Hydrogeochemical characterization of an evaporite karst area affected by sinkholes (Ebro Valley, NE Spain)

The main processes controlling the hydrochemistry of an alluvium-covered evaporite karst area with high sinkhole risk (Ebro Valley, NE Spain) are examined by means of multivariate analyses (Principal Component Analysis and Hierarchical Cluster Analysis), ion correlations and geochemical speciation-solubility calculations. The hydrogeochemistry of the studied system seems to be governed by the interaction between the groundwater from the salt-bearing evaporitic karst aquifer and from the overlying Ebro River alluvial aquifer. The observed hydrochemical features in the alluvial-karst aquifer system are mainly determined by the relative contribution of gypsum/anhydrite and halite dissolution, showing a wide spectrum from relatively fresh recharge waters (mainly irrigation waters) to highly evolved groundwater from the evaporitic aquifer. The variability of these contributions is especially evident at sinkhole ponds which, in some cases, seem to be associated with discharge areas of the karst aquifer in the valley bottom alluvium. Calculated saturation indexes suggest that, in contrast to gypsum, the amounts of halite in the sampled portions of evaporitic aquifer are not large enough to attain equilibrium, which is consistent with the predominance of gypsum/anhydrite reported for these materials. Furthermore, the observed Na:Cl and Ca:SO4 correlations and stoichiometries suggest that other possible processes, such as glauberite dissolution or Na/Ca-exchange, generally play a minor role (compared to halite and gypsum dissolution) in this system. Another important process in the system is the dissolution of carbonate minerals (dolomite and, possibly, calcite) fostered by the input of CO2(g), which is probably produced by pedogenic processes. Dolomite dissolution seems to be particularly relevant in the evaporitic materials probably due to dedolomitisation triggered by gypsum/anhydrite dissolution

Final report : environmental stresses and skeletal deformities in fish from the Willamette River, Oregon, USA

The Willamette River, one of only 14 American Heritage Rivers, flows through the most densely populated and agriculturally productive region of Oregon. Previous biological monitoring of Willamette River fish detected elevated frequencies of skeletal deformities in fish from certain areas of the lower (NP [NP], rivermile [RM] 26-55) and middle (near Wheatland Ferry [WF], RM 72-74) Willamette River, relative to those in the upper Willamette (i.e. near Corvallis [CV], RM 125-138). The objective of this study was to determine the likely cause of skeletal deformities in populations of Willamette River fish. Characterization of deformity loads in Willamette River fish collected in 2002 and 2003 demonstrated that deformity loads remained 2-3 times greater at the NPPool (NP) and WF locations than those observed at the CV location. There were some differences in water quality parameters between the NP and CV sites, but they did not readily explain the difference in deformity loads. Concentrations of bioavailable metals were below detection limits (≈1-5 µg/L). Concentrations of bioavailable polychlorinated biphenyls (PCBs) and chlorinated pesticides were generally below 0.25 ng/L. Concentrations of bioavailable polycyclic aromatic hydrocarbons were generally less than 5 ng/L. Chlorpyrifos (averaged less than 1.5 ng/L) was the only organophosphate pesticide detected as bioavailable in water. Concentrations of most persistent organic pollutants were below detection limits in ovary/oocyte tissue samples and sediments and those that were detected were not significantly different among sites. Bioassay of Willamette River water extracts provided no evidence that unidentified compounds or the complex mixture of compounds present in the extracts induced skeletal deformities in cyprinid fish. However, metacercariae of a digenean trematode were directly associated with a large portion of the lesions detected in fish collected from the Willamette River and the lesions were reproduced in fathead minnows exposed to cercariae extracted from field collected snails. As a whole, there was very little evidence to suggest that chemical contaminants were responsible for the greater deformity loads observed at NP and WF. Instead, the weight of evidence suggests that parasitic infection was the primary cause of skeletal deformities observed in Willamette River fish.Keywords: Willamette River, Infection, Chlorpyrifos, Polychorinated biphenyls, Chlorinated pesticides, Water, Parasite, Fish, Quality, Environment and Conservation, Skeleton, Deformity, Orego

Draft Genome Sequence of Telmatospirillum siberiense 26-4b1, an Acidotolerant Peatland Alphaproteobacterium Potentially Involved in Sulfur Cycling

The facultative anaerobic chemoorganoheterotrophic alphaproteobacterium Telmatospirillum siberiense 26-4b1 was isolated from a Siberian peatland. We report here a 6.20-Mbp near-complete high-quality draft genome sequence of T. siberiense that reveals expected and novel metabolic potential for the genus Telmatospirillum, including genes for sulfur oxidation.© 2018 Hausmann et al

Evaluation of Primers Targeting the Diazotroph Functional Gene and Development of NifMAP – A Bioinformatics Pipeline for Analyzing nifH Amplicon Data

Diazotrophic microorganisms introduce biologically available nitrogen (N) to the global N cycle through the activity of the nitrogenase enzyme. The genetically conserved dinitrogenase reductase (nifH) gene is phylogenetically distributed across four clusters (I–IV) and is widely used as a marker gene for N2 fixation, permitting investigators to study the genetic diversity of diazotrophs in nature and target potential participants in N2 fixation. To date there have been limited, standardized pipelines for analyzing the nifH functional gene, which is in stark contrast to the 16S rRNA gene. Here we present a bioinformatics pipeline for processing nifH amplicon datasets – NifMAP (“NifH MiSeq Illumina Amplicon Analysis Pipeline”), which as a novel aspect uses Hidden-Markov Models to filter out homologous genes to nifH. By using this pipeline, we evaluated the broadly inclusive primer pairs (Ueda19F–R6, IGK3–DVV, and F2–R6) that target the nifH gene. To evaluate any systematic biases, the nifH gene was amplified with the aforementioned primer pairs in a diverse collection of environmental samples (soils, rhizosphere and roots samples, biological soil crusts and estuarine samples), in addition to a nifH mock community consisting of six phylogenetically diverse members. We noted that all primer pairs co-amplified nifH homologs to varying degrees; up to 90% of the amplicons were nifH homologs with IGK3–DVV in some samples (rhizosphere and roots from tall oat-grass). In regards to specificity, we observed some degree of bias across the primer pairs. For example, primer pair F2–R6 discriminated against cyanobacteria (amongst others), yet captured many sequences from subclusters IIIE and IIIL-N. These aforementioned subclusters were largely missing by the primer pair IGK3–DVV, which also tended to discriminate against Alphaproteobacteria, but amplified sequences within clusters IIIC (affiliated with Clostridia) and clusters IVB and IVC. Primer pair Ueda19F–R6 exhibited the least bias and successfully captured diazotrophs in cluster I and subclusters IIIE, IIIL, IIIM, and IIIN, but tended to discriminate against Firmicutes and subcluster IIIC. Taken together, our newly established bioinformatics pipeline, NifMAP, along with our systematic evaluations of nifH primer pairs permit more robust, high-throughput investigations of diazotrophs in diverse environments.© 2018 Angel, Nepel, Panhölzl, Schmidt, Herbold, Eichorst and Woebke

The molecular interactions of organic compounds with tire crumb materials differ substantially from those with other microplastics

Tire materials are the most commonly found elastomers in the environment and they account for a significant fraction of microplastic pollution. In the discussions on the environmental impact of microplastics tire materials and their sorption properties have been largely overlooked. In this study we used experimental sorption data from six organic probe sorbates sorbing to two tire materials and their major components, styrene butadiene rubber and carbon black, to gain a better understanding of the underlying sorption processes of tire materials. Commonly applied models used to describe non-linear sorption processes were unable to fully explain sorption to tire materials but showed that absorption into the rubber fraction dominated the sorption process. Hydrophobicity was approximated using the hexadecane–water partitioning constant, which correlated very well with the distribution data obtained for styrene rubber, whereas the correlations between hydrophobicity of sorbates and the sorption data to the tire materials were poor. Although hydrophobicity plays an important role in sorption to tire materials, additional interactions must be taken into account. Overall, the processes involved in sorption to tire materials differed significantly from those governing sorption to other microplastics

Biochar particle aggregation in soil pore water: the influence of ionic strength and interactions with pyrene

The beneficial properties of biochar have led to its increasing application to soils for environmental management. Despite its stability in soil, biochar can physically disintegrate into smaller particles, which can then be relocated from the application area. Biochar transport is strongly dependent on the biochar particle size and aggregation, with the extent of aggregation depending on the chemistry of the soil pore water. Biochar has a strong sorption affinity for polyaromatic hydrocarbons (PAHs) such as pyrene, which can also affect its transport. We therefore investigated biochar particle aggregation in solutions of different ionic strengths (ultrapure water, 0.01 M CaCl2, and 0.1 M CaCl2) with suspensions of biochar particles, and with suspensions of biochar particles loaded with pyrene (0.2 and 3.6 g kg−1). Increasing the pyrene concentration in ultrapure water resulted in an increase in the biochar particle size, an effect that was more pronounced following equilibration for 28 days than following equilibration for only 24 hours. Biochar particle aggregation in solutions containing both pyrene and 0.01 M CaCl2 was greatly enhanced compared to aggregation in similar solutions with no pyrene. However, the influence of pyrene became negligible at high CaCl2 concentrations (0.1 M CaCl2). To determine the fate of biochar in soil, both the presence of PAHs and the influence of the pore water's ionic strength therefore need to be taken into account

Organ transcriptomes of the lucinid clam Loripes orbiculatus (Poli, 1791) provide insights into their specialised roles in the biology of a chemosymbiotic bivalve

Background: The lucinid clam Loripes orbiculatus lives in a nutritional symbiosis with sulphur-oxidizing bacteria housed in its gills. Although our understanding of the lucinid endosymbiont physiology and metabolism has made significant progress, relatively little is known about how the host regulates the symbiosis at the genetic and molecular levels. We generated transcriptomes from four L. orbiculatus organs (gills, foot, visceral mass, and mantle) for differential expression analyses, to better understand this clam’s physiological adaptations to a chemosymbiotic lifestyle, and how it regulates nutritional and immune interactions with its symbionts. Results: The transcriptome profile of the symbiont-housing gill suggests the regulation of apoptosis and innate immunity are important processes in this organ. We also identified many transcripts encoding ion transporters from the solute carrier family that possibly allow metabolite exchange between host and symbiont. Despite the clam holobiont’s clear reliance on chemosynthesis, the clam’s visceral mass, which contains the digestive tract, is characterised by enzymes involved in digestion, carbohydrate recognition and metabolism, suggesting that L. orbiculatus has a mixotrophic diet. The foot transcriptome is dominated by the biosynthesis of glycoproteins for the construction of mucus tubes, and receptors that mediate the detection of chemical cues in the environment. Conclusions:The transcriptome profiles of gills, mantle, foot and visceral mass provide insights into the molecular basis underlying the functional specialisation of bivalve organs adapted to a chemosymbiotic lifestyle.© The Author(s) 201

Data on sorption of organic compounds by aged polystyrene microplastic particles

This article contains data on experimental sorption isotherms of 21 probe sorbates by aged polystyrene microplastics. The polymeric particles were subjected to an UV-induced photo-oxidation procedure using hydrogen peroxide in a custom-made aging chamber. Sorption data were obtained for aged particles. The experimental sorption data was modelled using both single- and poly-parameter linear free-energy relationships. For discussion and interpretation of the presented data, refer to the research article entitled “Sorption of organic compounds by aged polystyrene microplastic particles” (Hüffer et al., 2018) [1].© 2018 The Author

Microbiomes In Natura: Importance of Invertebrates in Understanding the Natural Variety of Animal-Microbe Interactions

Animals evolved in a world teeming with microbes, which play pivotal roles in their health, development, and evolution. Although the overwhelming majority of living animals are invertebrates, the minority of “microbiome” studies focus on this group. Interest in invertebrate-microbe interactions is 2-fold—a range of immune components are conserved across almost all animal (including human) life, and their functional roles may be conserved. Thus, understanding cross talk between microbes and invertebrate animals can lead to insights of broader relevance. Invertebrates offer unique opportunities to “eavesdrop” on intricate host-microbe conversations because they tend to associate with fewer microbes. On the other hand, considering the vast diversity of form and function that has evolved in the invertebrates, they likely evolved an equally diverse range of ways to interact with beneficial microbes. We have investigated only a few of these interactions in detail; thus, there is still great potential for fundamentally new discoveries.© 2018 Petersen and Osvati