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At least 73 records · Page 4Linked to original sources

Methane hydrate-bearing seeps as a source of aged dissolved organic carbon to the oceans

Marine sediments contain about 500–10,000 Gt of methane carbon1, 2, 3, primarily in gas hydrate. This reservoir is comparable in size to the amount of organic carbon in land biota, terrestrial soils, the atmosphere and sea water combined1, 4, but it releases relatively little methane to the ocean and atmosphere5. Sedimentary microbes convert most of the dissolved methane to carbon dioxide6, 7. Here we show that a significant additional product associated with microbial methane consumption is methane-derived dissolved organic carbon. We use Δ14C and δ13C measurements and isotopic mass-balance calculations to evaluate the contribution of methane-derived carbon to seawater dissolved organic carbon overlying gas hydrate-bearing seeps in the northeastern Pacific Ocean. We show that carbon derived from fossil methane accounts for up to 28% of the dissolved organic carbon. This methane-derived material is much older, and more depleted in 13C, than background dissolved organic carbon. We suggest that fossil methane-derived carbon may contribute significantly to the estimated 4,000–6,000 year age of dissolved organic carbon in the deep ocean8, and provide reduced organic matter and energy to deep-ocean microbial communities.

Nature Geoscience

Functional restructuring of the global soil microbiome under multiple stressors

Microbes, as the planet’s most abundant and diverse organisms, drive soil functions globally and are vulnerable to environmental stressors triggered by global change. Yet, knowledge regarding the impacts of multiple environmental stressors on their functional profiles as well as the consequences for soil functionality largely remains unknown. Here, we analyze two global-scale datasets including information on soil metagenomics and multiple environmental stressors. We find that across terrestrial ecosystems worldwide, up to 60% of all functional genes significantly shift when soil microbes experience the high-level of concurrent stressors. In this regard, the relative abundances of genes involved in microbial growth are negatively linked to the increasing number of stressors. Conversely, those genes linked to stress resistance and energy production exhibit positive responses. Taken together, our findings highlight a significant restructuring of global soil functional microbiomes in response to multiple environmental stressors. Consequently, such restructuring drives community-level shifts in matter and energy reallocations, thereby impacting the maintenance of soil functionality under the projected global change.

Nature Communications

Filamentous hydrous ferric oxide biosignatures in a pipeline carrying acid mine drainage at Iron Mountain Mine, California

A pipeline carrying acidic mine effluent at Iron Mountain, CA, developed Fe(III)-rich precipitate caused by oxidation of Fe(II) aq . The native microbial community in the pipe included filamentous microbes. The pipe scale consisted of microbial filaments, and schwertmannite (ferric oxyhydroxysulfate, FOHS) mineral spheres and filaments. FOHS filaments contained central lumina with diameters similar to those of microbial filaments. FOHS filament geometry, the geochemical environment, and the presence of filamentous microbes suggest that FOHS filaments are mineralized microbial filaments. This formation of textural biosignatures provides the basis for a conceptual model for the development and preservation of biosignatures in other environments.

Geomicrobiology Journal

Divergent biotic and abiotic filtering of root endosphere and rhizosphere soil fungal communities along ecological gradients

Plant roots assemble two distinct microbial compartments: the rhizosphere (microbes in soil surrounding roots) and the endosphere (microbes within roots). Our knowledge of fungal community assembly in these compartments is limited, especially in wetlands. We tested the hypothesis that biotic factors would have direct effects on rhizosphere and endosphere assembly, while abiotic factors would have direct and indirect effects. Using a field study, we examined the influences of salinity, water level and biotic factors on baldcypress (Taxodium distichum) fungal communities. We found that endosphere fungi were correlated with host density and canopy cover as opposed to rhizosphere, suggesting that hosts can impose selective filters on fungi colonizing into their roots. Meanwhile, local abiotic conditions strongly influenced both rhizosphere and endosphere diversity in opposite patterns: e.g. highest endosphere diversity (hump-shaped) while lowest rhizosphere diversity (U-shaped) at intermediate salinity levels. These results indicate that the assembly and structure for the root endosphere and rhizosphere within a host can be shaped by different processes. Our results also highlight the importance of assessing how environmental changes affect plant and plant-associated fungal communities in wetland ecosystems where saltwater intrusion and sea level rise are major threats to both plant and fungal communities.

