Developing a versatile tool for studying kinetics of Selenate-Se removal from aqueous solution using a chemostat bioreactor.

Understanding the impact of various parameters on the kinetics of dissolved selenium (Se) removal in bioreactors can be a challenging task, primarily due to the mass transfer limitations inherent in bioreactors employing attached growth configurations. This study successfully established a proof-of-concept for the efficient removal of Se from aqueous solutions using a chemostat bioreactor that relies solely on suspended growth. The research investigated the effect of selenate-Se feed concentrations under two distinct Se concentration conditions. One experiment was conducted at a considerably elevated concentration of 25 mg/L to impose stress on the system and evaluate its response. Another experiment replicated an environmentally relevant concentration of 1 mg/L, mirroring the typical Se concentrations in mine water. The bioreactor, featuring a working volume of 0.35 L, was operated as an anaerobic, fully mixed chemostat with hydraulic retention times (HRTs) ranging from 5 to 0.25 days. The outcomes revealed the chemostat's capacity to remove up to 25 mg/L of dissolved Se from water for all HRTs exceeding 1 day, under otherwise optimal conditions encompassing temperature, pH, and salinity. The research's significance lies in the development of a versatile tool designed to examine Se removal kinetics within a system devoid of mass transfer limitations. Furthermore, this study verified the ability of the bacterial consortium, obtained from a mine-influenced environment and enriched in the laboratory, to grow and sustain Se removal activities within a chemostat operating with HRTs as short as 1 day.

Targeted deep learning classification and feature extraction for clinical diagnosis.

Protein biomarkers can be used to characterize symptom classes, which describe the metabolic or immunodeficient state of patients during the progression of a specific disease. Recent literature has shown that machine learning methods can complement traditional clinical methods in identifying biomarkers. However, many machine learning frameworks only apply narrowly to a specific archetype or subset of diseases. In this paper, we propose a feature extractor which can discover protein biomarkers for a wide variety of classification problems. The feature extractor uses a special type of deep learning model, which discovers a latent space that allows for optimal class separation and enhanced class cluster identity. The extracted biomarkers can then be used to train highly accurate supervised learning models. We apply our methods to a dataset involving COVID-19 patients and another involving scleroderma patients, to demonstrate improved class separation and reduced false discovery rates compared to results obtained using traditional models.

Identifying indicator species in ecological habitats using Deep Optimal Feature Learning.

Much of the current research on supervised modelling is focused on maximizing outcome prediction accuracy. However, in engineering disciplines, an arguably more important goal is that of feature extraction, the identification of relevant features associated with the various outcomes. For instance, in microbial communities, the identification of keystone species can often lead to improved prediction of future behavioral shifts. This paper proposes a novel feature extractor based on Deep Learning, which is largely agnostic to underlying assumptions regarding the training data. Starting from a collection of microbial species abundance counts, the Deep Learning model first trains itself to classify the selected distinct habitats. It then identifies indicator species associated with the habitats. The results are then compared and contrasted with those obtained by traditional statistical techniques. The indicator species are similar when compared at top taxonomic levels such as Domain and Phylum, despite visible differences in lower levels such as Class and Order. More importantly, when our estimated indicators are used to predict final habitat labels using simpler models (such as Support Vector Machines and traditional Artificial Neural Networks), the prediction accuracy is improved. Overall, this study serves as a preliminary step that bridges modern, black-box Machine Learning models with traditional, domain expertise-rich techniques.

Microbial consortia capable of reducing selenate in the presence of nitrate enriched from coalmining-impacted environments.

Biological treatment to remove dissolved selenium from mine-impacted water is often inhibited by the co-contaminant nitrate. In this work, we enriched microbial consortia capable of removing dissolved selenium in the presence of nitrate from native bacteria at sites influenced by coalmine seepages with elevated concentrations of Se, nitrate, and sulfate. Enrichments were collected from sediments in different vegetated or non-vegetated seepage collection ponds, and all demonstrated the potential for dissolved selenium removal. Nitrate inhibited dissolved selenium removal rates in four of these enrichments. However, microorganisms enriched from a mine seepage influenced natural vegetated marsh removed dissolved Se and nitrate simultaneously. Additionally, enrichments from one seepage collection pond achieved enhanced dissolved selenium removal in the presence of nitrate. Based on functional metagenomics, the dominant species with the metabolic capacity for selenate reduction were classified in Orders Enterobacterales and Clostridiales. Most putative selenate reductases identified as either ygfK, associated with selenoprotein synthesis or production of methylated organoselenium compounds, and narG, nitrate reductases with an affinity also for selenate.Key points• Enriched mine influenced sediment bacteria have the capacity for removal of dissolved Se species.• Consortia from a vegetated natural marsh reduced Se without inhibition from nitrate.• Nitrate stimulated the removal of Se by consortia from a disused tailing pond.

