Search

Marine microbial communities experience daily fluctuations in light and temperature that can have important ramifications for carbon and nutrient cycling. Elucidation of such short time scale community-wide dynamics is hindered by system complexity. Hypersaline aquatic environments have lower species richness than marine environments and can be well-defined spatially, hence they provide a model system for diel cycle analysis. We conducted a 3-day time series experiment in a well-defined pool in hypersaline Lake Tyrrell, Australia. Microbial communities were tracked by combining cultivation-independent lipidomic, metagenomic and microscopy methods. The ratio of total bacterial to archaeal core lipids in the planktonic community increased by up to 58% during daylight hours and decreased by up to 32% overnight. However, total organism abundances remained relatively consistent over 3 days. Metagenomic analysis of the planktonic community composition, resolved at the genome level, showed dominance by Haloquadratum species and six uncultured members of the Halobacteriaceae. The post 0.8 μm filtrate contained six different nanohaloarchaeal types, three of which have not been identified previously, and cryo-transmission electron microscopy imaging confirmed the presence of small cells. Notably, these nano-sized archaea showed a strong diel cycle, with a pronounced increase in relative abundance over the night periods. We detected no eukaryotic algae or other photosynthetic primary producers, suggesting that carbon resources may derive from patchily distributed microbial mats at the sediment-water interface or from surrounding land. Results show the operation of a strong community-level diel cycle, probably driven by interconnected temperature, light abundance, dissolved oxygen concentration and nutrient flux effects.

Background: Prior to soil formation, phosphate liberated by rock weathering is often sequestered into highly insoluble lanthanide phosphate minerals. Dissolution of these minerals releases phosphate and lanthanides to the biosphere. Currently, the microorganisms involved in phosphate mineral dissolution and the role of lanthanides in microbial metabolism are poorly understood., Results: Although there have been many studies of soil microbiology, very little research has investigated microbiomes of weathered rock. Here, we sampled weathered granite and associated soil to identify the zones of lanthanide phosphate mineral solubilisation and genomically define the organisms implicated in lanthanide utilisation. We reconstructed 136 genomes from 11 bacterial phyla and found that gene clusters implicated in lanthanide-based metabolism of methanol (primarily xoxF3 and xoxF5) are surprisingly common in microbial communities in moderately weathered granite. Notably, xoxF3 systems were found in Verrucomicrobia for the first time, and in Acidobacteria, Gemmatimonadetes and Alphaproteobacteria. The xoxF-containing gene clusters are shared by diverse Acidobacteria and Gemmatimonadetes, and include conserved hypothetical proteins and transporters not associated with the few well studied xoxF systems. Given that siderophore-like molecules that strongly bind lanthanides may be required to solubilise lanthanide phosphates, it is notable that candidate metallophore biosynthesis systems were most prevalent in bacteria in moderately weathered rock, especially in Acidobacteria with lanthanide-based systems., Conclusions: Phosphate mineral dissolution, putative metallophore production and lanthanide utilisation by enzymes involved in methanol oxidation linked to carbonic acid production co-occur in the zone of moderate granite weathering. In combination, these microbial processes likely accelerate the conversion of granitic rock to soil., (© 2024. The Author(s).)

Allopatric speciation has been difficult to examine among microorganisms, with prior reports of endemism restricted to sub-genus level taxa. Previous microbial community analysis via 16S rRNA gene sequencing of 925 geothermal springs from the Taupō Volcanic Zone (TVZ), Aotearoa-New Zealand, revealed widespread distribution and abundance of a single bacterial genus across 686 of these ecosystems (pH 1.2-9.6 and 17.4-99.8 °C). Here, we present evidence to suggest that this genus, Venenivibrio (phylum Aquificota), is endemic to Aotearoa-New Zealand. A specific environmental niche that increases habitat isolation was identified, with maximal read abundance of Venenivibrio occurring at pH 4-6, 50-70 °C, and low oxidation-reduction potentials. This was further highlighted by genomic and culture-based analyses of the only characterised species for the genus, Venenivibrio stagnispumantis CP.B2 T , which confirmed a chemolithoautotrophic metabolism dependent on hydrogen oxidation. While similarity between Venenivibrio populations illustrated that dispersal is not limited across the TVZ, extensive amplicon, metagenomic, and phylogenomic analyses of global microbial communities from DNA sequence databases indicates Venenivibrio is geographically restricted to the Aotearoa-New Zealand archipelago. We conclude that geographic isolation, complemented by physicochemical constraints, has resulted in the establishment of an endemic bacterial genus., (© 2024. The Author(s).)

The safeguarding of Australian outdoor stone heritage is currently limited by a lack of information concerning mechanisms responsible for the degradation of the built heritage. In this study, the bacterial community colonizing the stone surface of an outdoor sculpture located at the Church of St. John the Evangelist in Melbourne was analysed, providing an overview of the patterns of microbial composition associated with stone in an anthropogenic context. Illumina MiSeq 16S rRNA gene sequencing together with confocal laser microscope investigations highlighted the bacterial community was composed of both phototrophic and chemotrophic microorganisms characteristic of stone and soil, and typical of arid, salty and urban environments. Cardinal exposure, position and surface geometry were the most important factors in determining the structure of the microbial community. The North-West exposed areas on the top of the sculpture with high light exposure gave back the highest number of sequences and were dominated by Cyanobacteria. The South and West facing in middle and lower parts of the sculpture received significantly lower levels of radiation and were dominated by Actinobacteria. Proteobacteria were observed as widespread on the sculpture. This pioneer research provided an in-depth investigation of the microbial community structure on a deteriorated artistic stone in the Australian continent and provides information for the identification of deterioration-associated microorganisms and/or bacteria beneficial for stone preservation., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier Ltd. All rights reserved.)

