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.

Pan-Arctic sea ice-algal chl a biomass and suitable habitat are largely underestimated for multiyear ice.

There is mounting evidence that multiyear ice (MYI) is a unique component of the Arctic Ocean and may play a more important ecological role than previously assumed. This study improves our understanding of the potential of MYI as a suitable habitat for sea ice algae on a pan-Arctic scale. We sampled sea ice cores from MYI and first-year sea ice (FYI) within the Lincoln Sea during four consecutive spring seasons. This included four MYI hummocks with a mean chl a biomass of 2.0 mg/m2 , a value significantly higher than FYI and MYI refrozen ponds. Our results support the hypothesis that MYI hummocks can host substantial ice-algal biomass and represent a reliable ice-algal habitat due to the (quasi-) permanent low-snow surface of these features. We identified an ice-algal habitat threshold value for calculated light transmittance of 0.014%. Ice classes and coverage of suitable ice-algal habitat were determined from snow and ice surveys. These ice classes and associated coverage of suitable habitat were applied to pan-Arctic CryoSat-2 snow and ice thickness data products. This habitat classification accounted for the variability of the snow and ice properties and showed an areal coverage of suitable ice-algal habitat within the MYI-covered region of 0.54 million km2 (8.5% of total ice area). This is 27 times greater than the areal coverage of 0.02 million km2 (0.3% of total ice area) determined using the conventional block-model classification, which assigns single-parameter values to each grid cell and does not account for subgrid cell variability. This emphasizes the importance of accounting for variable snow and ice conditions in all sea ice studies. Furthermore, our results indicate the loss of MYI will also mean the loss of reliable ice-algal habitat during spring when food is sparse and many organisms depend on ice-algae.

Bacterial community succession in a high-altitude subarctic glacier foreland is a three-stage process.

Alpine glaciers are retreating rapidly, exposing foreland minerals, which develop into soils. Bacterial communities in glacier forelands exhibit high rates of turnover and undergo dramatic shifts in composition within the first 50 years after deglaciation, followed by relative stabilization and convergence. This period of microbial development occurs simultaneously with plant colonization in most systems; thus, it remains unclear whether the changes in the bacterial communities occur primarily as the result of edaphic, climatic or biotic factors. We examined bacterial community structure along two replicate chronosequences within the glacial foreland of Duke River Glacier, Yukon, Canada. This foreland is estimated to include >200 years of bare soils before an appreciable grassline, likely due to the high latitude and altitude of the glacier. This enabled us to examine bacterial community development prior to plant colonization over a longer period than previous studies. We observed three successional groups in the chronosequence: (i) an 'early' group in soils of less than approximately 50 years since deglaciation; (ii) an 'intermediate' group within bare soils, after the early period but before the grassline, containing communities with a relatively high degree of variability in composition; and (iii) a 'grassline' group in soils collected after plant colonization with higher diversity but lower age-group variability in community composition. These findings suggest rapid replacement and addition of species better adapted to glacier foreland conditions followed by slower community shifts over the next 150 years and, finally, indications of a possible response to plant colonization.

Anti-apoptotic machinery protects the necrotrophic fungus Botrytis cinerea from host-induced apoptotic-like cell death during plant infection.

Necrotrophic fungi are unable to occupy living plant cells. How such pathogens survive first contact with living host tissue and initiate infection is therefore unclear. Here, we show that the necrotrophic grey mold fungus Botrytis cinerea undergoes massive apoptotic-like programmed cell death (PCD) following germination on the host plant. Manipulation of an anti-apoptotic gene BcBIR1 modified fungal response to PCD-inducing conditions. As a consequence, strains with reduced sensitivity to PCD were hyper virulent, while strains in which PCD was over-stimulated showed reduced pathogenicity. Similarly, reduced levels of PCD in the fungus were recorded following infection of Arabidopsis mutants that show enhanced susceptibility to B. cinerea. When considered together, these results suggest that Botrytis PCD machinery is targeted by plant defense molecules, and that the fungal anti-apoptotic machinery is essential for overcoming this host-induced PCD and hence, for establishment of infection. As such, fungal PCD machinery represents a novel target for fungicides and antifungal drugs.

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.

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.

Bacterial communities from Arctic seasonal sea ice are more compositionally variable than those from multi-year sea ice.

