Genomic diversity within the haloalkaliphilic genus Thioalkalivibrio

Ahn, Anne Catherine; Meier‐Kolthoff, Jan P.; Overmars, Lex; Richter, Michael; Woyke, Tanja; Sorokin, Dimitry Y.; Muyzer, Gerard

doi:10.1371/journal.pone.0173517

Cited by 30 publications

(28 citation statements)

References 94 publications

(151 reference statements)

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“…So far, all characterized prokaryotic lineages cultured from soda lakes comprise over 70 different species within more than 30 genera [ 1 , 6 , 9 , 10 ]. From these, only a limited number of genomes have been sequenced today, mostly from chemolithoautotrophic sulfur-oxidizing bacteria belonging to the genus Thioalkalivibrio (class Gammaproteobacteria ) [ 1 , 11 , 12 ]. It is well established that metagenomics enables the recovery of genomes and the identification of novel genetic diversity where culturing efforts fail [ 13 , 14 ].…”

Section: Introductionmentioning

confidence: 99%

A metagenomics roadmap to the uncultured genome diversity in hypersaline soda lake sediments

et al. 2018

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BackgroundHypersaline soda lakes are characterized by extreme high soluble carbonate alkalinity. Despite the high pH and salt content, highly diverse microbial communities are known to be present in soda lake brines but the microbiome of soda lake sediments received much less attention of microbiologists. Here, we performed metagenomic sequencing on soda lake sediments to give the first extensive overview of the taxonomic diversity found in these complex, extreme environments and to gain novel physiological insights into the most abundant, uncultured prokaryote lineages.ResultsWe sequenced five metagenomes obtained from four surface sediments of Siberian soda lakes with a pH 10 and a salt content between 70 and 400 g L−1. The recovered 16S rRNA gene sequences were mostly from Bacteria, even in the salt-saturated lakes. Most OTUs were assigned to uncultured families. We reconstructed 871 metagenome-assembled genomes (MAGs) spanning more than 45 phyla and discovered the first extremophilic members of the Candidate Phyla Radiation (CPR). Five new species of CPR were among the most dominant community members. Novel dominant lineages were found within previously well-characterized functional groups involved in carbon, sulfur, and nitrogen cycling. Moreover, key enzymes of the Wood-Ljungdahl pathway were encoded within at least four bacterial phyla never previously associated with this ancient anaerobic pathway for carbon fixation and dissimilation, including the Actinobacteria.ConclusionsOur first sequencing effort of hypersaline soda lake sediment metagenomes led to two important advances. First, we showed the existence and obtained the first genomes of haloalkaliphilic members of the CPR and several hundred other novel prokaryote lineages. The soda lake CPR is a functionally diverse group, but the most abundant organisms in this study are likely fermenters with a possible role in primary carbon degradation. Second, we found evidence for the presence of the Wood-Ljungdahl pathway in many more taxonomic groups than those encompassing known homo-acetogens, sulfate-reducers, and methanogens. Since only few environmental metagenomics studies have targeted sediment microbial communities and never to this extent, we expect that our findings are relevant not only for the understanding of haloalkaline environments but can also be used to set targets for future studies on marine and freshwater sediments.Electronic supplementary materialThe online version of this article (10.1186/s40168-018-0548-7) contains supplementary material, which is available to authorized users.

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Section: Introductionmentioning

confidence: 99%

A metagenomics roadmap to the uncultured genome diversity in hypersaline soda lake sediments

et al. 2018

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“…Inexorable advances in methodologies will incorporate genomics into the taxonomy and systematics of the prokaryotes, boosting the credibility of taxonomy in the current post-genomic era (Coenye et al, 2005 ; Chun and Rainey, 2014 ). Up-to-date, while several groups have been analyzed through a genomic-wide view (Gupta et al, 2015 ; Adeolu et al, 2016 ; Hahnke et al, 2016 ; Ahn et al, 2017 ; Amin et al, 2017 ; Waite et al, 2017 ), many others have faced hurdles, such as Cyanobacteria. However, a genomic taxonomy approach has successfully been applied to elucidate the taxonomic structure of the two cyanobacterial genera, Prochlorococcus and Synechococcus (Thompson et al, 2013a ; Coutinho et al, 2016a , b ).…”

