Periodic and Spatial Spreading of Alkanes and
            <i>Alcanivorax</i>
            Bacteria in Deep Waters of the Mariana Trench

Li, Wen Li; Huang, Junzhe; Zhang, Peiwei; Cui, Guojie; Wei, Zhanfei; Wu, Yu-Zhi; Gao, Zhaoming; Han, Zhuang; Yong, Wang

doi:10.1128/aem.02089-18

Cited by 20 publications

(19 citation statements)

References 66 publications

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“…Moreover, glycolysis was most abundant in surface waters, whereas gluconeogenesis, the glyoxylate shunt and oxidative phosphorylation were more common in >10,000 m waters. Recent studies showed that microorganisms tend to utilize some refractory organic carbon compounds (e.g., alkanes) in the deep-sea zones and labile carbohydrates in surface waters, respectively [ 2 , 63 ]. This indicates that more bacteria exploit labile carbohydrates via glycolysis at the surface.…”

Section: Discussionmentioning

confidence: 99%

Insights into the Vertical Stratification of Microbial Ecological Roles across the Deepest Seawater Column on Earth

et al. 2020

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The Earth’s oceans are a huge body of water with physicochemical properties and microbial community profiles that change with depth, which in turn influences their biogeochemical cycling potential. The differences between microbial communities and their functional potential in surface to hadopelagic water samples are only beginning to be explored. Here, we used metagenomics to investigate the microbial communities and their potential to drive biogeochemical cycling in seven different water layers down the vertical profile of the Challenger Deep (0–10,500 m) in the Mariana Trench, the deepest natural point in the Earth’s oceans. We recovered 726 metagenome-assembled genomes (MAGs) affiliated to 27 phyla. Overall, biodiversity increased in line with increased depth. In addition, the genome size of MAGs at ≥4000 m layers was slightly larger compared to those at 0–2000 m. As expected, surface waters were the main source of primary production, predominantly from Cyanobacteria. Intriguingly, microbes conducting an unusual form of nitrogen metabolism were identified in the deepest waters (>10,000 m), as demonstrated by an enrichment of genes encoding proteins involved in dissimilatory nitrate to ammonia conversion (DNRA), nitrogen fixation and urea transport. These likely facilitate the survival of ammonia-oxidizing archaea α lineage, which are typically present in environments with a high ammonia concentration. In addition, the microbial potential for oxidative phosphorylation and the glyoxylate shunt was enhanced in >10,000 m waters. This study provides novel insights into how microbial communities and their genetic potential for biogeochemical cycling differs through the Challenger deep water column, and into the unique adaptive lifestyle of microbes in the Earth’s deepest seawater.

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Section: Discussionmentioning

confidence: 99%

Insights into the Vertical Stratification of Microbial Ecological Roles across the Deepest Seawater Column on Earth

et al. 2020

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“…The analyses on the datasets of 16S rRNA gene amplicons from marine samples were described in our previous study [59]. The representative reads of Tenericutes OTUs were recruited for this study.…”

Section: Phylogenetic and Phylogenomic Analysesmentioning

confidence: 99%

Phylogenomics of expanding uncultured environmental Tenericutes provides insights into their pathogenicity and evolutionary relationship with Bacilli

et al. 2020

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Background: The metabolic capacity, stress response and evolution of uncultured environmental Tenericutes have remained elusive, since previous studies have been largely focused on pathogenic species. In this study, we expanded analyses on Tenericutes lineages that inhabit various environments using a collection of 840 genomes. Results: Several environmental lineages were discovered inhabiting the human gut, ground water, bioreactors and hypersaline lake and spanning the Haloplasmatales and Mycoplasmatales orders. A phylogenomics analysis of Bacilli and Tenericutes genomes revealed that some uncultured Tenericutes are affiliated with novel clades in Bacilli, such as RF39, RFN20 and ML615. Erysipelotrichales and two major gut lineages, RF39 and RFN20, were found to be neighboring clades of Mycoplasmatales. We detected habitat-specific functional patterns between the pathogenic, gut and the environmental Tenericutes, where genes involved in carbohydrate storage, carbon fixation, mutation repair, environmental response and amino acid cleavage are overrepresented in the genomes of environmental lineages, perhaps as a result of environmental adaptation. We hypothesize that the two major gut lineages, namely RF39 and RFN20, are probably acetate and hydrogen producers. Furthermore, deteriorating capacity of bactoprenol synthesis for cell wall peptidoglycan precursors secretion is a potential adaptive strategy employed by these lineages in response to the gut environment. Conclusions: This study uncovers the characteristic functions of environmental Tenericutes and their relationships with Bacilli, which sheds new light onto the pathogenicity and evolutionary processes of Mycoplasmatales.

