Journal ArticleDOI
Microbial community dynamics in a seasonally anoxic fjord: Saanich Inlet, British Columbia.
Elena Zaikova,David A. Walsh,Claire P. Stilwell,William W. Mohn,Philippe D. Tortell,Steven J. Hallam +5 more
TLDR
A robust comparative phylogenetic framework for inferring systems metabolism of nitrogen, carbon and sulfur cycling within oxygen-deficient oceanic waters is provided and Saanich Inlet is established as a tractable model for studying the response of microbial communities to changing levels of water column hypoxia.Abstract:
Summary
Dissolved oxygen concentration plays a major role in shaping biotic interactions and nutrient flows within marine ecosystems. Throughout the global ocean, regions of low dissolved oxygen concentration (hypoxia) are a common and expanding feature of the water column, with major feedback on productivity and greenhouse gas cycling. To better understand microbial diversity underlying biogeochemical transformations within oxygen-deficient oceanic waters, we monitored and quantified bacterial and archaeal community dynamics in relation to dissolved gases and nutrients during a seasonal stratification and deep water renewal cycle in Saanich Inlet, British Columbia, a seasonally anoxic fjord. A number of microbial groups partitioned within oxygen-deficient waters including Nitrospina and SAR324 affiliated with the δ-proteobacteria, SAR406 and γ-proteobacteria related to thiotrophic gill symbionts of deep-sea clams and mussels. Microbial diversity was highest within the hypoxic transition zone decreasing dramatically within anoxic basin waters and temporal patterns of niche partitioning were observed along defined gradients of oxygen and phosphate. These results provide a robust comparative phylogenetic framework for inferring systems metabolism of nitrogen, carbon and sulfur cycling within oxygen-deficient oceanic waters and establish Saanich Inlet as a tractable model for studying the response of microbial communities to changing levels of water column hypoxia.read more
Citations
More filters
Journal ArticleDOI
Microbial Ecology of the Dark Ocean above, at, and below the Seafloor
TL;DR: This review focuses on the current understanding of microbiology in the dark ocean, outlining salient features of various habitats and discussing known and still unexplored types of microbial metabolism and their consequences in global biogeochemical cycling.
Journal ArticleDOI
Microbial nitrogen cycling processes in oxygen minimum zones.
Phyllis Lam,Marcel M. M. Kuypers +1 more
TL;DR: Oxygen minimum zones (OMZs) harbor unique microbial communities that rely on alternative electron acceptors for respiration, and conditions therein enable an almost complete nitrogen (N) cycle and substantial N-loss.
Journal ArticleDOI
Beyond the Calvin cycle: autotrophic carbon fixation in the ocean.
Michael Hügler,Stefan M. Sievert +1 more
TL;DR: Recent discoveries in the field of autotrophic carbon fixation are reviewed, including the biochemistry and evolution of the different pathways, as well as their ecological relevance in various oceanic ecosystems.
Journal ArticleDOI
Microbial ecology of expanding oxygen minimum zones
TL;DR: Current efforts to explore the fundamental factors that control the ecological and microbial biodiversity in oxygen-starved regions of the ocean, termed oxygen minimum zones are described and new insights into coupled biogeochemical processes in the ocean are provided.
Journal ArticleDOI
High taxonomic variability despite stable functional structure across microbial communities
Stilianos Louca,Saulo M. S. Jacques,Aliny P. F. Pires,Juliana S. Leal,Diane S. Srivastava,Laura Wegener Parfrey,Vinicius F. Farjalla,Michael Doebeli +7 more
TL;DR: It is found that all of the bromeliads exhibited remarkably similar functional community structures, but that the taxonomic composition within individual functional groups was highly variable, and that non-neutral processes at least partly shaped the composition within functional groups and were more important than spatial dispersal limitation and demographic drift.
References
More filters
Journal ArticleDOI
MUSCLE: multiple sequence alignment with high accuracy and high throughput
TL;DR: MUSCLE is a new computer program for creating multiple alignments of protein sequences that includes fast distance estimation using kmer counting, progressive alignment using a new profile function the authors call the log-expectation score, and refinement using tree-dependent restricted partitioning.
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
TL;DR: A 16S rRNA gene database (http://greengenes.lbl.gov) was used to provide chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies as mentioned in this paper.
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
SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB
Elmar Pruesse,Christian Quast,Katrin Knittel,Bernhard M. Fuchs,Wolfgang Ludwig,Jörg Peplies,Frank Oliver Glöckner +6 more
TL;DR: SILVA (from Latin silva, forest), was implemented to provide a central comprehensive web resource for up to date, quality controlled databases of aligned rRNA sequences from the Bacteria, Archaea and Eukarya domains.
Supporting Online Material for Spreading Dead Zones and Consequences for Marine Ecosystems
Robert J. Diaz,Rutger Rosenberg +1 more
TL;DR: The formation of dead zones has been exacerbated by the increase in primary production and consequent worldwide coastal eutrophication fueled by riverine runoff of fertilizers and the burning of fossil fuels as discussed by the authors.
Related Papers (5)
Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities
Patrick D. Schloss,Patrick D. Schloss,Sarah L. Westcott,Sarah L. Westcott,Thomas Ryabin,Justine R. Hall,Martin Hartmann,Emily B. Hollister,Ryan A. Lesniewski,Brian B. Oakley,Donovan H. Parks,Courtney J. Robinson,Jason W. Sahl,Blaz Stres,Gerhard G. Thallinger,David J. Van Horn,Carolyn F. Weber +16 more