Recovery of novel bacterial diversity from a forested wetland impacted by reject coal

Effects of coal-fired power plants on soil microbial diversity and community structures

Long-term deposition of atmospheric pollutants emitted from coal combustion and their effects on the eco-environment have been extensively studied around coal-fired power plants. However, the effects of coal-fired power plants on soil microbial communities have received little attention through atmospheric pollutant deposition and coal-stacking. Here, we collected the samples of power plant soils (PS), coal-stacking soils (CSS) and agricultural soils (AS) around three coal-fired power plants and background control soils (BG) in Huainan, a typical mineral resource-based city in East China, and investigated the microbial diversity and community structures through a high-throughput sequencing technique. Coal-stacking significantly increased (p < 0.05) the contents of total carbon, total nitrogen, total sulfur and Mo in the soils, whereas the deposition of atmospheric pollutants enhanced the levels of V, Cu, Zn and Pb. Proteobacteria, Actinobacteria, Thaumarchaeota, Thermoplasmata, Ascomycota and Basidiomycota were the dominant taxa in all soils. The bacterial community showed significant differences (p < 0.05) among PS, CSS, AS and BG, whereas archaeal and fungal communities showed significant differences (p < 0.01) according to soil samples around three coal-fired power plants. The predominant environmental variables affecting soil bacterial, archaeal and fungal communities were Mo-TN-TS, Cu-V-Mo, and organic matter (OM)-Mo, respectively. Certain soil microbial genera were closely related to multiple key factors associated with stacking coal and heavy metal deposition from power plants. This study provided useful insight into better understanding of the relationships between soil microbial communities and long-term disturbances from coal-fired power plants.

Bioaccumulation of contaminants in Scarabaeidae and Silphidae beetles at sites polluted by coal combustion residuals and radiocesium

Anthropogenic contamination from coal-fired power plants and nuclear reactors is a pervasive issue impacting ecosystems across the globe. As a result, it is critical that studies continue to assess the accumulation and effects of trace elements and radionuclides in a diversity of biota. In particular, bioindicator species are a powerful tool for risk assessment of chemically contaminated habitats. Using inductively coupled plasma mass spectrometry (ICP-MS) and auto-gamma counting, we analyzed trace element and radiocesium contaminant concentrations in Scarabaeidae and Silphidae beetles (Order: Coleoptera), important taxa in decomposition and nutrient cycling, at contaminated and reference sites on the Savannah River Site, South Carolina, U.S. Our results revealed variability in trace element concentrations between Scarabaeidae and Silphidae beetles at uncontaminated and contaminated sites. Compared to Scarabaeidae, Silphidae had higher levels of chromium (Cr), copper (Cu), iron (Fe), manganese (Mn), nickel (Ni), and zinc (Zn). Unexpectedly, concentrations of Cr, Cu, and Ni were higher in both taxa at the uncontaminated sites. Scarabaeidae and Silphidae beetles at the coal combustion waste site consistently had high concentrations of arsenic (As), and Scarabaeidae had high concentrations of selenium (Se). Of the 50 beetles analyzed for radiocesium levels, two had elevated radioactivity concentrations, both of which were from a site contaminated with radionuclides. Our results suggest carrion beetles may be particularly sensitive to bioaccumulation of contaminants due to their trophic position and role in decomposition, and thus are useful sentinels of trace element and radionuclide contamination.

Habitat-related variability in the morphological and taxonomic diversity of microbial communities in two Hungarian epigenic karst caves

The physical and chemical characteristics of the bedrock, along with the geological and hydrological conditions of karst caves may influence the taxonomic and functional diversity of prokaryotes. Most studies so far have focused on microbial communities of caves including only a few samples and have ignored the chemical heterogeneity of different habitat types such as sampling sites, dripping water, carbonate precipitates, cave walls, cave sediment and surface soils connected to the caves. The aim of the present study was to compare the morphology, the composition and physiology of the microbiota in caves with similar environmental parameters (temperature, host rock, elemental and mineral composition of speleothems) but located in different epigenic karst systems. Csodabogyós Cave and Baradla Cave (Hungary) were selected for the analysis of bacterial and archaeal communities using electron microscopy, amplicon sequencing, X-ray diffraction, and mass spectroscopic techniques. The microbial communities belonged to the phyla Pseudomonadota, Acidobacteriota, Nitrospirota and Nitrososphaerota, and they showed site-specific variation in composition and diversity. The results indicate that morphological and physiological adaptations provide survival for microorganisms according to the environment. In epigenic karst caves, prokaryotes are prone to increase their adsorption surface, cooperate in biofilms, and implement chemolithoautotrophic growth with different electron-donors and acceptors available in the microhabitats.

Evolutionary patterns of archaea predominant in acidic environment

BACKGROUND

Archaea of the order Thermoplasmatales are widely distributed in natural acidic areas and are amongst the most acidophilic prokaryotic organisms known so far. These organisms are difficult to culture, with currently only six genera validly published since the discovery of Thermoplasma acidophilum in 1970. Moreover, known great diversity of uncultured Thermoplasmatales represents microbial dark matter and underlines the necessity of efforts in cultivation and study of these archaea. Organisms from the order Thermoplasmatales affiliated with the so-called "alphabet-plasmas", and collectively dubbed "E-plasma", were the focus of this study. These archaea were found predominantly in the hyperacidic site PM4 of Parys Mountain, Wales, UK, making up to 58% of total metagenomic reads. However, these archaea escaped all cultivation attempts.

RESULTS

Their genome-based metabolism revealed its peptidolytic potential, in line with the physiology of the previously studied Thermoplasmatales isolates. Analyses of the genome and evolutionary history reconstruction have shown both the gain and loss of genes, that may have contributed to the success of the "E-plasma" in hyperacidic environment compared to their community neighbours. Notable genes among them are involved in the following molecular processes: signal transduction, stress response and glyoxylate shunt, as well as multiple copies of genes associated with various cellular functions; from energy production and conversion, replication, recombination, and repair, to cell wall/membrane/envelope biogenesis and archaella production. History events reconstruction shows that these genes, acquired by putative common ancestors, may determine the evolutionary and functional divergences of "E-plasma", which is much more developed than other representatives of the order Thermoplasmatales. In addition, the ancestral hereditary reconstruction strongly indicates the placement of Thermogymnomonas acidicola close to the root of the Thermoplasmatales.

CONCLUSIONS

This study has analysed the metagenome-assembled genome of "E-plasma", which denotes the basis of their predominance in Parys Mountain environmental microbiome, their global ubiquity, and points into the right direction of further cultivation attempts. The results suggest distinct evolutionary trajectories of organisms comprising the order Thermoplasmatales, which is important for the understanding of their evolution and lifestyle.

Biotechnology of Microorganisms from Coal Environments: From Environmental Remediation to Energy Production

Simple Summary

Despite the wide perception that coal environments are extreme habitats, they harbor resident microbial communities. Coal-associated habitats, such as coal mine areas/drainages, spoil heaps, and coalbeds, are defined as complex ecosystems with indigenous microbial groups and native microecological networks. Resident microorganisms possess rich functional potentials and profoundly shape a range of biotechnological processes in the coal industry, from production to remediation.