FEMS Microbiology Ecology

Microbiomes associated with avian malaria survival differ between susceptible Hawaiian honeycreepers and sympatric malaria-resistant introduced birds

Of the estimated 55 Hawaiian honeycreepers (subfamily Carduelinae) only 17 species remain, nine of which the International Union for Conservation of Nature considers endangered. Among the most pressing threats to honeycreeper survival is avian malaria, caused by the introduced blood parasite Plasmodium relictum , which is increasing in distribution in Hawaiʻi as a result of climate change. Preventing further honeycreeper decline will require innovative conservation strategies that confront malaria from multiple angles. Research on mammals has revealed strong connections between gut microbiome composition and malaria susceptibility, illuminating a potential novel approach to malaria control through the manipulation of gut microbiota. One honeycreeper species, Hawaiʻi ʻamakihi ( Chlorodrepanis virens ), persists in areas of high malaria prevalence, indicating they have acquired some level of immunity. To investigate if avian host-specific microbes may be associated with malaria survival, we characterized cloacal microbiomes and malaria infection for 174 ʻamakihi and 172 malaria-resistant warbling white-eyes ( Zosterops japonicus ) from Hawaiʻi Island using 16S rRNA gene metabarcoding and quantitative polymerase chain reaction. Neither microbial alpha nor beta diversity covaried with infection, but 149 microbes showed positive associations with malaria survivors. Among these were Escherichia and Lactobacillus spp . , which appear to mitigate malaria severity in mammalian hosts, revealing promising candidates for future probiotic research for augmenting malaria immunity in sensitive endangered species.

Hawaii

Experimental warming alters free-living nitrogen fixation in a humid tropical forest

Microbial nitrogen (N) fixation accounts for c. 97% of natural N inputs to terrestrial ecosystems. These microbes can be free-living in the soil and leaf litter (asymbiotic) or in symbiosis with plants. Warming is expected to increase N-fixation rates because warmer temperatures favor the growth and activity of N-fixing microbes. We investigated the effects of warming on asymbiotic components of N fixation at a field warming experiment in Puerto Rico. We analyzed the function and composition of bacterial communities from surface soil and leaf litter samples. Warming significantly increased asymbiotic N-fixation rates in soil by 55% (to 0.002 kg ha −1 yr −1 ) and by 525% in leaf litter (to 14.518 kg ha −1 yr −1 ) . This increase in N fixation was associated with changes in the N-fixing bacterial community composition and soil nutrients. Our findings suggest that warming increases the natural N inputs from the atmosphere into this tropical forest due to changes in microbial function and composition, especially in the leaf litter. Given the importance of leaf litter in nutrient cycling, future research should investigate other aspects of N cycles in the leaf litter under warming conditions.

Luquillo Experimental Forest, northeastern Puerto

Culture-independent characterization of bacterial communities associated with the cold-water coral Lophelia pertusa in the northeastern Gulf of Mexico

Bacteria are recognized as an important part of the total biology of shallow-water corals. Studies of shallow-water corals suggest that associated bacteria may benefit the corals by cycling carbon, fixing nitrogen, chelating iron, and producing antibiotics that protect the coral from other microbes. Cold-water or deep-sea corals have a fundamentally different ecology due to their adaptation to cold, dark, high-pressure environments and as such have novel microbiota. The goal of this study was to characterize the microbial associates of Lophelia pertusa in the northeastern Gulf of Mexico. This is the first study to collect the coral samples in individual insulated containers and to preserve coral samples at depth in an effort to minimize thermal shock and evaluate the effects of environmental gradients on the microbial diversity of samples. Molecular analysis of bacterial diversity showed a marked difference between the two study sites, Viosca Knoll 906/862 (VK906/862) and Viosca Knoll 826 (VK826). The bacterial communities from VK826 were dominated by a variety of unknown mycoplasmal members of the Tenericutes and Bacteroidetes , whereas the libraries from VK906/862 were dominated by members of the Proteobacteria . In addition to novel sequences, the 16S rRNA gene clone libraries revealed many bacterial sequences in common between Gulf of Mexico Lophelia corals and Norwegian fjord Lophelia corals, as well as shallow-water corals. Two Lophelia -specific bacterial groups were identified: a cluster of gammaproteobacteria related to sulfide-oxidizing gill symbionts of seep clams and a group of Mycoplasma spp. The presence of these groups in both Gulf and Norwegian Lophelia corals indicates that in spite of the geographic heterogeneity observed in Lophelia -associated bacterial communities, there are Lophelia -specific microbes.

