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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

Oligotype distribution for FreshwaterFish and MarineFish tissue (FreshwaterFish: 0-x-i and 5-x-ii, MarineFish: 18-x-i and 18-x-ii), associated water samples (x-x-W, blue lines), and water samples from aquaria containing no fish (x-C-W). The relative abundance of each oligotype within the total Vibrio diversity for each sample is shown in stacked bar graphs (bottom), and the proportion of the total Vibrio (relative abundance) within all bacterial diversity for each sample is shown with gray bars (top, red-dashed lines are median values for each host-habitat). A clear division between low and high salinity samples is seen, despite considerable variation within salinities. Significant differences in median total Vibrio relative abundance exists between FreshwaterFish and MarineFish samples, and between MarineFish samples and their surrounding water. The Vibrio community of fish food used during experimental period is also shown (“FOODX”).
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Figure 3: Oligotype distribution for FreshwaterFish and MarineFish tissue (FreshwaterFish: 0-x-i and 5-x-ii, MarineFish: 18-x-i and 18-x-ii), associated water samples (x-x-W, blue lines), and water samples from aquaria containing no fish (x-C-W). The relative abundance of each oligotype within the total Vibrio diversity for each sample is shown in stacked bar graphs (bottom), and the proportion of the total Vibrio (relative abundance) within all bacterial diversity for each sample is shown with gray bars (top, red-dashed lines are median values for each host-habitat). A clear division between low and high salinity samples is seen, despite considerable variation within salinities. Significant differences in median total Vibrio relative abundance exists between FreshwaterFish and MarineFish samples, and between MarineFish samples and their surrounding water. The Vibrio community of fish food used during experimental period is also shown (“FOODX”).

Mentions: Interestingly, although Vibrio communities between fish and their surrounding water at a given salinity were statistically indistinguishable, communities between fresh and marine salinity environments showed dramatic differences in both community structure and relative abundance of total Vibrio (Figure 2, Middle). Oligotypes 2, 4, and 8 dominated both FreshwaterFish and FreshWater (cumulative abundance in FreshwaterFish/FreshWater = 87.2%/71.9%), while Oligotypes 1, 3, and 6 dominated MarineFish and MarineWater (cumulative abundance in MarineFish/MarineWater = 60%/53% (Figure 3). Experimental aquaria without fish at low salinity (water only) showed a strong dominance of Oligotype 2, 4, and 8 (cumulative abundance = 67%), showing strong similarities to those aquaria that did house fish. However, marine aquaria without fish showed a strong dominance of Oligotype 2, inconsistent with marine aquaria that did contain fish. Interestingly, Oligotype 4 was found across all salinities, in water, fish and control samples, at greater than 10% relative abundance.


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)

Oligotype distribution for FreshwaterFish and MarineFish tissue (FreshwaterFish: 0-x-i and 5-x-ii, MarineFish: 18-x-i and 18-x-ii), associated water samples (x-x-W, blue lines), and water samples from aquaria containing no fish (x-C-W). The relative abundance of each oligotype within the total Vibrio diversity for each sample is shown in stacked bar graphs (bottom), and the proportion of the total Vibrio (relative abundance) within all bacterial diversity for each sample is shown with gray bars (top, red-dashed lines are median values for each host-habitat). A clear division between low and high salinity samples is seen, despite considerable variation within salinities. Significant differences in median total Vibrio relative abundance exists between FreshwaterFish and MarineFish samples, and between MarineFish samples and their surrounding water. The Vibrio community of fish food used during experimental period is also shown (“FOODX”).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 3: Oligotype distribution for FreshwaterFish and MarineFish tissue (FreshwaterFish: 0-x-i and 5-x-ii, MarineFish: 18-x-i and 18-x-ii), associated water samples (x-x-W, blue lines), and water samples from aquaria containing no fish (x-C-W). The relative abundance of each oligotype within the total Vibrio diversity for each sample is shown in stacked bar graphs (bottom), and the proportion of the total Vibrio (relative abundance) within all bacterial diversity for each sample is shown with gray bars (top, red-dashed lines are median values for each host-habitat). A clear division between low and high salinity samples is seen, despite considerable variation within salinities. Significant differences in median total Vibrio relative abundance exists between FreshwaterFish and MarineFish samples, and between MarineFish samples and their surrounding water. The Vibrio community of fish food used during experimental period is also shown (“FOODX”).
Mentions: Interestingly, although Vibrio communities between fish and their surrounding water at a given salinity were statistically indistinguishable, communities between fresh and marine salinity environments showed dramatic differences in both community structure and relative abundance of total Vibrio (Figure 2, Middle). Oligotypes 2, 4, and 8 dominated both FreshwaterFish and FreshWater (cumulative abundance in FreshwaterFish/FreshWater = 87.2%/71.9%), while Oligotypes 1, 3, and 6 dominated MarineFish and MarineWater (cumulative abundance in MarineFish/MarineWater = 60%/53% (Figure 3). Experimental aquaria without fish at low salinity (water only) showed a strong dominance of Oligotype 2, 4, and 8 (cumulative abundance = 67%), showing strong similarities to those aquaria that did house fish. However, marine aquaria without fish showed a strong dominance of Oligotype 2, inconsistent with marine aquaria that did contain fish. Interestingly, Oligotype 4 was found across all salinities, in water, fish and control samples, at greater than 10% relative abundance.

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