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At least 199 records · Page 11Linked to original sources
USGS2024

Perspectives on the future of host-microbe biology from the Council on Microbial Sciences of the American Society for Microbiology

Host-microbe biology (HMB) stands on the cusp of redefinition, challenging conventional paradigms to instead embrace a more holistic understanding of the microbial sciences. The American Society for Microbiology (ASM) Council on Microbial Sciences hosted a virtual retreat in 2023 to identify the future of the HMB field and innovations needed to advance the microbial sciences. The retreat presentations and discussions collectively emphasized the interconnectedness of microbes and their profound influence on humans, animals, and environmental health, as well as the need to broaden perspectives to fully embrace the complexity of these interactions. To advance HMB research, microbial scientists would benefit from enhancing interdisciplinary and transdisciplinary research to utilize expertise in diverse fields, integrate different disciplines, and promote equity and accessibility within HMB. Data integration will be pivotal in shaping the future of HMB research by bringing together varied scientific perspectives, new and innovative techniques, and ’omics approaches. ASM can empower under-resourced groups with the goal of ensuring that the benefits of cutting-edge research reach every corner of the scientific community. Thus, ASM will be poised to steer HMB toward a future that champions inclusivity, innovation, and accessible scientific progress.

mSphere↗
USGS2022

Microbiome assembly in thawing permafrost and its feedbacks to climate

The physical and chemical changes that accompany permafrost thaw directly influence the microbial communities that mediate the decomposition of formerly frozen organic matter, leading to uncertainty in permafrost–climate feedbacks. Although changes to microbial metabolism and community structure are documented following thaw, the generality of post-thaw assembly patterns across permafrost soils of the world remains uncertain, limiting our ability to predict biogeochemistry and microbial community responses to climate change. Based on our review of the Arctic microbiome, permafrost microbiology, and community ecology, we propose that Assembly Theory provides a framework to better understand thaw-mediated microbiome changes and the implications for community function and climate feedbacks. This framework posits that the prevalence of deterministic or stochastic processes indicates whether the community is well-suited to thrive in changing environmental conditions. We predict that on a short timescale and following high-disturbance thaw (e.g., thermokarst), stochasticity dominates post-thaw microbiome assembly, suggesting that functional predictions will be aided by detailed information about the microbiome. At a longer timescale and lower-intensity disturbance (e.g., active layer deepening), deterministic processes likely dominate, making environmental parameters sufficient for predicting function. We propose that the contribution of stochastic and deterministic processes to post-thaw microbiome assembly depends on the characteristics of the thaw disturbance, as well as characteristics of the microbial community, such as the ecological and phylogenetic breadth of functional guilds, their functional redundancy, and biotic interactions. These propagate across space and time, potentially providing a means for predicting the microbial forcing of greenhouse gas feedbacks to global climate change.

Global Change Biology↗
USGS2005

Bacteriological water quality in the Lake Pontchartrain basin, Louisiana, following Hurricanes Katrina and Rita, September 2005

The U.S. Geological Survey (USGS), in collaboration with the Louisiana Department of Environmental Quality, monitored bacteriological quality of water at 22 sites in and around Lake Pontchartrain, La., for three consecutive weeks beginning September 13, 2005, following hurricanes Katrina and Rita and the associated flooding. Samples were collected and analyzed by USGS personnel from the USGS Louisiana Water Science Center and the USGS Ohio Water Microbiology Laboratory. Fecal-indicator bacteria (Escherichia coli, enterococci, and fecal coliform) concentrations ranged from the detection limit to 36,000 colony-forming units per 100 milliliters. Data are presented in tabular form and as plots of data in the context of available historical data and water-quality standards and criteria for each site sampled. Quality-control data were reviewed to ensure that methods performed as expected in a mobile laboratory setting.

Louisiana↗
USGS2012

Microbial colonization and controls in dryland systems

Drylands constitute the most extensive terrestrial biome, covering more than one-third of the Earth's continental surface. In these environments, stress limits animal and plant life, so life forms that can survive desiccation and then resume growth following subsequent wetting assume the foremost role in ecosystem processes. In this Review, we describe how these organisms assemble in unique soil- and rock-surface communities to form a thin veneer of mostly microbial biomass across hot and cold deserts. These communities mediate inputs and outputs of gases, nutrients and water from desert surfaces, as well as regulating weathering, soil stability, and hydrological and nutrient cycles. The magnitude of regional and global desert-related environmental impacts is affected by these surface communities; here, we also discuss the challenges for incorporating the consideration of these communities and their effects into the management of dryland resources.