Arctic sea ice can be classified into two types: seasonal ice (first-year ice, FYI) and multi-year ice (MYI). Despite striking differences in the physical and chemical characteristics of FYI and MYI, and the key role sea ice bacteria play in biogeochemical cycles of the Arctic Ocean, there are a limited number of studies comparing the bacterial communities from these two ice types. Here, we compare the membership and composition of bacterial communities from FYI and MYI sampled north of Ellesmere Island, Canada. Our results show that communities from both ice types were dominated by similar class-level phylogenetic groups. However, at the operational taxonomic unit (OTU) level, communities from MYI and FYI differed in both membership and composition. Communities from MYI sites had consistent structure, with similar membership (presence/absence) and composition (OTU abundance) independent of location and year of sample. By contrast, communities from FYI were more variable. Although FYI bacterial communities from different locations and different years shared similar membership, they varied significantly in composition. Should these findings apply to sea ice across the Arctic, we predict increased compositional variability in sea ice bacterial communities resulting from the ongoing transition from predominantly MYI to FYI, which may impact nutrient dynamics in the Arctic Ocean.

Comparing springtime ice-algal chlorophyll a and physical properties of multi-year and first-year sea ice from the Lincoln Sea.

With near-complete replacement of Arctic multi-year ice (MYI) by first-year ice (FYI) predicted to occur within this century, it remains uncertain how the loss of MYI will impact the abundance and distribution of sea ice associated algae. In this study we compare the chlorophyll a (chl a) concentrations and physical properties of MYI and FYI from the Lincoln Sea during 3 spring seasons (2010-2012). Cores were analysed for texture, salinity, and chl a. We identified annual growth layers for 7 of 11 MYI cores and found no significant differences in chl a concentration between the bottom first-year-ice portions of MYI, upper old-ice portions of MYI, and FYI cores. Overall, the maximum chl a concentrations were observed at the bottom of young FYI. However, there were no significant differences in chl a concentrations between MYI and FYI. This suggests little or no change in algal biomass with a shift from MYI to FYI and that the spatial extent and regional variability of refrozen leads and younger FYI will likely be key factors governing future changes in Arctic sea ice algal biomass. Bottom-integrated chl a concentrations showed negative logistic relationships with snow depth and bulk (snow plus ice) integrated extinction coefficients; indicating a strong influence of snow cover in controlling bottom ice algal biomass. The maximum bottom MYI chl a concentration was observed in a hummock, representing the thickest ice with lowest snow depth of this study. Hence, in this and other studies MYI chl a biomass may be under-estimated due to an under-representation of thick MYI (e.g., hummocks), which typically have a relatively thin snowpack allowing for increased light transmission. Therefore, we suggest the on-going loss of MYI in the Arctic Ocean may have a larger impact on ice-associated production than generally assumed.

Distinct bacterial assemblages reside at different depths in Arctic multiyear sea ice.

Bacterial communities in Arctic sea ice play an important role in the regulation of nutrient and energy dynamics in the Arctic Ocean. Sea ice has vertical gradients in temperature, brine salinity and volume, and light and UV levels. Multiyear ice (MYI) has at least two distinct ice layers: old fresh ice with limited permeability, and new saline ice, and may also include a surface melt pond layer. Here, we determine whether bacterial communities (1) differ with ice depth due to strong physical and chemical gradients, (2) are relatively homogenous within a layer, but differ between layers, or (3) do not vary with ice depth. Cores of MYI off northern Ellesmere Island, NU, Canada, were subsectioned in 30-cm intervals, and the bacterial assemblage structure was characterized using 16S rRNA gene pyrotag sequencing. Assemblages clustered into three distinct groups: top (0-30 cm); middle (30-150 cm); and bottom (150-236 cm). These layers correspond to the occurrence of refrozen melt pond ice, at least 2-year-old ice, and newly grown first-year ice at the bottom of the ice sheet, respectively. Thus, MYI houses multiple distinct bacterial assemblages, and in situ conditions appear to play a less important role in structuring microbial assemblages than the age or conditions of the ice at the time of formation.

Fungal apoptosis: function, genes and gene function.

Cells of all living organisms are programmed to self-destruct under certain conditions. The most well known form of programmed cell death is apoptosis, which is essential for proper development in higher eukaryotes. In fungi, apoptotic-like cell death occurs naturally during aging and reproduction, and can be induced by environmental stresses and exposure to toxic metabolites. The core apoptotic machinery in fungi is similar to that in mammals, but the apoptotic network is less complex and of more ancient origin. Only some of the mammalian apoptosis-regulating proteins have fungal homologs, and the number of protein families is drastically reduced. Expression in fungi of animal proteins that do not have fungal homologs often affects apoptosis, suggesting functional conservation of these components despite the absence of protein-sequence similarity. Functional analysis of Saccharomyces cerevisiae apoptotic genes, and more recently of those in some filamentous species, has revealed partial conservation, along with substantial differences in function and mode of action between fungal and human proteins. It has been suggested that apoptotic proteins might be suitable targets for novel antifungal treatments. However, implementation of this approach requires a better understanding of fungal apoptotic networks and identification of the key proteins regulating apoptotic-like cell death in fungi.