The transcriptional response of prokaryotes to phytoplankton‐derived dissolved organic matter in seawater

Beier, Sara; Rivers, Adam R.; Moran, Mary Ann; Obernosterer, Ingrid

doi:10.1111/1462-2920.12434

Cited by 43 publications

(44 citation statements)

References 46 publications

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“…Sampling and further processing of the metatranscriptomic analyses have been described previously (Beier et al, 2014). After 15 days, samples for metatranscriptomic analyses were siphoned from the incubation vessels into a combusted glass bottle.…”

Section: Sampling For Metatranscriptomic Analysesmentioning

confidence: 99%

“…DNA was removed from the extracted RNA using the turboDNAse (Applied Biosystems, Austin, TX, USA). To further Samples marked with an asterisk were lost during the experimental procedure or excluded from data analyses for reasons given in the text (this figure has been published previously, Beier et al, 2014).…”

Section: Sampling For Metatranscriptomic Analysesmentioning

confidence: 99%

“…In the dendrogram based on functional binning (Figure 3a), one technical replicate in each of the two treatments of Exp_CyDi clustered separately from the remaining replicates of the treatment. We found evidence for possible contamination of these samples with genomic DNA (Beier et al, 2014) and reads from these two replicates were therefore excluded from further analyses (Table 1). In order to quantify the correlation between the functional and taxonomic response, a Mantel test (Mantel, 1967) using Pearson's correlation and 10 000 permutations was performed.…”

Section: Sample Similaritymentioning

confidence: 99%

“…The Bray-Curtis distance is a dissimilarity measurement that assesses the degree of compositional dissimilarity between two samples by estimating the Abbreviations: %fnc, percent of prokaryotic reads that were assigned to any function; genes, number of detected genes; mRNA-fnc, number of prokaryotic reads with assigned function (genes); mRNA-tax, number of mRNA reads with prokaryotic taxonomic assignment; taxa, number of detected taxa. Modified from Beier et al (2014).…”

Section: Sample Similaritymentioning

confidence: 99%

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Phenotypic plasticity in heterotrophic marine microbial communities in continuous cultures

et al. 2014

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Phenotypic plasticity (PP) is the development of alternate phenotypes of a given taxon as an adaptation to environmental conditions. Methodological limitations have restricted the quantification of PP to the measurement of a few traits in single organisms. We used metatranscriptomic libraries to overcome these challenges and estimate PP using the expressed genes of multiple heterotrophic organisms as a proxy for traits in a microbial community. The metatranscriptomes captured the expression response of natural marine bacterial communities grown on differing carbon resource regimes in continuous cultures. We found that taxa with different magnitudes of PP coexisted in the same cultures, and that members of the order Rhodobacterales had the highest levels of PP. In agreement with previous studies, our results suggest that continuous culturing may have specifically selected for taxa featuring a rather high range of PP. On average, PP and abundance changes within a taxon contributed equally to the organism's change in functional gene abundance, implying that both PP and abundance mediated observed differences in community function. However, not all functional changes due to PP were directly reflected in the bulk community functional response: gene expression changes in individual taxa due to PP were partly masked by counterbalanced expression of the same gene in other taxa. This observation demonstrates that PP had a stabilizing effect on a community's functional response to environmental change.

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Section: Sampling For Metatranscriptomic Analysesmentioning

confidence: 99%

Section: Sampling For Metatranscriptomic Analysesmentioning

confidence: 99%

Section: Sample Similaritymentioning

confidence: 99%

Section: Sample Similaritymentioning

confidence: 99%

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Phenotypic plasticity in heterotrophic marine microbial communities in continuous cultures

et al. 2014

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“…Bacteria and Archaea are the dominant degraders of DOM (Carlson, 2002), but the specific taxa, genes and molecular mechanisms most responsible for DOM metabolism remain relatively obscure. Recently, several culture-independent studies have begun to identify the microbial community members that respond to DOM enrichment, though the majority of these studies have focused on DOM isolated from phytoplankton cultures (Beier, Rivers, Moran, & Obernosterer, 2014;Landa et al, 2013;Nelson & Carlson, 2012;Poretsky, Sun, Mou, & Moran, 2010;Sarmento & Gasol, 2012;Sharma et al, 2014) which is presumed to be more labile than HMW DOM collected in oligotrophic environments. This is likely because of the presence of labile proteins and amino acids (Sarmento et al, 2013) and homopolysaccharides (Meon & Kirchman, 2001) in phytoplankton DOM.…”