Nature Reviews Microbiology↗
USGS2007

Southern California Bight 2003 Regional Monitoring Program: V. water quality

More than $30 million is expended annually on environmental monitoring in the Southern California Bight (SCB), yet only 5% of the Bight is monitored on an ongoing basis. Therefore, environmental managers in the SCB decided to expand their monitoring program and, starting in 1994, decided to conduct periodic regional assessments of ecosystem condition and assess the overall health of the SCB. Sixty-five different organizations collaborated in 2003 to create the third SCB Regional Monitoring Program (Bight '03). Bight '03 was designed to be integrated regional monitoring program that encompasses regulatory, academic, and non-governmental agencies. Bight '03 had three components: Coastal Ecology, Shoreline Microbiology, and Water Quality. This report addresses the purpose, approach, findings, and recommendations from the Water Quality component, which focused on contamination-laden stormwater runoff, in particularly its variability in time and space as well as its short-term ecological impacts. Specifically, the Bight '03 Water Quality component had three primary goals, the first of which was to described the temporal evolution of stormwater plumes produced by the major southern California rivers. Specifically, the study was intended to determine how far offshore the plumes extended, how rapidly they advected, how long before the plumes dispersed and how these properties differed among storms and river systems. The second goal was to describe how the physical properties (e.g., turbidity, temperature, salinity) of the plume related to biogeochemical and ecological properties that are of more direct concern to the water quality management community. Accomplished primarily through ship-based sampling of water quality parameters, this second goal was to describe how far offshore, and for how ;long after the storm, elevated bacterial concentrations, toxicity, and nutrients could be detected. Similar to the fist goal, the study also addressed how these answers differed among storms and river systems. The final goal was to determine whether relationships between environmental indicators derived from coincident satellite remote sensing and in situ data sets are sufficiently robust for remote sensing to become a routine water quality monitoring programs. Remote sensing data potentially provide coastal managers with synoptic near-real time regional information about prevailing ocean conditions and hazards that would complement existing field-based sampling protocols, but only if there is a thorough understanding of how to interpret and utilize the proxy measures, such as ocean color. The understanding of these priorities through Bight '03 sampling is intended to provide the basis for developing more efficient, widespread and coast-effective coastal ocean monitoring techniques. Water quality data were collected across eight major river systems within four geographic regions of southern California. Field measurements included the primary contaminants of interest, i.e., bacterial concentrations, water toxicity, and nutrients, as well as related parameters such as temperatures, salinity, total suspended solids, transmissivity, chlorophyll, and colored dissolved organic material (CDOM) concentrations. For each of the four major regions, i.e., Santa Clara/Ventura Rivers, Ballona Creek/Santa Monica Bay, San Pedro Shelf, and the San Diego, Tijuana Rivers, two stormwater events were sampled for up to three days by ship resulting in 574 water column CTD+ profiles and 705 discrete water samples during 36 ship-days. These data were analyzed in combination with MODIS ocean color satellite remote sensing, buoy meteorological observations, drifters, and HF radar current measurements to evaluate the dispersal patterns, dynamics, and impacts of the freshwater runoff plumes. Based on these data and resulting analyses, the principal conclusions were as follow: - Stormwater runoff turbidity plumes were found to be spatially extensive, covering up to 2500 km 2 within the Southern California Bight nearshore zone, and persisting over the entire duration of the post-storm sampling period (at least 3 days). - The spatial and temporal extent of the portion of the plume with contaminants was far less than that of the turbidity plume, typically representing <10% of its area (30-70% off Tijuana); however, with contaminant impacts generally greatly reduced or absent by the third or fourth day of sampling - Pseudo-nitzschia , a harmful algae that produces domoic acid, was found to be more abundant than previously reported. - Accurately describing stormwater runoff plumes requires a combination of in situ and remote sensing assessment tools, with satellite data providing valuable synoptic information. From these conclusions, the following recommendations are provided: - Future studies designed to describe stormwater plumes should include a combination of ship - and remote sensing-based methods. - CDOM is a good proxy of the freshwater runoff plume and should be added as a standard measurement parameter on water quality instrument packages. - Investigations are needed that assess on a local basis the spatial extent of ecological effects of stormwater plumes early in the storm, ideally accompanied by airborne imagery to provide improved temporal & spatial resolution, to fill in knowledge gaps. The next Bight regional monitoring program should focus on quantifying nutrient loadings and dynamics in association with stormwater runoff and other sources, and characterize their attendant ecosystem impacts such as phytoplankton blooms.