The origin of microbial mercury methylation has long been a mystery. Here, we employed genome-resolved phylogenetic analyses to decipher the evolution of the mercury-methylating gene, hgcAB, constrain the ancestral origin of the hgc operon, and explain the distribution of hgc in Bacteria and Archaea. We infer the extent to which vertical inheritance and horizontal gene transfer have influenced the evolution of mercury methylators and hypothesize that evolution of this trait bestowed the ability to produce an antimicrobial compound (MeHg+) on a potentially resource-limited early Earth. We speculate that, in response, the evolution of MeHg+-detoxifying alkylmercury lyase (encoded by merB) reduced a selective advantage for mercury methylators and resulted in widespread loss of hgc in Bacteria and Archaea., (© The Author(s) 2023. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.)

Mercury (Hg) methylation genes (hgcAB) mediate the formation of the toxic methylmercury and have been identified from diverse environments, including freshwater and marine ecosystems, Arctic permafrost, forest and paddy soils, coal-ash amended sediments, chlor-alkali plants discharges and geothermal springs. Here we present the first attempt at a standardized protocol for the detection, identification and quantification of hgc genes from metagenomes. Our Hg-cycling microorganisms in aquatic and terrestrial ecosystems (Hg-MATE) database, a catalogue of hgc genes, provides the most accurate information to date on the taxonomic identity and functional/metabolic attributes of microorganisms responsible for Hg methylation in the environment. Furthermore, we introduce "marky-coco", a ready-to-use bioinformatic pipeline based on de novo single-metagenome assembly, for easy and accurate characterization of hgc genes from environmental samples. We compared the recovery of hgc genes from environmental metagenomes using the marky-coco pipeline with an approach based on coassembly of multiple metagenomes. Our data show similar efficiency in both approaches for most environments except those with high diversity (i.e., paddy soils) for which a coassembly approach was preferred. Finally, we discuss the definition of true hgc genes and methods to normalize hgc gene counts from metagenomes., (© 2022 The Authors. Molecular Ecology Resources published by John Wiley & Sons Ltd.)

While recent efforts to catalogue Earth's microbial diversity have focused upon surface and marine habitats, 12-20 % of Earth's biomass is suggested to exist in the terrestrial deep subsurface, compared to ~1.8 % in the deep subseafloor. Metagenomic studies of the terrestrial deep subsurface have yielded a trove of divergent and functionally important microbiomes from a range of localities. However, a wider perspective of microbial diversity and its relationship to environmental conditions within the terrestrial deep subsurface is still required. Our meta-analysis reveals that terrestrial deep subsurface microbiota are dominated by Betaproteobacteria, Gammaproteobacteria and Firmicutes , probably as a function of the diverse metabolic strategies of these taxa. Evidence was also found for a common small consortium of prevalent Betaproteobacteria and Gammaproteobacteria operational taxonomic units across the localities. This implies a core terrestrial deep subsurface community, irrespective of aquifer lithology, depth and other variables, that may play an important role in colonizing and sustaining microbial habitats in the deep terrestrial subsurface. An in silico contamination-aware approach to analysing this dataset underscores the importance of downstream methods for assuring that robust conclusions can be reached from deep subsurface-derived sequencing data. Understanding the global panorama of microbial diversity and ecological dynamics in the deep terrestrial subsurface provides a first step towards understanding the role of microbes in global subsurface element and nutrient cycling.

Microbes transform aqueous mercury (Hg) into methylmercury (MeHg), a potent neurotoxin that accumulates in terrestrial and marine food webs, with potential impacts on human health. This process requires the gene pair hgcAB, which encodes for proteins that actuate Hg methylation, and has been well described for anoxic environments. However, recent studies report potential MeHg formation in suboxic seawater, although the microorganisms involved remain poorly understood. In this study, we conducted large-scale multi-omic analyses to search for putative microbial Hg methylators along defined redox gradients in Saanich Inlet, British Columbia, a model natural ecosystem with previously measured Hg and MeHg concentration profiles. Analysis of gene expression profiles along the redoxcline identified several putative Hg methylating microbial groups, including Calditrichaeota, SAR324 and Marinimicrobia, with the last the most active based on hgc transcription levels. Marinimicrobia hgc genes were identified from multiple publicly available marine metagenomes, consistent with a potential key role in marine Hg methylation. Computational homology modelling predicts that Marinimicrobia HgcAB proteins contain the highly conserved amino acid sites and folding structures required for functional Hg methylation. Furthermore, a number of terminal oxidases from aerobic respiratory chains were associated with several putative novel Hg methylators. Our findings thus reveal potential novel marine Hg-methylating microorganisms with a greater oxygen tolerance and broader habitat range than previously recognized.

