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Mine wastes pollute the environment with metals and metalloids in toxic concentrations, causing problems for humans and wildlife. Microorganisms colonize and inhabit mine wastes, and can influence the environmental mobility of metals through metabolic activity, biogeochemical cycling and detoxification mechanisms. In this article we review the microbiology of the metals and metalloids most commonly associated with mine wastes: arsenic, cadmium, chromium, copper, lead, mercury, nickel and zinc. We discuss the molecular mechanisms by which bacteria, archaea, and fungi interact with contaminant metals and the consequences for metal fate in the environment, focusing on long‐term field studies of metal‐impacted mine wastes where possible. Metal contamination can decrease the efficiency of soil functioning and essential element cycling due to the need for microbes to expend energy to maintain and repair cells. However, microbial communities are able to tolerate and adapt to metal contamination, particularly when the contaminant metals are essential elements that are subject to homeostasis or have a close biochemical analog. Stimulating the development of microbially reducing conditions, for example in constructed wetlands, is beneficial for remediating many metals associated with mine wastes. It has been shown to be effective at low pH, circumneutral and high pH conditions in the laboratory and at pilot field‐scale. Further demonstration of this technology at full field‐scale is required, as is more research to optimize bioremediation and to investigate combined remediation strategies. Microbial activity has the potential to mitigate the impacts of metal mine wastes, and therefore lessen the impact of this pollution on planetary health., Key Points Microbes colonize and inhabit mine wastes, they tolerate high concentrations of metals and contribute to soil functioning and plant growthMicrobes transform metal speciation and environmental mobility, through metabolism, biogeochemical cycling and metal resistance mechanismsBeneficial microbial activity can be stimulated to remediate metal‐containing mine wastes, but more long‐term field studies are required

Although uncommon, nontuberculous mycobacterial (NTM) pulmonary infection in the Hawaiian Islands has a relatively high incidence and mortality compared to the mainland U.S. As a result, this study examines the possible geological and hydrological pathways by which NTM patients may become infected, including the environmental conditions that may favor growth and transport. Previously suggested infection routes include the inhalation of NTM attached to micro‐droplets from infected home plumbing systems and aerosolized dust from garden soil. In this study, we evaluate the possible routes NTM may take from riparian environments, into groundwater, into public water supplies and then into homes. Because NTM are notoriously hydrophobic and prone to attach to surfaces, mineralogy, and surface chemistry of suspended sediment in streams, soils, and rock scrapings suggest that NTM may especially attach to Fe‐oxides/hydroxides, and be transported as particles from losing streams to the aquifer on time‐scales of minutes to days. Within the aquifer, flow models indicate that water may be drawn into production wells on time scales (months) that permit NTM to survive and enter domestic water supplies. These processes depend on the presence of interconnected fracture networks with sufficient aperture to preclude complete autofiltration. The common occurrence of NTM in and around streams, in addition to wells, implies that the natural and built environments are capable of introducing a source of NTM into domestic water supplies via groundwater withdrawals. This may produce a persistent source of NTM infection to individuals through the presence of NTM‐laden biofilms in home plumbing., Key Points Nontuberculous mycobacterial (NTM) are found in soils and biofilms of riparian environments in Hawai'iNTM are likely transported from losing streams to aquifersPumped wells draw NTM into culinary water supplies and into homes. NTM are chlorine resistant and outcompete other taxa in home plumbing

Longitudinal water quality monitoring is important for understanding seasonal variations in water quality, waterborne disease transmission, and future implications for climate change and public health. In this study, microfluidic quantitative polymerase chain reaction (MFQPCR) was used to quantify genes from pathogens commonly associated with human intestinal infections in water collected from protected springs, a public tap, drainage channels, and surface water in Kampala, Uganda, from November 2014 to May 2015. The differences in relative abundance of genes during the wet and dry seasons were also assessed. All water sources tested contained multiple genes from pathogenic microorganisms, with drainage channels and surface waters containing a higher abundance of genes as compared to protected spring and the public tap water. Genes detected represented the presence of enterohemorrhagic Escherichia coli, Shigella spp., Salmonella spp., Vibrio cholerae, and enterovirus. There was an increased presence of pathogenic genes in drainage channels during the wet season when compared to the dry season. In contrast, surface water and drinking water sources contained little seasonal variation in the quantity of microbes assayed. These results suggest that individual water source types respond uniquely to seasonal variability and that human interaction with contaminated drainage waters, rather than direct ingestion of contaminated water, may be a more important contributor to waterborne disease transmission. Furthermore, future work in monitoring seasonal variations in water quality should focus on understanding the baseline influences of any one particular water source given their unique complexities., Key Points Pathogenic genes associated with human infections were quantified in water samples collected over seven months in Kampala, UgandaAn increased presence of pathogenic bacterial and viral genes in drainage channels in wet season was observedHuman interaction with contaminated drainage water could contribute to waterborne disease transmission