Abstract

It was generally believed that coal sources are not favorable as live-in habitats for microorganisms due to their recalcitrant chemical nature and negligible decomposition. However, accumulating evidence has revealed the presence of diverse microbial groups in coal environments and their significant metabolic role in coal biogeochemical dynamics and ecosystem functioning. The high oxygen content, organic fractions, and lignin-like structures of lower-rank coals may provide effective means for microbial attack, still representing a greatly unexplored frontier in microbiology. Coal degradation/conversion technology by native bacterial and fungal species has great potential in agricultural development, chemical industry production, and environmental rehabilitation. Furthermore, native microalgal species can offer a sustainable energy source and an excellent bioremediation strategy applicable to coal spill/seam waters. Additionally, the measures of the fate of the microbial community would serve as an indicator of restoration progress on post-coal-mining sites. This review puts forward a comprehensive vision of coal biodegradation and bioprocessing by microorganisms native to coal environments for determining their biotechnological potential and possible applications.

Atmospheric Methane Consumption and Methanotroph Communities in West Siberian Boreal Upland Forest Ecosystems

Upland forest ecosystems are recognized as net sinks for atmospheric methane (CH4), one of the most impactful greenhouse gases. Biological methane uptake in these ecosystems occurs due to the activity of aerobic methanotrophic bacteria. Russia hosts one-fifth of the global forest area, with the most extensive forest landscapes located in West Siberia. Here, we report seasonal CH4 flux measurements conducted in 2018 in three types of stands in West Siberian middle taiga–Siberian pine, Aspen, and mixed forests. High rates of methane uptake of up to −0.184 mg CH4 m−2 h−1 were measured by a static chamber method, with an estimated total growing season consumption of 4.5 ± 0.5 kg CH4 ha−1. Forest type had little to no effect on methane fluxes within each season. Soil methane oxidation rate ranged from 0 to 8.1 ng CH4 gDW−1 h−1 and was negatively related to water-filled pore space. The microbial soil communities were dominated by the Alpha- and Gammaproteobacteria, Acidobacteriota and Actinobacteriota. The major group of 16S rRNA gene reads from methanotrophs belonged to uncultivated Beijerinckiaceae bacteria. Molecular identification of methanotrophs based on retrieval of the pmoA gene confirmed that Upland Soil Cluster Alpha was the major bacterial group responsible for CH4 oxidation.

High Representation of Archaea Across All Depths in Oxic and Low-pH Sediment Layers Underlying an Acidic Stream

Parys Mountain or Mynydd Parys (Isle of Anglesey, United Kingdom) is a mine-impacted environment, which accommodates a variety of acidophilic organisms. Our previous research of water and sediments from one of the surface acidic streams showed a high proportion of archaea in the total microbial community. To understand the spatial distribution of archaea, we sampled cores (0-20 cm) of sediment and conducted chemical analyses and taxonomic profiling of microbiomes using 16S rRNA gene amplicon sequencing in different core layers. The taxonomic affiliation of sequencing reads indicated that archaea represented between 6.2 and 54% of the microbial community at all sediment depths. Majority of archaea were associated with the order Thermoplasmatales, with the most abundant group of sequences being clustered closely with the phylotype B_DKE, followed by "E-plasma," "A-plasma," other yet uncultured Thermoplasmatales with Ferroplasma and Cuniculiplasma spp. represented in minor proportions. Thermoplasmatales were found at all depths and in the whole range of chemical conditions with their abundance correlating with sediment Fe, As, Cr, and Mn contents. The bacterial microbiome component was largely composed in all layers of sediment by members of the phyla Proteobacteria, Actinobacteria, Nitrospirae, Firmicutes, uncultured Chloroflexi (AD3 group), and Acidobacteria. This study has revealed a high abundance of Thermoplasmatales in acid mine drainage-affected sediment layers and pointed at these organisms being the main contributors to carbon, and probably to iron and sulfur cycles in this ecosystem.

Effects of industrial disturbances on biodiversity of carrion-associated beetles

Energy production systems such as nuclear reactors and coal-burning power plants produce a multitude of waste contaminants including radionuclides, trace elements, and heavy metals. Among invertebrates, much of the effort to understand the impact of these contaminants has focused in aquatic environments, while relatively less attention has been on terrestrial communities. We investigated the effects of trace element and radionuclide contamination on assemblages of beetles that are drawn to vertebrate carrion. Samples were collected from riparian sites at the Savannah River Site in South Carolina to compare trap catches (i.e., measure of relative abundance) of beetles and species diversity along a habitat gradient (0-300 m) away from an aquatic habitat and between uncontaminated and contaminated sites. We collected 17,800 carrion-associated beetles representing 112 species in nine families, which were classified as either scavenger or predatory beetles. Beetle catches and species diversity were generally higher at contaminated than uncontaminated sites. These trends were likely driven by scavenger species, which showed similar patterns between sites, whereas patterns of catches and species diversity were variable between sites for predatory beetles. Species compositions of contaminated and uncontaminated sites were generally distinct, however habitat edges appeared to substantially affect beetle assemblages. Overall, our study suggests carrion beetle assemblages are sensitive to edge effects and may exhibit variable responses to the presence of anthropogenic contaminants or disturbances associated with energy production systems. Such results reflect the inherent variability among individual beetle species, populations, and communities to local environmental conditions, and underscores the need for multi-taxa approach in environmental impact assessments.

Insights into ecological role of a new deltaproteobacterial order Candidatus Acidulodesulfobacterales by metagenomics and metatranscriptomics

Several abundant but yet uncultivated bacterial groups exist in extreme iron- and sulfur-rich environments, and the physiology, biodiversity, and ecological roles of these bacteria remain a mystery. Here we retrieved four metagenome-assembled genomes (MAGs) from an artificial acid mine drainage (AMD) system, and propose they belong to a new deltaproteobacterial order, Candidatus Acidulodesulfobacterales. The distribution pattern of Ca. Acidulodesulfobacterales in AMDs across Southeast China correlated strongly with ferrous iron. Reconstructed metabolic pathways and gene expression profiles showed that they were likely facultatively anaerobic autotrophs capable of nitrogen fixation. In addition to dissimilatory sulfate reduction, encoded by dsrAB, dsrD, dsrL, and dsrEFH genes, these microorganisms might also oxidize sulfide, depending on oxygen concentration and/or oxidation reduction potential. Several genes with homology to those involved in iron metabolism were also identified, suggesting their potential role in iron cycling. In addition, the expression of abundant resistance genes revealed the mechanisms of adaptation and response to the extreme environmental stresses endured by these organisms in the AMD environment. These findings shed light on the distribution, diversity, and potential ecological role of the new order Ca. Acidulodesulfobacterales in nature.

Characterization of the microbial community composition and the distribution of Fe-metabolizing bacteria in a creek contaminated by acid mine drainage

A small watershed heavily contaminated by long-term acid mine drainage (AMD) from an upstream abandoned coal mine was selected to study the microbial community developed in such extreme system. The watershed consists of AMD-contaminated creek, adjacent contaminated soils, and a small cascade aeration unit constructed downstream, which provide an excellent contaminated site to study the microbial response in diverse extreme AMD-polluted environments. The results showed that the innate microbial communities were dominated by acidophilic bacteria, especially acidophilic Fe-metabolizing bacteria, suggesting that Fe and pH are the primary environmental factors in governing the indigenous microbial communities. The distribution of Fe-metabolizing bacteria showed distinct site-specific patterns. A pronounced shift from diverse communities in the upstream to Proteobacteria-dominated communities in the downstream was observed in the ecosystem. This location-specific trend was more apparent at genus level. In the upstream samples (sampling sites just below the coal mining adit), a number of Fe(II)-oxidizing bacteria such as Alicyclobacillus spp., Metallibacterium spp., and Acidithrix spp. were dominant, while Halomonas spp. were the major Fe(II)-oxidizing bacteria observed in downstream samples. Additionally, Acidiphilium, an Fe(III)-reducing bacterium, was enriched in the upstream samples, while Shewanella spp. were the dominant Fe(III)-reducing bacteria in downstream samples. Further investigation using linear discriminant analysis (LDA) effect size (LEfSe), principal coordinate analysis (PCoA), and unweighted pair group method with arithmetic mean (UPGMA) clustering confirmed the difference of microbial communities between upstream and downstream samples. Canonical correspondence analysis (CCA) and Spearman's rank correlation indicate that total organic carbon (TOC) content is the primary environmental parameter in structuring the indigenous microbial communities, suggesting that the microbial communities are shaped by three major environmental parameters (i.e., Fe, pH, and TOC). These findings were beneficial to a better understanding of natural attenuation of AMD.

