@article{hu_miller_shi_2023, title={Abundance, diversity, and composition of root-associated microbial communities varied with tall fescue cultivars under water deficit}, volume={13}, ISSN={["1664-302X"]}, DOI={10.3389/fmicb.2022.1078836}, abstractNote={The plant breeding program has developed many cultivars of tall fescue (Festuca arundinacea) with low maintenance and stress tolerance. While the root-associated microbial community helps confer stress tolerance in the host plant, it is still largely unknown how the microbiota varies with plant cultivars under water stress. The study aimed to characterize drought-responsive bacteria and fungi in the roots and rhizosphere of different tall fescue cultivars. Intact grass-soil cores were collected from six cultivars grown in a field trial under no-irrigation for 3 years. Tall fescue under irrigation was also sampled from an adjacent area as the contrast. Bacterial and fungal communities in roots, rhizosphere, and bulk soil were examined for abundance, diversity, and composition using quantitative-PCR and high-throughput amplicon sequencing of 16S rRNA gene and ITS regions, respectively. Differences in microbial community composition and structure between non-irrigated and irrigated samples were statistically significant in all three microhabitats. No-irrigation enriched Actinobacteria in all three microhabitats, but mainly enriched Basidiomycota in the root endosphere and only Glomeromycota in bulk soil. Tall fescue cultivars slightly yet significantly modified endophytic microbial communities. Cultivars showing better adaptability to drought encompassed more relatively abundant Actinobacteria, Basidiomycota, or Glomeromycota in roots and the rhizosphere. PICRUSt2-based predictions revealed that the relative abundance of functional genes in roots related to phytohormones, antioxidant enzymes, and nutrient acquisition was enhanced under no-irrigation. Significant associations between Streptomyces and putative drought-ameliorating genes underscore possible mechanics for microbes to confer tall fescue with water stress tolerance. This work sheds important insight into the potential use of endophytic microbes for screening drought-adaptive genotypes and cultivars.}, journal={FRONTIERS IN MICROBIOLOGY}, author={Hu, Jialin and Miller, Grady and Shi, Wei}, year={2023}, month={Jan} }
 @article{zhou_shi_soltis_soltis_xiang_2023, title={Foliar endophyte diversity in Eastern Asian-Eastern North American disjunct tree species - influences of host identity, environment, phylogeny, and geographic isolation}, volume={14}, ISSN={["1664-462X"]}, DOI={10.3389/fpls.2023.1274746}, abstractNote={IntroductionThe well-known eastern Asian (EA) and eastern North American (ENA) floristic disjunction provides a unique system for biogeographic and evolutionary studies. Despite considerable interest in the disjunction, few studies have investigated the patterns and their underlying drivers of allopatric divergence in sister species or lineages isolated in the two areas. Endophyte diversity and assembly in disjunct sister taxa, as an ecological trait, may have played an important role in the processes of allopatric evolution, but no studies have examined endophytes in these lineages. Here we compared foliar endophytic fungi and bacteria-archaea (FEF and FEB) in 17 EA-ENA disjunct species or clade pairs from genera representing conifers and 10 orders of five major groups of angiosperms and 23 species of Cornus from EA and North America. }, journal={FRONTIERS IN PLANT SCIENCE}, author={Zhou, Wenbin and Shi, Wei and Soltis, Pamela S. and Soltis, Douglas E. and Xiang, Qiu-Yun}, year={2023}, month={Dec} }
 @article{huang_shi_fu_qiu_zhao_li_lyu_yang_xiong_wang_et al._2023, title={Soil development following glacier retreat shapes metagenomic and metabolomic functioning associated with asynchronous C and N accumulation}, volume={892}, ISSN={["1879-1026"]}, DOI={10.1016/j.scitotenv.2023.164405}, abstractNote={Glacier retreat caused by global warming may result in the variation of soil organic carbon and nutrient cycling. Yet, the dynamic change of soil microbial functional profiles, especially C metabolism-related, with soil development following glacier retreat are still unclear. In the present study, we investigated the soil microbial communities, metagenomic functioning, and metabolomic profiles along the Hailuogou Glacier forefield representing a 120-year chronosequence. The alpha diversity indices of soil bacteria, protozoa and nifH genes showed an upward trend with increased soil ages, and the beta diversity of soil archaea, bacteria, fungi, protozoa, nifH and nirS genes were significantly correlated with soil ages, in which increasing soil C and P while decreased C/N and pH significantly contributed to the differences of soil microbial communities among the analyzed environmental variables. The metagenomic functional genes related to the metabolisms of Glycogen and Cellulosome, Iron Acquisition and Metabolism were significantly decreased with chronosequence, while the utilization of Xylose and Lactate, Potassium Metabolism, Sulfur Metabolism showing an upward trend with soil ages, in which soil C/N ratios and pH were the most influential factors. In addition, soil C and C/N ratios were also significantly correlated to metabolomic compositions, in which the complexity of the metabolite structure increased with soil ages. Our results indicate that glacier retreat may lead to the asynchronous C and N accumulation along the chronosequence, thereby affecting the metagenomic and metabolomic functioning of soil microbial communities related to C metabolisms during soil development following glacier retreat.}, journal={SCIENCE OF THE TOTAL ENVIRONMENT}, author={Huang, Yu and Shi, Wei and Fu, Qi and Qiu, Yingbo and Zhao, Jiayi and Li, Jiaxin and Lyu, Qian and Yang, Xian and Xiong, Jia and Wang, Wenzhi and et al.}, year={2023}, month={Sep} }
 @article{xia_heitman_shi_2023, title={Soil macroporosity modulates the extent of negative microbial associations during organic substance decomposition}, volume={187}, ISSN={["1879-3428"]}, DOI={10.1016/j.soilbio.2023.109202}, abstractNote={Microbial species interactions are expected to influence the community-level properties, such as the production of extracellular enzymes and the degradation of organic substances. This work examined how microbial diversity, composition and the overall sign of microbial associations were altered with soil texture and structure following the amendment of organic substances. Two sets of microcosms (1:100 and 1:1) of a 4 × 3 factorial design were constructed, with four artificial textural classes (a sandy loam, two loams, and a (silty) clay loam) and three organics (TSB, tryptic soy broth; CA, a mixture of cellulose and humic/fulvic acids; BS, barley straw). As the ‘microbial inoculant’, an agricultural soil was added to the 1:100 and 1:1 microcosms at 1% and 50%, respectively. A few of microbial taxa were specifically enriched after soil addition of TSB, CA, or BS, but distributions across textural classes were inconsistent between microcosms or between organic amendments. Regardless, top abundant bacterial and fungal OTUs were overall negatively associated, suggesting that microbial competition for the shared resource dominated the decomposition of both simple and complex organics. Microbial associations were also modified by soil pore size distribution (PSD), being fewer negative (or more positive) in soils of greater macroporosity than in soils of lower macroporosity. The PSD-based differences in microbial associations were coordinated with PSD-based differences in the activities of exoglucanase and β-glucosidase in TSB-amended soils or soil respiration characteristics in CA-amended soils. Our results provide new insight into how soil structure regulates microbial interactions and, accordingly, the degradation of organic matter.}, journal={SOIL BIOLOGY & BIOCHEMISTRY}, author={Xia, Qing and Heitman, Joshua L. and Shi, Wei}, year={2023}, month={Dec} }
 @article{hu_cyle_miller_shi_2023, title={Water deficits shape the microbiome of Bermudagrass roots to be Actinobacteria rich}, volume={99}, ISSN={["1574-6941"]}, url={https://doi.org/10.1093/femsec/fiad036}, DOI={10.1093/femsec/fiad036}, abstractNote={Abstract}, number={5}, journal={FEMS MICROBIOLOGY ECOLOGY}, author={Hu, Jialin and Cyle, K. Taylor and Miller, Grady and Shi, Wei}, year={2023}, month={Apr} }
 @article{ramotowski_shi_2022, title={Nitrapyrin-based nitrification inhibitors shaped the soil microbial community via controls on soil pH and inorganic N composition}, volume={170}, ISSN={["1873-0272"]}, DOI={10.1016/j.apsoil.2021.104295}, abstractNote={Nitrate is a major source of N nutrition for plant production, but it is prone to loss from an arable soil via leaching and denitrification. Chemicals that inhibit biological NO3− production, known as nitrification inhibitors or N stabilizers, have been widely applied to slow nitrification and therefore minimize soil NO3− accumulation. However, the impacts of nitrification inhibitors on microbes other than nitrifying bacteria and archaea are largely unknown. Here we examined the diversity, abundance, and composition of the soil microbial community following the addition of two nitrification inhibitors, both containing nitrapyrin as the active ingredient but different solvents or emulsifying agents. Two silt loam soils of different acidities were used for a two-month microcosm incubation. Each soil was subjected to six treatments of soil alone, soil with the addition of each nitrification inhibitor at 4 μg nitrapyrin g−1 soil, soil with the addition of ammonium sulfate at 60 μg N g−1 soil, and soil with the addition of both ammonium sulfate and each nitrification inhibitor. Periodically during the incubation, soil NH4+ and NO3− were quantified. In addition to measurements of soil pH and potential rate of nitrification at the end of incubation, 16S rRNA and ITS marker gene libraries were prepared for high throughput sequencing. Our data showed clear targeted effects of nitrapyrin-based nitrification inhibitors on nitrification as well as ammonia oxidizing bacteria and archaea; and these effects were little affected by different solvents for dissolving or emulsifying nitrapyrin. However, the use of a nitrification inhibitor generated some non-target effects on the soil microbial community. Microbes of copiotrophic life strategy, e.g., Alphaproteobacteria, Betaproteobacteria, and Ascomycota were promoted, whereas microbes of oligotrophic life strategy, e.g., Acidobacteria, Planctomycetes, and Basidiomycota were suppressed. The degree of non-target effects appeared to be soil and microbial domain specific, with stronger effects in the acidic soil than neutral soil on the bacterial community and yet comparable effects on the fungal community between the two soils. Spearman's rank correlations suggested that non-target effects of nitrification inhibitors were primarily attributed to changes in soil pH as well as soil inorganic N composition, i.e., the percentage of ammonium (or nitrate) in inorganic N. Further research is needed for better understanding soil microbial ecology under high NH4+ concentrations so that the management practice of keeping more NH4+ in soil can be well adopted to improve crop N use efficiency and soil sustainability.}, journal={APPLIED SOIL ECOLOGY}, author={Ramotowski, David and Shi, Wei}, year={2022}, month={Feb} }
 @article{xia_zheng_heitman_shi_2022, title={Soil pore size distribution shaped not only compositions but also networks of the soil microbial community}, volume={170}, ISSN={["1873-0272"]}, DOI={10.1016/j.apsoil.2021.104273}, abstractNote={Soil pore size and arrangement control the heterogeneous distribution of nutrients, water, and air and, therefore, are likely a superimposed and integrated factor dictating the soil microbial community structure. It is known that soil with more large pores can potentially harbor more diverse microbes under low hydraulic connectivity. Still, there is scant information on how soil pore size distribution (PSD) governs the composition and association of the microbial community. This work examined PSD effects on microbial community compositions and networks via marker gene high-throughput sequencing of both DNA and cDNA. Three soils with a large variation in silt content (~11–73%) and their combinations at different mass ratios were used to enhance the continuity in silt content and thus PSD. Investigations were made under different levels of total pore volume and pore hydraulic connectivity by incubating soils at varied bulk densities and moisture contents for 50 days. The total of six soils was dichotomized into two PSD groups based on soil water retention curves, with PSD-1 of more macro- and mesopores (>30 μm) and PSD-2 of more micropores (<30 μm). Effects of moisture treatments on both fungal and bacterial evenness and Shannon diversity index were pore size group specific, supporting the importance of pore hydraulic connectivity in regulating microbial diversity. PSD-1 soils promoted the proliferation of Betaproteobacteria, Bacteroidetes, and Eurotiales, whereas PSD-2 soils favored Alphaproteobacteria, Sordariomycetes, and Chaetothyriales. Pore hydraulic connectivity slightly and yet significantly affected the microbial relative abundance of PSD-2 soils, with Actinobacteria being more abundant under drier conditions. There were less intra- and interkingdom associations in PSD-2 than PSD-1 soils, and such differences were little affected by pore volume and pore hydraulic connectivity. Our work highlighted PSD-dependent soil microbial distributions and associations, but ecological consequences need to be further examined.}, journal={APPLIED SOIL ECOLOGY}, author={Xia, Qing and Zheng, Ningguo and Heitman, Joshua L. and Shi, Wei}, year={2022}, month={Feb} }
 @article{xia_rufty_shi_2021, title={Predominant Microbial Colonizers in the Root Endosphere and Rhizosphere of Turfgrass Systems: Pseudomonas veronii, Janthinobacterium lividum, and Pseudogymnoascus spp.}, volume={12}, ISSN={["1664-302X"]}, DOI={10.3389/fmicb.2021.643904}, abstractNote={Microbes can colonize plant roots to modulate plant health and environmental fitness. Thus, using microbes to improve plant adaptation to biotic and abiotic stresses will be promising to abate the heavy reliance of management systems on synthetic chemicals and limited resource. This is particularly important for turfgrass systems because intensive management for plant available nutrients (e.g., nitrogen), water, and pest control is necessary to maintain a healthy and aesthetic landscape. However, little is known on microbial species and host compatibility in turfgrass root endosphere and rhizosphere. Here, by using marker gene high throughput sequencing approaches we demonstrated that a few bacterial and fungal species prevailed the root endosphere and rhizosphere and were of a broad host spectrum. Irrespective of turfgrass species (bermudagrass, ultradwarf bermudagrass, creeping bentgrass, and tall fescue), defoliation intensities (i.e., mowing height and frequency), turfgrass sites, and sampling time, Pseudomonas veronii was predominant in the root endosphere, constituting ∼38% of the total bacterial community, which was much higher than its presence in the bulk soil (∼0.5%) and rhizosphere (∼4.6%). By contrast, Janthinobacterium lividum and fungal species of the genus Pseudogymnoascus were more abundant in the rhizosphere, constituting ∼15 and ∼ 39% of the total bacterial and fungal community, respectively, compared to their respective presence in the bulk soil (∼ 0.1 and 5%) and root endosphere (∼ 0.8 and 0.3%). Such stark contrasts in the microbiome composition between the root endosphere, rhizosphere, and bulk soil were little influenced by turfgrass species, suggesting the broad turfgrass host compatibility of these bacterial and fungal species. Further, their dominance in respective niches were mutually unaffected, implying the possibility of developing a multiple species formula for coping turfgrass with environmental stresses. These species were likely involved in controlling pests, such as infectious nematodes and fungi, decomposing root debris, and helping turfgrass water and nutrient uptake; yet these possibilities need to be further examined.}, journal={FRONTIERS IN MICROBIOLOGY}, author={Xia, Qing and Rufty, Thomas and Shi, Wei}, year={2021}, month={Mar} }