California↗
USGS2007

Ground-Water Quality of the Northern High Plains Aquifer, 1997, 2002-04

An assessment of ground-water quality in the northern High Plains aquifer was completed during 1997 and 2002-04. Ground-water samples were collected at 192 low-capacity, primarily domestic wells in four major hydrogeologic units of the northern High Plains aquifer-Ogallala Formation, Eastern Nebraska, Sand Hills, and Platte River Valley. Each well was sampled once, and water samples were analyzed for physical properties and concentrations of nitrogen and phosphorus compounds, pesticides and pesticide degradates, dissolved solids, major ions, trace elements, dissolved organic carbon (DOC), radon, and volatile organic compounds (VOCs). Tritium and microbiology were analyzed at selected sites. The results of this assessment were used to determine the current water-quality conditions in this subregion of the High Plains aquifer and to relate ground-water quality to natural and human factors affecting water quality. Water-quality analyses indicated that water samples rarely exceeded established U.S. Environmental Protection Agency public drinking-water standards for those constituents sampled; 13 of the constituents measured or analyzed exceeded their respective standards in at least one sample. The constituents that most often failed to meet drinking-water standards were dissolved solids (13 percent of samples exceeded the U.S. Environmental Protection Agency Secondary Drinking-Water Regulation) and arsenic (8 percent of samples exceeded the U.S. Environmental Protection Agency Maximum Contaminant Level). Nitrate, uranium, iron, and manganese concentrations were larger than drinking-water standards in 6 percent of the samples. Ground-water chemistry varied among hydrogeologic units. Wells sampled in the Platte River Valley and Eastern Nebraska units exceeded water-quality standards more often than the Ogallala Formation and Sand Hills units. Thirty-one percent of the samples collected in the Platte River Valley unit had nitrate concentrations greater than the standard, 22 percent exceeded the manganese standard, 19 percent exceeded the sulfate standard, 26 percent exceeded the uranium standard, and 38 percent exceeded the dissolved-solids standard. In addition, 78 percent of samples had at least one detectable pesticide and 22 percent of samples had at least one detectable VOC. In the Eastern Nebraska unit, 30 percent of the samples collected had dissolved-solids concentrations larger than the standard, 23 percent exceeded the iron standard, 13 percent exceeded the manganese standard, 10 percent exceeded the arsenic standard, 7 percent exceeded the sulfate standard, 7 percent exceeded the uranium standard, and 7 percent exceeded the selenium standard. No samples exceeded the nitrate standard. Thirty percent of samples had at least one detectable pesticide compound and 10 percent of samples had at least one detectable VOC. In contrast, the Sand Hills and Ogallala Formation units had fewer detections of anthropogenic compounds and drinking-water exceedances. In the Sand Hills unit, 15 percent of the samples exceeded the arsenic standard, 4 percent exceeded the nitrate standard, 4 percent exceeded the uranium standard, 4 percent exceeded the iron standard, and 4 percent exceeded the dissolved-solids standard. Fifteen percent of samples had at least one pesticide compound detected and 4 percent had at least one VOC detected. In the Ogallala Formation unit, 6 percent of water samples exceeded the arsenic standard, 4 percent exceeded the dissolved-solids standard, 3 percent exceeded the nitrate standard, 2 percent exceeded the manganese standard, 1 percent exceeded the iron standard, 1 percent exceeded the sulfate standard, and 1 percent exceeded the uranium standard. Eight percent of samples collected in the Ogallala Formation unit had at least one pesticide detected and 6 percent had at least one VOC detected. Differences in ground-water chemistry among the hydrogeologic units were attributed to variable depth to water, depth of the well screen below the water table, reduction-oxidation conditions, ground-water residence time, interactions with surface water, composition of aquifer sediments, extent of cropland, extent of irrigated land, and fertilizer application rates.

Scientific Investigations Report↗
USGS2008

Water-quality effects and characterization of indicators of onsite wastewater disposal systems in the east-central Black Hills area, South Dakota, 2006-08

