Watershed-Scale Fungal Community Characterization along a pH Gradient in a Subsurface Environment Cocontaminated with Uranium and Nitrate

Jasrotia, Puja; Green, Stefan J.; Canion, Andy; Overholt, Will A.; Prakash, Om; Wafula, Denis; Hubbard, Daniela; Watson, David B.; Schadt, Christopher W.; Brooks, Scott C.; Kostka, Joel E.

doi:10.1128/aem.03423-13

Cited by 16 publications

(15 citation statements)

References 69 publications

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“…Interestingly, most sequenced genomes of fungal denitrifiers possess a putative napA gene encoding periplasmic nitrate reductase (3), but a detailed understanding of the variation in fungal NO 3 Ϫ reduction capacity has yet to be obtained. Overall, the observed production of N 2 O in microcosms established with Havana and Urbana soils is in line with the magnitude and variability observed in other studies, in which antibiotics were employed to probe the fungal contribution to N 2 O production (8,13,18).…”

Section: Figsupporting

confidence: 89%

“…For example, several members of the genera Fusarium and Trichoderma, both known to harbor species capable of N 2 O production, were cultured (8,17,18). Also identified were two Mortierella isolates (Mortierellomycotina, formally Zygomycota), a genus that includes members known to produce N 2 O (33, 58).…”

Section: Figmentioning

confidence: 99%

“…Although the SIRIN methodology has provided valuable insight into the fungal contribution to denitrification, the application of SI-RIN to soils can be problematic as incomplete inhibition can bias the observations (14)(15)(16). Hence, alternative approaches (e.g., PCR) that selectively target fungal genes involved in denitrification are desirable to advance understanding of the fungal diversity contributing to N cycling in environments such as soils, aquifers, and deep-ocean sediments, where denitrifying fungi have been cultivated (7,13,17,18).…”

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confidence: 99%

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Detection and Diversity of Fungal Nitric Oxide Reductase Genes ( p450nor ) in Agricultural Soils

Higgins

Welsh

Orellana

et al. 2016

Appl Environ Microbiol

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Members of the Fungi convert nitrate (NO 3؊ ) and nitrite (NO 2 ؊ ) to gaseous nitrous oxide (N 2 O) (denitrification), but the fungal contributions to N loss from soil remain uncertain. Cultivation-based methodologies that include antibiotics to selectively assess fungal activities have limitations, and complementary molecular approaches to assign denitrification potential to fungi are desirable. Microcosms established with soils from two representative U.S. Midwest agricultural regions produced N 2 O from added NO 3 ؊ or NO 2 ؊ in the presence of antibiotics to inhibit bacteria. Cultivation efforts yielded 214 fungal isolates belonging to at least 15 distinct morphological groups, 151 of which produced N 2 O from NO 2 ؊ . Novel PCR primers targeting the p450nor gene, which encodes the nitric oxide (NO) reductase responsible for N 2 O production in fungi, yielded 26 novel p450nor amplicons from DNA of 37 isolates and 23 amplicons from environmental DNA obtained from two agricultural soils. The sequences shared 54 to 98% amino acid identity with reference P450nor sequences within the phylum Ascomycota and expand the known fungal P450nor sequence diversity. p450nor was detected in all fungal isolates that produced N 2 O from NO 2 ؊ , whereas nirK (encoding the NO-forming NO 2 ؊ reductase) was amplified in only 13 to 74% of the N 2 O-forming isolates using two separate nirK primer sets. Collectively, our findings demonstrate the value of p450nor-targeted PCR to complement existing approaches to assess the fungal contributions to denitrification and N 2 O formation. IMPORTANCEA comprehensive understanding of the microbiota controlling soil N loss and greenhouse gas (N 2 O) emissions is crucial for sustainable agricultural practices and addressing climate change concerns. We report the design and application of a novel PCR primer set targeting fungal p450nor, a biomarker for fungal N 2 O production, and demonstrate the utility of the new approach to assess fungal denitrification potential in fungal isolates and agricultural soils. These new PCR primers may find application in a variety of biomes to assess the fungal contributions to N loss and N 2 O emissions. Denitrification is a key process responsible for loss of fixed nitrogen (N) in soils and sediments and is mediated by both abiotic and microbial processes (1, 2). Of the microorganisms involved in denitrification, members of the Bacteria are well studied and considered key contributors; however, some saprotrophic fungi also conserve energy from the reduction of nitrate (NO 3 Ϫ ) or nitrite (NO 2 Ϫ ) to nitrous oxide (N 2 O), the main end product of fungal denitrification (3-5). Fungi have been implicated in N turnover for over 30 years (1,3,6), but the ecological importance of fungal contributions to denitrification remain uncertain. Potential roles of fungi in soil N loss and greenhouse gas (i.e., N 2 O) emission are underexplored, and monitoring tools (e.g., quantitative or endpoint PCR) to specifically address the presence and abundance of denitrif...

