Literature DB >> 25712554

Comparative Metagenomics of Eight Geographically Remote Terrestrial Hot Springs.

Peter Menzel1, Sóley Ruth Gudbergsdóttir, Anne Gunn Rike, Lianbing Lin, Qi Zhang, Patrizia Contursi, Marco Moracci, Jakob K Kristjansson, Benjamin Bolduc, Sergey Gavrilov, Nikolai Ravin, Andrey Mardanov, Elizaveta Bonch-Osmolovskaya, Mark Young, Anders Krogh, Xu Peng.   

Abstract

Hot springs are natural habitats for thermophilic Archaea and Bacteria. In this paper, we present the metagenomic analysis of eight globally distributed terrestrial hot springs from China, Iceland, Italy, Russia, and the USA with a temperature range between 61 and 92 (∘)C and pH between 1.8 and 7. A comparison of the biodiversity and community composition generally showed a decrease in biodiversity with increasing temperature and decreasing pH. Another important factor shaping microbial diversity of the studied sites was the abundance of organic substrates. Several species of the Crenarchaeal order Thermoprotei were detected, whereas no single bacterial species was found in all samples, suggesting a better adaptation of certain archaeal species to different thermophilic environments. Two hot springs show high abundance of Acidithiobacillus, supporting the idea of a true thermophilic Acidithiobacillus species that can thrive in hyperthermophilic environments. Depending on the sample, up to 58 % of sequencing reads could not be assigned to a known phylum, reinforcing the fact that a large number of microorganisms in nature, including those thriving in hot environments remain to be isolated and characterized.

Mesh:

Year:  2015        PMID: 25712554     DOI: 10.1007/s00248-015-0576-9

Source DB:  PubMed          Journal:  Microb Ecol        ISSN: 0095-3628            Impact factor:   4.552


  45 in total

1.  Identification of thermophilic species by the amino acid compositions deduced from their genomes.

Authors:  D P Kreil; C A Ouzounis
Journal:  Nucleic Acids Res       Date:  2001-04-01       Impact factor: 16.971

2.  Biogeography of bacterial communities in hot springs: a focus on the actinobacteria.

Authors:  Angel Valverde; Marla Tuffin; Don A Cowan
Journal:  Extremophiles       Date:  2012-06-19       Impact factor: 2.395

3.  Identifying and removing artificial replicates from 454 pyrosequencing data.

Authors:  Tracy K Teal; Thomas M Schmidt
Journal:  Cold Spring Harb Protoc       Date:  2010-04

4.  High abundance of heterotrophic prokaryotes in hydrothermal springs of the Azores as revealed by a network of 16S rRNA gene-based methods.

Authors:  Kerstin Sahm; Patrick John; Heiko Nacke; Bernd Wemheuer; Ralf Grote; Rolf Daniel; Garabed Antranikian
Journal:  Extremophiles       Date:  2013-05-26       Impact factor: 2.395

Review 5.  A renaissance for the pioneering 16S rRNA gene.

Authors:  Susannah G Tringe; Philip Hugenholtz
Journal:  Curr Opin Microbiol       Date:  2008-10-08       Impact factor: 7.934

6.  Community ecology of hot spring cyanobacterial mats: predominant populations and their functional potential.

Authors:  Christian G Klatt; Jason M Wood; Douglas B Rusch; Mary M Bateson; Natsuko Hamamura; John F Heidelberg; Arthur R Grossman; Devaki Bhaya; Frederick M Cohan; Michael Kühl; Donald A Bryant; David M Ward
Journal:  ISME J       Date:  2011-06-23       Impact factor: 10.302

7.  Integrative analysis of environmental sequences using MEGAN4.

Authors:  Daniel H Huson; Suparna Mitra; Hans-Joachim Ruscheweyh; Nico Weber; Stephan C Schuster
Journal:  Genome Res       Date:  2011-06-20       Impact factor: 9.043

8.  FastTree 2--approximately maximum-likelihood trees for large alignments.

Authors:  Morgan N Price; Paramvir S Dehal; Adam P Arkin
Journal:  PLoS One       Date:  2010-03-10       Impact factor: 3.240

9.  SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes.

Authors:  Elmar Pruesse; Jörg Peplies; Frank Oliver Glöckner
Journal:  Bioinformatics       Date:  2012-05-03       Impact factor: 6.937

Review 10.  Achievements and new knowledge unraveled by metagenomic approaches.

