Bacterial diversity in deep-sea sediments under influence of asphalt seep at the São Paulo Plateau

Queiroz, Luciano Lopes; Bendia, Amanda Gonçalves; Duarte, Rubens Tadeu Delgado; Graças, Diego Assis das; Silva, Artur da Costa da Luiz; Nakayama, Cristina Rossi; Sumida, Paulo Yukio Gomes; Lima, André Oliveira de Souza; Nagano, Yuriko; Fujikura, Katsunori; Kitazato, Hiroshi; Pellizari, Vivian Helena

doi:10.1101/753616

Cited by 3 publications

(3 citation statements)

References 48 publications

(49 reference statements)

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“…Unexpectedly, the SAR11 clade was detected only in the RGR seamount. Closely related sequences of SAR11 were reported previously in sediments across the São Paulo Plateau (Queiroz et al ., 2020) and crusts from RGR (Bergo et al ., 2021). SAR11 includes carbon-oxidizing bacteria with multiple depth-specific ecotypes (Cameron et al ., 2014; Giovannoni et al ., 2017).…”

Section: Discussionsupporting

confidence: 85%

Spatial Patterns of Microbial Diversity, Composition and Community Structure in Fe-Mn Deposits and Associated Sediments in the Atlantic and Pacific Oceans

Bergo

Torres-Ballesteros

Signori

et al. 2022

Preprint

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Mining of deep-sea Fe-Mn deposits will remove crusts and nodules in large areas from the seafloor. The growth of a few millimeters of these minerals by Fe and Mn oxides precipitation takes millions of years, and yet little is known about their microbiome. Besides being key elements of the biogeochemical cycles and essential links of food and energy to deep-sea trophic webs, microbes have been identified to affect manganese oxide formation. Hence, polymetallic crusts and nodules may present unique habitats that deserve better understanding. In this study, we determined the composition and diversity of Bacteria and Archaea in deep-sea Fe-Mn crusts, nodules, and associated sediments from two oceanic elevations in the Atlantic Ocean, the Tropic Seamount in the northeast and the Rio Grande Rise (RGR) in the southwest. Sequencing of the 16S rRNA gene was performed using the Illumina MiSeq platform and statistical analyses using environmental data were performed in R. Additionally, we included public domain environmental DNA data of Fe-Mn crusts, nodules, and associated sediments from Clarion-Clipperton Zone and Takuyo-Daigo Seamount in the Pacific Ocean to compare microbial diversity in Fe-Mn deposits from different ocean basins. Our results indicated that Atlantic seamounts harbor an unusual and unknown Fe-Mn deposit microbiome with lower diversity and richness compared to deposits from Pacific areas. Crusts and nodules from Atlantic seamounts revealed the presence of unique taxa (Alteromonadales, Nitrospira, and Magnetospiraceae) and a higher relative abundance of sequences related to potential metal-cycling bacteria, such as Betaproteobacteriales and Pseudomonadales. The microbial beta-diversity from Atlantic seamounts was clearly grouped into microhabitats according to crusts, nodules, and sediments geochemical composition. Furthermore, community structure analysis using principal coordinate analysis also showed that the microbial communities of all seamounts were significantly divided into ocean basins and sampling areas. Despite the time scale of million years for these deposits to grow, a combination of environmental settings (temperature, salinity, depth, substrate geochemistry, nutrient, and organic matter availability) played a significant role in shaping the crusts and nodules microbiome, which was distinct between the Atlantic and Pacific Fe-Mn deposits. Our results suggest that the microbial community inhabiting Fe-Mn deposits participate in biogeochemical reactions indispensable to deep-sea ecosystems, which implies that understanding the microbial community is of utmost importance for any baseline environmental study in areas of potential deep-sea mining.

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Section: Discussionsupporting

confidence: 85%

Spatial Patterns of Microbial Diversity, Composition and Community Structure in Fe-Mn Deposits and Associated Sediments in the Atlantic and Pacific Oceans

Bergo

Torres-Ballesteros

Signori

et al. 2022

Preprint

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“…Functional roles of NB1-j in marine ecosystems are largely unknown. It is believed to be involved in hydrocarbon degradation [61] and has been reported mostly from marine sediments [62,63], mud volcanoes [61], sponges [64] and cyanobacterial mats [65]. To the best of our knowledge, this Deltaproteobacteria group is not reported in algal microbiomes.…”