 @article{xiao_qiu_tao_zhang_chen_reberg-horton_shi_shew_zhang_hu_2020, title={Biological controls over the abundances of terrestrial ammonia oxidizers}, volume={29}, ISSN={["1466-8238"]}, DOI={10.1111/geb.13030}, abstractNote={Abstract}, number={2}, journal={GLOBAL ECOLOGY AND BIOGEOGRAPHY}, author={Xiao, Rui and Qiu, Yunpeng and Tao, Jinjin and Zhang, Xuelin and Chen, Huaihai and Reberg-Horton, S. Chris and Shi, Wei and Shew, H. David and Zhang, Yi and Hu, Shuijin}, year={2020}, month={Feb}, pages={384–399} }
 @article{xia_rufty_shi_2020, title={Soil microbial diversity and composition: Links to soil texture and associated properties}, volume={149}, ISSN={["0038-0717"]}, DOI={10.1016/j.soilbio.2020.107953}, abstractNote={Soil texture is an essential component of soil survey for estimating potentials and limitations of land use and management. It has been appreciated as an important predictor for numerous soil processes. However, its connections with the diversity and composition of the soil microbial community remain less understood. This work employed a marker gene high-throughput sequencing approach to determine soil texture-based patterns of bacterial and fungal distribution. Thirty-six intact soil cores were sampled from bermudagrass ecosystems across seven soil texture classes with sand fraction varying from 30.3 to 83.4% and clay fraction from 4.4 to 53.0%. These soil cores were arranged into three sets of equal numbers, and each set of 12 was subjected to three moisture regimes (dry spell, field moisture, and saturation-field capacity), respectively, for 15 days. Soil cores were further stratified into top and bottom sections, leading to a total of 72 samples with varying soil physical and chemical properties. Our data revealed that fungal alpha diversity was more strongly related to soil texture than bacterial alpha diversity, with fungal species richness and Shannon diversity being positively correlated with the sand fraction. Soil texture was the second most important factor after soil pH in shaping the soil microbial community. Relative abundances of some fungi (Basidiomycota and Eurotiomycetes) and filamentous bacteria (Actinobacteria, Chloroflexi) significantly increased with silt and/or clay content. The genetic potential for the degradation of organic compounds also appeared to be higher in finer textured soils than the coarse-textured soils. By identifying sand, silt or clay-preferred microbial taxa and characterizing mineral particle-dependent genetic potential of organic carbon degradation and nitrogen cycling, this work highlighted the significance of soil texture and texture-associated pores, and resource locality, in regulating microbial diversity and community composition.}, journal={SOIL BIOLOGY & BIOCHEMISTRY}, author={Xia, Qing and Rufty, Thomas and Shi, Wei}, year={2020}, month={Oct} }
 @article{zheng_yu_shi_yao_2019, title={Biochar suppresses N2O emissions and alters microbial communities in an acidic tea soil}, volume={26}, ISSN={["1614-7499"]}, DOI={10.1007/s11356-019-06704-8}, abstractNote={Biochar has been considered as a promising soil amendment for improving fertility and mitigating N 2 O emission from the arable land. However, biochar's effectiveness in acidic tea soil and underlying mechanisms are largely unknown. We conducted a short-term microcosm experiment using two biochars (1% w/w, LB, generated from legume and NLB, non-legume biomass, respectively) to investigate the effects of biochar amendments on soil chemical properties, N 2 O emission, and microbial community in an acidic soil. Soil and headspace gas samples were taken on 1, 10, and 30 day's incubation. Biochar amendment increased soil pH and DOC, however, significantly reduced soil inorganic N. Both biochars at ~ 1% addition had little effect on microbial CO 2  respiration but suppressed soil N 2 O emission by ~ 40% during the incubation. The divergence in N 2 O efflux rates between soils with and without biochar addition aligned to some degree with changes in soil pH, inorganic N, and dissolved organic C (DOC). We also found that biochar addition significantly modified the fungal community structure, in particular the relative abundance of members of Ascomycota, but not the bacterial community. Furthermore, the copy number of nosZ, the gene encoding N 2 O reductase, was significantly greater in biochar-amended soils than the soil alone. Our findings contribute to better understanding of the impact of biochar on the soil chemical properties, soil N 2 O emission, and microbial community and the consequences of soil biochar amendment for improving the health of acidic tea soil.}, number={35}, journal={ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH}, author={Zheng, Ningguo and Yu, Yongxiang and Shi, Wei and Yao, Huaiying}, year={2019}, month={Dec}, pages={35978–35987} }
 @article{xia_chen_yang_miller_shi_2019, title={Defoliation management and grass growth habits modulated the soil microbial community of turfgrass systems}, volume={14}, ISSN={["1932-6203"]}, url={https://doi.org/10.1371/journal.pone.0218967}, DOI={10.1371/journal.pone.0218967}, abstractNote={Grass species selection and regular mowing are essential for maintaining aesthetic and environmentally sound turfgrass systems. However, their impacts on the soil microbial community, the driving force for soil N cycle and thus the environmental fate of N, are largely unknown. Here, the high throughput sequencing of 16S rRNA gene and internal transcribed spacer (ITS) region was used to evaluate how long-term defoliation management and grass growth habits (propagation types and photosynthetic pathways) modulated the soil microbial community. The investigation included three cool-season C3 grasses (creeping bentgrass, Kentucky bluegrass, and tall fescue) and three warm-season C4 grasses (bermudagrass, St. Augustinegrass, and zoysiagrass). Creeping bentgrass and bermudagrass were managed as putting greens with a lower mowing height; tall fescue spread in a tussock manner via tiller production whereas other grasses propagated in a creeping manner via rhizomes and/or stolons. Ordination analysis showed that both bacterial and fungal communities were primarily separated between putting green and non-putting green systems; and so were N-cycle gene relative abundances, with the putting greens being greater in N mineralization but lower in nitrification. Compared to warm-season grasses, cool-season grasses slightly and yet significantly enhanced the relative abundances of Chloroflexi, Verrucomicrobia, and Glomeromycota. Tall fescue yielded significantly greater bacterial and fungal richness than non-tussock grasses. As the main explanatory soil property, pH only contributed to < 18% of community compositional variations among turfgrass systems. Our results indicate that defoliation management was the main factor in shaping the soil microbial community and grass growth habits was secondary in modulating microbial taxon distribution.}, number={6}, journal={PLOS ONE}, publisher={Public Library of Science (PLoS)}, author={Xia, Qing and Chen, Huaihai and Yang, Tianyou and Miller, Grady and Shi, Wei}, editor={Gao, ChengEditor}, year={2019}, month={Jun} }
 @article{cacho_youssef_shi_chescheir_skaggs_tian_leggett_sucre_nettles_arellano_2019, title={Impacts on soil nitrogen availability of converting managed pine plantation into switchgrass monoculture for bioenergy}, volume={654}, ISSN={["1879-1026"]}, DOI={10.1016/j.scitotenv.2018.11.133}, abstractNote={Biofuels derived from lignocellulosic materials is one of the options in addressing issues on climate change and energy independence. One of the most promising bioenergy crops is switchgrass (Panicum virgatum L.), particularly in North America. Future advancement in large-scale conversion of lignocellulosic feedstocks and relatively more competitive price for biomass and other economic advantages could lead to landowners opting to venture on switchgrass monoculture (SWITCH) in lieu of loblolly pine monoculture (PINE). Therefore, we investigated the conversion of previously managed loblolly pine stand into SWITCH in eastern North Carolina, U.S.A. on soil N availability. Treatments included PINE, SWTICH, and mature loblolly pine stand (REF). Each treatment was replicated three times on 0.8 ha plots drained by open ditches dug 1.0–1.2 m deep and spaced at 100 m. Rates of net N mineralization (Nm) and nitrification (Nn) at the top 20 cm were measured using sequential in-situ techniques in 2011 and 2012 (the 3rd and 4th years of establishment, respectively) along with a one-time laboratory incubation. On average, PINE, SWITCH, and REF can have field net Nm rates up to 0.40, 0.34 and 0.44 mg N·kg soil−1·d−1, respectively, and net Nn rates up to 0.14, 0.08 and 0.10 mg N·kg soil−1·d−1, respectively. Annually, net Nm rates ranged from 136.98 to 167.21, 62.00 to 142.61, and 63.57 to 127.95 kg N·ha−1, and net Nn rates were 56.31–62.98, 16.45–30.45, 31.99–32.94 kg N·ha−1 in PINE, SWITCH, and REF, respectively. Treatment effect was not significant on field Nm rate (p = 0.091). However, SWITCH significantly reduced nitrate-N production (p < 0.01). Overall, results indicated that establishment of SWITCH on poorly drained lands previously under PINE is less likely to significantly impact total soil N availability and potentially has minimum N leaching losses since soil mineral N under this system will be dominated by ammonium-N.}, journal={SCIENCE OF THE TOTAL ENVIRONMENT}, author={Cacho, Julian F. and Youssef, Mohamed A. and Shi, Wei and Chescheir, George M. and Skaggs, R. Wayne and Tian, Shiying and Leggett, Zakiya H. and Sucre, Eric B. and Nettles, Jami E. and Arellano, Consuelo}, year={2019}, month={Mar}, pages={1326–1336} }
 @article{chen_xia_yang_bowman_shi_2019, title={The soil microbial community of turf: linear and nonlinear changes of taxa and N-cycling gene abundances over a century-long turf development}, volume={95}, ISSN={["1574-6941"]}, DOI={10.1093/femsec/fiy224}, abstractNote={&NA; Turf, consisting of closely spaced grasses and the subtending soil, is a unique ecosystem subject to intense management. Yet soil organic matter accumulates quickly and reaches equilibrium after 20 to 50 years. Resource availability is an important driver of species richness and theoretically their relationship is expected to be unimodal. In this work, we examined the effects of turf development (i.e. a 1, 15, 20 and 109 year‐old chronosequence) on microbial taxon richness, community composition, and abundances of genes putatively involved in N cycling through 16S rRNA gene and ITS region amplicon sequencing. Microbial alpha‐diversity remained relatively stable although soil organic C and N increased by up to 3‐fold over a century‐long turf development. However, both bacterial and fungal community compositions changed substantially from those in the previous land use, pine stands and along turf development. Youngest turf was closer to the oldest turf than to middle‐aged ones, specifically for bacterial community. Microbial changes to resource availability were also taxonomically specific. The relative abundance of Proteobacteria was independent of resource availability; Nitrospirae increased monotonically, and Bacteroidetes, Actinobacteria and Glomeromycota varied curvilinearly. However, abundances of most taxa from the phylum to operational taxonomic unit level and N‐cycling genes varied nonlinearly with turf development. &NA; Graphical Abstract Figure. Turf, an apparent copiotrophic environment, harbors diverse microbial taxa; the abundances of most taxa from the phylum to operational taxonomic unit level changed nonlinearly along turf development.}, number={2}, journal={FEMS MICROBIOLOGY ECOLOGY}, author={Chen, Huaihai and Xia, Qing and Yang, Tianyou and Bowman, Daniel and Shi, Wei}, year={2019}, month={Feb} }
 @article{cacho_youssef_shi_chescheir_skaggs_tian_leggett_sucre_nettles_arellano_2018, title={Impacts of forest-based bioenergy feedstock production on soil nitrogen cycling}, volume={419-420}, ISSN={0378-1127}, url={http://dx.doi.org/10.1016/J.FORECO.2018.04.002}, DOI={10.1016/J.FORECO.2018.04.002}, abstractNote={We investigated impacts of simultaneous production of biomass for biofuel and quality timber on soil nitrogen (N) cycling in a poorly drained forest soil of eastern North Carolina, U.S.A. Treatments included traditional loblolly pine (PINE) and pine-switchgrass intercropping (PSWITCH). Treatments were replicated three times on 0.8 ha plots drained by parallel open ditches which were 1.2 m deep and spaced 100 m apart. Net N mineralization (Nm) and nitrification (Nn) rates were measured in the field using sequential in-situ technique over two years with multiple measurements in each year and laboratory by incubating soil samples for one-, two-, eight-, and thirteen weeks. Soil incubation in-situ or sample collection for laboratory incubation was conducted at nine sampling points within a 30 × 40 m subplot at each plot center and 20 cm from the soil surface. Soil samples were composited by location including near tree (NT), between two trees on the same bed (BT), and in the middle of four trees on two adjacent beds (M4T). Composite samples from NT and BT were categorized as tree-bed (BED), while those from M4T were grouped as interbed (INT). Field results showed that total soil N availability and its temporal variations over two years were not significantly affected by PSWITCH. However, it significantly reduced Nn rates, particularly in the INT. The plot-level mean Nm rates in PINE were 0.21 and 0.26 mg N·kg soil−1 d−1, while in PSWITCH they were 0.10 and 0.21 mg N kg soil−1 d−1 in 2011 and 2012, respectively. The plot-level mean Nn rates in PINE were 0.09 and 0.10 mg N kg soil−1 d−1 in 2011 and 2012, respectively, while in PSWITCH they remained at 0.03 mg N kg soil−1 d−1 across these two years. At the INT, mean Nn rates in PINE were 0.11 and 0.12 mg N kg soil−1 d−1 in 2011 and 2012, respectively, while in PSWITCH, Nn rate remained at 0.02 mg N kg soil−1 d−1 over two years. Laboratory results indicated that change in litter quality inputs (changing from mixed species to switchgrass) in the INT did not significantly affect Nm rates. Results of this study contributed to a better understanding of the changes in soil N cycling due to loblolly pine-switchgrass interactions, which is important in sustainable nutrient management of this new land use. Further, the results suggested that growing switchgrass as intercrop to managed loblolly pine has positive water quality implication since ammonium N is less mobile in soil than nitrate N.}, journal={Forest Ecology and Management}, publisher={Elsevier BV}, author={Cacho, Julian F. and Youssef, Mohamed A. and Shi, Wei and Chescheir, George M. and Skaggs, R. Wayne and Tian, Shiying and Leggett, Zakiya H. and Sucre, Eric B. and Nettles, Jami E. and Arellano, Consuelo}, year={2018}, month={Jul}, pages={227–239} }
