Evidence for Seismogenic Hydrogen Gas, a Potential Microbial Energy Source on Earth and Mars

M thanks the STFC for a PhD studentship and the NASA Astrobiology Institute for additional funding (NNAI13AA90A; Foundations of Complex Life, Evolution, Preservation and Detection on Earth and Beyond). Alison Wright, Roger Gibson and Edward Lynch are thanked for contributing samples. We thank three anonymous reviewers for their insightful comments.Peer reviewedPostprin

Performance of polycarbonate, cellulose nitrate and polyethersulfone filtering membranes for culture-independent microbiota analysis of clean waters

Demineralized and disinfected waters may have very low microbial loads, requiring that large volumes of water are filtered to recover enough biomass for further analysis. Extended filtration periods, often interrupted by clogging, are a major limiting factor to concentrate samples' microbiota for further examination, besides hindering the work pace. In this study, we investigated the performance of three types of filtering membranes - polycarbonate (PC), cellulose nitrate (CN), and polyethersulfone (PES) with 0.22 μm pore size for culture-independent microbiological analysis (quantitative PCR of seven housekeeping and integrase genes) of tap water, recirculating tap water in a bottle washing loop, and of demineralized water. Compared to PC membranes, CN or PES required lower filtration periods, although had slightly lower DNA extraction yields. However, genes abundance per volume of water was, in general, not significantly different. The exception was observed for bottle washing water in which PC membranes supported significantly higher quantification values than PES membranes. These differences were lower than ∼0.5 log-units and did not hamper the distinction of the types of water based on genes profile. Also, the type of membrane did not significantly affect the profile of the bacterial community determined for tap and demineralized water. A major conclusion is that CN membranes, cheaper, allowing shorter filtration periods, and producing results that are not significantly different from those obtained with PC or PES, can be a good alternative to analyze waters with low biomass loads.info:eu-repo/semantics/publishedVersio

Experimental antibiotic treatment identifies potential pathogens of white band disease in the endangered Caribbean coral Acropora cervicornis

Coral diseases have been increasingly reported over the past few decades and are a major contributor to coral decline worldwide. The Caribbean, in particular, has been noted as a hotspot for coral disease, and the aptly named white syndromes have caused the decline of the dominant reef building corals throughout their range. White band disease (WBD) has been implicated in the dramatic loss of Acropora cervicornis and Acropora palmata since the 1970s, resulting in both species being listed as critically endangered on the International Union for Conservation of Nature Red list. The causal agent of WBD remains unknown, although recent studies based on challenge experiments with filtrate from infected hosts concluded that the disease is probably caused by bacteria. Here, we report an experiment using four different antibiotic treatments, targeting different members of the disease-associated microbial community. Two antibiotics, ampicillin and paromomycin, arrested the disease completely, and by comparing with community shifts brought about by treatments that did not arrest the disease, we have identified the likely candidate causal agent or agents of WBD. Our interpretation of the experimental treatments is that one or a combination of up to three specific bacterial types, detected consistently in diseased corals but not detectable in healthy corals, are likely causal agents of WBD. In addition, a histophagous ciliate (Philaster lucinda) identical to that found consistently in association with white syndrome in Indo-Pacific acroporas was also consistently detected in allWBDsamples and absent in healthy coral. Treatment with metronidazole reduced it to below detection limits, but did not arrest the disease. However, the microscopic disease signs changed, suggesting a secondary role in disease causation for this ciliate. In future studies to identify a causal agent ofWBDvia tests of Henle–Koch’s postulates, it will be vital to experimentally control for populations of the other potential pathogens identified in this study

Assessment of the microbial communities associated with white syndrome and brown jelly syndrome in aquarium corals

Bacterial and ciliate assemblages associated with aquarium corals displaying white syndrome (WS) and brown jelly syndrome (BJS) were investigated. Healthy (n = 10) and diseased corals (WS n = 18; BJS n = 3) were analysed for 16S rRNA gene bacterial diversity, total bacterial abundance and vibrio-specific 16S rRNA gene abundance. This was conducted alongside analysis of 18S rRNA gene sequenc-ing targeting ciliates, a group of organisms largely overlooked for their potential as causal agents of coral disease. Despite significant differences between healthy and diseased corals in their 16S rRNA gene bacterial diversity, total bacterial abundance and vibrio-specific rRNA gene abundance, no domi-nant bacterial ribotypes were found consistently within the diseased samples. In contrast, one ciliate morphotype, named Morph 3 in this study (GenBank Accession Numbers JF831358 for the ciliate isolated from WS and JF831359 for the ciliate isolated from BJS) was observed to burrow into and underneath the coral tissues at the disease lesion in both disease types and contained algal endosym-bionts indicative of coral tissue ingestion. This ciliate was observed in larger numbers in BJS compared to WS, giving rise to the characteristic jelly like substance in BJS. Morph 3 varied by only 1 bp over 549 bp from the recently described Morph 1 ciliate (GenBank Accession No. JN626268), which has been shown to be present in field samples of WS and Brown Band Disease (BrB) in the Indo-Pacific. This result indicates a close relationship between these aquarium diseases and those observed in the wild

