Shrimp and microplastics: A case study with the Atlantic ditch shrimp Palaemon varians

Many invertebrate species inhabit coastal areas where loads of plastic debris and microplastics are high. In the current case study, we exemplarily illustrate the principal processes taking place in the Atlantic ditch shrimp, Palaemon varians, upon ingestion of microplastics. In the laboratory, shrimp readily ingested fluorescent polystyrene microbeads of 0.1-9.9 µm, which could be tracked within the widely translucent body. Ingested food items as well as micro-particles cumulate in the stomach where they are macerated and mixed with digestive enzymes. Inside the stomach, ingested particles are segregated by size by a complex fine-meshed filter system. Liquids and some of the smallest particles (0.1 µm) pass the filter and enter the midgut gland where resorption of nutrients as well as synthesis and release of digestive enzymes take place. Large particles and most of the small particles are egested with the feces through the hindgut. Small particles, which enter the midgut gland, may interact with the epithelial cells and induce oxidative stress, as indicated by elevated activities of superoxide dismutase and cellular markers of reactive oxygen species. The shrimp indiscriminately ingest microparticles but possess efficient mechanisms to protect their organs from overloading with microplastics and other indigestible particles. These include an efficient sorting mechanism within the stomach and the protection of the midgut gland by the pyloric filter. Formation of detrimental radical oxygen species is counteracted by the induction of enzymatic antioxidants.

Discovery of novel community-relevant small proteins in a simplified human intestinal microbiome

BACKGROUND

The intestinal microbiota plays a crucial role in protecting the host from pathogenic microbes, modulating immunity and regulating metabolic processes. We studied the simplified human intestinal microbiota (SIHUMIx) consisting of eight bacterial species with a particular focus on the discovery of novel small proteins with less than 100 amino acids (= sProteins), some of which may contribute to shape the simplified human intestinal microbiota. Although sProteins carry out a wide range of important functions, they are still often missed in genome annotations, and little is known about their structure and function in individual microbes and especially in microbial communities.

RESULTS

We created a multi-species integrated proteogenomics search database (iPtgxDB) to enable a comprehensive identification of novel sProteins. Six of the eight SIHUMIx species, for which no complete genomes were available, were sequenced and de novo assembled. Several proteomics approaches including two earlier optimized sProtein enrichment strategies were applied to specifically increase the chances for novel sProtein discovery. The search of tandem mass spectrometry (MS/MS) data against the multi-species iPtgxDB enabled the identification of 31 novel sProteins, of which the expression of 30 was supported by metatranscriptomics data. Using synthetic peptides, we were able to validate the expression of 25 novel sProteins. The comparison of sProtein expression in each single strain versus a multi-species community cultivation showed that six of these sProteins were only identified in the SIHUMIx community indicating a potentially important role of sProteins in the organization of microbial communities. Two of these novel sProteins have a potential antimicrobial function. Metabolic modelling revealed that a third sProtein is located in a genomic region encoding several enzymes relevant for the community metabolism within SIHUMIx.

CONCLUSIONS

We outline an integrated experimental and bioinformatics workflow for the discovery of novel sProteins in a simplified intestinal model system that can be generically applied to other microbial communities. The further analysis of novel sProteins uniquely expressed in the SIHUMIx multi-species community is expected to enable new insights into the role of sProteins on the functionality of bacterial communities such as those of the human intestinal tract. Video abstract.

Environmentally Relevant Concentration of Bisphenol S Shows Slight Effects on SIHUMIx

Bisphenol S (BPS) is an industrial chemical used in the process of polymerization of polycarbonate plastics and epoxy resins and thus can be found in various plastic products and thermal papers. The microbiota disrupting effect of BPS on the community structure of the microbiome has already been reported, but little is known on how BPS affects bacterial activity and function. To analyze these effects, we cultivated the simplified human intestinal microbiota (SIHUMIx) in bioreactors at a concentration of 45 µM BPS. By determining biomass, growth of SIHUMIx was followed but no differences during BPS exposure were observed. To validate if the membrane composition was affected, fatty acid methyl esters (FAMEs) profiles were compared. Changes in the individual membrane fatty acid composition could not been described; however, the saturation level of the membranes slightly increased during BPS exposure. By applying targeted metabolomics to quantify short-chain fatty acids (SCFA), it was shown that the activity of SIHUMIx was unaffected. Metaproteomics revealed temporal effect on the community structure and function, showing that BPS has minor effects on the structure or functionality of SIHUMIx.