Onsite wastewater disposal systems (OWDS) are used extensively in the Black Hills of South Dakota where many of the watersheds and aquifers are characterized by fractured or solution-enhanced bedrock with thin soil cover. A study was conducted during 2006-08 to characterize water-quality effects and indicators of OWDS. Water samples were collected and analyzed for potential indicators of OWDS, including chloride, bromide, boron, nitrite plus nitrate (NO2+NO3), ammonia, major ions, nutrients, selected trace elements, isotopes of nitrate, microbiological indicators, and organic wastewater compounds (OWCs). The microbiological indicators were fecal coliforms, Escherichia coli (E. coli), enterococci, Clostridium perfringens (C. perfringens), and coliphages. Sixty ground-water sampling sites were located either downgradient from areas of dense OWDS or in background areas and included 25 monitoring wells, 34 private wells, and 1 spring. Nine surface-water sampling sites were located on selected streams and tributaries either downstream or upstream from residential development within the Precambrian setting. Sampling results were grouped by their hydrogeologic setting: alluvial, Spearfish, Minnekahta, and Precambrian. Mean downgradient dissolved NO2+NO3 concentrations in ground water for the alluvial, Spearfish, Minnekahta, and Precambrian settings were 0.734, 7.90, 8.62, and 2.25 milligrams per liter (mg/L), respectively. Mean downgradient dissolved chloride concentrations in ground water for these settings were 324, 89.6, 498, and 33.2 mg/L, respectively. Mean downgradient dissolved boron concentrations in ground water for these settings were 736, 53, 64, and 43 micrograms per liter (ug/L), respectively. Mean dissolved surface-water concentrations for NO2+NO3, chloride, and boron for downstream sites were 0.222 mg/L, 32.1 mg/L, and 28 ug/L, respectively. Mean values of delta-15N and delta-18O (isotope ratios of 14N to 15N and 18O to 16O relative to standard ratios) for nitrate in ground-water samples were 10.4 and -2.0 per mil (0/100), respectively, indicating a relatively small contribution from synthetic fertilizer and probably a substantial contribution from OWDS. The surface-water sample with the highest dissolved NO2+NO3 concentration of 1.6 mg/L had a delta-15N value of 12.36 0/100, which indicates warm-blooded animals (including humans) as the nitrate source. Fecal coliforms were detected in downgradient ground water most frequently in the Spearfish (19 percent) and Minnekahta (9.7 percent) settings. E. coli was detected most frequently in the Minnekahta (29 percent) and Spearfish (13 percent) settings. Enterococci were detected more frequently than other microbiological indicators in all four settings. Fecal coliforms and E. coli were detected in 73 percent and 95 percent of all surface-water samples, respectively. Enterococci, coliphages (somatic), and C. perfringens were detected in 50, 70, and 50 percent of surface-water samples, respectively. Of the 62 OWC analytes, 12 were detected only in environmental samples, 10 were detected in at least one environmental and one blank sample (not necessarily companion pairs), 2 were detected only in blank samples, and 38 were not detected in any blank, environmental, or replicate sample from either ground or surface water. Eleven different organic compounds were detected in ground-water samples at eight different sites. The most frequently occurring compound was DEET, which was found in 32 percent of the environmental samples, followed by tetrachloroethene, which was detected in 20 percent of the samples. For surface-water samples, 16 organic compounds were detected in 9 of the 10 total samples. The compound with the highest occurrence in surface-water samples was camphor, which was detected in 50 percent of samples. The alluvial setting was characterized by relatively low dissolved NO2+NO3 concentrations, detection of ammonia nitrogen, and relatively high concentr

South Dakota↗
USGS2002

Microbiological quality of water from noncommunity supply wells in carbonate and crystalline aquifers of Pennsylvania

Samples were collected from 59 noncommunity water supplies in the Commonwealth of Pennsylvania from September 2000 to January 2001 and analyzed for pathogens and microbiological indicator organisms. The pathogens sampled were culturable viruses and Helicobacter pylori (H. pylori). The indicator organisms sampled were total coliform, Escherichia coli ( E. coli ), Clostridium perfringens ( C. perfringens ), somatic coliphage, male- specific coliphage, and enterococcus. The two primary areas sampled for the project completed by the U.S. Geological Survey, in cooperation with the Pennsylvania Department of Environmental Protection (PaDEP), were carbonate aquifers and crystalline aquifers. The results of all sampling showed culturable viruses were detected in 8 percent of the wells, H. pyloriin 7 percent of the wells, E. coli in 12 percent of the wells, total coliform in 46 percent of the wells, C. perfringens in 15 percent of the wells, somatic coliphage in 8 percent of the wells, male-specific coliphage in 5 percent of the wells, and enterococcus in 14 percent of the wells. Carbonate aquifers tended to have higher detection rates for the pathogens and indicators sampled than the crystalline aquifers. Detections of the pathogens and indicator organisms were not related statistically to the amounts of urban, agricultural, or forested area in a 1,500-foot radius around the sampled well. Somatic and male-specific coliphage showed the best relation to occurrence of culturable viruses. Culturable viruses and H. pylori were detected in wells in which no indicator organisms were present; therefore, none of the indicator organisms sampled provide complete assurance of pathogenfree water. The best predictive tool for virus screening was a combination of indicator organisms.

Water-Resources Investigations Report↗
USGS2024

Microbial communities in standing dead trees in ghost forests are largely aerobic, saprophytic, and methanotrophic

Standing dead trees (snags) are recognized for their influence on methane (CH 4 ) cycling in coastal wetlands, yet the biogeochemical processes that control the magnitude and direction of fluxes across the snag-atmosphere interface are not fully elucidated. Herein, we analyzed microbial communities and fluxes at one height from ten snags in a ghost forest wetland. Snag-atmosphere CH 4 fluxes were highly variable (− 0.11–0.51 mg CH 4 m −2 h −1 ). CH 4 production was measured in three out of ten snags; whereas, CH 4 consumption was measured in two out of ten snags. Potential CH 4 production and oxidation in one core from each snag was assayed in vitro. A single core produced CH 4 under anoxic and oxic conditions, at measured rates of 0.7 and 0.6 ng CH 4 g −1 h −1 , respectively. Four cores oxidized CH 4 under oxic conditions, with an average rate of − 1.13 ± 0.31 ng CH 4 g −1 h −1 . Illumina sequencing of the V3/V4 region of the 16S rRNA gene sequence revealed diverse microbial communities and indicated oxidative decomposition of deadwood. Methanogens were present in 20% of the snags, with a mean relative abundance of < 0.0001%. Methanotrophs were identified in all snags, with a mean relative abundance of 2% and represented the sole CH 4 -cycling communities in 80% of the snags. These data indicate potential for microbial attenuation of CH 4 emissions across the snag-atmosphere interface in ghost forests. A better understanding of the environmental drivers of snag-associated microbial communities is necessary to forecast the response of CH 4 cycling in coastal ghost forest wetlands to a shifting coastal landscape.