Gulf of Mexico

Krumholzibacteriota and Deltaproteobacteria contain rare genetic potential to liberate carbon from monoaromatic compounds in subsurface coal seams

Biogenic methane in subsurface coal seam environments is produced by diverse consortia of microbes. Although this methane is useful for global energy security, it remains unclear which microbes can liberate carbon from the coal. Most of this carbon is relatively resistant to biodegradation, as it is contained within aromatic rings. Thus, to explore for coal-degrading taxa in the subsurface, this study reconstructed relevant metagenome-assembled genomes (MAGs) from coal seams by using a key genomic marker for the anaerobic degradation of monoaromatic compounds as a guide: the benzoyl-CoA reductase gene ( bcrABCD ). Three MAGs were identified with this genetic potential. The first represented a novel taxon from the Krumholzibacteriota phylum, which this study is the first to describe. This Krumholzibacteriota MAG contained a full set of genes for benzoyl-CoA dearomatization, in addition to other genes for anaerobic catabolism of monoaromatics. Analysis of Krumholzibacteriota MAGs from other environments revealed that this genetic potential may be common, and thus, Krumholzibacteriota may be important organisms for the liberation of recalcitrant carbon in a broad range of environments. Moreover, the assembly and characterization of two Syntrophorhabdus aromaticivorans MAGs from different continents and a Syntrophaceae sp. MAG implicate the Deltaproteobacteria class in coal seam monoaromatic degradation. Each of these taxa are potential rate-limiting organisms for subsurface coal-to-methane biodegradation. Their description here provides some understanding of their function within the coal seam microbiome and will help inform future efforts in coal bed methane stimulation, anoxic bioremediation of organic pollutants, and assessments of anoxic, subsurface carbon cycling and emissions.

mBio

Perspectives on the future of ecology, evolution, and biodiversity from the Council on Microbial Sciences of the American Society for Microbiology

The field of microbial ecology, evolution, and biodiversity (EEB) is at the leading edge of understanding how microbes shape our biosphere and influence the well-being of humankind. To that end, EEB is developing new tools to analyze the massive, complex, transdisciplinary datasets that result from such studies. The American Society for Microbiology’s Council on Microbial Sciences hosted a virtual retreat in 2023 to identify the trajectory of EEB both within the Society and microbiology at large. Retreat presentations and discussions collectively emphasized the interconnectedness of microbes and their outsized global influence on environmental and host health. The retreat repeatedly emphasized that the future of science is through transdisciplinary collaborations that promote integration of diverse datasets and advanced technologies, while also genuinely fostering inclusivity, global collaborations, and public engagement. The American Society for Microbiology and EEB stand poised to lead a paradigm shift that will result in a new era of collaboration, innovation, and societal relevance for microbiology.

mSphere

Milankovitch-scale correlations between deeply buried microbial populations and biogenic ooze lithology

The recent discoveries of large, active populations of microbes in the subseafloor of the world's oceans supports the impact of the deep biosphere biota on global biogeochemical cycles and raises important questions concerning the functioning of these extreme environments for life. These investigations demonstrated that subseafloor microbes are unevenly distributed and that cell abundances and metabolic activities are often independent from sediment depths, with increased prokaryotic activity at geochemical and/or sedimentary interfaces. In this study we demonstrate that microbial populations vary at the scale of individual beds in the biogenic oozes of a drill site in the eastern equatorial Pacific (Ocean Drilling Program Leg 201, Site 1226). We relate bedding-scale changes in biogenic ooze sediment composition to organic carbon (OC) and microbial cell concentrations using high-resolution color reflectance data as proxy for lithology. Our analyses demonstrate that microbial concentrations are an order of magnitude higher in the more organic-rich diatom oozes than in the nannofossil oozes. The variations mimic small-scale variations in diatom abundance and OC, indicating that the modern distribution of microbial biomass is ultimately controlled by Milankovitch-frequency variations in past oceanographic conditions. ?? 2010 Geological Society of America.