Differences in the Effect of Coal Pile Runoff (Low pH, High Metal Concentrations) Versus Natural Carolina Bay Water (Low pH, Low Metal Concentrations) on Plant Condition and Associated Bacterial Epiphytes of Salvinia minima

Numerous wetlands and streams have been impacted by acid mine drainage (AMD) resulting in lowered pH and increased levels of toxic heavy metals. Remediation of these contaminated sites requires knowledge on the response of microbial communities (especially epiphytic) and aquatic plants to these altered environmental conditions. We examined the effect of coal pile runoff waters as an example of AMD in contrast to natural water from Carolina Bays with low pH and levels of metals on Salvinia minima, a non-native, metal accumulating plant and associated epiphytic bacteria. Treatments included water from two Carolina Bays, one AMD basin and Hoagland's Solution at two pH levels (natural and adjusted to 5.0-5.5). Using controlled replicated microcosms (N = 64) we determined that the combination of low pH and high metal concentrations has a significant negative impact (p < 0.05) on plant condition and epiphytes. Solution metal concentrations dropped indicating removal from solution by S. minima in all microcosms.

Halophyte plant colonization as a driver of the composition of bacterial communities in salt marshes chronically exposed to oil hydrocarbons

In this study, two molecular techniques [denaturing gradient gel electrophoresis (DGGE) and barcoded pyrosequencing] were used to evaluate the composition of bacterial communities in salt marsh microhabitats [bulk sediment and sediment surrounding the roots (rhizosphere) of Halimione portulacoides and Sarcocornia perennis ssp. perennis] that have been differentially affected by oil hydrocarbon (OH) pollution. Both DGGE and pyrosequencing revealed that bacterial composition is structured by microhabitat. Rhizosphere sediment from both plant species revealed enrichment of operational taxonomic units closely related to Acidimicrobiales, Myxococcales and Sphingomonadales. The in silico metagenome analyses suggest that homologous genes related to OH degradation appeared to be more frequent in both plant rhizospheres than in bulk sediment. In summary, this study suggests that halophyte plant colonization is an important driver of hydrocarbonoclastic bacterial community composition in estuarine environments, which can be exploited for in situ phytoremediation of OH in salt marsh environments.

Potentially novel copper resistance genes in copper-enriched activated sludge revealed by metagenomic analysis

In this study, we utilized the Illumina high-throughput metagenomic approach to investigate diversity and abundance of both microbial community and copper resistance genes (CuRGs) in activated sludge (AS) which was enriched under copper selective stress up to 800 mg/L. The raw datasets (~3.5 Gb for each sample, i.e., the copper-enriched AS and the control AS) were merged and normalized for the BLAST analyses against the SILVA SSU rRNA gene database and self-constructed copper resistance protein database (CuRD). Also, the raw metagenomic sequences were assembled into contigs and analyzed based on Open Reading Frames (ORFs) to identify potentially novel copper resistance genes. Among the different resistance systems for copper detoxification under the high copper stress condition, the Cus system was the most enriched system. The results also indicated that genes encoding multi-copper oxidase played a more important role than those encoding efflux proteins. More significantly, several potentially novel copper resistance ORFs were identified by Pfam search and phylogenic analysis. This study demonstrated a new understanding of microbial-mediated copper resistance under high copper stress using high-throughput shotgun sequencing technique.

Depth-dependent geochemical and microbiological gradients in Fe(III) deposits resulting from coal mine-derived acid mine drainage

We evaluated the depth-dependent geochemistry and microbiology of sediments that have developed via the microbially-mediated oxidation of Fe(II) dissolved in acid mine drainage (AMD), giving rise to a 8–10 cm deep “iron mound” that is composed primarily of Fe(III) (hydr)oxide phases. Chemical analyses of iron mound sediments indicated a zone of maximal Fe(III) reducing bacterial activity at a depth of approximately 2.5 cm despite the availability of dissolved O₂ at this depth. Subsequently, Fe(II) was depleted at depths within the iron mound sediments that did not contain abundant O₂. Evaluations of microbial communities at 1 cm depth intervals within the iron mound sediments using “next generation” nucleic acid sequencing approaches revealed an abundance of phylotypes attributable to acidophilic Fe(II) oxidizing Betaproteobacteria and the chloroplasts of photosynthetic microeukaryotic organisms in the upper 4 cm of the iron mound sediments. While we observed a depth-dependent transition in microbial community structure within the iron mound sediments, phylotypes attributable to Gammaproteobacterial lineages capable of both Fe(II) oxidation and Fe(III) reduction were abundant in sequence libraries (comprising ≥20% of sequences) from all depths. Similarly, abundances of total cells and culturable Fe(II) oxidizing bacteria were uniform throughout the iron mound sediments. Our results indicate that O₂ and Fe(III) reduction co-occur in AMD-induced iron mound sediments, but that Fe(II)-oxidizing activity may be sustained in regions of the sediments that are depleted in O₂.

'Candidatus Megaira polyxenophila' gen. nov., sp. nov.: considerations on evolutionary history, host range and shift of early divergent rickettsiae

"Neglected Rickettsiaceae" (i.e. those harboured by non-hematophagous eukaryotic hosts) display greater phylogenetic variability and more widespread dispersal than pathogenic ones; yet, the knowledge about their actual host range and host shift mechanism is scarce. The present work reports the characterization following the full-cycle rRNA approach (SSU rRNA sequence, specific in situ hybridization, and ultrastructure) of a novel rickettsial bacterium, herewith proposed as 'Candidatus Megaira polyxenophila' gen. nov., sp. nov. We found it in association with four different free-living ciliates (Diophrys oligothrix, Euplotes octocarinatus, Paramecium caudatum, and Spirostomum sp., all belonging to Alveolata, Ciliophora); furthermore it was recently observed as intracellular occurring in Carteria cerasiformis and Pleodorina japonica (Chlorophyceae, Chlorophyta). Phylogenetic analyses demonstrated the belonging of the candidate new genus to the family Rickettsiaceae (Alphaproteobacteria, Rickettsiales) as a sister group of the genus Rickettsia. In situ observations revealed the ability of the candidate new species to colonize either nuclear or cytoplasmic compartments, depending on the host organism. The presence of the same bacterial species within different, evolutionary distant, hosts indicates that 'Candidatus Megaira polyxenophila' recently underwent several distinct host shifts, thus suggesting the existence of horizontal transmission pathways. We consider these findings as indicative of an unexpected spread of rickettsial infections in aquatic communities, possibly by means of trophic interactions, and hence propose a new interpretation of the origin and phylogenetic diversification of rickettsial bacteria.