Current Microbiology↗
USGS2013

The effects of artificial recharge on groundwater levels and water quality in the west hydrogeologic unit of the Warren subbasin, San Bernardino County, California

Between the late 1940s and 1994, groundwater levels in the Warren subbasin, California, declined by as much as 300 feet because pumping exceeded sparse natural recharge. In response, the local water district, Hi-Desert Water District, implemented an artificial-recharge program in early 1995 using imported water from the California State Water Project. Subsequently, the water table rose by as much as 250 feet; however, a study done by the U.S. Geological Survey found that the rising water table entrained high-nitrate septic effluent, which caused nitrate (as nitrogen) concentrations in some wells to increase to more than the U.S. Environmental Protection Agency maximum contaminant level of 10 milligrams per liter.. A new artificial-recharge site (site 3) was constructed in 2006 and this study, which started in 2004, was done to address concerns about the possible migration of nitrates in the unsaturated zone. The objectives of this study were to: (1) characterize the hydraulic, chemical, and microbiological properties of the unsaturated zone; (2) monitor changes in water levels and water quality in response to the artificial-recharge program at site 3; (3) determine if nitrates from septic effluent infiltrated through the unsaturated zone to the water table; (4) determine the potential for nitrates within the unsaturated zone to mobilize and contaminate the groundwater as the water table rises in response to artificial recharge; and (5) determine the presence and amount of dissolved organic carbon because of its potential to react with disinfection byproducts during the treatment of water for public use. Two monitoring sites were installed and instrumented with heat-dissipation probes, advanced tensiometers, suction-cup lysimeters, and wells so that the arrival and effects of recharging water from the State Water Project through the 250 to 425 foot-thick unsaturated zone and groundwater system could be closely observed. Monitoring site YVUZ-1 was located between two recharge ponds in the middle of site 3, and YVUZ-2 was located approximately 1,200 feet down-gradient and to the southeast in an area where septic systems have been in use since about 1960. Site YVUZ-3 only went to a depth of 42 feet and was used to sample the upper part of the unsaturated zone near a golf course. Prior to the start of artificial recharge at site 3, nitrate concentrations reported as nitrogen from the soil leachate below YVUZ-1 did not exceed 1.58 milligrams per kilogram. Nitrate-reducing bacteria concentrations of 4,300 most probable number were found at about 220 feet below land surface and at the top of the water table at YVUZ-1. Nitrate concentrations at YVUZ-2 reached a maximum concentration of about 25 milligrams per kilogram between about 100 and 121 feet below land surface; concentrations of nitrate-reducing or denitrifying bacteria were as high as 21,000 most probable number at 36 feet below land surface but did not exceed 40 most probable number below about 150 feet below land surface. Between June 2006 and September 2009, more than 9,800 acre feet of water from the State Water Project was released to site 3 ponds. The infiltration of the recharge water was predominantly vertical with limited lateral spreading to a depth of about 200 feet below land surface at YVUZ-1. Lateral spreading of the recharge water with depth was caused by geologic heterogeneities within the unsaturated zone, and resulted in varied arrival times of the recharge water to the instruments and slower rates of vertical movement with depth. No abrupt changes in soil moisture were observed at YVUZ-2, indicating that the recharge water had not reached that site by September 2009. Water levels from the monitoring wells at both sites and from five production wells nearby showed that the water table rose at a mean rate of about 0.08 feet per day between June 2006 and January 2009. The arrival of the water from the State Water Project caused relatively rapid changes in the stable-isotopic ratios from the lysimeters at YVUZ-1. The estimated average rate of infiltration of the recharge water through the unsaturated zone ranged from 3.7 to 25 feet per day. The recharge water arrived at the monitoring well below the recharge ponds between August 2007 and March 2008; the rate of vertical movement to the monitoring well was between 0.6 and 0.9 feet per day. By September 2008, a production well located 375 feet west of site 3 was producing almost 100 percent infiltrated recharge water. By contrast, the stable-isotope data from the lysimeters at YVUZ-2 showed that the recharge water had not reached this site by September 2009, but that septic effluent in the unsaturated zone likely had mixed with the native pore water to at least 154 feet below land surface. Assuming vertical infiltration, the minimum rate of infiltration of septic effluent since 1960 was about 3 feet per year. The isotopic data from the lysimeters at YVUZ-3 indicated two different sources of water to the upper 43 feet–irrigation-return flow and precipitation. Nitrate concentrations of the water from the State Water Project did not exceed 1 milligram per liter. Prior to artificial recharge, nitrate concentrations of the pore water at YVUZ-1 ranged between 6 to 18.2 milligrams per liter. After the arrival of the recharge water, the nitrate concentrations from the lysimeters and well at YVUZ-1 decreased to less than 1 milligram per liter, with the exception of samples collected at 205.5 feet, which did not exceed 4.12 milligrams per liter. The decrease in nitrate concentrations after artificial recharge indicated that the rising water table did not result in an increase of nitrates below YVUZ-1. At YVUZ-2, nitrate concentrations ranged between 12 to 479 milligrams per liter. The highest nitrate concentrations were at 92 feet below land surface and were almost seven times that of samples collected from a nearby septic tank. Nitrate concentrations from the lysimeter at 273 feet below land surface increased from 6 to almost 58 milligrams per liter after it was saturated by the rising water table in December 2007. These increases could be the result of the mobilization of high-nitrate water from regional sources of septic effluent after saturation, or the result of high-nitrate water present at the top of the water table that may be diluted deeper in the aquifer. Nitrate concentrations in groundwater from five nearby production wells and from both monitoring wells were less than 5 milligrams per liter before artificial recharge started. Nitrate concentrations decreased to less than 3 milligrams per liter in three of the production wells and the monitoring well below the recharge ponds after artificial recharge. Dissolved organic carbon concentrations were measured in the recharge water and groundwater because of the potential for dissolved organic carbon to react with chlorine to form trihalomethanes during the water-treatment process. The dissolved organic carbon concentrations of the recharge water were 3.1 milligrams per liter or less, and dissolved organic carbon concentrations of the groundwater were less than 1 milligram per liter. Even though recharge water was present in some of the wells by September 2008, the concentrations of both dissolved organic carbon and trihalomethane formation potential in the groundwater did not increase. Interpretation of these data suggests that the dissolved organic carbon from the recharge water is altered or metabolized in the unsaturated zone, either by absorption to the grain particles in the soil or by microbiological processes.

