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Microbial Gene Abundance and Expression Patterns across a River to Ocean Salinity Gradient.

Fortunato CS, Crump BC - PLoS ONE (2015)

Bottom Line: Samples were pre-filtered through 3 μm filters and collected on 0.2 μm filters, thus results were focused on changes among free-living microbial communities.Denitrification genes were found throughout the Columbia River coastal margin, and most highly expressed in the estuary.Across a river to ocean gradient, the free-living microbial community followed three different patterns of diversity: 1) the taxonomy of the community changed strongly with salinity, 2) metabolic potential was highly similar across samples, with few differences in functional gene abundance from river to ocean, and 3) gene expression was highly variable and generally was independent of changes in salinity.

View Article: PubMed Central - PubMed

Affiliation: Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, Massachusetts, United States of America.

ABSTRACT
Microbial communities mediate the biogeochemical cycles that drive ecosystems, and it is important to understand how these communities are affected by changing environmental conditions, especially in complex coastal zones. As fresh and marine waters mix in estuaries and river plumes, the salinity, temperature, and nutrient gradients that are generated strongly influence bacterioplankton community structure, yet, a parallel change in functional diversity has not been described. Metagenomic and metatranscriptomic analyses were conducted on five water samples spanning the salinity gradient of the Columbia River coastal margin, including river, estuary, plume, and ocean, in August 2010. Samples were pre-filtered through 3 μm filters and collected on 0.2 μm filters, thus results were focused on changes among free-living microbial communities. Results from metagenomic 16S rRNA sequences showed taxonomically distinct bacterial communities in river, estuary, and coastal ocean. Despite the strong salinity gradient observed over sampling locations (0 to 33), the functional gene profiles in the metagenomes were very similar from river to ocean with an average similarity of 82%. The metatranscriptomes, however, had an average similarity of 31%. Although differences were few among the metagenomes, we observed a change from river to ocean in the abundance of genes encoding for catabolic pathways, osmoregulators, and metal transporters. Additionally, genes specifying both bacterial oxygenic and anoxygenic photosynthesis were abundant and expressed in the estuary and plume. Denitrification genes were found throughout the Columbia River coastal margin, and most highly expressed in the estuary. Across a river to ocean gradient, the free-living microbial community followed three different patterns of diversity: 1) the taxonomy of the community changed strongly with salinity, 2) metabolic potential was highly similar across samples, with few differences in functional gene abundance from river to ocean, and 3) gene expression was highly variable and generally was independent of changes in salinity.

No MeSH data available.


Taxonomic changes across the salinity gradient.Bar charts represent the taxonomic changes seen in a) 16S sequences identified from metagenomes, b) COG annotated sequences from metagenomes, and c) COG annotated sequences from metatranscriptomes.
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pone.0140578.g002: Taxonomic changes across the salinity gradient.Bar charts represent the taxonomic changes seen in a) 16S sequences identified from metagenomes, b) COG annotated sequences from metagenomes, and c) COG annotated sequences from metatranscriptomes.

Mentions: Taxonomic profiles from the 16S sequences identified in the metagenomes showed a dramatic change in microbial community composition from river to ocean. Actinobacteria and Betaproteobacteria decreased across the salinity gradient, while Gammaproteobacteria, especially the Oceanospirillales family, increased from river to ocean (Fig 2a). The taxonomic classifications of the COG annotated reads from the metagenomes depicted a similar community composition across the salinity gradient, with only slight differences (Fig 2b). With the contig classifications we saw more Alphaproteobacteria in the lower salinity environments of the estuary and new plume. Additionally, there were fewer annotated reads classified as Bacteroidetes and more as Gammaproteobacteria in the higher salinity samples. Examination of the annotated metatranscriptomes showed slight differences in taxonomy compared to the metagenomes (Fig 2c). This was especially true in the estuary, where there was a higher percentage of Actinobacteria in the metatranscriptome compared to the metagenome. Although Cyanobacteria were present in the estuary metagenome, there was little expression of this group in the metatranscriptome. The high expression of Alphaproteobacteria in the new plume was attributed to one contig. A BLASTX of this contig gave the top hit as being from a SAR116 bacterium, an abundant group in the coastal ocean (Fig 2c). In the coastal ocean metatranscriptome, Gammaproteobacteria were most abundant with little expression of Alphaproteobacteria compared to the plume samples.