Evolution of microbial "streamer" growths in an acidic, metal-contaminated stream draining an abandoned underground copper mine

A nine year study was carried out on the evolution of macroscopic “acid streamer” growths in acidic, metal-rich mine water from the point of construction of a new channel to drain an abandoned underground copper mine. The new channel became rapidly colonized by acidophilic bacteria: two species of autotrophic iron-oxidizers (Acidithiobacillus ferrivorans and “Ferrovum myxofaciens”) and a heterotrophic iron-oxidizer (a novel genus/species with the proposed name “Acidithrix ferrooxidans”). The same bacteria dominated the acid streamer communities for the entire nine year period, with the autotrophic species accounting for ~80% of the micro-organisms in the streamer growths (as determined by terminal restriction enzyme fragment length polymorphism (T-RFLP) analysis). Biodiversity of the acid streamers became somewhat greater in time, and included species of heterotrophic acidophiles that reduce ferric iron (Acidiphilium, Acidobacterium, Acidocella and gammaproteobacterium WJ2) and other autotrophic iron-oxidizers (Acidithiobacillus ferrooxidans and Leptospirillum ferrooxidans). The diversity of archaea in the acid streamers was far more limited; relatively few clones were obtained, all of which were very distantly related to known species of euryarchaeotes. Some differences were apparent between the acid streamer community and planktonic-phase bacteria. This study has provided unique insights into the evolution of an extremophilic microbial community, and identified several novel species of acidophilic prokaryotes.

Archaeal diversity: temporal variation in the arsenic-rich creek sediments of Carnoulès Mine, France

The Carnoulès mine is an extreme environment located in the South of France. It is an unusual ecosystem due to its acidic pH (2-3), high concentration of heavy metals, iron, and sulfate, but mainly due to its very high concentration of arsenic (up to 10 g L⁻¹ in the tailing stock pore water, and 100-350 mg L⁻¹ in Reigous Creek, which collects the acid mine drainage). Here, we present a survey of the archaeal community in the sediment and its temporal variation using a culture-independent approach by cloning of 16S rRNA encoding genes. The taxonomic affiliation of Archaea showed a low degree of biodiversity with two different phyla: Euryarchaeota and Thaumarchaeota. The archaeal community varied in composition and richness throughout the sampling campaigns. Many sequences were phylogenetically related to the order Thermoplasmatales represented by aerobic or facultatively anaerobic, thermoacidophilic autotrophic or heterotrophic organisms like the organotrophic genus Thermogymnomonas. Some members of Thermoplasmatales can also derive energy from sulfur/iron oxidation or reduction. We also found microorganisms affiliated with methanogenic Archaea (Methanomassiliicoccus luminyensis), which are involved in the carbon cycle. Some sequences affiliated with ammonia oxidizers, involved in the first and rate-limiting step in nitrification, a key process in the nitrogen cycle were also observed, including Candidatus Nitrososphaera viennensis and Candidatus nitrosopumilus sp. These results suggest that Archaea may be important players in the Reigous sediments through their participation in the biochemical cycles of elements, including those of carbon and nitrogen.

Single-cell analysis reveals a novel uncultivated magnetotactic bacterium within the candidate division OP3

Magnetotactic bacteria (MTB) are a diverse group of prokaryotes that orient along magnetic fields using membrane-coated magnetic nanocrystals of magnetite (Fe(3) O(4) ) or greigite (Fe(3) S(4) ), the magnetosomes. Previous phylogenetic analysis of MTB has been limited to few cultivated species and most abundant members of natural populations, which were assigned to Proteobacteria and the Nitrospirae phyla. Here, we describe a single cell-based approach that allowed the targeted phylogenetic and ultrastructural analysis of the magnetotactic bacterium SKK-01, which was low abundant in sediments of Lake Chiemsee. Morphologically conspicuous single cells of SKK-01 were micromanipulated from magnetically collected multi-species MTB populations, which was followed by whole genome amplification and ultrastructural analysis of sorted cells. Besides intracellular sulphur inclusions, the large ovoid cells of SKK-01 harbour ∼175 bullet-shaped magnetosomes arranged in multiple chains that consist of magnetite as revealed by TEM and EDX analysis. Sequence analysis of 16 and 23S rRNA genes from amplified genomic DNA as well as fluorescence in situ hybridization assigned SKK-01 to the candidate division OP3, which so far lacks any cultivated representatives. SKK-01 represents the first morphotype that can be assigned to the OP3 group as well as the first magnetotactic member of the PVC superphylum.

The quantitative significance of Syntrophaceae and syntrophic partnerships in methanogenic degradation of crude oil alkanes

Libraries of 16S rRNA genes cloned from methanogenic oil degrading microcosms amended with North Sea crude oil and inoculated with estuarine sediment indicated that bacteria from the genera Smithella (Deltaproteobacteria, Syntrophaceace) and Marinobacter sp. (Gammaproteobacteria) were enriched during degradation. Growth yields and doubling times (36 days for both Smithella and Marinobacter) were determined using qPCR and quantitative data on alkanes, which were the predominant hydrocarbons degraded. The growth yield of the Smithella sp. [0.020 g_(cell-C)/g_(alkane-C)], assuming it utilized all alkanes removed was consistent with yields of bacteria that degrade hydrocarbons and other organic compounds in methanogenic consortia. Over 450 days of incubation predominance and exponential growth of Smithella was coincident with alkane removal and exponential accumulation of methane. This growth is consistent with Smithella's occurrence in near surface anoxic hydrocarbon degrading systems and their complete oxidation of crude oil alkanes to acetate and/or hydrogen in syntrophic partnership with methanogens in such systems. The calculated growth yield of the Marinobacter sp., assuming it grew on alkanes, was [0.0005 g_(cell-C)/g_(alkane-C)] suggesting that it played a minor role in alkane degradation. The dominant methanogens were hydrogenotrophs (Methanocalculus spp. from the Methanomicrobiales). Enrichment of hydrogen-oxidizing methanogens relative to acetoclastic methanogens was consistent with syntrophic acetate oxidation measured in methanogenic crude oil degrading enrichment cultures. qPCR of the Methanomicrobiales indicated growth characteristics consistent with measured rates of methane production and growth in partnership with Smithella.

Characterization of active microbes in a full-scale anaerobic fluidized bed reactor treating phenolic wastewater

This study investigated the active microbial community in a full-scale granular activated carbon-anaerobic fluidized bed (GAC-AFB) reactor treating wastewater from the manufacturing of phenolic resin, using 16S rRNA-based molecular analyses. The results of cDNA from 16S rRNA revealed that Methanosaeta-related (83.9% of archaeal clones) and Syntrophorhabdaceae (formerly named Deltaproteobacteria group TA)-related (68.9% of bacterial clones) microorganisms were as the most predominant populations in the phenol-degrading GAC-AFB reactor. The high abundance of Syntrophorhabdaceae was supported by a terminal restriction fragment length polymorphism (T-RFLP) analysis, which showed that a Syntrophorhabdaceae-like fragment of 119 bp (~80% of total fragments) was the most predominant phylotype. Furthermore, fluorescence in situ hybridization (FISH) analyses suggested that Syntrophus- and Chloroflexi-like cells were also in high abundance in the GAC biofilm. A non-layered structure of microorganisms was found in the GAC biofilm, where Methanosaeta (thick filamentous), Syntrophorhabdaceae (oval-shaped), Syntrophus (small rods) and Chloroflexi (thin-filamentous) were randomly distributed with high abundance. These findings greatly improve our understanding of the diversity and distribution of microbial populations in a full-scale mesophilic bioreactor treating an actual phenol-containing waste stream.

Microbial diversity in anaerobic sediments at Rio Tinto, a naturally acidic environment with a high heavy metal content

The Tinto River is an extreme environment located at the core of the Iberian Pyritic Belt (IPB). It is an unusual ecosystem due to its size (100 km long), constant acidic pH (mean pH, 2.3), and high concentration of heavy metals, iron, and sulfate in its waters, characteristics that make the Tinto River Basin comparable to acidic mine drainage (AMD) systems. In this paper we present an extensive survey of the Tinto River sediment microbiota using two culture-independent approaches: denaturing gradient gel electrophoresis and cloning of 16S rRNA genes. The taxonomic affiliation of the Bacteria showed a high degree of biodiversity, falling into 5 different phyla: Proteobacteria, Firmicutes, Bacteroidetes, Acidobacteria, and Actinobacteria; meanwhile, all the Archaea were affiliated with the order Thermoplasmatales. Microorganisms involved in the iron (Acidithiobacillus ferrooxidans, Sulfobacillus spp., Ferroplasma spp., etc.), sulfur (Desulfurella spp., Desulfosporosinus spp., Thermodesulfobium spp., etc.), and carbon (Acidiphilium spp., Bacillus spp., Clostridium spp., Acidobacterium spp., etc.) cycles were identified, and their distribution was correlated with physicochemical parameters of the sediments. Ferric iron was the main electron acceptor for the oxidation of organic matter in the most acid and oxidizing layers, so acidophilic facultative Fe(III)-reducing bacteria appeared widely in the clone libraries. With increasing pH, the solubility of iron decreases and sulfate-reducing bacteria become dominant, with the ecological role of methanogens being insignificant. Considering the identified microorganisms-which, according to the rarefaction curves and Good's coverage values, cover almost all of the diversity-and their corresponding metabolism, we suggest a model of the iron, sulfur, and organic matter cycles in AMD-related sediments.

Development of a small-scale bioreactor method to monitor the molecular diversity and environmental impacts of bacterial biofilm communities from an acid mine drainage impacted creek

Shamokin Creek is a tributary of the Susquehanna River in central Pennsylvania that is heavily impacted by the acid mine drainage (AMD) caused by the oxidation of pyrite from the region's extensive anthracite coal mining industry. Recent studies have begun to characterize the microbial communities present in this and other AMD-impacted waters, but varying environmental conditions have complicated attempts to determine the ecological impacts of individual bacterial species within these communities. This study developed a small-scale biofilm reactor protocol that allowed us to simultaneously monitor the development of bacterial biofilm communities in AMD-impacted creek collected water using terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA genes, while assessing the impacts that the developing biofilms were having on water quality. Our analysis confirmed that the diversity and composition of these small in situ biofilm communities could be monitored using molecular methods, and indicated the possible presence of many taxa frequently found in AMD environments, including Sulfobacillus, Nitrospira, Desulfovibrio, Geobacter, and Leptothrix species. A significant increase in the total sulfate was observed in the bioreactor, and as most likely due to the accumulation of sulfur-oxidizing bacteria such as Sulfobacillus in the biofilms. This system will allow us to study the microbial ecology of Shamokin Creek through controlled experiments that will ultimately integrate microscopic, molecular, physiological and chemical analyses, and that can be utilized to develop more effective and cost-efficient environmental remediation techniques for AMD-impacted areas.

Archaeal diversity in a terrestrial acidic spring field revealed by a novel PCR primer targeting archaeal 16S rRNA genes

The phylogenetic diversity of archaeal 16S rRNA genes in a thermoacidic spring field of Ohwakudani, Hakone, Japan, was investigated by PCR-based analysis using a novel Archaea-specific primer designed in the present study. Clone libraries of archaeal 16S rRNA genes were constructed from hot water (78 °C) and mud (28 °C) samples by PCR using a newly designed forward primer and a previously reported forward primer with reverse primers. Most phylotypes found in the libraries from the hot water sample were related to cultured (hyper)thermophiles. The phylotypes and their detection frequencies from the hot water sample were similar for the libraries amplified with the two different primer sets. In contrast, phylotypes having a low similarity (<95%) to cultured Archaea were found in the libraries from the mud sample. Some of the phylotypes were relatively close to members of Thermoplasmata (80-93% similarity) and the others were not clearly affiliated with Crenarchaeota and Euryarchaeota, but related to Thaumarchaeota and Korarchaeota. The phylotypes and their detection frequencies were significantly different between the two libraries of the mud sample. Our results from the PCR-based analysis using the redesigned primer suggest that more diverse, uncultured Archaea are present in acidic environments at a low temperature than previously recognized.

Identification of sulfur-cycle prokaryotes in a low-sulfate lake (Lake Pavin) using aprA and 16S rRNA gene markers

Geochemical researches at Lake Pavin, a low-sulfate-containing freshwater lake, suggest that the dominant biogeochemical processes are iron and sulfate reduction, and methanogenesis. Although the sulfur cycle is one of the main active element cycles in this lake, little is known about the sulfate-reducer and sulfur-oxidizing bacteria. The aim of this study was to assess the vertical distribution of these microbes and their diversities and to test the hypothesis suggesting that only few SRP populations are involved in dissimilatory sulfate reduction and that Epsilonproteobacteria are the likely key players in the oxidative phase of sulfur cycle by using a PCR aprA gene-based approach in comparison with a 16S rRNA gene-based analysis. The results support this hypothesis. Finally, this preliminary work points strongly the likelihood of novel metabolic processes upon the availability of sulfate and other electron acceptors.

Geobacter: the microbe electric's physiology, ecology, and practical applications

Geobacter species specialize in making electrical contacts with extracellular electron acceptors and other organisms. This permits Geobacter species to fill important niches in a diversity of anaerobic environments. Geobacter species appear to be the primary agents for coupling the oxidation of organic compounds to the reduction of insoluble Fe(III) and Mn(IV) oxides in many soils and sediments, a process of global biogeochemical significance. Some Geobacter species can anaerobically oxidize aromatic hydrocarbons and play an important role in aromatic hydrocarbon removal from contaminated aquifers. The ability of Geobacter species to reductively precipitate uranium and related contaminants has led to the development of bioremediation strategies for contaminated environments. Geobacter species produce higher current densities than any other known organism in microbial fuel cells and are common colonizers of electrodes harvesting electricity from organic wastes and aquatic sediments. Direct interspecies electron exchange between Geobacter species and syntrophic partners appears to be an important process in anaerobic wastewater digesters. Functional and comparative genomic studies have begun to reveal important aspects of Geobacter physiology and regulation, but much remains unexplored. Quantifying key gene transcripts and proteins of subsurface Geobacter communities has proven to be a powerful approach to diagnose the in situ physiological status of Geobacter species during groundwater bioremediation. The growth and activity of Geobacter species in the subsurface and their biogeochemical impact under different environmental conditions can be predicted with a systems biology approach in which genome-scale metabolic models are coupled with appropriate physical/chemical models. The proficiency of Geobacter species in transferring electrons to insoluble minerals, electrodes, and possibly other microorganisms can be attributed to their unique "microbial nanowires," pili that conduct electrons along their length with metallic-like conductivity. Surprisingly, the abundant c-type cytochromes of Geobacter species do not contribute to this long-range electron transport, but cytochromes are important for making the terminal electrical connections with Fe(III) oxides and electrodes and also function as capacitors, storing charge to permit continued respiration when extracellular electron acceptors are temporarily unavailable. The high conductivity of Geobacter pili and biofilms and the ability of biofilms to function as supercapacitors are novel properties that might contribute to the field of bioelectronics. The study of Geobacter species has revealed a remarkable number of microbial physiological properties that had not previously been described in any microorganism. Further investigation of these environmentally relevant and physiologically unique organisms is warranted.

