Abundance, composition, diversity and novelty of soil Proteobacteria
TLDR
This level of novel phylogenetic diversity indicates that the understanding of the functions of soil microorganisms, even those belonging to phyla with numerous and diverse well-characterized cultured representatives such as the Proteobacteria, remains far from adequate.Abstract:
Small subunit (16S) rRNA gene surveys generating near full-length 16S rRNA clones offer a unique opportunity for in-depth phylogenetic analysis to highlight the breadth of diversity within various major bacterial phyla encountered in soil. This study offers a detailed phylogenetic analysis of the Proteobacteria-affiliated clones identified from 13,001 nearly full-length 16S rRNA gene clones derived from Oklahoma tall-grass prairie soil. Proteobacteria was the most abundant phylum in the community, and comprised 25% of the total clones. The most abundant and diverse class within the Proteobacteria was Alphaproteobacteria, followed by the Delta-, Beta- and Gammaproteobacteria. Members of the Epsilon- and Zetaproteobacteria were not detected in the dataset. Our analysis identified 15 novel order-level and 48 novel family-level Proteobacteria lineages. In addition, we show that the majority of Proteobacteria clones in the dataset belong to orders and families containing no described cultivated representatives (50% and 65%, respectively). An examination of the ecological distribution of the six most abundant Proteobacteria lineages in this dataset with no characterized pure culture representatives provided important information regarding their global distribution and environmental preferences. This level of novel phylogenetic diversity indicates that our understanding of the functions of soil microorganisms, even those belonging to phyla with numerous and diverse well-characterized cultured representatives such as the Proteobacteria, remains far from adequate.read more
Citations
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The unaccounted yet abundant nitrous oxide-reducing microbial community: a potential nitrous oxide sink
TL;DR: A comprehensive phylogenetic analysis of the nosZ gene coding the N2OR in genomes retrieved from public databases revealed two distinct clades of nosZ, indicating a physiological dichotomy in the diversity of N2O-reducing microorganisms.
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Global patterns in the biogeography of bacterial taxa
Diana R. Nemergut,Elizabeth K. Costello,Micah Hamady,Catherine A. Lozupone,Lin Jiang,Steven K. Schmidt,Noah Fierer,Alan R. Townsend,Cory C. Cleveland,Lee F. Stanish,Rob Knight +10 more
TL;DR: In this article, the authors reveal patterns in the distribution of individual bacterial taxa at multiple levels of phylogenetic resolution within and between Earth's major habitat types and show that the most cosmopolitan taxa are also the most abundant in individual assemblages.
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Bacterial diversity in rhizosphere soil from Antarctic vascular plants of Admiralty Bay, maritime Antarctica.
Lia C. R. S. Teixeira,Raquel S. Peixoto,Juliano C. Cury,Woo Jun Sul,Vivian Helena Pellizari,James M. Tiedje,Alexandre S. Rosado +6 more
TL;DR: To the best of the knowledge, this is the first major bacterial sequencing effort of this kind of soil, and it revealed more than expected diversity within these rhizospheres of both maritime Antarctica vascular plants in Admiralty Bay, King George Island, which is part of the South Shetlands archipelago.
Journal ArticleDOI
Microbial ecology of hot desert edaphic systems
Thulani P. Makhalanyane,Angel Valverde,Eoin Gunnigle,Aline Frossard,Jean-Baptiste Ramond,Don A. Cowan +5 more
TL;DR: This review examines the microbial communities of hot desert terrestrial biotopes (including soils, cryptic and refuge niches and plant-root-associated microbes) and the processes that govern their assembly and the possible effects of global climate change on hot desert microbial communities and the resulting feedback mechanisms.
Journal ArticleDOI
Exposure of Soil Microbial Communities to Chromium and Arsenic Alters Their Diversity and Structure
Cody S. Sheik,Tyler W. Mitchell,Fariha Zakria Rizvi,Yasir Rehman,Muhammad Faisal,Shahida Hasnain,Michael J. McInerney,Lee R. Krumholz +7 more
TL;DR: Results showed that ACR3 becomes less diverse as arsenic concentrations increase with a single OTU dominating at the highest concentration, and chronic exposure to either Cr or As not only alters the composition of the soil bacterial community in general, but affects the arsenic resistant individuals in different ways.
References
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Journal ArticleDOI
Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB
Todd Z. DeSantis,Philip Hugenholtz,Neils Larsen,Mark Rojas,Eoin L. Brodie,Keith Keller,Thomas Huber,Daniel Dalevi,Ping Hu,Gary L. Andersen +9 more
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Journal ArticleDOI
ARB: a software environment for sequence data
Wolfgang Ludwig,Oliver Strunk,Ralf Westram,Lothar Richter,Harald Meier,Yadhukumar,Arno Buchner,Tina Lai,Susanne Steppi,Gangolf Jobb,Wolfram Förster,Igor Brettske,Stefan Gerber,Anton W. Ginhart,Oliver Gross,Silke Grumann,Stefan Hermann,Ralf Jost,Andreas König,Thomas Liss,Ralph Lüßmann,Michael May,Björn Nonhoff,Boris Reichel,Robert Strehlow,Alexandros Stamatakis,Norbert Stuckmann,Alexander Vilbig,Michael Lenke,Thomas Ludwig,Arndt Bode,Karl-Heinz Schleifer +31 more
TL;DR: The ARB program package comprises a variety of directly interacting software tools for sequence database maintenance and analysis which are controlled by a common graphical user interface.
Journal ArticleDOI
Introducing DOTUR, a Computer Program for Defining Operational Taxonomic Units and Estimating Species Richness
Patrick D. Schloss,Jo Handelsman +1 more
TL;DR: A computer program, DOTUR, is developed, which assigns sequences to OTUs by using either the furthest, average, or nearest neighbor algorithm for each distance level, which addresses the challenge of assigning sequences to operational taxonomic units (OTUs) based on the genetic distances between sequences.
Journal ArticleDOI
Pyrosequencing enumerates and contrasts soil microbial diversity
Luiz Fernando Wurdig Roesch,Roberta R. Fulthorpe,Alberto Riva,George Casella,Alison K M Hadwin,Angela D. Kent,Samira H. Daroub,Flávio Anastácio de Oliveira Camargo,William G. Farmerie,Eric W. Triplett +9 more
TL;DR: This work is the most comprehensive examination to date of bacterial diversity in soil and suggests that agricultural management of soil may significantly influence the diversity of bacteria and archaea.
Journal ArticleDOI
Bellerophon: a program to detect chimeric sequences in multiple sequence alignments
TL;DR: Bellerophon was specifically developed to detect 16S rRNA gene chimeras in PCR-clone libraries of environmental samples but can be applied to other nucleotide sequence alignments.
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