Microbial Gene Abundance and Expression Patterns across a River to Ocean Salinity Gradient.

Fortunato CS, Crump BC - PLoS ONE (2015)

Taxonomic changes across the salinity gradient.Bar charts represent the taxonomic changes seen in a) 16S sequences identified from metagenomes, b) COG annotated sequences from metagenomes, and c) COG annotated sequences from metatranscriptomes.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4633275&req=5

pone.0140578.g002: Taxonomic changes across the salinity gradient.Bar charts represent the taxonomic changes seen in a) 16S sequences identified from metagenomes, b) COG annotated sequences from metagenomes, and c) COG annotated sequences from metatranscriptomes.
Mentions: Taxonomic profiles from the 16S sequences identified in the metagenomes showed a dramatic change in microbial community composition from river to ocean. Actinobacteria and Betaproteobacteria decreased across the salinity gradient, while Gammaproteobacteria, especially the Oceanospirillales family, increased from river to ocean (Fig 2a). The taxonomic classifications of the COG annotated reads from the metagenomes depicted a similar community composition across the salinity gradient, with only slight differences (Fig 2b). With the contig classifications we saw more Alphaproteobacteria in the lower salinity environments of the estuary and new plume. Additionally, there were fewer annotated reads classified as Bacteroidetes and more as Gammaproteobacteria in the higher salinity samples. Examination of the annotated metatranscriptomes showed slight differences in taxonomy compared to the metagenomes (Fig 2c). This was especially true in the estuary, where there was a higher percentage of Actinobacteria in the metatranscriptome compared to the metagenome. Although Cyanobacteria were present in the estuary metagenome, there was little expression of this group in the metatranscriptome. The high expression of Alphaproteobacteria in the new plume was attributed to one contig. A BLASTX of this contig gave the top hit as being from a SAR116 bacterium, an abundant group in the coastal ocean (Fig 2c). In the coastal ocean metatranscriptome, Gammaproteobacteria were most abundant with little expression of Alphaproteobacteria compared to the plume samples.

Bottom Line: Samples were pre-filtered through 3 μm filters and collected on 0.2 μm filters, thus results were focused on changes among free-living microbial communities.Denitrification genes were found throughout the Columbia River coastal margin, and most highly expressed in the estuary.Across a river to ocean gradient, the free-living microbial community followed three different patterns of diversity: 1) the taxonomy of the community changed strongly with salinity, 2) metabolic potential was highly similar across samples, with few differences in functional gene abundance from river to ocean, and 3) gene expression was highly variable and generally was independent of changes in salinity.

View Article: PubMed Central - PubMed

Affiliation: Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, Massachusetts, United States of America.

ABSTRACT
Microbial communities mediate the biogeochemical cycles that drive ecosystems, and it is important to understand how these communities are affected by changing environmental conditions, especially in complex coastal zones. As fresh and marine waters mix in estuaries and river plumes, the salinity, temperature, and nutrient gradients that are generated strongly influence bacterioplankton community structure, yet, a parallel change in functional diversity has not been described. Metagenomic and metatranscriptomic analyses were conducted on five water samples spanning the salinity gradient of the Columbia River coastal margin, including river, estuary, plume, and ocean, in August 2010. Samples were pre-filtered through 3 μm filters and collected on 0.2 μm filters, thus results were focused on changes among free-living microbial communities. Results from metagenomic 16S rRNA sequences showed taxonomically distinct bacterial communities in river, estuary, and coastal ocean. Despite the strong salinity gradient observed over sampling locations (0 to 33), the functional gene profiles in the metagenomes were very similar from river to ocean with an average similarity of 82%. The metatranscriptomes, however, had an average similarity of 31%. Although differences were few among the metagenomes, we observed a change from river to ocean in the abundance of genes encoding for catabolic pathways, osmoregulators, and metal transporters. Additionally, genes specifying both bacterial oxygenic and anoxygenic photosynthesis were abundant and expressed in the estuary and plume. Denitrification genes were found throughout the Columbia River coastal margin, and most highly expressed in the estuary. Across a river to ocean gradient, the free-living microbial community followed three different patterns of diversity: 1) the taxonomy of the community changed strongly with salinity, 2) metabolic potential was highly similar across samples, with few differences in functional gene abundance from river to ocean, and 3) gene expression was highly variable and generally was independent of changes in salinity.

No MeSH data available.