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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

NMDS plot with covariance ellipsoids for both host-associated and environmental samples. Sample names refer to habitat type and VAMPS project listed in Table 1.
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Figure 5: NMDS plot with covariance ellipsoids for both host-associated and environmental samples. Sample names refer to habitat type and VAMPS project listed in Table 1.

Mentions: In order to gain as broad a view as possible of Vibrio oligotype distributions across habitats, we included 179 samples from 7 environmental and host-associated habitats spanning a wide range of environmental and geographical gradients (Figure 5). This analysis yielded 99 oligotypes, of which the top 5 represented 65% of all reads, while the top 10 represented 90%. We observed the top 10 oligotypes from this analysis at high abundance in previous analyses (as determined by identical representative sequences), except Oligotype 10, which was novel to Sand-PAH mesocosms and is a highly divergent oligotype which could not be fully resolved. Sand-PAH samples were taken from beach sand communities near the Deepwater Horizon oil spill, and were likely enriched for PAH-associated species (Kappell et al., 2014).


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)

NMDS plot with covariance ellipsoids for both host-associated and environmental samples. Sample names refer to habitat type and VAMPS project listed in Table 1.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 5: NMDS plot with covariance ellipsoids for both host-associated and environmental samples. Sample names refer to habitat type and VAMPS project listed in Table 1.
Mentions: In order to gain as broad a view as possible of Vibrio oligotype distributions across habitats, we included 179 samples from 7 environmental and host-associated habitats spanning a wide range of environmental and geographical gradients (Figure 5). This analysis yielded 99 oligotypes, of which the top 5 represented 65% of all reads, while the top 10 represented 90%. We observed the top 10 oligotypes from this analysis at high abundance in previous analyses (as determined by identical representative sequences), except Oligotype 10, which was novel to Sand-PAH mesocosms and is a highly divergent oligotype which could not be fully resolved. Sand-PAH samples were taken from beach sand communities near the Deepwater Horizon oil spill, and were likely enriched for PAH-associated species (Kappell et al., 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