16S rRNA Gene Amplicon Data Set-Based Bacterial Diversity in a Water-Soil Sample from Pangong Tso Lake, a High-Altitude Grassland Lake of the Northwest Himalayas

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Abstract

We report here 16S rRNA-based bacterial diversity existing during freezing conditions in a high-altitude Himalayan lake through sequencing a 16S rRNA gene amplicon data set. A total of 121,857 high-quality reads were obtained; 40.78% of the bacterial population was classified to the genus level, while 1.26% was classified to the species level.

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Metagenomics: application of genomics to uncultured microorganisms.

Jo Handelsman (2004)

Metagenomics (also referred to as environmental and community genomics) is the genomic analysis of microorganisms by direct extraction and cloning of DNA from an assemblage of microorganisms. The development of metagenomics stemmed from the ineluctable evidence that as-yet-uncultured microorganisms represent the vast majority of organisms in most environments on earth. This evidence was derived from analyses of 16S rRNA gene sequences amplified directly from the environment, an approach that avoided the bias imposed by culturing and led to the discovery of vast new lineages of microbial life. Although the portrait of the microbial world was revolutionized by analysis of 16S rRNA genes, such studies yielded only a phylogenetic description of community membership, providing little insight into the genetics, physiology, and biochemistry of the members. Metagenomics provides a second tier of technical innovation that facilitates study of the physiology and ecology of environmental microorganisms. Novel genes and gene products discovered through metagenomics include the first bacteriorhodopsin of bacterial origin; novel small molecules with antimicrobial activity; and new members of families of known proteins, such as an Na(+)(Li(+))/H(+) antiporter, RecA, DNA polymerase, and antibiotic resistance determinants. Reassembly of multiple genomes has provided insight into energy and nutrient cycling within the community, genome structure, gene function, population genetics and microheterogeneity, and lateral gene transfer among members of an uncultured community. The application of metagenomic sequence information will facilitate the design of better culturing strategies to link genomic analysis with pure culture studies.

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High occurrence of Pacearchaeota and Woesearchaeota (Archaea superphylum DPANN) in the surface waters of oligotrophic high-altitude lakes.

Rüdiger Ortiz-Álvarez, Emilio O. Casamayor (2016)

We carried out a regional survey on the archaea composition from surface waters of > 300 high-altitude Pyrenean lakes (average altitude 2300 m, pH range 4.4-10.1) by 16S rRNA gene tag sequencing. Relative Archaea abundances ranged between 0% and 6.3% of total prokaryotes amplicons in the polymerase chain reaction (PCR) mixture, and we detected 769 operational taxonomic units (OTUs; grouped at 97% identity) that split into 13 different lineages, with altitude and pH having a significant effect on the community composition. Woesearchaeota and Pacearchaeota (formerly Euryarchaeota DHVEG-6 cluster) dominated the data set (83% of total OTUS), showed a high occurrence (presence in c. 75% of the lakes) and had relative abundances significantly and positively correlated with the phylogenetic diversity of bacterial communities. Micrarchaeota-Diapherotrites (formerly Euryarchaeota MEG cluster), Methanomicrobia, Thermoplasmata and ammonia-oxidizing thaumarchaeota (AOA) showed relative abundances between 1% and 3% and occurrences between 14% and 26%. Minor lineages were SM1K20, Aenigmarchaeota (formerly Euryarchaeota DSEG cluster), Methanobacteria, Bathyarchaeota and SCG. Environmental preferences substantially differed among lineages, with Aenigmarchaeota and Methanomicrobia having the largest habitat breadth, and Thermoplasmata, AOA and Micrarchaeota having the smallest. Pacearchaeota and Woesearchaeota had been mostly reported from saline habitats and sediments, but surface waters of oligotrophic alpine lakes are suitable environments for such ecologically spread and genetically diverse archaeal lineages.