Bacterial lineages putatively associated with the dissemination of antibiotic resistance genes in a full-scale urban wastewater treatment plant

Urban wastewater treatment plants (UWTPs) are reservoirs of antibiotic resistance. Wastewater treatment changes the bacterial community and inevitably impacts the fate of antibiotic resistant bacteria and antibiotic resistance genes (ARGs). Some bacterial groups are major carriers of ARGs and hence, their elimination during wastewater treatment may contribute to increasing resistance removal efficiency. This study, conducted at a full-scale UWTP, evaluated variations in the bacterial community and ARGs loads and explored possible associations among them. With that aim, the bacterial community composition (16S rRNA gene Illumina sequencing) and ARGs abundance (real-time PCR) were characterized in samples of raw wastewater (RWW), secondary effluent (sTWW), after UV disinfection (tTWW), and after a period of 3 days storage to monitoring possible bacterial regrowth (tTWW-RE). Culturable enterobacteria were also enumerated. Secondary treatment was associated with the most dramatic bacterial community variations and coincided with reductions of ~2 log-units in the ARGs abundance. In contrast, no significant changes in the bacterial community composition and ARGs abundance were observed after UV disinfection of sTWW. Nevertheless, after UV treatment, viability losses were indicated ~2 log-units reductions of culturable enterobacteria. The analysed ARGs (qnrS, blaCTX-M, blaOXA-A, blaTEM, blaSHV, sul1, sul2, and intI1) were strongly correlated with taxa more abundant in RWW than in the other types of water, and which associated with humans and animals, such as members of the families Campylobacteraceae, Comamonadaceae, Aeromonadaceae, Moraxellaceae and Bacteroidaceae. Further knowledge of the dynamics of the bacterial community during wastewater treatment and its relationship with ARGs variations may contribute with information useful for wastewater treatment optimization, aiming at a more effective resistance control.info:eu-repo/semantics/acceptedVersio

Habitat-based density models of pack-ice seal distribution in the southern Weddell Sea, Antarctica

Climate variability and changes in sea ice dynamics have caused several ice-obligate or krill-dependent populations of marine predators to decline, eliciting concern about their demographic persistence and the indirect ecological consequences that predator depletions may have on marine ecosystems. Pack-ice seals are dominant ice-obligate predators in the Antarctic marine ecosystem, but there is considerable uncertainty about their abundance and population trends. We modelled the density and distribution of pack-ice seals as a function of environmental covariates in the southern Weddell Sea, Antarctica. Our density surface modelling approach used data from aerial surveys of pack-ice seals collected in the 2013/14 austral summer. Crabeater seals Lobo don carcinophaga, the most numerous pack-ice seal we observed, occurred at the highest densities in areas with extensive sea ice near the continental shelf break, but were almost absent in areas of similar sea ice concentration in the southern extent of the Weddell Sea. The highest densities of Weddell seals Leptonychotes weddelli, which were less abundant than crabeater seals within the pack-ice habitat, were predicted to occur over the continental shelf, near the shelf break. The distribution of both seal species broadly corresponded with the distribution and relative abundance of their main prey (Antarctic krill Euphausia superba and Antarctic silverfish Pleuragramma antarctica) obtained from concurrent ecosystem surveys. Ross seals Ommatophoca rossii and leopard seals Hydrurga leptonyx were not detected at all and are apparently rare within the southern Weddell Sea. These results can contribute to biodiversity assessments in the context of marine protected area planning in this region of the Southern Ocean

Comparison of culture- and quantitative PCR-Based indicators of antibiotic resistance in wastewater, recycled water, and tap water

Standardized methods are needed to support monitoring of antibiotic resistance in environmental samples. Culture-based methods target species of human-health relevance, while the direct quantification of antibiotic resistance genes (ARGs) measures the antibiotic resistance potential in the microbial community. This study compared measurements of tetracycline-, sulphonamide-, and cefotaxime-resistant presumptive total and fecal coliforms and presumptive enterococci versus a suite of ARGs quantified by quantitative polymerase chain reaction (qPCR) across waste-, recycled-, tap-, and freshwater. Cross-laboratory comparison of results involved measurements on samples collected and analysed in the US and Portugal. The same DNA extracts analysed in the US and Portugal produced comparable qPCR results (variation <28%), except for blaOXA-1 gene (0%–57%). Presumptive total and fecal coliforms and cefotaxime-resistant total coliforms strongly correlated with blaCTX-M and intI1 (0.725 ≤ R2 ≤ 0.762; p < 0.0001). Further, presumptive total and fecal coliforms correlated with the Escherichia coli-specific biomarkers, gadAB, and uidA, suggesting that both methods captured fecal-sourced bacteria. The genes encoding resistance to sulphonamides (sul1 and sul2) were the most abundant, followed by genes encoding resistance to tetracyclines (tet(A) and tet(O)) and β-lactams (blaOXA-1 and, blaCTX-M), which was in agreement with the culture-based enumerations. The findings can help inform future application of methods being considered for international antibiotic resistance surveillance in the environment.info:eu-repo/semantics/publishedVersio

