Dataset Information

Genomic Signatures for Sedimentary Microbial Utilization of Phytoplankton Detritus in a Fast-Flowing Estuary.

ABSTRACT: In fast-flowing, river-dominated estuaries, "hotspots" of microbial biogeochemical cycling can be found within areas of extended water retention. Lateral bays located off of the North and South channels of the Columbia River estuary are proposed to be such hotspots. Previous metagenomic studies on water samples indicated that these regions function both as sources and sinks of biogenic particles, with potential to impact organic matter fluxes in the estuary. To extend this work, we analyzed 11 sediment metagenomes from three disparate bays: the freshwater Cathlamet Bay, and the brackish Youngs Bay and more saline Baker Bay located nearer the mouth to the south and north of the main channel, respectively. Samples were collected from upper layers of sediments in August of 2011 and 2013 for DNA extraction and metagenome sequencing. All metagenomes were dominated by bacterial sequences, although diatom sequences as high as 26% of the total annotated sequences were observed in the higher salinity samples. Unsupervised 2D hierarchical clustering analysis resulted in the eleven metagenome samples clustered into four groups by microbial taxonomic composition, with Bacteroides, diatom, and phage levels driving most of the grouping. Results of functional gene clustering further indicated that diatom bloom degradation stage (early vs. late) was an important factor. While the Flavobacteriia and Cytophagia classes were well represented in metagenomes containing abundant diatoms, taxa from the Bacteroidia class, along with certain members of the Sphingobacteriia class, were particularly abundant in metagenomes representing later stages of diatom decomposition. In contrast, the sediment metagenomes with low relative abundance of diatom and Bacteroidetes sequences appeared to have a metabolic potential biased toward microbial growth under nutrient limitation. While differences in water salinity clearly also influenced the microbial community composition and metabolic potential, our results highlight a central role for allochthonous labile organic matter (i.e., diatom detritus), in shaping bacterial taxonomic and functional properties in the Columbia River estuary lateral bay sediments. These results suggest that in fast-flowing, river-dominated estuaries, sediment microbial communities in areas of extended water retention, such as the lateral bays, may contribute disproportionately to estuarine organic matter degradation and recycling.

SUBMITTER: Smith MW

PROVIDER: S-EPMC6848030 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Genomic Signatures for Sedimentary Microbial Utilization of Phytoplankton Detritus in a Fast-Flowing Estuary.

Smith Maria W MW Herfort Lydie L Rivers Adam R AR Simon Holly M HM

Frontiers in microbiology 20191105

In fast-flowing, river-dominated estuaries, "hotspots" of microbial biogeochemical cycling can be found within areas of extended water retention. Lateral bays located off of the North and South channels of the Columbia River estuary are proposed to be such hotspots. Previous metagenomic studies on water samples indicated that these regions function both as sources and sinks of biogenic particles, with potential to impact organic matter fluxes in the estuary. To extend this work, we analyzed 11 s ...[more]

PMID: 31749780

Similar Datasets

Project description:Fueled by seasonal phytoplankton blooms, the Columbia River estuary is a natural bioreactor for organic matter transformations. Prior metagenome analyses indicated high abundances of diverse Bacteroidetes taxa in estuarine samples containing phytoplankton. To examine the hypothesis that Bacteroidetes taxa have important roles in phytoplankton turnover, we further analyzed metagenomes from water collected along a salinity gradient at 0, 5, 15, 25, and 33 PSU during bloom events. Size fractions were obtained by using a 3-μm prefilter and 0.2-μm collection filter. Although this approach targeted bacteria by removing comparatively large eukaryotic cells, the metagenome from the ES-5 sample (5 PSU) nevertheless contained an abundance of diatom DNA. Biogeochemical measurements and prior studies indicated that this finding resulted from the leakage of cellular material due to freshwater diatom lysis at low salinity. Relative to the other metagenomes, the bacterial fraction of ES-5 was dramatically depleted of genes annotated as Bacteroidetes and lysogenic bacteriophages, but was overrepresented in DNA of protists and Myxococcales bacterivores. We suggest the following equally plausible scenarios for the microbial response to phytoplankton lysis: (1) Bacteroidetes depletion in the free-living fraction may at least in part be caused by their attachment to fluvial diatoms as the latter are lysed upon contact with low-salinity estuarine waters; (2) diatom particle colonization is likely followed by rapid bacterial growth and lytic phage infection, resulting in depletion of lysogenic bacteriophages and host bacteria; and (3) the subsequent availability of labile organic matter attracted both grazers and predators to feed in this estuarine biogeochemical "hotspot," which may have additionally depleted Bacteroidetes populations. These results represent the first detailed molecular analysis of the microbial response to phytoplankton lysis at the freshwater-brackish water interface in the fast-flowing Columbia River estuary.