Application of Fe-biochar composites for selenium (Se+6) removal from aqueous solution and effect of the presence of competing anions under environmentally relevant conditions.

This study's aim was to compare biochar and steam activated biochar functionalized with iron for removal of selenium as selenate from solutions also containing nitrate and sulfate. The Fe-biochar composites were made impregnating iron (ferric nitrate) onto regular biochar (RB) and steam activated biochar (SAB), forming the Fe-biochar composites FeRB and FeSAB. Iron oxyhydroxide deposits were observed on the surface of FeRB using Raman spectroscopy analysis, but not on the FeSAB surface. Unmodified biochar samples did not remove selenium, as Se(VI), from solution, whereas FeRB and FeSAB recovered 8.3 mg-Se⋅g-composite-1 and 5.9 mg-Se⋅g-composite-1, respectively. Higher Se uptake was achieved at higher Fe-loads and lower acetone:biochar ratio, to a maximum of 17.3 mg-Se⋅g-composite-1 (FeRB). Washing after Fe-impregnation using deionized water diminished nitrate and Fe-leaching from the Fe-biochar composites while removing selenium. Se(VI) and sulfate uptake were observed when washed composites were tested in the presence of possible competing ions at environmentally relevant concentrations ([Se]t=0 = 1.01 ± 0.03 mg⋅L-1; [N-NO3-]t=0 = 40.2 ± 0.2 mg⋅L-1; and [SO42-]t=0 = 496 ± 25 mg⋅L-1). One of the possible mechanisms of removal might be the complexation of Se with the iron oxyhydroxide deposits (goethite and hematite) found on the FeRB surface.

A single clonal lineage of transmissible cancer identified in two marine mussel species in South America and Europe.

Transmissible cancers, in which cancer cells themselves act as an infectious agent, have been identified in Tasmanian devils, dogs, and four bivalves. We investigated a disseminated neoplasia affecting geographically distant populations of two species of mussels (Mytilus chilensis in South America and M. edulis in Europe). Sequencing alleles from four loci (two nuclear and two mitochondrial) provided evidence of transmissible cancer in both species. Phylogenetic analysis of cancer-associated alleles and analysis of diagnostic SNPs showed that cancers in both species likely arose in a third species of mussel (M. trossulus), but these cancer cells are independent from the previously identified transmissible cancer in M. trossulus from Canada. Unexpectedly, cancers from M. chilensis and M. edulis are nearly identical, showing that the same cancer lineage affects both. Thus, a single transmissible cancer lineage has crossed into two new host species and has been transferred across the Atlantic and Pacific Oceans and between the Northern and Southern hemispheres.

Removal of selenate from brine using anaerobic bacteria and zero valent iron.

The mining industry needs to treat large volumes of wastewater highly concentrated in chemical compounds that can adversely affect receiving environments. One promising method of treatment is the use of reverse osmosis to remove most of the dissolved salts. However, the resulting brine reject is a highly saline wastewater that needs further treatment to remove the toxic components, such as selenate, which is a chemical compound of great concern in coal-mining regions. Biological reduction and removal of dissolved selenium from a brine solution was achieved. Microorganisms were enriched from environmental samples collected from two mines, respectively, at different geographic locations through adaptive evolution in the laboratory. Batch treatment of typical brine was tested with two different enrichments with the addition of either of two chemical forms of iron, ferrous chloride or zero valent iron. Successful selenium removal in the presence of high nitrate and sulphate concentrations was achieved with a combination of enriched microorganisms from one particular site and the addition of zero-valent iron. The composition and metabolic potential of the enriched microorganisms revealed Clostridium, Sphaerochaeta, Synergistes and Desulfosporosinus species with the metabolic potential for selenate reduction through the YgfK enzymatic process associated with selenium detoxification.

