Comparative genomic analysis reveals the evolution and environmental adaptation strategies of vibrios

Lin, Heyu; Yu, Min; Wang, Xiaolei; Zhang, Xiaohua

doi:10.1186/s12864-018-4531-2

Cited by 84 publications

(92 citation statements)

References 79 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The observed differences in Vibrio abundance measured by qPCR may reflect special conditions of separate benthic environments and may also be contributed to by the varied copy numbers of 16S rRNA genes (from 6 to 14 operons) between Vibrio spp. (16). Taken together, the ecological importance of benthic Vibrio populations merits further investigation.…”

Section: Discussionmentioning

confidence: 95%

“…Vibrio spp. may evolve several adaptive strategies to survive in benthic environments, e.g., utilize a wide range of organic carbon sources, enter the VBNC state, or use sediments as reservoirs (3,16,52,53). Most Vibrio spp.…”

Section: Discussionmentioning

confidence: 99%

“…Most Vibrio spp. can utilize a wide range of organic carbon compounds as carbon and energy sources, such as polysaccharides derived from macroalgal cell walls or zooplankton exoskeletons (3,16,17). When environmental conditions become unfavorable, many Vibrio spp.…”

Section: Discussionmentioning

confidence: 99%

“…are copiotrophic and opportunistic strategists. They have been found to utilize a wide range of organic carbon compounds, such as chitin, alginate, and agar (16). These findings suggest that vibrios may exert large impacts on biogeochemical processes in the marine ecosystem (3,17).…”

mentioning

confidence: 99%

See 3 more Smart Citations

Spatial Heterogeneity of Vibrio spp. in Sediments of Chinese Marginal Seas

Wang

Liu

et al. 2019

Appl Environ Microbiol

Self Cite

View full text Add to dashboard Cite

Vibrio spp. are ubiquitous marine bacteria with high metabolism flexibility and genome plasticity. Previous studies have revealed the dynamics of planktonic vibrios in relation to environmental forces, such as temperature and salinity. However, little is known about Vibrio ecology in benthic environments. Here, we elucidate the abundance, diversity, and spatial distribution of Vibrio spp. in sediments of the Chinese marginal seas, with a wide spatial range from north to south covering the Yellow Sea (YS), East China Sea (ECS), and South China Sea (SCS). Quantitative analysis showed that Vibrio spp. were most abundant in the SCS (ϳ9.04 ϫ 10 5 copies/g) compared to the YS (ϳ1.00 ϫ 10 5 copies/g) and ECS (ϳ8.86 ϫ 10 5 copies/g). Vibrio community compositions derived from Illumina sequencing of Vibrio-specific 16S rRNA genes varied significantly between sampling areas, which was reflected by a strong distance-decay pattern. The spatial distribution of Vibrio was governed by a joint effect of spatial and environmental factors (especially temperature, salinity, and SiO 3 2Ϫ ), and their respective pure effects explained only a small fraction of the community variation. Moreover, we identified the most prominent operational taxonomic units (OTUs) that were partitioned in these sea areas. Whereas Vibrionaceae OTU20 and Photobacterium lipolyticum were prevalent in the YS, Vibrio gigantis and Photobacterium piscicola, and P. piscicola, Photobacterium lutimaris, and Photobacterium alginatilyticum were prevalent in the ECS and SCS, respectively. Our study demonstrated clear spatial heterogeneity of Vibrio spp. in sediments of the Chinese marginal seas, laying a foundation for fully understanding the marine Vibrio ecology and the ecological roles of the species. IMPORTANCE Vibrio is an important component of natural marine microbial populations in terms of pathogenicity and roles in carbon cycling. Compared to the marine pelagic environment, our knowledge of the diversity and distribution pattern of Vibrio spp. in sediment is limited. Here, we show higher Vibrio abundance in Chinese marginal seas than in other studied sediments. There was a clear spatial differentiation of Vibrio abundance and community composition in different sea areas. The benthic Vibrio community displayed a strong distance-decay pattern across a wide spatial range, which was formed under the combined effects of spatial and environmental factors. These results provide deep insights into the ecological dynamics of Vibrio and its environmental controls, facilitating a more comprehensive understanding of the marine Vibrio ecology.

show abstract

Section: Discussionmentioning

confidence: 95%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

See 2 more Smart Citations

Spatial Heterogeneity of Vibrio spp. in Sediments of Chinese Marginal Seas

Wang

Liu

et al. 2019

Appl Environ Microbiol

Self Cite

View full text Add to dashboard Cite

show abstract

“…These patterns are undoubtedly influenced by the dramatic fluctuations in the feeding-responsive members of the community, primarily Photobacterium , but likely also the unclassified members of the Vibrionaceae that increased during fed time points (Table S2). Indeed, comparative analysis of Photobacterium genomes has revealed high numbers of CRISPR arrays, prophage sequences, and genomic islands, suggesting that phage infection and gene mobilization may be common in this genus (53); other Vibrionaceae genomes share similar features (54,55).…”

