SEARCH · Search USGS

Results for “Archaea”

Search indexed USGS publications on groundwater, aquifers, geologic maps, mineral resources and earthquakes. Explore source records by subject and place.

SourceResearch connectionFrom yearThrough year

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 37 records · Page 2Linked to original sources

USGS2011

Hydrogeochemical processes governing the origin, transport and fate of major and trace elements from mine wastes and mineralized rock to surface waters

The formation of acid mine drainage from metals extraction or natural acid rock drainage and its mixing with surface waters is a complex process that depends on petrology and mineralogy, structural geology, geomorphology, surface-water hydrology, hydrogeology, climatology, microbiology, chemistry, and mining and mineral processing history. The concentrations of metals, metalloids, acidity, alkalinity, Cl - , F - and SO 4 2- found in receiving streams, rivers, and lakes are affected by all of these factors and their interactions. Remediation of mine sites is an engineering concern but to design a remediation plan without understanding the hydrogeochemical processes of contaminant mobilization can lead to ineffective and excessively costly remediation. Furthermore, remediation needs a goal commensurate with natural background conditions rather than water-quality standards that might bear little relation to conditions of a highly mineralized terrain. This paper reviews hydrogeochemical generalizations, primarily from US Geological Survey research, that enhance our understanding of the origin, transport, and fate of contaminants released from mined and mineralized areas. Mobility of potential or actual contaminants from mining and mineral processing activities depends on (1) occurrence : is the mineral source of the contaminant actually present? (2) abundance : is the mineral present in sufficient quantity to make a difference? (3) reactivity : what are the energetics, rates, and mechanisms of sorption and mineral dissolution and precipitation relative to the flow rate of the water? and (4) hydrology : what are the main flow paths for contaminated water? Estimates of relative proportions of minerals dissolved and precipitated can be made with mass-balance calculations if minerals and water compositions along a flow path are known. Combined with discharge, these mass-balance estimates quantify the actual weathering rate of pyrite mineralization in the environment and compare reasonably well with laboratory rates of pyrite oxidation except when large quantities of soluble salts and evaporated mine waters have accumulated underground. Quantitative mineralogy with trace-element compositions can substantially improve the identification of source minerals for specific trace elements through mass balances. Post-dissolution sorption and precipitation (attenuation) reactions depend on the chemical behavior of each element, solution composition and pH, aqueous speciation, temperature, and contact-time with mineral surfaces. For example, little metal attenuation occurs in waters of low pH (<3.5) and metals tend to maintain element ratios indicative of the main mineral or group of minerals from which they dissolved, except Fe, SiO 2 , and redox-sensitive oxyanions (As, Sb, Se, Mo, Cr, V). Once dissolved, metal and metalloid concentrations are strongly affected by redox conditions and pH. Iron is the most reactive because it is rapidly oxidized by bacteria and archaea and Fe(III) hydrolyzes and precipitates at low pH (1–3) which is related directly to its first hydrolysis constant, pK 1 = 2.2. Several insoluble sulfate minerals precipitate at low pH including anglesite, barite, jarosite, alunite and basaluminite. Aluminum hydrolyzes near pH 5 (pK 1 = 5.0) and provides buffering and removal of Al by mineral precipitation from pH 4–5.5. Dissolved sulfate behaves conservatively because the amount removed from solution by precipitation is usually too small relative to the high concentrations in the water column and relative to the flow rate of the water.

Applied Geochemistry↗

USGS2021

Effect of an algal amendment on the microbial conversion of coal to methane at different sulfate concentrations from the Powder River Basin, USA

