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Comparative genomics of planktonic Flavobacteriaceae from the Gulf of Maine using metagenomic data.

ABSTRACT: BACKGROUND: The Gulf of Maine is an important biological province of the Northwest Atlantic with high productivity year round. From an environmental Sanger-based metagenome, sampled in summer and winter, we were able to assemble and explore the partial environmental genomes of uncultured members of the class Flavobacteria. Each of the environmental genomes represents organisms that compose less than 1% of the total microbial metagenome. RESULTS: Four partial environmental genomes were assembled with varying degrees of estimated completeness (37%-84% complete) and were analyzed from a perspective of gathering information regarding niche partitioning between co-occurring organisms. Comparative genomics revealed potentially important niche partitioning genomic variations, including iron transporters and genes associated with cell attachment and polymer degradation. Analysis of large syntenic regions helped reveal potentially ecologically relevant variations for Flavobacteriaceae in the Gulf of Maine, such as arginine biosynthesis, and identify a putative genomic island incorporating novel exogenous genes from the environment. CONCLUSIONS: Biogeographic analysis revealed flavobacteria species with distinct abundance patterns suggesting the presence of local blooms relative to the other species, as well as seasonally selected organisms. The analysis of genomic content for the Gulf of Maine Flavobacteria supports the hypothesis of a particle-associated lifestyle and specifically highlights a number of putative coding sequences that may play a role in the remineralization of particulate organic matter. And lastly, analysis of the underlying sequences for each assembled genome revealed seasonal and nonseasonal variants of specific genes implicating a dynamic interaction between individuals within the species.

SUBMITTER: Tully BJ

PROVIDER: S-EPMC4164334 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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Comparative genomics of planktonic Flavobacteriaceae from the Gulf of Maine using metagenomic data.

Tully Benjamin J BJ Sachdeva Rohan R Heidelberg Karla B KB Heidelberg John F JF

Microbiome 20140905

<h4>Background</h4>The Gulf of Maine is an important biological province of the Northwest Atlantic with high productivity year round. From an environmental Sanger-based metagenome, sampled in summer and winter, we were able to assemble and explore the partial environmental genomes of uncultured members of the class Flavobacteria. Each of the environmental genomes represents organisms that compose less than 1% of the total microbial metagenome.<h4>Results</h4>Four partial environmental genomes we ...[more]

PMID: 25258679

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Project description:The marine copepod Calanus finmarchicus is the most abundant zooplankton species in the northern regions of the Atlantic Ocean and the Barents Sea. Very little is known about the molecular mechanisms underlying critical processes associated with this species’ complex life history (e.g., ontogenetic development, reproduction, molting, diapause) and physiology (e.g., digestion, neural processes, and membrane physiology). This study analyzed patterns of gene expression of C. finmarchicus samples collected from the Gulf of Maine (Northwest Atlantic Ocean) using a 1,000 expressed sequence tag (EST) microarray designed to assay genes of known physiological function and hypothesized ecological importance for C. finmarchicus. Replicate analyses compared adult females and final-stage juveniles (Copepodite-5) collected from surface (0-30m) and deep (130-170m) layers. Environmental data include detailed characterization of biological, chemical, and physical oceanographic parameters in the sampled water packets. All data were screened for artifacts, normalized and selected using a fold-change filter prior to analysis. Replicate comparisons were analyzed by Significance Analysis of Microarrays (SAM; Stanford University Labs) with a control for False Discovery Rate (FDR) and with Principle Component Analysis with evaluation of significance by one- or two-sample t-test in Acuity Microarray Informatics Software (Molecular Devices, Inc.). Gene Ontology Enrichment Analysis was carried out using GOEAST (http://omicslab.genetics.ac.cn/GOEAST/index.php) to assess functional relationships of selected genes and/or proteins. The results indicated: up-regulation of genes involved in cell division, protein synthesis and mating in deep females and juveniles; up-regulation of genes related to cellular homeostasis, circadian behavior and nervous system development in surface females; and up-regulation of genes related to muscle development and protein catabolism in deep juveniles versus deep females. KEGG pathway analysis using the Blast2GO suite (http://www.blast2go.org/) indicated: up-regulation of genes encoding enzymes related to the citrate cycle and anaerobic metabolism in deep females and juveniles; and up-regulation of genes encoding enzymes related to energy metabolism and osmoregulation in surface females.

Dataset Information

Comparative genomics of planktonic Flavobacteriaceae from the Gulf of Maine using metagenomic data.

Publications

Comparative genomics of planktonic Flavobacteriaceae from the Gulf of Maine using metagenomic data.

Similar Datasets

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