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Coal mines in Alaska with high rare earth elements (REEs) levels (286-524 mg/kg) serve as an alternative domestic source for REEs. Existing leaching/separation technologies fail to selectively recover REEs from the feedstock and require downstream multiple purification stages that increase the overall operational cost. This study aims at bio-weathering coal from two Alaskan coal mines (Wishbone Hill and Healy) at three density fractions (1.3 float, and 1.3 and 1.5 sink) using Shewanella oneidensis MR-1 for achieving higher selective REEs recovery in one-step process. Optimizing the bio-weathering process by varying solids percentages (5.7 to14.3% w/v), particle size (-14 to -200 M), incubation temperatures (30 to 34 °C), and inoculum dosing (0.2 to 1% v/v) resulted in highest recovery of Neodymium (75.3%) and total REEs (98.4%) from 1.3 float Wishbone Hill and 1.3 sink Healy coal, respectively. When compared to the chemical leaching process, bio-weathering enhanced selective recovery of REEs including Scandium, Yttrium, Ytterbium, Terbium, Erbium, and Lutetium from Healy coal at low density, and Yttrium from Wishbone Hill coal at high density. The results indicate the future scope for developing cost-effective selective REEs recovery processes that may address the global critical minerals supply chain risk.

Rotenone is a pesticide commonly used to eradicate Northern Pike (Esox lucius), an invasive species, in Southcentral Alaska. The present work incorporates a field investigation of rotenone attenuation in eight lakes of the Kenai Peninsula, following a CFT Legumine® treatment in October 2018 and a laboratory simulation to determine persistence under light/dark and sterile/nonsterile conditions representative of Southcentral Alaskan winters. In the field, rotenone degraded within

The microbial community in oil reservoirs plays important roles in carbon, sulfur, and nitrogen cycling. We identified the microbial composition, abundance, and diversity in two heavy oil w...

Structural Fe(II) in clay minerals and natural sediments is known to reduce Cr(VI) to Cr(III), but the effect of redox-cycled Fe-bearing natural sediments on Cr(VI) reduction kinetics is poorly understood. The objective of this study was to understand the kinetics and mechanisms of Cr(VI) reduction by Fe(II) in redox cycled natural sediment. Fe-bearing sediment was collected from the Ringold formation in the 300 area of Hanford, Washington, United States. Fe redox cycling of the sediment was accomplished via four cycles of bioreduction of structural Fe(III) in Hanford sediment and air oxidation of the resulting Fe(II). Bio-produced Fe(II) in Hanford sediment from each redox cycle was utilized to reduce Cr(VI) at three temperatures (10, 20 and 30 °C). The initial rate of Cr(VI) reduction generally increased with each redox cycle, which was more pronounced at high temperatures. The amount of Fe(II) oxidized to the amount of Cr(VI) reduced was close to the expected stoichiometric ratio of 3. Aqueous concentrations of Si, Al, and Fe revealed some dissolution of the sediment after reaction with Cr(VI). X-ray diffraction (XRD) and scanning electron microscopy (SEM) detected secondary mineral formation. Mossbauer data showed that the oxidation of Fe(II) was coupled with the reduction of Cr(VI) but no Fe-oxides/oxyhydroxides formed. Transmission electron microscopy (TEM), electron energy loss spectroscopy (EELS), XANES, and EXAFS were performed for representative reduced Cr solids that formed from reduction of Cr(VI) by sediment-associated Fe(II) at 30 °C. TEM revealed that the d-spacing of Cr-reacted montmorillonite at 30 °C, a dominant Fe-bearing mineral in Hanford sediment, expanded from 10 A to 13 A. This layer expansion was likely due to intercalation of reduced Cr(III) into the interlayer space of the montmorillonite structure. EELS exhibited an L2 absorption peak at 586.0 eV and an L3 absorption peak at 577.0 eV, suggestive of Cr(III) in a hydroxide mineral phase. Similarly, XANES and EXAFS analyses confirmed Cr(VI) reduction to Cr(OH)3 at 30 °C and indicated an edge-sharing coordination of the Cr(III) octahedra to 2–3 other Cr or metal ions. This study has important implications for understanding the reactivity of clay-rich sediment towards Cr(VI) reduction at contaminated sites and the stability of the reduced Cr(III).

