Cargando…
Dominant bacterial phyla in caves and their predicted functional roles in C and N cycle
BACKGROUND: Bacteria present in cave often survive by modifying their metabolic pathway or other mechanism. Understanding these adopted bacteria and their survival strategy inside the cave is an important aspect of microbial ecology. Present study focuses on the bacterial community and geochemistry...
Autores principales: | , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2017
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5387202/ https://www.ncbi.nlm.nih.gov/pubmed/28399822 http://dx.doi.org/10.1186/s12866-017-1002-x |
_version_ | 1782520896732266496 |
---|---|
author | De Mandal, Surajit Chatterjee, Raghunath Kumar, Nachimuthu Senthil |
author_facet | De Mandal, Surajit Chatterjee, Raghunath Kumar, Nachimuthu Senthil |
author_sort | De Mandal, Surajit |
collection | PubMed |
description | BACKGROUND: Bacteria present in cave often survive by modifying their metabolic pathway or other mechanism. Understanding these adopted bacteria and their survival strategy inside the cave is an important aspect of microbial ecology. Present study focuses on the bacterial community and geochemistry in five caves of Mizoram, Northeast India. The objective of this study was to explore the taxonomic composition and presumed functional diversity of cave sediment metagenomes using paired end Illumina sequencing using V3 region of 16S rRNA gene and bioinformatics pipeline. RESULTS: Actinobacteria, Proteobacteria, Verrucomicrobia and Acidobacteria were the major phyla in all the five cave sediment samples. Among the five caves the highest diversity is found in Lamsialpuk with a Shannon index 12.5 and the lowest in Bukpuk (Shannon index 8.22). In addition, imputed metagenomic approach was used to predict the functional role of microbial community in biogeochemical cycling in the cave environments. Functional module showed high representation of genes involved in Amino Acid Metabolism in (20.9%) and Carbohydrate Metabolism (20.4%) in the KEGG pathways. Genes responsible for carbon degradation, carbon fixation, methane metabolism, nitrification, nitrate reduction and ammonia assimilation were also predicted in the present study. CONCLUSION: The cave sediments of the biodiversity hotspot region possessing a oligotrophic environment harbours high phylogenetic diversity dominated by Actinobacteria and Proteobacteria. Among the geochemical factors, ferric oxide was correlated with increased microbial diversity. In-silico analysis detected genes involved in carbon, nitrogen, methane metabolism and complex metabolic pathways responsible for the survival of the bacterial community in nutrient limited cave environments. Present study with Paired end Illumina sequencing along with bioinformatics analysis revealed the essential ecological role of the cave bacterial communities. These results will be useful in documenting the biospeleology of this region and systematic understanding of bacterial communities in natural sediment environments as well. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12866-017-1002-x) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-5387202 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-53872022017-04-11 Dominant bacterial phyla in caves and their predicted functional roles in C and N cycle De Mandal, Surajit Chatterjee, Raghunath Kumar, Nachimuthu Senthil BMC Microbiol Research Article BACKGROUND: Bacteria present in cave often survive by modifying their metabolic pathway or other mechanism. Understanding these adopted bacteria and their survival strategy inside the cave is an important aspect of microbial ecology. Present study focuses on the bacterial community and geochemistry in five caves of Mizoram, Northeast India. The objective of this study was to explore the taxonomic composition and presumed functional diversity of cave sediment metagenomes using paired end Illumina sequencing using V3 region of 16S rRNA gene and bioinformatics pipeline. RESULTS: Actinobacteria, Proteobacteria, Verrucomicrobia and Acidobacteria were the major phyla in all the five cave sediment samples. Among the five caves the highest diversity is found in Lamsialpuk with a Shannon index 12.5 and the lowest in Bukpuk (Shannon index 8.22). In addition, imputed metagenomic approach was used to predict the functional role of microbial community in biogeochemical cycling in the cave environments. Functional module showed high representation of genes involved in Amino Acid Metabolism in (20.9%) and Carbohydrate Metabolism (20.4%) in the KEGG pathways. Genes responsible for carbon degradation, carbon fixation, methane metabolism, nitrification, nitrate reduction and ammonia assimilation were also predicted in the present study. CONCLUSION: The cave sediments of the biodiversity hotspot region possessing a oligotrophic environment harbours high phylogenetic diversity dominated by Actinobacteria and Proteobacteria. Among the geochemical factors, ferric oxide was correlated with increased microbial diversity. In-silico analysis detected genes involved in carbon, nitrogen, methane metabolism and complex metabolic pathways responsible for the survival of the bacterial community in nutrient limited cave environments. Present study with Paired end Illumina sequencing along with bioinformatics analysis revealed the essential ecological role of the cave bacterial communities. These results will be useful in documenting the biospeleology of this region and systematic understanding of bacterial communities in natural sediment environments as well. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12866-017-1002-x) contains supplementary material, which is available to authorized users. BioMed Central 2017-04-11 /pmc/articles/PMC5387202/ /pubmed/28399822 http://dx.doi.org/10.1186/s12866-017-1002-x Text en © The Author(s). 2017 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Article De Mandal, Surajit Chatterjee, Raghunath Kumar, Nachimuthu Senthil Dominant bacterial phyla in caves and their predicted functional roles in C and N cycle |
title | Dominant bacterial phyla in caves and their predicted functional roles in C and N cycle |
title_full | Dominant bacterial phyla in caves and their predicted functional roles in C and N cycle |
title_fullStr | Dominant bacterial phyla in caves and their predicted functional roles in C and N cycle |
title_full_unstemmed | Dominant bacterial phyla in caves and their predicted functional roles in C and N cycle |
title_short | Dominant bacterial phyla in caves and their predicted functional roles in C and N cycle |
title_sort | dominant bacterial phyla in caves and their predicted functional roles in c and n cycle |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5387202/ https://www.ncbi.nlm.nih.gov/pubmed/28399822 http://dx.doi.org/10.1186/s12866-017-1002-x |
work_keys_str_mv | AT demandalsurajit dominantbacterialphylaincavesandtheirpredictedfunctionalrolesincandncycle AT chatterjeeraghunath dominantbacterialphylaincavesandtheirpredictedfunctionalrolesincandncycle AT kumarnachimuthusenthil dominantbacterialphylaincavesandtheirpredictedfunctionalrolesincandncycle |