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Section: Figsupporting

confidence: 89%

Section: Figmentioning

confidence: 99%

mentioning

confidence: 99%

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Detection and Diversity of Fungal Nitric Oxide Reductase Genes ( p450nor ) in Agricultural Soils

Higgins

Welsh

Orellana

et al. 2016

Appl Environ Microbiol

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“…It is a major cause of N loss from agricultural soils, and, moreover, the process also has the potential to produce nitrous oxide (N 2 O), a potent greenhouse gas. Although soil abiotic conditions can affect denitrification (35)(36)(37), microbial factors such as the diversity, composition, and abundance of bacterial as well as fungal denitrifiers are also critical in regulating the fate of environmental N (38)(39)(40). Therefore, it is necessary to obtain a holistic understanding of the community dynamics of soil bacterial denitrifiers as well as of their response(s) to human activities, such as the reuse of TWW via land application.…”

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confidence: 99%

“…To understand the structure and diversity of bacterial denitrifier communities in the environment, functional genes coding for denitrification enzymes have been extensively used; these include the nitrite reductases (nirK and nirS) and the nitrous oxide reductase (nosZ) (38)(39)(40)(41). Using these genes, previous studies have shown that long-term fertilization with different treatments influenced the size, composition, and functioning of bacterial denitrifiers (42).…”

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Impacts of Long-Term Irrigation of Domestic Treated Wastewater on Soil Biogeochemistry and Bacterial Community Structure

