Genomic Analysis Reveals Adaptation of
            <i>Vibrio campbellii</i>
            to the Hadal Ocean

Liang, Jinchang; Liu, Jiwen; Wang, Xiaolei; Sun, Hao; Yu-lin, Zhang; Ju, Feng; Thompson, Fabiano L.; Zhang, Xiao‐Hua

doi:10.1128/aem.00575-22

Cited by 5 publications

(7 citation statements)

References 82 publications

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“…Compared with Vibrio isolated from epipelagic, hadopelagic strains encountered high pressure, low temperature, and high inorganic salt content. It possesses more genes in cell wall/membrane/envelope biogenesis [ 44 ]. Desiccation resistance genes of Salmonella Typhimurium under desiccation stress related to cell wall/membrane/envelope biogenesis [ 45 ].…”

Section: Discussionmentioning

confidence: 99%

Genomic characters of Anaplasma bovis and genetic diversity in China

Han,

Du,

Lin

et al. 2024

Emerging Microbes & Infections

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The emergence of Anaplasma bovis or A. bovis -like infection in humans from China and the United States of America has raised concern about the public health importance of this pathogen. Although A. bovis has been detected in a wide range of ticks and mammals in the world, no genome of the pathogen is available up to now, which has prohibited us from better understanding the genetic basis for its pathogenicity. Here we describe an A. bovis genome from metagenomic sequencing of an infected goat in China. Anaplasma bovis had the smallest genome of the genus Anaplasma , and relatively lower GC content. Phylogenetic analysis of single-copy orthologue sequence showed that A. bovis was closely related to A. platys and A. phagocytophilum , but relatively far from intraerythrocytic Anaplasma species. Anaplasma bovis had 116 unique orthogroups and lacked 51 orthogroups in comparison to other Anaplasma species. The virulence factors of A. bovis were significantly less than those of A. phagocytophilum , suggesting less pathogenicity of A. bovis . When tested by specific PCR assays, A. bovis was detected in 23 of 29 goats, with an infection rate up to 79.3% (95% CI: 64.6% ∼94.1%). The phylogenetic analyses based on partial 16S rRNA, gltA and groEL genes indicated that A. bovis had high genetic diversity. The findings of this study lay a foundation for further understanding of the biological characteristics and genetic diversity of A. bovis , and will facilitate the formulation of prevention and control strategies.

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Section: Discussionmentioning

confidence: 99%

Genomic characters of Anaplasma bovis and genetic diversity in China

Han,

Du,

Lin

et al. 2024

Emerging Microbes & Infections

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“…Microbes may have strong adaptabilities facilitating their wide spread across various marine environments [ 70 ]. In the non-coral areas, including the South China Sea, the Chinese northern marginal seas and the Changjiang estuary, 160, 74 and 40 Vibrio OTUs were reported, respectively [ 38 , 45 , 55 ].…”

Section: Discussionmentioning

confidence: 99%

“…Predominance of these species in both areas may indicate their strong environmental adaptablities. V. campbellii is widely distributed, even in the oligotrophic deep sea, and can acquire gene horizontally to enhance adaptation of environment [ 70 ]. As a common pathogen of shrimp [ 71 ], V. campbellii encodes a sugar-specific porin in the outer membrane responsible for the transport of chitooligosaccharides, allowing it to grow rapidly in aquatic environments with chitin as a nutrient [ 72 ].…”

Section: Discussionmentioning

confidence: 99%

“…As a common pathogen of shrimp [ 71 ], V. campbellii encodes a sugar-specific porin in the outer membrane responsible for the transport of chitooligosaccharides, allowing it to grow rapidly in aquatic environments with chitin as a nutrient [ 72 ]. The environmental adaptability of V. campbellii was also reflected by its strong ability to degrade macromolecule substances [ 70 ], possession of quorum sensing for interbacterial cell killing and biofilms formation [ 73 ], and expression of rpoS ortholog gene ( rpoS1 ) and rpoS xenolog gene ( rpoS2 ) [ 74 ]. Paraphotobacterium marinum possesses the activity of a variety of enzymes including alkaline phosphatase, esterase (C4), leucine arylamidase and acid phosphatase, which can utilize D-Glucose and D-maltose, and reduce nitrate to nitrite [ 75 ].…”

Section: Discussionmentioning

confidence: 99%

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Distinct coral environments shape the dynamic of planktonic Vibrio spp.

Zhao,

Chen,

Liu

et al. 2023

Environmental Microbiome

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Background Coral reefs are one of the most biodiverse and productive ecosystems, providing habitat for a vast of species. Reef-building scleractinian corals with a symbiotic microbiome, including bacteria, archaea, viruses and eukaryotic microbes, are referred to coral holobionts. Among them, coral diseases, mainly caused by Vibrio spp., have significantly contributed to the loss of coral cover and diversity. Habitat filtering across the globe has led to a variety structure of marine bacterial communities. Coral species, quantity and characteristics are significant differences between the Xisha Islands and Daya Bay (Guangdong Province). Thus, the Vibrio communities may be distinct between coral rich and poor areas. Results Through comparison of Vibrio dynamics between coral-rich (Xisha Islands) and coral-poor (Daya Bay) locations, we uncovered differences in Vibrio abundance, diversity, community composition and assembly mechanisms associated with corals. The higher abundance of Vibrio in coral rich areas may indicate a strong interaction between vibrios and corals. V. campbellii, Paraphotobacterium marinum and V. caribbeanicus were widely distributed in both coral rich and poor areas, likely indicating weak species specificity in the coral-stimulated growth of Vibrio. Random-forest prediction revealed Vibrio species and Photobacterium species as potential microbial indicators in the coral rich and coral poor areas, respectively. Ecological drift rather than selection governed the Vibrio community assembly in the Xisha Islands. Comparatively, homogenizing selection was more important for the Daya Bay community, which may reflect a role of habitat filtration. Conclusion This study revealed the different distribution pattern and assembly mechanism of Vibrio spp. between coral rich and poor areas, providing the background data for the research of Vibrio community in coral reef areas and may help the protection of coral reef at the biological level. The main reasons for the difference were different number and species of corals, environmental (e.g., temperature) and spatial factors. It reflected the strong interaction between Vibrio and corals, and provided a new perspective for the investigation of Vibrio in coral reef ecosystem.

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“…Genome streamlining is common for species living in stable, nutrient poor conditions such as some soil and marine habitats (59)(60)(61)(62), and is thought to be driven by selection and facilitated when bacteria have large effective population sizes (59,(63)(64)(65). Some environmental stresses may also promote genome streamlining due to selection (66,67).…”

Section: Phylogeny and Genome Characteristics Of Nectar-dwelling Acin...mentioning

confidence: 99%

Genome evolution following an ecological shift in nectar-dwellingAcinetobacter

Sanchez,

Renner,

Baker

et al. 2023

Preprint

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The bacterial genusAcinetobacterincludes species found in environmental habitats like soil and water, as well as species adapted to be host-associated or pathogenic. High genetic diversity may allow for this habitat flexibility, but the specific genes underlying switches between habitats are poorly understood. One lineage ofAcinetobacterhas undergone a substantial habitat change by evolving from a presumed soil-dwelling ancestral state to thrive in floral nectar. Here we compared the genomes of floral-dwelling and pollinator-associatedAcinetobacter, including newly described species, with genomes from relatives found in other environments to determine the genomic changes associated with this ecological shift. Following one evolutionary origin of floral nectar adaptation, nectar-dwellingAcinetobacterspecies have undergone reduction in genome size compared to relatives and have experienced dynamic gene gains and losses as they diversified. We found changes in gene content underlying carbohydrate metabolism and nitrogen metabolism, which we predict to be beneficial in nectar environments. Gene losses follow a pattern consistent with genome streamlining, whereas gains appear to result from both evolutionary divergence and horizontal gene transfer. Most notably, nectar-dwellingAcinetobacteracquired the ability to degrade pectin from plant pathogens and the genes underlying this ability have duplicated and are under selection within the clade. We hypothesize that this ability was a key trait for adaptation to floral nectar, as it could improve access to nutrients in the nutritional unbalanced habitat of nectar. These results identify the genomic changes and traits coinciding with a dramatic habitat switch from soil to floral nectar.

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Genomic Analysis Reveals Adaptation of Vibrio campbellii to the Hadal Ocean

Cited by 5 publications

References 82 publications

Genomic characters of Anaplasma bovis and genetic diversity in China

Genomic characters of Anaplasma bovis and genetic diversity in China

Distinct coral environments shape the dynamic of planktonic Vibrio spp.

Genome evolution following an ecological shift in nectar-dwellingAcinetobacter

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