Chthonomonas calidirosea gen. nov., sp. nov., an aerobic, pigmented, thermophilic micro-organism of a novel bacterial class, Chthonomonadetes classis nov., of the newly described phylum Armatimonadetes originally designated candidate division OP10

An aerobic, saccharolytic, obligately thermophilic, motile, non-spore-forming bacterium, strain T49(T), was isolated from geothermally heated soil at Hell's Gate, Tikitere, New Zealand. On the basis of 16S rRNA gene sequence similarity, T49(T) is the first representative of a new class in the newly described phylum Armatimonadetes, formerly known as candidate division OP10. Cells of strain T49(T) stained Gram-negative and were catalase-positive and oxidase-negative. Cells possessed a highly corrugated outer membrane. The major fatty acids were 16 : 0, i17 : 0 and ai17 : 0. The G+C content of the genomic DNA was 54.6 mol%. Strain T49(T) grew at 50-73 °C with an optimum temperature of 68 °C, and at pH 4.7-5.8 with an optimum growth pH of 5.3. A growth rate of 0.012 h(-1) was observed under optimal temperature and pH conditions. The primary respiratory quinone was MK-8. Optimal growth was achieved in the absence of NaCl, although growth was observed at NaCl concentrations as high as 2 % (w/v). Strain T49(T) was able to utilize mono- and disaccharides such as cellobiose, lactose, mannose and glucose, as well as branched or amorphous polysaccharides such as starch, CM-cellulose, xylan and glycogen, but not highly linear polysaccharides such as crystalline cellulose or cotton. On the basis of its phylogenetic position and phenotypic characteristics, we propose that strain T49(T) represents a novel bacterial genus and species within the new class Chthonomonadetes classis nov. of the phylum Armatimonadetes. The type strain of Chthonomonas calidirosea gen. nov., sp. nov. is T49(T) ( = DSM 23976(T) = ICMP 18418(T)).

Microbial community structure across the tree of life in the extreme Río Tinto

Understanding biotic versus abiotic forces that shape community structure is a fundamental aim of microbial ecology. The acidic and heavy metal extreme Río Tinto (RT) in southwestern Spain provides a rare opportunity to conduct an ecosystem-wide biodiversity inventory at the level of all three domains of life, because diversity there is low and almost exclusively microbial. Despite improvements in high-throughput DNA sequencing, environmental biodiversity studies that use molecular metrics and consider entire ecosystems are rare. These studies can be prohibitively expensive if domains are considered separately, and differences in copy number of eukaryotic ribosomal RNA genes can bias estimates of relative abundances of phylotypes recovered. In this study we have overcome these barriers (1) by targeting all three domains in a single polymerase chain reaction amplification and (2) by using a replicated sampling design that allows for incidence-based methods to extract measures of richness and carry out downstream analyses that address community structuring effects. Our work showed that combined bacterial and archaeal richness is an order of magnitude higher than eukaryotic richness. We also found that eukaryotic richness was highest at the most extreme sites, whereas combined bacterial and archaeal richness was highest at less extreme sites. Quantitative community phylogenetics showed abiotic forces to be primarily responsible for shaping the RT community structure. Canonical correspondence analysis revealed co-occurrence of obligate symbionts and their putative hosts that may contribute to biotic forces shaping community structure and may further provide a possible mechanism for persistence of certain low-abundance bacteria encountered in the RT.

Effect of enrichment medium on real-time detection of Salmonella enterica from lettuce and tomato enrichment cultures

Three enrichment broths commonly used for detection of Salmonella (buffered peptone water [BPW], tryptic soy broth [TSB], and universal preenrichment broth [UPB]) were compared for use in real-time SYBR Green PCR detection of Salmonella introduced into enrichment cultures made from store-bought lettuce and tomatoes. The produce served as a source of normal plant microbiota to measure how well DNA-based detection methods for Salmonella work in a suspension of plant-associated bacteria that may be closely related to Salmonella. A qualitative assessment of the background microbiota that grew in the three enrichment broths cultures from tomato and lettuce samples revealed that different bacteria predominated in the different broths. Results obtained with five produce-related outbreak Salmonella strains and PCR primers directed toward three different Salmonella genes suggest that the ability to detect Salmonella from these enrichment cultures by real-time PCR was 10 to 1,000 times better with TSB enrichment cultures. Detection levels were similar between the different enrichment media when an immunomagnetic separation method was used; however, the immunological technique did not enhance detection from TSB enrichment cultures. Detection could be affected by the medium and by the background microbiota. An immunomagnetic separation method may be useful in BPW and UPB enrichment cultures but not in TSB enrichment cultures.

Comparison of archaeal and bacterial community structures in heavily oil-contaminated and pristine soils

Archaeal and bacterial community structures in heavily oil-contaminated and pristine soils were compared using denaturing gradient gel electrophoresis and 16S rRNA gene libraries. The results showed that archaeal diversity was more complex in the contaminated soil than in the uncontaminated control soil. Archaeal populations in the contaminated soil consisted mainly of Euryarchaeota, with abundant methanogen-like operational taxonomic units (OTUs) and OTUs related to the phylogenetically diverse group, candidate division I, corresponding to rice cluster V. In contrast, only halophilic archaea were found in the pristine soil. Bacterial community structures also differed significantly between the contaminated and pristine soils. More clones from the contaminated soil were related to known hydrocarbon-degrading bacteria, implying that microorganisms with the potential to degrade petroleum were well-established. These results provide further insights into the composition of microbial communities in oil-contaminated soils.

Sulfate-reducing bacteria in leachate-polluted aquifers along the shore of the East China Sea

The diversity of sulfate-reducing bacteria (SRB) in the aquifer underlying the Laogang Landfill along the shore of the East China Sea was investigated. The DNA extracted from 15 groundwater samples was subjected to PCR amplification of the dissimilatory sulfite reductase (dsr) gene. Full-length dsrAB amplicons (approximately 1.9 kb) were then used to construct 4 clone libraries, while the dsrB amplicons (approximately 350 bp) were used for denaturing gradient gel electrophoresis (DGGE) analysis. The clones in the 4 libraries covered all cultured SRB lineages, as well as a deeply branching clade not affiliated with any cultured SRB. In addition, nearly 80% of the 388 clones in the 4 libraries were similar to sequences of the Deltaproteobacteria, Desulfobacteriaceae, Desulfovibrionales, Syntrophaceae, and Desulfobulbaceae. Furthermore, a wide variety of marine SRB was detected, which indicated that seawater has infiltrated the aquifer. Indeed, the DGGE profiles revealed obvious variations in SRB diversity among the 15 samples, which clustered in accordance with the sulfate concentration of the samples ([SO4(2-)]). Moreover, the sulfate concentrations and SRB diversity along the leachate plume did not show regular variation, which suggests the impact of both groundwater flow and seawater intrusion.