Biogenic methane is estimated to account for one-fifth of the natural gas worldwide and there is great interest in controlling methane from different sources. Biogenic coalbed methane (CBM) production relies on syntrophic associations between fermentative bacteria and methanogenic archaea to anaerobically degrade recalcitrant coal and produce methanogenic substrates. However, very little is known about how differences in geochemistry, hydrology, and microbial community composition influence subsurface carbon utilization and CBM production. The addition of an amendment consisting of microalgal biomass has previously been shown to increase CBM production while providing the possibility of a closed-loop fossil system where waste (production water) is used to grow algae to ultimately produce energy (methane). However, the efficiency of enhancing CBM production under different redox conditions remains unresolved. In this study, we focused on the U.S. Geological Survey's Birney test site (Montana, USA) that has nine wells vertically accessing four coal seams with varying geochemistry (low and high sulfate (SO 4 2− )) and methane production rates. We used organic matter (OM) in the form of algal biomass to discern the effect of this amendment on OM degradation and microbially enhanced CBM production potential under different geochemical constraints. We tracked changes in community composition, OM composition, organic carbon (OC) concentration, methane production, and nutrients in batch systems over six months. Methane production was detected only in microcosms from low SO 4 2− wells (168 to 800 μg methane per gram of coal). The OC consumption varied across time for all wells and the variation was greatest for the low SO 4 2− wells. Different groups of syntrophic bacteria were associated with net‑carbon consuming microcosms, and specifically Syntrophorhabdus was identified with several different statistical methods as a potentially important coal degrader. Results from this study provide insight into potential coal-degraders, the compositional changes in some of the different OM fractions, and trends in carbon consumption related to methane production across coal seams along the vertical SO 4 2− gradient.

Montana, Wyoming↗

USGS2019

Changes in microbial communities and associated water and gas geochemistry across a sulfate gradient in coal beds: Powder River Basin, USA

Competition between microbial sulfate reduction and methanogenesis drives cycling of fossil carbon and generation of CH 4 in sedimentary basins. However, little is understood about the fundamental relationship between subsurface aqueous geochemistry and microbiology that drives these processes. Here we relate elemental and isotopic geochemistry of coal-associated water and gas to the microbial community composition from wells in two different coal beds across CH 4 and SO 4 2− gradients (Powder River Basin, Montana, USA). Areas with high CH 4 concentrations generally have higher alkalinity and δ 13 C-DIC values, little to no SO 4 2− , and greater conversion of coal-biodegradable organics to CH 4 (based on δ 13 C-CH 4 and δ 13 C-CO 2 values). Wells with SO 4 2− concentrations from 2 to 10 mM had bacterial populations dominated by several different sulfate-reducing bacteria and archaea that were mostly novel and unclassified. In contrast, in wells with SO 4 2− concentrations <1 mM, the sequences were dominated by presumptive syntrophic bacteria as well as archaeal Methanosarcinales and Methanomicrobiales . The presence of sequences indicative of these bacteria in low SO 4 2− methanogenic wells may suggest a syntrophic role in coal biodegradation and/or the generation of methanogenic substrates from intermediate organic compounds. Archaeal sequences were observed in all sampled zones, with an enrichment of sequences indicative of methanogens in low SO 4 2− zones and unclassified sequences in high SO 4 2− zones. However, sequences indicative of Methanomassiliicoccales were enriched in intermediate SO 4 2− zones and suggest tolerance to SO 4 2− and/or alternative metabolisms in the presence of SO 4 2− . Moreover, sequences indicative of methylotrophic methanogens were more prevalent in an intermediate SO 4 2− and CH 4 well and results suggest an important role for methylotrophic methanogens in critical zone transitions. The presented results demonstrate in situ changes in bacterial and archaeal population distributions along a SO 4 2− gradient associated with recalcitrant, organic carbon that is biodegraded and converted to CO 2 and/or CH 4 .

Powder River Basin↗

USGS2014

Comparison of surficial CO2 efflux to other measures of subsurface crude oil degradation

At a spill site near Bemidji, Minnesota, crude oil at the water table has been undergoing anaerobic biodegradation for over 30 years. Previous work at this site has shown that methane produced from biodegradation of the oil migrates upward and is oxidized in a methanotrophic zone midway between the water table and the surface. To compare microbial activity measurement methods from multiple locations in the oil body, surficial carbon dioxide efflux, methanogen and methanotroph concentrations, and oil degradation state were collected. Carbon dioxide effluxes over the oil body averaged more than four times those at the background site. Methanotrophic bacteria concentrations measured using pmoA were over 10 5 times higher above the oil-contaminated sediments compared with the background site. Methanogenic archaea measured using mcrA ranged from 10 5 to over 10 7 in the oil and were below detection in the background. Methanogens correlated very well with methanotroph concentrations (r = 0.99), n-alkylcyclohexane losses as a proxy for degradation state (r = − 0.96), and somewhat less well with carbon dioxide efflux (r = 0.92). Carbon dioxide efflux similarly correlated to methanotroph concentrations (r = 0.90) and n-alkylcyclohexane losses (r = − 0.91).

