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: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:Marine sediments harbor highly diverse microbial communities that contribute to global biodiversity and play essential roles in the ecosystem functioning. However, the metaproteome of marine sediments remains poorly understood. Extracting proteins from environmental samples can be challenging, especially in marine sediments due to their complex matrix. Few studies have been conducted on improving protein extraction methods from marine sediments. To establish an effective protein extraction workflow for clay-rich sediments, we compared, combined and improved several protein extraction methods. The presented workflow includes blocking of protein binding sites on sediment particles with high concentrations of amino acids, effective cell lysis via ultra-sonication, and the electro-elution and simultaneous fractionation of proteins. Using this workflow, we were able to recover 100% of the previously added Escherichia coli proteins from the sediment.
