Microbiota and Microsatellite genotypes of Pacific oysters stemming from three oyster bed in the Northern Wadden Sea

Background: Studies of oyster microbiomes have revealed that a limited number of microbes, including pathogens, can dominate microbial communities in host tissues such as gills and gut. Much of the bacterial diversity however remains underexplored and unexplained, although environmental conditions and host genetics have been implicated. We used 454 next generation 16S rRNA amplicon sequencing of individually tagged PCR reactions to explore the diversity of bacterial communities in gill tissue of the invasive Pacific oyster Crassostrea gigas stemming from genetically differentiated beds under ambient outdoor conditions and after a multifaceted disturbance treatment imposing stress on the host. Results: While the gill associated microbial communities in oysters were dominated by few abundant taxa (i.e. Sphingomonas, Mycoplasma) the distribution of rare bacterial groups correlated to relatedness between the hosts under ambient conditions. Exposing the host to disturbance broke apart this relationship by removing rare phylotypes thereby reducing overall microbial diversity. Shifts in the microbiome composition in response to stress did not result in a net increase in genera known to contain potentially pathogenic strains. Conclusion: The decrease in microbial diversity and the disassociation between population genetic structure of the hosts and their associated microbiome suggest that disturbance (i.e. stress) may play a significant role for the assembly of the natural microbiome. Such community shifts may in turn also feed back on the course of disease and the occurrence of mass mortality events in oyster populations.

Biomass and substrate utilization of cold adapted bacteria in Fram Strait and the Western Greenlad Sea

During the 'Polarstern' expedition ARK-IV/2 in June 1987, water samples from 8 stations were taken to study biomass and substrate utilization of cold adapted bacteria. Bacterial biomasses determined from acridine orange direct counts (AODC) were between 0.4 and 31.4 µ/g C/l, and ATP concentrations amounted from <0.1 to 40 ng/l. Colony counts on seawater agar reached only 0.1% of AODC, but with the MPN-method 1 to 10% of AODC were recorded. With 14C-glutamic acid or 14C-glucose as tracer substrate in oligotrophic broth containing 0.5 mg trypticase and 0.05 mg yeast extract per liter of seawater, obligately oligotrophic bacteria could be detected in one water sample. Although incubation was at 2 °C, only psychrotrophic bacteria showing growth temperatures between 1 and 30 °C were obtained. Organic substrate utilizations by 106 isolates were tested at 4 and 20 °C. Most carbohydrates, organic acids, alcohols, and alanine were assimilated at both temperatures, but arginine, aspartate and ornithine were utilized only at 20 °C by almost all strains.

Biogeochemistry and microbiology of groundwater during acetate and bicarbonate amendment to an alluvial aquifer

These data are from a field experiment conducted in a shallow alluvial aquifer along the Colorado River in Rifle, Colorado, USA. In this experiment, bicarbonate-promoted uranium desorption and acetate amendment were combined and compared to an acetate amendment-only experiment in the same experimental plot. Data include names and location data for boreholes, geochemical data for all the boreholes between June 1, 2010 and January 1, 2011, microarray data provided as signal to noise ratio (SNR) for individual microarray probes, microarray data provided as signal to noise ratio (SNR) by Genus.

Prokaryotic growth and presence of metabolic products and contamination tracers in rocks samples from ODP Leg 187 sites

The microbial population in samples of basalt drilled from the north of the Australian Antarctic Discordance (AAD) during Ocean Drilling Program Leg 187 were studied using deoxyribonucleic acid (DNA)-based methods and culturing techniques. The results showed the presence of a microbial population characteristic for the basalt environment. DNA sequence analysis revealed that microbes grouping within the Actinobacteria, green nonsulfur bacteria, the Cytophaga/Flavobacterium/Bacteroides (CFB) group, the Bacillus/Clostridium group, and the beta and gamma subclasses of the Proteobacteria were present in the basalt samples collected. The most dominant phylogenetic group, both in terms of the number of sequences retrieved and the intensities of the DNA bands obtained with the denaturing gradient gel electrophoresis analysis, was the gamma Proteobacteria. Enrichment cultures showed phylogenetic affiliation with the Actinobacteria, the CFB group, the Bacillus/Clostridium group, and the alpha, beta, gamma, and epsilon subclasses of the Proteobacteria. Comparison of native and enriched samples showed that few of the microbes found in native basalt samples grew in the enrichment cultures. Only seven clusters, two clusters within each of the CFB and Bacillus/Clostridium groups and five clusters within the gamma Proteobacteria, contained sequences from both native and enriched basalt samples with significant similarity. Results from cultivation experiments showed the presence of the physiological groups of iron reducers and methane producers. The presence of the iron/manganese-reducing bacterium Shewanella was confirmed with DNA analysis. The results indicate that iron reducers and lithotrophic methanogenic Archaea are indigenous to the ocean crust basalt and that the methanogenic Archaea may be important primary producers in this basaltic environment.

Oligotrophic bacteria from the Antarctic Ocean

From enrichment cultures in dialysis chambers held in natural seawater tanks, 104 strains were isolated and kept in culture. All strains proved to be Gram-negative and psychrotrophic, having optimum growth temperatures of between 20 and 24 °C. Maximal growth temperatures were 30 to 37 °C, or even higher. With 55 isolates, substrate utilizations in Biolog MicroPlates were determined, and the obtained metabolic fingerprints used for clustering. Five groups could be distinguished at the 80% similarity level. Fifteen strains belonged to cluster 1, seven strains to cluster 2, and each of the clusters 3 and 4 contained nine strains. Cluster 5 can be divided into subcluster 5a and 5b, with 6 strains showing a few substrates metabolized, and 9 strains without any reactions, or weak reactions for one or two substrates, respectively. Each cluster could be characterized by specific metabolic fingerprints. Strains from cluster 1 metabolized N-acetyl-D-glucosamine, alpha-hydroxybutyric acid and gamma-hydroxybutyric acid, strains from cluster 2 citric acid, formic acid, thymidine and putrescine, strains from cluster 3 glycyl-L-aspartic acid, glycyl-L-glutamic acid, L-threonine and inosine, whereas strains from cluster 4 metabolized alpha-cyclodextrin and N-acetyl-D-galactosamine, typically. Methylamine was not utilized by the isolates, but strains from cluster 1, 2 and 3 could grow on basal seawater agar. Morphological characteristics and photomicrographs of the oligotrophic strains are presented. Due to their typical morphologies and ampicillin resistence, the nine strains from cluster 3 can be regarded as new species of the genus Planctomyces. These bacteria have not been cultivated before.