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Oligotyping reveals community level habitat selection within the genus Vibrio.

Schmidt VT, Reveillaud J, Zettler E, Mincer TJ, Murphy L, Amaral-Zettler LA - Front Microbiol (2014)

Bottom Line: Here we use oligotyping analyses in combination with a large collection of existing Vibrio 16S ribosomal RNA (rRNA) gene sequence data to reveal patterns of Vibrio ecology across a wide range of environmental, host, and abiotic substrate associated habitats.Our data show that individual taxa often display a wide range of habitat preferences yet tend to be highly abundant in either substrate-associated or free-living environments.Lastly, evidence for habitat specificity at the community level exists in some habitats, despite considerable stochasticity in others.

View Article: PubMed Central - PubMed

Affiliation: Marine Biological Laboratory, Josephine Bay Paul Center for Comparative Molecular Biology and Evolution Woods Hole, MA, USA ; Department of Ecology and Evolutionary Biology, Brown University Providence, RI, USA.

ABSTRACT
The genus Vibrio is a metabolically diverse group of facultative anaerobic bacteria, common in aquatic environments and marine hosts. The genus contains several species of importance to human health and aquaculture, including the causative agents of human cholera and fish vibriosis. Vibrios display a wide variety of known life histories, from opportunistic pathogens to long-standing symbionts with individual host species. Studying Vibrio ecology has been challenging as individual species often display a wide range of habitat preferences, and groups of vibrios can act as socially cohesive groups. Although strong associations with salinity, temperature and other environmental variables have been established, the degree of habitat or host specificity at both the individual and community levels is unknown. Here we use oligotyping analyses in combination with a large collection of existing Vibrio 16S ribosomal RNA (rRNA) gene sequence data to reveal patterns of Vibrio ecology across a wide range of environmental, host, and abiotic substrate associated habitats. Our data show that individual taxa often display a wide range of habitat preferences yet tend to be highly abundant in either substrate-associated or free-living environments. Our analyses show that Vibrio communities share considerable overlap between two distinct hosts (i.e., sponge and fish), yet are distinct from the abiotic plastic substrates. Lastly, evidence for habitat specificity at the community level exists in some habitats, despite considerable stochasticity in others. In addition to providing insights into Vibrio ecology across a broad range of habitats, our study shows the utility of oligotyping as a facile, high-throughput and unbiased method for large-scale analyses of publically available sequence data repositories and suggests its wide application could greatly extend the range of possibilities to explore microbial ecology.

No MeSH data available.


Related in: MedlinePlus

PhyML phylogeny of full-length 16S rRNA gene sequences from type strain isolates in the SILVA ARB database, with the 17 most abundant oligotypes found in this study added by Maximum Parsimony over the 60 bp region. The isolation source for each type strain is color coded at its terminal node. The proportion of MEGABLAST hits that fell into each isolation source category is coded for the 17 oligotype sequences added to the tree, and shown in bar graphs at each oligotype node.
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Figure 7: PhyML phylogeny of full-length 16S rRNA gene sequences from type strain isolates in the SILVA ARB database, with the 17 most abundant oligotypes found in this study added by Maximum Parsimony over the 60 bp region. The isolation source for each type strain is color coded at its terminal node. The proportion of MEGABLAST hits that fell into each isolation source category is coded for the 17 oligotype sequences added to the tree, and shown in bar graphs at each oligotype node.

Mentions: Our phylogenetic analysis of ARB reference sequences revealed no 16S rRNA gene phylogeny-habitat relationship. This is evidenced by the spread of reference sequences from the same isolation source across the phylogenetic tree (Figure 7). Our 17 abundant oligotypes were also not monophyletic according to the habitat in which they were most abundant (e.g., sponges or fish). For example, oligotype sequences dominant in FreshwaterFish and Freshwater (Oligotype 2, 4, and 8) were found to branch in different parts of our phylogenetic tree (Figure 7).


