ABSTRACT: Lake sediment microbial communities from Walker lake, Nevada to study Microbial Dark Matter (Phase II) - Walker Lake 11/02/13 Deep Sediment metagenome
Project description:We established simple synthetic microbial communities in a microcosm model system to determine the mechanisms that underlay cross-feeding in microbial methane-consuming communities. Co-occurring strains from Lake Washington sediment were used that are involved in methane consumption, a methanotroph and two non-methanotrophic methylotrophs.
Project description:In this study, we investigated Mn3+-cycling microbial populations enriched from Lake Matano, Indonesia using metagenomics and metaproteomics. Lake Matano contains an active Mn cycle that links the oxic-anoxic interface with anoxic deep waters that are enriched in iron and manganese, and depleted in sulfate, phosphate, and oxidized nitrogen (Crowe et al., 2008; Jones et al., 2011). Sediments were incubated with sequential transfers for ~1 year with Mn3+ as the sole electron acceptor and methane as organic carbon until achieving sediment-free conditions. Here we investigate this novel species of Dechloromonas (Betaproteobacteria), “Candidatus Dechloromonas occultata,” which was the dominant population in enrichment cultures with active Mn3+ reduction. “Ca. D. occultata” expressed electron conduits related to those involved in Fe2+ oxidation (Mto-like), as well as a novel cytochrome c-rich gene cluster putatively involved in extracellular electron transfer, and an atypical nitrous oxide reductase. According to ribosomal counts, Dechloromonas outnumber Geobacter. In terms of functional genes, Dechloromonas expresses a wider variety and number of genes. Dechloromonas therefore seems to have a (selective?) advantage over Geobacter. Previous experiments revealed that Dechloromonas express nitrogen regulators, reductases and scavenging genes, as well as many carbon central metabolic pathways, and aromatic carbon degradation pathways. Dechloromonas is a beta proteobacteria, and these are "experts" in nitrogen metabolism. Geobacter, on the other hand, is well known for carbon degradation. Our previous experiments lead to our hypothesis that Dechloromonas is more active because they are more successful at acquiring nitrogen, a limiting nutrient for Geobacter. This would further suggest that carbon is not the limiting nutrient. We will test 2 hypotheses with the next suite of experiments 1) pyrophosphate supports the community, by allowing carbon fixation , 2)Dechloromonas has a (selective?) advantage over Geobacter. To test this hypothesis, bioreactors will be used to grow biotriplicate cultures of (1)- CH4 vs. pyrophosphate and (2)-CH4 vs. Mn(III) pyrophosphate. Here we have analyzed whole cell pellets using gas phase fractionations on the Q Exactive. Are Dechloromonas capable of out-competing Geobacter when grown in media with methane as the only carbon source bioreactors because they are capable of acquiring more nitrogen? Source of inoculum. Lake Matano is a metal-rich, ancient ocean analog (Crowe et al. 2011, Jones et al. 2011). Organic carbon in Lake Matano is mostly mineralized via methanogenesis before reaching the iron-rich sediments, limiting organic matter bioavailability for metal-reducers (Kuntz et al. 2015). A 15-cm sediment core from 200 m water depth in Lake Matano, Sulawesi Island, Indonesia (02°26′27.1′′S, 121°15′12.3′′E; in situ sediment temperature ~27°C) was sampled in November 2014 and sub-sampled at 5 cm increments. Sediments were sealed in gas-tight Mylar bags with no headspace (Hansen et al. 2000) and stored at 4°C until incubations began in December 2015.
Project description:Lake sediment microbial communities from Lake Baikal, Russia to study Microbial Dark Matter (Phase II) - Lake Baikal sediment 0-5 cm metagenome
Project description:Lake sediment microbial communities from Lake Kivu, Rwanda to study Microbial Dark Matter (Phase II) - Lake Kivu sediment site 1 69 cm metaG metagenome
Project description:Seagrass meadows are highly productive ecosystems that are considered hotspots for carbon sequestration. The decline of seagrass meadows of various species has been documented worldwide, including that of Cymodocea nodosa, a widespread seagrass in the Mediterranean Sea. To assess the influence of seagrass decline on the metabolic profile of sediment microbial communities, metaproteomes from two sites, one without vegetation and one with a declining Cymodocea nodosa meadow, were characterised at monthly intervals from July 2017 to October 2018. The differences in the metabolic profile observed between the vegetated and nonvegetated sediment before the decline were more pronounced in the deeper parts of the sediment and disappeared with the decay of the roots and rhizomes. During the decline, the protein richness and diversity of the metabolic profile of the microbial communities inhabiting the nonvegetated sediment became similar to those observed for the vegetated communities. Temporal shifts in the structure of the metabolic profile were only observed in the nonvegetated sediment and were also more pronounced in the deeper parts of the sediment. The assessment of the dynamics of proteins involved in the degradation of organic matter, such as ABC transporters, fermentation-mediating enzymes, and proteins involved in dissimilatory sulphate reduction, reflected the general dynamics of the metabolic profile. Overall, the metabolic profile of the microbial communities inhabiting the nonvegetated sediment was influenced by the decline of seagrass, with stronger shifts observed in the deeper parts of the sediment.
Project description:Coastal marine sediments, as locations of substantial fixed nitrogen loss, are very important to the nitrogen budget and to the primary productivity of the oceans. Coastal sediment systems are also highly dynamic and subject to periodic natural and anthropogenic organic substrate additions. The response to organic matter by the microbial community involved in nitrogen loss processes was evaluated using mesocosms of Chesapeake Bay sediments. Over the course of a 50-day incubation, rates of anammox and denitrification were measured weekly using 15N tracer incubations, and samples were collected for genetic analysis. Rates of both nitrogen loss processes and gene abundances associated with them corresponded loosely, probably because heterogeneities in sediments obscured a clear relationship. The rates of denitrification were stimulated more by the higher organic matter addition, and the fraction of nitrogen loss attributed to anammox slightly reduced. Furthermore, the large organic matter pulse drove a significant and rapid shift in the denitrifier community as determined using a nirS microarray, indicating the diversity of these organisms plays an essential role in responding to anthropogenic inputs. We also suggest that the proportion of nitrogen loss due to anammox in these coastal estuarine sediments may be underestimated due to temporal dynamics as well as from methodological artifacts related to conventional sediment slurry incubation approaches.
Project description:Sediment microbial communities from Lake Kivu, Western Province, Rwanda to study Microbial Dark Matter (Phase II) - Sediment_site1_48cm metagenome
Project description:Sediment microbial communities from Lake Kivu, Western Province, Rwanda to study Microbial Dark Matter (Phase II) - Sediment_site1_10cm metagenome