Copper (Cu) is an essential trace metal cofactor for a variety of proteins; however, excess Cu is toxic to most organisms. Cu homeostasis is maintained by a complex machinery of Cu binding proteins that control the uptake, transport, sequestration, and efflux of Cu ions. Despite the importance of Cu binding proteins in electron transfer, substrate oxidation, superoxide dismutation, and denitrification, little information exists about microbial Cu utilization in extreme environments, where the geochemical conditions may affect Cu bioavailability. Using metagenomic data from 9 hot springs in Tengchong, China, which range in temperature from 42°C to 96°C and in pH from 2.3 to 9, the effects of pH, temperature, and spring geochemistry on the distribution of Cu binding domains of proteins and oxidoreductases were studied. Dissolved Cu and Cu binding domains were detected across all temperature and pH gradients. Cu binding domains of cytochrome c oxidase subunits, heavy-metal-associated domains, and nitrous oxide reductase were detected at all sites. DoxB, a quinol oxidase, and other quinol oxidase subunits were the dominant Cu binding oxidoreductase subunits present at low-pH and high-temperature sites, whereas cbb3-type cytochrome c oxidase subunits were dominant at high-pH and high-temperature sites. Additionally, aa3-type cytochrome c oxidase was more prominent than cbb3-type cytochrome c oxidase under circumneutral-pH conditions. This suggests that the type of cytochrome c oxidase pathway and the Cu proteins employed by microbes to carry out important functions such as energy acquisition and efflux of excess Cu are affected by the physicochemical conditions of the springs. IMPORTANCE Copper is present in a variety of proteins and is required to carry out essential functions by all organisms. However, in hot spring environments, copper availability may be limited due to the high temperatures and the wide range in pH. The significance of our research is in relating the physicochemical environment to the distribution of copper proteins across hot spring environments, which provides increased understanding of primary functions and adaptions in these environments.

To reduce emissions from petrochemical refinement, bio-production has been heralded as a way to create economically valuable compounds with fewer harmful effects. For example, gaseous alkenes are precursor molecules that can be polymerized into a variety of industrially significant compounds and have biological production pathways. Production levels, however, remain low, thus enhancing bio-production of gaseous petrochemicals for chemical precursors is critical. This review covers the metabolic pathways and production levels of the gaseous alkenes ethylene, isoprene, and isobutene. Techniques needed to drive production to higher levels are also discussed.

The novel coronavirus SARS-CoV-2, the causative agent of COVID-19, emerged in the human population in December 2019 and spread worldwide within a few short months. Much of the public health focus for preventing and mitigating the spread of COVID-19 has been on individual and collective behaviors, such as social distancing, mask-wearing, and hygiene. It is important to recognize that these behaviors and health outcomes occur within broader social and environmental contexts, and factors within local communities such as regional policy, historical context, cultural beliefs, and natural- and built environmental characteristics affect underlying population health and the spread of disease. For example, the COVID-19 pandemic has renewed attention to the importance of secure water and sanitation services in protecting human health; many remote Alaskan communities are particularly vulnerable to infectious disease transmission because of inadequate water and sanitation services. In addition, there are a number of socio-economic, physical, and infrastructure factors in rural Alaska (e.g., remoteness, household overcrowding, climate change impacts, limited medical facilities, and high prevalence of chronic diseases) that contribute to the potential for more severe COVID-19 disease outcomes in these predominantly Alaska Native communities., Graphical abstract Unlabelled Image

Microbial processes in the deep biosphere affect marine sediments, such as the formation of gas hydrate deposits. Gas hydrate deposits offer a large source of natural gas with the potential to augment energy reserves and affect climate and seafloor stability. Despite the significant interdependence between life and geology in the ocean, coverage of the deep biosphere is generally missing in most introductory oceanography textbooks, so there is a need for instructional materials on this important topic. In response to this need, a course module on the deep biosphere with a focus on gas hydrate deposits was created. The module uses Google Earth (Google, Mountain View, CA) to support inquiry-based activities that demonstrate the interaction of the deep biosphere with geology. The module was tried as both a series of in-class exercises and as an out-of-class assignment in an introductory, undergraduate oceanography course. The students took short, preactivity and postactivity quizzes to determine the...