Bioremediation systems represent an environmentally sustainable approach to degrading industrially generated thiocyanate (SCN - ), with low energy demand and operational costs and high efficiency and substrate specificity. However, heavy metals present in mine tailings effluent may hamper process efficiency by poisoning thiocyanate-degrading microbial consortia. Here, we experimentally tested the tolerance of an autotrophic SCN - -degrading bacterial consortium enriched from gold mine tailings for Zn, Cu, Ni, Cr, and As. All of the selected metals inhibited SCN - biodegradation to different extents, depending on concentration. At pH of 7.8 and 30 °C, complete inhibition of SCN - biodegradation by Zn, Cu, Ni, and Cr occurred at 20, 5, 10, and 6 mg L -1 , respectively. Lower concentrations of these metals decreased the rate of SCN - biodegradation, with relatively long lag times. Interestingly, the microbial consortium tolerated As even at 500 mg L -1 , although both the rate and extent of SCN - biodegradation were affected. Potentially, the observed As tolerance could be explained by the origin of our microbial consortium in tailings derived from As-enriched gold ore (arsenopyrite). This study highlights the importance of considering metal co-contamination in bioreactor design and operation for SCN - bioremediation at mine sites. KEY POINTS: • Both the efficiency and rate of SCN - biodegradation were inhibited by heavy metals, to different degrees depending on type and concentration of metal. • The autotrophic microbial consortium was capable of tolerating high concentrations of As, potential having adapted to higher As levels derived from the tailings source.

Microbial communities play important roles in the biogeochemical cycling of carbon in the Earth's deep subsurface. Previously, we demonstrated changes to the microbial community structure of a deep aquifer (1.4 km) receiving 150 tons of injected supercritical CO 2 (scCO 2 ) in a geosequestration experiment. The observed changes support a key role in the aquifer microbiome for the thermophilic CO-utilizing anaerobe Carboxydocella, which decreased in relative abundance post-scCO 2 injection. Here, we present results from more detailed metagenomic profiling of this experiment, with genome resolution of the native carboxydotrophic Carboxydocella. We demonstrate a switch in CO-oxidation potential by Carboxydocella through analysis of its carbon monoxide dehydrogenase (CODH) gene before and after the geosequestration experiment. We discuss the potential impacts of scCO 2 on subsurface flow of carbon and electrons from oxidation of the metabolic intermediate carbon monoxide (CO)., (© 2020 The Authors. Environmental Microbiology Reports published by Society for Applied Microbiology and John Wiley & Sons Ltd.)

Geothermal systems emit substantial amounts of aqueous, gaseous, and methylated mercury, but little is known about microbial influences on mercury speciation. Here, we report results from genome-resolved metagenomics and mercury speciation analysis of acidic warm springs in the Ngawha Geothermal Field (<55°C, pH <4.5), Northland Region, Aotearoa New Zealand. Our aim was to identify the microorganisms genetically equipped for mercury methylation, demethylation, or Hg(II) reduction to volatile Hg(0) in these springs. Dissolved total and methylated mercury concentrations in two adjacent springs with different mercury speciation ranked among the highest reported from natural sources (250 to 16,000 ng liter -1 and 0.5 to 13.9 ng liter -1 , respectively). Total solid mercury concentrations in spring sediments ranged from 1,274 to 7,000 μg g -1 In the context of such ultrahigh mercury levels, the geothermal microbiome was unexpectedly diverse and dominated by acidophilic and mesophilic sulfur- and iron-cycling bacteria, mercury- and arsenic-resistant bacteria, and thermophilic and acidophilic archaea. By integrating microbiome structure and metagenomic potential with geochemical constraints, we constructed a conceptual model for biogeochemical mercury cycling in geothermal springs. The model includes abiotic and biotic controls on mercury speciation and illustrates how geothermal mercury cycling may couple to microbial community dynamics and sulfur and iron biogeochemistry. IMPORTANCE Little is currently known about biogeochemical mercury cycling in geothermal systems. The manuscript presents a new conceptual model, supported by genome-resolved metagenomic analysis and detailed geochemical measurements. The model illustrates environmental factors that influence mercury cycling in acidic springs, including transitions between solid (mineral) and aqueous phases of mercury, as well as the interconnections among mercury, sulfur, and iron cycles. This work provides a framework for studying natural geothermal mercury emissions globally. Specifically, our findings have implications for mercury speciation in wastewaters from geothermal power plants and the potential environmental impacts of microbially and abiotically formed mercury species, particularly where they are mobilized in spring waters that mix with surface or groundwaters. Furthermore, in the context of thermophilic origins for microbial mercury volatilization, this report yields new insights into how such processes may have evolved alongside microbial mercury methylation/demethylation and the environmental constraints imposed by the geochemistry and mineralogy of geothermal systems., (Copyright © 2020 American Society for Microbiology.)