Minnesota↗

USGS2016

Organic petrology and geochemistry of Eocene Suzak bituminous marl, north-central Afghanistan: Depositional environment and source rock potential

Organic geochemistry and petrology of Eocene Suzak bituminous marl outcrop samples from Madr village in north-central Afghanistan were characterized via an integrated analytical approach to evaluate depositional environment and source rock potential. Multiple proxies suggest the organic-rich (TOC ∼6 wt.%) bituminous marls are ‘immature’ for oil generation (e.g., vitrinite R o < 0.4%, T max < 425 °C, PI ≤ 0.05, C 29 ααα S/S + R ≤ 0.12, C 29 ββS/ββS+ααR ≤ 0.10, others), yet oil seeps are present at outcrop and live oil and abundant solid bitumen were observed via optical microscopy. Whole rock sulfur content is ∼2.3 wt.% whereas sulfur content is ∼5.0–5.6 wt.% in whole rock extracts with high polar components, consistent with extraction from S-rich Type IIs organic matter which could generate hydrocarbons at low thermal maturity. Low Fe-sulfide mineral abundance and comparison of Pr/Ph ratios between saturate and whole extracts suggest limited Fe concentration resulted in sulfurization of organic matter during early diagenesis. From these observations, we infer that a Type IIs kerogen in ‘immature’ bituminous marl at Madr could be generating high sulfur viscous oil which is seeping from outcrop. However, oil-seep samples were not collected for correlation studies. Aluminum-normalized trace element concentrations indicate enrichment of redox sensitive trace elements Mo, U and V and suggest anoxic-euxinic conditions during sediment deposition. The bulk of organic matter observed via optical microscopy is strongly fluorescent amorphous bituminite grading to lamalginite, possibly representing microbial mat facies. Short chain n- alkanes peak at C 14 –C 16 ( n- C 17 / n- C 29 > 1) indicating organic input from marine algae and/or bacterial biomass, and sterane/hopane ratios are low (0.12–0.14). Monoaromatic steroids are dominated by C 28 clearly indicating a marine setting. High gammacerane index values (∼0.9) are consistent with anoxia stratification and may indicate intermittent saline-hypersaline conditions. Stable C isotope ratios also suggest a marine depositional scenario for the Suzak samples, consistent with the presence of marine foraminifera including abundant planktic globigerinida (?) and rare benthic discocyclina (?) and nummulites (?). Biomarker 2α-methylhopane for photosynthetic cyanobacteria implies shallow photic zone deposition of Madr marls and 3β-methylhopane indicates presence of methanotrophic archaea in the microbial consortium. The data presented herein are consistent with deposition of Suzak bituminous marls in shallow stratified waters of a restricted marine basin associated with the southeastern incipient or proto-Paratethys. Geochemical proxies from Suzak rock extracts (S content, high polar content, C isotopes, normal (αααR) C 27–29 steranes, and C 29 /C 30 and C 26 /C 25 hopane ratios) are similar to extant data from Paleogene oils produced to the north in the Afghan-Tajik Basin. This observation may indicate laterally equivalent strata are effective source rocks as suggested by previous workers; however, further work is needed to strengthen oil-source correlations.

Marine and Petroleum Geology↗

USGS2012

Bacterial and enchytraeid abundance accelerate soil carbon turnover along a lowland vegetation gradient in interior Alaska

Boreal wetlands are characterized by a mosaic of plant communities, including forests, shrublands, grasslands, and fens, which are structured largely by changes in topography and water table position. The soil associated with these plant communities contain quantitatively and qualitatively different forms of soil organic matter (SOM) and nutrient availability that drive changes in biogeochemical cycling rates. Therefore different boreal plant communities likely contain different soil biotic communities which in turn affect rates of organic matter decomposition. We examined relationships between plant communities, microbial communities, enchytraeids, and soil C turnover in near-surface soils along a shallow topographic soil moisture and vegetation gradient in interior Alaska. We tested the hypothesis that as soil moisture increases along the gradient, surface soils would become increasingly dominated by bacteria and mesofauna and have more rapid rates of C turnover. We utilized bomb radiocarbon techniques to infer rates of C turnover and the 13C isotopic composition of SOM and respired CO 2 to infer the degree of soil humification. Soil phenol oxidase and peroxidase enzyme activities were generally higher in the rich fen compared with the forest and bog birch sites. Results indicated greater C fluxes and more rapid C turnover in the surface soils of the fen sites compared to the wetland forest and shrub sites. Quantitative PCR analyses of soil bacteria and archaea, combined with enchytraeid counts, indicated that surface soils from the lowland fen ecosystems had higher abundances of these microbial and mesofaunal groups. Fungal abundance was highly variable and not significantly different among sites. Microbial data was utilized in a food web model that confirmed that rapidly cycling systems are dominated by bacterial activity and enchytraeid grazing. However, our results also suggest that oxidative enzymes play an important role in the C mineralization process in saturated systems, which has been often ignored.