Wafula

White

Canion

et al. 2015

Appl Environ Microbiol

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Freshwater scarcity and regulations on wastewater disposal have necessitated the reuse of treated wastewater (TWW) for soil irrigation, which has several environmental and economic benefits. However, TWW irrigation can cause nutrient loading to the receiving environments. We assessed bacterial community structure and associated biogeochemical changes in soil plots irrigated with nitrate-rich TWW (referred to as pivots) for periods ranging from 13 to 30 years. Soil cores (0 to 40 cm) were collected in summer and winter from five irrigated pivots and three adjacently located nonirrigated plots. Total bacterial and denitrifier gene abundances were estimated by quantitative PCR (qPCR), and community structure was assessed by 454 massively parallel tag sequencing (MPTS) of small-subunit (SSU) rRNA genes along with terminal restriction fragment length polymorphism (T-RFLP) analysis of nirK, nirS, and nosZ functional genes responsible for denitrification of the TWW-associated nitrate. Soil physicochemical analyses showed that, regardless of the seasons, pH and moisture contents (MC) were higher in the irrigated (IR) pivots than in the nonirrigated (NIR) plots; organic matter (OM) and microbial biomass carbon (MBC) were higher as a function of season but not of irrigation treatment. MPTS analysis showed that TWW loading resulted in the following: (i) an increase in the relative abundance of Proteobacteria, especially Betaproteobacteria and Gammaproteobacteria; (ii) a decrease in the relative abundance of Actinobacteria; (iii) shifts in the communities of acidobacterial groups, along with a shift in the nirK and nirS denitrifier guilds as shown by T-RFLP analysis. Additionally, bacterial biomass estimated by genus/group-specific real-time qPCR analyses revealed that higher numbers of total bacteria, Acidobacteria, Actinobacteria, Alphaproteobacteria, and the nirS denitrifier guilds were present in the IR pivots than in the NIR plots. Identification of the nirK-containing microbiota as a proxy for the denitrifier community indicated that bacteria belonged to alphaproteobacteria from the Rhizobiaceae family within the agroecosystem studied. Multivariate statistical analyses further confirmed some of the above soil physicochemical and bacterial community structure changes as a function of long-term TWW application within this agroecosystem. Rapid population growth across the globe, an increase in per capita water consumption, and, in part, global climate change have resulted in increased demands on available freshwater resources (1-3). Many countries are turning to wastewater recycling in order to meet these increased freshwater demands (3-5). Therefore, planned and managed reuse of wastewater is increasingly practiced not only in arid or semiarid regions but also in temperate and subtropical regions that do not routinely face water shortages (6-9). Regardless of the motivation, large-scale reuse of treated wastewater (TWW) is now becoming increasingly common worldwide. With proper planning, implementation, and management, ...

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Responses of fungal community composition to long‐term chemical and organic fertilization strategies in Chinese Mollisols

Jiang

Wang

et al. 2018

MicrobiologyOpen

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How fungi respond to long‐term fertilization in Chinese Mollisols as sensitive indicators of soil fertility has received limited attention. To broaden our knowledge, we used high‐throughput pyrosequencing and quantitative PCR to explore the response of soil fungal community to long‐term chemical and organic fertilization strategies. Soils were collected in a 35‐year field experiment with four treatments: no fertilizer, chemical phosphorus, and potassium fertilizer (PK), chemical phosphorus, potassium, and nitrogen fertilizer (NPK), and chemical phosphorus and potassium fertilizer plus manure (MPK). All fertilization differently changed soil properties and fungal community. The MPK application benefited soil acidification alleviation and organic matter accumulation, as well as soybean yield. Moreover, the community richness indices (Chao1 and ACE) were higher under the MPK regimes, indicating the resilience of microbial diversity and stability. With regards to fungal community composition, the phylum Ascomycota was dominant in all samples, followed by Zygomycota, Basidiomycota, Chytridiomycota, and Glomeromycota. At each taxonomic level, the community composition dramatically differed under different fertilization strategies, leading to different soil quality. The NPK application caused a loss of Leotiomycetes but an increase in Eurotiomycetes, which might reduce the plant–fungal symbioses and increase nitrogen losses and greenhouse gas emissions. According to the linear discriminant analysis (LDA) coupled with effect size (LDA score > 3.0), the NPK application significantly increased the abundances of fungal taxa with known pathogenic traits, such as order Chaetothyriales, family Chaetothyriaceae and Pleosporaceae, and genera Corynespora, Bipolaris, and Cyphellophora. In contrast, these fungi were detected at low levels under the MPK regime. Soil organic matter and pH were the two most important contributors to fungal community composition.

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Watershed-Scale Fungal Community Characterization along a pH Gradient in a Subsurface Environment Cocontaminated with Uranium and Nitrate

Cited by 16 publications

References 69 publications

Detection and Diversity of Fungal Nitric Oxide Reductase Genes ( p450nor ) in Agricultural Soils

Detection and Diversity of Fungal Nitric Oxide Reductase Genes ( p450nor ) in Agricultural Soils

Impacts of Long-Term Irrigation of Domestic Treated Wastewater on Soil Biogeochemistry and Bacterial Community Structure

Responses of fungal community composition to long‐term chemical and organic fertilization strategies in Chinese Mollisols

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