Connecting MetaProteomeAnalyzer and PeptideShaker to Unipept for Seamless End-to-End Metaproteomics Data Analysis

Although metaproteomics, the study of the collective proteome of microbial communities, has become increasingly powerful and popular over the past few years, the field has lagged behind on the availability of user-friendly, end-to-end pipelines for data analysis. We therefore describe the connection from two commonly used metaproteomics data processing tools in the field, MetaProteomeAnalyzer and PeptideShaker, to Unipept for downstream analysis. Through these connections, direct end-to-end pipelines are built from database searching to taxonomic and functional annotation

Peat substrate amended with chitin modulates the N-cycle, siderophore and chitinase responses in the lettuce rhizobiome

Chitin is a valuable peat substrate amendment by increasing lettuce growth and reducing the survival of the zoonotic pathogen Salmonella enterica on lettuce leaves. The production of chitin-catabolic enzymes (chitinases) play a crucial role and are mediated through the microbial community. A higher abundance of plant-growth promoting microorganisms and genera involved in N and chitin metabolism are present in a chitin-enriched substrate. In this study, we hypothesize that chitin addition to peat substrate stimulates the microbial chitinase production. The degradation of chitin leads to nutrient release and the production of small chitin oligomers that are related to plant growth promotion and activation of the plant's defense response. First a shotgun metagenomics approach was used to decipher the potential rhizosphere microbial functions then the nutritional content of the peat substrate was measured. Our results show that chitin addition increases chitin-catabolic enzymes, bacterial ammonium oxidizing and siderophore genes. Lettuce growth promotion can be explained by a cascade degradation of chitin to N-acetylglucosamine and eventually ammonium. The occurrence of increased ammonium oxidizing bacteria, Nitrosospira, and amoA genes results in an elevated concentration of plant-available nitrate. In addition, the increase in chitinase and siderophore genes may have stimulated the plant's systemic resistance

Risk analysis for inland vessels in estuary service

At present, less than 2 % of the hinterland traffic to the harbour of Zeebrugge is carried by inland navigation, due to the insufficient capacity of inland waterway connections. An alternative could be offered by estuary vessels, i.e. inland vessels strengthened and equipped for safe operation between the Belgian coastal harbours and the West Scheldt in favourable weather and wave conditions. However, the window determined by the present regulations of the Belgian Shipping Inspectorate is too restrictive, traffic being impossible for 60 days a year on average.Accordingly, the Belgian federal authorities have recently prepared new regulations, based on probabilistic design procedures, including a risk analysis with respect to criteria which take due account of the limitations inherent to the design of inland vessels.Measures have been proposed by the Flemish authorities to stimulate the operation of estuary inland vessels for container transport from and to the coastal harbours, implying financial support for construction and exploitation