@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_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_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} }