Methanotrophic bacterial diversity in two diverse soils under varying land-use practices as determined by high-throughput sequencing of the pmoA gene

Sengupta, Aditi; Dick, Warren A.

doi:10.1016/j.apsoil.2017.05.031

Cited by 37 publications

(26 citation statements)

References 68 publications

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“…Owing to the complexity and interlinked nature of carbon cycling, we focused on the cycling of methane, an important greenhouse gas that has a radiative forcing potential 23 times higher than that of carbon dioxide. Methanotrophic diversity in soils has also been previously studied (Sengupta and Dick, 2017).…”

Section: Resultsmentioning

confidence: 99%

Functional Predictions of Microbial Communities in Soil as Affected by Long‐term Tillage Practices

Hariharan

Sengupta

Grewal

et al. 2017

Agricultural & Env Letters

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Core Ideas Microbial function is important but difficult to assess in soil. An omics‐driven tool, PICRUSt, was used to characterize functions of soil microbial communities. No‐tillage compared with plow tillage was functionally enriched for most nutrient cycles. Many other functions integral to soil health can be explored by the PICRUSt omics approach. Soil microbial communities affect the soil's biological, chemical, and physical properties, but there is still a knowledge gap regarding the long‐term impact of tillage practices on soil microbial dynamics. Additionally, the accurate identification of belowground microbial functions is a topic of active interest. In this study, microbial community profiles and functions in soil from a 50‐plus‐year‐old experiment in Ohio, representing one of the world's longest running comparisons of a plow‐tillage system and a continuous no‐tillage system, were compared. The Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) algorithm was used to predict associated functional traits from 16S rRNA gene sequences. Analysis of the sequences revealed a large number of unidentified operational taxonomic units (67%), which is consistent with expectations of the soil ecosystem. Next, we investigated gene and enzyme predictions for nitrogen, sulfur, and methane metabolism and hydrocarbon degradation in soil. Results indicated that no‐tillage was functionally enriched for most nutrient cycles. This study has allowed us to predict distinct functional profiles as a result of legacy land uses. It serves as an example of improved analysis of the functional differences in soil managed by long‐term tillage versus no‐till.

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Section: Resultsmentioning

confidence: 99%

Functional Predictions of Microbial Communities in Soil as Affected by Long‐term Tillage Practices

Hariharan

Sengupta

Grewal

et al. 2017

Agricultural & Env Letters

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“…(5′-GTGCCAGCMGCCGCGGTAA-3′) and 806R (5′-GGACTACVSGGGTATCTA AT-3′) with barcode, following previously described protocol (Sengupta and Dick, 2017). Purified PCR amplicons were sequenced by the Illumina HiSeq2500 platform (Novogene, China).…”

Section: Soil Microbial Community Analysismentioning

confidence: 99%

Effects of two ecological earthworm species on atrazine degradation performance and bacterial community structure in red soil

et al. 2018

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Vermicomposting is an effective and environmentally friendly approach for eliminating soil organic contamination. Atrazine is one of the most commonly applied triazinic herbicides and frequently detected in agricultural soils. This study investigated the roles and mechanisms of two earthworm species (epigeic Eisenia foetida and endogeic Amynthas robustus) in microbial degradation of atrazine. Both earthworms accelerated atrazine degradation performance from 39.0% in sterile soils to 94.9%-95.7%, via neutralizing soil pH, consuming soil humus, altering bacterial community structure, enriching indigenous atrazine degraders and excreting the intestinal atrazine-degrading bacteria. Rhodoplanes and Kaistobacter were identified as soil indigenous degraders for atrazine mineralization and stimulated by both earthworm species. A. robustus excreted the intestinal Cupriavidus and Pseudomonas, whereas Flavobacterium was released by E. foetida. This study provides a comprehensive understanding of the distinct effects of two earthworm species on soil microbial community and atrazine degradation, offering technical supports to apply vermicomposting in effective soil bioremediation.

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“…Zhang et al, 2018). The analysis of the methanotrophic communities was based on the pmoA gene, which encodes the beta subunit of particulate methane monooxygenase, an enzyme that catalyses the first step in the CH 4 oxidation pathway (Sengupta & Dick, 2017). The primer pair used for the amplification was A189F/mb661R (Table S1 in Appendix S1).…”

Section: Dna Extraction and Quantitative Real-time Pcrmentioning

confidence: 99%

“…Type I methanotrophs are further subdivided into Type Ia, which includes the genera Methylosarcina, Methylobacter, Methylomonas and Methylomicrobium, and Type Ib, which includes the genera Methylococcus, Methyloparacoccus and Methyloterricola (Dedysh & Knief, 2018). Type II methanotrophs include Methylosinus and Methylocystis (Sengupta & Dick, 2017). In addition, it is known that Type I methanotrophs are more active in CH 4 assimilation than Type II methanotrophs (K. Ma, Conrad, & Lu, 2013;Qiu, Noll, Abraham, Lu, & Conrad, 2008;Shrestha, Abraham, Shrestha, Noll, & Conrad, 2008).…”