Soil Biology and Biochemistry↗

USGS2023

Nitrifying microorganisms linked to biotransformation of perfluoroalkyl sulfonamido precursors from legacy aqueous film forming foams

Drinking water supplies across the United States have been contaminated by firefighting and fire-training activities that use aqueous film-forming foams (AFFF) containing per- and polyfluoroalkyl substances (PFAS). Much of the AFFF is manufactured using electrochemical fluorination by 3M. Precursors with six perfluorinated carbons (C6) and non-fluorinated amine substituents make up approximately one-third of the PFAS in 3M AFFF. C6 precursors can be transformed through nitrification (microbial oxidation) of amine moieties into perfluorohexane sulfonate (PFHxS), a compound of regulatory concern. Here, we report biotransformation of the most abundant C6 sulfonamido precursors in 3M AFFF with available commercial standards (FHxSA, PFHxSAm, and PFHxSAmS) in microcosms representative of the groundwater/surface water boundary. Results show rapid (<1 day) biosorption to living cells by precursors but slow biotransformation into PFHxS (1–100 pM day –1 ). The transformation pathway includes one or two nitrification steps and is supported by the detection of key intermediates using high-resolution mass spectrometry. Increasing nitrate concentrations and total abundance of nitrifying taxa occur in parallel with precursor biotransformation. Together, these data provide multiple lines of evidence supporting microbially limited biotransformation of C6 sulfonamido precursors involving ammonia-oxidizing archaea ( Nitrososphaeria ) and nitrite-oxidizing bacteria ( Nitrospina ). Further elucidation of interrelationships between precursor biotransformation and nitrogen cycling in ecosystems would help inform site remediation efforts.

Environmental Science and Technology↗

USGS2021

Expanding the repertoire of electron acceptors for the anaerobic oxidation of methane in carbonates in the Atlantic and Pacific Ocean

Authigenic carbonates represent a significant microbial sink for methane, yet little is known about the microbiome responsible for the methane removal. We identify carbonate microbiomes distributed over 21 locations hosted by seven different cold seeps in the Pacific and Atlantic Oceans by carrying out a gene-based survey using 16S rRNA- and mcr A gene sequencing coupled with metagenomic analyses. Based on 16S rRNA gene amplicon analyses, these sites were dominated by bacteria affiliated to the Firmicutes, Alpha- and Gammaproteobacteria. ANME-1 and -2 archaeal clades were abundant in the carbonates yet their typical syntrophic partners, sulfate-reducing bacteria, were not significantly present. Based on mcrA amplicon analyses, the Candidatus Methanoperedens clades were also highly abundant. Our metagenome analysis indicated that methane oxidizers affiliated to the ANME-1 and -2, may be capable of performing complete methane- and potentially short-chain alkane oxidation independently using oxidized sulfur and nitrogen compounds as terminal electron acceptors. Gammaproteobacteria are hypothetically capable of utilizing oxidized nitrogen compounds and may be involved in syntrophy with methane-oxidizing archaea. Carbonate structures represent a window for a more diverse utilization of electron acceptors for anaerobic methane oxidation along the Atlantic and Pacific Margin.

ISME Journal↗

USGS2023

Metabolically diverse microorganisms mediate methylmercury formation under nitrate-reducing conditions in a dynamic hydroelectric reservoir

