Characterization of per- and polyfluoroalkyl substances (PFAS) and other constituents in MSW landfill leachate from Puerto Rico.

Elevated per- and polyfluoroalkyl substance (PFAS) concentrations have been reported in municipal solid waste (MSW) landfill leachate with higher levels in wet and warmer subtropical climates. Information about landfill leachate characteristics is much more limited in tropical climates. In this study, 20 landfill leachate samples were collected from three MSW landfills on the tropical island of Puerto Rico and results were compared against landfills nationally and within Florida, USA. The samples collected in Puerto Rico underwent physical-chemical analysis, as well as a quantitative analysis of 92 PFAS. Samples described in this study include discrete leachate types, such as leachate, gas condensate, and leachate which has undergone on-site treatment (e.g., RO treatment, phytoremediation, lagoons). A total of 51 PFAS were detected above quantitation limits, including perfluorohexylphosphonic acid, a perfluoroalkyl acid (PFAA) which has not been reported previously in landfill leachate. ∑PFAS concentrations in this study (mean: 38,000 ng L-1), as well as concentrations of individual PFAS, are significantly higher than other reported MSW landfill leachate concentrations. The profiles of leachates collected from on-site treatment systems indicate possible transformation of precursor PFAS as a result of treatment processes - oxidizing conditions, for example, may facilitate aerobic transformation, increase the concentrations of PFAAs, and possibly increase the apparent ∑PFAS concentration. Extreme climate events, including rising temperatures and more frequent hurricanes, have placed additional strain on the solid waste management infrastructure on the island - adding complexity to an already challenging PFAS management issue. As concern grows over PFAS contamination in drinking water, these findings should inform solid waste and leachate management decisions in order to minimize PFAS emissions in island environments.

Detection of Shiga toxin-encoding genes in small community water supplies.

Shiga toxin (Stx), one of the most potent bacterial toxins known, can cause bloody diarrhea, hemolytic uremic syndrome, kidney failure and death. The aim of this pilot was to investigate the occurrence of Shiga toxin-encoding genes, stx (stx1 and stx2) from total coliform (TC) and E. coli positive samples from small community water systems. After aliquots for TC and E. coli analyses were removed, the remnant volume of the samples was enriched, following a protocol developed for this study. Fifty-two per cent of the samples tested by multiplex PCR were positive for the presence of the stx genes; this percentage was higher in raw water samples. The stx2 gene was more abundant. Testing larger volumes of the samples increase the sensitivity of our assay, providing an alternative protocol for the detection of Shiga toxin-producing E. coli (STEC) that might be missed by the TC assay. This study confirms the presence of Stx encoding genes in source and distributed water for all systems sampled and suggests STEC as a potential health risk in small systems.

Methane Dynamics in a Tropical Serpentinizing Environment: The Santa Elena Ophiolite, Costa Rica.

Uplifted ultramafic rocks represent an important vector for the transfer of carbon and reducing power from the deep subsurface into the biosphere and potentially support microbial life through serpentinization. This process has a strong influence upon the production of hydrogen and methane, which can be subsequently consumed by microbial communities. The Santa Elena Ophiolite (SEO) on the northwestern Pacific coast of Costa Rica comprises ~250 km2 of ultramafic rocks and mafic associations. The climatic conditions, consisting of strongly contrasting wet and dry seasons, make the SEO a unique hydrogeological setting, where water-rock reactions are enhanced by large storm events (up to 200 mm in a single storm). Previous work on hyperalkaline spring fluids collected within the SEO has identified the presence of microorganisms potentially involved in hydrogen, methane, and methanol oxidation (such as Hydrogenophaga, Methylobacterium, and Methylibium spp., respectively), as well as the presence of methanogenic Archaea (such as Methanobacterium). Similar organisms have also been documented at other serpentinizing sites, however their functions have not been confirmed. SEO's hyperalkaline springs have elevated methane concentrations, ranging from 145 to 900 µM, in comparison to the background concentrations (<0.3 µM). The presence and potential activity of microorganisms involved in methane cycling in serpentinization-influenced fluids from different sites within the SEO were investigated using molecular, geochemical, and modeling approaches. These results were combined to elucidate the bioenergetically favorable methane production and/or oxidation reactions in this tropical serpentinizing environment. The hyperalkaline springs at SEO contain a greater proportion of Archaea and methanogens than has been detected in any terrestrial serpentinizing system. Archaea involved in methanogenesis and anaerobic methane oxidation accounted from 40 to 90% of total archaeal sequences. Genes involved in methanogenic metabolisms were detected from the metagenome of one of the alkaline springs. Methanogenic activities are likely to be facilitated by the movement of nutrients, including dissolved inorganic carbon (DIC), from surface water and their infiltration into serpentinizing groundwater. These data provide new insight into methane cycle in tropical serpentinizing environments.