Cell-based internal standard for qPCR determinations of antibiotic resistance indicators in environmental water samples

Quantitative PCR (qPCR) has been used to quantify antibiotic resistance genes (ARGs) in water, wastewater, soil, sediment and tissue samples. Concerns regarding the comparability of data obtained in different laboratories has been a major bottleneck to incentivize the compilation of publicly available of ARGs quantifications gathered from different reports. In this study, the influence of the DNA extraction kits (NZY Tissue gDNA Isolation kit or DNeasy PowerWater kit) and of the operator on the DNA extraction yield and on qPCR genes quantification was assessed. Since in wastewater and water samples the matrix effect can affect the DNA recovery and, therefore, gene quantification, an internal standard, consisting in a cloned gene not found in environmental samples, was tested. The aim was to assess how qPCR determinations in wastewater and water samples can be affected by the matrix effect. The results show that the DNA extraction operator did not significantly influence DNA yield. The use of distinct kits resulted in qPCR gene quantifications that did not differ in more than 1 log-unit mL−1. The matrix effect, assessed based on the use of an internal standard, was associated with an underestimation that ranged 0.1–0.9 log gene copy number mL−1 of sample, irrespective of the water type. The reliability on the use of a DNA extraction kit that costs about 3 times less than the most commonly used can be an incentive for the use of DNA based analyses of ARGs in environmental waters. Moreover, the fact that both the DNA extraction operator and the reduced matrix effect have little influence on the final results, are good news, encouraging the compilation of data produced in distinct laboratories. Nevertheless, harmonization efforts are still necessary to minimize bias that may be due associated with other conditions, such as equipment.info:eu-repo/semantics/publishedVersio

Reproductive Ecology of Dragonfishes (Stomiiformes: Stomiidae) in the Gulf of Mexico

The most abundant fishes on Earth live in the meso- and bathypelagic (deep-pelagic, collectively) zones of the open ocean, where they play a key role in deep-sea food webs by mediating energy flow from surface waters to great depth. Of these fishes, the most speciose taxon is the family Stomiidae (dragonfishes). Despite being the numerically dominant predators of the global mesopelagic zone, stomiid reproductive ecology is poorly known. Research surveys rarely catch larger adults, impeding reproductive ecology studies. Between 2010 and 2011, the Offshore Nekton Sampling and Analysis Program sampled the Gulf of Mexico using a research-sized, opening/closing trawl (10-m2 MOCNESS) and a commercial-sized, high-speed rope trawl (HSRT). Size-distribution analysis by gear type revealed: the HSRT caught more specimens per species, and the HSRT caught significantly larger specimens, whereas the MOCNESS sampled more juveniles. Gonads were dissected from 714 individuals representing 47 species, and the 12 dominant species were analyzed in further detail. Gonadal histology assessment indicated that stomiids are gonochoristic and exhibit asynchronous oocyte development and batch spawning. A total of 11 of the 12 species had sex ratios that did not significantly differ from a 1:1 (male:female) ratio (P \u3c 0.05). Histological analysis indicated that females mature at larger sizes than males. Given the lack of age and growth data for this family, these data are critical for estimating stomiid production rates, a key element for quantifying the role of stomiids in the transfer of organic matter within the deep-pelagic zone, the planet\u27s largest cumulative ecosystem

Fecundity and early life of the deep-water jellyfish Periphylla periphylla

Comparisons over 6 years of three Norwegian fjord populations of the deep-water scyphomedusa Periphylla periphylla are presented. A minor part of the population in Lurefjord is migrating to the surface during night, which benefits mating encounters by increasing abundance per unit volume and decreasing the distance between individuals. Simulations using a typical water-column density profile and Stoke’s law show that fertilized eggs released in the surface quickly reach a depth where light is insufficient for visual predators. Consequently, the distribution of the smallest juveniles was strongly skewed towards higher depths in all three fjords studied. Mature females in Sognefjord were 4–5 times less abundant than in Lurefjord and Halsafjord, but due to a larger size and strong exponential relationship between size and number of mature oocytes, the potential recruitment rate as recruits m−2 year−1 was not much different from the other two fjords. Nevertheless, the observed number of small (<1 cm) juveniles was 18–31 times higher in Sognefjord than in the other two fjords, and it is assumed that the deeper habitat (up to 1300 m) compared to the other fjords (up to 440 and 530 m) is a superior habitat for the early development of P. periphylla.publishedVersio