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Phylogenetic Signals of Salinity and Season in Bacterial Community Composition Across the Salinity Gradient of the Baltic Sea

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ABSTRACT

Understanding the key processes that control bacterial community composition has enabled predictions of bacterial distribution and function within ecosystems. In this study, we used the Baltic Sea as a model system to quantify the phylogenetic signal of salinity and season with respect to bacterioplankton community composition. The abundances of 16S rRNA gene amplicon sequencing reads were analyzed from samples obtained from similar geographic locations in July and February along a brackish to marine salinity gradient in the Baltic Sea. While there was no distinct pattern of bacterial richness at different salinities, the number of bacterial phylotypes in winter was significantly higher than in summer. Bacterial community composition in brackish vs. marine conditions, and in July vs. February was significantly different. Non-metric multidimensional scaling showed that bacterial community composition was primarily separated according to salinity and secondly according to seasonal differences at all taxonomic ranks tested. Similarly, quantitative phylogenetic clustering implicated a phylogenetic signal for both salinity and seasonality. Our results suggest that global patterns of bacterial community composition with respect to salinity and season are the result of phylogenetically clustered ecological preferences with stronger imprints from salinity.

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Phylogenetic tree and heat map of high-abundant indicator operational taxonomic units (OTUs). The heat map shows the relative abundances of the abundant (>1%) OTUs identified by a least discriminant analysis (LDA) effect size (LEfSe) analysis of the congruent dataset (bold). The OTUs are arranged based on a maximum-likelihood (ML) tree of full-length sequences chosen based on their close phylogenetic affiliation with the indicator OTU sequences. The short indicator OTU sequences from our study were added without changing the tree topology, after calculation of the ML-tree. The scale bar is only approximate because the procedure distorts branch length. Original sequence definitions were replaced by a consistent nomenclature, including Genbank accession number, name, and next defined taxonomic level.
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Figure 5: Phylogenetic tree and heat map of high-abundant indicator operational taxonomic units (OTUs). The heat map shows the relative abundances of the abundant (>1%) OTUs identified by a least discriminant analysis (LDA) effect size (LEfSe) analysis of the congruent dataset (bold). The OTUs are arranged based on a maximum-likelihood (ML) tree of full-length sequences chosen based on their close phylogenetic affiliation with the indicator OTU sequences. The short indicator OTU sequences from our study were added without changing the tree topology, after calculation of the ML-tree. The scale bar is only approximate because the procedure distorts branch length. Original sequence definitions were replaced by a consistent nomenclature, including Genbank accession number, name, and next defined taxonomic level.

Mentions: Representative bacterial OTUs, classes, and phyla for season and salinity were identified by applying the LEfSe to the congruent dataset. This resulted in the identification of 280 OTUs for the marine samples and 51 OTUs for the mesohaline samples with significantly higher relative abundances at the respective salinity (Supplementary Table S2). Among the abundant OTUs (>1% relative abundance; Supplementary Table S3; Figure 5), different representatives of the cyanobacterial genus Synechococcus were typical for either the marine or the mesohaline samples (OTU-41, OTU-10 vs. OTU-13, OTU-57, OTU-64). Representatives of the SAR11 clade (“Pelagibacterales”) were present among the marine and mesohaline samples. While the mesohaline samples were dominated by a SAR11-IIIa OTU (OTU-14), in the marine samples two other OTUs from the SAR11 group (SAR11-II) were dominant (OTU-18, OTU-200). Other typical alphaproteobacterial OTUs in the marine samples were SAR116, Roseobacter OCT lineage, Planktomarina, the gammaproteobacteria SAR86, “unclassified Oceanospirillales,” “unclassified Alteromonadales,” NOR5/OM60 (Alteromonadaceae), a representative of OM43 (Betaproteobacteria) and “Candidatus Actinomarina” (Actinobacteria). In the mesohaline environment, after Synechococcus, an OTU from Spartobacteria was the most abundant, with other representative OTUs including those assigned to Flavobacteriaceae (Bacteroidetes), Rhodobacteriaceae (Alphaproteobacteria), and the actinobacterial family Corynebacteriales as well as two OTUs from the hgcI-clade [also referred to as the “acI-clade” (Warnecke et al., 2005)].


