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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 distributions for Plastic samples and their surrounding water. Sample labels indicate the date the samples were collected and the sample type. Water and plastic samples collected on the same date are associated with one another. All water was collected at the surface. Black arrows indicate plastic samples that contain a single oligotype at greater than 50% relative abundance. “OligotypeNA” represents an oligotype that was not among the top 10 most abundant oligotypes from any three of our oligotype groupings.
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Figure 4: Oligotype distributions for Plastic samples and their surrounding water. Sample labels indicate the date the samples were collected and the sample type. Water and plastic samples collected on the same date are associated with one another. All water was collected at the surface. Black arrows indicate plastic samples that contain a single oligotype at greater than 50% relative abundance. “OligotypeNA” represents an oligotype that was not among the top 10 most abundant oligotypes from any three of our oligotype groupings.

Mentions: Lastly, Vibrio communities from plastic substrates overlapped completely with seawater communities collected alongside them (Figure 2, Bottom), and Oligotypes 3, 5, and 12, dominated both Plastics and associated seawater. We found no oligotype to be significantly enriched on plastic samples compared to their surrounding water, nor were there significant increases in total Vibrio on plastic substrates. In several cases, we found a single oligotype that did not occur in the surrounding water but dominated in relative abundance on an individual plastic substrate. This pattern was particularly apparent with Oligotypes 13, 2, and 7, which reached extremely high relative abundances on multiple occasions (e.g., Oligotype 2 at 91% relative abundance in the “10/09-Plastic” sample) (Figure 4).


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 distributions for Plastic samples and their surrounding water. Sample labels indicate the date the samples were collected and the sample type. Water and plastic samples collected on the same date are associated with one another. All water was collected at the surface. Black arrows indicate plastic samples that contain a single oligotype at greater than 50% relative abundance. “OligotypeNA” represents an oligotype that was not among the top 10 most abundant oligotypes from any three of our oligotype groupings.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 4: Oligotype distributions for Plastic samples and their surrounding water. Sample labels indicate the date the samples were collected and the sample type. Water and plastic samples collected on the same date are associated with one another. All water was collected at the surface. Black arrows indicate plastic samples that contain a single oligotype at greater than 50% relative abundance. “OligotypeNA” represents an oligotype that was not among the top 10 most abundant oligotypes from any three of our oligotype groupings.
Mentions: Lastly, Vibrio communities from plastic substrates overlapped completely with seawater communities collected alongside them (Figure 2, Bottom), and Oligotypes 3, 5, and 12, dominated both Plastics and associated seawater. We found no oligotype to be significantly enriched on plastic samples compared to their surrounding water, nor were there significant increases in total Vibrio on plastic substrates. In several cases, we found a single oligotype that did not occur in the surrounding water but dominated in relative abundance on an individual plastic substrate. This pattern was particularly apparent with Oligotypes 13, 2, and 7, which reached extremely high relative abundances on multiple occasions (e.g., Oligotype 2 at 91% relative abundance in the “10/09-Plastic” sample) (Figure 4).

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