Authors:  Carola Simon; Rolf Daniel
Journal:  Appl Microbiol Biotechnol       Date:  2009-09-16       Impact factor: 4.813

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  33 in total

1.  Microbial diversity and autotrophic activity in Kamchatka hot springs.

Authors:  Alexander Yu Merkel; Nikolay V Pimenov; Igor I Rusanov; Alexander I Slobodkin; Galina B Slobodkina; Ivan Yu Tarnovetckii; Evgeny N Frolov; Arseny V Dubin; Anna A Perevalova; Elizaveta A Bonch-Osmolovskaya
Journal:  Extremophiles       Date:  2016-12-27       Impact factor: 2.395

2.  Life Cycle Characterization of Sulfolobus Monocaudavirus 1, an Extremophilic Spindle-Shaped Virus with Extracellular Tail Development.

Authors:  Kristine B Uldahl; Signe B Jensen; Yuvaraj Bhoobalan-Chitty; Laura Martínez-Álvarez; Pavlos Papathanasiou; Xu Peng
Journal:  J Virol       Date:  2016-05-27       Impact factor: 5.103

Review 3.  Biogeography and taxonomic overview of terrestrial hot spring thermophilic phages.

Authors:  Olivier Zablocki; Leonardo van Zyl; Marla Trindade
Journal:  Extremophiles       Date:  2018-08-18       Impact factor: 2.395

Review 4.  Microbial diversity in extreme environments.

Authors:  Wen-Sheng Shu; Li-Nan Huang
Journal:  Nat Rev Microbiol       Date:  2021-11-09       Impact factor: 60.633

5.  Draft Genome Sequences of Three Strains of Acidithiobacillus spp. Isolated from Acidic Cold Springs in a Freshwater Wetland.

Authors:  H V Parker; C L Marnocha
Journal:  Microbiol Resour Announc       Date:  2021-04-01

6.  Metagenomics of an Alkaline Hot Spring in Galicia (Spain): Microbial Diversity Analysis and Screening for Novel Lipolytic Enzymes.

Authors:  Olalla López-López; Kamila Knapik; Maria-Esperanza Cerdán; María-Isabel González-Siso
Journal:  Front Microbiol       Date:  2015-11-20       Impact factor: 5.640

Review 7.  Metagenomics of Thermophiles with a Focus on Discovery of Novel Thermozymes.

Authors:  María-Eugenia DeCastro; Esther Rodríguez-Belmonte; María-Isabel González-Siso
Journal:  Front Microbiol       Date:  2016-09-27       Impact factor: 5.640

8.  The variability of soils and vegetation of hydrothermal fields in the Valley of Geysers at Kamchatka Peninsula.

Authors:  I N Semenkov; G V Klink; M P Lebedeva; V V Krupskaya; M S Chernov; O V Dorzhieva; M T Kazinskiy; V N Sokolov; A V Zavadskaya
Journal:  Sci Rep       Date:  2021-05-26       Impact factor: 4.379

9.  RaFAH: Host prediction for viruses of Bacteria and Archaea based on protein content.

Authors:  Felipe Hernandes Coutinho; Asier Zaragoza-Solas; Mario López-Pérez; Jakub Barylski; Andrzej Zielezinski; Bas E Dutilh; Robert Edwards; Francisco Rodriguez-Valera
Journal:  Patterns (N Y)       Date:  2021-06-15

10.  Global Association between Thermophilicity and Vancomycin Susceptibility in Bacteria.

Authors:  Chayan Roy; Masrure Alam; Subhrangshu Mandal; Prabir K Haldar; Sabyasachi Bhattacharya; Trinetra Mukherjee; Rimi Roy; Moidu J Rameez; Anup K Misra; Ranadhir Chakraborty; Ashish K Nanda; Subhra K Mukhopadhyay; Wriddhiman Ghosh
Journal:  Front Microbiol       Date:  2016-03-31       Impact factor: 5.640

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