Phylogenetic Signals of Salinity and Season in Bacterial Community Composition Across the Salinity Gradient of the Baltic Sea
Phylogenetic tree and heat map of high-abundant indicator operational taxonomic units (OTUs). The heat map shows the relative abundances of the abundant (>1%) OTUs identified by a least discriminant analysis (LDA) effect size (LEfSe) analysis of the congruent dataset (bold). The OTUs are arranged based on a maximum-likelihood (ML) tree of full-length sequences chosen based on their close phylogenetic affiliation with the indicator OTU sequences. The short indicator OTU sequences from our study were added without changing the tree topology, after calculation of the ML-tree. The scale bar is only approximate because the procedure distorts branch length. Original sequence definitions were replaced by a consistent nomenclature, including Genbank accession number, name, and next defined taxonomic level.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5121245&req=5

Figure 5: Phylogenetic tree and heat map of high-abundant indicator operational taxonomic units (OTUs). The heat map shows the relative abundances of the abundant (>1%) OTUs identified by a least discriminant analysis (LDA) effect size (LEfSe) analysis of the congruent dataset (bold). The OTUs are arranged based on a maximum-likelihood (ML) tree of full-length sequences chosen based on their close phylogenetic affiliation with the indicator OTU sequences. The short indicator OTU sequences from our study were added without changing the tree topology, after calculation of the ML-tree. The scale bar is only approximate because the procedure distorts branch length. Original sequence definitions were replaced by a consistent nomenclature, including Genbank accession number, name, and next defined taxonomic level.
Mentions: Representative bacterial OTUs, classes, and phyla for season and salinity were identified by applying the LEfSe to the congruent dataset. This resulted in the identification of 280 OTUs for the marine samples and 51 OTUs for the mesohaline samples with significantly higher relative abundances at the respective salinity (Supplementary Table S2). Among the abundant OTUs (>1% relative abundance; Supplementary Table S3; Figure 5), different representatives of the cyanobacterial genus Synechococcus were typical for either the marine or the mesohaline samples (OTU-41, OTU-10 vs. OTU-13, OTU-57, OTU-64). Representatives of the SAR11 clade (“Pelagibacterales”) were present among the marine and mesohaline samples. While the mesohaline samples were dominated by a SAR11-IIIa OTU (OTU-14), in the marine samples two other OTUs from the SAR11 group (SAR11-II) were dominant (OTU-18, OTU-200). Other typical alphaproteobacterial OTUs in the marine samples were SAR116, Roseobacter OCT lineage, Planktomarina, the gammaproteobacteria SAR86, “unclassified Oceanospirillales,” “unclassified Alteromonadales,” NOR5/OM60 (Alteromonadaceae), a representative of OM43 (Betaproteobacteria) and “Candidatus Actinomarina” (Actinobacteria). In the mesohaline environment, after Synechococcus, an OTU from Spartobacteria was the most abundant, with other representative OTUs including those assigned to Flavobacteriaceae (Bacteroidetes), Rhodobacteriaceae (Alphaproteobacteria), and the actinobacterial family Corynebacteriales as well as two OTUs from the hgcI-clade [also referred to as the “acI-clade” (Warnecke et al., 2005)].

View Article: PubMed Central - PubMed

ABSTRACT

Understanding the key processes that control bacterial community composition has enabled predictions of bacterial distribution and function within ecosystems. In this study, we used the Baltic Sea as a model system to quantify the phylogenetic signal of salinity and season with respect to bacterioplankton community composition. The abundances of 16S rRNA gene amplicon sequencing reads were analyzed from samples obtained from similar geographic locations in July and February along a brackish to marine salinity gradient in the Baltic Sea. While there was no distinct pattern of bacterial richness at different salinities, the number of bacterial phylotypes in winter was significantly higher than in summer. Bacterial community composition in brackish vs. marine conditions, and in July vs. February was significantly different. Non-metric multidimensional scaling showed that bacterial community composition was primarily separated according to salinity and secondly according to seasonal differences at all taxonomic ranks tested. Similarly, quantitative phylogenetic clustering implicated a phylogenetic signal for both salinity and seasonality. Our results suggest that global patterns of bacterial community composition with respect to salinity and season are the result of phylogenetically clustered ecological preferences with stronger imprints from salinity.

No MeSH data available.


Related in: MedlinePlus