The Common Oceanographer: Crowdsourcing the Collection of Oceanographic Data

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Sulfate-dependant microbially induced corrosion of mild steel in the deep sea: a 10-year microbiome study.

BACKGROUND: Metal corrosion in seawater has been extensively studied in surface and shallow waters. However, infrastructure is increasingly being installed in deep-sea environments, where extremes of temperature, salinity, and high hydrostatic pressure increase the costs and logistical challenges associated with monitoring corrosion. Moreover, there is currently only a rudimentary understanding of the role of microbially induced corrosion, which has rarely been studied in the deep-sea. We report here an integrative study of the biofilms growing on the surface of corroding mooring chain links that had been deployed for 10 years at ~2 km depth and developed a model of microbially induced corrosion based on flux-balance analysis. METHODS: We used optical emission spectrometry to analyze the chemical composition of the mooring chain and energy-dispersive X-ray spectrometry coupled with scanning electron microscopy to identify corrosion products and ultrastructural features. The taxonomic structure of the microbiome was determined using shotgun metagenomics and was confirmed by 16S amplicon analysis and quantitative PCR of the dsrB gene. The functional capacity was further analyzed by generating binned, genomic assemblies and performing flux-balance analysis on the metabolism of the dominant taxa. RESULTS: The surface of the chain links showed intensive and localized corrosion with structural features typical of microbially induced corrosion. The microbiome on the links differed considerably from that of the surrounding sediment, suggesting selection for specific metal-corroding biofilms dominated by sulfur-cycling bacteria. The core metabolism of the microbiome was reconstructed to generate a mechanistic model that combines biotic and abiotic corrosion. Based on this metabolic model, we propose that sulfate reduction and sulfur disproportionation might play key roles in deep-sea corrosion. CONCLUSIONS: The corrosion rate observed was higher than what could be expected from abiotic corrosion mechanisms under these environmental conditions. High corrosion rate and the form of corrosion (deep pitting) suggest that the corrosion of the chain links was driven by both abiotic and biotic processes. We posit that the corrosion is driven by deep-sea sulfur-cycling microorganisms which may gain energy by accelerating the reaction between metallic iron and elemental sulfur. The results of this field study provide important new insights on the ecophysiology of the corrosion process in the deep sea

Draft genome sequence of Enterobacter sp. strain EA-1, an electrochemically active microorganism isolated from tropical sediment

© 2018 Doyle et al. Enterobacter sp. strain EA-1 is an electrochemically active bacterium isolated from tropical sediment in Singapore. Here, the annotated draft genome assembly of the bacterium is reported. Whole-genome comparison indicates that Enterobacter sp. EA-1, along with a previously sequenced Enterobacter isolate from East Asia, forms a distinct clade within the Enterobacter genus

Reconnection surgery in adult post-operative short bowel syndrome < 100 cm: is colonic continuity sufficient to achieve enteral autonomy without autologous gastrointestinal reconstruction? Report from a single center and systematic review of literature

A systematic bibliographic research concerning patients operated on for SBS was performed: inclusion criteria were adult age, reconnection surgery and SBS &lt; 100 cm. Autologous gastrointestinal reconstruction represented an exclusion criteria. The outcomes of interest were the rate of total parenteral nutrition (TPN) independence and the length of follow-up (minimum 1 year) after surgery. We reviewed our experience from 2003 to 2013 with minimum 1-year follow-up, dealing with reconnection surgery in 13 adults affected by &lt; 100 cm SBS after massive small bowel resection: autologous gastrointestinal reconstruction was not feasible. Three (out of 5168 screened papers) non randomized controlled trials with 116 adult patients were analysed showing weaning from TPN (40%, 50% and 90% respectively) after reconnection surgery without autologous gastrointestinal reconstruction. Among our 13 adults, mean age was 54.1 years (53.8 % ASA III): 69.2 % had a high stomal output (&gt; 500 cc/day) and TPN dependence was 100%. We performed a jejuno-colonic anastomosis (SBS type II) in 53.8%, in 46.1% of cases without ileo-cecal valve, leaving a mean residual small bowel length of 75.7 cm. In-hospital mortality was 0%. After a minimum period of 1 year of intestinal rehabilitation, all our patients (100%) went back to oral intake and 69.2% were off TPN (9 patients). No one was listed for transplantation. A residual small bowel length of minimum 75 cm, even if reconnected to part of the colon, seems able to produce a TPN independence without autologous gastrointestinal reconstruction after a minimum period of 1 year of intestinal rehabilitation

Photobacterium profundum under Pressure:A MS-Based Label-Free Quantitative Proteomics Study