 @article{chen_yang_xia_bowman_williams_walker_shi_2018, title={The extent and pathways of nitrogen loss in turfgrass systems: Age impacts}, volume={637}, ISSN={["1879-1026"]}, DOI={10.1016/j.scitotenv.2018.05.053}, abstractNote={Nitrogen loss from fertilized turf has been a concern for decades, with most research focused on inorganic (NO3−) leaching. The present work examined both inorganic and organic N species in leachate and soil N2O emissions from intact soil cores of a bermudagrass chronosequence (1, 15, 20, and 109 years old) collected in both winter and summer. Measurements of soil N2O emissions were made daily for 3 weeks, while leachate was sampled once a week. Four treatments were established to examine the impacts of fertilization and temperature: no N, low N at 30 kg N ha−1, and high N at 60 kg N ha−1, plus a combination of high N and temperature (13 °C in winter or 33 °C in summer compared to the standard 23 °C). Total reactive N loss generally showed a “cup” pattern of turf age, being lowest for the 20 years old. Averaged across all intact soil cores sampled in winter and summer, organic N leaching accounted for 51% of total reactive N loss, followed by inorganic N leaching at 41% and N2O-N efflux at 8%. Proportional loss among the fractions varied with grass age, season, and temperature and fertilization treatments. While high temperature enhanced total reactive N loss, it had little influence on the partitioning of loss among dissolved organic N, inorganic N and N2O-N when C availability was expected to be high in summer due to rhizodeposition and root turnover. This effect of temperature was perhaps due to higher microbial turnover in response to increased C availability in summer. However when C availability was low in winter, warming might mainly affect microbial growth efficiency and therefore partitioning of N. This work provides a new insight into the interactive controls of warming and substrate availability on dissolved organic N loss from turfgrass systems.}, journal={SCIENCE OF THE TOTAL ENVIRONMENT}, author={Chen, Huaihai and Yang, Tianyou and Xia, Qing and Bowman, Daniel and Williams, David and Walker, John T. and Shi, Wei}, year={2018}, month={Oct}, pages={746–757} }
 @article{franzluebbers_chappell_shi_cubbage_2017, title={Greenhouse gas emissions in an agroforestry system of the southeastern USA}, volume={108}, ISSN={["1573-0867"]}, DOI={10.1007/s10705-016-9809-7}, number={1}, journal={NUTRIENT CYCLING IN AGROECOSYSTEMS}, author={Franzluebbers, Alan J. and Chappell, Janet C. and Shi, Wei and Cubbage, Frederick W.}, year={2017}, month={May}, pages={85–100} }
 @article{yuan_chen_yuan_williams_walker_shi_2017, title={Is biochar-manure co-compost a better solution for soil health improvement and N2O emissions mitigation?}, volume={113}, ISSN={0038-0717}, url={http://dx.doi.org/10.1016/J.SOILBIO.2017.05.025}, DOI={10.1016/j.soilbio.2017.05.025}, abstractNote={Land application of compost has been a promising remediation strategy for soil health and environmental quality, but substantial emissions of greenhouse gases, especially N2O, need to be controlled during making and using compost of high N-load wastes, such as chicken manure. Biochar as a bulking agent for composting has been proposed as a novel approach to solve this issue, due to large surface area and porosity, and thus high ion exchange and adsorption capacity. Here, we compared the impacts of biochar-chicken manure co-compost (BM) and chicken manure compost (M) on soil biological properties and processes in a 120-d microcosm experiment at the soil moisture of 60% water-filled pore space. Our results showed that BM and M addition significantly enhanced soil total C and N, inorganic and KCl-extractable organic N, microbial biomass C and N, cellulase enzyme activity, abundance of N2O-producing bacteria and fungi, and gas emissions of N2O and CO2. However, compared to the M treatment, BM significantly reduced soil CO2 and N2O emissions by 35% and 27%, respectively, over the experimental period. The 15N-N2O site preference, i.e., difference between 15N-N2O in the center position (δ15Nα) and the end position (δ15Nβ), was ∼17‰ for M and ∼26‰ for BM during the first week of incubation, suggesting that BM suppressed N2O from bacterial denitrification and/or nitrifier denitrification. This inference was well aligned with the observation that soil glucosaminidase activity and nirK gene abundance were lower in BM than M treatment. Further, soil peroxidase activity was greater in BM than M treatment, implying soil organic C was more stable in BM treatment. Our data demonstrated that the biochar-chicken manure co-compost could substantially reduce soil N2O emissions compared to chicken manure compost, via controls on soil organic C stabilization and the activities of microbial functional groups, especially bacterial denitrifiers.}, journal={Soil Biology and Biochemistry}, publisher={Elsevier BV}, author={Yuan, Yinghong and Chen, Huaihai and Yuan, Wenqiao and Williams, David and Walker, John T. and Shi, Wei}, year={2017}, month={Oct}, pages={14–25} }
 @article{barnes_nelson_hesterberg_shi_whipker_2017, title={Modeling impact of nitrogen carrier and concentration on root substrate pH}, volume={40}, ISSN={["1532-4087"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85029409669&partnerID=MN8TOARS}, DOI={10.1080/01904167.2016.1143502}, abstractNote={ABSTRACT We conducted an experiment to quantify the effects on substrate pH from nitrogen (N) carrier and concentration. We used four concentrations of N (3.5–14 mM) and five fractions of ammonium (NH4+) (0–80% NH4+ of total N) that are found in commercially available fertilizers. Fertilizers were applied to fallow 14-cm-diameter pots (1.29 L) filled with a 3 peat:1 perlite (v/v) substrate amended with non-residual powdered calcium carbonate to raise the substrate pH to approximately 6.0. Harvests occurred at 20 and 42 days. Significant effects in the model included main effects of N carrier and N concentration, their squared terms, an interaction effect, and a time × N carrier. The fraction of NH4+ accounted for 45.0% of variation in substrate pH, and N concentration accounted for 1.5% of the total R2 of 76.7%. Substrate acidification was likely due to the physiological fertilizer effect and nitrification.}, number={15}, journal={JOURNAL OF PLANT NUTRITION}, author={Barnes, Jared and Nelson, Paul V. and Hesterberg, Dean and Shi, Wei and Whipker, Brian E.}, year={2017}, pages={2101–2108} }
 @article{chen_shi_2017, title={Opening up the N2O-producing fungal community in an agricultural soil with a cytochrome p450nor-based primer tool}, volume={119}, ISSN={["1873-0272"]}, DOI={10.1016/j.apsoil.2017.07.022}, abstractNote={Fungi play an important role in soil N2O emissions; yet little is known on the community ecology of N2O-producing fungi in soil. We explored denitrifying fungi using a cytochrome p450nor-based primer tool. Clone library and sequencing analysis revealed that soil harbored diverse denitrifying fungi in Ascomycota and Basidiomycota. Ascomycotal fungi were widely distributed across orders, Eurotiales, Hypocreales, and Sordariales. Denitrifying fungi were also expanded to include Cylindrocarpon, Neurospora, Thielavia, and Trichosporon that were undetected in our previous culture-based work. These results indicate that the p450nor-based primer tool can provide a more comprehensive characterization of denitrifying fungal community in soil environment.}, journal={APPLIED SOIL ECOLOGY}, author={Chen, Huaihai and Shi, Wei}, year={2017}, month={Oct}, pages={392–395} }
 @article{chen_yu_shi_2016, title={Detection of N2O-producing fungi in environment using nitrite reductase gene (nirK)-targeting primers}, volume={120}, DOI={10.1016/j.funbio.2016.07.012}, abstractNote={Fungal denitrification has been increasingly investigated, but its community ecology is poorly understood due to the lack of culture-independent tools. In this work, four pairs of nirK-targeting primers were designed and evaluated for primer specificity and efficiency using thirty N2O-producing fungal cultures and an agricultural soil. All primers amplified nirK from fungi and soil, but their efficiency and specificity were different. A primer set, FnirK_F3/R2 amplified ∼80 % of tested fungi, including Aspergillus, Fusarium, Penicillium, and Trichoderma, as compared to ∼40-70 % for other three primers. The nirK fragments of fungal and soil DNA amplified by FnirK_F3/R2 were phylogenetically related to denitrifying fungi in the orders Eurotiales, Hypocreales, and Sordariales; and clone sequences were also distributed in the clusters of Chaetomium, Metarhizium, and Myceliophthora that were uncultured from soil in our previous work. This proved the wide-range capability of primers for amplifying diverse denitrifying fungi from environment. However, our primers and recently-developed other primers amplified bacterial nirK from soil and this co-amplification of fungal and bacterial nirK was theoretically discussed. The FnirK_F3/R2 was further compared with published primers; results from clone libraries demonstrated that FnirK_F3/R2 was more specifically targeted on fungi and had broader taxonomical coverage than some others.}, number={12}, journal={Fungal Biology}, author={Chen, H. H. and Yu, F. B. and Shi, Wei}, year={2016}, pages={1479–1492} }
 @article{jia_wang_yuan_shah_shi_meng_ju_yang_2016, title={N2O EMISSION AND NITROGEN TRANSFORMATION IN CHICKEN MANURE AND BIOCHAR CO-COMPOSTING}, volume={59}, ISSN={["2151-0040"]}, DOI={10.13031/trans.59.11685}, abstractNote={This study examined the effect of biochar addition on nitrous oxide (N2O) emission and nitrogen (N) transformation in co-composting of biochar and chicken manure. Compared with the control (no biochar), addition of 20% biochar resulted in a 59.8% decrease in the major peak of N2O emission. Ammonium (NH4+-N) and nitrate (NO3--N) contents in the final product with 20% biochar addition increased by 67.3% and 66.7%, respectively, compared to the control. Turning frequency (TF), the primary parameter of aeration and temperature control in the biochar-manure co-composting process, was also investigated. Results indicated that less frequent turning (e.g., turning every seven days) promoted NH4+-N and NO3-N retention but increased peak N2O emission by 58.1% compared with daily turning. Overall, biochar can be an ideal bulking agent for stabilizing N-rich materials to minimize N2O emission and, with proper aeration, can enhance nitrogen retention based on this laboratory study.}, number={5}, journal={TRANSACTIONS OF THE ASABE}, author={Jia, X. and Wang, M. and Yuan, W. and Shah, S. and Shi, W. and Meng, X. and Ju, X. and Yang, B.}, year={2016}, pages={1277–1283} }
 @article{chen_williams_walker_shi_2016, title={Probing the biological sources of soil N2O emissions by quantum cascade laser-based N-15 isotopocule analysis}, volume={100}, ISSN={["1879-3428"]}, DOI={10.1016/j.soilbio.2016.06.015}, abstractNote={Isotopocule analysis by quantum cascade laser spectrometry (QCL) is a promising approach for in situ, real-time tracking of the biological sources of soil N2O emissions. However, background atmospheric N2O is an important source of variability in the measurement of isotopocule ratios (i.e., 14N15N16O/14N14N16O and 15N14N16O/14N14N16O) of gas samples. Here, a method based on Keeling plot for determining the intramolecular 15N distribution in N2O is introduced. The sensitivity and reliability of this method are examined against N2O of known 15N site preference (SP), and N2O produced from fungal and bacterial isolates, soils with different moisture contents and organic amendments, and a soil chamber under field conditions. The isotopocules of N2O determined by standard gases supported that the Keeling plot method was more reliable than the averaging method. Using this method, SP of N2O was greater in fungal than bacterial denitrifiers, as well as in soil at 60% water filled pore space (WFPS) than 80–100% WFPS. This method also determined that the SP of N2O was distinct between soils of different substrate complexity. Further, we observed a N2O SP between −18.9‰ and 2.2% in a soil flux chamber deployed in a corn field after 2 d of rainfalls that is consistent with the SP of N2O produced from bacterial denitrification and nitrifier denitrification. Our data demonstrate that this Keeling plot method provides accurate discrimination of biological sources when N2O is analyzed by the QCL system.}, journal={SOIL BIOLOGY & BIOCHEMISTRY}, author={Chen, Huaihai and Williams, David and Walker, John T. and Shi, Wei}, year={2016}, month={Sep}, pages={175–181} }
 @article{o'connell_grossman_hoyt_shi_bowen_marticorena_fager_creamer_2015, title={A survey of cover crop practices and perceptions of sustainable farmers in North Carolina and the surrounding region}, volume={30}, DOI={10.1017/s1742170514000398}, abstractNote={Abstract}, number={6}, journal={Renewable Agriculture and Food Systems}, author={O'Connell, S. and Grossman, J. M. and Hoyt, G. D. and Shi, Wei and Bowen, S. and Marticorena, D. C. and Fager, K. L. and Creamer, N. G.}, year={2015}, pages={550–562} }
 @article{chen_mothapo_shi_2015, title={Fungal and bacterial N2O production regulated by soil amendments of simple and complex substrates}, volume={84}, ISSN={["0038-0717"]}, DOI={10.1016/j.soilbio.2015.02.018}, abstractNote={Fungal N2O production results from a respiratory denitrification that reduces NO3−/NO2− in response to the oxidation of an electron donor, often organic C. Despite similar heterotrophic nature, fungal denitrifiers may differ from bacterial ones in exploiting diverse resources. We hypothesized that complex C compounds and substances could favor the growth of fungi over bacteria, and thereby leading to fungal dominance for soil N2O emissions. Effects of substrate quality on fungal and bacterial N2O production were, therefore, examined in a 44-d incubation after soils were amended with four different substrates, i.e., glucose, cellulose, winter pea, and switchgrass at 2 mg C g−1 soil. During periodic measurements of soil N2O fluxes at 80% soil water-filled pore space and with the supply of KNO3, substrate treatments were further subjected to four antibiotic treatments, i.e., no antibiotics or soil addition of streptomycin, cycloheximide or both so that fungal and bacterial N2O production could be separated. Up to d 8 when antibiotic inhibition on substrate-induced microbial activity and/or growth was still detectable, bacterial N2O production was generally greater in glucose- than in cellulose-amended soils and also in winter pea- than in switchgrass-amended soils. In contrast, fungal N2O production was more enhanced in soils amended with cellulose than with glucose. Therefore, fungal-to-bacterial contribution ratios were greater in complex than in simple C substrates. These ratios were positively correlated with fungal-to-bacterial activity ratios, i.e., CO2 production ratios, suggesting that substrate-associated fungal or bacterial preferential activity and/or growth might be the cause. Considering substrate depletion over time and thereby becoming limited for microbial N2O production, measurements of soil N2O fluxes were also carried out with additional supply of glucose, irrespective of different substrate treatments. This measurement condition might lead to potentially high rates of fungal and bacterial N2O production. As expected, bacterial N2O production was greater with added glucose than with added cellulose on d 4 and d 8. However, this pattern was broken on d 28, with bacterial N2O production lower with added glucose than with added cellulose. In contrast, plant residue impacts on soil N2O fluxes were consistent over 44-d, with greater bacterial contribution, lower fungal contribution, and thus lower fungal-to-bacterial contribution ratios in winter pea- than in switchgrass-amended soils. Real-time PCR analysis also demonstrated that the ratios of 16S rDNA to ITS and the copy numbers of bacterial denitrifying genes were greater in winter pea- than in switchgrass-amended soils. Despite some inconsistency found on the impacts of cellulose versus glucose on fungal and bacterial leading roles for N2O production, the results generally supported the working hypothesis that complex substrates promoted fungal dominance for soil N2O emissions.}, journal={SOIL BIOLOGY & BIOCHEMISTRY}, author={Chen, Huaihai and Mothapo, Nape V. and Shi, Wei}, year={2015}, month={May}, pages={116–126} }