Brownlee Reservoir is a mercury (Hg)-impaired hydroelectric reservoir that exhibits dynamic hydrological and geochemical conditions and is located within the Hells Canyon Complex in Idaho, USA. Methylmercury (MeHg) contamination in fish is a concern in the reservoir. While MeHg production has historically been attributed to sulfate-reducing bacteria and methanogenic archaea, microorganisms carrying the hgcA gene are taxonomically and metabolically diverse and the major biogeochemical cycles driving mercury (Hg) methylation are not well understood. In this study, Hg speciation and redox-active compounds were measured throughout Brownlee Reservoir across the stratified period in four consecutive years (2016–2019) to identify the location where and redox conditions under which MeHg is produced. Metagenomic sequencing was performed on a subset of samples to characterize the microbial community with hgcA and identify possible links between biogeochemical cycles and MeHg production. Biogeochemical profiles suggested in situ water column Hg methylation was the major source of MeHg. These profiles, combined with genome-resolved metagenomics focused on hgcA -carrying microbes, indicated that MeHg production occurs in this system under nitrate- or manganese-reducing conditions, which were previously thought to preclude Hg-methylation. Using this multidisciplinary approach, we identified the cascading effects of interannual variability in hydrology on the redox status, microbial metabolic strategies, abundance and metabolic diversity of Hg methylators, and ultimately MeHg concentrations throughout the reservoir. This work expands the known conditions conducive to producing MeHg and suggests that the Hg-methylation mitigation efforts by nitrate or manganese amendment may be unsuccessful in some locations.

Idaho↗

USGS2001

Large carbon isotope fractionation associated with oxidation of methyl halides by methylotrophic bacteria

The largest biological fractionations of stable carbon isotopes observed in nature occur during production of methane by methanogenic archaea. These fractionations result in substantial (as much as ≈70‰) shifts in δ 13 C relative to the initial substrate. We now report that a stable carbon isotopic fractionation of comparable magnitude (up to 70‰) occurs during oxidation of methyl halides by methylotrophic bacteria. We have demonstrated biological fractionation with whole cells of three methylotrophs (strain IMB-1, strain CC495, and strain MB2) and, to a lesser extent, with the purified cobalamin-dependent methyltransferase enzyme obtained from strain CC495. Thus, the genetic similarities recently reported between methylotrophs, and methanogens with respect to their pathways for C 1 -unit metabolism are also reflected in the carbon isotopic fractionations achieved by these organisms. We found that only part of the observed fractionation of carbon isotopes could be accounted for by the activity of the corrinoid methyltransferase enzyme, suggesting fractionation by enzymes further along the degradation pathway. These observations are of potential biogeochemical significance in the application of stable carbon isotope ratios to constrain the tropospheric budgets for the ozone-depleting halocarbons, methyl bromide and methyl chloride. Methyl bromide (MeBr) and methyl chloride (MeCl) are, respectively, the most abundant volatile bromo- and chlorocarbons in the troposphere and are major contributors to stratospheric ozone destruction (1). Both compounds have natural and human-influenced sources and a predominant sink by reaction with OH in the troposphere (2–4). MeBr also has a bacterial soil sink (5) that represents about 20% of the estimated total removal from the troposphere, and it is likely that a soil sink of similar magnitude exists for MeCl (6). Hence, if an isotopic fractionation is associated with the soil sink, it will influence the isotopic compositions of MeBr and MeCl in the lower atmosphere (7). The δ 13 C value of industrially produced MeBr ranges between −43.5‰ and −66.4‰ (7), but δ 13 C values of tropospheric MeBr and natural sources are not yet known. The δ 13 C of atmospheric MeCl has been measured from −22‰ to −45‰ (8, 9). If carbon isotope ratios are to be used to constrain the budgets of these methyl halides, it is essential to determine the extent of carbon isotope fractionation that occurs during biological degradation of these compounds. Methylotrophic bacteria use C 1 compounds, which are simple organic molecules that contain no carbon–carbon bonds. Strains IMB-1, CC495, and MB2 are as-yet-unnamed facultative methylotrophs isolated from agricultural soil, woodland leaf litter, and coastal seawater, respectively (10–13), environments where methyl halides are produced. They are members of the α subgroup of the Proteobacteria . On the basis of 16S rRNA gene sequences, strains IMB-1 and CC495 show some phylogenetic alignment with the genus Rhizobium (10, 11) and are very closely related to the new genus Pseudoaminobacte r (I. McDonald, personal communication). Strain MB2 aligns within the Ruegeria clade [J. K. Schaefer, K. D. Goodwin, I. R. McDonald, J. C. Murrell and R.S.O., unpublished work]. All of these aerobic bacteria are methylotrophs in that they can grow by using MeBr or MeCl as their sole carbon source, but they do not metabolize methane. They oxidize MeBr, MeCl, and methyl iodide (MeI) to CO 2 . Soil bacteria are known to consume MeBr at the ambient tropospheric mixing ratio of around 10 parts per trillion by volume (5). Preliminary experiments with strain IMB-1 indicate that it can oxidize MeBr at these mixing ratios** and is therefore likely to be characteristic of bacteria associated with MeBr uptake by soils. We examined δ 13 C of MeCl, MeBr, and MeI during oxidation by whole-cell suspensions of IMB-1 and CC495 and also the change in δ 13 C values of the three methyl halides during oxidation by the marine strain MB2. In addition, we measured the fractionation of carbon isotopes during formation of methane thiol (MeSH) from MeCl by the purified cobalamin-dependent enzyme, halomethane:bisulphide/halide ion methyltransferase (11) from CC495, to determine whether this initial step in MeCl degradation could account for the observed fractionation by whole cells. Finally, we determined the fractionation associated with the degradation of MeBr during field studies with agricultural soil by monitoring MeBr concentration and δ 13 C of MeBr in the headspace of flux chambers under fumigation conditions.