Semi-passive in-situ pilot scale bioreactor successfully removed sulfate and metals from mine impacted water under subarctic climatic conditions.

Mine drainage contaminated with metals is a major environmental threat since it is a source of water pollution with devastating effects on aquatic ecosystems. Conventional active treatment technologies are prohibitively expensive and so there is increasing demand to develop reliable, cost-effective and sustainable passive or semi-passive treatment. These are promising alternatives since they leverage the metabolism of microorganisms native to the disturbed site at in situ or close to in situ conditions. Since this is a biological approach, it is not clear if semi-passive treatment would be effective in remote locations with extremely cold weather such as at mines in the subarctic. In this study we tested the hypothesis that sulfate-reducing bacteria, which are microorganisms that promote metal precipitation, exist in subarctic mine environments and their activity can be stimulated by adding a readily available carbon source. An experiment was setup at a closed mine in the Yukon Territory, Canada, where leaching of Zn and Cd occurs. To test if semi-passive treatment could precipitate these metals and prevent further leaching from waste rock, molasses as a carbon source was added to anaerobic bioreactors mimicking the belowground in-situ conditions. Microbial community analysis confirmed that sulfate-reducing bacteria became enriched in the bioreactors upon addition of molasses. The population composition remained fairly stable over the 14 month operating period despite temperature shifts from 17 to 5 °C. Sulfate reduction functionality was confirmed by quantification of the gene for dissimilatory sulfite reductase. Metals were removed from underground mine drainage fed into the bioreactors with Zn removal efficiency varying between 20.9% in winter and 89.3% in summer, and Cd removal efficiency between 39% in winter and 90.5% in summer. This study demonstrated that stimulation of native SRB in MIW was possible and that in situ semi-passive treatment can be effective in removing metals despite the cold climate.

Short-term microbial effects of a large-scale mine-tailing storage facility collapse on the local natural environment.

We investigated the impacts of the Mount Polley tailings impoundment failure on chemical, physical, and microbial properties of substrates within the affected watershed, comprised of 70 hectares of riparian wetlands and 40 km of stream and lake shore. We established a biomonitoring network in October of 2014, two months following the disturbance, and evaluated riparian and wetland substrates for microbial community composition and function via 16S and full metagenome sequencing. A total of 234 samples were collected from substrates at 3 depths and 1,650,752 sequences were recorded in a geodatabase framework. These data revealed a wealth of information regarding watershed-scale distribution of microbial community members, as well as community composition, structure, and response to disturbance. Substrates associated with the impact zone were distinct chemically as indicated by elevated pH, nitrate, and sulphate. The microbial community exhibited elevated metabolic capacity for selenate and sulfate reduction and an abundance of chemolithoautotrophs in the Thiobacillus thiophilus/T. denitrificans/T. thioparus clade that may contribute to nitrate attenuation within the affected watershed. The most impacted area (a 6 km stream connecting two lakes) exhibited 30% lower microbial diversity relative to the remaining sites. The tailings impoundment failure at Mount Polley Mine has provided a unique opportunity to evaluate functional and compositional diversity soon after a major catastrophic disturbance to assess metabolic potential for ecosystem recovery.

Core Sulphate-Reducing Microorganisms in Metal-Removing Semi-Passive Biochemical Reactors and the Co-Occurrence of Methanogens.

Biochemical reactors (BCRs) based on the stimulation of sulphate-reducing microorganisms (SRM) are emerging semi-passive remediation technologies for treatment of mine-influenced water. Their successful removal of metals and sulphate has been proven at the pilot-scale, but little is known about the types of SRM that grow in these systems and whether they are diverse or restricted to particular phylogenetic or taxonomic groups. A phylogenetic study of four established pilot-scale BCRs on three different mine sites compared the diversity of SRM growing in them. The mine sites were geographically distant from each other, nevertheless the BCRs selected for similar SRM types. Clostridia SRM related to Desulfosporosinus spp. known to be tolerant to high concentrations of copper were members of the core microbial community. Members of the SRM family Desulfobacteraceae were dominant, particularly those related to Desulfatirhabdium butyrativorans. Methanogens were dominant archaea and possibly were present at higher relative abundances than SRM in some BCRs. Both hydrogenotrophic and acetoclastic types were present. There were no strong negative or positive co-occurrence correlations of methanogen and SRM taxa. Knowing which SRM inhabit successfully operating BCRs allows practitioners to target these phylogenetic groups when selecting inoculum for future operations.

