The ocean sampling day consortium.

Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world's oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits.

A Laboratory of Extremophiles: Iceland Coordination Action for Research Activities on Life in Extreme Environments (CAREX) Field Campaign.

Existence of life in extreme environments has been known for a long time, and their habitants have been investigated by different scientific disciplines for decades. However, reports of multidisciplinary research are uncommon. In this paper, we report an interdisciplinary three-day field campaign conducted in the framework of the Coordination Action for Research Activities on Life in Extreme Environments (CAREX) FP7EU program, with participation of experts in the fields of life and earth sciences. In situ experiments and sampling were performed in a 20 m long hot springs system of different temperature (57 °C to 100 °C) and pH (2 to 4). Abiotic factors were measured to study their influence on the diversity. The CO2 and H2S concentration varied at different sampling locations in the system, but the SO2 remained the same. Four biofilms, mainly composed by four different algae and phototrophic protists, showed differences in photosynthetic activity. Varying temperature of the sampling location affects chlorophyll fluorescence, not only in the microbial mats, but plants (Juncus), indicating selective adaptation to the environmental conditions. Quantitative polymerase chain reaction (PCR), DNA microarray and denaturing gradient gel electrophoresis (DGGE)-based analysis in laboratory showed the presence of a diverse microbial population. Even a short duration (30 h) deployment of a micro colonizer in this hot spring system led to colonization of microorganisms based on ribosomal intergenic spacer (RISA) analysis. Polyphasic analysis of this hot spring system was possible due to the involvement of multidisciplinary approaches.

Microbial communities in the subglacial waters of the Vatnajökull ice cap, Iceland.

Subglacial lakes beneath the Vatnajökull ice cap in Iceland host endemic communities of microorganisms adapted to cold, dark and nutrient-poor waters, but the mechanisms by which these microbes disseminate under the ice and colonize these lakes are unknown. We present new data on this subglacial microbiome generated from samples of two subglacial lakes, a subglacial flood and a lake that was formerly subglacial but now partly exposed to the atmosphere. These data include parallel 16S rRNA gene amplicon libraries constructed using novel primers that span the v3-v5 and v4-v6 hypervariable regions. Archaea were not detected in either subglacial lake, and the communities are dominated by only five bacterial taxa. Our paired libraries are highly concordant for the most abundant taxa, but estimates of diversity (abundance-based coverage estimator) in the v4-v6 libraries are 3-8 times higher than in corresponding v3-v5 libraries. The dominant taxa are closely related to cultivated anaerobes and microaerobes, and may occupy unique metabolic niches in a chemoautolithotrophic ecosystem. The populations of the major taxa in the subglacial lakes are indistinguishable (>99% sequence identity), despite separation by 6 km and an ice divide; one taxon is ubiquitous in our Vatnajökull samples. We propose that the glacial bed is connected through an aquifer in the underlying permeable basalt, and these subglacial lakes are colonized from a deeper, subterranean microbiome.

Bacterial composition and succession during storage of North-Atlantic cod (Gadus morhua) at superchilled temperatures.

BACKGROUND: The bacteriology during storage of the North-Atlantic cod has been investigated for the past decades using conventional cultivation strategies which have generated large amount of information. This paper presents a study where both conventional cultivation and cultivation independent approaches were used to investigate the bacterial succession during storage of cod loins at chilled and superchilled temperatures. RESULTS: Unbrined (0.4% NaCl) and brined (2.5% NaCl) cod loins were stored at chilled (0 degrees C) and superchilled (-2 and -3.6 degrees C) temperatures in air or modified atmosphere (MA, % CO2/O2/N2: 49.0 +/- 0.6/7.4 +/- 0.2/43.7 +/- 0.4). Discrepancy was observed between cultivation enumeration and culture independent methods where the former showed a general dominance of Pseudomonas spp. (up to 59%) while the latter showed a dominance of Photobacterium phosphoreum (up to 100%).Gas chromatography-mass spectrophotometry (GC-MC) showed that trimethylamine was the most abundant volatile in mid- and late storage periods. Terminal restriction polymorphism (t-RFLP) analysis showed that the relative abundance of P. phosphoreum increased with storage time. CONCLUSION: The present study shows the bacteriological developments on lightly salted or non-salted cod loins during storage at superchilled temperatures. It furthermore confirms the importance of P. phosphoreum as a spoilage organism during storage of cod loins at low temperatures using molecular techniques. The methods used compensate each other, giving more detailed data on bacterial population developments during spoilage.

Rapid quantitative monitoring method for the fish spoilage bacteria Pseudomonas.

Pseudomonas spp. is a group of microorganisms commonly found in fish and other fresh foods and is involved in their spoilage process. The aim of this study was to develop a rapid and accurate quantitative assay for Pseudomonas spp. in fish using real-time PCR. The assay targets the carbamoyl phosphate synthase gene (carA) with SYBR green based real-time PCR. The selectivity of the assay was confirmed using 24 Pseudomonas strains and 55 non-pseudomonad strains. A linear quantification was established over seven orders of magnitude, from 40 - 4(7) copies reaction(-1). The assay was validated on cod samples collected during two shelf life trials and showed a high degree of correlation to the plate count method (rP = 0.891) where the difference between the methods was 0.04 log(10) CFU g(-1) on average. The study shows that it is possible to quantify accurately the specific spoilage organisms belonging to the genus Pseudomonas in fish using real-time PCR. The method takes less than 5 h from sampling to results. The short detection time of the method can provide the fish industry with an important tool for quality control and processing management.

Molecular cloning and functional expression of the first two specific insect myosuppressin receptors.

The Drosophila Genome Project database contains the sequences of two genes, CG8985 and CG13803, which are predicted to code for G protein-coupled receptors. We cloned the cDNAs corresponding to these genes and found that their gene structures had not been correctly annotated. We subsequently expressed the coding regions of the two corrected receptor genes in Chinese hamster ovary cells and found that each of them coded for a receptor that could be activated by low concentrations of Drosophila myosuppressin (EC50,4 x 10(-8) M). The insect myosuppressins are decapeptides that generally inhibit insect visceral muscles. Other tested Drosophila neuropeptides did not activate the two receptors. In addition to the two Drosophila myosuppressin receptors, we identified a sequence in the genomic database from the malaria mosquito Anopheles gambiae that also very likely codes for a myosuppressin receptor. To our knowledge, this paper is the first report on the molecular identification of specific insect myosuppressin receptors.

Molecular identification of the first insect proctolin receptor.

The website of the Drosophila Genome Project (www.flybase.org) contains the sequence of an annotated gene CG6986, which is predicted to code for a G protein-coupled receptor. We cloned the cDNA of this gene and expressed it in Chinese hamster ovary cells. Screening of a neuropeptide library revealed that the expressed receptor was specific for the neuropeptide proctolin (EC(50), 6x10(-10)M). Proctolin (RYLPT) was the first invertebrate neuropeptide to be fully sequenced (already in 1975) and occurs with identical structure in both crustaceans and insects, where it has myo- and neurostimulatory actions. Northern blots showed that the Drosophila proctolin receptor was only weakly expressed in embryos, larvae, pupae, and in the thoraces and abdomina of adult flies, but strongly in the heads of adult animals. The Drosophila receptor reported here is the first invertebrate proctolin receptor to be identified.