 @article{mothapo_chen_cubeta_grossman_fuller_shi_2015, title={Phylogenetic, taxonomic and functional diversity of fungal denitrifiers and associated N2O production efficacy}, volume={83}, ISSN={0038-0717}, url={http://dx.doi.org/10.1016/j.soilbio.2015.02.001}, DOI={10.1016/j.soilbio.2015.02.001}, abstractNote={Fungi generally dominate microbial biomass in various soils and play critical roles in ecosystem functioning including nutrient cycling, disease ecology and food production. Therefore, fungal denitrification, phenotypically typified by nitrous oxide (N2O) production, presents another avenue other than N mineralization and heterotrophic nitrification for progress to better understand the multiple roles of fungi in sustaining the biosphere. The discovery of N2O production and consequently denitrification in Fusarium oxysporum Schltdl. in early 1970's has led to identification of many taxonomically diverse species of N2O-producing fungi. This review evaluates the current status of knowledge on species composition of fungal denitrifiers and their N2O-producing activity. Here we describe challenges with assessment of fungal N2O-producing activity across genera and suggest prospects for future studies. We also discuss species diversity in order to gain knowledge of important taxonomic and phylogenetic groups mediating N2O production and provide insight on ecological cues associated with fungal N2O production. Currently, the extent to which species phylogeny and the functional trait, i.e. N2O-producing activity, are linked remains to be determined; even so, it is evident that some related taxa exhibit similar N2O production efficacy than distant relatives.}, journal={Soil Biology and Biochemistry}, publisher={Elsevier BV}, author={Mothapo, Nape and Chen, Huaihai and Cubeta, Marc A. and Grossman, Julie M. and Fuller, Fred and Shi, Wei}, year={2015}, month={Apr}, pages={160–175} }
 @article{lu_bowman_rufty_shi_2015, title={Reactive Nitrogen in Turfgrass Systems: Relations to Soil Physical, Chemical, and Biological Properties}, volume={44}, ISSN={["1537-2537"]}, DOI={10.2134/jeq2014.06.0247}, abstractNote={Turfgrass systems contribute to the loading of reactive N to water and air via runoff, leaching, and gas emission. Yet, a comprehensive approach has never been developed to assess N loss potential from turfgrass systems. We used pools and production of reactive N (inorganic N, extractable organic N, and NO) to estimate N loss potential and hypothesized that this potential could be predicated by basic soil properties. A total of 68 soil samples were taken from 17 bermudagrass sites in North Carolina. Basic soil properties were analyzed, including soil C and N, C:N ratio, microbial biomass, moisture, pH, and percent silt/clay/sand. Soil samples varied most widely in texture, followed by soil C and N, microbial biomass, moisture, pH, and C:N ratio. The pools of extractable organic N and inorganic N were comparable, indicating that soluble organic N should be considered as a pathway of N loss from turfgrass. Turfgrass with large pools and production of reactive N was characterized by high soil C and N, microbial biomass, and moisture. Because soil C and N accumulate over time after turfgrass establishment, turfgrass age could be a suitable practical indicator of N loss potential and thus could be used to implement changes in management. Pools and production of reactive N in liquid and gas phases were well correlated, suggesting that if a turfgrass system has a high potential of N loss via leaching and runoff, it may also be of a high potential for NO emissions.}, number={1}, journal={JOURNAL OF ENVIRONMENTAL QUALITY}, author={Lu, Caiyan and Bowman, Daniel and Rufty, Thomas and Shi, Wei}, year={2015}, pages={210–218} }
 @article{o’connell_shi_grossman_hoyt_fager_creamer_2015, title={Short-term nitrogen mineralization from warm-season cover crops in organic farming systems}, volume={396}, ISSN={0032-079X 1573-5036}, url={http://dx.doi.org/10.1007/S11104-015-2594-2}, DOI={10.1007/s11104-015-2594-2}, number={1-2}, journal={Plant and Soil}, publisher={Springer Science and Business Media LLC}, author={O’Connell, S. and Shi, W. and Grossman, J. M. and Hoyt, G. D. and Fager, K. L. and Creamer, N. G.}, year={2015}, month={Jul}, pages={353–367} }
 @article{chen_mothapo_shi_2015, title={Soil Moisture and pH Control Relative Contributions of Fungi and Bacteria to N2O Production}, volume={69}, ISSN={["1432-184X"]}, DOI={10.1007/s00248-014-0488-0}, abstractNote={Fungal N(2)O production has been progressively recognized, but its controlling factors remain unclear. This study examined the impacts of soil moisture and pH on fungal and bacterial N(2)O production in two ecosystems, conventional farming and plantation forestry. Four treatments, antibiotic-free soil and soil amended with streptomycin, cycloheximide, or both were used to determine N(2)O production of fungi versus bacteria. Soil moisture and pH effects were assessed under 65-90 % water-filled pore space (WFPS) and pH 4.0-9.0, respectively. Irrespective of antibiotic treatments, soil N(2)O fluxes peaked at 85-90 % WFPS and pH 7.0 or 8.0, indicating that both fungi and bacteria preferred more anoxic and neutral or slightly alkaline conditions in producing N(2)O. However, compared with bacteria, fungi contributed more to N(2)O production under sub-anoxic and acidic conditions. Real-time polymerase chain reaction of 16S, ITS rDNA, and denitrifying genes for quantifications of bacteria, fungi, and denitrifying bacteria, respectively, showed that fungi were more abundant at acidic pH, whereas total and denitrifying bacteria favored neutral conditions. Such variations in the abundance appeared to be related to the pH effects on the relative fungal and bacterial contribution to N(2)O production.}, number={1}, journal={MICROBIAL ECOLOGY}, author={Chen, Huaihai and Mothapo, Nape V. and Shi, Wei}, year={2015}, month={Jan}, pages={180–191} }
 @article{tian_shi_2014, title={Short-term effects of plant litter on the dynamics, amount, and stoichiometry of soil enzyme activity in agroecosystems}, volume={65}, ISSN={["1778-3615"]}, DOI={10.1016/j.ejsobi.2014.08.004}, abstractNote={Addition of plant litter can affect soil enzyme activity at three scales: dynamics, amount, and stoichiometry. In this study, we examined the dependence of soil enzyme activity at all three scales on litter quality. Soils of similar texture were collected from conventional and organic farming systems, the Center for Environmental Farming Systems, Goldsboro, North Carolina, USA. Soil samples were then amended with senescent pine needles, grass materials, and soybean residues of C:N ratio 139, 50, and 9, respectively, at 2 mg C g−1 soil, and the activities of soil β-glucosidase, exoglucanase, β-glucosaminidase, and phenol oxidase were measured over the course of 90-d incubation. Relationships between the dynamics of enzyme activity and litter quality appeared to be enzyme specific. Time patterns of soil β-glucosidase and β-glucosaminidase activity were independent of litter quality, with rapid increase in enzyme activity and reaching a peak several weeks after litter addition. In contrast, time patterns of polymer-degrading enzymes (exoglucanase and phenol oxidase) were dependent on litter quality. Exoglucanase activity showed a concave function with time following the addition of soybean residues or grass materials, but increased slightly following the addition of pine needles. Cumulative activities of soil enzymes were upregulated following litter addition and could be qualitatively assessed by litter C:N ratio. The activity of β-glucosaminidase was negatively related to litter C:N ratio, being greatest in soybean residues-amended soil. Litter of a low C:N ratio was generally better than litter of a high C:N ratio for increasing soil cellulase activity and vice versa for phenol oxidase. However, the stoichiometry of soil enzyme activity was decoupled with litter C:N ratio. Soybean residues and pine needles at opposite ends of the litter C:N range were more similar in the ratio of C- to N-acquiring enzyme activity. We also examined pH effects on the expression of added enzymes. Soil enzyme activities were enhanced as soil pH increased from 6 to 8. pH-associated changes in enzyme activity were generally smaller as compared to changes caused by other factors during the 42-d incubation. Our results suggest that litter effects on the dynamics, amount, and stoichiometry of soil enzyme activity were independent of soil pH. Litter C:N was a good indicator for the total amount, but not for the dynamics or stoichiometry of soil enzyme activity.}, journal={EUROPEAN JOURNAL OF SOIL BIOLOGY}, author={Tian, Lei and Shi, Wei}, year={2014}, pages={23–29} }
 @article{liang_grossman_shi_2014, title={Soil microbial responses to winter, legume cover crop management during organic transition}, volume={65}, ISSN={["1778-3615"]}, DOI={10.1016/j.ejsobi.2014.08.007}, abstractNote={Legume cover cropping has been widely used as an efficient strategy to improve soil fertility. Although this management practice is important to resolve N deficiency for the transition from conventional to organic production systems, optimization is necessary to determine legume cover crop species and termination methods. This study used soil microbial properties and processes to evaluate the suitability of several legume cover crops and termination methods for organic transition in southeastern USA. Soil samples were taken from two newly-established study sites, each containing 12 treatments of three termination methods (disk, flail, and spray) and four cover types (no cover crop, Austrian winter pea, hairy vetch, and crimson clover). Compared to disking and spraying, flail mowing significantly increased soil microbial biomass C by ∼17%, C mineralization by ∼25%, N mineralization by ∼16%, and nitrification potential by ∼36%, 12 weeks after cover crop termination. However, cover cropping only stimulated nitrification potential, but not C and N mineralization. Furthermore, the activities of soil enzymes (exoglucanase, β-glucosidase, and β-glucosaminidase) appeared to be more responsive to cover types than to termination methods. Among three cover crops, Austrian winter pea showed the greatest positive effects on nitrification potential, β-glucosidase, and β-glucosaminidase. The ratio of C mineralization to microbial biomass C also differed with cover types, being lowest in Austrian winter pea. Our results indicated that legume species even with small differences in C-to-N ratio and lignin and cellulose contents could have varied effects on soil microbial properties and processes. Nitrification potential, representing the function of a small group of soil microbial community, was proved to be sensitive to both legume species and termination methods.}, journal={EUROPEAN JOURNAL OF SOIL BIOLOGY}, author={Liang, Shangtao and Grossman, Julie and Shi, Wei}, year={2014}, pages={15–22} }
 @article{tian_shi_2014, title={Soil peroxidase regulates organic matter decomposition through improving the accessibility of reducing sugars and amino acids}, volume={50}, ISSN={["1432-0789"]}, DOI={10.1007/s00374-014-0903-1}, number={5}, journal={BIOLOGY AND FERTILITY OF SOILS}, author={Tian, Lei and Shi, Wei}, year={2014}, month={Jul}, pages={785–794} }
 @article{barnes_nelson_whipker_dickey_hesterberg_shi_2014, title={Statistical model for describing macronutrient impacts on container substrate pH over time}, volume={49}, number={2}, journal={HortScience}, author={Barnes, J. and Nelson, P. and Whipker, B. E. and Dickey, D. A. and Hesterberg, D. and Shi, W.}, year={2014}, pages={207–214} }
 @article{chen_mothapo_shi_2014, title={The significant contribution of fungi to soil N2O production across diverse ecosystems}, volume={73}, ISSN={["1873-0272"]}, DOI={10.1016/j.apsoil.2013.08.011}, abstractNote={Sporadic observations from pure culture study and direct soil measurement have indicated that fungi can substantially contribute to soil N2O production. Yet, it is still uncertain whether this fungal significance is a more general ecological phenomenon. In this study, relative contributions of fungi and bacteria to soil N2O production were examined in five ecosystems, including conventional farming (CON), integrated crop and livestock system (ICL), organic farming (ORG), plantation forestry (PF), and abandoned agriculture field subjected to natural succession (SUCC). Soil N2O production was measured at 90% water-filled pore space from antibiotic-free controls and soils amended with streptomycin, cycloheximide, or both. Streptomycin and cycloheximide additions significantly reduced soil N2O fluxes from the five systems, ranging from 31% to 54% and 40% to 51%, respectively. Fungi contributed more to soil N2O fluxes than bacteria in PF, whereas fungi and bacteria made comparable contributions in other four systems. Furthermore, soil pH was correlated positively with the percentage of bacterial contribution to soil N2O flux, but negatively with the percentage of fungal contribution to soil N2O flux as well as the ratio of fungal-to-bacterial contributions. Our results showed that fungi could potentially contribute to soil N2O production in diverse agroecosystems and their contribution might be more pronounced in the acidic plantation forestry.}, journal={APPLIED SOIL ECOLOGY}, author={Chen, Huaihai and Mothapo, Nape V. and Shi, Wei}, year={2014}, month={Jan}, pages={70–77} }
 @article{mothapo_grossman_sooksa-nguan_maul_bräuer_shi_2013, title={Cropping history affects nodulation and symbiotic efficiency of distinct hairy vetch (Vicia villosa Roth.) genotypes with resident soil rhizobia}, volume={49}, ISSN={0178-2762 1432-0789}, url={http://dx.doi.org/10.1007/S00374-013-0781-Y}, DOI={10.1007/S00374-013-0781-Y}, abstractNote={Compatible rhizobia strains are essential for nodulation and biological nitrogen fixation (BNF) of hairy vetch (Vicia villosa Roth, HV). We evaluated how past HV cultivation affected nodulation and BNF across host genotypes. Five groups of similar HV genotypes were inoculated with soil dilutions from six paired fields, three with 10-year HV cultivation history (HV+) and three with no history (HV−), and used to determine efficiency of rhizobia nodulation and BNF. Nodulation was equated to nodule number and mass, BNF to plant N and Rhizobium leguminosarum biovar viceae (Rlv) soil cell counts using qPCR to generate an amplicon of targeted Rlv nodD genes. Both HV cultivation history and genotype affected BNF parameters. Plants inoculated with HV+ soil dilutions averaged 60 and 70 % greater nodule number and mass, respectively. Such plants also had greater biomass and tissue N than those inoculated with HV− soil. Plant biomass and tissue N were strongly correlated to nodule mass (r 2 = 0.80 and 0.50, respectively), while correlations to nodule number were low (r 2 = 0.50 and 0.31, respectively). Although hairy vetch rhizobia occur naturally in soils, past cultivation of HV was shown in this study to enhance nodulation gene-carrying Rlv population size and/or efficiency of rhizobia capable of nodulation and N fixation.}, number={7}, journal={Biology and Fertility of Soils}, publisher={Springer Science and Business Media LLC}, author={Mothapo, N. V. and Grossman, J. M. and Sooksa-nguan, T. and Maul, J. and Bräuer, S. L. and Shi, W.}, year={2013}, month={Feb}, pages={871–879} }
