Metagenomic analysis shows the presence of bacteria related to free-living forms of sulfur-Oxidizing Chemolithoautotrophic Symbionts in the rhizosphere of the seagrass Zostera marina

Seagrasses play an important role as ecosystem engineers; they provide shelter to many animals and improve water quality by filtering out nutrients and by controlling pathogens. Moreover, their rhizosphere promotes a myriad of microbial interactions and processes, which are dominated by microorganisms involved in the sulfur cycle. This study provides a detailed insight into the metabolic sulfur pathways in the rhizobiome of the seagrass Zostera marina, a dominant seagrass species across the temperate northern hemisphere. Shotgun metagenomic sequencing revealed the relative dominance of Gamma- and Deltaproteobacteria, and comparative analysis of sulfur genes identified a higher abundance of genes related to sulfur oxidation than sulfate reduction. We retrieved four high-quality draft genomes that are closely related to the gill symbiont of the clam Solemya velum, which suggests the presence of putative free-living forms of symbiotic bacteria. These are potentially highly versatile chemolithoautotrophic bacteria, able to alternate their metabolism between parallel pathways of sulfide oxidation (via sqr and fcc), nitrate reduction (denitrification or DNRA) and carbon fixation (via CBB or TCA cycle), depending on the environmental availability of sulfide. Our results support the hypothesis that seagrass meadows might function as a source of symbionts for invertebrates that inhabit within or around seagrass meadows. While providing ideal conditions for the proliferation of these free-living forms of symbionts, seagrasses would benefit from their genetic versatility, which contributes to sulfide detoxification and ammonium production, the seagrasses' preferred nitrogen source.European Union ERC 322551 European Science Foundation ConGenOmics program 6349 Fundacao para a Ciencia e Tecnologia (FCT) SFRH/BPD/63/03/2009 SFRH/BPD/107878/2015info:eu-repo/semantics/publishedVersio

Diversity and Distribution of Sulfur Oxidation-Related Genes in Thioalkalivibrio, a Genus of Chemolithoautotrophic and Haloalkaliphilic Sulfur-Oxidizing Bacteria

Soda lakes are saline alkaline lakes characterized by high concentrations of sodium carbonate/bicarbonate which lead to a stable elevated pH (>9), and moderate to extremely high salinity. Despite this combination of extreme conditions, biodiversity in soda lakes is high, and the presence of diverse microbial communities provides a driving force for highly active biogeochemical cycles. The sulfur cycle is one of the most important of these and bacterial sulfur oxidation is dominated by members of the obligately chemolithoautotrophic genus Thioalkalivibrio. Currently, 10 species have been described in this genus, but over one hundred isolates have been obtained from soda lake samples. The genomes of 75 strains were sequenced and annotated previously, and used in this study to provide a comprehensive picture of the diversity and distribution of genes related to dissimilatory sulfur metabolism in Thioalkalivibrio. Initially, all annotated genes in 75 Thioalkalivibrio genomes were placed in ortholog groups and filtered by bi-directional best BLAST analysis. Investigation of the ortholog groups containing genes related to sulfur oxidation showed that flavocytochrome c (fcc), the truncated sox system, and sulfite:quinone oxidoreductase (soe) are present in all strains, whereas dissimilatory sulfite reductase (dsr; which catalyzes the oxidation of elemental sulfur) was found in only six strains. The heterodisulfide reductase system (hdr), which is proposed to oxidize sulfur to sulfite in strains lacking both dsr and soxCD, was detected in 73 genomes. Hierarchical clustering of strains based on sulfur gene repertoire correlated closely with previous phylogenomic analysis. The phylogenetic analysis of several sulfur oxidation genes showed a complex evolutionary history. All in all, this study presents a comprehensive investigation of sulfur metabolism-related genes in cultivated Thioalkalivibrio strains and provides several avenues for future research

Comparative analyses imply that the enigmatic sigma factor 54 is a central controller of the bacterial exterior

