Bayesian community-wide culture-independent microbial source tracking

Knights, Dan; Kuczynski, Justin; Charlson, Emily S.; Zaneveld, Jesse; Mozer, Michael C.; Collman, Ronald G.; Bushman, Frederic D.; Knight, Robert T.; Kelley, Scott T.

doi:10.1038/nmeth.1650

Cited by 1,411 publications

(1,282 citation statements)

References 22 publications

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“…The similarity percentage (SIMPER, Primer-E) analysis was used to determine the sequences that contributed most to similarity within, and dissimilarity between groups of samples identified by water mass and sample type. SourceTracker (Knights et al, 2011) was used to identify sources and sinks of OTUs in samples. The analysis was conducted at a rarefaction depth of 1000.…”

Section: Resultsmentioning

confidence: 99%

Ocean currents shape the microbiome of Arctic marine sediments

et al. 2012

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Prokaryote communities were investigated on the seasonally stratified Alaska Beaufort Shelf (ABS). Water and sediment directly underlying water with origin in the Arctic, Pacific or Atlantic oceans were analyzed by pyrosequencing and length heterogeneity-PCR in conjunction with physicochemical and geographic distance data to determine what features structure ABS microbiomes. Distinct bacterial communities were evident in all water masses. Alphaproteobacteria explained similarity in Arctic surface water and Pacific derived water. Deltaproteobacteria were abundant in Atlantic origin water and drove similarity among samples. Most archaeal sequences in water were related to unclassified marine Euryarchaeota. Sediment communities influenced by Pacific and Atlantic water were distinct from each other and pelagic communities. Firmicutes and Chloroflexi were abundant in sediment, although their distribution varied in Atlantic and Pacific influenced sites. Thermoprotei dominated archaea in Pacific influenced sediments and Methanomicrobia dominated in methanecontaining Atlantic influenced sediments. Length heterogeneity-PCR data from this study were analyzed with data from methane-containing sediments in other regions. Pacific influenced ABS sediments clustered with Pacific sites from New Zealand and Chilean coastal margins. Atlantic influenced ABS sediments formed another distinct cluster. Density and salinity were significant structuring features on pelagic communities. Porosity co-varied with benthic community structure across sites and methane did not. This study indicates that the origin of water overlying sediments shapes benthic communities locally and globally and that hydrography exerts greater influence on microbial community structure than the availability of methane.

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Section: Resultsmentioning

confidence: 99%

Ocean currents shape the microbiome of Arctic marine sediments

et al. 2012

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“…To ensure that the result was not unduly influenced by the samples to which the 100-year ceiling was applied (all AABW; see Results) and those for which particle releases were not simulated (samples 11, 13, 17 and 22), the test was repeated with these samples removed. To confirm that the advection effect was directional, that is, 'upstream' sites were acting as sources of diversity to 'downstream' sites, SourceTracker 46 was used to identify sources of OTUs in each sample. Each sample was sequentially designated a sink, with the remaining samples as potential sources, and the most probable proportion of OTUs originating from each potential source determined over 100 randomised trials per sample.…”

Section: Methodsmentioning

confidence: 99%

Advection shapes Southern Ocean microbial assemblages independent of distance and environment effects

et al. 2013

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“…To illustrate the spread of bacterial communities in the fjord the SourceTracker 0.9.5 software (Knights et al, 2011) was applied in QIIME. It is designed to track the relative contribution of predefined microbial sources in sink samples using a Bayesian approach, as done in Storesund et al, in review.…”

Section: Source Tracker Analysismentioning

confidence: 99%

Heterotrophic nanoflagellate grazing facilitates subarctic Atlantic spring bloom development

Paulsen¹,

Riisgaard²,

John³

et al. 2017

Aquat. Microb. Ecol.

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My study underpins that picophytoplankton are important contributors to primary production, especially during the winter-spring transition (Paper I and III) and autumn (Paper V). They boosted the growth of heterotrophic microorganisms before the onset of the diatom spring bloom in the Subarctic Atlantic (Paper I) and dominated the phytoplankton biomass in the high turbid parts of a NE Greenland fjord influenced by glacial meltwater (Paper V). Picophytoplankton were better adapted to low light conditions and demonstrated higher growth rates, than larger phytoplankton (Paper I, II, III, V). In the Polar-influenced water near Greenland, Synechococcus were negligible, while in the Atlantic influenced waters picoeukaryotes and Synechococcus were often equally abundant and the latter dominated on several occasions during autumn and winter (Paper I and III). Unexpectedly, abundances of Synechococcus were as high at 65°N as at 79°N, and molecular analysis suggests the presence of new clades specially adapted to Arctic conditions. Bacteria were generally rather carbon-than nutrient limited, and their abundance increased rapidly in response to the pre-bloom picophytoplankton production of labile carbon in both the Arctic and Subarctic (Paper I and V). In NE Greenland the terrestrial DOM supplied from the Greenland ice sheet proved to be highly bioavailable compared to the 7 autochthonous fjord DOM (Paper IV). The in situ changes in DOM, which were examined via fluorescence signal of different DOM components (FDOM), surprisingly demonstrated that the highest net-growth of bacteria was not coupled to the labile glacial runoff in the surface, but rather to sub-surface the humic-DOM, commonly considered to be refractory. This may be explained by the presence of specific dominating taxa of bacteria that had the ability to degrade humic-DOM (Paper V).Across regions, HNF exerted strong control of picophytoplankton and bacteria (Paper I, II, III, V). HNF grew significantly faster than microzooplankton and were therefore less affected by mixing and relatively more important grazers than their micro-sized counterparts in well-mixed water columns (Paper I and II). HNF larger than 5µm controlled picophytoplankton particularly in the early productive season, while small HNF (3-5µm) mainly kept bacteria in check in autumn (Paper III, V). In conclusion, the studies underline that pico-sized plankton play a fundamental part in the carbon transfer in high latitude ecosystems both as primary producers and via the microbial loop. Picophytoplankton appeared better adapted than larger phytoplankton to low light conditions, and bacteria were capable of degrading terrestrial derived DOM, however, these abilities are highly community specific. The data suggest that a change in mixing patters will affect the microbial food structure and that shifts in coastal microbial community composition should be anticipated with increased runoff. 8 List of publicationsThe thesis is based on preliminary data and the following fived papers referred to in the t...

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Bayesian community-wide culture-independent microbial source tracking

Cited by 1,411 publications

References 22 publications

Ocean currents shape the microbiome of Arctic marine sediments

Ocean currents shape the microbiome of Arctic marine sediments

Advection shapes Southern Ocean microbial assemblages independent of distance and environment effects

Heterotrophic nanoflagellate grazing facilitates subarctic Atlantic spring bloom development

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