The vast majority of microbial life remains uncatalogued due to the inability to cultivate these organisms in the laboratory. This “microbial dark matter” represents a substantial portion of the tree of life and of the populations that contribute to chemical cycling in many ecosystems. In this work, we leveraged an existing single-cell genomic data set representing the candidate bacterial phylum “ Calescamantes ” (EM19) to calibrate machine learning algorithms and define metagenomic bins directly from pyrosequencing reads derived from Great Boiling Spring in the U.S. Great Basin. Compared to other assembly-based methods, taxonomic binning with a read-based machine learning approach yielded final assemblies with the highest predicted genome completeness of any method tested. Read-first binning subsequently was used to extract Calescamantes bins from all metagenomes with abundant Calescamantes populations, including metagenomes from Octopus Spring and Bison Pool in Yellowstone National Park and Gongxiaoshe Spring in Yunnan Province, China. Metabolic reconstruction suggests that Calescamantes are heterotrophic, facultative anaerobes, which can utilize oxidized nitrogen sources as terminal electron acceptors for respiration in the absence of oxygen and use proteins as their primary carbon source. Despite their phylogenetic divergence, the geographically separate Calescamantes populations were highly similar in their predicted metabolic capabilities and core gene content, respiring O 2 , or oxidized nitrogen species for energy conservation in distant but chemically similar hot springs.

Analysis of the increasing wealth of metagenomic data collected from diverse environments can lead to the discovery of novel branches on the tree of life. Here we analyse 5.2 Tb of metagenomic data collected globally to discover a novel bacterial phylum (‘Candidatus Kryptonia') found exclusively in high-temperature pH-neutral geothermal springs. This lineage had remained hidden as a taxonomic ‘blind spot' because of mismatches in the primers commonly used for ribosomal gene surveys. Genome reconstruction from metagenomic data combined with single-cell genomics results in several high-quality genomes representing four genera from the new phylum. Metabolic reconstruction indicates a heterotrophic lifestyle with conspicuous nutritional deficiencies, suggesting the need for metabolic complementarity with other microbes. Co-occurrence patterns identifies a number of putative partners, including an uncultured Armatimonadetes lineage. The discovery of Kryptonia within previously studied geothermal springs underscores the importance of globally sampled metagenomic data in detection of microbial novelty, and highlights the extraordinary diversity of microbial life still awaiting discovery., The analysis of existing metagenomic data can lead to discovery of new microorganisms. Here, Eloe-Fadrosh et al. perform a large-scale analysis of global metagenomic data, followed by genome reconstruction and single-cell genomics, to describe a new bacterial phylum that inhabits geothermal springs.

Increasing application of rare earth elements (REE) in electronics, renewable energy, biomedical devices, and industrial products has increased their demand globally. Enhanced production of industrial and electronic wastes has led the researchers to focus on the REE recovery from these alternative economic sources. Recent developments in bioprocess technology have created suitable avenues of REE recovery from waste materials. This review focuses on secondary sources of REE including industrial wastes, mine wastes, and electronic wastes. Detailed mechanisms of REE biorecovery from waste mineral sources have been discussed elaborately. The influence of physico-chemical operational parameters on the efficiency of REE biorecovery from source materials has also been thoroughly elaborated. Analyses in terms of economic perspectives indicate that REE biorecovery from waste materials may be a cost-effective approach. This review directs future research towards the development of enhanced REE biorecovery from wastes on a large commercial scale.