Geology

Geomicrobial interactions with arsenic and antimony

Although arsenic and antimony are generally toxic to life, some microorganisms exist that can metabolize certain forms of these elements. Some can use arsenite or stibnite as potential or sole energy sources, whereas others can use aresenate and antimonite (as was discovered only recently) as terminal electron acceptors. Still other microbes can metabolize arsenic and antimony compounds to detoxify them. These reactions are important from a geomicrobial standpoint because they indicate that a number of microbes contribute to arsenic and antimony mobilization or immobilization in the environment and play a role in arsenic and antimony cycles. Recent reviews include five on prokaryotes and arsenic metabolism, a review with an arsenic perspective on biomining, and a series on environmental antimony, including one about antimony and its interaction with microbiota.

Book chapter

Sources and risk factors for nitrate and microbial contamination of private household wells in the fractured dolomite aquifer of northeastern Wisconsin

Background: Groundwater quality in the Silurian dolomite aquifer in northeastern Wisconsin, USA, has become contentious as dairy farms and exurban development expand. Objectives: We investigated private household wells in the region, determining the extent, sources, and risk factors of nitrate and microbial contamination. Methods: Total coliforms, Escherichia coli , and nitrate were evaluated by synoptic sampling during groundwater recharge and no-recharge periods. Additional seasonal sampling measured genetic markers of human and bovine fecal-associated microbes and enteric zoonotic pathogens. We constructed multivariable regression models of detection probability (log-binomial) and concentration (gamma) for each contaminant to identify risk factors related to land use, precipitation, hydrogeology, and well construction. Results: Total coliforms and nitrate were strongly associated with depth-to-bedrock at well sites and nearby agricultural land use, but not septic systems. Both human wastewater and cattle manure contributed to well contamination. Rotavirus group A, Cryptosporidium , and Salmonella were the most frequently detected pathogens. Wells positive for human fecal markers were associated with depth-to-groundwater and number of septic system drainfield within 229 m "> 229 m 229m . Manure-contaminated wells were associated with groundwater recharge and the area size of nearby agricultural land. Wells positive for any fecal-associated microbe, regardless of source, were associated with septic system density and manure storage proximity modified by bedrock depth. Well construction was generally not related to contamination, indicating land use, groundwater recharge, and bedrock depth were the most important risk factors. Discussion: These findings may inform policies to minimize contamination of the Silurian dolomite aquifer, a major water supply for the U.S. and Canadian Great Lakes region.

Wisconsin

Coniform stromatolites from geothermal systems, North Island, New Zealand

Coniform stromatolites are found in several sites in the Tokaanu and Whakarewarewa geothermal areas of North Island, New Zealand. At Tokaanu, silicification of these stromatolites is taking place in Kirihoro, a shallow hot springfed pool. At Whakarewarewa, subfossil silicified coniform stromatolites are found on the floor of "Waikite Pool" on the discharge apron below Waikite Geyser, and in an old sinter succession at Te Anarata. The microbes in the coniform stromatolites from Tokaanu, Waikite Pool, and Te Anarata have been well preserved through rapid silicification. Nevertheless, subtle differences in the silicification style induced morphological variations that commonly mask or alter morphological features needed for identification of the microbes in terms of extant taxa. The coniform stromatolites in the New Zealand hotspring pools are distinctive because (1) they are formed of upward tapering (i.e., conical) columns, (2) neighboring columns commonly are linked by vertical sheets or bridges, (3) internally, they are formed of alternating high- and low-porosity laminae that have a conical vertical profile, and (4) Phormidium form more than 90% of the biota. As such, they are comparable to modern coniform mats and stromatolites found in the geothermal systems of Yellowstone National Park and ice-covered lakes in Antarctica. Formation of the coniform stromatolites is restricted to pools that are characterized by low current energy and a microflora that is dominated by Phormidium. These delicate and intricate stromatolites could not form in areas characterized by fast flowing water or a diverse microflora. Thus, it appears that the distribution of these distinctive stromatolites is controlled by biological constraints that are superimposed on environmental needs.