Identification of sulfate-reducing bacteria in methylmercury-contaminated mine tailings by analysis of SSU rRNA genes

Sulfate-reducing bacteria (SRB) are often used in bioremediation of acid mine drainage because microbial sulfate reduction increases pH and produces sulfide that binds with metals. Mercury methylation has also been linked with sulfate reduction. Previous geochemical analysis indicated the occurrence of sulfate reduction in mine tailings, but no molecular characterization of the mine tailings-associated microbial community has determined which SRB are present. This study characterizes the bacterial communities of two geochemically contrasting, high-methylmercury mine tailing environments, with emphasis on SRB, by analyzing small subunit (SSU) rRNA genes present in the tailings sediments and in enrichment cultures inoculated with tailings. Novel Deltaproteobacteria and Firmicutes-related sequences were detected in both the pH-neutral gold mine tailings and the acidic high-sulfide base-metal tailings. At the subphylum level, the SRB communities differed between sites, suggesting that the community structure was dependent on local geochemistry. Clones obtained from the gold tailings and enrichment cultures were more similar to previously cultured isolates whereas clones from acidic tailings were more closely related to uncultured lineages identified from other acidic sediments worldwide. This study provides new insights into the novelty and diversity of bacteria colonizing mine tailings, and identifies specific organisms that warrant further investigation with regard to their roles in mercury methylation and sulfur cycling in these environments.

Use of coal mining waste for the removal of acidity and metal ions Al (III), Fe (III) and Mn (II) in acid mine drainage

The coal industry may generate acid mine drainage (AMD) and mining wastes, which may adversely affect the quality of the environment. In this study we propose the use of this waste in the removal of acidity and metal ions, as well as in the reduction of the toxicity of AMD. A physico-chemical analysis of the waste shows the presence of mainly SiO2, Al2O3 and Fe2O3 and a superficial area of 4.316 m2 g(-1). The treatment of AMD with the waste resulted in an increase in pH from 2.6 to 7.8 and removed 100% of the Al (III), 100% of the Fe (III) and 89% of the Mn (II). We also observed that the high toxicity of the AMD towards Daphnia magna (LC50 = 3.68%) and Artemia sp. (LC50 = 4.97%) was completely eliminated after treatment with the waste. The data obtained allow us to propose that the waste can be used in the treatment of AMD, providing an economic use for the waste.

Change of bacterial communities in sediments along Songhua River in Northeastern China after a nitrobenzene pollution event

More than 100 tons of nitrobenzene and related compounds were released into Songhua River due to the explosion of an aniline production factory in November, 2005. Sediment samples were taken from the heavily polluted drainage canal, one upstream and three downstream river sites. The change of bacterial community structures along the river was studied by denaturing gradient gel electrophoresis (DGGE) and cloning and sequencing of 16S rRNA genes with five clone libraries constructed and 101 sequences acquired representing 172 clones. Both DGGE profiles and sequences of 16S rRNA genes from clone libraries demonstrated that the contaminated drainage canal and three downstream river sites were similar in that all had Betaproteobacteria, mainly grouped into Comamonadaceae, as the dominant group of bacteria, and all had Firmicutes, primarily as Clostridium spp. These results suggest that these latter two groups of bacteria may play potential roles in degradation and detoxification of nitrobenzene in the present contaminated river environments.

Molecular characterization of bacterial communities mineralizing benzene under sulfate-reducing conditions

The microbial communities of in situ reactor columns degrading benzene with sulfate as an electron acceptor were analyzed based on clone libraries and terminal restriction fragment length polymorphism fingerprinting of PCR-amplified 16S rRNA genes. The columns were filled with either lava granules or sand particles and percolated with groundwater from a benzene-contaminated aquifer. The predominant organisms colonizing the lava granules were related to Magnetobacterium sp., followed by a phylotype affiliated to the genera Cryptanaerobacter/Pelotomaculum and several Deltaproteobacteria. From the sand-filled columns, a stable benzene-degrading consortium was established in sand-filled laboratory microcosms under sulfate-reducing conditions. It was composed of Delta- and Epsilonproteobacteria, Clostridia, Chloroflexi, Actinobacteria and Bacteroidetes. The most prominent phylotype of the consortium was related to the genus Sulfurovum, followed by Desulfovibrio sp. and the Cryptanaerobacter/Pelotomaculum phylotype. The proportion of the latter was similar in both communities and significantly increased after repeated benzene-spiking. During cultivation on aromatic substrates other than benzene, the Cryptanaerobacter/Pelotomaculum phylotype was outcompeted by other community members. Hence, this organism appears to be specific for benzene as a growth substrate and might play a key role in benzene degradation in both communities. Based on the possible functions of the community members and thermodynamic calculations, a functional model for syntrophic benzene degradation under sulfate-reducing conditions is proposed.

Culturable and molecular phylogenetic diversity of microorganisms in an open-dumped, extremely acidic Pb/Zn mine tailings

A combination of cultivation-based and molecular-based approaches was used to reveal the culturable and molecular diversity of the microbes inhabiting an open-dumped Pb/Zn mine tailings that was undergoing intensive acid generation (pH 1.9). Culturable bacteria found in the extremely acidic mine tailings were Acidithiobacillus ferrooxidans, Leptospirillum ferriphilum, Sulfobacillus thermotolerans and Acidiphilium cryptum, where the number of acidophilic heterotrophs was ten times higher than that of the iron- and sulfur-oxidizing bacteria. Cloning and phylogenetic analysis revealed that, in contrast to the adjacent AMD, the mine tailings possessed a low microbial diversity with archaeal sequence types dominating the 16S rRNA gene library. Of the 141 clones examined, 132 were represented by two sequence types phylogenetically affiliated with the iron-oxidizing archaea Ferroplasma acidiphilum and three belonged to two tentative groups within the Thermoplasma lineage so far represented by only a few environmental sequences. Six clones in the library were represented by the only bacterial sequence type and were closely related to the well-described iron-oxidizer L. ferriphilum. The significant differences in the prokaryotic community structures of the extremely acidic mine tailings and the AMD associated with it highlights the importance of studying the microbial communities that are more directly involved in the iron and sulfur cycles of mine tailings.

Factors affecting methylmercury distribution in surficial, acidic, base-metal mine tailings

The most toxic form of Hg commonly of concern in the environment is methylmercury (MeHg), as it accumulates in living tissues and bioconcentrates in food webs. Sulfide-rich metal ores are often enriched in Hg, but little is known regarding the potential for Hg methylation in acidic tailings produced from these ores. This study examined acidic tailings from four mines in northern Ontario, Canada, to determine whether they could be an important source of MeHg to downstream environments. Where sulfate reducing bacteria (SRB) were abundant and active in pH-circumneutral, unoxidized layers (Potter mine), negligible MeHg was detected. By contrast, a zone of active sulfate reduction found in the acidic, oxidizing, surficial layers of tailings from the Kidd Metsite contained the highest concentrations of MeHg in bulk tailings (12.1 nmol kg(-1) dry wt. of sediment) and porewaters (88 pM) measured in this study. Cell count estimates of SRB by the "most-probable-number" (MPN) method were low in these surficial tailings, suggesting that sulfate reducers from this environment were acidophilic and did not thrive under the pH-neutral conditions of the MPN incubations. A later study of bacterial DNA from these tailings produced evidence of a novel Deltaproteobacterium which has only previously been detected in acid mine drainage environments. Further research will be necessary to determine whether this Deltaproteobacterium is a sulfate reducer and/or an efficient Hg methylator. Surface water concentrations of MeHg did not exceed Canadian water quality guidelines at any of the sites sampled, but one site (Broulan) featured total Hg (HgT) concentrations of 838 pM in filtered samples, far in excess of recommended levels. Trends in surface water MeHg and HgT reflected corresponding values in porewaters from the same sites, indicating that concentrations of these substances in tailings influence surface water concentrations.