Iron-bearing clay minerals are predominant in soils and sediments, and they undergo oxidation-reduction cycles as a result of natural processes such as wetting/drying cycles and plant root respiration. However, the kinetics and mechanisms of multiple redox cycles of iron in clay-rich sediments and consequences of such cycling on sediment properties are poorly understood. The objective of this study was to understand how multiple redox cycles of Fe in clay-rich sediment affect the rate and extent of Fe bioreduction and the physicochemical properties of the sediment. A natural sediment sample containing Fe-bearing montmorillonite from Hanford, Washington, USA was size-fractionated [2.0 to 0.5 μm (Hanford-C) and 0.5 to 0.02 μm (Hanford-F)] and redox-cycled for four times. Bioreduction was achieved utilizing Geobacter sulfurreducens and re-oxidization was performed with sparged air. Time-course change of total Fe (II) was monitored to measure the rate and extent of Fe (III) bioreduction. Redox-cycled sediments were characterized to determine the physicochemical changes. Both the initial rate and extent of bioreduction fluctuated across the four redox cycles, but they ultimately decreased from 5.3 μmol g−1 h−1 and 22.9% to nearly zero by the fourth cycle. These fluctuation patterns were likely due to a combined effect of reductive dissolution of small/poorly crystalline clay particles (by 3–5%) and clay mineral structural changes, as evidenced by redox induced changes of aqueous chemistry, surface area, cation exchange capacity, mineralogy, and Mossbauer parameters. Once these small/poorly crystalline clay particles were dissolved, structural Fe in residual larger and more crystalline clay particles was largely reversible across additional redox cycles, as revealed by Mossbauer spectroscopy through the first three cycles.

Myocyanophages, a group of viruses infecting cyanobacteria, are abundant and play important roles in elemental cycling. Here we investigated the particle-associated viral communities retained on 0.2 μm filters and in sediment samples (representing ancient cyanophage communities) from four ocean and three lake locations, using high-throughput sequencing and a newly designed primer pair targeting a gene fragment (∼145-bp in length) encoding the cyanophage gp23 major capsid protein (MCP). Diverse viral communities were detected in all samples. The fragments of 142-, 145-, and 148-bp in length were most abundant in the amplicons, and most sequences (>92%) belonged to cyanophages. Additionally, different sequencing depths resulted in different diversity estimates of the viral community. Operational taxonomic units obtained from deep sequencing of the MCP gene covered the majority of those obtained from shallow sequencing, suggesting that deep sequencing exhibited a more complete picture of cyanophage community than shallow sequencing. Our results also revealed a wide geographic distribution of marine myocyanophages, i.e., higher dissimilarities of the myocyanophage communities corresponded with the larger distances between the sampling sites. Collectively, this study suggests that the newly designed primer pair can be effectively used to study the community and diversity of myocyanophage from different environments, and the high-throughput sequencing represents a good method to understand viral diversity.

Studies focusing on seasonal dynamics of microbial communities in terrestrial and marine environments are common; however, little is known about seasonal dynamics in high-temperature environments. Thus, our objective was to document the seasonal dynamics of both the physicochemical conditions and the microbial communities inhabiting hot springs in Tengchong County, Yunnan Province, China. The PhyloChip microarray detected 4882 operational taxonomic units (OTUs) within 79 bacterial phylum-level groups and 113 OTUs within 20 archaeal phylum-level groups, which are additional 54 bacterial phyla and 11 archaeal phyla to those that were previously described using pyrosequencing. Monsoon samples (June 2011) showed increased concentrations of potassium, total organic carbon, ammonium, calcium, sodium and total nitrogen, and decreased ferrous iron relative to the dry season (January 2011). At the same time, the highly ordered microbial communities present in January gave way to poorly ordered communities in June, characterized by higher richness of Bacteria, including microbes related to mesophiles. These seasonal changes in geochemistry and community structure are likely due to high rainfall influx during the monsoon season and indicate that seasonal dynamics occurs in high-temperature environments experiencing significant changes in seasonal recharge. Thus, geothermal environments are not isolated from the surrounding environment and seasonality affects microbial ecology.