Project description:Purpose: Gene expression signatures developed to measure the activity of oncogenic signaling pathways have been used to dissect the heterogeneity of tumor samples and to predict sensitivity to various cancer drugs that target components of the relevant pathways, thus potentially identifying therapeutic options for subgroups of patients. To facilitate broad use, including in a clinical setting, the ability to generate data from formalin-fixed, paraffin-embedded (FFPE) tissues is essential. Experimental Design: Patterns of pathway activity in matched fresh-frozen and FFPE xenograft tumor samples were generated using the MessageAmp Premier methodology in combination with assays using Affymetrix arrays. Results generated were compared with those obtained from fresh-frozen samples using a standard Affymetrix assay. In addition, gene expression data from patient matched fresh-frozen and FFPE melanomas were also utilized to evaluate the consistency of predictions of oncogenic signaling pathway status. Results: Significant correlation of pathway activity predictions was observed between paired fresh-frozen and FFPE xenograft tumor samples. In addition, significant concordance of pathway activity predictions was also observed between patient matched fresh-frozen and FFPE melanomas. Conclusion: Reliable and consistent predictions of oncogenic pathway activities can be obtained from FFPE tumor tissue samples. The ability to reliably utilize FFPE patient tumor tissue samples for genomic analyses will lead to a better understanding of the biology of disease progression and, in the clinical setting, will provide tools to guide the choice of therapeutics to those most likely to be effective in treating a patient’s disease. 8 replicates of HMECs infected with adenovirus expressing GFP, 8 replicates of HMECs infected with adenovirus expressing RAS, 6 replicates of HMECs infected with adenovirus expressing MYC, 25 fresh-frozen melanoma xenografts, 25 FFPE melanoma xenografts, 6 FFPE human melanoma

Project description:BackgroundAlgae encompass a wide array of photosynthetic organisms that are ubiquitously distributed in aquatic and terrestrial habitats. Algal species often bloom in aquatic ecosystems, providing a significant autochthonous carbon input to the deeper anoxic layers in stratified water bodies. In addition, various algal species have been touted as promising candidates for anaerobic biogas production from biomass. Surprisingly, in spite of its ecological and economic relevance, the microbial community involved in algal detritus turnover under anaerobic conditions remains largely unexplored.ResultsHere, we characterized the microbial communities mediating the degradation of Chlorella vulgaris (Chlorophyta), Chara sp. strain IWP1 (Charophyceae), and kelp Ascophyllum nodosum (phylum Phaeophyceae), using sediments from an anaerobic spring (Zodlteone spring, OK; ZDT), sludge from a secondary digester in a local wastewater treatment plant (Stillwater, OK; WWT), and deeper anoxic layers from a seasonally stratified lake (Grand Lake O' the Cherokees, OK; GL) as inoculum sources. Within all enrichments, the majority of algal biomass was metabolized within 13-16 weeks, and the process was accompanied by an increase in cell numbers and a decrease in community diversity. Community surveys based on the V4 region of the 16S rRNA gene identified different lineages belonging to the phyla Bacteroidetes, Proteobacteria (alpha, delta, gamma, and epsilon classes), Spirochaetes, and Firmicutes that were selectively abundant under various substrate and inoculum conditions. Within all kelp enrichments, the microbial communities structures at the conclusion of the experiment were highly similar regardless of the enrichment source, and were dominated by the genus Clostridium, or family Veillonellaceae within the Firmicutes. In all other enrichments the final microbial community was dependent on the inoculum source, rather than the type of algae utilized as substrate. Lineages enriched included the uncultured groups VadinBC27 and WCHB1-69 within the Bacteroidetes, genus Spirochaeta and the uncultured group SHA-4 within Spirochaetes, Ruminococcaceae, Lachnospiraceae, Yongiibacter, Geosporobacter, and Acidaminobacter within the Firmicutes, and genera Kluyvera, Pantoea, Edwardsiella and Aeromonas, and Buttiauxella within the Gamma-Proteobaceteria order Enterobacteriales.ConclusionsOur results represent the first systematic survey of microbial communities mediating turnover of algal biomass under anaerobic conditions, and highlights the diversity of lineages putatively involved in the degradation process.