Section: Discussionmentioning

confidence: 99%

Feeding rapidly alters microbiome composition and gene transcription in the clownfish gut

Parris

Morgan

Stewart

2018

Preprint

View full text Add to dashboard Cite

BackgroundDiet is a major determinant of intestinal microbiome composition. While studies have evaluated microbiome responses to diet variation, less is understood of how the act of feeding influences the microbiome, independent of diet type. Here, we use the clownfish Premnas biaculeatus, a species reared commonly in ornamental marine aquaculture, to test how the diversity, predicted gene content, and gene transcription of the microbiome vary over a two-day diurnal period with a single daily feeding event. This study used fish fed four times daily, once daily, or every three days prior to the diurnal period, allowing us also to test how feeding frequency affected microbiome diversity. The amount of time between feedings had no affect on baseline diversity of the microbiome. In contrast, the act of feeding itself caused a significant short term change in the microbiome, with microbiome diversity, predicted gene content, and gene transcription varying significantly between time points immediately before and 1.5 hours post feeding. Variation was driven by abundance shifts involving exact sequence variants (ESVs), with one ESV identified as Photobacterium sp. increasing from <0.5% of sequences immediately pre-feeding to 34% at 1.5 hours post-feeding. Other ESVs from a range of microbial groups also increased dramatically after feeding, with the majority also detected in the food. One ESV identified as Clostridium perfringens represented up to 55% of sequences but did not vary significantly over the diurnal period and was not detected in the food. Post-feeding samples were enriched in transcripts and predicted genes for social interactions, cell motility, and coping with foreign DNA, whereas time points farther from feeding were enriched in genes of diverse catabolic and biosynthetic functions. These results confirm feeding as a significant destabilizing force in clownfish intestinal microbiomes, likely due to both input of cells attached to food and stimulation of resident microbes. Microbes such as Photobacterium may episodically transition from environmental reservoirs to growth in the gut, likely in association with food particles. This transition may be facilitated by functions for navigating a new environment and interacting with neighboring microbes and host cells. Other taxa, such as Clostridium, are comparatively stable intestinal members and less likely to be affected by passing food. Conclusions about microbiome ecology may therefore differ based on when samples were collected relative to the last feeding.ImportanceDespite extensive study of intestinal microbiome diversity and the role of diet type in structuring gut microbial communities, we know very little about short-term changes in the intestinal microbiome as a result of feeding alone. Sampling microbiomes over a feeding cycle will allow us to differentiate opportunistic, feeding-responsive microbes from resident, potentially commensal members of the gut community. Also, since feeding has the potential to alter microbiome structure, sampling at different points relative to the last feeding event will likely yield different conclusions about microbiome composition and function. This variation should be addressed in comparative microbiome studies. Our study contributes to knowledge of short-term changes in the gut microbiome associated with feeding events.

show abstract

General Assessment of Approaches to the Identification of Aquatic Bacterial Pathogens: A Methodological Review

2022

View full text Add to dashboard Cite

In the evolving biosphere, pathogenic microorganisms that cause disease may undergo phenotypic changes. While some of these changes result in new variants or mutants, others lead to the emergence of novel pathogens. Such phenotypic changes as well as advances in technology and analytical methods and the identification of genomic sequences of microbial DNA have brought about new methodological approaches in the diagnosis of bacterial diseases. Although bacterial identification was originally based on phenotypic characteristics, later researchers claimed that bacteria could be accurately identified by only gene sequencing and generally by the sequencing of the 16S ribosomal RNA gene region. Currently, there is still disagreement between classical microbiologists and those using new genomic sequence technology over the best method for identification. Fish are cold‐blooded animals, and fish pathogens generally exhibit psychrophilic characteristics. Many bacterial identification systems that are used to identify mesophilic bacteria remain useless for identifying fish pathogens because the optimum incubation temperatures for mesophilic bacteria are 35–37°C. Bacteria that are pathogenic to piscine species require specific media for their cultivation at lower incubation temperatures (15–28°C), and this limits both their growth in culture and subsequent identification by phenotype‐based methods. This review presents a comprehensive overview of the isolation and identification of bacterial fish pathogens by optimal culture conditions, biochemical tests, colorimetric methods for rapid identification systems, matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry, and immunological and molecular methods, as well as an overview of the detection of uncultivable bacteria and the use of anamnesis. We conclude that the accurate identification of fish pathogens requires the use of different methods, including phenotype‐ and genotype‐based tests, and the evaluation of anamnesis.

show abstract

Comparative genomic analysis reveals the evolution and environmental adaptation strategies of vibrios

Cited by 84 publications

References 79 publications

Spatial Heterogeneity of Vibrio spp. in Sediments of Chinese Marginal Seas

Spatial Heterogeneity of Vibrio spp. in Sediments of Chinese Marginal Seas

Feeding rapidly alters microbiome composition and gene transcription in the clownfish gut

General Assessment of Approaches to the Identification of Aquatic Bacterial Pathogens: A Methodological Review

Contact Info

Product

Resources

About