California↗
USGS2013

Microbiological reduction of Sb(V) in anoxic freshwater sediments

Microbiological reduction of millimolar concentrations of Sb(V) to Sb(III) was observed in anoxic sediments from two freshwater settings: (1) a Sb- and As-contaminated mine site (Stibnite Mine) in central Idaho and 2) an uncontaminated suburban lake (Searsville Lake) in the San Francisco Bay Area. Rates of Sb(V) reduction in anoxic sediment microcosms and enrichment cultures were enhanced by amendment with lactate or acetate as electron donors but not by H2, and no reduction occurred in sterilized controls. Addition of 2- 14 C-acetate to Stibnite Mine microcosms resulted in the production of 14 CO 2 coupled to Sb(V) reduction, suggesting that this process proceeds by a dissimilatory respiratory pathway in those sediments. Antimony(V) reduction in Searsville Lake sediments was not coupled to acetate mineralization and may be associated with Sb-resistance. The microcosms and enrichment cultures also reduced sulfate, and the precipitation of insoluble Sb(III)-sulfide complexes was a major sink for reduced Sb. The reduction of Sb(V) by Stibnite Mine sediments was inhibited by As(V), suggesting that As(V) is a preferred electron acceptor for the indigenous community. These findings indicate a novel pathway for anaerobic microbiological respiration and suggest that communities capable of reducing high concentrations of Sb(V) commonly occur naturally in the environment.

Environmental Science & Technology↗
USGS2016

Developing integrated methods to address complex resource and environmental issues