The microbial diversity was investigated in sediments of six acidic to circumneutral hot springs (Temperature: 60-92 °C, pH 3.72-6.58) in the Philippines using an integrated approach that included geochemistry and 16S rRNA gene pyrosequencing. Both bacterial and archaeal abundances were lower in high-temperature springs than in moderate-temperature ones. Overall, the archaeal community consisted of sequence reads that exhibited a high similarity (nucleotide identity > 92%) to phyla Crenarchaeota, Euryarchaeota, and unclassified Archaea. The bacterial community was composed of sequence reads moderately related (nucleotide identity > 90%) to 17 phyla, with Aquificae and Firmicutes being dominant. These phylogenetic groups were correlated with environmental conditions such as temperature, dissolved sulfate and calcium concentrations in spring water, and sediment properties including total nitrogen, pyrite, and elemental sulfur. Based on the phylogenetic inference, sulfur metabolisms appear to be key physiological functions in these hot springs. Sulfobacillus (within phylum Firmicutes) along with members within Sulfolobales were abundant in two high-temperature springs (> 76 °C), and they were hypothesized to play an important role in regulating the sulfur cycling under high-temperature conditions. The results of this study improve our understanding of microbial diversity and community composition in acidic to circumneutral terrestrial hot springs and their relationships with geochemical conditions.

The authors examined the physiochemical and microbiological properties of archived rusticles from World War II shipwrecks in the Gulf of Mexico. Rusticles, iron (Fe)-rich accumulations on shipwrecks in marine environments, have long been assumed to be the result of low alloy steel corrosion. In many cases the assumed corrosion has been attributed to biodeterioration because of the presence of specific types of bacteria associated with the rusticles. However, archived rusticles from WWII shipwrecks in the Gulf of Mexico (GOM) do not have the mineralogical layering typical of iron corrosion products. Moreover, spatial relationships between bacteria and rusticles cannot be interpreted as biodeterioration. The authors concluded that environmental Fe plays a role in rusticle formation and differences in Fe concentrations can be used to explain differences in rusticle size and distribution with depth in the GOM. Both biotic and abiotic mechanisms for Fe accumulation are provided.

We studied the microbial communities collected from hydrate-bearing sediments on the North Slope of Alaska to determine how abiotic variables (e.g., grain size, hydrate presence, formation fluid gases) may correspond to the type and distribution of microbes in the sediments. The cores were acquired from sub-permafrost, Eocene (46–55 million year old) sediments in the BPXA-DOE-USGS Mount Elbert Gas Hydrate Stratigraphic Test Well within which hydrates are believed to have formed 1.5 mya. Forty samples, eight of which originally contained hydrates, were acquired from depths of ca. 606–666 m below land surface. Five drilling fluid samples acquired from the same depth range were included in the analysis as a control for possible contamination by drilling fluid microbes during the drilling and handling of cores. DNA was extracted from 15 samples (typically