Industrial thiocyanate (SCN - ) waste streams from gold mining and coal coking have polluted environments worldwide. Modern SCN - bioremediation involves use of complex engineered heterotrophic microbiomes; little attention has been given to the ability of a simple environmental autotrophic microbiome to biodegrade SCN - . Here we present results from a bioreactor experiment inoculated with SCN - -loaded mine tailings, incubated autotrophically, and subjected to a range of environmentally relevant conditions. Genome-resolved metagenomics revealed that SCN - hydrolase-encoding, sulphur-oxidizing autotrophic bacteria mediated SCN - degradation. These microbes supported metabolically-dependent non-SCN - -degrading sulphur-oxidizing autotrophs and non-sulphur oxidizing heterotrophs, and "niche" microbiomes developed spatially (planktonic versus sessile) and temporally (across changing environmental parameters). Bioreactor microbiome structures changed significantly with increasing temperature, shifting from Thiobacilli to a novel SCN - hydrolase-encoding gammaproteobacteria. Transformation of carbonyl sulphide (COS), a key intermediate in global biogeochemical sulphur cycling, was mediated by plasmid-hosted CS 2 and COS hydrolase genes associated with Thiobacillus, revealing a potential for horizontal transfer of this function. Our work shows that simple native autotrophic microbiomes from mine tailings can be employed for SCN - bioremediation, thus improving the recycling of ore processing waters and reducing the hydrological footprint of mining., (Copyright © 2019 Elsevier Ltd. All rights reserved.)

Gold ore processing typically generates large amounts of thiocyanate (SCN - )-contaminated effluent. When this effluent is stored in unlined tailings dams, contamination of the underlying aquifer can occur. The potential for bioremediation of SCN - -contaminated groundwater, either in situ or ex situ, remains largely unexplored. This study aimed to enrich and characterise SCN - -degrading microorganisms from mining-contaminated groundwater under a range of culturing conditions. Mildly acidic and suboxic groundwater, containing ∼135 mg L -1 SCN - , was collected from an aquifer below an unlined tailings dam. An SCN - -degrading consortium was enriched from contaminated groundwater using combinatory amendments of air, glucose and phosphate. Biodegradation occurred in all oxic cultures, except with the sole addition of glucose, but was inhibited by NH 4 + and did not occur under anoxic conditions. The SCN - -degrading consortium was characterised using 16S and 18S rRNA gene sequencing, identifying a variety of heterotrophic taxa in addition to sulphur-oxidising bacteria. Interestingly, few recognised SCN - -degrading taxa were identified in significant abundance. These results provide both proof-of-concept and the required conditions for biostimulation of SCN - degradation in groundwater by native aquifer microorganisms., Competing Interests: John W. Moreau is an Academic Editor for PeerJ (Environmental Science). All other authors declare that they have no competing interests.

Subseafloor sulfate concentrations typically decrease with depth as this electron acceptor is consumed by respiring microorganisms. However, studies show that seawater can flow through hydraulically conductive basalt to deliver sulfate upwards into deeply buried overlying sediments. Our previous work on IODP Site C0012A (Nankai Trough, Japan) revealed that recirculation of sulfate through the subducting Philippine Sea Plate stimulated microbial activity near the sediment-basement interface (SBI). Here, we describe the microbial ecology, phylogeny, and energetic requirements of population of aero-tolerant sulfate-reducing bacteria in the deep subseafloor. We identified dissimilatory sulfite reductase gene (dsr) sequences 93% related to oxygen-tolerant Desulfovibrionales species across all reaction zones while no SRB were detected in drilling fluid control samples. Pore fluid chemistry revealed low concentrations of methane (<0.25 mM), while hydrogen levels were consistent with active bacterial sulfate reduction (0.51-1.52 nM). Solid phase total organic carbon (TOC) was also considerably low in these subseafloor sediments. Our results reveal the phylogenetic diversity, potential function, and physiological tolerance of a community of sulfate-reducing bacteria living at ~480 m below subducting seafloor., (© 2018 John Wiley & Sons Ltd.)

The presence of organic matter (OM) has a profound impact on uranium (U) redox cycling, either limiting or promoting the mobility of U via binding, reduction, or complexation. To understand the interactions between OM and U, we characterised U oxidation state and speciation in nine OM-rich sediment cores (18 samples), plus a lignite sample from the Mulga Rock polymetallic deposit in Western Australia. Uranium was unevenly dispersed within the analysed samples with 84% of the total U occurring in samples containing >21 wt % OM. Analyses of U speciation, including x-ray absorption spectroscopy and bicarbonate extractions, revealed that U existed predominately (∼71%) as U(VI), despite the low pH (4.5) and nominally reducing conditions within the sediments. Furthermore, low extractability by water, but high extractability by a bi-carbonate solution, indicated a strong association of U with particulate OM. The unexpectedly high proportion of U(VI) relative to U(IV) within the OM-rich sediments implies that OM itself does not readily reduce U, and the reduction of U is not a requirement for immobilizing uranium in OM-rich deposits. The fact that OM can play a significant role in limiting the mobility and reduction of U(VI) in sediments is important for both U-mining and remediation., (Copyright © 2017 Elsevier Ltd. All rights reserved.)

Thiocyanate (SCN - ) is a contaminant requiring remediation in gold mine tailings and wastewaters globally. Seepage of SCN - -contaminated waters into aquifers can occur from unlined or structurally compromised mine tailings storage facilities. A wide variety of microorganisms are known to be capable of biodegrading SCN - ; however, little is known regarding the potential of native microbes for in situ SCN - biodegradation, a remediation option that is less costly than engineered approaches. Here we experimentally characterize the principal biogeochemical barrier to SCN - biodegradation for an autotrophic microbial consortium enriched from mine tailings, to arrive at an environmentally realistic assessment of in situ SCN - biodegradation potential. Upon amendment with phosphate, the consortium completely degraded up to ∼10 mM SCN - to ammonium and sulfate, with some evidence of nitrification of the ammonium to nitrate. Although similarly enriched in known SCN - -degrading strains of thiobacilli, this consortium differed in its source (mine tailings) and metabolism (autotrophy) from those of previous studies. Our results provide a proof of concept that phosphate limitation may be the principal barrier to in situ SCN - biodegradation in mine tailing waters and also yield new insights into the microbial ecology of in situ SCN - bioremediation involving autotrophic sulfur-oxidizing bacteria.