Palaios

Nutrient additions to mitigate for loss of Pacific salmon: consequences for stream biofilm and nutrient dynamics

Mitigation activities designed to supplement nutrient and organic matter inputs to streams experiencing decline or loss of Pacific salmon typically presuppose that an important pathway by which salmon nutrients are moved to fish (anadromous and/or resident) is via nutrient incorporation by biofilms and subsequent bottom-up stimulation of biofilm production, which is nutrient-limited in many ecosystems where salmon returns have declined. Our objective was to quantify the magnitude of nutrient incorporation and biofilm dynamics that underpin this indirect pathway in response to experimental additions of salmon carcasses and pelletized fish meal (a.k.a., salmon carcass analogs) to 500-m reaches of central Idaho streams over three years. Biofilm standing crops increased 2–8-fold and incorporated marine-derived nutrients (measured using 15 N and 13 C) in the month following treatment, but these responses did not persist year-to-year. Biofilms were nitrogen (N) limited before treatments, and remained N limited in analog, but not carcass-treated reaches. Despite these biofilm responses, in the month following treatment total N load was equal to 33–47% of the N added to the treated reaches, and N spiraling measurements suggested that as much as 20%, but more likely 2–3% of added N was taken up by microbes. Design of biologically and cost-effective strategies for nutrient addition will require understanding the rates at which stream microbes take up nutrients and the downstream distance traveled by exported nutrients.

Idaho

Alternate wetting and drying decreases methylmercury in flooded rice (Oryza sativa) systems

In flooded soils, including those found in rice ( Oryza sativa L.) fields, microbes convert inorganic Hg to more toxic methylmercury (MeHg). Methylmercury is accumulated in rice grain, potentially affecting health. Methylmercury in rice field surface water can bioaccumulate in wildlife. We evaluated how introducing aerobic periods into an otherwise continuously flooded rice growing season affects MeHg dynamics. Conventional continuously flooded (CF) rice field water management was compared with alternate wetting and drying, where irrigation was stopped twice during the growing season, allowing soil to dry to 35% volumetric moisture content, at which point plots were reflooded (AWD-35). Methylmercury studies began at harvest in Year 3 and throughout Year 4 of a 4-yr replicated field experiment. Bulk soil, water, and plant samples were analyzed for MeHg and total Hg (THg), and iron (Fe) speciation was measured in soil samples. Rice grain yield over 4 yr did not differ between treatments. Soil chemistry responded quickly to AWD-35 dry-downs, showing significant oxidation of Fe(II) accompanied by a significant reduction of MeHg concentration (76% reduction at harvest) compared with CF. Surface water MeHg decreased by 68 and 39% in the growing and fallow seasons, respectively, suggesting that the effects of AWD-35 management can last through to the fallow season. The AWD-35 treatment reduced rice grain MeHg and THg by 60 and 32%, respectively. These results suggest that the more aerobic conditions caused by AWD-35 limited the activity of Hg(II)-methylating microbes and may be an effective way to reduce MeHg concentrations in rice ecosystems.

Soil Science Society of America Journal

Microbial production of natural gas from coal and organic-rich shale

Natural gas is an important component of the energy mix in the United States, producing greater energy yield per unit weight and less pollution compared to coal and oil. Most of the world’s natural gas resource is thermogenic, produced in the geologic environment over time by high temperature and pressure within deposits of oil, coal, and shale. About 20 percent of the natural gas resource, however, is produced by microorganisms (microbes). Microbes potentially could be used to generate economic quantities of natural gas from otherwise unexploitable coal and shale deposits, from coal and shale from which natural gas has already been recovered, and from waste material such as coal slurry. Little is known, however, about the microbial production of natural gas from coal and shale.

