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USGS2022

Exploring the role of cryptic nitrogen fixers in terrestrial ecosystems: A frontier in nitrogen cycling research

Biological nitrogen fixation represents the largest natural flux of new nitrogen (N) into terrestrial ecosystems, providing a critical N source to support net primary productivity of both natural and agricultural systems. When they are common, symbiotic associations between plants and bacteria can add more than 100 kg N ha −1 y −1 to ecosystems. Yet, these associations are uncommon in many terrestrial ecosystems. In most cases, N inputs derive from more cryptic sources, including mutualistic and/or free-living microorganisms in soil, plant litter, decomposing roots and wood, lichens, insects, and mosses, among others. Unfortunately, large gaps remain in the understanding of cryptic N fixation. We conducted a literature review to explore rates, patterns, and controls of cryptic N fixation in both unmanaged and agricultural ecosystems. Our analysis indicates that, as is common with N fixation, rates are highly variable across most cryptic niches, with N inputs in any particular cryptic niche ranging from near zero to more than 20 kg ha −1 y −1 . Such large variation underscores the need for more comprehensive measurements of N fixation by organisms not in symbiotic relationships with vascular plants in terrestrial ecosystems, as well as identifying the factors that govern cryptic N fixation rates. We highlight several challenges, opportunities, and priorities in this important research area, and we propose a conceptual model that posits an interacting hierarchy of biophysical and biogeochemical controls over N fixation that should generate valuable new hypotheses and research.

Ecosystems↗

USGS2008

Assessment of crop growth and soil water modules in SWAT2000 using extensive field experiment data in an irrigation district of the Yellow River Basin

SWAT, a physically-based, hydrological model simulates crop growth, soil water and groundwater movement, and transport of sediment and nutrients at both the process and watershed scales. While the different versions of SWAT have been widely used throughout the world for agricultural and water resources applications, little has been done to test the performance, variability, and transferability of the parameters in the crop growth, soil water, and groundwater modules in an integrated way with multiple sets of field experimental data at the process scale. Using an multiple years of field experimental data of winter wheat (Triticum aestivum L.) in the irrigation district of the Yellow River Basin, this paper assesses the performance of the plant-soil-groundwater modules and the variability and transferability of SWAT2000. Comparison of the simulated results by SWAT to the observations showed that SWAT performed quite unsatisfactorily in LAI predictions during the senescence stage, in yield predictions, and in soil-water estimation under dry soil-profile conditions. The unsatisfactory performance in LAI prediction might be attributed to over-simplified senescence modeling; in yield prediction to the improper computation of the harvest index; and in soil water under dry conditions to the exclusion of groundwater evaporation from the soil water balance in SWAT. In this paper, improvements in crop growth, soil water, and groundwater modules in SWAT were implemented. The saturated soil profile was coupled to the oscillating groundwater table. A variable evaporation coefficient taking into account soil water deficit index, groundwater depth, and crop root depth was used to replace the fixed coefficient in computing groundwater evaporation. The soil water balance included the groundwater evaporation. The modifications improved simulations of crop evapotranspiration and biomass as well as soil water dynamics under dry soil-profile conditions. The evaluation shows that the crop growth and soil water components of SWAT could be further refined to better simulate the hydrology of agricultural watersheds. ?? 2008 Elsevier B.V. All rights reserved.

Journal of Hydrology↗

USGS1970

Geochemical Survey of Missouri: Plans and progress for second six-month period (January-June 1970)

This is the second six-month progress report on studies in environmental geochemistry in the State of Missouri initiated on behalf of the Environmental Health Surveillance Project in July, 1969. The studies are being made in support of epidemiological investigations of the Surveillance Project to provide general information pertaining to the occurrence and distribution of chemical elements in rocks, soils, plants, and water throughout the State. Emphasis is placed on the occurrence and distribution of elements in the natural environment, though studies of the effects of some types of chemical pollution are necessarily included. The objectives and plans for the three phases of the Survey that are directed at the rocks, soils, and vegetation are described in the progress report for the first six-month period; those for the phase of the project concerned with the water are described by Gerald L. Feder in a later section of the present report. The addition of this latter phase significantly expands the scope of our study and increases its relevance to studies of human and animal health. Mr. Feder has a valuable background in the geology and hydrology of Missouri, and we are most pleased that he has joined us in this effort.

