Journal ArticleDOI
A metatranscriptomics-based assessment of small-scale mixing of sulfidic and oxic waters on redoxcline prokaryotic communities.
Sara Beier,Sara Beier,Peter Holtermann,Daniela Numberger,Daniela Numberger,Thomas Schott,Lars Umlauf,Klaus Jürgens +7 more
TLDR
It is suggested that, despite the absence of measurable oxygenated compounds in the sulfidic water, frequent intermittent small-scale intrusions stimulate the permanent upregulation of genes involved in nitrification, denitrification and sulfur oxidation.Abstract:
Lateral intrusions of oxygen caused by small-scale mixing are thought to shape microbial activity in marine redoxclines. To examine the response of prokaryotes to such mixing events we employed a shipboard mixing experiment in the euxinic central Baltic Sea: oxic, nitrate containing and sulfidic water samples without detectable oxygenized substances were incubated directly or after mixing. While nitrate, nitrite and ammonium concentrations stayed approximately constant in all incubations, we observed a decrease of sulfide after the contact with oxygen in the sulfide containing incubations. The transcription of marker genes from chemolithoauthotrophic key players including archaeal nitrifiers as well as gammaproteobacterial and campylobacterial autotrophic organisms that couple denitrification with sulfur-oxidation were followed at four time points within 8.5 h. The temporally contrasting transcriptional profiles of gammaproteobacterial and campylobacterial denitrifiers that depend on the same inorganic substrates pointed to a niche separation. Particular archaeal and campylobacterial marker genes involved in nitrification, denitrification and sulfur oxidation, which depend on oxidized substrates, were highly upregulated in the anaerobic sulfidic samples. We suggest that, despite the absence of measurable oxygenated compounds in the sulfidic water, frequent intermittent small-scale intrusions stimulate the permanent upregulation of genes involved in nitrification, denitrification and sulfur oxidation.read more
Citations
More filters
Journal Article
Metagenome of a Versatile Chemolithoautotroph from Expanding Oceanic Dead Zones
TL;DR: In this paper, the authors report time-resolved metagenomic analyses of a ubiquitous and abundant but uncultivated OMZ microbe (SUP05) closely related to chemoautotrophic gill symbionts of deep-sea clams and mussels.
Journal ArticleDOI
Interleaving of oxygenized intrusions into the Baltic Sea redoxcline
Peer ReviewDOI
Biogeochemical functioning of the Baltic Sea
Karol Kuliński,Gregor Rehder,Eero Asmala,Alena Bartosova,Jacob Carstensen,Bo G. Gustafsson,Per O. J. Hall,Christoph Humborg,Tom Jilbert,Klaus Jürgens,H. E. Markus Meier,Bärbel Müller-Karulis,Michael Naumann,Jørgen E. Olesen,Oleg P. Savchuk,Andreas Schramm,Caroline P. Slomp,Mikhail Sofiev,Anna Sobek,Beata Szymczycha,Emma Undeman +20 more
TL;DR: In this paper , a comprehensive assessment of marine biogeochemical functioning of the Baltic Sea is presented, including changes in carbon, nitrogen, and phosphorus external loads, their transformations in the coastal zone, changes in organic-matter production (eutrophication) and remineralization (oxygen availability), and the role of sediments in burial and turnover of C, N, and P.
Journal ArticleDOI
Homeostasis drives intense microbial trace metal processing on marine particles
Pavla Debeljak,Pavla Debeljak,Stéphane Blain,Andrew R. Bowie,Pier van der Merwe,Barbara Bayer,Ingrid Obernosterer +6 more
TL;DR: In this paper, the availability of nine metals of biological importance on particles collected in the region of Heard Island (Indian sector of the Southern Ocean) was investigated, and the expression of genes for the uptake of metals through various mechanisms demonstrated that particles are a bioavailable reservoir.
Journal ArticleDOI
Resource Partitioning Between Phytoplankton and Bacteria in the Coastal Baltic Sea
TL;DR: In this article, the authors used metatranscriptomics and amplicon sequencing to compare known metabolic pathways of both phytoplankton and bacteria co-occurring during a summer bloom in the archipelago of Aland in the Baltic Sea to examine the impact of resource partitioning on the community composition.
References
More filters
Journal ArticleDOI
Fast gapped-read alignment with Bowtie 2
TL;DR: Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.
Journal ArticleDOI
Cutadapt removes adapter sequences from high-throughput sequencing reads
TL;DR: The command-line tool cutadapt is developed, which supports 454, Illumina and SOLiD (color space) data, offers two adapter trimming algorithms, and has other useful features.
Posted ContentDOI
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
TL;DR: This work presents DESeq2, a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates, which enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression.
Journal ArticleDOI
featureCounts: an efficient general-purpose program for assigning sequence reads to genomic features
TL;DR: FeatureCounts as discussed by the authors is a read summarization program suitable for counting reads generated from either RNA or genomic DNA sequencing experiments, which implements highly efficient chromosome hashing and feature blocking techniques.
Journal ArticleDOI
KEGG for linking genomes to life and the environment
Minoru Kanehisa,Michihiro Araki,Susumu Goto,Masahiro Hattori,Mika Hirakawa,Masumi Itoh,Toshiaki Katayama,Shuichi Kawashima,Shujiro Okuda,Toshiaki Tokimatsu,Yoshihiro Yamanishi +10 more
TL;DR: KEGG PATHWAY is now supplemented with a new global map of metabolic pathways, which is essentially a combined map of about 120 existing pathway maps, and the KEGG resource is being expanded to suit the needs for practical applications.