Section: Introductionmentioning

confidence: 99%

Microbial cycling of marine high molecular weight dissolved organic matter

Sosa¹

2016

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Microorganisms play a central role mediating biogeochemical cycles in the ocean. Marine dissolved organic matter (DOM) -a reservoir of organic solutes and colloids derived from plankton is a major source of carbon, nutrients, and energy to microbial communities. The biological transformation and remineralization of DOM sustains marine productivity by linking the microbial food web to higher trophic levels (the microbial loop) and exerts important controls over the cycles of carbon and bioessential elements, such as nitrogen and phosphorus, in the sea. Yet insight into the underlying metabolism and reactions driving the degradation of DOM is limited partly because its exact molecular composition is difficult to constrain and appropriate microbial model systems known to decompose marine DOM are lacking. This thesis identifies marine microorganisms that can serve as model systems to study the metabolic pathways and biochemical reactions that control an important ecosystem function, DOM turnover. To accomplish this goal, bacterial isolates were obtained by enriching seawater in dilution-to-extinction culturing experiments with a natural source of DOM, specifically, the high molecular weight (HMW) fraction (>1 kDa nominal molecular weight) obtained by ultrafiltration. Because it is relatively easy to concentrate and it is fairly uniform in its chemical composition across the global ocean and other aquatic environments, HMW DOM has the potential to serve as a model growth substrate to study the biological breakdown of DOM. The phylogeny, genomes, and growth characteristics of the organisms identified through this work indicate that HMW DOM contains bioavailable substrates that may support widespread microbial populations in coastal and open-ocean environments. The availability of ecologically relevant isolates in culture can now serve to test hypothesis emerging from cultivation-independent studies pertaining the potential role of microbial groups in the decomposition of organic matter in the sea. Detailed studies of the biochemical changes exerted on DOM by selected bacterial strains will provide new insight into the processes driving the aerobic microbial food chain in the upper ocean. AcknowledgmentsI owe my deepest gratitude to those who mentored me in the lab. My advisers Ed DeLong and Dan Repeta really changed my life and career trajectory in a way I never imagined bringing me on as a JP student, giving me the opportunity to take part in research at sea and an important collaborative project as part of my dissertation. Thank you to my thesis committee members Martin Polz and Tracy Mincer who always provided constructive discussion and advice that helped me progress. Thank you to my friend and collegue Jamie Becker, my reference in the JP, who convinced my advisers Ed and Dan I should help him out with his research in Hawaii as he was finishing up his thesis, an experience that would be invaluable down the road as a continued my work there when our lab moved to C-MORE at the University of Hawaii. A big mahalo al...

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Differential effects of nitrate, ammonium, and urea as N sources for microbial communities in the North Pacific Ocean

Shilova

Mills

Robidart

et al. 2017

Limnology & Oceanography

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Nitrogen (N) is the major limiting nutrient for phytoplankton growth and productivity in large parts of the world's oceans. Differential preferences for specific N substrates may be important in controlling phytoplankton community composition. To date, there is limited information on how specific N substrates influence the composition of naturally occurring microbial communities. We investigated the effect of nitrate ( NO3−), ammonium ( NH4+), and urea on microbial and phytoplankton community composition (cell abundances and 16S rRNA gene profiling) and functioning (photosynthetic activity, carbon fixation rates) in the oligotrophic waters of the North Pacific Ocean. All N substrates tested significantly stimulated phytoplankton growth and productivity. Urea resulted in the greatest (>300%) increases in chlorophyll a (<0.06 μg L−1 and ∼0.19 μg L−1 in the control and urea addition, respectively) and productivity (<0.4 μmol C L−1 d−1 and ∼1.4 μmol C L−1 d−1 in the control and urea addition, respectively) at two experimental stations, largely due to increased abundances of Prochlorococcus (Cyanobacteria). Two abundant clades of Prochlorococcus, High Light I and II, demonstrated similar responses to urea, suggesting this substrate is likely an important N source for natural Prochlorococcus populations. In contrast, the heterotrophic community composition changed most in response to NH4+. Finally, the time and magnitude of response to N amendments varied with geographic location, likely due to differences in microbial community composition and their nutrient status. Our results provide support for the hypothesis that changes in N supply would likely favor specific populations of phytoplankton in different oceanic regions and thus, affect both biogeochemical cycles and ecological processes.

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The transcriptional response of prokaryotes to phytoplankton‐derived dissolved organic matter in seawater

Cited by 43 publications

References 46 publications

Phenotypic plasticity in heterotrophic marine microbial communities in continuous cultures

Phenotypic plasticity in heterotrophic marine microbial communities in continuous cultures

Microbial cycling of marine high molecular weight dissolved organic matter

Differential effects of nitrate, ammonium, and urea as N sources for microbial communities in the North Pacific Ocean

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