Responses of aerobic microbial communities and soil respiration to water-level drawdown in a northern boreal fen

On a global basis, peatlands are a major reserve of carbon (C). Hydrological changes can affect the decomposition processes in peatlands and in turn can alter their C balance. Since 1959, a groundwater extraction plant has generated a water-level gradient at our study site that has gradually changed part of the wet fen into a dry peatland forest. The average water-level drawdown of the gradient (from a pristine 9 cm to 26 cm in the dry end) is close to an estimate predicted by an increase in mean global temperature of 3 degrees C. We studied the total microbial community of the aerobic surface peat in four locations along the gradient through phospholipid fatty acid and PCR-DGGE methods. Additionally, field measurements of soil respiration showed a threefold increase in the C-emission rate at the driest location compared with the wettest one, indicating enhanced decomposition. Also, both fungal and bacterial biomass increased in the drier locations. At the species level, the fungal community changed due to water-level drawdown whereas actinobacteria were less sensitive to drying. The majority of fungal sequences were similar to ectomycorrhizal (ECM) fungi, which dominated throughout the gradient. Our results indicate that ECM fungi might act as important facultative decomposers in organic-rich environments such as peatlands.

Miniprimer PCR, a new lens for viewing the microbial world

Molecular methods based on the 16S rRNA gene sequence are used widely in microbial ecology to reveal the diversity of microbial populations in environmental samples. Here we show that a new PCR method using an engineered polymerase and 10-nucleotide "miniprimers" expands the scope of detectable sequences beyond those detected by standard methods using longer primers and Taq polymerase. After testing the method in silico to identify divergent ribosomal genes in previously cloned environmental sequences, we applied the method to soil and microbial mat samples, which revealed novel 16S rRNA gene sequences that would not have been detected with standard primers. Deeply divergent sequences were discovered with high frequency and included representatives that define two new division-level taxa, designated CR1 and CR2, suggesting that miniprimer PCR may reveal new dimensions of microbial diversity.

Diversity and in situ quantification of Acidobacteria subdivision 1 in an acidic mining lake

Analysis of 16S rRNA gene clone libraries from acidic mining lake water and sediment, and from an enclosure to which organic carbon was added to stimulate microbial alkalinization processes of sulfate and iron reduction revealed the presence of diverse sequences affiliated with the Acidobacteria subdivision 1. A novel oligonucleotide probe, ACIDO228, was designed that covered most sequences of Acidobacteria subdivision 1. The hybridization conditions were optimized using the type strain Acidobacterium capsulatum. The depth distribution and seasonal dynamics of Acidobacteria in the lake and the enclosure were assessed by whole cell hybridization. Sequence analyses and in situ quantification indicated that Acidobacteria accounted for a substantial part of bacterioplankton communities in both compartments. During the summer stratification distinct maxima of acidobacterial abundance were detected in the hypolimnion (up to 13% of total cell numbers), whereas during spring and autumn circulations no clear depth-dependent differences were visible. These data suggest that Acidobacteria thrive best in the hypolimnion, which is characterized by lower temperatures and higher availability of organic substrates. The application of probe ACIDO228 provided quantitative information on the seasonal and depth distribution of Acidobacteria in a lake environment and in particular in a rather extreme habitat, an acidic mining lake.

Novel nickel resistance genes from the rhizosphere metagenome of plants adapted to acid mine drainage

Metal resistance determinants have traditionally been found in cultivated bacteria. To search for genes involved in nickel resistance, we analyzed the bacterial community of the rhizosphere of Erica andevalensis, an endemic heather which grows at the banks of the Tinto River, a naturally metal-enriched and extremely acidic environment in southwestern Spain. 16S rRNA gene sequence analysis of rhizosphere DNA revealed the presence of members of five phylogenetic groups of Bacteria and the two main groups of Archaea mostly associated with sites impacted by acid mine drainage (AMD). The diversity observed and the presence of heavy metals in the rhizosphere led us to construct and screen five different metagenomic libraries hosted in Escherichia coli for searching novel nickel resistance determinants. A total of 13 positive clones were detected and analyzed. Insights about their possible mechanisms of resistance were obtained from cellular nickel content and sequence similarities. Two clones encoded putative ABC transporter components, and a novel mechanism of metal efflux is suggested. In addition, a nickel hyperaccumulation mechanism is proposed for a clone encoding a serine O-acetyltransferase. Five clones encoded proteins similar to well-characterized proteins but not previously reported to be related to nickel resistance, and the remaining six clones encoded hypothetical or conserved hypothetical proteins of uncertain functions. This is the first report documenting nickel resistance genes recovered from the metagenome of an AMD environment.

Impact of plant density and microbial composition on water quality from a free water surface constructed wetland

AIMS

To correlate microbial community composition and water quality changes within wetland cells containing varying plant densities and composition in a free water surface (FWS) constructed wetland.

METHODS AND RESULTS

Water chemistry was monitored weekly for nitrate, orthophosphate, and suspended solids, at various sites throughout the wetland for 6 months. Treatment ponds with 50% plant cover had about a 96.3% nitrate removal. The average change between the influent and effluent was 50-60% nitrate removal and 40-50% orthophosphate removal. Community profile of total DNA, generated by using denaturing gradient gel electrophoresis (DGGE), was used to determine the major microbial composition associated with the wetland sediment, rhizosphere, and surface water. Bacterial cloned libraries were constructed, and 300 clones were analysed by amplified ribosomal DNA restriction analysis (ARDRA) and grouped into operational taxonomic units (OTUs). A total of 35, 31, and 36 different OTU were obtained from sediment, rhizosphere, and surface water, respectively. The bacterial members within the dominant group of our clone library belonged to unclassified taxa, while the second predominant group consisted of members of the phylum Proteobacteria. The dominant organisms within the class were in the gamma, beta, and delta classes.

CONCLUSION

Microbial diversity as determined by Shannon-Weaver index (H) was higher in the wetland cells with 50% plant density than the 100%. This was in agreement with the most efficient wetland contaminant removal units.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study provides evidence that wetlands with 50% plant cover may promote the growth of diverse microbial communities that facilitate decomposition of chemical pollutants in surface water, and improve water quality.

A novel Acidimicrobium species in continuous cultures of moderately thermophilic, mineral-sulfide-oxidizing acidophiles

A novel species of Acidimicrobium appeared to be the predominant ferrous iron oxidizer in a mixed culture that effected the continuous, efficient extraction of nickel from a mineral concentrate at 49 degrees C, but it was not isolated in pure culture. It outcompeted Acidimicrobium ferrooxidans, which was expected to have a major role in iron oxidation in reactors gassed with air, and was outnumbered at 49 degrees C only by the sulfur-oxidizing Acidithiobacillus caldus. Sulfobacillus species were expected to compete with Acidimicrobium species when culture aeration was enriched with carbon dioxide, but they were a minor component of the populations with and without this enrichment. Sulfobacillus thermosulfidooxidans replaced the Acidimicrobium species and Acidithiobacillus caldus when the temperature was increased to 55 degrees C.