During the Oligo‐Miocene, major phases of phosphogenesis occurred in the Earth's oceans. However, most phosphate deposits represent condensed or allochthonous hemipelagic deposits, formed by complex physical and chemical enrichment processes, limiting their applicability for the study regarding the temporal pacing of Miocene phosphogenesis. The Oligo‐Miocene Decontra section located on the Maiella Platform (central Apennines, Italy) is a widely continuous carbonate succession deposited in a mostly middle to outer neritic setting. Of particular interest are the well‐winnowed grain to packstones of the middle Miocene Bryozoan Limestone, where occurrences of authigenic phosphate grains coincide with the prominent carbon isotope excursion of the Monterey event. This unique setting allows the analysis of orbital forcing on phosphogenesis, within a bio, chemo, and cyclostratigraphically constrained age‐model. LA‐ICP‐MS analyses revealed a significant enrichment of uranium in the studied authigenic phosphates compared to the surrounding carbonates, allowing natural gamma‐radiation (GR) to be used as a qualitative proxy for autochthonous phosphate content. Time series analyses indicate a strong 405 kyr eccentricity forcing of GR in the Bryozoan Limestone. These results link maxima in the GR record and thus phosphate content to orbitally paced increases in the burial of organic carbon, particularly during the carbon isotope maxima of the Monterey event. Thus, phosphogenesis during the middle Miocene in the Mediterranean was controlled by the 405 kyr eccentricity and its influence on large‐scale paleoproductivity patterns. Rare earth element data were used as a tool to reconstruct the formation conditions of the investigated phosphates, indicating generally oxic formation conditions, which are consistent with microbially mediated phosphogenesis., Key Points: Phosphogenesis during the Monterey event forced by 405 kyr eccentricity controlled paleoproductivityGamma radiation is directly linked to phosphogenesis via U enrichment of authigenic phosphateTrace elements show the phosphates formed under microbially mediated and well‐oxygenated conditions

The Martian surface is cold, dry, exposed to biologically harmful radiation and apparently barren today. Nevertheless, there is clear geological evidence for warmer, wetter intervals in the past that could have supported life at or near the surface. This evidence has motivated National Aeronautics and Space Administration and European Space Agency to prioritize the search for any remains or traces of organisms from early Mars in forthcoming missions. Informed by (1) stratigraphic, mineralogical and geochemical data collected by previous and current missions, (2) Earth's fossil record, and (3) experimental studies of organic decay and preservation, we here consider whether, how, and where fossils and isotopic biosignatures could have been preserved in the depositional environments and mineralizing media thought to have been present in habitable settings on early Mars. We conclude that Noachian‐Hesperian Fe‐bearing clay‐rich fluvio‐lacustrine siliciclastic deposits, especially where enriched in silica, currently represent the most promising and best understood astropaleontological targets. Siliceous sinters would also be an excellent target, but their presence on Mars awaits confirmation. More work is needed to improve our understanding of fossil preservation in the context of other environments specific to Mars, particularly within evaporative salts and pore/fracture‐filling subsurface minerals., Key Points Noachian‐Hesperian Fe‐bearing clay‐rich fluvio‐lacustrine siliciclastic sediments are favored in the search for ancient Martian lifeThere is insufficient confidence in the nature of reported silica sinters on Mars or the possibility of preservation in the deep biosphereExperimental taphonomy approaches from paleontology should now be adapted to understand limits on preservation under Martian conditions

This study tests the hypothesis that surface composition influences microbial community structure and growth of biofilms. We used laboratory biofilm reactors (inoculated with a diverse subsurface community) to explore the phylogenetic and taxonomic variability in microbial communities as a function of surface type (carbonate, silicate, aluminosilicate), media pH, and carbon and phosphate availability. Using high-throughput pyrosequencing, we found that surface type significantly controlled ~70-90% of the variance in phylogenetic diversity regardless of environmental pressures. Consistent patterns also emerged in the taxonomy of specific guilds (sulfur-oxidizers/reducers, Gram-positives, acidophiles) due to variations in media chemistry. Media phosphate availability was a key property associated with variation in phylogeny and taxonomy of whole reactors and was negatively correlated with biofilm accumulation and α-diversity (species richness and evenness). However, mineral-bound phosphate limitations were correlated with less biofilm. Carbon added to the media was correlated with a significant increase in biofilm accumulation and overall α-diversity. Additionally, planktonic communities were phylogenetically distant from those in biofilms. All treatments harbored structurally (taxonomically and phylogenetically) distinct microbial communities. Selective advantages within each treatment encouraged growth and revealed the presence of hundreds of additional operational taxonomix units (OTU), representing distinct consortiums of microorganisms. Ultimately, these results provide evidence that mineral/rock composition significantly influences microbial community structure, diversity, membership, phylogenetic variability, and biofilm growth in subsurface communities.

International audience; During IODP expedition 323 in the Bering Sea (July 5- September 4, 2009) a series of drilling (down to 750 meters below sea floor) was realized at 7 sites localized on the Umnak plateau (U1339), on the Bowers Ridge (U1340, U1341, U1342) and on the Beringian margin (U1343, U1344, U1345) ; the oldest sediments dated at 5 Myrs were recovered at Sites U1340 and U1341. Diagenetic carbonates are present at all Sites either as nodules and cm to dm thick layers, or as isolated acicular crystals, within the diatom-rich oozes of the Bering Sea, which are also characterized by their extreme richness in methane. The mineralogical, geochemical and isotopic study of diagenetic carbonates from Sites U1343, U1344 and U1345 was realized to characterize the nature of inorganic and microbial processes responsible for this diagenesis, and to determine the composition and origin of fluids in which these carbonates were precipitated. The carbonate mineralogy is very complex ; it is represented by composite mixtures of magnesian calcite and dolomite of various composition. Fe-rich dolomite/siderite dominate below ~260 mbsf at Site U1343 and ~200 mbsf at Site U1344. The isotopic compositions of the diagenetic carbonates display wide ranges of variations both for calcite (+2.84 < δ18O ‰ < +6.92 ; -20.52 < δ13C ‰ 18O ‰ < +9.19; +1.28 < δ13C ‰ 13C values clearly indicate that methanogenesis was involved in the sediments during microbial fermentation of organic matter : in this reaction, the 13C-rich CO2 was converted to carbonate alkalinity via silicate weathering and the 13C-poor methane was oxidized as bicarbonate via anaerobic oxidation of methane coupled with bacterial sulfate reduction as it is shown by the association of pyrite with the diagenetic carbonates.