Proceedings of the National Academy of Sciences of↗

USGS2010

Advances in the hydrogeochemistry and microbiology of acid mine waters

The last decade has witnessed a plethora of research related to the hydrogeochemistry and microbiology of acid mine waters and associated tailings and waste-rock waters. Numerous books, reviews, technical papers, and proceedings have been published that examine the complex bio-geochemical process of sulfide mineral oxidation, develop and apply geochemical models to site characterization, and characterize the microbial ecology of these environments. This review summarizes many of these recent works, and provides references for those investigating this field. Comparisons of measured versus calculated Eh and measured versus calculated pH for water samples from several field sites demonstrate the reliability of some current geochemical models for aqueous speciation and mass balances. Geochemical models are not, however, used to predict accurately time-dependent processes but to improve our understanding of these systems and to constrain possible processes that contribute to actual or potential water quality issues. Microbiological studies are demonstrating that there is much we have yet to learn about the types of different microorganisms and their function and ecology in mine-waste environments. A broad diversity of green algae, bacteria, archaea, yeasts, and fungi are encountered in acid mine waters, and a better understanding of their ecology and function may potentially enhance remediation possibilities as well as our understanding of the evolution of life.

International Geology Review↗

USGS2024

Relation between the relative abundance and collapse of Aphanizomenon flos-aquae and microbial antagonism in Upper Klamath Lake, Oregon

Aphanizomenon flos-aquae (AFA) is the dominant filamentous cyanobacterium that develops into blooms in Upper Klamath Lake, Oregon each year. During AFA bloom and collapse, ecosystem conditions for endangered Lost River and shortnose suckers deteriorate, thus motivating the need to identify processes that limit AFA abundance and decline. Here we investigate the relations between AFA and other members of the microbial community (photosynthetic and non-photosynthetic bacteria and archaea), how those relations impact abundance and collapse of AFA, and the types of microbial conditions that suppress AFA. We found significant spatial variation in AFA relative abundance during the 2016 bloom period using 16S rRNA sequencing. The Pelican Marina (PM) site had the lowest AFA relative abundance, and this was coincident with increased relative abundance of Candidatus Sericytochromatia , Flavobacterium , and Rheinheimera , some of which are known AFA antagonists. The AFA collapse coincided with phosphorus limitation relative to nitrogen and the increased relative abundance of Cyanobium and Candidatus Sericytochromatia, which outcompete AFA when dissolved inorganic nitrogen is available. The data collected in this study indicate the importance of dissolved inorganic nitrogen combined with microbial community structure in suppressing AFA abundance.

Oregon↗

USGS2025

Sulfide stress tolerance as a controller of methane production in temperate wetlands