Thiocyanate (SCN - ) forms as a by-product of cyanidation during gold ore processing and can be degraded by a variety of microorganisms utilizing it as an energy, nitrogen, sulphur and/or carbon source. In complex consortia inhabiting bioreactor systems, a range of metabolisms are sustained by SCN - degradation; however, despite the addition or presence of labile carbon sources in most bioreactor designs to date, autotrophic bacteria have been found to dominate key metabolic functions. In this study, we cultured an autotrophic SCN - -degrading consortium directly from gold mine tailings. In a batch-mode bioreactor experiment, this consortium degraded 22 mM SCN - , accumulating ammonium (NH 4 + ) and sulphate (SO 4 2- ) as the major end products. The consortium consisted of a diverse microbial community comprised of chemolithoautotrophic members, and despite the absence of an added organic carbon substrate, a significant population of heterotrophic bacteria. The role of eukaryotes in bioreactor systems is often poorly understood; however, we found their 18S rRNA genes to be most closely related to sequences from bacterivorous Amoebozoa. Through combined chemical and phylogenetic analyses, we were able to infer roles for key microbial consortium members during SCN - biodegradation. This study provides a basis for understanding the behaviour of a SCN - degrading bioreactor under autotrophic conditions, an anticipated approach to remediating SCN - at contemporary gold mines.

Atmospheric deposition of mercury onto sea ice and circumpolar sea water provides mercury for microbial methylation, and contributes to the bioaccumulation of the potent neurotoxin methylmercury in the marine food web. Little is known about the abiotic and biotic controls on microbial mercury methylation in polar marine systems. However, mercury methylation is known to occur alongside photochemical and microbial mercury reduction and subsequent volatilization. Here, we combine mercury speciation measurements of total and methylated mercury with metagenomic analysis of whole-community microbial DNA from Antarctic snow, brine, sea ice and sea water to elucidate potential microbially mediated mercury methylation and volatilization pathways in polar marine environments. Our results identify the marine microaerophilic bacterium Nitrospina as a potential mercury methylator within sea ice. Anaerobic bacteria known to methylate mercury were notably absent from sea-ice metagenomes. We propose that Antarctic sea ice can harbour a microbial source of methylmercury in the Southern Ocean.

Thiocyanate is a common contaminant of the gold mining and coal coking industries for which biological degradation generally represents the most viable approach to remediation. Recent studies of thiocyanate-degrading bioreactor systems have revealed new information on the structure and metabolic activity of thiocyanate-degrading microbial consortia. Previous knowledge was limited primarily to pure-culture or co-culture studies in which the effects of linked carbon, sulfur and nitrogen cycling could not be fully understood. High throughput sequencing, DNA fingerprinting and targeted gene amplification have now elucidated the genetic and metabolic diversity of these complex microbial consortia. Specifically, this has highlighted the roles of key consortium members involved in sulfur oxidation and nitrification. New insights into the biogeochemical cycling of sulfur and nitrogen in bioreactor systems allow tailoring of the microbial metabolism towards meeting effluent composition requirements. Here we review these rapidly advancing studies and synthesize a conceptual model to inform new biotechnologies for thiocyanate remediation.

Methylation of tracer and ambient mercury ((200)Hg and (202)Hg, respectively) equilibrated with four different natural organic matter (NOM) isolates was investigated in vivo using the Hg-methylating sulfate-reducing bacterium Desulfobulbus propionicus 1pr3. Desulfobulbus cultures grown fermentatively with environmentally representative concentrations of dissolved NOM isolates, Hg[II], and HS(-) were assayed for absolute methylmercury (MeHg) concentration and conversion of Hg(II) to MeHg relative to total unfiltered Hg(II). Results showed the (200)Hg tracer was methylated more efficiently in the presence of hydrophobic NOM isolates than in the presence of transphilic NOM, or in the absence of NOM. Different NOM isolates were associated with variable methylation efficiencies for either the (202)Hg tracer or ambient (200)Hg. One hydrophobic NOM, F1 HpoA derived from dissolved organic matter from the Florida Everglades, was equilibrated for different times with Hg tracer, which resulted in different methylation rates. A 5 day equilibration with F1 HpoA resulted in more MeHg production than either the 4 h or 30 day equilibration periods, suggesting a time dependence for NOM-enhanced Hg bioavailability for methylation.