 @article{mothapo_grossman_maul_shi_isleib_2013, title={Genetic diversity of resident soil rhizobia isolated from nodules of distinct hairy vetch (Vicia villosa Roth) genotypes}, volume={64}, ISSN={["1873-0272"]}, DOI={10.1016/j.apsoil.2012.12.010}, abstractNote={Hairy vetch (Vicia villosa Roth, HV) is widely grown as a legume cover crop throughout the U.S.A., with biological nitrogen fixation (BNF) through symbiosis with Rhizobium leguminosarum biovar viciae (Rlv) being one of the most sought after benefits of its cultivation. This study determined if HV cultivation history and plant genotype affect genetic diversity of resident Rlv. Soil samples were collected from within farmers’ fields at Graham, Cedar Grove and Ivanhoe sites in North Carolina and pairs of genetically similar hairy vetch genotypes used as trap hosts. A total of 519 Rlv strains were isolated from six paired field soils, three with and three without histories of HV cultivation. A total of 46 strains failed to PCR-amplify the nifH gene; however nodC PCR amplification of these nifH-negative strains resulted in amplification of 22 of the strains. Repetitive element polymerase chain reaction (rep-PCR) with BOX-A1R primer and redundancy analysis showed rhizobial diversity to vary greatly within and between fields, with over 30 BOX banding patterns obtained across the six fields. Cluster analysis of BOX-PCR banding patterns resulted in 36 genetic groups of Rlv at a similarity level of 70%, with 15 of the isolates from fields with HV history not belonging to any of the clusters. Site was found to be the main driver of isolate diversity overall, explaining 57%, of the total variation among rhizobia occupying HV nodules, followed by history of hairy vetch cultivation. Evidence of a HV host genotype influence on the populations of rhizobia that infect hairy vetch was also observed, with plant genotype explaining 12.7% of the variation among all isolates. Our results show that second to site, HV cultivation history was the most important driver of rhizobial nodule community structure and increases the genetic diversity of resident Rlv in soils.}, journal={APPLIED SOIL ECOLOGY}, author={Mothapo, N. V. and Grossman, J. M. and Maul, J. E. and Shi, W. and Isleib, T.}, year={2013}, month={Feb}, pages={201–213} }
 @article{mothapo_chen_cubeta_shi_2013, title={Nitrous oxide producing activity of diverse fungi from distinct agroecosystems}, volume={66}, ISSN={["1879-3428"]}, DOI={10.1016/j.soilbio.2013.07.004}, abstractNote={Fungi represent a significant component of the soil microbial community and play critical ecological roles in carbon and nitrogen mediated processes. Therefore, fungi capable of nitrous oxide (N2O) production may have great implications to soil N2O emission. The primary objective of this research was to identify and characterize N2O-producing fungi in agricultural soil systems and determine their relative physiological responses to inorganic N, pH and oxygen availability. Soil samples were collected from five agricultural-based systems: conventional farming, organic farming, integrated crop and livestock, plantation forestry, and an abandoned agriculture field subjected to natural succession. Fungi were isolated from soil and examined for N2O production in a nitrate-containing liquid Czapek medium amended with or without cycloheximide or streptomycin. Fungal population levels were similar among the five systems, ranging from 1.1 to 3.7 × 105 colony-forming units per gram of soil. One hundred-fifty one fungal colonies were selected based on colony morphology and tested for N2O production. About half (i.e., 45%) of tested isolates representing at least 16 genera and 30 species of filamentous fungi were capable of producing N2O. Neocosmospora vasinfecta exhibited the highest production of N2O in laboratory based assays, followed by Aspergillus versicolor, A. oryzae, A. terreus, Fusarium oxysporum and Penicillium pinophilum. Ten selected N2O-producing fungus isolates were subsequently evaluated to determine the influence of nitrogen species, pH and O2 on N2O production. Seven of the 10 selected isolates had 65% or greater N2O production in a nitrite than a nitrate medium. Ninety and 60%, of isolates showed greatest N2O production at neutral pH 7.0 and ≤5% headspace O2 conditions, respectively. Our results demonstrate that N2O-producing fungi were prevalent in the five soil systems and production of N2O varied among isolates examined under different imposed abiotic conditions in the laboratory.}, journal={SOIL BIOLOGY & BIOCHEMISTRY}, author={Mothapo, Nape V. and Chen, Huaihai and Cubeta, Marc A. and Shi, Wei}, year={2013}, month={Nov}, pages={94–101} }
 @article{li_hu_bowman_shi_2013, title={Nitrous oxide production in turfgrass systems: Effects of soil properties and grass clipping recycling}, volume={67}, ISSN={0929-1393}, url={http://dx.doi.org/10.1016/J.APSOIL.2013.03.002}, DOI={10.1016/j.apsoil.2013.03.002}, abstractNote={Soil N2O emissions can affect global environments because N2O is a potent greenhouse gas and ozone depletion substance. In the context of global warming, there is increasing concern over the emissions of N2O from turfgrass systems. It is possible that management practices could be tailored to reduce emissions, but this would require a better understanding of factors controlling N2O production. In the present study we evaluated the spatial variability of soil N2O production and its correlation with soil physical, chemical and microbial properties. The impacts of grass clipping addition on soil N2O production were also examined. Soil samples were collected from a chronosequence of three golf courses (10, 30, and 100-year-old) and incubated for 60 days at either 60% or 90% water filled-pore space (WFPS) with or without the addition of grass clippings or wheat straw. Both soil N2O flux and soil inorganic N were measured periodically throughout the incubation. For unamended soils, cumulative soil N2O production during the incubation ranged from 75 to 972 ng N g−1 soil at 60% WFPS and from 76 to 8842 ng N g−1 soil at 90% WFPS. Among all the soil physical, chemical and microbial properties examined, soil N2O production showed the largest spatial variability with the coefficient of variation ~110% and 207% for 60% and 90% WFPS, respectively. At 60% WFPS, soil N2O production was positively correlated with soil clay fraction (Pearson's r = 0.91, P < 0.01) and soil NH4+–N (Pearson's r = 0.82, P < 0.01). At 90% WFPS, however, soil N2O production appeared to be positively related to total soil C and N, but negatively related to soil pH. Addition of grass clippings and wheat straw did not consistently affect soil N2O production across moisture treatments. Soil N2O production at 60% WFPS was enhanced by the addition of grass clippings and unaffected by wheat straw (P < 0.05). In contrast, soil N2O production at 90% WFPS was inhibited by the addition of wheat straw and little influenced by glass clippings (P < 0.05), except for soil samples with >2.5% organic C. Net N mineralization in soil samples with >2.5% organic C was similar between the two moisture regimes, suggesting that O2 availability was greater than expected from 90% WFPS. Nonetheless, small and moderate changes in the percentage of clay fraction, soil organic matter content, and soil pH were found to be associated with large variations in soil N2O production. Our study suggested that managing soil acidity via liming could substantially control soil N2O production in turfgrass systems.}, journal={Applied Soil Ecology}, publisher={Elsevier BV}, author={Li, Xuechao and Hu, Feng and Bowman, Daniel and Shi, Wei}, year={2013}, month={May}, pages={61–69} }
 @article{li_hu_shi_2013, title={Plant material addition affects soil nitrous oxide production differently between aerobic and oxygen-limited conditions}, volume={64}, ISSN={["0929-1393"]}, DOI={10.1016/j.apsoil.2012.10.003}, abstractNote={It is a common agricultural practice for crop residues to be plowed into the soil or left on the soil surface. Soil addition of crop residues can considerably modify soil microbial activity and net N mineralization, and in general such modifications are negatively related to the C:N ratios of crop residues. Yet, little is known on the impacts of crop residues of different C:N ratios on soil nitrous oxide (N2O) production under different aeration conditions via nitrification and denitrification. In this study, an 84-day laboratory incubation was conducted under aerobic and O2-limited conditions and soil N2O production was measured every 3 days after the addition of plant materials with a wide range of C:N ratios from 14 to 297. Two aerobic conditions were created by adjusting the water content of soil at a bulk density of 1.1 g cm−3 to 30% water-filled pore space (WFPS) and 60% WFPS, and two O2-limited conditions were made by 90% WFPS and fluctuation between 90% and 30% WFPS. Each fluctuation cycle lasted 9 days and soil water content was readjusted to 90% WFPS at the end of each cycle. We also measured microbial respiration activity and net N mineralization periodically (i.e., 3, 7, 14, 28, 42, 56, 70, and 84 days) during the incubation and microbial biomass C at the end of incubation. At aerobic conditions, soil amendments of plant materials, regardless of their C:N ratios, all enhanced soil N2O production. However, net N mineralization was dependent on plant material C:N ratios, being significantly higher or lower than the control for C:N ratios ∼15 and C:N ratios ≥44, respectively. Such inconsistent responses indicated that nitrifiers mediating nitrification and therefore byproduct N2O production could strongly compete with heterotrophic microbes for NH4+ and therefore net N mineralization was not a good predictor for nitrification-associated N2O production. Interestingly, plant material additions reduced soil N2O production by up to ∼95% at O2-limited conditions, perhaps due to NO3− limitation. Soil NO3− production via nitrification could be low at O2-limited conditions, and soil NO3− availability could be further reduced due to increases in microbial biomass and thus microbial N assimilation after plant material additions. This NO3− limitation might enhance N2O reduction to N2, by which denitrifiers could harvest more energy from the consumption of limited NO3−. Nonetheless, our results revealed contrasting differences in N2O production between aerobic and O2-limited conditions following soil amendments of plant materials.}, journal={APPLIED SOIL ECOLOGY}, author={Li, Xuechao and Hu, Feng and Shi, Wei}, year={2013}, month={Feb}, pages={91–98} }
 @misc{chen_li_hu_shi_2013, title={Soil nitrous oxide emissions following crop residue addition: a meta-analysis}, volume={19}, ISSN={["1365-2486"]}, DOI={10.1111/gcb.12274}, abstractNote={Abstract}, number={10}, journal={GLOBAL CHANGE BIOLOGY}, author={Chen, Huaihai and Li, Xuechao and Hu, Feng and Shi, Wei}, year={2013}, month={Oct}, pages={2956–2964} }
 @article{gannon_hixson_weber_shi_yelverton_rufty_2013, title={Sorption of Simazine and S-Metolachlor to Soils from a Chronosequence of Turfgrass Systems}, volume={61}, ISSN={["1550-2759"]}, DOI={10.1614/ws-d-12-00173.1}, abstractNote={Pesticide sorption by soil is among the most sensitive input parameters in many pesticide-leaching models. For many pesticides, organic matter is the most important soil constituent influencing pesticide sorption. Increased fertility, irrigation, and mowing associated with highly maintained turfgrass areas result in constant deposition of organic material, creating a soil system that can change drastically with time. Changes in soil characteristics could affect the environmental fate of pesticides applied to turfgrass systems of varying ages. Sorption characteristics of simazine andS-metolachlor were determined on five soils from bermudagrass systems of increasing ages (1, 4, 10, 21, and 99 yr) and compared to adjacent native pine and bare-ground areas. Surface soil (0 to 5 cm) and subsurface soil (5 to 15 cm) from all sites were air-dried and passed through a 4-mm sieve for separation from plant material. Using a batch-equilibrium method, sorption isotherms were determined for each soil. Data were fit to the Freundlich equation, andKd(soil sorption coefficient) andKoc(organic carbon sorption coefficient) values were determined. Sorption and soil system age were directly related to organic matter content in the soil. Sorption of both herbicides increased with age of the soil system and was greatest on the surface soil from the oldest bermudagrass soil system. Herbicide sorption decreased at greater soil depths with lower organic matter. Greater amount of14C–simazine sorbed to subsurface soil of the oldest turfgrass system compared to14C–S-metolachlor. Results indicate that as bermudagrass systems age and accumulate higher organic matter levels increased herbicide sorption may decrease the leaching potential and bioavailability of simazine andS-metolachlor.}, number={3}, journal={WEED SCIENCE}, author={Gannon, Travis W. and Hixson, Adam C. and Weber, Jerome B. and Shi, Wei and Yelverton, Fred H. and Rufty, Thomas W.}, year={2013}, pages={508–514} }
 @article{yang_shi_zhu_2013, title={The impact of secondary forests conversion into larch plantations on soil chemical and microbiological properties}, volume={368}, ISSN={["1573-5036"]}, DOI={10.1007/s11104-012-1535-6}, number={1-2}, journal={PLANT AND SOIL}, author={Yang, Kai and Shi, Wei and Zhu, Jiao-Jun}, year={2013}, month={Jul}, pages={535–546} }