Wetlands are a major source of methane emissions and contribute to the observed increase in atmospheric methane over the last 20 years. Methane production in wetlands is the final step of carbon decomposition performed by anaerobic archaea. Although hydrogen/carbon dioxide and acetate are the substrates most often attributed to methanogenesis, other substrates—such as methylated compounds—may additionally play important roles in driving methane production in wetland systems. Here we conducted mesocosm experiments combined with genome-resolved metatranscriptomics to investigate the impact of diverse methanogenic substrate amendment on methanogenesis in two high methane-emitting wetlands with distinct geochemistry, termed P7 and P8. Methanol amendment resulted in high methane production at both sites, whereas acetate and formate amendment only stimulated methanogenesis in P7 mesocosms, where aqueous sulfide concentrations were lower. In P7 sediments, formate amendment fueled acetogenic microbes that produced acetate, which was subsequently utilized by acetoclastic methanogens. In contrast to expression profiles in P7 mesocosms, active methylotrophic methanogen genomes from P8 showed increased expression of genes related to membrane remodeling and DNA damage repair, indicative of stress tolerance mechanisms to counter sulfide toxicity. Methylotrophic methanogenesis generates higher free energy yields than acetoclastic methanogenesis, which likely enables allocation of more energy toward stress responses. These findings contribute to the growing body of literature highlighting methylotrophic methanogenesis as an important methane production pathway in wetlands. By using less competitive substrates like methanol that provide greater energy yields, methylotrophic methanogens may invest in physiological strategies that provide competitive advantages across a range of environmental stresses.

North Dakota↗

USGS2021

Does restoration of plant diversity trigger concomitant soil microbiome changes in dryland ecosystems?

Drylands are highly vulnerable to land degradation, and despite increasing efforts, restoration success remains low. Although often ignored in the design and deployment of management strategies, soil microbial communities might be critical for dryland restoration due to their central role in promoting soil stability, nutrient cycling and plant establishment. We collected soil samples from eight dryland restoration sites within RestoreNet, a restoration field trial network, and determined their soil microbiome using 16S rRNA (bacteria and archaea) and ITS (fungi) amplicon sequencing. Each previously degraded site was treated with monoculture (single species) and polyculture (multiple species) seedling plantings. Contrary to our initial expectations, we found that these different revegetation interventions did not trigger changes in microbial diversity, composition or relative abundance of functional groups across sites after 1 year of revegetation. Synthesis and applications . Considering the crucial role of soil micro-organisms in dryland ecosystem functions, our results suggest that site-specific targeted microbiome restoration should be considered to accelerate the establishment of desired microbial communities. Plant community-based restoration practices such as revegetation have a limited impact on soil micro-organisms in the short term.

Journal of Applied Ecology↗

USGS2013

Dryland soil microbial communities display spatial biogeographic patterns associated with soil depth and soil parent material

Biological soil crusts (biocrusts) are common to drylands worldwide. We employed replicated, spatially nested sampling and 16S rRNA gene sequencing to describe the soil microbial communities in three soils derived from different parent material (sandstone, shale, and gypsum). For each soil type, two depths (biocrusts, 0–1 cm; below-crust soils, 2–5 cm) and two horizontal spatial scales (15 cm and 5 m) were sampled. In all three soils, Cyanobacteria and Proteobacteria demonstrated significantly higher relative abundance in the biocrusts, while Chloroflexi and Archaea were significantly enriched in the below-crust soils. Biomass and diversity of the communities in biocrusts or below-crust soils did not differ with soil type. However, biocrusts on gypsum soil harbored significantly larger populations of Actinobacteria and Proteobacteria and lower populations of Cyanobacteria. Numerically dominant operational taxonomic units (OTU; 97% sequence identity) in the biocrusts were conserved across the soil types, whereas two dominant OTUs in the below-crust sand and shale soils were not identified in the gypsum soil. The uniformity with which small-scale vertical community differences are maintained across larger horizontal spatial scales and soil types is a feature of dryland ecosystems that should be considered when designing management plans and determining the response of biocrusts to environmental disturbances.

Utah↗

USGS2022

What is a biocrust? A refined, contemporary definition for a broadening research community