Simultaneous selenate reduction and denitrification by a consortium of enriched mine site bacteria.

Increasing selenium concentrations in aquatic environments downstream of mine sites is of great concern due to selenium's bioaccumulation propensity and teratogenic toxicity. Removal of selenium from mine influenced water is complicated by the presence of nitrate, which is also elevated in mine influenced water due to the use of explosives in mining. In many biological treatment processes, nitrate as a thermodynamically more preferable electron acceptor inhibits selenate reduction. Here we report on an enrichment of a bacterial assemblage from a mine impacted natural marsh sediment that was capable of simultaneous selenate reduction and denitrification. Selenate reduction followed first order kinetics with respect to the concentration of total dissolved selenium. The kinetic rate constant was independent of initial nitrate concentration over the range 3-143 mg L-1-NO3--N. The initial concentration of selenate inhibited selenate reduction kinetics over the range 1-24 mg-Se L-1. Dominant taxa that grew in selenate only medium were classified in the genera Pseudomonas, Lysinibacillus and Thauera. When nitrate was introduced in addition to selenate, previously rare taxa that became dominant were relatives of Exiguobacterium, Tissierella and Clostridium. Open reading frames (ORFs) associated with dissimilatory denitrification were identified for Pseudomonas, Thauera and Clostridium. In addition, ORFs were found that were homologous with known selenate reductase subunits (SerA and SerB). These findings suggest that native mine site bacteria can be used for removing selenate and nitrate from mine wastewater.

Widespread transmission of independent cancer lineages within multiple bivalve species.

Most cancers arise from oncogenic changes in the genomes of somatic cells, and while the cells may migrate by metastasis, they remain within that single individual. Natural transmission of cancer cells from one individual to another has been observed in two distinct cases in mammals (Tasmanian devils and dogs), but these are generally considered to be rare exceptions in nature. The discovery of transmissible cancer in soft-shell clams (Mya arenaria) suggested that this phenomenon might be more widespread. Here we analyse disseminated neoplasia in mussels (Mytilus trossulus), cockles (Cerastoderma edule), and golden carpet shell clams (Polititapes aureus) and find that neoplasias in all three species are attributable to independent transmissible cancer lineages. In mussels and cockles, the cancer lineages are derived from their respective host species; however, unexpectedly, cancer cells in P. aureus are all derived from Venerupis corrugata, a different species living in the same geographical area. No cases of disseminated neoplasia have thus far been found in V. corrugata from the same region. These findings show that transmission of cancer cells in the marine environment is common in multiple species, that it has originated many times, and that while most transmissible cancers are found spreading within the species of origin, cross-species transmission of cancer cells can occur.

Performance of sulphate- and selenium-reducing biochemical reactors using different ratios of labile to recalcitrant organic materials.

Successful operation of sulphate-reducing bioreactors using complex organic materials depends on providing a balance between more easily degrading material that achieves reasonable kinetics and low hydraulic retention times, and more slowly decomposing material that sustains performance in the long term. In this study, two organic mixtures containing the same ingredients typical of bioreactors used at mine sites (woodchips, hay and cow manure) but with different ratios of wood (recalcitrant) to hay (labile) were tested in six continuous flow bioreactors treating synthetic mine-affected water containing 600 mg/L of sulphate and 15 µg/L of selenium. The reactors were operated for short (5-6 months) and long (435-450 days) periods of time at the same hydraulic retention time of 15 days. There were no differences in the performance of the bioreactors in terms of sulphate-reduction over the short term, but the wood-rich bioreactors experienced variable and sometimes unreliable sulphate-reduction over the long term. Presence of more hay in the organic mixture was able to better sustain reliable performance. Production of dissolved organic compounds due to biodegradation within the bioreactors was detected for the first 175-230 days, after which their depletion coincided with a crash phase observed in the wood-rich bioreactors only.