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“…To examine vertical distribution of the four Bdellovibrionota groups (Fig. 1A) in marine water zones, the 16S rRNA sequences (16S metagenomic Illumina tags, miTags) of Tara ocean (23) and Mariana marine metagenomes (24, 25) were used to calculate relative abundance of Bdellovibrionota groups. Bacteriovoracia and Bdello-group2 were relatively abundant in oceans, compared to the other two groups (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…16S rRNA sequences of Bdellovibrionota genomes and MAGs were extracted by using rRNA_hmm_fs_wst (v.0) (75) and used to create a 16S rRNA database. The Bdellovibrionota 16S miTags in Tara Ocean (23) and Mariana (24, 69) marine water metagenomes (Table S7) were identified by blastn (v.2.9.0) (-evalue 1e-05) against the 16S rRNA sequence database of Bdellovibrionota. Only the 16S miTags longer than 100bp and >97% identity to a reference in the database were selected for further calculation of their relative abundance in the marine samples.…”

Section: Methodsmentioning

confidence: 99%

Phylogenomic insights into distribution and adaptation of Bdellovibrionota in marine waters

Zhou

Wei

et al. 2020

Preprint

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Bdellovibrionota is composed of obligate predators that can consume some gram-negative bacteria inhabiting various environments. However, whether genomic traits influence their distribution and marine adaptation remains to be answered. In this study, we performed phylogenomics and comparative genomics studies on 82 Bdellovibrionota genomes along with five metagenome-assembled genomes (MAGs) from deep sea zones. Four phylogenetic groups, Oligoflexia, Bdello-group1, Bdello-group2 and Bacteriovoracia, were revealed by constructing a phylogenetic tree, of which 53.84% of Bdello-group2 and 48.94% of Bacteriovoracia were derived from ocean. Bacteriovoracia was more prevalent in deep sea zones, whereas Bdello-group2 was largely distributed in the epipelagic zone. Metabolic reconstruction indicated that genes involved in chemotaxis, flagellar (mobility), type II secretion system, ABC transporters and penicillin-binding protein were necessary for predatory lifestyle of Bdellovibrionota. Genes involved in glycerol metabolism, hydrogen peroxide (H2O2) degradation, cell wall recycling and peptide utilization were ubiquitously present in Bdellovibrionota genomes. Comparative genomics between marine and non-marine Bdellovibrionota demonstrated that betaine as an osmoprotectant is probably widely used by marine Bdellovibrionota, meanwhile, all the marine genomes have a number of related genes for adapting marine environment. The chitinase and chitin-binding protein encoding genes were identified for the first time in Oligoflexia, which implied that Oligoflexia may prey a wider spectrum of microbes. This study expanded our knowledge on adaption strategies of Bdellovibrionota inhabiting deep sea and their potential usage for biological control.

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Periodic and Spatial Spreading of Alkanes and Alcanivorax Bacteria in Deep Waters of the Mariana Trench

Cited by 20 publications

References 66 publications

Insights into the Vertical Stratification of Microbial Ecological Roles across the Deepest Seawater Column on Earth

Insights into the Vertical Stratification of Microbial Ecological Roles across the Deepest Seawater Column on Earth

Phylogenomics of expanding uncultured environmental Tenericutes provides insights into their pathogenicity and evolutionary relationship with Bacilli

Phylogenomic insights into distribution and adaptation of Bdellovibrionota in marine waters

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