[ILLUSTRATION OMITTED] Students often resort to memorization and recall when learning about cellular respiration. The concepts of glycolysis, Krebs cycle, and the electron transfer chain are abstract with multiple steps that are difficult to follow. The electron transport chain is the major workhorse for creating ATP in living organisms, and yet there are very few ways to clearly illustrate the electron transport chain in the laboratory. The above comment started a conversation between a high school biology teacher and scientists from the local university who were participants in a National Science Foundation (NSF)-funded teacher-scientist partnership program. This conversation led to a collaboration that developed this laboratory exercise demonstrating cellular respiration. Cellular respiration is the process of obtaining biochemical energy (stored as ATP) from fuel molecules (sugars). There are three major reactions that occur in cellular respiration: glycolysis, the Krebs cycle, and the electron transport chain (ETC). The ETC is the final step in cellular respiration and produces the most ATE In eukaryotes, the ETC is on the mitochondrial membrane; however, prokaryotes do not have a mitochondria and thus the ETC is on the plasma membrane. In addition, eukaryotes are only capable of respiring on oxygen (glucose + [O.sub.2] [right arrow] C[O.sub.2] + [H.sub.2]O), called aerobic respiration. When oxygen is not present, eukaryotes can perform the less efficient fermentation reactions. Fermentation produces less ATP than aerobic respiration because it does not use the Krebs cycle and the ETC. However, in the absence of oxygen, prokaryotes have the ability to ferment as well as use the ETC (anaerobic respiration). For example, some bacteria are able to respire on solid phase iron (glucose + [Fe.sup.+3] [right arrow] C[O.sub.2] + [Fe.sup.+2]). Respiration on multiple elements gives microbes an advantage in harsh environments where oxygen is not present. In addition, microbial respiration on solid phase compounds can be exploited to produce electricity. Microbial fuel ceils are a current research area that harvests electricity from bacteria capable of anaerobic respiration (Holmes et al., 2004; Liu et al., 2004; Logan et al., 2005). Graphite is an electrically conductive material that bacteria can respire on, thus it can be used to capture electrons from bacteria. When bacteria transfer electrons to graphite, an electrical potential is created that can produce electricity when in a circuit. A sediment battery is a simple circuit that uses graphite and anaerobic bacteria naturally found in dirt. The electrical potential produced by bacterial respiration on the graphite can be measured on a voltmeter and thus can be used as a visual aid for teaching cellular respiration. The combination of the need for a new learning tool and the expertise of the scientists led to the development of the laboratory exercise described here. It uses student-designed sediment batteries to better visualize and measure electron transfer in living cells. This exercise satisfies National Science Education Teaching Standards A and B, and Content Standards A, B, and C. * Background Chemical Batteries A battery uses chemicals to produce electrons. One common battery is a zinc/carbon battery, which has two terminals: a positive (cathode) and negative (anode). At the negative terminal, a zinc rod is placed in sulfuric acid. The sulfuric acid dissolves the zinc rod at the surface. A zinc atom will leave the rod as a [Zn.sup.+2] ion leaving two electrons on the rod; thus electrons are built up at the anode. When the battery is incorporated into a circuit, the electrons are allowed to travel from the anode to the cathode. In the cathode, the electrons travel through the carbon into sulfuric acid to produce hydrogen gas. The production and movement of electrons in a battery can power a device. …

Temporal variation in geochemistry can cause changes in microbial community structure and diversity. Here we studied temporal changes of microbial communities in Tengchong hot springs of Yunnan Province, China in response to geochemical variations by using microbial and geochemical data collected in January, June and August of 2011. Greater temporal variations were observed in individual taxa than at the whole community structure level. Water and sediment communities exhibited different temporal variation patterns. Water communities were largely stable across three sampling times and dominated by similar microbial lineages: Hydrogenobaculum in moderate-temperature acidic springs, Sulfolobus in high-temperature acidic springs and Hydrogenobacter in high-temperature circumneutral to alkaline springs. Sediment communities were more diverse and responsive to changing physicochemical conditions. Most of the sediment communities in January and June were similar to those in waters. However, the August sediment community was more diverse and contained more anaerobic heterotrophs than the January and June: Desulfurella and Acidicaldus in moderate-temperature acidic springs, Ignisphaera and Desulfurococcus in high-temperature acidic springs, the candidate division OP1 and Fervidobacterium in alkaline springs and Thermus and GAL35 in neutral springs. Temporal variations in physicochemical parameters including temperature, pH and dissolved organic carbon may have triggered the observed microbial community shifts.

