ABSTRACT: Optimisation of DNA-protein co-extraction from the thin microbial biofilm inhabiting marine plastic debris for meta-omics and comparative metaproteomics analysis.
Project description:Environmental meta-omics is rapidly expanding as sequencing capabilities improve, computing technologies become more accessible, and associated costs are reduced. The in situ snapshots of marine microbial life afforded by these data provide a growing knowledge of the functional roles of communities in ecosystem processes. Metaproteomics allows for the characterization of the dynamic proteome of a complex microbial community. It has the potential to reveal impacts of microbial metabolism on biogeochemical transport, storage and cycling (for example, Hawley et al., 2014), while additionally clarifying which taxonomic groups perform these roles. Previous work illuminated many of the important functions and interactions within marine microbial communities (for example, Morris et al., 2010), but a review of ocean metaproteomics literature revealed little standardization in bioinformatics pipelines for detecting peptides and inferring and annotating proteins. As prevalence of these data sets grows, there is a critical need to develop standardized approaches for mass spectrometry (MS) proteomic spectrum identification and annotation to maximize the scientific value of the data obtained. Here, we demonstrate that bioinformatics decisions made throughout the peptide identification process are as important for data interpretation as choices of sampling protocol and bacterial community manipulation experimental design. Our analysis offers a best practices guide for environmental metaproteomics.
Project description:To characterize the taxonomic and functional diversity of biofilms on plastics in marine environments, plastic pellets (PE and PS, ø 3mm) and wooden pellets (as organic control) were incubated at three stations: at the Baltic Sea coast in Heiligendamm (coast), in a dead branch of the river Warnow in Warnemünde (inlet), and in the Warnow estuary (estuary). After two weeks of incubation, all pellets were frozen for subsequent metagenome sequencing and metaproteomic analysis. Biofilm communities in the samples were compared on multiple levels: a) between the two plastic materials, b) between the individual incubation sites, and c) between the plastic materials and the wooden control. Using a semiquantitative approach, we established metaproteome profiles, which reflect the dominant taxonomic groups as well as abundant metabolic functions in the respective samples.
Project description:With the technological advances of the last decade, it is now feasible to analyze environmental samples of vast complexity, such as human stool specimen, using meta-omics techniques like metaproteomics. Still the most sophisticated, sensitive instruments can only extract information that a sample contains in the first place. This highlights the need for initial sample preparation to preserve as much unaltered information as possible. Yet little is known about the effects different processing approaches have on the final analysis results. This study analyzes human stool samples applying metaproteomics and shows that the initial sample storage has a massive effect on the taxonomic composition of proteins identified. The findings are backed up by the results of the metagenomics analysis of the same samples. This suggests, that great care should be taken in choosing storage conditions for (omics) studies, as well as in comparing the results of experiments with different initial processing.
2019-09-26 | PXD014482 | Pride
Project description:Plastisphere microbial community composition on marine plastic debris
Project description:This set of metaproteomics data of the Gemran cockroach hindgut community and the host has been used to validate the gNOMO pipeline. This pipeline is designed to integrate multiple meta-omics data of non-model organisms.
Project description:This study is aimed to isolate marine actinomycetes from sediments from Andaman and the Gulf of Thailand. All 101 marine actinomycetes were screened for anti-biofilm activity. Streptomyces sp. GKU223 showed significantly inhibited biofilm formation of S. aureus. The evaluation of supernatants of anti-biofilm activity produced by Streptomyces sp. GKU223 has been performed. Since the interaction between marine actinomycetes and biofilm forming bacteria has never been investigated, proteomic analysis has been used to identify whole cell proteins involved in anti–biofilm activity. Understanding the interaction at molecular level will lead to sustainably use for anti-biofilm producing marine actinomycetes in pharmaceutical and medicinal applications in the future.
Project description:This study is aimed to isolate marine actinomycetes from sediments from Andaman and the Gulf of Thailand. All 101 marine actinomycetes were screened for anti-biofilm activity. Streptomyces sp. GKU 257-1 showed significantly inhibited biofilm formation of E. coli. The evaluation of supernatants of anti-biofilm activity produced by Streptomyces sp. GKU 257-1 has been performed. Since the interaction between marine actinomycetes and biofilm forming bacteria has never been investigated, proteomic analysis has been used to identify whole cell proteins involved in anti–biofilm activity. Understanding the interaction at molecular level will lead to sustainably use for anti-biofilm producing marine actinomycetes in pharmaceutical and medicinal applications in the future.
2019-09-07 | PXD011027 | JPOST Repository
Project description:Development of technology for impact assessment of marine plastic debris on marine ecosystem (2022)