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...

Descripción completa

Detalles Bibliográficos
Autores principales: De Mandal, Surajit, Chatterjee, Raghunath, Kumar, Nachimuthu Senthil
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