Despite the significant progress on iron reduction by thermophilic microorganisms, studies on their ability to reduce toxic metals are still limited, despite their common co-existence in high temperature environments (up to 70°C). In this study, Methanothermobacter thermautotrophicus, an obligate thermophilic methanogen, was used to reduce hexavalent chromium. Experiments were conducted in a growth medium with H2/CO2 as substrate with various Cr6+ concentrations (0.2, 0.4, 1, 3, and 5 mM) in the form of potassium dichromate (K2Cr2O7). Time-course measurements of aqueous Cr6+ concentrations with the 1, 5-diphenylcarbazide colorimetric method showed complete reduction of the 0.2 and 0.4 mM Cr6+ solutions by this methanogen. However, much lower reduction extents of 43.6%, 13.0%, and 3.7% were observed at higher Cr6+ concentrations of 1, 3 and 5 mM, respectively. These lower extents of bioreduction suggest a toxic effect of aqueous Cr6+ to cells at this concentration range. At these higher Cr6+ concentrations, methanogenesis was inhibited and cell growth was impaired as evidenced by decreased total cellular protein production and live/dead cell ratio. Likewise, Cr6+ bioreduction rates decreased with increased initial concentrations of Cr6+ from 13.3 to1.9 µM h-1. X-ray absorption near-edge structure (XANES) spectroscopy revealed a progressive reduction of soluble Cr6+ to insoluble Cr3+ precipitates, which was confirmed as amorphous chromium hydroxide by X-ray diffraction and selected area electron diffraction pattern. However, a small fraction of reduced Cr occurred as aqueous Cr3+. Scanning and transmission electron microscope observations of M. thermautotrophicus cells after Cr6+ exposure suggest both extra- and intracellular chromium reduction mechanisms. Results of this study demonstrate the ability of M. thermautotrophicus cells to reduce toxic Cr6+ to less toxic Cr3+ and its potential application in metal bioremediation, especially at high temperature subsurface radioactive waste disposal sites, where the temperature may reach ∼70°C.

Microbe-mediated biogeochemical cycles contribute to the global climate system and have sensitive responses and feedbacks to environmental stress caused by climate change. Yet, little is known about the effects of microbial biodiversity (i.e., taxonmic and functional diversity) on biogeochemical cycles in ecosytems that are highly sensitive to climate change. One such sensitive ecosystem is Qinghai Lake, a high-elevation (3196 m) saline (1.4%) lake located on the Tibetan Plateau, China. This study provides baseline information on the microbial taxonomic and functional diversity as well as the associated stress response genes. Illumina metagenomic and metatranscriptomic datasets were generated from lake water samples collected at two sites (B and E). Autotrophic Cyanobacteria dominated the DNA samples, while heterotrophic Proteobacteria dominated the RNA samples at both sites. Photoheterotrophic Loktanella was also present at both sites. Photosystem II was the most active pathway at site B; while, oxidative phosphorylation was most active at site E. Organisms that expressed photosystem II or oxidative phosphorylation also expressed genes involved in photoprotection and oxidative stress, respectively. Assimilatory pathways associated with the nitrogen cycle were dominant at both sites. Results also indicate a positive relationship between functional diversity and the number of stress response genes. This study provides insight into the stress resilience of microbial metabolic pathways supported by greater taxonomic diversity, which may affect the microbial community response to climate change.

Studies focusing on seasonal dynamics of microbial communities in terrestrial and marine environments are common; however, little is known about seasonal dynamics in high-temperature environments. Thus, our objective was to document the seasonal dynamics of both the physicochemical conditions and the microbial communities inhabiting hot springs in Tengchong County, Yunnan Province, China. The PhyloChip microarray detected 4882 operational taxonomic units (OTUs) within 79 bacterial phylum-level groups and 113 OTUs within 20 archaeal phylum-level groups, which are additional 54 bacterial phyla and 11 archaeal phyla to those that were previously described using pyrosequencing. Monsoon samples (June 2011) showed increased concentrations of potassium, total organic carbon, ammonium, calcium, sodium and total nitrogen, and decreased ferrous iron relative to the dry season (January 2011). At the same time, the highly ordered microbial communities present in January gave way to poorly ordered communities in June, characterized by higher richness of Bacteria, including microbes related to mesophiles. These seasonal changes in geochemistry and community structure are likely due to high rainfall influx during the monsoon season and indicate that seasonal dynamics occurs in high-temperature environments experiencing significant changes in seasonal recharge. Thus, geothermal environments are not isolated from the surrounding environment and seasonality affects microbial ecology.