Using flow cytometry to detect haemic neoplasia in mussels (Mytilus trossulus) from the Pacific Coast of Southern British Columbia, Canada.

Flow cytometry was investigated as an alternative to visual haemocytology for potentially higher-throughput and less subjective detection of neoplasia in Mytilus trossulus. In contrast to previous studies of ploidy in the Mytilus spp. complex, distinct tetra- and pentaploidal neoplastic cells were rare and a wide range of aneuploidy peaks from 1.4n to 5.5n were detected for late-stage leukemic animals. There was no correlation between aneuploidy and the number of diseased cells for early and intermediate disease stages. Formation of aneuploidy and neoplasia progression might not be simultaneous, and DNA content analysis using flow cytometry was only useful for detecting late stages of the disease.

Biomining active cellulases from a mining bioremediation system.

Functional metagenomics has emerged as a powerful method for gene model validation and enzyme discovery from natural and human engineered ecosystems. Here we report development of a high-throughput functional metagenomic screen incorporating bioinformatic and biochemical analyses features. A fosmid library containing 6144 clones sourced from a mining bioremediation system was screened for cellulase activity using 2,4-dinitrophenyl ß-cellobioside, a previously proven cellulose model substrate. Fifteen active clones were recovered and fully sequenced revealing 9 unique clones with the ability to hydrolyse 1,4-ß-D-glucosidic linkages. Transposon mutagenesis identified genes belonging to glycoside hydrolase (GH) 1, 3, or 5 as necessary for mediating this activity. Reference trees for GH 1, 3, and 5 families were generated from sequences in the CAZy database for automated phylogenetic analysis of fosmid end and active clone sequences revealing known and novel cellulase encoding genes. Active cellulase genes recovered in functional screens were subcloned into inducible high copy plasmids, expressed and purified to determine enzymatic properties including thermostability, pH optima, and substrate specificity. The workflow described here provides a general paradigm for recovery and characterization of microbially derived genes and gene products based on genetic logic and contemporary screening technologies developed for model organismal systems.

Evaluation of Solvita compost stability and maturity tests for assessment of quality of end-products from mixed latrine style compost toilets.

It is challenging and expensive to monitor and test decentralized composting toilet systems, yet critical to prevent the mismanagement of potentially harmful and pathogenic end-product. Recent studies indicate that mixed latrine composting toilets can be inhibited by high ammonia content, a product of urea hydrolysis. Urine-diverting vermicomposting toilets are better able to accomplish the goals of remote site human waste management by facilitating the consumption of fecal matter by earthworms, which are highly sensitive to ammonia. The reliability of Solvita compost stability and maturity tests were evaluated as a means of determining feedstock suitability for vermicomposting (ammonia) and end-product stability/completeness (carbon dioxide). A significant linear regression between Solvita ammonia and free ammonia gas was found. Solvita ranking of maturity did not correspond to ranking assigned by ammonium:nitrate standards. Solvita ammonia values 4 and 5 contained ammonia levels below earthworm toxicity limits in 80% and 100% of samples respectively indicative of their use in evaluating feedstock suitability for vermicomposting. Solvita stability tests did not correlate with carbon dioxide evolution tests nor ranking of stability by the same test, presumably due to in situ inhibition of decomposition and microbial respiration by ammonia which were reported by the Solvita CO2 test as having high stability values.

Composting toilets a misnomer: excessive ammonia from urine inhibits microbial activity yet is insufficient in sanitizing the end-product.

End-product from 16 public mixed latrine style composting toilets (CTs) at 12 sites between 50 and 2100 m.a.s.l. in Western North America was tested in order to evaluate the effect of composting variables (TS%, NH3-N, temperature, and material age) on compost quality and hygiene (VS%, Escherichia coli, [Formula: see text] -N, and pH). Principal component analysis indicated that TS%, temperature, and material age equally contributed to reduction in VS%. NH3-N had the greatest effect on [Formula: see text] -N, E. coli, and pH. Nitrification was significantly inhibited above 386 mg/kg NH3-N, but no such limit was found for E. coli, despite a significant (p = 0.016) but weak (r(2) = 0.11) negative relationship. It may be possible to amplify the sanitizing effect of ammonia and overcome pathogen resistance due to low temperatures and re-contamination (caused by poor design) with generous dosing of urea and ash. However, even sanitized, the fertilization effect of discharged material on the natural environment may not be desired or permitted in parks or protected areas where many CTs were found. To this end, operators of CTs need to evaluate their primary management objectives and ensure congruency with proven system capabilities.