Diverse, rare microbial taxa responded to the Deepwater Horizon deep-sea hydrocarbon plume.

The Deepwater Horizon (DWH) oil well blowout generated an enormous plume of dispersed hydrocarbons that substantially altered the Gulf of Mexico's deep-sea microbial community. A significant enrichment of distinct microbial populations was observed, yet, little is known about the abundance and richness of specific microbial ecotypes involved in gas, oil and dispersant biodegradation in the wake of oil spills. Here, we document a previously unrecognized diversity of closely related taxa affiliating with Cycloclasticus, Colwellia and Oceanospirillaceae and describe their spatio-temporal distribution in the Gulf's deepwater, in close proximity to the discharge site and at increasing distance from it, before, during and after the discharge. A highly sensitive, computational method (oligotyping) applied to a data set generated from 454-tag pyrosequencing of bacterial 16S ribosomal RNA gene V4-V6 regions, enabled the detection of population dynamics at the sub-operational taxonomic unit level (0.2% sequence similarity). The biogeochemical signature of the deep-sea samples was assessed via total cell counts, concentrations of short-chain alkanes (C1-C5), nutrients, (colored) dissolved organic and inorganic carbon, as well as methane oxidation rates. Statistical analysis elucidated environmental factors that shaped ecologically relevant dynamics of oligotypes, which likely represent distinct ecotypes. Major hydrocarbon degraders, adapted to the slow-diffusive natural hydrocarbon seepage in the Gulf of Mexico, appeared unable to cope with the conditions encountered during the DWH spill or were outcompeted. In contrast, diverse, rare taxa increased rapidly in abundance, underscoring the importance of specialized sub-populations and potential ecotypes during massive deep-sea oil discharges and perhaps other large-scale perturbations.

Insights into environmental controls on microbial communities in a continental serpentinite aquifer using a microcosm-based approach.

Geochemical reactions associated with serpentinization alter the composition of dissolved organic compounds in circulating fluids and potentially liberate mantle-derived carbon and reducing power to support subsurface microbial communities. Previous studies have identified Betaproteobacteria from the order Burkholderiales and bacteria from the order Clostridiales as key components of the serpentinite-hosted microbiome, however there is limited knowledge of their metabolic capabilities or growth characteristics. In an effort to better characterize microbial communities, their metabolism, and factors limiting their activities, microcosm experiments were designed with fluids collected from several monitoring wells at the Coast Range Ophiolite Microbial Observatory (CROMO) in northern California during expeditions in March and August 2013. The incubations were initiated with a hydrogen atmosphere and a variety of carbon sources (carbon dioxide, methane, acetate, and formate), with and without the addition of nutrients and electron acceptors. Growth was monitored by direct microscopic counts; DNA yield and community composition was assessed at the end of the 3 month incubation. For the most part, results indicate that bacterial growth was favored by the addition of acetate and methane, and that the addition of nutrients and electron acceptors had no significant effect on microbial growth, suggesting no nutrient- or oxidant-limitation. However, the addition of sulfur amendments led to different community compositions. The dominant organisms at the end of the incubations were closely related to Dethiobacter sp. and to the family Comamonadaceae, which are also prominent in culture-independent gene sequencing surveys. These experiments provide one of first insights into the biogeochemical dynamics of the serpentinite subsurface environment and will facilitate experiments to trace microbial activities in serpentinizing ecosystems.

Deep-sea hydrothermal vent Epsilonproteobacteria encode a conserved and widespread nitrate reduction pathway (Nap).