Studies of biological soil crusts (biocrusts) have proliferated over the last few decades. The biocrust literature has broadened, with more studies assessing and describing the function of a variety of biocrust communities in a broad range of biomes and habitats and across a large spectrum of disciplines, and also by the incorporation of biocrusts into global perspectives and biogeochemical models. As the number of biocrust researchers increases, along with the scope of soil communities defined as ‘biocrust’, it is worth asking whether we all share a clear, universal, and fully articulated definition of what constitutes a biocrust. In this review, we synthesize the literature with the views of new and experienced biocrust researchers, to provide a refined and fully elaborated definition of biocrusts. In doing so, we illustrate the ecological relevance and ecosystem services provided by them. We demonstrate that biocrusts are defined by four distinct elements: physical structure, functional characteristics, habitat, and taxonomic composition. We describe outgroups, which have some, but not all, of the characteristics necessary to be fully consistent with our definition and thus would not be considered biocrusts. We also summarize the wide variety of different types of communities that fall under our definition of biocrusts, in the process of highlighting their global distribution. Finally, we suggest the universal use of the Belnap, Büdel & Lange definition, with minor modifications: Biological soil crusts (biocrusts) result from an intimate association between soil particles and differing proportions of photoautotrophic (e.g. cyanobacteria , algae , lichens , bryophytes) and heterotrophic (e.g. bacteria , fungi , archaea) organisms , which live within , or immediately on top of , the uppermost millimetres of soil. Soil particles are aggregated through the presence and activity of these often extremotolerant biota that desiccate regularly , and the resultant living crust covers the surface of the ground as a coherent layer. With this detailed definition of biocrusts, illustrating their ecological functions and widespread distribution, we hope to stimulate interest in biocrust research and inform various stakeholders (e.g. land managers, land users) on their overall importance to ecosystem and Earth system functioning.

Biological Reviews↗

USGS2019

Microbial assemblages reflect environmental heterogeneity in alpine streams

Alpine streams are dynamic habitats harboring substantial biodiversity across small spatial extents. The diversity of alpine stream biota is largely reflective of environmental heterogeneity stemming from varying hydrological sources. Globally, alpine stream diversity is under threat as meltwater sources recede and stream conditions become increasingly homogeneous. Much attention has been devoted to macroinvertebrate diversity in alpine headwaters, yet to fully understand the breadth of climate change threats, a more thorough accounting of microbial diversity is needed. We characterized microbial diversity (specifically Bacteria and Archaea) of 13 streams in two disjunct Rocky Mountain subranges through 16S rRNA gene sequencing. Our study encompassed the spectrum of alpine stream sources (glaciers, snowfields, subterranean ice, and groundwater) and three microhabitats (ice, biofilms, and streamwater). We observed no difference in regional (γ) diversity between subranges but substantial differences in diversity among (β) stream types and microhabitats. Within‐stream (α) diversity was highest in groundwater‐fed springs, lowest in glacier‐fed streams, and positively correlated with water temperature for both streamwater and biofilm assemblages. We identified an underappreciated alpine stream type—the icy seep—that are fed by subterranean ice, exhibit cold temperatures (summer mean <2°C), moderate bed stability, and relatively high conductivity. Icy seeps will likely be important for combatting biodiversity losses as they contain similar microbial assemblages to streams fed by surface ice yet may be buffered against climate change by insulating debris cover. Our results show that the patterns of microbial diversity support an ominous trend for alpine stream biodiversity; as meltwater sources decline, stream communities will become more diverse locally, but regional diversity will be lost. Icy seeps, however, represent a source of optimism for the future of biodiversity in these imperiled ecosystems.

Montana↗

USGS2004

Spatial and temporal changes in microbial community structure associated with recharge-influenced chemical gradients in a contaminated aquifer

In a contaminated water‐table aquifer, we related microbial community structure on aquifer sediments to gradients in 24 geochemical and contaminant variables at five depths, under three recharge conditions. Community amplified ribsosomal DNA restriction analysis (ARDRA) using universal 16S rDNA primers and denaturing gradient gel electrophoresis (DGGE) using bacterial 16S rDNA primers indicated: (i) communities in the anoxic, contaminated central zone were similar regardless of recharge; (ii) after recharge, communities at greatest depth were similar to those in uncontaminated zones; and (iii) after extended lack of recharge, communities at upper and lower aquifer margins differed from communities at the same depths on other dates. General aquifer geochemistry was as important as contaminant or terminal electron accepting process (TEAP) chemistry in discriminant analysis of community groups. The Shannon index of diversity ( H ) and the evenness index ( E ), based on DGGE operational taxonomic units (OTUs), were statistically different across community groups and aquifer depths. Archaea or sulphate‐reducing bacteria 16S rRNA abundance was not clearly correlated with TEAP chemistry indicative of methanogenesis or sulphate reduction. Eukarya rRNA abundance varied by depth and date from 0 to 13% of the microbial community. This contaminated aquifer is a dynamic ecosystem, with complex interactions between physical, chemical and biotic components, which should be considered in the interpretation of aquifer geochemistry and in the development of conceptual or predictive models for natural attenuation or remediation.

Environmental Microbiology↗