Vermicomposting toilets, an alternative to latrine style microbial composting toilets, prove far superior in mass reduction, pathogen destruction, compost quality, and operational cost.

Composting toilets aim to recycle excrement into safe, stable humus. Preceding this, low costs, low risks, and mass reduction should be ensured. Source separating vermicomposting toilets (SSVCs) outperformed mixed latrine microbial composting toilets (MLMCs) in all categories. MLMCs: incurred ten times greater operational costs; created 10x more operator exposure; employed no proven pathogen reduction mechanism since solid end-products averaged 71,000±230,000CFU/g (fecal-origin) Escherichia coli and 24±5% total solids, consistently failed NSF/ANSI Standard 41; failed to reduce volatile solids compared to raw fecal matter; increased total contaminated dry mass by 274%, and produced alkaline end-product (8.0±0.7) high in toxic free ammonia (Solvita® 2.6±1.5). SSVCs have low maintenance costs and risks; adequate worm density for pathogen destruction (0.03±0.04g-worm/g-material); reduced E. coli 200±244CFU/g in neutral (7.4±0.3), stable (60±10% volatile solids), and mature (4±0 Solvita® NH(3)) end-product.

Restaurant challenge offers healthful meal options and builds diabetes awareness.

PURPOSE: The Frederick Restaurant Challenge is an innovative project based on a collaborative effort among community organizations and partners designed to offer delicious healthful meal options at local restaurants during the month of November for American Diabetes Month. Local restaurants were challenged to participate and submitted recipes for healthful meals to the Frederick County Diabetes Coalition for review by registered dietitians. Diners voted on meals to determine the challenge winner(s), and were eligible to win prizes as well. Publicity prior to and during the month was effective in creating positive news about healthful meals when eating out, raised awareness about diabetes, and provided restaurants with desirable advertising opportunities. Feedback from restaurants and diners was overwhelmingly positive. The purpose of this article is to describe this successful low-budget project to encourage its replication in local communities. CONCLUSIONS: The Frederick Restaurant Challenge proved to be a very successful, innovative, low-budget project that met its intended goals: to develop healthful meal options for people with diabetes (or for anyone wishing to eat healthier); to demonstrate that healthful food can taste delicious; and to encourage restaurants to continue offering healthful options on their menus beyond the challenge month. Community interventions such as the Frederick Restaurant Challenge offer unique and important strategies for affecting change and raising awareness not only for people with diabetes but also for the entire community.

Correlation of bacterial communities supported by different organic materials with sulfate reduction in metal-rich landfill leachate.

Several different organic materials, typical of those used in passive treatment systems for mine influenced water, were tested for their ability to support sulfate-reducing bacteria and sulfate reduction in an anaerobic biological reactor (ABR). The quantity of sulfate-reducing bacteria (SRB) in each organic material, as determined using quantitative polymerase chain reaction (q-PCR) of the dissimilatory sulfite reductase (dsr) gene, correlated with the initial C/N ratio of each material. Potential sulfate reduction rates measured in the laboratory ranked silage > compost = molasses/hay > cattails > pulp mill biosolids and correlated with the q-PCR estimates of SRB in the submerged materials. A comparison of bacterial communities using 16S rRNA gene clone library sequencing revealed similar distribution of clones among the phyla Bacteroidetes, Firmicutes and Proteobacteria for silage, compost and molasses/hay after 174 days of exposure in the seepage water. Silage, the most successful material tested, contained more δ-Proteobacteria-related sequences than the other materials and Spirochaetes-related clones were more abundant in silage than in compost or molasses/hay. According to sequenced dsr clones, the SRB community in silage differed from that for compost and molasses/hay, with fewer Desulfovibrio- and more Desulfomicrobium-related sequences in the silage. Pulp mill biosolids used in the ABR since 2004 contained an overall bacterial community that was more diverse than those for the freshly submerged organics, but only Desulfovibrio desulfuricans-related sequences were found in the dsr library.