 @article{dell_carley_rufty_shi_2012, title={Heat stress and N fertilization affect soil microbial and enzyme activities in the creeping bentgrass (Agrostis Stolonifera L.) rhizosphere}, volume={56}, ISSN={0929-1393}, url={http://dx.doi.org/10.1016/j.apsoil.2012.02.002}, DOI={10.1016/j.apsoil.2012.02.002}, abstractNote={High summer temperatures often cause damage to bentgrass on putting greens in transition zone regions. One of the most damaging effects is a depression of rooting. Although heat stress effects on plant functions are considered as a main reason for the damage, heat stress also may be related to organic matter (OM) accumulation and poor gas exchange into the rhizosphere. The OM accumulation and the often-observed root dieback suggest that soil microbial processes play a role in summer bentgrass decline. In this study, the impact of high temperature on soil microbial properties and enzyme activities was examined using creeping bentgrass (Agrostis stolonifera) growing in a phytotron controlled environment chamber. The high temperature exposures (34/30 °C versus 22/18 °C for controls) lasted for four weeks and the bentgrass cultures received mineral N at two rates. Our working hypothesis was that not only did high temperatures stimulate overall soil microbial and enzyme activity but also selectively modified microbial catabolic functions. To test this hypothesis, we compared temperature sensitivities and Q10 values of microbial substrate utilization patterns using a Biolog plate approach and soil enzyme activities. The results indicated that soil enzyme activities had similar responses to assay temperatures and their Q10 values averaged ∼2 with changes of laboratory assay temperatures from 12 to 22 °C and from 22 to 34 °C. Such positive responses of microbial activity to high temperatures were supported by parallel increases in rates of microbial substrate utilization. Total substrate availability in Biolog plates also increased with laboratory assay temperatures. This enhancement could not be explained by the overall stimulation of high temperature on microbial activity, but instead by selective modification of microbial community functions. Nitrogen fertilization significantly changed soil biological activities. Phenol oxidase activity was reduced by the high rate of N fertilization, whereas β-glucosidase and β-glucosaminidase activities were increased. Interactions on soil enzyme activities between growth chamber temperatures and N fertilization rates also occurred. Soil peroxidase activity was ∼three-fold greater for bentgrass subjected to heat stress and the low rate of N fertilization. Our results indicated that summer heat stress and the associated increases in root and OM degradation in bentgrass systems are related with overall temperature stimulations on soil microbial and enzyme activities as well as with modifications in functional components of the microbial community.}, journal={Applied Soil Ecology}, publisher={Elsevier BV}, author={Dell, Emily A. and Carley, Danesha Seth and Rufty, Thomas and Shi, Wei}, year={2012}, month={May}, pages={19–26} }
 @article{taggart_heitman_shi_vepraskas_2012, title={Temperature and Water Content Effects on Carbon Mineralization for Sapric Soil Material}, volume={32}, ISSN={0277-5212 1943-6246}, url={http://dx.doi.org/10.1007/S13157-012-0327-3}, DOI={10.1007/S13157-012-0327-3}, number={5}, journal={Wetlands}, publisher={Springer Science and Business Media LLC}, author={Taggart, Matthew and Heitman, J. L. and Shi, Wei and Vepraskas, Michael}, year={2012}, month={Jul}, pages={939–944} }
 @article{richter_ivors_shi_benson_2011, title={Cellulase Activity as a Mechanism for Suppression of Phytophthora Root Rot in Mulches}, volume={101}, ISSN={["0031-949X"]}, DOI={10.1094/phyto-04-10-0125}, abstractNote={ Wood-based mulches are used in avocado production and are being tested on Fraser fir for reduction of Phytophthora root rot, caused by Phytophthora cinnamomi. Research with avocado has suggested a role of microbial cellulase enzymes in pathogen suppression through effects on the cellulosic cell walls of Phytophthora. This work was conducted to determine whether cellulase activity could account for disease suppression in mulch systems. A standard curve was developed to correlate cellulase activity in mulches with concentrations of a cellulase product. Based on this curve, cellulase activity in mulch samples was equivalent to a cellulase enzyme concentration of 25 U ml–1 or greater of product. Sustained exposure of P. cinnamomi to cellulase at 10 to 50 U ml–1 significantly reduced sporangia production, but biomass was only reduced with concentrations over 100 U ml–1. In a lupine bioassay, cellulase was applied to infested soil at 100 or 1,000 U ml–1 with three timings. Cellulase activity diminished by 47% between 1 and 15 days after application. Cellulase applied at 100 U ml–1 2 weeks before planting yielded activity of 20.08 μmol glucose equivalents per gram of soil water (GE g–1 aq) at planting, a level equivalent to mulch samples. Cellulase activity at planting ranged from 3.35 to 48.67 μmol GE g–1 aq, but no treatment significantly affected disease progress. Based on in vitro assays, cellulase activity in mulch was sufficient to impair sporangia production of P. cinnamomi, but not always sufficient to impact vegetative biomass. }, number={2}, journal={PHYTOPATHOLOGY}, author={Richter, Brantlee Spakes and Ivors, Kelly and Shi, Wei and Benson, D. M.}, year={2011}, month={Feb}, pages={223–230} }
 @article{wherley_bowman_shi_rufty_2011, title={Effect of Soil Saturation on Development and 15N-Nitrate Uptake Efficiency of  Two Warm Season Grasses Emerging from Dormancy}, volume={34}, ISSN={0190-4167 1532-4087}, url={http://dx.doi.org/10.1080/01904167.2011.610489}, DOI={10.1080/01904167.2011.610489}, abstractNote={Use of effluent on turfgrass is increasing due to population growth and limited water supplies. Because effluent is generated continuously, turf managers may be forced to over-irrigate, leading to soil saturation. Although the nutrients in effluent are readily absorbed by turf, the effects of prolonged soil saturation on uptake are unknown. This research examined the impact of soil saturation on plant development and nitrate uptake of two warm-season turfgrasses emerging from dormancy. Dormant grass/soil cores of hybrid bermudagrass and common centipedegrass were treated to stimulate regrowth, with soil moisture controlled at saturation (∼0.36 cm3 cm−3) or field capacity (0.13 cm3 cm−3). Soil saturation reduced canopy development in both species, but shoot biomass was affected only in bermudagrass. Nitrate uptake by both species was generally unaffected by soil saturation. While extended periods of soil saturation may alter plant development, they do not impair the ability of these turfgrasses to absorb nitrogen.}, number={13}, journal={Journal of Plant Nutrition}, publisher={Informa UK Limited}, author={Wherley, Benjamin and Bowman, Daniel and Shi, Wei and Rufty, Thomas, Jr.}, year={2011}, month={Oct}, pages={2039–2054} }
 @article{liu_dell_yao_rufty_shi_2011, title={Microbial and soil properties in bentgrass putting greens: Impacts of nitrogen fertilization rates}, volume={162}, ISSN={["1872-6259"]}, DOI={10.1016/j.geoderma.2011.02.009}, abstractNote={Nitrogen fertilization is important for maintaining the quality of golf course putting greens, but causes environmental concerns and affects soil organic matter buildup. Belowground biology and processes are vital to address both environmental and organic buildup issues. We examined microbial and soil properties in sand-based bentgrass putting greens that had been unfertilized or fertilized at the rates of 195, 244, and 305 kg N ha−1 yr−1 for over one year after turf establishment. Nitrogen fertilization increased soil organic C by ~ 10% and slightly modified microbial community as revealed by denaturing gradient gel electrophoresis, but had no effects on microbial biomass or C and N mineralization. We observed that changes in soil pH and enzyme activities were the functions of fertilization rates. Soil pH was reduced by ~ 0.3 to 0.8 units as fertilization rates increased. The activities of soil enzymes (β-glucosidase, N-acetyl-β-glucosaminidase, chitinase, and cellulase) were enhanced by fertilization at 195 or 244 kg N ha−1 yr−1, but was equivalent to or even lower than those in the unfertilized control when fertilization rate reached 305 kg N ha−1 yr−1. Results indicated that the activity of soil enzymes could be used as an important metric to diagnose the impacts of fertilization rates on soil. Fertilization rate at approximately 200 kg N ha−1 yr−1 appeared to be appropriate for managing putting greens.}, number={1-2}, journal={GEODERMA}, author={Liu, Yueyan and Dell, Emily and Yao, Huaiying and Rufty, Thomas and Shi, Wei}, year={2011}, month={Apr}, pages={215–221} }
 @article{yao_bowman_shi_2011, title={Seasonal variations of soil microbial biomass and activity in warm- and cool-season turfgrass systems}, volume={43}, ISSN={["0038-0717"]}, DOI={10.1016/j.soilbio.2011.03.031}, abstractNote={Plant growth can be an important factor regulating seasonal variations of soil microbial biomass and activity. We investigated soil microbial biomass, microbial respiration, net N mineralization, and soil enzyme activity in turfgrass systems of three cool-season species (tall fescue, Festuca arundinacea Schreb., Kentucky bluegrass, Poa pratensis L., and creeping bentgrass, Agrostis palustris L.) and three warm-season species (centipedegrass, Eremochloa ophiuroides (Munro.) Hack, zoysiagrass, Zoysia japonica Steud, and bermudagrass, Cynodon dactylon (L.) Pers.). Microbial biomass and respiration were higher in warm- than the cool-season turfgrass systems, but net N mineralization was generally lower in warm-season turfgrass systems. Soil microbial biomass C and N varied seasonally, being lower in September and higher in May and December, independent of turfgrass physiological types. Seasonal variations in microbial respiration, net N mineralization, and cellulase activity were also similar between warm- and cool-season turfgrass systems. The lower microbial biomass and activity in September were associated with lower soil available N, possibly caused by turfgrass competition for this resource. Microbial biomass and activity (i.e., microbial respiration and net N mineralization determined in a laboratory incubation experiment) increased in soil samples collected during late fall and winter when turfgrasses grew slowly and their competition for soil N was weak. These results suggest that N availability rather than climate is the primary determinant of seasonal dynamics of soil microbial biomass and activity in turfgrass systems, located in the humid and warm region.}, number={7}, journal={SOIL BIOLOGY & BIOCHEMISTRY}, author={Yao, Huaiying and Bowman, Daniel and Shi, Wei}, year={2011}, month={Jul}, pages={1536–1543} }
 @article{carley_goodman_sermons_shi_bowman_miller_rufty_2011, title={Soil Organic Matter Accumulation in Creeping Bentgrass Greens: A Chronosequence with Implications for Management and Carbon Sequestration}, volume={103}, ISSN={1435-0645}, url={http://dx.doi.org/10.2134/agronj2010.0335}, DOI={10.2134/agronj2010.0335}, abstractNote={Excessive organic matter (OM) accumulation in creeping bentgrass (Agrostis palustris Huds.) putting greens, and its restriction of permeability, is one of the most difficult problems in turfgrass management. In this transition zone study, we characterized temporal and spatial aspects of OM accumulation, in an attempt to assess the effectiveness of management and to begin to uncover the processes controlling C sequestration. Root zone samples were collected from sand‐based putting greens at 49 golf courses of various ages, generating 212 individual observations. Organic matter accumulated hyperbolically over time in the top 2.5 cm; apparent critical levels of 40 g kg−1 were exceeded within 5 yr. At a depth of 2.5 to 7.6 cm, accumulation was much slower and linear over time, and critical levels were not reached even after 20 yr. Oxygen levels were never depressed more than 15%, indicating that intensive management of the upper soil profile was successfully allowing gas exchange into the root zone. Carbon accumulated in the soil profile hyperbolically, reflecting changes in the large OM pool near the soil surface. The sequestration rate of 59 g m−2 yr−1 over 25 yr was less than that observed by others examining soil under bentgrass greens in different environments. The evidence indicates that OM and C accumulation are strongly influenced by increasing microbial degradation rates as turfgrass systems age.}, number={3}, journal={Agronomy Journal}, publisher={American Society of Agronomy}, author={Carley, Danesha Seth and Goodman, David and Sermons, Shannon and Shi, Wei and Bowman, Dan and Miller, Grady and Rufty, Thomas}, year={2011}, pages={604} }
 @article{tian_dell_shi_2010, title={Chemical composition of dissolved organic matter in agroecosystems: Correlations with soil enzyme activity and carbon and nitrogen mineralization}, volume={46}, ISSN={["1873-0272"]}, DOI={10.1016/j.apsoil.2010.09.007}, abstractNote={Soil enzyme-catalyzed depolymerization of organic matter results in the production of low molecular weight and dissolved organic compounds. This fraction of soil organic matter is the immediate energy, carbon and other nutrient substrates for microbial catabolic pathways and thus likely plays an important role in soil processes. The purpose of this study was to elucidate interrelationships among dissolved organic matter, soil enzyme activity, and soil C and N mineralization from diverse agroecosystems. These systems included a conventional cropping, organic cropping, integrated crop–livestock, plantation forestry, and succession from an abandoned agricultural field. We collected surface soil samples from 0 to 10 cm depth in early spring 2009 and examined the concentrations of soil-derived dissolved organic C and N, soluble phenolics, reducing sugars, and amino acids, the activities of β-glucosidase, exoglucanase, phenol oxidase, peroxidase, and β-glucosaminidase, and the rates of soil C and N mineralization. The integrated crop–livestock system showed the highest concentrations of dissolved soil organic C (78 μg C g−1 soil) as well as phenolic compounds (1.5 μg C g−1 soil), reducing sugars (23 μg C g−1 soil), and amino acids (0.76 μg N g−1 soil), and these components were up to 3-fold greater than soils under the other systems. However, soil β-glucosidase activity in the integrated crop–livestock system was significantly lower than the other systems and appeared to reflect the inhibitory role of soluble phenolics on this enzyme; this enzymatic disparity was also revealed in our preliminary study conducted in 2008. Among the five enzyme activities examined, only peroxidase activity was correlated significantly with the chemical composition of dissolved organic matter as well as soil C and N mineralization. Soil peroxidase activity was negatively related to the relative abundance of reducing sugars (i.e., reducing sugar C as a fraction of dissolved organic C, r = −0.92, P < 0.05) and positively with soil C and N mineralization (r = 0.86, P < 0.1 for C mineralization; r = 0.85, P < 0.1 for N mineralization). Furthermore, relative abundance of reducing sugars was negatively associated with soil C mineralization (r = −0.80, P < 0.1) and so was relative abundance of amino acids with soil N mineralization (r = −0.97, P < 0.01). Our results suggested that diverse agroecosystems differed in the chemical composition of dissolved organic matter and the differences could be correlated with soil peroxidase activity and soil C and N mineralization.}, number={3}, journal={APPLIED SOIL ECOLOGY}, author={Tian, Lei and Dell, Emily and Shi, Wei}, year={2010}, month={Nov}, pages={426–435} }
