Metagenomics analysis of rhizospheric bacterial communities of Saccharum arundinaceum growing on organometallic sludge of sugarcane molasses-based distillery

Abstract

The present paper aims to explore the rhizospheric bacterial communities associated with Saccharum arundinaceum grown on organometallic pollutants-rich hazardous distillery sludge. The sequence analysis of 16S rRNA V3–V4 hypervariable region with Illumina MiSeq platform showed 621,897 OTUs derived from rhizospheric and non-rhizospheric distillery sludge samples out of 1,191,014 and 901,757 sequences read, respectively. The major phyla detected in rhizospheric sludge sample were Proteobacteria (50%), Bacteriodetes (33%), Firmicutes (5%) Gemmatimonadetes (2%), Chloroflexi (2%), and Tenericutes (2%). The dominant three genera were detected as Rheinheimera (21%), Sphingobacterium (17%), and Idiomarina (8%). In addition, other minor genera such as uncultured Bacillus (4%), Acidothermus (4%), Bacillus (3%), Pseudomonas (2%), Flavobacterium (2%), uncultured bacterium (2%), Parapedobacter (2%), Alcanivorax (2%), Acholeplasma (2%), Hyphomonas (1%), and Aquamicrobium were also detected (1%) in rhizospheric sludge. Our results suggested that rhizospheric bacterial communities associated with S. arundinaceum were substantially different in richness, diversity, and relative abundance of taxa compared to non-rhizospheric sludge. Further, the comparative organic pollutant analysis from non-rhizospheric and rhizospheric sludge samples through GC–MS analysis revealed the disappearance of few compounds and generation of some compounds as new metabolic products by the activity of rhizospheric bacterial communities. The results of this study will be helpful in understanding the role of rhizospheric bacterial communities responsible for degradation and detoxification of complex organometallic waste and, thus, can help in designing appropriate phytoremediation studies for eco-restoration of polluted sites.

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Acknowledgments

We would like to thank M/s AgriGenome Labs Pvt Ltd., Kerala, India for the 16S rDNA Illumina Miseq analysis. The authors gratefully acknowledge the financial assistance received from University Grants Commission (UGC), New Delhi, in form of Rajiv Gandhi National Fellowship (Letter No. F1-17.1/2012-13/RGNF-2012-13-SC-UTT-30458) to Vineet Kumar and Department of Biotechnology (DBT), Govt. of India as Grant-in-Aid Project (Letter No. BT/PR13922/BCE/8/1129/2015) to Ram Chandra. The authors gratefully acknowledge the anonymous reviewers and executive editor-in-chief for their valuable comments and suggestion on the earlier version of this paper. The authors would like to acknowledge the English Language Editing help from Dr. Saurav Das, University of Nebraska at Lincoln, United States.

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VK and RC designed the study, carried out sampling and performed the experiments and analyzed data. VK wrote the first manuscript draft, which was then revised by RC. RC contributed to the development of the idea for this manuscript and contributed text to the final version, and edited the manuscript. All authors gave approval to the final version.

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Correspondence to Ram Chandra.

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The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

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We confirm that this research study does not include either vertebrates or higher invertebrates.

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Kumar, V., Chandra, R. Metagenomics analysis of rhizospheric bacterial communities of Saccharum arundinaceum growing on organometallic sludge of sugarcane molasses-based distillery. 3 Biotech 10, 316 (2020). https://doi.org/10.1007/s13205-020-02310-5

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Keywords

  • Proteobacteria
  • Distillery sludge
  • Organic pollutants
  • Illumina MiSeq
  • Saccharum arundinaceum