Section: Introductionmentioning

confidence: 99%

Co‐incorporation of Chinese milk vetch (Astragalus sinicus L.) and rice (Oryza sativa L.) straw minimizes CH₄ emissions by changing the methanogenic and methanotrophic communities in a paddy soil

Zhou

Gao

et al. 2020

European J Soil Science

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The practice of co‐incorporating rice straw and leguminous green manure (such as Chinese milk vetch) into paddy soils has become increasingly popular in the last 10 years, although its effect on soil CH4 emissions and microbial community structure is poorly understood. In this study, data from a 2‐year pot experiment were used to reveal the effects of the co‐incorporation of rice straw and Chinese milk vetch on CH4 emissions and methanogenic and methanotrophic communities in paddy soil. Five treatments were chosen: CK (unamended control), CF (inorganic fertilizer), FM (inorganic fertilizer and Chinese milk vetch, 20 g 10 kg−1 dry soil, 4.5 t ha−1), FR (inorganic fertilizer and rice straw, 20 g 10 kg−1 dry soil, 4.5 t ha−1) and FMR (inorganic fertilizer and Chinese milk vetch and rice straw mixture, 5 + 15 g 10 kg−1 dry soil, 1.125 + 2.375 t ha−1). Overall, the soil CH4 emissions in the 2 years under all residue treatments (104.4–122.8 and 83.3–133.3 g CH4 m−2) were higher than those in CK (57.0 and 20.7 g CH4 m−2) and CF (71.8 and 21.9 g CH4 m−2) treatments. The FMR treatment decreased CH4 emissions when compared with FM and FR, especially in the second year. A higher abundance of methanogens (mcrA gene copies) was found under the plant residue‐treated soils (4.35 × 108 g−1 dry soil on average) and FM increased the abundance of methanotrophs (pmoA gene copies, 2.68 × 106 g−1 dry soil). Application of plant residues changed the methanogenic and methanotrophic community structures in comparison with CF (e.g., markedly increased the populations of Methanobacteriales and Methylomonas and suppressed Methanomicrobiales and Methylobacter populations). Methane emissions were significantly and positively related to the mcrA and pmoA gene copy numbers, as well as the mcrA/pmoA ratio. The partial least squares path model (PLS‐PM) indicated that the rice plant biomass (path coefficient = 0.64), the abundance of methanogens (path coefficient = 0.57) and the community structure of methanotrophs (path coefficient = −0.59) were determinants of CH4 emissions. Among the three residue‐treated soils, FMR showed the lowest CH4 emissions and was associated with a slight decrease in the mcrA/pmoA ratio and a significant increase in the Type I/Type II methanotrophs ratio. Thus, we recommend the co‐incorporation of Chinese milk vetch and rice straw as a sustainable fertilization pattern to improve the growth of rice and minimize CH4 emissions. Highlights Residue application improves rice productivity (except for FR), soil fertility and CH4 emissions. Co‐incorporation of MV and RS reduces CH4 emissions in comparison with pure MV or RS addition. Residue application changes the community structure of methanogens and methanotrophs. The methanogenic abundance and the methanotrophic community structure determine the CH4 emissions.

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Methanotrophic bacterial diversity in two diverse soils under varying land-use practices as determined by high-throughput sequencing of the pmoA gene

Cited by 37 publications

References 68 publications

Functional Predictions of Microbial Communities in Soil as Affected by Long‐term Tillage Practices

Functional Predictions of Microbial Communities in Soil as Affected by Long‐term Tillage Practices

Effects of two ecological earthworm species on atrazine degradation performance and bacterial community structure in red soil

Co‐incorporation of Chinese milk vetch (Astragalus sinicus L.) and rice (Oryza sativa L.) straw minimizes CH₄ emissions by changing the methanogenic and methanotrophic communities in a paddy soil

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Methanotrophic bacterial diversity in two diverse soils under varying land-use practices as determined by high-throughput sequencing of the pmoA gene

Cited by 37 publications

References 68 publications

Functional Predictions of Microbial Communities in Soil as Affected by Long‐term Tillage Practices

Functional Predictions of Microbial Communities in Soil as Affected by Long‐term Tillage Practices

Effects of two ecological earthworm species on atrazine degradation performance and bacterial community structure in red soil

Co‐incorporation of Chinese milk vetch (Astragalus sinicus L.) and rice (Oryza sativa L.) straw minimizes CH4 emissions by changing the methanogenic and methanotrophic communities in a paddy soil

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Co‐incorporation of Chinese milk vetch (Astragalus sinicus L.) and rice (Oryza sativa L.) straw minimizes CH₄ emissions by changing the methanogenic and methanotrophic communities in a paddy soil