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Temporal shift in methanotrophic community and methane oxidation potential in forest soils of dry tropics: high-throughput metagenomic approach

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Abstract

Forest soil contributes to global methane (CH4) cycle as the natural sink for atmospheric CH4 by methane-oxidizing bacteria (MOB). In this study, high-throughput sequencing of pmoA gene amplicons based approach was used to investigate temporal variations in molecular diversity of MOB in soil of tropical dry forest. Quantitative PCR (qPCR) analysis revealed pmoA and 16S rRNA gene copy numbers (copies g−1 dws) ranging from 2.23 × 106 to 14.62 × 106 and from 0.92 × 109 to 14.99 × 109, respectively, in the year 2016. In 2017, the respective values varied from 1.96 × 106 to 13.62 × 106 and from 2.55 × 109 to 20.15 × 109, respectively. The sequence analysis revealed the existence of both type I and type II methanotrophs in soils. The average observed OTUs were about 800/sample, and Shannon diversity index ranged between 4.24 and 6.22 being highest in winter season. The rice paddy clusters (RPCs), Methylocystis, Methlylocystis-Methylosinus and JR2 and JR3, dominated the methanotrophic community with relative abundance of 32.7–50.2, 15.4–34.2, 0.45–15.8, 0.0–17.8 and 1.6–19.2%, respectively. Relatively, higher CH4 oxidation potential (MOP) (ng CH4 g−1 h−1 dws) was observed in winter (14.12) compared with rainy (2.10) and summer (3.72) coinciding with high methanotrophic diversity and abundance. Overall, the study suggests that tropical dry deciduous forest soils favour considerable range of methanotrophic diversity and abundance that positively correlates with MOP of soils across season.

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Acknowledgements

We thank the Editor and anonymous reviewers for their critical constructive suggestions on our manuscript.

Funding

This study was financially supported by Department of Science and Technology (DST-SERB), Government of India, New Delhi (File No.: EMR/2014/000502). YB is thankful to CSIR, New Delhi, India (File No: 09/013(0653)/2017-EMR-I), for the financial support in the form of JRF and SRF. We also thank coordinator CAS and DST-FIST for facilities.

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  1. Laboratory of Molecular Ecology, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, India

    Yashpal Bhardwaj, Bhaskar Reddy & Suresh Kumar Dubey

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  1. Yashpal Bhardwaj
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  2. Bhaskar Reddy
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  3. Suresh Kumar Dubey
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YB and SKD designed experimentation details. BR helped in sequence analysis. All authors contributed significantly in framing of the manuscript.

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Correspondence to Suresh Kumar Dubey.

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Bhardwaj, Y., Reddy, B. & Dubey, S.K. Temporal shift in methanotrophic community and methane oxidation potential in forest soils of dry tropics: high-throughput metagenomic approach. Biol Fertil Soils 56, 859–867 (2020). https://doi.org/10.1007/s00374-020-01444-1

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