Metagenomic covariation along densely sampled environmental gradients in the Red Sea

Handle URI:
http://hdl.handle.net/10754/621776
Title:
Metagenomic covariation along densely sampled environmental gradients in the Red Sea
Authors:
Thompson, Luke R; Williams, Gareth J; Haroon, Mohamed; Shibl, Ahmed; Larsen, Peter; Shorenstein, Joshua; Knight, Rob; Stingl, Ulrich
Abstract:
Oceanic microbial diversity covaries with physicochemical parameters. Temperature, for example, explains approximately half of global variation in surface taxonomic abundance. It is unknown, however, whether covariation patterns hold over narrower parameter gradients and spatial scales, and extending to mesopelagic depths. We collected and sequenced 45 epipelagic and mesopelagic microbial metagenomes on a meridional transect through the eastern Red Sea. We asked which environmental parameters explain the most variation in relative abundances of taxonomic groups, gene ortholog groups, and pathways—at a spatial scale of <2000 km, along narrow but well-defined latitudinal and depth-dependent gradients. We also asked how microbes are adapted to gradients and extremes in irradiance, temperature, salinity, and nutrients, examining the responses of individual gene ortholog groups to these parameters. Functional and taxonomic metrics were equally well explained (75–79%) by environmental parameters. However, only functional and not taxonomic covariation patterns were conserved when comparing with an intruding water mass with different physicochemical properties. Temperature explained the most variation in each metric, followed by nitrate, chlorophyll, phosphate, and salinity. That nitrate explained more variation than phosphate suggested nitrogen limitation, consistent with low surface N:P ratios. Covariation of gene ortholog groups with environmental parameters revealed patterns of functional adaptation to the challenging Red Sea environment: high irradiance, temperature, salinity, and low nutrients. Nutrient-acquisition gene ortholog groups were anti-correlated with concentrations of their respective nutrient species, recapturing trends previously observed across much larger distances and environmental gradients. This dataset of metagenomic covariation along densely sampled environmental gradients includes online data exploration supplements, serving as a community resource for marine microbial ecology.The ISME Journal advance online publication, 15 July 2016; doi:10.1038/ismej.2016.99. © 2016 International Society for Microbial Ecology
KAUST Department:
Red Sea Research Center (RSRC)
Citation:
Thompson LR, Williams GJ, Haroon MF, Shibl A, Larsen P, et al. (2016) Metagenomic covariation along densely sampled environmental gradients in the Red Sea. The ISME Journal. Available: http://dx.doi.org/10.1038/ismej.2016.99.
Publisher:
Springer Nature
Journal:
The ISME Journal
Issue Date:
15-Jul-2016
DOI:
10.1038/ismej.2016.99
Type:
Article
ISSN:
1751-7362; 1751-7370
Appears in Collections:
Articles; Red Sea Research Center (RSRC)

Full metadata record

DC FieldValue Language
dc.contributor.authorThompson, Luke Ren
dc.contributor.authorWilliams, Gareth Jen
dc.contributor.authorHaroon, Mohameden
dc.contributor.authorShibl, Ahmeden
dc.contributor.authorLarsen, Peteren
dc.contributor.authorShorenstein, Joshuaen
dc.contributor.authorKnight, Roben
dc.contributor.authorStingl, Ulrichen
dc.date.accessioned2016-11-03T13:24:43Z-
dc.date.available2016-11-03T13:24:43Z-
dc.date.issued2016-07-15en
dc.identifier.citationThompson LR, Williams GJ, Haroon MF, Shibl A, Larsen P, et al. (2016) Metagenomic covariation along densely sampled environmental gradients in the Red Sea. The ISME Journal. Available: http://dx.doi.org/10.1038/ismej.2016.99.en
dc.identifier.issn1751-7362en
dc.identifier.issn1751-7370en
dc.identifier.doi10.1038/ismej.2016.99en
dc.identifier.urihttp://hdl.handle.net/10754/621776-
dc.description.abstractOceanic microbial diversity covaries with physicochemical parameters. Temperature, for example, explains approximately half of global variation in surface taxonomic abundance. It is unknown, however, whether covariation patterns hold over narrower parameter gradients and spatial scales, and extending to mesopelagic depths. We collected and sequenced 45 epipelagic and mesopelagic microbial metagenomes on a meridional transect through the eastern Red Sea. We asked which environmental parameters explain the most variation in relative abundances of taxonomic groups, gene ortholog groups, and pathways—at a spatial scale of <2000 km, along narrow but well-defined latitudinal and depth-dependent gradients. We also asked how microbes are adapted to gradients and extremes in irradiance, temperature, salinity, and nutrients, examining the responses of individual gene ortholog groups to these parameters. Functional and taxonomic metrics were equally well explained (75–79%) by environmental parameters. However, only functional and not taxonomic covariation patterns were conserved when comparing with an intruding water mass with different physicochemical properties. Temperature explained the most variation in each metric, followed by nitrate, chlorophyll, phosphate, and salinity. That nitrate explained more variation than phosphate suggested nitrogen limitation, consistent with low surface N:P ratios. Covariation of gene ortholog groups with environmental parameters revealed patterns of functional adaptation to the challenging Red Sea environment: high irradiance, temperature, salinity, and low nutrients. Nutrient-acquisition gene ortholog groups were anti-correlated with concentrations of their respective nutrient species, recapturing trends previously observed across much larger distances and environmental gradients. This dataset of metagenomic covariation along densely sampled environmental gradients includes online data exploration supplements, serving as a community resource for marine microbial ecology.The ISME Journal advance online publication, 15 July 2016; doi:10.1038/ismej.2016.99. © 2016 International Society for Microbial Ecologyen
dc.publisherSpringer Natureen
dc.titleMetagenomic covariation along densely sampled environmental gradients in the Red Seaen
dc.typeArticleen
dc.contributor.departmentRed Sea Research Center (RSRC)en
dc.identifier.journalThe ISME Journalen
kaust.authorHaroon, Mohameden
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