"Candidatus Desulfobulbus rimicarensis," an Uncultivated Deltaproteobacterial Epibiont from the Deep-Sea Hydrothermal Vent Shrimp Rimicaris exoculata.


:The deep-sea hydrothermal vent shrimp Rimicaris exoculata largely depends on a dense epibiotic chemoautotrophic bacterial community within its enlarged cephalothoracic chamber. However, our understanding of shrimp-bacterium interactions is limited. In this report, we focused on the deltaproteobacterial epibiont of R. exoculata from the relatively unexplored South Mid-Atlantic Ridge. A nearly complete genome of a Deltaproteobacteria epibiont was binned from the assembled metagenome. Whole-genome phylogenetic analysis reveals that it is affiliated with the genus Desulfobulbus, representing a potential novel species for which the name "Candidatus Desulfobulbus rimicarensis" is proposed. Genomic and transcriptomic analyses reveal that this bacterium utilizes the Wood-Ljungdahl pathway for carbon assimilation and harvests energy via sulfur disproportionation, which is significantly different from other shrimp epibionts. Additionally, this epibiont has putative nitrogen fixation activity, but it is extremely active in directly taking up ammonia and urea from the host or vent environments. Moreover, the epibiont could be distinguished from its free-living relatives by various features, such as the lack of chemotaxis and motility traits, a dramatic reduction in biosynthesis genes for capsular and extracellular polysaccharides, enrichment of genes required for carbon fixation and sulfur metabolism, and resistance to environmental toxins. Our study highlights the unique role and symbiotic adaptation of Deltaproteobacteria in deep-sea hydrothermal vent shrimps.IMPORTANCE The shrimp Rimicaris exoculata represents the dominant faunal biomass at many deep-sea hydrothermal vent ecosystems along the Mid-Atlantic Ridge. This organism harbors dense bacterial epibiont communities in its enlarged cephalothoracic chamber that play an important nutritional role. Deltaproteobacteria are ubiquitous in epibiotic communities of R. exoculata, and their functional roles as epibionts are based solely on the presence of functional genes. Here, we describe "Candidatus Desulfobulbus rimicarensis," an uncultivated deltaproteobacterial epibiont. Compared to campylobacterial and gammaproteobacterial epibionts of R. exoculata, this bacterium possessed unique metabolic pathways, such as the Wood-Ljungdahl pathway, as well as sulfur disproportionation and nitrogen fixation pathways. Furthermore, this epibiont can be distinguished from closely related free-living Desulfobulbus strains by its reduced genetic content and potential loss of functions, suggesting unique adaptations to the shrimp host. This study is a genomic and transcriptomic analysis of a deltaproteobacterial epibiont and largely expands the understanding of its metabolism and adaptation to the R. exoculata host.


Appl Environ Microbiol


Jiang L,Liu X,Dong C,Huang Z,Cambon-Bonavita MA,Alain K,Gu L,Wang S,Shao Z




Has Abstract


2020-04-01 00:00:00












  • The shared resistome of human and pig microbiota is mobilized by distinct genetic elements.

    abstract::The extensive use of antibiotics in hospitals and in the animal breeding industry has promoted antibiotic resistance in bacteria, which resulted in the emergence of a large number of antibiotic resistance genes in the intestinal tract of human and farmed animals. Genetic exchange of resistance genes between the two ec...

    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章


    authors: Wang C,Song Y,Tang N,Zhang G,Leclercq SO,Feng J

    更新日期:2020-12-11 00:00:00

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    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章


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    更新日期:2004-04-01 00:00:00

  • Effect of bacterial distribution and activity on conjugal gene transfer on the phylloplane of the bush bean (Phaseolus vulgaris).

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    pub_type: 杂志文章


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    pub_type: 杂志文章


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    pub_type: 杂志文章


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  • Identification of Campylobacter coli isolates from animals and humans by bacterial restriction endonuclease DNA analysis.

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    pub_type: 杂志文章


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  • Products from the incomplete metabolism of pyrene by polycyclic aromatic hydrocarbon-degrading bacteria.

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  • Absence of microbial mineralization of lignin in anaerobic enrichment cultures.

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    pub_type: 杂志文章


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    更新日期:2016-11-21 00:00:00

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    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章


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    pub_type: 杂志文章


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    pub_type: 杂志文章


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    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章


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    更新日期:2014-01-01 00:00:00

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    pub_type: 杂志文章


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    更新日期:2003-07-01 00:00:00

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    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章


    authors: Foegeding PM,Busta FF

    更新日期:1983-04-01 00:00:00

  • Biochemical fingerprinting of water coliform bacteria, a new method for measuring phenotypic diversity and for comparing different bacterial populations.

    abstract::A simple, automated microplate system for biochemical characterization of water isolates can be used to obtain fingerprints of the bacterial flora from various water samples. Mathematical models for calculating the diversities and similarities between bacterial populations are described for such fingerprints. The dive...

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    pub_type: 杂志文章


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    更新日期:1991-11-01 00:00:00

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    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章


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  • Novel functions of (p)ppGpp and Cyclic di-GMP in mycobacterial physiology revealed by phenotype microarray analysis of wild-type and isogenic strains of Mycobacterium smegmatis.

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    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章


    authors: Gupta KR,Kasetty S,Chatterji D

    更新日期:2015-04-01 00:00:00

  • Metabolic activity of pathogenic bacteria during semicontinuous anaerobic digestion.

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    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章


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    更新日期:1994-10-01 00:00:00

  • Effects of pesticides on cyanobacterium Plectonema boryanum and cyanophage LPP-1.

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    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章


    authors: Mallison SM 3rd,Cannon RE

    更新日期:1984-05-01 00:00:00

  • Viability of Rhizobium bacteroids.

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    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章


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    更新日期:1977-12-01 00:00:00