Despite the frequent isolation of nitrate-respiring Epsilonproteobacteria from deep-sea hydrothermal vents, the genes coding for the nitrate reduction pathway in these organisms have not been investigated in depth. In this study we have shown that the gene cluster coding for the periplasmic nitrate reductase complex (nap) is highly conserved in chemolithoautotrophic, nitrate-reducing Epsilonproteobacteria from deep-sea hydrothermal vents. Furthermore, we have shown that the napA gene is expressed in pure cultures of vent Epsilonproteobacteria and it is highly conserved in microbial communities collected from deep-sea vents characterized by different temperature and redox regimes. The diversity of nitrate-reducing Epsilonproteobacteria was found to be higher in moderate temperature, diffuse flow vents than in high temperature black smokers or in low temperatures, substrate-associated communities. As NapA has a high affinity for nitrate compared with the membrane-bound enzyme, its occurrence in vent Epsilonproteobacteria may represent an adaptation of these organisms to the low nitrate concentrations typically found in vent fluids. Taken together, our findings indicate that nitrate reduction is widespread in vent Epsilonproteobacteria and provide insight on alternative energy metabolism in vent microorganisms. The occurrence of the nap cluster in vent, commensal and pathogenic Epsilonproteobacteria suggests that the ability of these bacteria to respire nitrate is important in habitats as different as the deep-sea vents and the human body.

Salinisphaera hydrothermalis sp. nov., a mesophilic, halotolerant, facultatively autotrophic, thiosulfate-oxidizing gammaproteobacterium from deep-sea hydrothermal vents, and emended description of the genus Salinisphaera.

A mesophilic, aerobic, facultatively chemolithoautotrophic bacterium, designated strain EPR70(T), was isolated from hydrothermal fluids from diffuse-flow vents on the East Pacific Rise at degrees 50' N 10 degrees 17' W. Cells were Gram-negative rods, approximately 0.8-1.0 microm long and 0.3-0.5 microm wide. Strain EPR70(T) grew at 20-40 degrees C (optimum 30-35 degrees C), 1-25 % NaCl (optimum 2.5 %) and pH 5.0-7.5 (optimum pH 5.5). The shortest generation time observed for strain EPR70(T) was 42 min. Growth occurred under aerobic chemolithoautotrophic conditions in the presence of thiosulfate and CO(2). Strain EPR70(T) grew heterotrophically with acetate or n-alkanes as sole carbon and energy sources, and in complex artificial seawater medium. Nitrate was not used as an electron acceptor. The G+C content of the genomic DNA was 64 mol%. Phylogenetic analysis of the 16S rRNA gene indicated that this organism is a member of the class Gammaproteobacteria, with Salinisphaera shabanensis E1L3A(T) as its closest relative (94 % sequence similarity). On the basis of phylogenetic analyses based on 16S rRNA, rbcL and alkB genes and physiological analysis, it is proposed that the organism represents a novel species within the genus Salinisphaera, for which the name Salinisphaera hydrothermalis sp. nov. is proposed. The type strain is EPR70(T) (=DSM 21483(T) =JCM 15514(T)).

The isolation and initial characterization of mercury resistant chemolithotrophic thermophilic bacteria from mercury rich geothermal springs.

Mercury rich geothermal springs are likely environments where mercury resistance is critical to microbial life and where microbe-mercury interactions may have evolved. Eleven facultative thermophilic and chemolithoautotrophic, thiosulfate oxidizing bacteria were isolated from thiosulfate enrichments of biofilms from mercury rich hot sulfidic springs in Mount Amiata, Italy. Some strains were highly resistant to mercury (>or=200 muM HgCl(2)) regardless of its presence or absence during primary enrichments, and three reduced ionic mercury to its elemental form. The gene encoding for the mercuric reductase enzyme (MerA), was amplified by PCR from seven strains. However, one highly resistant strain did not reduce mercury nor carried merA, suggesting an alternative resistance mechanism. All strains were members of the order Bacillales and were most closely related to previously described thermophiles belonging to the Firmicutes. Phylogenetic analyses clustered the MerA of the isolates in two supported novel nodes within the Firmicutes lineage and a comparison with the 16S rRNA gene tree suggested at least one case of horizontal gene transfer. Overall, the results show that the thermophilic thiosulfate oxidizing isolates were adapted to life in presence of mercury mostly, but not exclusively, by possessing MerA. These findings suggest that reduction of mercury by chemolithotrophic thermophilic bacteria may mobilize mercury from sulfur and iron deposits in geothermal environments.