Missouri↗

USGS2020

From pools to flow: The PROMISE framework for new insights on soil carbon cycling in a changing world

Soils represent the largest terrestrial reservoir of organic carbon, and the balance between soil organic carbon (SOC) formation and loss will drive powerful carbon‐climate feedbacks over the coming century. To date, efforts to predict SOC dynamics have rested on pool‐based models, which assume classes of SOC with internally homogenous physicochemical properties. However, emerging evidence suggests that soil carbon turnover is not dominantly controlled by the chemistry of carbon inputs, but rather by restrictions on microbial access to organic matter in the spatially heterogeneous soil environment. The dynamic processes that control the physicochemical protection of carbon translate poorly to pool‐based SOC models; as a result, we are challenged to mechanistically predict how environmental change will impact movement of carbon between soils and the atmosphere. Here, we propose a novel conceptual framework to explore controls on belowground carbon cycling: P robabilistic R epresentation of O rganic M atter I nteractions within the S oil E nvironment (PROMISE). In contrast to traditional model frameworks, PROMISE does not attempt to define carbon pools united by common thermodynamic or functional attributes. Rather, the PROMISE concept considers how SOC cycling rates are governed by the stochastic processes that influence the proximity between microbial decomposers and organic matter, with emphasis on their physical location in the soil matrix. We illustrate the applications of this framework with a new biogeochemical simulation model that traces the fate of individual carbon atoms as they interact with their environment, undergoing biochemical transformations and moving through the soil pore space. We also discuss how the PROMISE framework reshapes dialogue around issues related to SOC management in a changing world. We intend the PROMISE framework to spur the development of new hypotheses, analytical tools, and model structures across disciplines that will illuminate mechanistic controls on the flow of carbon between plant, soil, and atmospheric pools.

Global Change Biology↗

USGS2021

Identification of bacteria in groundwater used for domestic supply in the southeast San Joaquin Valley, California, 2014

Groundwater is an important source of drinking water in California. Water-borne diseases caused by microbial contamination are a growing concern. The MI test, a membrane filtration method for the chromogenic/fluorogenic detection of total coliforms and Escherichia coli , was used for samples collected January to April 2014 from 42 domestic wells in the southeastern San Joaquin Valley. The wells were sampled as part of the Groundwater Ambient Monitoring and Assessment Program Priority Basin Project (GAMA-PBP), a cooperative study between the U.S. Geological Survey and the California State Water Resources Control Board. Polymerase chain reaction analysis and sequencing of deoxyribonucleic acid (DNA) were used for 34 target and nontarget colonies that grew on the MI media from samples collected from 13 of the domestic wells to identify what genera of bacteria could exist in groundwater used by domestic wells. Gene sequences obtained using the Sanger method were entered into the basic local alignment search tool (BLAST) database, and 17 genera of bacteria were identified. Of these, 13 genera contain species that are human pathogens or opportunistic human pathogens. All the genera that include human pathogens are naturally present in soil, plants, or water; one of the pathogens also can be found in fecal matter. Six of the human pathogens were from non-target colony growth on the MI media. Target and non-target microbial growth on MI media are indicators of the possible presence of pathogenic bacteria even if the bacteria naturally are from soil rather than from a fecal source.

California↗

USGS2015

From bacteria to elephants: Effects of land-use legacies on biodiversity and ecosystem structure in the Serengeti-Mara ecosystem: Chapter 8

Generally, ecological research has considered the aboveground and belowground components of ecosystems separately. Consequently, frameworks for integrating the two components are not well developed. Integrating the microbial components into ecosystem ecology requires different approaches from those offered by plant ecology, partly because of the scales at which microbial processes operate and partly because of measurement constraints. Studies have begun to relate microbial community structure to ecosystem function. results suggest that excluding people and livestock from the MMNR, or preventing heavier livestock from grazing around settlements, may not change the general structure of the ecosystem (soils, plant structure), but can change the numbers and diversity of wildlife, nematodes and microbes in this ecosystem in subtle ways.

Book chapter↗

USGS2014

The effects of atmospheric nitrogen deposition on terrestrial and freshwater biodiversity

This chapter reports the findings of a Working Group on how atmospheric nitrogen (N) deposition affects both terrestrial and freshwater biodiversity. Regional and global scale impacts on biodiversity are addressed, together with potential indicators. Key conclusions are that: the rates of loss in biodiversity are greatest at the lowest and initial stages of N deposition increase; changes in species compositions are related to the relative amounts of N, carbon (C) and phosphorus (P) in the plant soil system; enhanced N inputs have implications for C cycling; N deposition is known to be having adverse effects on European and North American vegetation composition; very little is known about tropical ecosystem responses, while tropical ecosystems are major biodiversity hotspots and are increasingly recipients of very high N deposition rates; N deposition alters forest fungi and mycorrhyzal relations with plants; the rapid response of forest fungi and arthropods makes them good indicators of change; predictive tools (models) that address ecosystem scale processes are necessary to address complex drivers and responses, including the integration of N deposition, climate change and land use effects; criteria can be identified for projecting sensitivity of terrestrial and aquatic ecosystems to N deposition. Future research and policy-relevant recommendations are identified.