An aerobic, thermophilic and cellulolytic bacterium, designated strain WKT50.2T, was isolated from geothermal soil at Waikite, New Zealand. Strain WKT50.2T grew at 53-76 °C and at pH 5.9-8.2. The DNA G+C content was 58.4 mol%. The major fatty acids were 12-methyl C18 : 0 and C18 : 0. Polar lipids were all linked to long-chain 1,2-diols, and comprised 2-acylalkyldiol-1-O-phosphoinositol (diolPI), 2-acylalkyldiol-1-O-phosphoacylmannoside (diolP-acylMan), 2-acylalkyldiol-1-O-phosphoinositol acylmannoside (diolPI-acylMan) and 2-acylalkyldiol-1-O-phosphoinositol mannoside (diolPI-Man). Strain WKT50.2T utilized a range of cellulosic substrates, alcohols and organic acids for growth, but was unable to utilize monosaccharides. Robust growth of WKT50.2T was observed on protein derivatives. WKT50.2T was sensitive to ampicillin, chloramphenicol, kanamycin, neomycin, polymyxin B, streptomycin and vancomycin. Metronidazole, lasalocid A and trimethoprim stimulated growth. Phylogenetic analysis of 16S rRNA gene sequences showed that WKT50.2T belonged to the class Thermomicrobia within the phylum Chloroflexi, and was most closely related to Thermorudis peleae KI4T (99.6% similarity). DNA-DNA hybridization between WKT50.2T and Thermorudis peleae DSM 27169T was 18.0%. Physiological and biochemical tests confirmed the phenotypic and genotypic differentiation of strain WKT50.2T from Thermorudis peleae KI4T and other members of the Thermomicrobia. On the basis of its phylogenetic position and phenotypic characteristics, we propose that strain WKT50.2T represents a novel species, for which the name Thermorudis pharmacophila sp. nov. is proposed, with the type strain WKT50.2T ( = DSM 26011T = ICMP 20042T). Emended descriptions of Thermomicrobium roseum, Thermomicrobium carboxidum, Thermorudis peleae and Sphaerobacter thermophilus are also proposed, and include the description of a novel respiratory quinone, MK-8 2,3-epoxide (23%), in Thermomicrobium roseum.

We present data from sediment cores collected from IODP Site C0012 in the Shikoku Basin. Our site lies at the Nankai Trough, just prior to subduction of the 19 Ma Philippine Sea plate. Our data indicate that the sedimentary package is undergoing multiple routes of electron transport and that these differing pathways for oxidant supply generate a complex array of metabolic routes and microbial communities involved in carbon cycling. Numerical simulations matched to pore water data document that Ca(2+) and Cl(1-) are largely supplied via diffusion from a high-salinity (44.5 psu) basement fluid, which supports the presence of halophile Archean communities within the deep sedimentary package that are not observed in shallow sediments. Sulfate supply from basement supports anaerobic oxidation of methane (AOM) at a rate of ~0.2 pmol cm(-3) day(-1) at ~400 mbsf. We also note the disappearance of δ-Proteobacteria at 434 mbsf, coincident with the maximum in methane concentration, and their reappearance at 463 mbsf, coinciding with the observed deeper increase in sulfate concentration toward the basement. We did not, however, find ANME representatives in any of the samples analyzed (from 340 to 463 mbsf). The lack of ANME may be due to an overshadowing effect from the more dominant archaeal phylotypes or may indicate involvement of unknown groups of archaea in AOM (i.e., unclassified Euryarchaeota). In addition to the supply of sulfate from a basement aquifer, the deep biosphere at this site is also influenced by an elevated supply of reactive iron (up to 143 μmol g(-1)) and manganese (up to 20 μmol g(-1)). The effect of these metal oxides on the sulfur cycle is inferred from an accompanying sulfur isotope fractionation much smaller than expected from traditional sulfate-reducing pathways. The detection of the manganese- and iron-reducer γ-Proteobacteria Alteromonas at 367 mbsf is consistent with these geochemical inferences., (© 2015 John Wiley & Sons Ltd.)

Coastal acid sulfate soils (CASS) constitute a serious and global environmental problem. Oxidation of iron sulfide minerals exposed to air generates sulfuric acid with consequently negative impacts on coastal and estuarine ecosystems. Tidal inundation represents one current treatment strategy for CASS, with the aim of neutralizing acidity by triggering microbial iron- and sulfate-reduction and inducing the precipitation of iron-sulfides. Although well-known functional guilds of bacteria drive these processes, their distributions within CASS environments, as well as their relationships to tidal cycling and the availability of nutrients and electron acceptors, are poorly understood. These factors will determine the long-term efficacy of "passive" CASS remediation strategies. Here we studied microbial community structure and functional guild distribution in sediment cores obtained from 10 depths ranging from 0 to 20 cm in three sites located in the supra-, inter- and sub-tidal segments, respectively, of a CASS-affected salt marsh (East Trinity, Cairns, Australia). Whole community 16S rRNA gene diversity within each site was assessed by 454 pyrotag sequencing and bioinformatic analyses in the context of local hydrological, geochemical, and lithological factors. The results illustrate spatial overlap, or close association, of iron-, and sulfate-reducing bacteria (SRB) in an environment rich in organic matter and controlled by parameters such as acidity, redox potential, degree of water saturation, and mineralization. The observed spatial distribution implies the need for empirical understanding of the timing, relative to tidal cycling, of various terminal electron-accepting processes that control acid generation and biogeochemical iron and sulfur cycling.