Contains fulltext : 95738.pdf (publisher's version ) (Open Access)BACKGROUND: Sigma-54 is a central regulator in many pathogenic bacteria and has been linked to a multitude of cellular processes like nitrogen assimilation and important functional traits such as motility, virulence, and biofilm formation. Until now it has remained obscure whether these phenomena and the control by Sigma-54 share an underlying theme. RESULTS: We have uncovered the commonality by performing a range of comparative genome analyses. A) The presence of Sigma-54 and its associated activators was determined for all sequenced prokaryotes. We observed a phylum-dependent distribution that is suggestive of an evolutionary relationship between Sigma-54 and lipopolysaccharide and flagellar biosynthesis. B) All Sigma-54 activators were identified and annotated. The relation with phosphotransfer-mediated signaling (TCS and PTS) and the transport and assimilation of carboxylates and nitrogen containing metabolites was substantiated. C) The function annotations, that were represented within the genomic context of all genes encoding Sigma-54, its activators and its promoters, were analyzed for intra-phylum representation and inter-phylum conservation. Promoters were localized using a straightforward scoring strategy that was formulated to identify similar motifs. We found clear highly-represented and conserved genetic associations with genes that concern the transport and biosynthesis of the metabolic intermediates of exopolysaccharides, flagella, lipids, lipopolysaccharides, lipoproteins and peptidoglycan. CONCLUSION: Our analyses directly implicate Sigma-54 as a central player in the control over the processes that involve the physical interaction of an organism with its environment like in the colonization of a host (virulence) or the formation of biofilm

A comparison of TIS prediction accuracy between RefSeq, PCA-based and Prodigal annotation.

<p>Scatterplot of the correlation between observed alternative start codon frequencies and expected alternative start codon frequencies (i.e., the TIS annotation quality measure) for both the original TIS annotation as found in the RefSeq database (<i>Y</i> axis) and the adjusted annotations (<i>X</i> axis) based on (A) our iterative PCA pipeline and (B) Prodigal. (C) Scatterplot for PCA-based annotation versus Prodigal. The color scale represents the GC% of the corresponding genome (blue: high, green: average, red: low)</p

Distribution of alternative start codons for each microbial Refseq genome

<p>Distributions of alternative start codons for each microbial Refseq genome.</p

Effects of year of sequencing, GC-content and taxonomy on TIS-prediction accuracy.

<p>The boxplots show the distribution of the calculated correlation values (between the observed and expected distribution of alternative TISs) (<i>Y</i> axis) for: (A) all bacterial and archaeal RefSeq genomes grouped by year of sequencing (NCBI Bioproject data; [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0133691#pone.0133691.ref038" target="_blank">38</a>]); (B) The RefSeq genomes grouped into 6 bins according to their GC%; (C) The RefSeq genomes grouped according to phylum; and (D) 277 selected bacterial and archaeal genomes with varying SD-index (proportion of Shine-Dalgarno sequence-preceded genes) [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0133691#pone.0133691.ref004" target="_blank">4</a>].</p

Correlation coefficients between observed alternative start frequencies and expected alternative start frequencies for microbial genomes.

<p>(A) Spearman’s rho coefficients for all bacterial RefSeq genomes with > 500 ORFs. (B) Spearman’s rho coefficients for all Archaeal RefSeq genomes with > 500 ORFs.</p

TIS annotation for <i>E</i>. <i>coli</i> K12 MG1655.

<p>(a) The majority of TISs that are different in the PCA-based and Prodigal-based annotation are located close to the RefSeq TIS. For the PCA-based predictions: 548 were not in agreement with RefSeq, 199 of these where within 30 nt distance and 56 at 3nt distance; For the Prodigal predictions: 241 (6%) were not in agreement with RefSeq (and 74 (2%) were missed): 96 of these were within 30 nt distance and 30 at 3nt distance.</p><p>The NCBI RefSeq file contained 4141 annotated genes. The position of the TISs was compared between the PCA-based prediction, the Prodigal-based prediction and the RefSeq annotation. Recently, the EcoGene annotation has been updated and 13 TISs have been adjusted (b0259, b0552, b0656, b1994, b2030, b2192, b3218, b3505, b4543, b2803, b1331, b2982 and b3093). The adaptations were compared to the PCA-based and Prodigal-based predictions.</p

Distributions of alternative start codons for all microbial Refseq genomes

<p>Distributions of alternative start codons for all microbial Refseq genomes</p