The unaccounted yet abundant nitrous oxide-reducing microbial community: a potential nitrous oxide sink
Reads0
Chats0
TLDR
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.Abstract:
Nitrous oxide (N2O) is a major radiative forcing and stratospheric ozone-depleting gas emitted from terrestrial and aquatic ecosystems. It can be transformed to nitrogen gas (N2) by bacteria and archaea harboring the N2O reductase (N2OR), which is the only known N2O sink in the biosphere. Despite its crucial role in mitigating N2O emissions, knowledge of the N2OR in the environment remains limited. Here, we report a comprehensive phylogenetic analysis of the nosZ gene coding the N2OR in genomes retrieved from public databases. The resulting phylogeny revealed two distinct clades of nosZ, with one unaccounted for in studies investigating N2O-reducing communities. Examination of N2OR structural elements not considered in the phylogeny revealed that the two clades differ in their signal peptides, indicating differences in the translocation pathway of the N2OR across the membrane. Sequencing of environmental clones of the previously undetected nosZ lineage in various environments showed that it is widespread and diverse. Using quantitative PCR, we demonstrate that this clade was most often at least as abundant as the other, thereby more than doubling the known extent of the overall N2O-reducing community in the environment. Furthermore, we observed that the relative abundance of nosZ from either clade varied among habitat types and environmental conditions. Our results indicate a physiological dichotomy in the diversity of N2O-reducing microorganisms, which might be of importance for understanding the relationship between the diversity of N2O-reducing microorganisms and N2O reduction in different ecosystems.read more
Citations
More filters
Journal ArticleDOI
The microbial nitrogen-cycling network
TL;DR: This Review summarizes the current understanding of the microbial nitrogen-cycling network, including novel processes, their underlying biochemical pathways, the involved microorganisms, their environmental importance and industrial applications.
Journal ArticleDOI
Loss in microbial diversity affects nitrogen cycling in soil.
Laurent Philippot,Aymé Spor,Catherine Hénault,David Bru,Florian Bizouard,Christopher M. Jones,Christopher M. Jones,Amadou Sarr,Pierre-Alain Maron +8 more
TL;DR: This study shows that microbial diversity loss can alter terrestrial ecosystem processes, which suggests that the importance of functional redundancy in soil microbial communities has been overstated.
Journal ArticleDOI
FunGene: the functional gene pipeline and repository
TL;DR: The Functional Gene Pipeline and Repository offers databases of many common ecofunctional genes and proteins, as well as integrated tools that allow researchers to browse these collections and choose subsets for further analysis, build phylogenetic trees, test primers and probes for coverage, and download aligned sequences.
Journal ArticleDOI
Microbial regulation of terrestrial nitrous oxide formation: understanding the biological pathways for prediction of emission rates
TL;DR: It is argued that it is urgently necessary to incorporate microbial traits into biogeochemical ecosystem modeling in order to increase the estimation reliability of N2O emissions and proposed a molecular methodology oriented framework from gene to ecosystem scales for more robust prediction and mitigation of future N1O emissions.
Journal ArticleDOI
Linking N2O emissions from biochar-amended soil to the structure and function of the N-cycling microbial community
Johannes Harter,Hans Martin Krause,Stefanie Schuettler,Reiner Ruser,Markus Fromme,Thomas Scholten,Andreas Kappler,Sebastian Behrens +7 more
TL;DR: In this paper, a microcosm study with a water-saturated soil amended with different amounts (0, 2% and 10% (w/w)) of high-temperature biochar was performed.
References
More filters
Journal ArticleDOI
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
TL;DR: UNLABELLED RAxML-VI-HPC (randomized axelerated maximum likelihood for high performance computing) is a sequential and parallel program for inference of large phylogenies with maximum likelihood (ML) that has been used to compute ML trees on two of the largest alignments to date.
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
Profile hidden Markov models.
TL;DR: Profile HMM methods performed comparably to threading methods in the CASP2 structure prediction exercise and complement standard pairwise comparison methods for large-scale sequence analysis.
Journal ArticleDOI
Toward an ecological classification of soil bacteria.
TL;DR: Survey, experimental, and meta-analytical results suggest that certain bacterial phyla can be differentiated into copiotrophic and oligotrophic categories that correspond to the r- and K-selected categories used to describe the ecological attributes of plants and animals.
Journal ArticleDOI
The PSIPRED protein structure prediction server.
TL;DR: The PSIPRED protein structure prediction server allows users to submit a protein sequence, perform a prediction of their choice and receive the results of the prediction both textually via e-mail and graphically via the web.