@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_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{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{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{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{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{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{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{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{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_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} }
 @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} }