Our primary research paper (Mu et al., 2014) demonstrated selective changes to a deep subsurface prokaryotic community as a result of CO2 stress. Analyzing geochemical and microbial 16S rRNA gene profiles, we evaluated how in situ prokaryotic communities responded to increased CO2 and the presence of trace organic compounds, and related temporal shifts in phylogeny to changes in metabolic potential. In this focused review, we extend upon our previous discussion to present analysis of taxonomic unit co-occurrence profiles from the same field experiment, to attempt to describe dynamic community behavior within the deep subsurface. Understanding the physiology of the subsurface microbial biosphere, including how key functional groups integrate into the community, will be critical to determining the fate of injected CO2. For example, community-wide network analyses may provide insights to whether microbes cooperatively produce biofilm biomass, and/or biomineralize the CO2, and hence, induce changes to formation porosity or changes in electron flow. Furthermore, we discuss potential impacts to the feasibility of subsurface CO2 storage of selectively enriching for particular metabolic functions (e.g., methanogenesis) as a result of CO2 injection.

A novel bacterial strain, NGM72.4(T), was isolated from a hot spring in the Ngatamariki geothermal field, New Zealand. Phylogenetic analysis based on 16S rRNA gene sequences grouped it into the phylum Verrucomicrobia and class level group 3 (also known as OPB35 soil group). NGM72.4(T) stained Gram-negative, and was catalase- and oxidase-positive. Cells were small cocci, 0.5-0.8 µm in diameter, which were motile by means of single flagella. Transmission electron micrograph (TEM) imaging showed an unusual pirellulosome-like intracytoplasmic membrane. The peptidoglycan content was very small with only trace levels of diaminopimelic acid detected. No peptidoglycan structure was visible in TEM imaging. The predominant isoprenoid quinone was MK-7 (92%). The major fatty acids (>15%) were C(16 : 0), anteiso-C(15 : 0), iso-C(16 : 0) and anteiso-C(17 : 0). Major phospholipids were phosphatidylethanolamine (PE), phosphatidylmonomethylethanolamine (PMME) and cardiolipin (CL), and a novel analogous series of phospholipids where diacylglycerol was replaced with diacylserinol (sPE, sPMME, sCL). The DNA G+C content was 65.6 mol%. Cells displayed an oxidative chemoheterotrophic metabolism. NGM72.4(T) is a strictly aerobic thermophile (growth optimum 60-65 °C), has a slightly alkaliphilic pH growth optimum (optimum pH 8.1-8.4) and has a NaCl tolerance of up to 8 g l(-1). Colonies were small, circular and pigmented pale pink. The distinct phylogenetic position and phenotypic traits of strain NGM72.4(T) distinguish it from all other described species of the phylum Verrucomicrobia and, therefore, it is considered to represent a novel species in a new genus for which we propose the name Limisphaera ngatamarikiensis gen. nov., sp. nov. The type strain is NGM72.4(T) ( = ICMP 20182(T) = DSM 27329(T))., (© 2015 IUMS.)

Thiocyanate (SCN(-)) is a toxic contaminant produced by industrial processes such as gold ore cyanidation and coal coking. The potential for remediation by adsorption of SCN(-) on ferrihydrite, the influence of sulfate (SO4(2-)) on SCN(-) adsorption, and the fate of adsorbed SCN(-) during ferrihydrite aging were studied using macroscopic techniques complemented with attenuated total reflectance-Fourier transform infrared analysis (ATR-FTIR), X-ray powder diffraction (XRD) and transmission electron microscopy (TEM). Results showed that adsorption of SCN(-) was strongly affected by the concentration of electrolyte (NaNO3) and pH, with decreases in concentration of NaNO3 and pH leading to increased SCN(-) adsorption. The adsorption isotherms can be described by the Langmuir model. While at lower concentrations (0.52-1.04 mM), the presence of SO4(2-) had little impact on SCN(-) adsorption, at a higher concentration (2.08 mM), SCN(-) adsorption was significantly inhibited. ATR-FTIR data confirmed that SCN(-) was bound as an outer-sphere complex on ferrihydrite, and this mechanism was not influenced by changes in pH or electrolyte concentration. XRD data showed that ferrihydrite transformed to a mixture of hematite and goethite at 75 °C and pH 5 in the presence and absence of SCN(-). Partitioning data revealed that during ferrihydrite transformation, all adsorbed SCN(-) was released into solution., (Crown Copyright © 2014. Published by Elsevier Ltd. All rights reserved.)

Acid-sulfide hot springs are analogs of early Earth geothermal systems where microbial metal(loid) resistance likely first evolved. Arsenic is a metalloid enriched in the acid-sulfide hot spring Champagne Pool (Waiotapu, New Zealand). Arsenic speciation in Champagne Pool follows reaction paths not yet fully understood with respect to biotic contributions and coupling to biogeochemical sulfur cycling. Here we present quantitative arsenic speciation from Champagne Pool, finding arsenite dominant in the pool, rim and outflow channel (55-75% total arsenic), and dithio- and trithioarsenates ubiquitously present as 18-25% total arsenic. In the outflow channel, dimethylmonothioarsenate comprised ≤9% total arsenic, while on the outflow terrace thioarsenates were present at 55% total arsenic. We also quantified sulfide, thiosulfate, sulfate and elemental sulfur, finding sulfide and sulfate as major species in the pool and outflow terrace, respectively. Elemental sulfur concentration reached a maximum at the terrace. Phylogenetic analysis of 16S rRNA genes from metagenomic sequencing revealed the dominance of Sulfurihydrogenibium at all sites and an increased archaeal population at the rim and outflow channel. Several phylotypes were found closely related to known sulfur- and sulfide-oxidizers, as well as sulfur- and sulfate-reducers. Bioinformatic analysis revealed genes underpinning sulfur redox transformations, consistent with sulfur speciation data, and illustrating a microbial role in sulfur-dependent transformation of arsenite to thioarsenate. Metagenomic analysis also revealed genes encoding for arsenate reductase at all sites, reflecting the ubiquity of thioarsenate and a need for microbial arsenate resistance despite anoxic conditions. Absence of the arsenite oxidase gene, aio, at all sites suggests prioritization of arsenite detoxification over coupling to energy conservation. Finally, detection of methyl arsenic in the outflow channel, in conjunction with increased sequences from Aquificaceae, supports a role for methyltransferase in thermophilic arsenic resistance. Our study highlights microbial contributions to coupled arsenic and sulfur cycling at Champagne Pool, with implications for understanding the evolution of microbial arsenic resistance in sulfidic geothermal systems.