The Rehai and Ruidian geothermal fields, located in Tengchong County, Yunnan Province, China, host a variety of geochemically distinct hot springs. In this study, we report a comprehensive, cultivation-independent census of microbial communities in 37 samples collected from these geothermal fields, encompassing sites ranging in temperature from 55.1 to 93.6°C, in pH from 2.5 to 9.4, and in mineralogy from silicates in Rehai to carbonates in Ruidian. Richness was low in all samples, with 21–123 species-level OTUs detected. The bacterial phylum Aquificae or archaeal phylum Crenarchaeota were dominant in Rehai samples, yet the dominant taxa within those phyla depended on temperature, pH, and geochemistry. Rehai springs with low pH (2.5–2.6), high temperature (85.1–89.1°C), and high sulfur contents favored the crenarchaeal order Sulfolobales, whereas those with low pH (2.6–4.8) and cooler temperature (55.1–64.5°C) favored the Aquificae genus Hydrogenobaculum. Rehai springs with neutral-alkaline pH (7.2–9.4) and high temperature (>80°C) with high concentrations of silica and salt ions (Na, K, and Cl) favored the Aquificae genus Hydrogenobacter and crenarchaeal orders Desulfurococcales and Thermoproteales. Desulfurococcales and Thermoproteales became predominant in springs with pH much higher than the optimum and even the maximum pH known for these orders. Ruidian water samples harbored a single Aquificae genus Hydrogenobacter, whereas microbial communities in Ruidian sediment samples were more diverse at the phylum level and distinctly different from those in Rehai and Ruidian water samples, with a higher abundance of uncultivated lineages, close relatives of the ammonia-oxidizing archaeon “Candidatus Nitrosocaldus yellowstonii”, and candidate division O1aA90 and OP1. These differences between Ruidian sediments and Rehai samples were likely caused by temperature, pH, and sediment mineralogy. The results of this study significantly expand the current understanding of the microbiology in Tengchong hot springs and provide a basis for comparison with other geothermal systems around the world.

A rapid DNA isolation method was developed to concentrate dissolved DNA (dDNA) in aquifer water for molecular analysis. The aquifer dDNA from the Eastern Snake River Plain Aquifer (ESRPA) was extracted and concentrated using a new method with an anion-exchange Mustang® Q membrane. The concentration of aquifer dDNA in this study ranged from 60 to 264.5 ng l−1 in ESRPA aquifer wells. DNA stability in ESRPA aquifer water was also tested in this study. The dDNA extracted from aquifer water samples was used for PCR amplification of bacterial 16S rRNA genes for terminal restriction fragment length polymorphism (T-RFLP) analysis and construction of 16S rRNA gene clone libraries. The ureC gene, IncP, IncQ and IncW plasmid genes were also PCR amplified from dDNA samples. Based on the results, dDNA is relatively stable in aquifer water and can be concentrated by Q membrane method for molecular analysis. The quality of isolated dDNA was suitable as a PCR template.

The degradation of organic carbon in subseafloor sediments on continental margins contributes to the largest reservoir of methane on Earth. Sediments in the Andaman Sea are composed of ~ 1% marine-derived organic carbon and biogenic methane is present. Our objective was to determine microbial abundance and diversity in sediments that transition the gas hydrate occurrence zone (GHOZ) in the Andaman Sea. Microscopic cell enumeration revealed that most sediment layers harbored relatively low microbial abundance (10(3)-10(5) cells cm(-3)). Archaea were never detected despite the use of both DNA- and lipid-based methods. Statistical analysis of terminal restriction fragment length polymorphisms revealed distinct microbial communities from above, within, and below the GHOZ, and GHOZ samples were correlated with a decrease in organic carbon. Primer-tagged pyrosequences of bacterial 16S rRNA genes showed that members of the phylum Firmicutes are predominant in all zones. Compared with other seafloor settings that contain biogenic methane, this deep subseafloor habitat has a unique microbial community and the low cell abundance detected can help to refine global subseafloor microbial abundance.