A multi-study analysis of gut microbiome data from the blue mussel (Mytilus edulis) emphasises the impact of depuration on biological interpretation

The blue mussel (Mytilus edulis) is a suspension feeder which has been used in gut-microbiome surveys. Although raw 16S sequence data are often publicly available, unifying secondary analyses are lacking. The present work analysed raw data from seven projects conducted by one group over 7 years. Although each project had different motivations, experimental designs and conclusions, all selected samples were from the guts of M. edulis collected from a single location in Long Island Sound. The goal of this analysis was to determine which independent factors (e.g., collection date, depuration status) were responsible for governing composition and diversity in the gut microbiomes. Results indicated that whether mussels had undergone depuration, defined here as voidance of faeces in a controlled, no-food period, was the primary factor that governed gut microbiome composition. Gut microbiomes from non-depurated mussels were mixtures of resident and transient communities and were influenced by temporal factors. Resident communities from depurated mussels were influenced by the final food source and length of time host mussels were held under laboratory conditions. These findings reinforce the paradigm that gut microbiota are divided into resident and transient components and suggest that depuration status should be taken into consideration when designing and interpreting future experiments.     

Effect of verapamil and sulfhydryl reagents on calcium transport in bovine spermatozoa

Calcium uptake by intact bovine epididymal spermatozoa is not affected by low concentrations (up to 0.75 mM) of the calcium transport blocker verapamil. Under these conditions, calcium transport into sperm mitochondria is highly inhibited. At higher verapamil concentrations (1.0, 1.5 mM), calcium transport into intact sperm is also inhibited, and this inhibition cannot be relieved by disrupting the plasma membrane with filipin. Calcium uptake into intact sperm is highly inhibited by mersalyl and this inhibitory effect can be completely relieved when the plasma membrane is disrupted by filipin. This effect of mersalyl is not dependent on the presence of phosphate in the incubation medium. Phosphate itself, up to 2 mM, enhances calcium uptake into the cells; this effect decreases at higher concentrations and is depressed 57% at 10 mM phosphate. This inhibitory effect of high phosphate concentration can be blocked by mersalyl. It is suggested that the calcium carrier itself and not a phosphate carrier of the plasma membrane is inhibited by mersalyl. It is possible that there is a symporter for calcium and phosphate in the plasma membrane of bovine spermatozoa.     

Genomic analysis of multiple Roseophage SIO1 strains

Roseophage SIO1 is a lytic marine phage that infects Roseobacter SIO67, a member of the Roseobacter clade of near-shore alphaproteobacteria. Roseophage SIO1 was first isolated in 1989 and sequenced in 2000. We have re-sequenced and re-annotated the original isolate. Our current annotation could only assign functions to seven additional open reading frames, indicating that, despite the advances in bioinformatics tools and increased genomic resources, we are still far from being able to translate phage genomic sequences into biological functions. In 2001, we isolated four new strains of Roseophage SIO1 from California near-shore locations. The genomes of all four were sequenced and compared against the original Roseophage SIO1 isolated in 1989. A high degree of conservation was evident across all five genomes; comparisons at the nucleotide level yielded an average 97% identity. The observed differences were clustered in protein-encoding regions and were mostly synonymous. The one strain that was found to possess an expanded host range also showed notable changes in putative tail protein-coding regions. Despite the possibly rapid evolution of phage and the mostly uncharacterized diversity found in viral metagenomic data sets, these findings indicate that viral genomes such as the genome of SIO1-like Roseophages can be stably maintained over ecologically significant time and distance (i.e. over a decade and ∼50 km).