Assessing the Diversity of Benthic Sulfate-Reducing Microorganisms in Northwestern Gulf of Mexico by Illumina Sequencing of dsrB Gene

Sánchez-Soto, Ma. Fernanda; Cerqueda-García, Daniel; Alcántara-Hernández, Rocı́o; Falcón, Luisa I.; Pech, Daniel; Árcega-Cabrera, Flor; Aguirre-Macedo, M. Leopoldina; García-Maldonado, José Q.

doi:10.1007/s00248-020-01631-5

Cited by 6 publications

(7 citation statements)

References 115 publications

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“…Relative abundances presented from amplicon sequencing-based studies (Short Read Archives) were derived from the highest relative abundance found in any individual sample per study. As exception was that an average relative abundance of Thermoanaerobaculia dsrB was calculated from all dsrB sequences from the Northwestern Gulf of Mexico study (23 surface sediment samples) [147]. List of studies/ datasets used are listed https:// doi.org/10.6084/m9.figshare.…”

Section: Genome Comparisons Reveal Distinct Properties Between Novel Genera and Adaptations To Marine Environmentsmentioning

confidence: 99%

Novel taxa of Acidobacteriota implicated in seafloor sulfur cycling

et al. 2021

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Acidobacteriota are widespread and often abundant in marine sediments, yet their metabolic and ecological properties are poorly understood. Here, we examined metabolisms and distributions of Acidobacteriota in marine sediments of Svalbard by functional predictions from metagenome-assembled genomes (MAGs), amplicon sequencing of 16S rRNA and dissimilatory sulfite reductase (dsrB) genes and transcripts, and gene expression analyses of tetrathionate-amended microcosms. Acidobacteriota were the second most abundant dsrB-harboring (averaging 13%) phylum after Desulfobacterota in Svalbard sediments, and represented 4% of dsrB transcripts on average. Meta-analysis of dsrAB datasets also showed Acidobacteriota dsrAB sequences are prominent in marine sediments worldwide, averaging 15% of all sequences analysed, and represent most of the previously unclassified dsrAB in marine sediments. We propose two new Acidobacteriota genera, Candidatus Sulfomarinibacter (class Thermoanaerobaculia, “subdivision 23”) and Ca. Polarisedimenticola (“subdivision 22”), with distinct genetic properties that may explain their distributions in biogeochemically distinct sediments. Ca. Sulfomarinibacter encode flexible respiratory routes, with potential for oxygen, nitrous oxide, metal-oxide, tetrathionate, sulfur and sulfite/sulfate respiration, and possibly sulfur disproportionation. Potential nutrients and energy include cellulose, proteins, cyanophycin, hydrogen, and acetate. A Ca. Polarisedimenticola MAG encodes various enzymes to degrade proteins, and to reduce oxygen, nitrate, sulfur/polysulfide and metal-oxides. 16S rRNA gene and transcript profiling of Svalbard sediments showed Ca. Sulfomarinibacter members were relatively abundant and transcriptionally active in sulfidic fjord sediments, while Ca. Polarisedimenticola members were more relatively abundant in metal-rich fjord sediments. Overall, we reveal various physiological features of uncultured marine Acidobacteriota that indicate fundamental roles in seafloor biogeochemical cycling.

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Section: Genome Comparisons Reveal Distinct Properties Between Novel Genera and Adaptations To Marine Environmentsmentioning

confidence: 99%

Novel taxa of Acidobacteriota implicated in seafloor sulfur cycling

et al. 2021

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“…Instead, the dissimilatory (bi)sulfite reductase (dsrAB) genes-based methods were considered to be more adequate for this purpose [30][31][32][33]. dsrAB may be exploited as a phylogenetic marker in amplicon sequencing-based environmental studies [33][34][35][36][37][38][39][40][41]. Phylogenetic analysis discerns three main DsrAB protein families: reductive bacterial-type, reductive archaeal-type and oxidative bacterial-type DsrAB [32].…”

Section: Introductionmentioning

confidence: 99%

Diversity and Activity of Sulfate-Reducing Prokaryotes in Kamchatka Hot Springs

et al. 2021

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Microbial communities of the Kamchatka Peninsula terrestrial hot springs were studied using radioisotopic and cultural approaches, as well as by the amplification and sequencing of dsrB and 16S rRNA genes fragments. Radioisotopic experiments with 35S-labeled sulfate showed that microbial communities of the Kamchatka hot springs are actively reducing sulfate. Both the cultivation experiments and the results of dsrB and 16S rRNA genes fragments analyses indicated the presence of microorganisms participating in the reductive part of the sulfur cycle. It was found that sulfate-reducing prokaryotes (SRP) belonging to Desulfobacterota, Nitrospirota and Firmicutes phyla inhabited neutral and slightly acidic hot springs, while bacteria of phylum Thermodesulofobiota preferred moderately acidic hot springs. In high-temperature acidic springs sulfate reduction was mediated by archaea of the phylum Crenarchaeota, chemoorganoheterotrophic representatives of genus Vulcanisaeta being the most probable candidates. The 16S rRNA taxonomic profiling showed that in most of the studied communities SRP was present only as a minor component. Only in one microbial community, the representatives of genus Vulcanisaeta comprised a significant group. Thus, in spite of comparatively low sulfate concentrations in terrestrial hot springs of the Kamchatka, phylogenetically and metabolically diverse groups of sulfate-reducing prokaryotes are operating there coupling carbon and sulfur cycles in these habitats.

