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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

Nonmetric Multidimensional Scaling (NMDS) plot of host-associated Vibrio communities based on oligotype distributions. Labels are located at the center of covariance ellipsoids around each host type. Pairwise ANOSIM permutation tests reveal all host habitats can be significantly differentiated except MarineFish and Sponge communities (Table S1).
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Figure 1: Nonmetric Multidimensional Scaling (NMDS) plot of host-associated Vibrio communities based on oligotype distributions. Labels are located at the center of covariance ellipsoids around each host type. Pairwise ANOSIM permutation tests reveal all host habitats can be significantly differentiated except MarineFish and Sponge communities (Table S1).

Mentions: Pairwise Analysis of Similarity (ANOSIM) tests showed significant groupings in oligotype communities according to habitat, except between high salinity fish (MarineFish) and sponges, whose communities could not be significantly distinguished. This ANOSIM result is also visible in our NMDS analyses which shows clear overlap between both sponges (DeepSponge and ShallowSponge) and high salinity fish (MarineFish), yet separation from plastic and low salinity fish (FreshwaterFish) habitats (Figure 1). An ANOSIM test comparing marine biotic substrates (MarineFish and Sponges pooled together) revealed a significant grouping that excluded Plastic, an abiotic substrate. Similarity Percentages (SIMPER) analysis corroborated these results by illustrating the strong contribution of Oligotypes 1, 4, and 6 to both MarineFish and Sponge within-habitat similarity, and distinguished those habitats from FreshwaterFish and Plastics. Oligotypes 2, 4, and 8 contributed to both within habitat similarity, and between habitat differences for FreshwaterFish samples. Plastics were dominated by Oligotype 5, which also distinguished it from other habitat types, including biotic substrates (Tables 4A,B).


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)

Nonmetric Multidimensional Scaling (NMDS) plot of host-associated Vibrio communities based on oligotype distributions. Labels are located at the center of covariance ellipsoids around each host type. Pairwise ANOSIM permutation tests reveal all host habitats can be significantly differentiated except MarineFish and Sponge communities (Table S1).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 1: Nonmetric Multidimensional Scaling (NMDS) plot of host-associated Vibrio communities based on oligotype distributions. Labels are located at the center of covariance ellipsoids around each host type. Pairwise ANOSIM permutation tests reveal all host habitats can be significantly differentiated except MarineFish and Sponge communities (Table S1).
Mentions: Pairwise Analysis of Similarity (ANOSIM) tests showed significant groupings in oligotype communities according to habitat, except between high salinity fish (MarineFish) and sponges, whose communities could not be significantly distinguished. This ANOSIM result is also visible in our NMDS analyses which shows clear overlap between both sponges (DeepSponge and ShallowSponge) and high salinity fish (MarineFish), yet separation from plastic and low salinity fish (FreshwaterFish) habitats (Figure 1). An ANOSIM test comparing marine biotic substrates (MarineFish and Sponges pooled together) revealed a significant grouping that excluded Plastic, an abiotic substrate. Similarity Percentages (SIMPER) analysis corroborated these results by illustrating the strong contribution of Oligotypes 1, 4, and 6 to both MarineFish and Sponge within-habitat similarity, and distinguished those habitats from FreshwaterFish and Plastics. Oligotypes 2, 4, and 8 contributed to both within habitat similarity, and between habitat differences for FreshwaterFish samples. Plastics were dominated by Oligotype 5, which also distinguished it from other habitat types, including biotic substrates (Tables 4A,B).

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