Fact Sheet

Origin of water that discharges from Calf Creek Spring, Garfield County, Utah

Calf Creek Spring provides drinking water to users of Calf Creek Campground, which is operated by the Bureau of Land Management in southcentral Utah. Use of all methods and tools available indicates that surface water from Calf Creek does not contribute to the discharge of Calf Creek Spring. Microscopic Particulate Analysis of spring water indicates that the spring has a low risk of surface-water contamination, which is substantiated by a bacterial test of water from the point of discharge of Calf Creek Spring, the Calf Creek Spring collection box, a tap from the water distribution system, and Calf Creek near the picnic area. Bacteria colonies were found in Calf Creek near the picnic area. Calf Creek Spring discharges from fractured Navajo Sandstone where the potential for contamination by animal or human microbes is slight. Calf Creek probably gains water along its entire length from the aquifer in the Navajo Sandstone. Once at the surface, water in Calf Creek is exposed to animal- and human-borne microbes. If the water level in the Navajo aquifer at the spring remains higher than the water level of the creek, mixing is unlikely to occur and contamination is unlikely. The water level of Calf Creek Spring in June 1994 was at least 4 feet above the water level of Calf Creek. Water from Calf Creek Spring is a mixed type composed of magnesium, calcium, sodium, bicarbonate, and sulfate ions, and water from Calf Creek is a mixed type composed of calcium, magnesium, bicarbonate, sulfate, and chloride ions. Compositional similarity is not unusual if both water sources are derived from the Navajo aquifer. Discharge and temperature measurements at the spring and in the creek in May and June 1994 vary independently and do not indicate a hydraulic connection. Turbidity measurements, though not conclusive, indicate that no direct hydraulic connection exists between Calf Creek and Calf Creek Spring. Hydrologic characteristics of Calf Creek provide evidence that the probable long-term, sustainable source of water is the Navajo aquifer and not precipitation-derived runoff. Ground-water leakage from adjacent drainages could contribute to perennial flow in Calf Creek. Fractures modify the movement of ground water to discharge areas, such as Calf Creek Spring.

Utah

The Effectiveness of Cattlemans Detention Basin, South Lake Tahoe, California

Lake Tahoe (Nevada-California) has been designated as an 'outstanding national water resource' by the U.S. Environmental Protection Agency, in part, for its exceptional clarity. Water clarity in Lake Tahoe, however, has been declining at a rate of about one foot per year for more than 35 years. To decrease the amount of sediment and nutrients delivered to the lake by way of alpine streams, wetlands and stormwater detention basins have been installed at several locations around the lake. Although an improvement in stormwater and snowmelt runoff quality has been measured, the effectiveness of the detention basins for increasing the clarity of Lake Tahoe needs further study. It is possible that poor ground-water quality conditions exist beneath the detention basins and adjacent wetlands and that the presence of the basins has altered ground-water flow paths to nearby streams. A hydrogeochemical and ground-water flow modeling study was done at Cattlemans detention basin, situated adjacent to Cold Creek, a tributary to Lake Tahoe, to determine whether the focusing of storm and snowmelt runoff into a confined area has (1) modified the ground-water flow system beneath the detention basin and affected transport of sediment and nutrients to nearby streams and (2) provided an increased source of solutes which has changed the distribution of nutrients and affected nutrient transport rates beneath the basin. Results of slug tests and ground-water flow modeling suggest that ground water flows unrestricted northwest across the detention basin through the meadow. The modeling also indicates that seasonal flow patterns and flow direction remain similar from year to year under transient conditions. Model results imply that about 34 percent (0.004 ft3/s) of the total ground water within the model area originates from the detention basin. Of the 0.004 ft3/s, about 45 percent discharges to Cold Creek within the modeled area downstream of the detention basin. The remaining 55 percent of ground water is either consumed by evapotranspiration, is discharged to Cold Creek outside the modeled area downstream of the detention basin, or is discharged directly to Lake Tahoe. Of the 45 percent discharging to Cold Creek, about 9 percent enters directly downstream of the detention basin and 36 percent enters further downstream. Geochemical and microbial data suggest that a seasonal variation of chemical constituents and microbe population size is present at most wells. The geochemical data also indicate that construction of Cattlemans detention basin has not substantially changed the composition of the ground water in the area. High concentrations of ammonia, iron, and dissolved organic carbon, low concentrations of sulfate and nitrate, and large populations of sulfate-reducing microbes imply that the major geochemical process controlling nutrient concentrations beneath the detention basin is sulfate reduction. High concentrations of total nitrogen indicate that oxidation of organic carbon is a second important geochemical process occurring beneath the basin. The influx of surface runoff during spring 2002 apparently provided sufficient oxidized organic carbon to produce iron-reducing conditions and an increase in reduced iron, sulfate, and iron-reducing microorganisms. The increase in recharge of oxygenated water to the ground water system beneath the basin in future intervals of increased recharge may eventually redistribute nutrients and speed up transport of dissolved nutrients from the ground water system to Cold Creek.

Scientific Investigations Report