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“…In addition, a high abundance of wb1-A12 was detected which is capable of nitrite oxidation under oxic and anoxic environmental conditions (Orsi, 2018), and Desulfurella, related to sulfate-reducers that has been detected in high abundances in the deep biosphere (Orsi et al, 2016). Except for Desulfurellaceae, these taxa have been detected in high abundances in the study region (Sańchez-Soto et al, 2018;Ramıŕez et al, 2020;Sańchez-Soto et al, 2021). For Desulfurella this is the first report in the GoM, but sulfate-reducers seem to have an important role in oxic and metal rich deep sediments in the PFB (Sańchez-Soto et al, 2021).…”

Section: Beta Diversity In the Bathymetric Gradientmentioning

confidence: 89%

“…Although the way to analyze, interpret, and present microbial diversity data in these studies are difficult to compare, some interesting trends can be observed. In the first place, the analysis of the beta-diversity of pelagic and benthic communities showed a tendency to cluster the samples by water column depth (Sańchez-Soto Jimeńez et al, 2018;Raggi et al, 2020;Ramıŕez et al, 2020;Sańchez-Soto et al, 2021). Sańchez-Soto Jimeńez et al (2018; and Ramıŕez et al (2020) reported the co-occurrence of aerobic and anaerobic metabolisms in the studied sites; however, anaerobes (e.g., sulfate-reducers) showed higher abundances in shallow environments where anoxic conditions predominated.…”

Section: Introductionmentioning

confidence: 99%

“…Despite recent progress in assessing community composition and spatial distribution of benthic prokaryotes in the nwGoM, the study of alpha and beta diversity and the factors that shape microbial assemblages continues to be an area of acute research. Analysis of benthic prokaryotes in a bathymetric gradient in the PFB has shown the response of microbial communities to specific parameters variation, including water depth, temperature, OM, salinity, sediment particles, nutrients, and contaminants (Sańchez-Soto Jimeńez et al, 2018;Raggi et al, 2020;Ramıŕez et al, 2020;Sańchez-Soto et al, 2021;Loza et al, 2022). However, how consistently microbial communities respond to such variables over different climatic seasons and in a wider spatial area is still to be investigated.…”

Section: Introductionmentioning

confidence: 99%

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Spatiotemporal dynamics of benthic bacterial communities in the Perdido Fold Belt, Northwestern Gulf of Mexico

et al. 2023

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This study analyzed the spatiotemporal dynamics of surficial benthic microbial communities in a bathymetric gradient (44 - 3573 m) across four oceanographic campaigns at the Perdido Fold Belt (PFB) in the northwestern Gulf of Mexico (nwGoM). Bioinformatic analysis of 16S rRNA gene amplicons grouped the 27 samples into three clusters according to a longitudinal bathymetric gradient. Differences in community structure among clusters, based on PERMANOVA analysis, were partially explained by cruise, water depth, temperature, salinity, nitrate plus nitrite, silicate, redox potential, Ni, Cd, Pb, and Al, as well by aliphatic and aromatic hydrocarbon concentrations. Into microbial community composition, Gemmatimonadaceae, Planctomycetaceae, and the JTB255 were detected at all depths across the four campaigns. Members of Anaerolinaceae and specific sulfate-reducing bacteria were more abundant in sites located between 43 and 1200 m, and Rhodospirillaceae, wb1-A12, OM1 clade, Desulfurellaceae, Gemmatimonadetes, Nitrospinaceae, and Clostridiaceae 1 were better represented in deeper sites. Alpha diversity was similar between the three groups and remained stable; however, 10 samples presented changes in the community structure across the four campaigns. Finally, a multivariable association analysis revealed 25 bacterial genera positively related with physicochemical parameters that characterized the environment from shallow to deep sea sites. Taken together, these results yield insights into the temporal stability of 17 of 27 sites in the PFB and revealed signature taxa with putatively ecological relevance in sedimentary environments.

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Assessing the Diversity of Benthic Sulfate-Reducing Microorganisms in Northwestern Gulf of Mexico by Illumina Sequencing of dsrB Gene

Cited by 6 publications

References 115 publications

Novel taxa of Acidobacteriota implicated in seafloor sulfur cycling

Novel taxa of Acidobacteriota implicated in seafloor sulfur cycling

Diversity and Activity of Sulfate-Reducing Prokaryotes in Kamchatka Hot Springs

Spatiotemporal dynamics of benthic bacterial communities in the Perdido Fold Belt, Northwestern Gulf of Mexico

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