Subsurface microorganisms may respond to increased CO2 levels in ways that significantly affect pore fluid chemistry. Changes in CO2 concentration or speciation may result from the injection of supercritical CO2 (scCO2) into deep aquifers. Therefore, understanding subsurface microbial responses to scCO2, or unnaturally high levels of dissolved CO2, will help to evaluate the use of geosequestration to reduce atmospheric CO2 emissions. This study characterized microbial community changes at the 16S rRNA gene level during a scCO2 geosequestration experiment in the 1.4 km-deep Paaratte Formation of the Otway Basin, Australia. One hundred and fifty tons of mixed scCO2 and groundwater was pumped into the sandstone Paaratte aquifer over 4 days. A novel U-tube sampling system was used to obtain groundwater samples under in situ pressure conditions for geochemical analyses and DNA extraction. Decreases in pH and temperature of 2.6 log units and 5.8°C, respectively, were observed. Polyethylene glycols (PEGs) were detected in the groundwater prior to scCO2 injection and were interpreted as residual from drilling fluid used during the emplacement of the CO2 injection well. Changes in microbial community structure prior to scCO2 injection revealed a general shift from Firmicutes to Proteobacteria concurrent with the disappearance of PEGs. However, the scCO2 injection event, including changes in response to the associated variables (e.g., pH, temperature and salinity), resulted in increases in the relative abundances of Comamonadaceae and Sphingomonadaceae suggesting the potential for enhanced scCO2 tolerance of these groups. This study demonstrates a successful new in situ sampling approach for detecting microbial community changes associated with an scCO2 geosequestration event.

A strictly aerobic, thermophilic, moderately acidophilic, non-spore-forming bacterium, strain P373(T), was isolated from geothermally heated soil at Waikite, New Zealand. Cells were filamentous rods, 0.2-0.4 µm in diameter and grew in chains up to 80 µm in length. On the basis of 16S rRNA gene sequence similarity, strain P373(T) was shown to belong to the family Chitinophagaceae (class Sphingobacteriia) of the phylum Bacteroidetes, with the most closely related cultivated strain, Chitinophaga pinensis UQM 2034(T), having 87.6 % sequence similarity. Cells stained Gram-negative, and were catalase- and oxidase-positive. The major fatty acids were i-15 : 0 (10.8 %), i-17 : 0 (24.5 %) and i-17 : 0 3-OH (35.2 %). Primary lipids were phosphatidylethanolamine, two unidentified aminolipids and three other unidentified polar lipids. The presence of sulfonolipids (N-acyl-capnines) was observed in the total lipid extract by mass spectrometry. The G+C content of the genomic DNA was 47.3 mol% and the primary respiratory quinone was MK-7. Strain P373(T) grew at 35-63 °C with an optimum temperature of 60 °C, and at pH 5.5-8.7 with an optimum growth pH of 7.3-7.4. NaCl tolerance was up to 5 % (w/v) with an optimum of 0.1-0.25 % (w/v). Cell colonies were non-translucent and pigmented vivid yellow-orange. Cells displayed an oxidative chemoheterotrophic metabolism. The distinct phylogenetic position and the phenotypic characteristics separate strain P373(T) from all other members of the phylum Bacteroidetes and indicate that it represents a novel species in a new genus, for which the name Thermoflavifilum aggregans gen. nov., sp. nov. is proposed. The type strain of the type species is P373(T) ( = ICMP 20041(T) = DSM 27268(T)).

Unlabelled: A novel B. phytofirmans strain with the capacity to degrade thiocyanate was isolated from pH approximately 6·5 soil contaminated by effluent from gold mine tailings. This Burkholderia strain uses thiocyanate as its sole nitrogen source and can grow on acetate as a sole carbon source in a minimal medium. While biodegradation of thiocyanate has been reported to occur within alkaline environments (e.g. soda lakes and wastewater from coking plants), this work presents the first observation of thiocyanate degradation by Burkholderia at pH <9·0. Our findings therefore inform remediation strategies for thiocyanate contamination in nonalkaline soils and waters impacted by gold-mining activities., Significance and Impact of the Study: This work describes thiocyanate biodegradation by a novel Burkholderia phytofirmans strain isolated from circumneutral pH gold mining-contaminated soils. Previous reports of bacterial thiocyanate degradation have mainly focused on alkaline environments or culturing conditions (pH ≥ 9). Because cyanidation is used globally in gold mining, with thiocyanate as the major contaminant, our results will interest those working on biotechnological approaches to gold mine waste remediation., (© 2013 The Society for Applied Microbiology.)