Introduction This circular provides an overview of selected activities that were conducted within the U.S. Geological Survey (USGS) Integrated Methods Development Project, an interdisciplinary project designed to develop new tools and conduct innovative research requiring integration of geologic, geophysical, geochemical, and remote-sensing expertise. The project was supported by the USGS Mineral Resources Program, and its products and acquired capabilities have broad applications to missions throughout the USGS and beyond. In addressing challenges associated with understanding the location, quantity, and quality of mineral resources, and in investigating the potential environmental consequences of resource development, a number of field and laboratory capabilities and interpretative methodologies evolved from the project that have applications to traditional resource studies as well as to studies related to ecosystem health, human health, disaster and hazard assessment, and planetary science. New or improved tools and research findings developed within the project have been applied to other projects and activities. Specifically, geophysical equipment and techniques have been applied to a variety of traditional and nontraditional mineral- and energy-resource studies, military applications, environmental investigations, and applied research activities that involve climate change, mapping techniques, and monitoring capabilities. Diverse applied geochemistry activities provide a process-level understanding of the mobility, chemical speciation, and bioavailability of elements, particularly metals and metalloids, in a variety of environmental settings. Imaging spectroscopy capabilities maintained and developed within the project have been applied to traditional resource studies as well as to studies related to ecosystem health, human health, disaster assessment, and planetary science. Brief descriptions of capabilities and laboratory facilities and summaries of some applications of project products and research findings are included in this circular. The work helped support the USGS mission to “provide reliable scientific information to describe and understand the Earth; minimize loss of life and property from natural disasters; manage water, biological, energy, and mineral resources; and enhance and protect our quality of life.” Activities within the project include the following: Spanned scales from microscopic to planetary; Demonstrated broad applications across disciplines; Included life-cycle studies of mineral resources; Incorporated specialized areas of expertise in applied geochemistry including mineralogy, hydrogeology, analytical chemistry, aqueous geochemistry, biogeochemistry, microbiology, aquatic toxicology, and public health; and Incorporated specialized areas of expertise in geophysics including magnetics, gravity, radiometrics, electromagnetics, seismic, ground-penetrating radar, borehole radar, and imaging spectroscopy. This circular consists of eight sections that contain summaries of various activities under the project. The eight sections are listed below: Laboratory Facilities and Capabilities, which includes brief descriptions of the various types of laboratories and capabilities used for the project; Method and Software Development, which includes summaries of remote-sensing, geophysical, and mineralogical methods developed or enhanced by the project; Instrument Development, which includes descriptions of geophysical instruments developed under the project; Minerals, Energy, and Climate, which includes summaries of research that applies to mineral or energy resources, environmental processes and monitoring, and carbon sequestration by earth materials; Element Cycling, Toxicity, and Health, which includes summaries of several process-oriented geochemical and biogeochemical studies and health-related research activities; Hydrogeology and Water Quality, which includes descriptions of innovative geophysical, remote-sensing, and geochemical research pertaining to hydrogeology and water-quality applications; Hazards and Disaster Assessment, which includes summaries of research and method development that were applied to natural hazards, human-caused hazards, and disaster assessments; and Databases and Framework Studies, which includes descriptions of fundamental applications of geophysical studies and of the importance of archived data.

Circular↗
USGS2020

Mapping metabolic activity at single cell resolution in intact volcanic fumarole soil

Interactions among microorganisms and their mineralogical substrates govern the structure, function, and emergent properties of microbial communities. These interactions are predicated on spatial relationships, which dictate metabolite exchange and access to key substrates. To quantitatively assess links between spatial relationships and metabolic activity, this study presents a novel approach to map all organisms, the metabolically active subset, and associated mineral grains, all while maintaining spatial integrity of an environmental microbiome. We applied this method at an outgassing fumarole of Vanuatu’s Marum Crater, one of the largest point sources of several environmentally relevant gaseous compounds, including H2O, CO2, and SO2. With increasing distance from the soil-air surface and from mineral grain outer boundaries, organism abundance decreased but the proportion of metabolically active organisms often increased. These protected niches may provide more stable conditions that promote consistent metabolic activity of a streamlined community. Conversely, mineral exteriors accumulate more organisms that may cover a wider range of preferred conditions, implying that only a subset of the community will be active under any particular environmental regime. More broadly, the approach presented here allows investigators to see microbial communities “as they really are” and explore determinants of metabolic activity across a range of microbiomes.

FEMS Microbiology Letters↗
USGS2020

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↗
USGS2025

Bacterial community diversity and potential eco-physiological roles in toxigenic blooms composed of Microcystis, Aphanizomenon or Planktothrix