Photobacterium profundum SS9 is a Gram-negative bacterium, originally collected from the Sulu Sea. Its genome consists of two chromosomes and a 80 kb plasmid. Although it can grow under a wide range of pressures, P. profundum grows optimally at 28 MPa and 15°C. Its ability to grow at atmospheric pressure allows for both easy genetic manipulation and culture, making it a model organism to study piezophily. Here, we report a shotgun proteomic analysis of P. profundum grown at atmospheric compared to high pressure using label-free quantitation and mass spectrometry analysis. We have identified differentially expressed proteins involved in high pressure adaptation, which have been previously reported using other methods. Proteins involved in key metabolic pathways were also identified as being differentially expressed. Proteins involved in the glycolysis/gluconeogenesis pathway were up-regulated at high pressure. Conversely, several proteins involved in the oxidative phosphorylation pathway were up-regulated at atmospheric pressure. Some of the proteins that were differentially identified are regulated directly in response to the physical impact of pressure. The expression of some proteins involved in nutrient transport or assimilation, are likely to be directly regulated by pressure. In a natural environment, different hydrostatic pressures represent distinct ecosystems with their own particular nutrient limitations and abundances. However, the only variable considered in this study was atmospheric pressure

The changing form of Antarctic biodiversity

Antarctic biodiversity is much more extensive, ecologically diverse and biogeographically structured than previously thought. Understanding of how this diversity is distributed in marine and terrestrial systems, the mechanisms underlying its spatial variation, and the significance of the microbiota is growing rapidly. Broadly recognizable drivers of diversity variation include energy availability and historical refugia. The impacts of local human activities and global environmental change nonetheless pose challenges to the current and future understanding of Antarctic biodiversity. Life in the Antarctic and the Southern Ocean is surprisingly rich, and as much at risk from environmental change as it is elsewher

Adhesion Molecules Associated with Female Genital Tract Infection

Altres ajuts: Marie Curie Career Integration Grant i una beca Fundació Dexeus Salut de la DonaEfforts to develop vaccines that can elicit mucosal immune responses in the female genital tract against sexually transmitted infections have been hampered by an inability to measure immune responses in these tissues. The differential expression of adhesion molecules is known to confer site-dependent homing of circulating effector T cells to mucosal tissues. Specific homing molecules have been defined that can be measured in blood as surrogate markers of local immunity (e.g. α4β7 for gut). Here we analyzed the expression pattern of adhesion molecules by circulating effector T cells following mucosal infection of the female genital tract in mice and during a symptomatic episode of vaginosis in women. While CCR2, CCR5, CXCR6 and CD11c were preferentially expressed in a mouse model of Chlamydia infection, only CCR5 and CD11c were clearly expressed by effector T cells during bacterial vaginosis in women. Other homing molecules previously suggested as required for homing to the genital mucosa such as α4β1 and α4β7 were also differentially expressed in these patients. However, CD11c expression, an integrin chain rarely analyzed in the context of T cell immunity, was the most consistently elevated in all activated effector CD8+ T cell subsets analyzed. This molecule was also induced after systemic infection in mice, suggesting that CD11c is not exclusive of genital tract infection. Still, its increase in response to genital tract disorders may represent a novel surrogate marker of mucosal immunity in women, and warrants further exploration for diagnostic and therapeutic purposes

Metagenomics Reveals the Influence of Land Use and Rain on the Benthic Microbial Communities in a Tropical Urban Waterway

Growing demands for potable water have led to extensive reliance on waterways in tropical megacities. Attempts to manage these waterways in an environmentally sustainable way generally lack an understanding of microbial processes and how they are influenced by urban factors, such as land use and rain. Here, we describe the composition and functional potential of benthic microbial communities from an urban waterway network and analyze the effects of land use and rain perturbations on these communities. With a sequence depth of 3 billion reads from 48 samples, these metagenomes represent nearly full coverage of microbial communities. The predominant taxa in these waterways were Nitrospira and Coleofasciculus, indicating the presence of nitrogen and carbon fixation in this system. Gene functions from carbohydrate, protein, and nucleic acid metabolism suggest the presence of primary and secondary productivity in such nutrient-deficient systems. Comparison of microbial communities by land use type and rain showed that while there are significant differences in microbial communities in land use, differences due to rain perturbations were rain event specific. The more diverse microbial communities in the residential areas featured a higher abundance of reads assigned to genes related to community competition. However, the less diverse communities from industrial areas showed a higher abundance of reads assigned to specialized functions such as organic remediation. Finally, our study demonstrates that microbially diverse populations in well-managed waterways, where contaminant levels are within defined limits, are comparable to those in other relatively undisturbed freshwater systems

Environmental DNA signatures distinguish between tsunami and storm deposition in overwash sand

AbstractSandy onshore deposits from tsunamis are difficult to distinguish from storm deposits, which makes it difficult to assess coastal hazards from the geological record. Here we analyse environmental DNA from microbial communities preserved in known tsunami and storm-deposited sediments and intercalating soils and non-marine sediments near Cuddalore, India, and Phra Thong Island, Thailand. Both sites were impacted by the 2004 Indian Ocean Tsunami and a subsequent storm flooding event (2011 Cyclone Thane at Cuddalore and a 2007 storm at Phra Thong Island). We show that the microbial communities in the overwash deposits are significantly different from soil and sediments that are not derived by overwash processes at both locations. Our method also successfully discriminates between modern tsunami deposits and storm deposits. We suggest molecular techniques have the potential to accurately discriminate overwash deposits from catastrophic natural events.</jats:p