 @article{yao_shi_2010, title={Soil organic matter stabilization in turfgrass ecosystems: Importance of microbial processing}, volume={42}, ISSN={["0038-0717"]}, DOI={10.1016/j.soilbio.2010.01.003}, abstractNote={Biochemical modification of plant materials may contribute considerably to the formation and stabilization of soil organic matter, but its significance remains elusive in turfgrass systems. This study aimed to close this knowledge gap by examining the dynamics of soil organic matter in turfgrass systems as well as its stability using δ13C and δ15N records. Two geographic locations, each containing 3 or 4 turfgrass systems of different ages were used as the study sites because site-associated differences, in particular soil pH (alkaline versus acidic) might cause divergence in microbial processing during organic matter decomposition and resynthesis. We observed that soil C storage was ∼12% greater in the alkaline site than the acidic one. In addition, accumulation rates of soil organic C and N were about 3-fold higher in the alkaline site. Soil organic matter was physically fractionated into light and heavy fractions. Heavy fraction from the alkaline site mineralized more slowly than the acidic one, indicating that soil organic matter was more stable in the alkaline site. Furthermore, the stability of soil organic matter based upon δ15N records and C-to-N ratio of organic matter was again found to be more stable in the alkaline site than the acidic one. While both soil δ13C and δ15N increased as turfgrass systems aged, rates were greater in the alkaline site than the acidic one. Temporal shifts in soil δ13C and δ15N were attributed mainly to isotope fractionation associated with microbial processes rather than selective preservation of 13C- or 15N-enriched chemical compounds of plant materials. Our results suggested that microbial decomposition and resynthesis played an important role in organic matter stabilization in turfgrass systems and this microbial processing could be managed via microbial activity-regulating factors, such as soil pH.}, number={4}, journal={SOIL BIOLOGY & BIOCHEMISTRY}, author={Yao, Huaiying and Shi, Wei}, year={2010}, month={Apr}, pages={642–648} }
 @article{dell_bowman_rufty_shi_2010, title={The community composition of soil-denitrifying bacteria from a turfgrass environment}, volume={161}, ISSN={["1769-7123"]}, DOI={10.1016/j.resmic.2010.03.010}, abstractNote={Soil-denitrifying bacteria in highly-managed turfgrass systems were examined to assess their response to land-use change and time under management. Denitrifier community composition and diversity in a turfgrass chronosequence of 1 to 95-years-old were compared with those in an adjacent pine-dominant forest via molecular investigations of nirK and nosZ gene fragments. Both denaturing gradient gel electrophoresis and sequenced clone libraries revealed that the denitrifier community became more diverse after turf establishment, and the diversity was then preserved. Furthermore, the composition of the turfgrass denitrifier community was slightly affected by time under management. Meta-analysis of sequenced nirK and nosZ gene fragments from a variety of ecosystems showed that denitrifier communities in pine and turf were more similar to those in other environments than to each other, suggesting that land-use change substantially modified the composition and increased the diversity of denitrifiers. This study provides a useful baseline of nirK- and nosZ-type soil denitrifier communities to aid in the evaluation of ecological and environmental impacts of turfgrass systems.}, number={5}, journal={RESEARCH IN MICROBIOLOGY}, author={Dell, Emily A. and Bowman, Daniel and Rufty, Thomas and Shi, Wei}, year={2010}, month={Jun}, pages={315–325} }
 @article{wherley_shi_bowman_rufty_2009, title={Fate of N-15-Nitrate Applied to a Bermudagrass System: Assimilation Profiles in Different Seasons}, volume={49}, ISSN={["1435-0653"]}, DOI={10.2135/cropsci2008.08.0468}, abstractNote={ABSTRACT}, number={6}, journal={CROP SCIENCE}, author={Wherley, Benjamin G. and Shi, Wei and Bowman, Daniel C. and Rufty, Thomas W.}, year={2009}, pages={2291–2301} }
 @article{yao_bowman_rufty_shi_2009, title={Interactions between N fertilization, grass clipping addition and pH in turf ecosystems: Implications for soil enzyme activities and organic matter decomposition}, volume={41}, ISSN={0038-0717}, url={http://dx.doi.org/10.1016/j.soilbio.2009.03.020}, DOI={10.1016/j.soilbio.2009.03.020}, abstractNote={Turf has been acknowledged as an important ecosystem with potential for soil C sequestration. As a major process dictating soil C storage, organic matter decomposition has received little attention in turf systems. Given that soil enzyme-catalyzed biochemical reactions are the rate limiting steps of organic matter decomposition, we examined the activities of oxidative and hydrolytic soil enzymes and their relations with soluble organic compounds and soil C and N mineralization in two turf chronosequences with contrasting soil pH and in response to N fertilization and grass clipping addition. In comparison with turf ecosystems under acidic soil, phenol oxidase activity was about two-fold greater in turf ecosystems under alkaline soil and positively correlated to about two-fold differences in soluble phenolics and dissolved organic C between alkaline and acidic soils. However, the activities of hydrolytic enzymes including cellulase, chitinase, and glucosidase were lower in alkaline soil. It appears that the high concentration of soluble phenolics inhibited the activities of hydrolytic enzymes that in turn limited the decomposition of dissolved organic C and resulted in its accumulation in alkaline soil. Nitrogen mineralization was comparable between alkaline and acidic soils, but CO2 evolution was about two-fold greater in alkaline soil, possibly due to considerable abiotic carbonate dissolution. We observed that mineral N input at 60 mg N kg−1 soil had very minor negative effects on the activities of both phenol oxidase and hydrolytic enzymes. Grass clipping addition did not affect the activity of phenol oxidase, but increased the activities of soil chitinase, cellulase, glucosidase, and glucosaminidase by up to 20% and also soluble phenolics in soil by about 10%. Our results suggest that soil phenol oxidase might regulate the activities of hydrolytic soil enzymes via its control on soluble phenolics and function as an ‘enzymatic latch’ to hold soil organic C in highly managed turf ecosystems. While soil pH is important to affect phenol oxidase activity and therefore decomposition, management practices, i.e., N fertilization and grass clipping addition may indirectly affect the decomposition through enhancing turfgrass productivity and thus soil C input.}, number={7}, journal={Soil Biology and Biochemistry}, publisher={Elsevier BV}, author={Yao, Huaiying and Bowman, Daniel and Rufty, Thomas and Shi, Wei}, year={2009}, month={Jul}, pages={1425–1432} }
 @article{hixson_shi_weber_yelverton_rufty_2009, title={Soil Organic Matter Changes in Turfgrass Systems Affect Binding and Biodegradation of Simazine}, volume={49}, ISSN={["0011-183X"]}, DOI={10.2135/cropsci2008.09.0541}, abstractNote={Concern about pesticide losses from maintained turfgrass areas led us to examine the fate of the triazine herbicide simazine in turfgrass systems and, specifically, interactions between simazine binding to soil organic matter and biodegradation. Soil samples were removed from turfgrass systems of different ages, placed in microcosms, conditioned as sterile or nonsterile, and exposed to 14C‐simazine. At seven sampling intervals, the soil was extracted and 14C was separated into three pools; bound, extractable, and CO2 With sterilized surface soil (0–5 cm), 52, 70, and 71% of applied 14C‐simazine was bound to soil from the 4‐, 21‐, and 99‐yr‐old turfgrass systems, respectively, after 16 wk. With nonsterile conditions, biodegradation became dominant, as 60 to 80% of the 14C was recovered in the CO2 fraction and binding was held at ∼20%. Among all soils evaluated, bound 14C and 14CO2 production was lower in subsurface soil (5–15 cm) from the 4‐ and 21‐yr‐old turfgrass systems. 14C‐simazine disappearance time (DT50) values under nonsterile conditions ranged from 0.9 to 5.8 wk. Results indicate that turfgrass systems have a relatively low amount of simazine available for leaching as the systems age due to a large capacity for biodegradation and binding to organic matter.}, number={4}, journal={CROP SCIENCE}, author={Hixson, Adam C. and Shi, Wei and Weber, Jerome B. and Yelverton, Fred H. and Rufty, Thomas W.}, year={2009}, pages={1481–1488} }
 @article{dell_bowman_rufty_shi_2008, title={Intensive management affects composition of betaproteobacterial ammonia oxidizers in turfgrass systems}, volume={56}, ISSN={["1432-184X"]}, DOI={10.1007/s00248-007-9335-x}, abstractNote={Turfgrass is a highly managed ecosystem subject to frequent fertilization, mowing, irrigation, and application of pesticides. Turf management practices may create a perturbed environment for ammonia oxidizers, a key microbial group responsible for nitrification. To elucidate the long-term effects of turf management on these bacteria, we assessed the composition of betaproteobacterial ammonia oxidizers in a chronosequence of turfgrass systems (i.e., 1, 6, 23, and 95 years old) and the adjacent native pines by using both 16S rRNA and amoA gene fragments specific to ammonia oxidizers. Based on the Shannon-Wiener diversity index of denaturing gradient gel electrophoresis patterns and the rarefaction curves of amoA clones, turf management did not change the relative diversity and richness of ammonia oxidizers in turf soils as compared to native pine soils. Ammonia oxidizers in turfgrass systems comprised a suite of phylogenetic clusters common to other terrestrial ecosystems. Nitrosospira clusters 0, 2, 3, and 4; Nitrosospira sp. Nsp65-like sequences; and Nitrosomonas clusters 6 and 7 were detected in the turfgrass chronosequence with Nitrosospira clusters 3 and 4 being dominant. However, both turf age and land change (pine to turf) effected minor changes in ammonia oxidizer composition. Nitrosospira cluster 0 was observed only in older turfgrass systems (i.e., 23 and 95 years old); fine-scale differences within Nitrosospira cluster 3 were seen between native pines and turf. Further investigations are needed to elucidate the ecological implications of the compositional differences.}, number={1}, journal={MICROBIAL ECOLOGY}, author={Dell, Emily A. and Bowman, Daniel and Rufty, Thomas and Shi, Wei}, year={2008}, month={Jul}, pages={178–190} }
 @article{iyyemperumal_green_israel_ranells_shi_2008, title={Soil chemical and microbiological properties in hay production systems: residual effects of contrasting N fertilization of swine lagoon effluent versus ammonium nitrate}, volume={44}, ISSN={["1432-0789"]}, DOI={10.1007/s00374-007-0221-y}, number={3}, journal={BIOLOGY AND FERTILITY OF SOILS}, author={Iyyemperumal, Kannan and Green, James, Jr. and Israel, Daniel W. and Ranells, Noah N. and Shi, Wei}, year={2008}, month={Feb}, pages={425–434} }
 @article{lyyemperumal_shi_2008, title={Soil enzyme activities in two forage systems following application of different rates of swine lagoon effluent or ammonium nitrate}, volume={38}, ISSN={["1873-0272"]}, DOI={10.1016/j.apsoil.2007.10.001}, abstractNote={Land application of swine lagoon effluent (SLE) to forage production systems is widespread in the southeastern USA and often leads to change in soil properties. Although soil enzymes are crucial to the degradation of soil organic matter and cycling of nutrients, the impacts of SLE application on soil enzyme activities have not been well characterized. We assessed the activities of soil enzymes involved in soil C, N, and P cycling in forage systems 3 years after the termination of three consecutive years of fertilization. Bermudagrass and tall fescue were supplied with SLE or ammonium nitrate (AN) at the rates of 0, 200, 400, and 600 kg plant available N (PAN) ha−1 year−1. The activities of oxidative enzymes (i.e., peroxidase and phenol oxidase) differed between soils amended with SLE versus AN. In soils amended with AN at 600 kg PAN ha−1 year−1, the activities of phenol oxidase and peroxidase were lower than or similar to those in the unfertilized control. In contrast, those activities were stimulated by the application of SLE at the rate of 600 kg PAN ha−1 year−1 except for phenol oxidase in the bermudagrass system. The activities of cellobiohydrolase, β-glucosidase, cellulase, β-glucosaminidase, protease, and acid phosphatase, however, were independent of the source, but varied with the rate of fertilization. In general, the activities of cellobiohydrolase, β-glucosidase, cellulase, β-glucosaminidase, protease, and acid phosphatase in soils with N fertilization at 200 or 400 kg PAN ha−1 year−1 were higher than those in the unfertilized control. But the activities of some hydrolytic enzymes in soils fertilized with 600 kg PAN ha−1 year−1 were similar to or lower than those in the unfertilized control. Non-metric multidimensional scaling (NMS) analysis integrated the activities of eight soil enzymes and showed significant differences between fertilized soils and the unfertilized control and between soils amended with SLE versus AN. These differences in soil integrated enzyme activity were correlated with soil pH (Pearson's correlation coefficient r = 0.76, P < 0.05) rather than with other soil properties. The activities of individual enzymes such as peroxidase, cellulase, and acid phosphatase were also significantly correlated with soil pH. Our results suggested that fertilization-associated change in soil pH could influence the potential activities of soil enzymes in the hay production systems. Application of SLE at 600 kg PAN ha−1 year−1 may be unbeneficial to soil organic matter accumulation and nutrient cycling.}, number={2}, journal={APPLIED SOIL ECOLOGY}, author={Lyyemperumal, Kannan and Shi, Wei}, year={2008}, month={Feb}, pages={128–136} }
 @article{iyyemperumal_israel_shi_2007, title={Soil microbial biomass, activity and potential nitrogen mineralization in a pasture: Impact of stock camping activity}, volume={39}, ISSN={["0038-0717"]}, DOI={10.1016/j.soilbio.2006.07.002}, abstractNote={Grazing animals recycle a large fraction of ingested C and N within a pasture ecosystem, but the redistribution of C and N via animal excreta is often heterogeneous, being highest in stock camping areas, i.e., near shade and watering sources. This non-uniform distribution of animal excreta may modify soil physical and chemical attributes, and likely affect microbial community eco-physiology and soil N cycling. We determined microbial population size, activity, N mineralization, and nitrification in areas of a pasture with different intensity of animal excretal deposits (i.e., stock camping, open grazing and non-grazing areas). The pasture was cropped with coastal bermudagrass (Cynodon dactylon L.) and subjected to grazing by cattle for 4 y. Soil microbial biomass, activity and N transformations were significantly higher at 0–5 cm than at 5–15 cm soil depth, and the impacts of heterogeneous distribution of animal excreta were more pronounced in the uppermost soil layer. Microbial biomass, activity and potential net N mineralization were greater in stock camping areas and were significantly correlated (r2≈0.50, P<0.05) with the associated changes in total soil C and N. However, gross N mineralization and nitrification potential tended to be lower in stock camping areas than in the open grazing areas. The lower gross N mineralization, combined with greater net N mineralization in stock camping areas, implied that microbial N immobilization was lower in those areas than in the other areas. This negative association between microbial N immobilization and soil C is inconsistent with a bulk of publications showing that microbial N immobilization was positively related to the amount of soil C. We hypothesized that the negative correlation was due to microbial direct utilization of soluble organic N and/or changes in microbial community composition towards active fungi dominance in stock camping areas.}, number={1}, journal={SOIL BIOLOGY & BIOCHEMISTRY}, author={Iyyemperumal, Kannan and Israel, Daniel W. and Shi, Wei}, year={2007}, month={Jan}, pages={149–157} }
 @article{iyyemperumal_shi_2007, title={Soil microbial community composition and structure: residual effects of contrasting N fertilization of swine lagoon effluent versus ammonium nitrate}, volume={292}, ISSN={["1573-5036"]}, DOI={10.1007/s11104-007-9219-3}, number={1-2}, journal={PLANT AND SOIL}, author={Iyyemperumal, Kannan and Shi, Wei}, year={2007}, month={Mar}, pages={233–242} }