Cyanobacterial toxicity, cyanotoxins, and their impact on aquatic ecosystems and human health are well documented. In comparison, less is known about bloom-associated bacterial communities. Co-occurring bacteria can influence bloom development, physiology and collapse, and may also provide a niche for pathogenic bacteria. Existing research focuses on the cyanosphere of Microcystis -dominated blooms, despite the increasing prevalence of filamentous genera ( Aphanizomenon and Planktothrix ). This pilot study aimed to broaden our understanding of the bacterial consortia attached to morphologically distinct cyanobacteria (coccoid and filamentous) dominating phytoplankton communities and to explore their potential roles in amplifying the impacts of cyanobacterial blooms. We investigated four shallow freshwater bodies across three continents and two climate zones: an urban pond in the USA, a dammed reservoir and a natural lake in Poland, and an urban water body in Singapore. Amplicon sequencing (16S rRNA gene) was used to characterize bacterial communities, while shotgun metagenomics identified nitrogen- and phosphorus-cycling genes to infer potential eco-physiological functions. Cyanobacteria dominated bacterioplankton assemblages at all sites (>35.6%), with bloom composition influencing toxigenic profiles. A mixed bloom of Microcystis , Snowella , and Aphanizomenon had the broadest range of cyanotoxin synthetase genes ( mcy E, cyr J, ana F and sxt A). Microcystis blooms correlated with increased Roseomonas , while Planktothrix co-occurred with Flavobacterium – both bacteria likely contribute to nutrient-cycling within blooms and represent potential opportunistic pathogens for aquatic organisms and humans. The Microcystis cyanosphere exhibited the highest number of significant positive correlations with bacteria (19 relations), compared to Planktothrix and Aphanizomenon (11 and 2 relations, respectively). Non-diazotrophic blooms of Microcystis and Planktothrix showed greater abundances of nitrogen – ( ure B, gln A, nar B, and nar HZ) and phosphorus-cycling genes ( pho BHPR and ppk 1), indicating a strong dependence on associated bacteria for nutrient acquisition compared to diazotrophic Aphanizomenon . These findings suggest that Aphanizomenon -dominated blooms may be sustained by simpler microbiomes. Our results provide preliminary evidence of cyanosphere heterogeneity potentially shaped by the dominance or coexistence of three morphologically and eco-physiologically distinct genera of cyanobacteria. A comprehensive knowledge of the taxonomy and functional roles of bloom-associated microbiomes is therefore essential to understand bloom activity, evaluate the environmental threat, and develop effective strategies for prevention and mitigation.

Frontiers in Microbiology↗
USGS2004

Use of PRD1 bacteriophage in groundwater viral transport, inactivation, and attachment studies

PRD1, an icosahedra-shaped, 62 nm (diameter), double-stranded DNA bacteriophage with an internal membrane, has emerged as an important model virus for studying the manner in which microorganisms are transported through a variety of groundwater environments. The popularity of this phage for use in transport studies involving geologic media is due, in part, to its relative stability over a range of temperatures and low degree of attachment in aquifer sediments. Laboratory and field investigations employing PRD1 are leading to a better understanding of viral attachment and transport behaviors in saturated geologic media and to improved methods for describing mathematically subsurface microbial transport at environmentally significant field scales. Radioisotopic labeling of PRD1 is facilitating additional information about the nature of viral interactions with solid surfaces in geologic media, the importance of iron oxide surfaces, and allowing differentiation between inactivation and attachment in field-scale tracer tests.

FEMS Microbiology Ecology↗
USGS2004

Microbial precipitation of dolomite in methanogenic groundwater

We report low-temperature microbial precipitation of dolomite in dilute natural waters from both field and laboratory experiments. In a freshwater aquifer, microorganisms colonize basalt and nucleate nonstoichiometric dolomite on cell walls. In the laboratory, ordered dolomite formed at near-equilibrium conditions from groundwater with molar Mg:Ca ratios of <1; dolomite was absent in sterile experiments. Geochemical and microbiological data suggest that methanogens are the dominant metabolic guild in this system and are integral to dolomite precipitation. We hypothesize that the attached microbial consortium reacts with the basalt surface, releasing Mg and Ca into solution, which drives dolomite precipitation via nucleation on the cell wall. These findings provide insight into the long-standing dolomite problem and suggest a fundamental role for microbial processes in the formation of dolomite across a wide range of environmental conditions.

Geology↗
USGS2016

Bacterial genomics reveal the complex epidemiology of an emerging pathogen in arctic and boreal ungulates

Northern ecosystems are currently experiencing unprecedented ecological change, largely driven by a rapidly changing climate. Pathogen range expansion, and emergence and altered patterns of infectious disease, are increasingly reported in wildlife at high latitudes. Understanding the causes and consequences of shifting pathogen diversity and host-pathogen interactions in these ecosystems is important for wildlife conservation, and for indigenous populations that depend on wildlife. Among the key questions are whether disease events are associated with endemic or recently introduced pathogens, and whether emerging strains are spreading throughout the region. In this study, we used a phylogenomic approach to address these questions of pathogen endemicity and spread for Erysipelothrix rhusiopathiae , an opportunistic multi-host bacterial pathogen associated with recent mortalities in arctic and boreal ungulate populations in North America. We isolated E. rhusiopathiae from carcasses associated with large-scale die-offs of muskoxen in the Canadian Arctic Archipelago, and from contemporaneous mortality events and/or population declines among muskoxen in northwestern Alaska and caribou and moose in western Canada. Bacterial genomic diversity differed markedly among these locations; minimal divergence was present among isolates from muskoxen in the Canadian Arctic, while in caribou and moose populations, strains from highly divergent clades were isolated from the same location, or even from within a single carcass. These results indicate that mortalities among northern ungulates are not associated with a single emerging strain of E. rhusiopathiae , and that alternate hypotheses need to be explored. Our study illustrates the value and limitations of bacterial genomic data for discriminating between ecological hypotheses of disease emergence, and highlights the importance of studying emerging pathogens within the broader context of environmental and host factors.

Frontiers in Microbiology↗