Project description:Nitrogen availability and form are important controls on estuarine phytoplankton growth. This study experimentally determined the influence of urea and nitrate additions on phytoplankton growth throughout the growing season (March 2012, June 2011, August 2011) in a temperate, eutrophied estuary (Neuse River Estuary, North Carolina, USA). Photopigments (chlorophyll a and diagnostic photopigments: peridinin, fucoxanthin, alloxanthin, zeaxanthin, chlorophyll b) and microscopy-based cell counts were used as indicators of phytoplankton growth. In March, the phytoplankton community was dominated by Gyrodinium instriatum and only fucoxanthin-based growth rates were stimulated by nitrogen addition. The limited response to nitrogen suggests other factors may control phytoplankton growth and community composition in early spring. In June, inorganic nitrogen concentrations were low and stimulatory effects of both nitrogen forms were observed for chlorophyll a- and diagnostic photopigment-based growth rates. In contrast, cell counts showed that only cryptophyte and dinoflagellate (Heterocapsa rotundata) growth were stimulated. Responses of other photopigments may have been due to an increase in pigment per cell or growth of plankton too small to be counted with the microscopic methods used. Despite high nitrate concentrations in August, growth rates were elevated in response to urea and/or nitrate addition for all photopigments except peridinin. However, this response was not observed in cell counts, again suggesting that pigment-based growth responses may not always be indicative of a true community and/or taxa-specific growth response. This highlights the need to employ targeted microscopy-based cell enumeration concurrent with pigment-based technology to facilitate a more complete understanding of phytoplankton dynamics in estuarine systems. These results are consistent with previous studies showing the seasonal importance of nitrogen availability in estuaries, and also reflect taxa-specific responses nitrogen availability. Finally, this study demonstrates that under nitrogen-limiting conditions, the phytoplankton community and its various taxa are capable of using both urea and nitrate to support growth.

Project description:Sydney Harbour is subjected to persistent stress associated with anthropogenic activity and global climate change, but is particularly subjected to pulse stress events associated with stormwater input during episodic periods of high rainfall. Photosynthetic microbes underpin metazoan diversity within estuarine systems and are therefore important bioindicators of ecosystem health; yet how stormwater input affects their occurrence and distribution in Sydney Harbour remains poorly understood. We utilised molecular tools (16S/18S rRNA and petB genes) to examine how the phytoplankton community structure (both prokaryotes and eukaryotes) within Sydney Harbour varies between high and low rainfall periods. The relative proportion of phytoplankton sequences was more abundant during the high rainfall period, comprising mainly of diatoms, an important functional group supporting increased productivity within estuarine systems, together with cyanobacteria. Increased spatial variability in the phytoplankton community composition was observed, potentially driven by the steepened physico-chemical gradients associated with stormwater inflow. Conversely, during a low rainfall period, the proportion of planktonic photosynthetic microbes was significantly lower and the persistent phytoplankton were predominantly represented by chlorophyte and dinoflagellate sequences, with lower overall diversity. Differences in phytoplankton composition between the high and low rainfall periods were correlated with temperature, salinity, total nitrogen and silicate. These results suggest that increased frequency of high-rainfall events may change the composition, productivity and health of the estuary. Our study begins to populate the knowledge gap in the phytoplankton community structure and substantial changes associated with transient environmental perturbations, an essential step towards unravelling the dynamics of primary production in a highly urbanised estuarine ecosystem in response to climate change and other anthropogenic stressors.

Dataset Information

Genomic Signatures for Sedimentary Microbial Utilization of Phytoplankton Detritus in a Fast-Flowing Estuary.

Publications

Genomic Signatures for Sedimentary Microbial Utilization of Phytoplankton Detritus in a Fast-Flowing Estuary.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets