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Changes in structure and function of bacterial communities during coconut leaf vermicomposting

Abstract

To understand bacterial community dynamics during the vermicomposting of lignin-rich coconut leaves using an indigenous isolate of an epigeic earthworm, Eudrilus sp., we employed amplicon-based pyrosequencing of the V1 to V3 region of the 16S rRNA genes. Total community DNA was isolated from two separate vermicomposting tanks in triplicate at four different stages of the process: pre-decomposition (15th day), initial vermicomposting (45th day), 50–70% vermicomposting (75th day) and mature vermicompost (105th day). Alpha diversity measurements revealed an increase in bacterial diversity till the 75th day, which then declined in the mature vermicompost. Beta diversity comparisons showed formation of distinct, stage-specific communities. In terms of relative abundance, the Acidobacteria, Actinobacteria, Chloroflexi, Gemmatimonadetes, Nitrospirae, Planctomycetes, TM7 and WS3 groups increased until the 50–70% vermicomposting stage (p = 0.05). During the same time, the abundance of Bacteroidetes and Proteobacteria decreased. In contrast, the levels of Firmicutes increased throughout the 105-day vermicomposting process. The distribution of the most abundant OTUs revealed that each stage of the vermicomposting process possessed its own unique microbiome. Predictions based on the OTUs present by PICRUSt suggested a functional shift in the microbiome during vermicomposting. Enzymes and pathways of lipid and lignin metabolism were predicted to be initially abundant, but by the end of the process, biosynthesis of secondary metabolites and plant beneficial properties were enriched. The study revealed that bacterial communities undergo a continuous change throughout the vermicomposting process and that certain OTUs associated with specific stages could be targets for further improvements in the process.

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Acknowledgements

MG is grateful to the Indian Council of Agricultural Research, New Delhi, India for the training grant under the HRD program of National Agricultural Innovation Project. SSB thanks the University Grants Commission, India for research fellowship during the course of this project. KJ acknowledges the funding support from the Department of Biotechnology, Government of India, under the project ‘‘Establishment of microbial culture collection’’(Grant no. BT/PR/0054/NDB/52/94/2007). The authors are thankful to Prof. Mary Ann Moran, Department of Marine Sciences at the University of Georgia for extending the laboratory facilities for DNA quantification.

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Correspondence to Kamlesh Jangid.

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Gopal, M., Bhute, S.S., Gupta, A. et al. Changes in structure and function of bacterial communities during coconut leaf vermicomposting. Antonie van Leeuwenhoek 110, 1339–1355 (2017). https://doi.org/10.1007/s10482-017-0894-7

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Keywords

  • 16S rRNA
  • Coconut leaf
  • Lignin degradation
  • Metagenomics
  • Pyrosequencing
  • Vermicompost