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Comparison of the active and resident community of a coastal microbial mat

Daniela Cardoso, Anna Sandionigi, Mariana Cretoiu … (2017)

Coastal microbial mats form a nearly closed micro-scale ecosystem harboring a complex microbial community. Previous DNA based analysis did not necessarily provide information about the active fraction of the microbial community because it includes dormant, inactive cells as well as a potential stable pool of extracellular DNA. Here we focused on the active microbial community by comparing 16S rRNA sequences obtained from the ribosomal RNA pool with gene sequences obtained from the DNA fraction. In addition, we aimed to establish an optimal and feasible sampling protocol that takes potential spatial and temporal heterogeneity into account. The coastal microbial mat investigated here was sampled randomly and at regular time points during one 24-h period. DNA and RNA was extracted and after conversion of the RNA fraction to cDNA, the V1-V3 and the V3-V4 regions of the 16S rRNA gene were targeted for high-throughput amplicon sequencing. We show that the community composition varies little in time and space whereas two amplified 16S regions gave significant different results. The largest differences were found when comparing the “resident community” (DNA) with the “active community” (cDNA/RNA); in the latter, Cyanobacteria dominated for almost 95% while they represented 60% of the resident fraction.

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Author and article information

Contributors

Frank J. Stewart: Role: Editor

Journal

Journal ID (nlm-ta): Microbiol Resour Announc

Journal ID (iso-abbrev): Microbiol Resour Announc

Journal ID (hwp): ga

Journal ID (pmc): mra

Journal ID (publisher-id): MRA

Title: Microbiology Resource Announcements

Publisher: American Society for Microbiology (1752 N St., N.W., Washington, DC )

ISSN (Electronic): 2576-098X

Publication date (Electronic): 1 November 2018

Publication date Collection: November 2018

Volume: 7

Issue: 17

Electronic Location Identifier: e01192-18

Affiliations

[a ]Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, Himachal Pradesh, India

[b ]Department of Food Science and Nutrition, University of Minnesota—Twin Cities, St. Paul, Minnesota, USA

[c ]Microbial and Plant Genomic Institute, University of Minnesota—Twin Cities, St. Paul, Minnesota, USA

[d ]Biotechnology Institute, University of Minnesota—Twin Cities, St. Paul, Minnesota, USA

Georgia Institute of Technology

Author notes

Address correspondence to David J. Baumler, dbaumler@ 123456umn.edu , or Kamal Dev, kamaldevbhardwaj1969@ 123456gmail.com .

Citation Bisht G, Sourirajan A, Baumler DJ, Dev K. 2018. 16S rRNA gene amplicon data set-based bacterial diversity in a water-soil sample from Pangong Tso Lake, a high-altitude grassland lake of the Northwest Himalayas. Microbiol Resour Announc 7:e01192-18. https://doi.org/10.1128/MRA.01192-18.

Article

Publisher ID: MRA01192-18

DOI: 10.1128/MRA.01192-18

PMC ID: 6256501

PubMed ID: 30533766

SO-VID: 18415179-dbef-4f55-8713-0cf585e95d48

License:

This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

History

Date received : 27 August 2018

Date accepted : 24 September 2018

Page count

Figures: 1, Tables: 1, Equations: 0, References: 9, Pages: 3, Words: 1486

Funding

Funded by: Shoolini University of Biotechnology and Management Sciences, https://doi.org/10.13039/501100010603;

Award ID: Center for Omics and Biodiversity Research

Award Recipient : Kamal Dev

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cover-date November 2018

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16S rRNA Gene Amplicon Data Set-Based Bacterial Diversity in a Water-Soil Sample from Pangong Tso Lake, a High-Altitude Grassland Lake of the Northwest Himalayas

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Most cited references 6

Metagenomics: application of genomics to uncultured microorganisms.

High occurrence of Pacearchaeota and Woesearchaeota (Archaea superphylum DPANN) in the surface waters of oligotrophic high-altitude lakes.

Comparison of the active and resident community of a coastal microbial mat

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