@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{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{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{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{peoples_donaldson_osuntokun_xia_nelson_blanton_allen_church_bartlett_2018, title={Vertically distinct microbial communities in the Mariana and Kermadec trenches}, volume={13}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0195102}, abstractNote={Hadal trenches, oceanic locations deeper than 6,000 m, are thought to have distinct microbial communities compared to those at shallower depths due to high hydrostatic pressures, topographical funneling of organic matter, and biogeographical isolation. Here we evaluate the hypothesis that hadal trenches contain unique microbial biodiversity through analyses of the communities present in the bottom waters of the Kermadec and Mariana trenches. Estimates of microbial protein production indicate active populations under in situ hydrostatic pressures and increasing adaptation to pressure with depth. Depth, trench of collection, and size fraction are important drivers of microbial community structure. Many putative hadal bathytypes, such as members related to the Marinimicrobia, Rhodobacteraceae, Rhodospirilliceae, and Aquibacter, are similar to members identified in other trenches. Most of the differences between the two trench microbiomes consists of taxa belonging to the Gammaproteobacteria whose distributions extend throughout the water column. Growth and survival estimates of representative isolates of these taxa under deep-sea conditions suggest that some members may descend from shallower depths and exist as a potentially inactive fraction of the hadal zone. We conclude that the distinct pelagic communities residing in these two trenches, and perhaps by extension other trenches, reflect both cosmopolitan hadal bathytypes and ubiquitous genera found throughout the water column.}, number={4}, journal={PLOS ONE}, author={Peoples, Logan M. and Donaldson, Sierra and Osuntokun, Oladayo and Xia, Qing and Nelson, Alex and Blanton, Jessica and Allen, Eric E. and Church, Matthew J. and Bartlett, Douglas H.}, year={2018}, month={Apr} }