Section: Introductionmentioning

confidence: 99%

Ecogenomics and Taxonomy of Cyanobacteria Phylum

et al. 2017

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Cyanobacteria are major contributors to global biogeochemical cycles. The genetic diversity among Cyanobacteria enables them to thrive across many habitats, although only a few studies have analyzed the association of phylogenomic clades to specific environmental niches. In this study, we adopted an ecogenomics strategy with the aim to delineate ecological niche preferences of Cyanobacteria and integrate them to the genomic taxonomy of these bacteria. First, an appropriate phylogenomic framework was established using a set of genomic taxonomy signatures (including a tree based on conserved gene sequences, genome-to-genome distance, and average amino acid identity) to analyse ninety-nine publicly available cyanobacterial genomes. Next, the relative abundances of these genomes were determined throughout diverse global marine and freshwater ecosystems, using metagenomic data sets. The whole-genome-based taxonomy of the ninety-nine genomes allowed us to identify 57 (of which 28 are new genera) and 87 (of which 32 are new species) different cyanobacterial genera and species, respectively. The ecogenomic analysis allowed the distinction of three major ecological groups of Cyanobacteria (named as i. Low Temperature; ii. Low Temperature Copiotroph; and iii. High Temperature Oligotroph) that were coherently linked to the genomic taxonomy. This work establishes a new taxonomic framework for Cyanobacteria in the light of genomic taxonomy and ecogenomic approaches.

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“…reported as sulfide and/or elemental sulfur oxidizers (Sorokin and Kuenen, 2005;Ahn et al, 2017). Therefore, the enrichment of Thioalkalivibrio requires further investigation focused on the isolation and characterization of the potential novel species able to thrive under sulfidogenic conditions.…”

Section: Electron Acceptor Screeningmentioning

confidence: 99%

Long Chain Fatty Acid Degradation Coupled to Biological Sulfidogenesis: A Prospect for Enhanced Metal Recovery

Florentino

Costa

et al. 2020

Front. Bioeng. Biotechnol.

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This research assessed the microbiological suitability of oleate degradation coupled to sulfidogenesis by enriching communities from anaerobic sludge treating dairy products with S 0 , SO 2− 3 , SO 2− 4 , and S 2 O 2− 3 as electron acceptors. The limiting factor hampering highly efficient oleate degradation was investigated in batch reactors. The best sulfidogenic performance coupled to specialization of the enriched bacterial community was obtained for S 0-and S 2 O 2− 3-reducing enrichments, with 15.6 (± 0.2) and 9.0 (± 0.0) mM of sulfide production, respectively. Microbial community analyses revealed predominance of Enterobacteraceae (50.6 ± 5.7%), Sulfurospirillum (23.1 ± 0.1%), Bacteroides (7.5 ± 1.5%) and Seleniivibrio (6.9 ± 1.1%) in S 0-reducing cultures. In S 2 O 2− 3-reducing enrichments, the genus Desulfurella predominated (49.2 ± 1.2%), followed by the Enterobacterales order (20.9 ± 2.3%). S 0-reducing cultures were not affected by oleate concentrations up to 5 mM, while S 2 O 2− 3-reducing cultures could degrade oleate in concentrations up to 10 mM, with no significant impact on sulfidogenesis. In sequencing batch reactors operated with sulfide stripping, the S 0reducing enrichment produced 145.8 mM sulfide, precipitating Zn as ZnS in a separate tank. The S 2 O 2− 3 fed bioreactor only produced 23.4 mM of sulfide precipitated as ZnS. The lower sulfide production likely happened due to sulfite toxicity, an intermediate of thiosulfate reduction. Therefore, elemental sulfur reduction represents an excellent alternative to the currently adopted approaches for LCFA degradation. To the best of our knowledge, this is the first report of oleate degradation with the flux of electrons totally diverted toward sulfide production for metal precipitation, showing great efficiency of LCFA degradation coupled to high levels of metals precipitated as metal sulfide.

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Genomic diversity within the haloalkaliphilic genus Thioalkalivibrio

Cited by 30 publications

References 94 publications

A metagenomics roadmap to the uncultured genome diversity in hypersaline soda lake sediments

A metagenomics roadmap to the uncultured genome diversity in hypersaline soda lake sediments

Ecogenomics and Taxonomy of Cyanobacteria Phylum

Long Chain Fatty Acid Degradation Coupled to Biological Sulfidogenesis: A Prospect for Enhanced Metal Recovery

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