 @article{shi_dell_bowman_iyyemperumal_2006, title={Soil enzyme activities and organic matter composition in a turfgrass chronosequence}, volume={288}, ISSN={["1573-5036"]}, DOI={10.1007/s11104-006-9116-1}, number={1-2}, journal={PLANT AND SOIL}, author={Shi, Wei and Dell, Emily and Bowman, Daniel and Iyyemperumal, Kannan}, year={2006}, month={Oct}, pages={285–296} }
 @article{shi_muruganandam_bowman_2006, title={Soil microbial biomass and nitrogen dynamics in a turfgrass chronosequence: A short-term response to turfgrass clipping addition}, volume={38}, ISSN={["0038-0717"]}, DOI={10.1016/j.soilbio.2006.01.005}, abstractNote={A mechanistic understanding of soil microbial biomass and N dynamics following turfgrass clipping addition is central to understanding turfgrass ecology. New leaves represent a strong sink for soil and fertilizer N, and when mowed, a significant addition to soil organic N. Understanding the mineralization dynamics of clipping N should help in developing strategies to minimize N losses via leaching and denitrification. We characterized soil microbial biomass and N mineralization and immobilization turnover in response to clipping addition in a turfgrass chronosequence (i.e. 3, 8, 25, and 97 yr old) and the adjacent native pines. Our objectives were (1) to evaluate the impacts of indigenous soil and microbial attributes associated with turf age and land use on the early phase decomposition of turfgrass clippings and (2) to estimate mineralization dynamics of turfgrass clippings and subsequent effects on N mineralization of indigenous soils. We conducted a 28-d laboratory incubation to determine short-term dynamics of soil microbial biomass, C decomposition, N mineralization and nitrification after soil incorporation of turfgrass clippings. Gross rates of N mineralization and immobilization were estimated with 15N using a numerical model, FLAUZ. Turfgrass clippings decomposed rapidly; decomposition and mineralization equivalent to 20–30% of clipping C and N, respectively, occurred during the incubation. Turfgrass age had little effect on decomposition and net N mineralization. However, the response of potential nitrification to clipping addition was age dependent. In young turfgrass systems having low rates, potential nitrification increased significantly with clipping addition. In contrast, old turfgrass systems having high initial rates of potential nitrification were unaffected by clipping addition. Isotope 15N modeling showed that gross N mineralization following clipping addition was not affected by turf age but differed between turfgrass and the adjacent native pines. The flush of mineralized N following clipping addition was derived predominantly from the clippings rather than soil organic N. Our data indicate that the response of soil microbial biomass and N mineralization and immobilization to clipping addition was essentially independent of indigenous soil and microbial attributes. Further, increases in microbial biomass and activity following clipping addition did not stimulate the mineralization of indigenous soil organic N.}, number={8}, journal={SOIL BIOLOGY & BIOCHEMISTRY}, author={Shi, Wei and Muruganandam, Subathra and Bowman, Daniel}, year={2006}, month={Aug}, pages={2032–2042} }
 @article{shi_yao_bowman_2006, title={Soil microbial biomass, activity and nitrogen transformations in a turfgrass chronosequence}, volume={38}, ISSN={["0038-0717"]}, DOI={10.1016/j.soilbio.2005.05.008}, abstractNote={Understanding the chronological changes in soil microbial properties of turfgrass ecosystems is important from both the ecological and management perspectives. We examined soil microbial biomass, activity and N transformations in a chronosequence of turfgrass systems (i.e. 1, 6, 23 and 95 yr golf courses) and assessed soil microbial properties in turfgrass systems against those in adjacent native pines. We observed age-associated changes in soil microbial biomass, CO2 respiration, net and gross N mineralization, and nitrification potential. Changes were more evident in soil samples collected from 0 to 5 cm than the 5 to 15 cm soil depth. While microbial biomass, activity and N transformations per unit soil weight were similar between the youngest turfgrass system and the adjacent native pines, microbial biomass C and N were approximately six times greater in the oldest turfgrass system compared to the adjacent native pines. Potential C and N mineralization also increased with turfgrass age and were three to four times greater in the oldest vs. the youngest turfgrass system. However, microbial biomass and potential mineralization per unit soil C or N decreased with turfgrass age. These reductions were accompanied by increases in microbial C and N use efficiency, as indicated by the significant reduction in microbial C quotient (qCO2) and N quotient (qN) in older turfgrass systems. Independent of turfgrass age, microbial biomass N turnover was rapid, averaging approximately 3 weeks. Similarly, net N mineralization was ∼12% of gross mineralization regardless of turfgrass age. Our results indicate that soil microbial properties are not negatively affected by long-term management practices in turfgrass systems. A tight coupling between N mineralization and immobilization could be sustained in mature turfgrass systems due to its increased microbial C and N use efficiency.}, number={2}, journal={SOIL BIOLOGY & BIOCHEMISTRY}, author={Shi, W and Yao, HY and Bowman, D}, year={2006}, month={Feb}, pages={311–319} }
 @article{yao_bowman_shi_2006, title={Soil microbial community structure and diversity in a turfgrass chronosequence: Land-use change versus turfgrass management}, volume={34}, ISSN={["1873-0272"]}, DOI={10.1016/j.apsoil.2006.01.009}, abstractNote={A diverse soil microbial community is an important measure of sustainable land use. Turfgrasses are usually managed as a monostand, which may result in reduced soil microbial diversity. However, there is little information on the structure and diversity of soil microorganisms in managed turfgrass systems. We examined the soil microbial community in a turfgrass chronosequence (i.e., 1, 6, 23 and 95 years), established from native pines, to address (1) the degree to which microbial diversity is achieved and maintained in turfgrass soils and (2) the relative importance of turfgrass management versus land-use change (i.e., native pines to turfgrass) in structuring the soil microbial community. Soil microbial communities were fingerprinted using phospholipid fatty acid (PLFA) composition, and also by the pattern of sole C source utilization (i.e., community-level physiological profiles, CLPP). The relative diversities of soil microbial communities as a function of land use and turfgrass ages were compared using the Shannon index. Multivariate analysis was used to detail variations in soil microbial communities. Despite the differences in land use and turfgrass age, microbial biodiversity was generally similar for the various soils, with the exception that diversity was lower in soils taken from 5 to 15 cm depth of the two youngest turfgrass systems. This reduction was correlated with low soil C, and suggests that soil organic matter (OM) is a primary determinant of microbial community diversity. Both CLPP- and PLFA-based principal component analyses (PCA) revealed distinct groupings of soil microbial communities based on land use but not on turfgrass age. There was a preferential use of phenolic compounds and carboxylic acids by the microbial community in native pine soils, whereas carbohydrates were the preferred C source for microbial communities in turfgrass soils. This difference in catabolic function was mirrored by a compositional change of phospholipid fatty acids. Cluster analysis of community structure indicated that microbial communities in older turfgrass systems (23 and 95 years old) diverged from younger systems (1 and 6 years old), implying some effect of management on composition and structure of the soil microbial community. Our study concludes that a diverse soil microbial community was achieved and maintained in turfgrass systems, and that shifts in soil microbial community structure were attributed primarily to the change of land use rather than the length of turfgrass management.}, number={2-3}, journal={APPLIED SOIL ECOLOGY}, author={Yao, Huaiying and Bowman, Daniel and Shi, Wei}, year={2006}, month={Dec}, pages={209–218} }
 @article{shi_bischoff_turco_konopka_2005, title={Microbial Catabolic Diversity in Soils Contaminated with Hydrocarbons and Heavy Metals}, volume={39}, ISSN={0013-936X 1520-5851}, url={http://dx.doi.org/10.1021/es049034n}, DOI={10.1021/es049034n}, abstractNote={Understanding indigenous microbial function in contaminated soil is crucial to the successful development and use of bioremediation technologies. We measured the catabolic diversity of indigenous microbial communities in soils with a 30-yr history of Pb, Cr, and hydrocarbon (HC) contamination using a modified substrate-induced respiration method. There were characteristic differences of microbial respirations in the response of highly versus less contaminated soils to the range of organic substrates used. The catabolic response to glucose as compared to succinic acid was approximately 1:5 in less contaminated soils, but 1:25 in highly contaminated soils. In contrast, the response ratio to glucose versus aromatics was about 1:0.4 in less contaminated soils and 1:1 in highly contaminated soils. Principal components analysis (PCA) of the responses confirmed that catabolic diversity differed between highly and less contaminated soils. Univariate analysis also indicated that catabolic diversity was reduced in highly contaminated soils. This catabolic difference was strongly associated with the alteration of microbial community composition. Statistical analyses suggested that the variation in microbial community catabolic diversity was attributed to HCs more than to Pb and Cr.}, number={7}, journal={Environmental Science & Technology}, publisher={American Chemical Society (ACS)}, author={Shi, Wei and Bischoff, Marianne and Turco, Ronald and Konopka, Allan}, year={2005}, month={Apr}, pages={1974–1979} }
 @article{shi_miller_stark_norton_2004, title={Microbial nitrogen transformations in response to treated dairy waste in agricultural soils}, volume={68}, ISSN={["0361-5995"]}, DOI={10.2136/sssaj2004.1867}, abstractNote={Dairy wastes are commonly applied to croplands as N fertilizers, but the dynamics of N release and transformations during the growing season are difficult to predict. We compared N mineralization kinetics and examined microbial N transformations in soil receiving dairy‐waste compost vs. lagoon effluent. Mineralization kinetics was examined with a 70‐d laboratory incubation, and a first‐order model was used to derive mineralization parameters. Measurements of N transformations were conducted with 15N pool dilution techniques in silage corn field plots that were unfertilized or fertilized with ammonium sulfate, lagoon effluent, or compost at two rates equivalent to 100 or 200 kg available N ha−1 The N mineralization potential was higher and the first‐order rate constant was lower in soil receiving compost than lagoon effluent. Approximately 6% of compost N was mineralized within 2.5 mo; in contrast, up to 90% lagoon effluent organic N was released. However, silage yield was greatest in the compost treatment, showing that synchronization of N availability is as important as the amount mineralized. The field 15N measurements indicated that microbial NO−3 consumption was negligible despite the treatments. Microbial NH+4 immobilization in soil receiving dairy wastes was similar to that in soil unfertilized or fertilized with inorganic N. Soil treated with the high‐rate compost had the highest rates of mineralization and nitrification, which led to the highest soil NO−3 accumulation. Our observations suggest that peak plant demand is met by the compost N; however, its high N mineralization potential makes the management of dairy compost a difficult task.}, number={6}, journal={SOIL SCIENCE SOCIETY OF AMERICA JOURNAL}, author={Shi, W and Miller, BE and Stark, JM and Norton, JM}, year={2004}, pages={1867–1874} }
 @article{shi_morrison_bryden_2002, title={Water, heat and freshwater flux out of the northern Indian Ocean in September-October 1995}, volume={49}, ISSN={["1879-0100"]}, DOI={10.1016/S0967-0645(01)00154-0}, abstractNote={World Ocean Circulation Experiment (WOCE) Transindian Hydrographic Section I1 (I1) is the northernmost of the zonal sections carried out during the WOCE Indian Ocean Expedition of 1994–1995. It crosses the southern boundaries of both the Bay of Bengal (I1e) in the east and the Arabian Sea (I1w) in the west. From I1, heat, freshwater and water-mass budgets are computed for the Arabian Sea and Bay of Bengal. Unfortunately, unlike the flow in the Atlantic and Pacific, the flow through I1 experiences considerable seasonal variability due to the annual reversal of the monsoonal winds. Therefore, at best we can expect to compute a “snapshot” of the heat and freshwater flux at the end of the SW Monsoon. But at least the timing of this section was chosen to coincide in the period where the mean circulation is most like the “normal” subtropical gyres found at mid-latitudes in the other oceans. During WOCE I1 both the Arabian Sea and the Bay of Bengal acted as heat sources. The mechanisms of the heat exportation in these two basins differed slightly from each other with the deep-ocean flow playing an important role in exporting heat from the Arabian Sea. The total heat transport out of the Arabian Sea was 0.60±0.27 PW. Of the 0.60 PW heat transport, a total of 0.28 PW was exported below 2000 m. The monsoonally driven southward surface flow accounted for the remaining 50% of the total heat export. Meanwhile, the Bay of Bengal was exporting heat at a rate of 0.63±0.16 PW, with half of the heat export due to surface flow and the other half due to meridional overturning at mid-depths. Meanwhile, the Arabian Sea was importing freshwater at a rate of 0.38±0.09×106 m3 s−1 while the Bay of Bengal was exporting freshwater at a rate of 0.38±0.08×106 m3 s−1. The mechanisms for the freshwater transport from the two basins were fundamentally different. In the Arabian Sea, vertical recirculation cells in the upper and deep ocean contributed to the freshwater import across I1w with the deep cell accounting for ∼25% of the total freshwater transport. In the Bay of Bengal, most of the freshwater export occurred in the surface layer because of strong southward Ekman surface flow and fresh surface waters from river runoff and monsoon rainfall. The role the horizontal circulation plays in the heat and freshwater transport across I1 was different in the Arabian Sea and Bay of Bengal. The horizontal circulation contributed 0.06 PW of the total heat transport in contrast to −0.60 PW of the total heat transport crossing I1w and ∼30% of the freshwater transport across I1w in the Arabian Sea. In the Bay of Bengal, the horizontal circulation contributed ∼20% heat transport and ∼45% of the freshwater transport across I1e. The difference in horizontal circulation between the two basins is predominately due to the role of the Somali Current in the Arabian Sea.}, number={7-8}, journal={DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY}, author={Shi, W and Morrison, JM and Bryden, HL}, year={2002}, pages={1231–1252} }