Section: Emerging Microalgal-bacterial Associations That Can Guide Fu...mentioning

confidence: 99%

Unravelling microalgal-bacterial interactions in aquatic ecosystems through 16S rRNA gene-based co-occurrence networks

Pushpakumara

Tandon

Willis

et al. 2022

Preprint

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Microalgae and bacteria have a wide spectrum of associations in aquatic environments. Since their interactions can directly influence global carbon and nutrient cycling, understanding these associations help us evaluate their influence on ecosystem productivity. Algal biodiversity is large, and bacterial associations have been characterised for a small fraction of them. While experiments based on algal-bacterial co-culturing are commonly used to infer interactions, deciphering all associations present in nature through such methods is impractical and approaches based on co-occurrence network analysis can help infer associations. In this study, we used microbial co-occurrence networks built from Earth microbiome project 16S metabarcoding data to detect microalgal-bacterial associations in aquatic environments. We analysed marine and freshwater environments to understand what groups of bacteria are tightly co-occurring with different algal groups in both aquatic environments, to see patterns of interactions, and to evaluate the overall use of co-occurrence networks to infer meaningful algal-bacterial interactions. In line with expectations from co-culturing work, our results show that the phyla Proteobacteria and Bacteroidetes are the major bacterial associates of microalgae and the co-occurring bacteria may be specific to the algal host. From the independent analysis of environments, we also show that sample origin may be an important determinant of these interactions. By unravelling previously established microalgal-bacterial links as well as identifying a range of previously unknown interactions, we show that co-occurrence network analysis is a promising hypothesis-generating framework to study microalgal-bacterial interactions that can guide future research into the functional nature of interactions.

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“…The class Acidimicrobiia is a deep-rooting lineage within the phylum Actinomycetota and is extensively distributed in various habitats, such as acidic mineral wastewaters, oceans, saline lakes, deserts, and other environments [1][2][3][4]. The family Iamiaceae, belonging to the order Iamiales, class Acidimicrobiia, was first described by Kurahashi et al and recommended by Salam et al with the type strain Iamia majanohamensis [5,6].…”

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confidence: 99%

Rhabdothermincola salaria sp. nov., a novel actinobacterium isolated from a saline lake sediment

Gao

Fang

Liu

et al. 2022

International Journal of Systematic and Evolutionary Microbiology

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An actinobacterium, designated strain EGI L10124T, was isolated from saline lake sediment collected in Xinjiang province, PR China. The taxonomic position of the isolate was determined based on polyphasic taxonomic and phylogenomic analyses. Phylogenetic analysis and 16S rRNA gene sequence similarities indicated that strain EGI L10124T formed a distinct clade with Rhabdothermincola sediminis SYSU G02662T, with a shared sequence identity of 95.2 %. The novel isolate could be distinguished from species in the genus Rhabdothermincola by its distinct phenotypic, physiological and genotypic characteristics. The cells of strain EGI L10124T were aerobic, Gram-stain-positive and short rod-shaped. Optimal growth conditions of strain EGI L10124T on marine agar 2216 were registered at pH 8.0 at 37 °C. In addition, meso-diaminopimelic acid was the diagnostic diamino acid in the cell-wall peptidoglycan. The major respiratory quinone was MK-9 (H8), while the major fatty acids were iso-C16 : 0, C17 : 0 and C16 : 0. The polar lipids included diphosphatidylglycerol, phosphatidylinositol mannoside and phosphatidylinositol. Based on the genome sequence of strain EGI L10124T, it appears that the G+C content of the novel isolate was 71.8 mol%. According to our data, strain EGI L10124T represents a new species of the genus Rhabdothermincola , for which the name Rhabdothermincola salaria sp. nov. is proposed. The type strain of the proposed novel isolate is EGI L10124T (=CGMCC 1.19113T=KCTC 49679T).

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Bacterial diversity in deep-sea sediments under influence of asphalt seep at the São Paulo Plateau

Cited by 3 publications

References 48 publications

Spatial Patterns of Microbial Diversity, Composition and Community Structure in Fe-Mn Deposits and Associated Sediments in the Atlantic and Pacific Oceans

Spatial Patterns of Microbial Diversity, Composition and Community Structure in Fe-Mn Deposits and Associated Sediments in the Atlantic and Pacific Oceans

Unravelling microalgal-bacterial interactions in aquatic ecosystems through 16S rRNA gene-based co-occurrence networks

Rhabdothermincola salaria sp. nov., a novel actinobacterium isolated from a saline lake sediment

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