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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

Commonness and abundance plot of all oligotypes that were part of the mixed habitat sample grouping analysis (Table 2). The occurrence (presence/absence) of each of the 99 oligotypes across all 179 samples is plotted along the x-axis while its mean relative abundance across all samples is plotted on the y-axis. Samples that are both common and abundant are found in the top right, while those that are common, but rare are in the bottom right. Both rare and uncommon are found in the bottom left. The top 17 most abundant oligotypes from Table 3 are also labeled.
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Figure 6: Commonness and abundance plot of all oligotypes that were part of the mixed habitat sample grouping analysis (Table 2). The occurrence (presence/absence) of each of the 99 oligotypes across all 179 samples is plotted along the x-axis while its mean relative abundance across all samples is plotted on the y-axis. Samples that are both common and abundant are found in the top right, while those that are common, but rare are in the bottom right. Both rare and uncommon are found in the bottom left. The top 17 most abundant oligotypes from Table 3 are also labeled.

Mentions: All oligotypes that were highly abundant in a single sample (>10% relative Vibrio abundance) occurred across all other habitat types. Abundant oligotypes were therefore also likely to be common across a wide variety of habitat types (Figure 6). Oligotype 5 in particular was found to be both highly abundant and frequent, occurring in all 179 samples analyzed across all habitats (Figure 6). Several oligotypes did not follow this general pattern, and despite a relative ubiquity, they maintained at low mean relative abundances across all the samples in which they occurred (e.g., Oligotypes 1, 2, 13, and 14, Figure 6). Comparing the mean relative abundance of individual oligotypes between marine hosts (Sponge, MarineFish) and marine environments (Seawater, Saltmarsh, Sand-PAH) revealed that 10 of the top 17 oligotypes (Table 3) were significantly different between these habitat categories at the bonferroni-corrected alpha level of 0.0029. SIMPER revealed the strong influence of Oligotype 3 and 5 in Saltmarsh and non-host associated Seawater communities, and Oligotype 5 in Sand-PAH mesocosms. Oligotype 5 was often extremely abundant in seawater samples, including those from a Vibrio bloom (from project ICM_PML_Bv6, Table 1), and on plastic samples (Figure 4). ANOSIM analyses revealed that across all habitat pairwise comparisons only Sponge and MarineFish, Seawater and Saltmarsh, Sand-PAH and Plastic, and Sand-PAH and Seawater could not be significantly differentiated from one another (Table S1).


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)

Commonness and abundance plot of all oligotypes that were part of the mixed habitat sample grouping analysis (Table 2). The occurrence (presence/absence) of each of the 99 oligotypes across all 179 samples is plotted along the x-axis while its mean relative abundance across all samples is plotted on the y-axis. Samples that are both common and abundant are found in the top right, while those that are common, but rare are in the bottom right. Both rare and uncommon are found in the bottom left. The top 17 most abundant oligotypes from Table 3 are also labeled.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 6: Commonness and abundance plot of all oligotypes that were part of the mixed habitat sample grouping analysis (Table 2). The occurrence (presence/absence) of each of the 99 oligotypes across all 179 samples is plotted along the x-axis while its mean relative abundance across all samples is plotted on the y-axis. Samples that are both common and abundant are found in the top right, while those that are common, but rare are in the bottom right. Both rare and uncommon are found in the bottom left. The top 17 most abundant oligotypes from Table 3 are also labeled.
Mentions: All oligotypes that were highly abundant in a single sample (>10% relative Vibrio abundance) occurred across all other habitat types. Abundant oligotypes were therefore also likely to be common across a wide variety of habitat types (Figure 6). Oligotype 5 in particular was found to be both highly abundant and frequent, occurring in all 179 samples analyzed across all habitats (Figure 6). Several oligotypes did not follow this general pattern, and despite a relative ubiquity, they maintained at low mean relative abundances across all the samples in which they occurred (e.g., Oligotypes 1, 2, 13, and 14, Figure 6). Comparing the mean relative abundance of individual oligotypes between marine hosts (Sponge, MarineFish) and marine environments (Seawater, Saltmarsh, Sand-PAH) revealed that 10 of the top 17 oligotypes (Table 3) were significantly different between these habitat categories at the bonferroni-corrected alpha level of 0.0029. SIMPER revealed the strong influence of Oligotype 3 and 5 in Saltmarsh and non-host associated Seawater communities, and Oligotype 5 in Sand-PAH mesocosms. Oligotype 5 was often extremely abundant in seawater samples, including those from a Vibrio bloom (from project ICM_PML_Bv6, Table 1), and on plastic samples (Figure 4). ANOSIM analyses revealed that across all habitat pairwise comparisons only Sponge and MarineFish, Seawater and Saltmarsh, Sand-PAH and Plastic, and Sand-PAH and Seawater could not be significantly differentiated from one another (Table S1).

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