Oligotyping reveals community level habitat selection within the genus Vibrio.

Schmidt VT, Reveillaud J, Zettler E, Mincer TJ, Murphy L, Amaral-Zettler LA - Front Microbiol (2014)

PhyML phylogeny of full-length 16S rRNA gene sequences from type strain isolates in the SILVA ARB database, with the 17 most abundant oligotypes found in this study added by Maximum Parsimony over the 60 bp region. The isolation source for each type strain is color coded at its terminal node. The proportion of MEGABLAST hits that fell into each isolation source category is coded for the 17 oligotype sequences added to the tree, and shown in bar graphs at each oligotype node.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4230168&req=5

Figure 7: PhyML phylogeny of full-length 16S rRNA gene sequences from type strain isolates in the SILVA ARB database, with the 17 most abundant oligotypes found in this study added by Maximum Parsimony over the 60 bp region. The isolation source for each type strain is color coded at its terminal node. The proportion of MEGABLAST hits that fell into each isolation source category is coded for the 17 oligotype sequences added to the tree, and shown in bar graphs at each oligotype node.
Mentions: Our phylogenetic analysis of ARB reference sequences revealed no 16S rRNA gene phylogeny-habitat relationship. This is evidenced by the spread of reference sequences from the same isolation source across the phylogenetic tree (Figure 7). Our 17 abundant oligotypes were also not monophyletic according to the habitat in which they were most abundant (e.g., sponges or fish). For example, oligotype sequences dominant in FreshwaterFish and Freshwater (Oligotype 2, 4, and 8) were found to branch in different parts of our phylogenetic tree (Figure 7).

Bottom Line: Here we use oligotyping analyses in combination with a large collection of existing Vibrio 16S ribosomal RNA (rRNA) gene sequence data to reveal patterns of Vibrio ecology across a wide range of environmental, host, and abiotic substrate associated habitats.Our data show that individual taxa often display a wide range of habitat preferences yet tend to be highly abundant in either substrate-associated or free-living environments.Lastly, evidence for habitat specificity at the community level exists in some habitats, despite considerable stochasticity in others.

View Article: PubMed Central - PubMed

Affiliation: Marine Biological Laboratory, Josephine Bay Paul Center for Comparative Molecular Biology and Evolution Woods Hole, MA, USA ; Department of Ecology and Evolutionary Biology, Brown University Providence, RI, USA.

ABSTRACT
The genus Vibrio is a metabolically diverse group of facultative anaerobic bacteria, common in aquatic environments and marine hosts. The genus contains several species of importance to human health and aquaculture, including the causative agents of human cholera and fish vibriosis. Vibrios display a wide variety of known life histories, from opportunistic pathogens to long-standing symbionts with individual host species. Studying Vibrio ecology has been challenging as individual species often display a wide range of habitat preferences, and groups of vibrios can act as socially cohesive groups. Although strong associations with salinity, temperature and other environmental variables have been established, the degree of habitat or host specificity at both the individual and community levels is unknown. Here we use oligotyping analyses in combination with a large collection of existing Vibrio 16S ribosomal RNA (rRNA) gene sequence data to reveal patterns of Vibrio ecology across a wide range of environmental, host, and abiotic substrate associated habitats. Our data show that individual taxa often display a wide range of habitat preferences yet tend to be highly abundant in either substrate-associated or free-living environments. Our analyses show that Vibrio communities share considerable overlap between two distinct hosts (i.e., sponge and fish), yet are distinct from the abiotic plastic substrates. Lastly, evidence for habitat specificity at the community level exists in some habitats, despite considerable stochasticity in others. In addition to providing insights into Vibrio ecology across a broad range of habitats, our study shows the utility of oligotyping as a facile, high-throughput and unbiased method for large-scale analyses of publically available sequence data repositories and suggests its wide application could greatly extend the range of possibilities to explore microbial ecology.

No MeSH data available.


Related in: MedlinePlus