Book chapter↗

USGS2006

Application of municipal biosolids to dry-land wheat fields - A monitoring program near Deer Trail, Colorado (USA). A presentation for an international conference: "The Future of Agriculture: Science, Stewardship, and Sustainability", August 7-9, 2006, Sacramento, CA

Since late 1993, Metro Wastewater Reclamation District of Denver (Metro District), a large wastewater treatment plant in Denver, Colorado, has applied Grade I, Class B biosolids to about 52,000 acres of non-irrigated farmland and rangeland near Deer Trail, Colorado. In cooperation with the Metro District in 1993, the U.S. Geological Survey (USGS) began monitoring ground water at part of this site. In 1999, the USGS began a more comprehensive study of the entire site to address stakeholder concerns about the chemical effects of biosolids applications. This more comprehensive monitoring program has recently been extended through 2010. Monitoring components of the more comprehensive study included biosolids collected at the wastewater treatment plant, soil, crops, dust, alluvial and bedrock ground water, and stream bed sediment. Streams at the site are dry most of the year, so samples of stream bed sediment deposited after rain were used to indicate surface-water effects. This presentation will only address biosolids, soil, and crops. More information about these and the other monitoring components are presented in the literature (e.g., Yager and others, 2004a, b, c, d) and at the USGS Web site for the Deer Trail area studies at http://co.water.usgs.gov/projects/CO406/CO406.html. Priority parameters identified by the stakeholders for all monitoring components, included the total concentrations of nine trace elements (arsenic, cadmium, copper, lead, mercury, molybdenum, nickel, selenium, and zinc), plutonium isotopes, and gross alpha and beta activity, regulated by Colorado for biosolids to be used as an agricultural soil amendment. Nitrogen and chromium also were priority parameters for ground water and sediment components. In general, the objective of each component of the study was to determine whether concentrations of priority parameters (1) were higher than regulatory limits, (2) were increasing with time, or (3) were significantly higher in biosolids-applied areas than in a similar farmed area where biosolids were not applied. Where sufficient samples could be collected, statistical methods were used to evaluate effects. Rigorous quality assurance was included in all aspects of the study. The roles of hydrology and geology also were considered in the design, data collection, and interpretation phases of the study. Study results indicate that the chemistry of the biosolids from the Denver plant was consistent during 1999-2005, and total concentrations of regulated trace elements were consistently lower than the regulatory limits. Plutonium isotopes were not detected in the biosolids. Leach tests using deionized water to simulate natural precipitation indicate arsenic, molybdenum, and nickel were the most soluble priority parameters in the biosolids. Study results show no significant difference in concentrations of priority parameters between biosolids-applied soils and unamended soils where no biosolids were applied. However, biosolids were applied only twice during 1999-2003. The next soil sampling is not scheduled until 2010. To date concentrations of most of the priority parameters were not much greater in the biosolids than in natural soil from the sites. Therefore, many more biosolids applications would need to occur before biosolids effects on the soil priority constituents can be quantified. Leach tests using deionized water to simulate precipitation indicate that molybdenum and selenium were the priority parameters that were most soluble in both biosolids-applied soil and natural or unamended soil. Study results do not indicate significant differences in concentrations of priority parameters between crops grown in biosolids-applied areas and crops grown where no biosolids were applied. However, crops were grown only twice during 1999-2003, so only two crop samples could be collected. The wheat-grain elemental data collected during 1999-2003 for both biosolids-applied areas and unamended areas are similar

Open-File Report↗

USGS2022

Plague and trace metals in natural systems

All pathogenic organisms are exposed to abiotic influences such as the microclimates and chemical constituents of their environments. Even those pathogens that exist primarily within their hosts or vectors can be influenced directly or indirectly. Yersinia pestis , the flea-borne bacterium causing plague, is influenced by climate and its survival in soil suggests a potentially strong influence of soil chemistry. We summarize a series of controlled studies conducted over four decades in Russia by Dr. Evgeny Rotshild and his colleagues that investigated correlations between trace metals in soils, plants, and insects, and the detection of plague in free-ranging small mammals. Trace metal concentrations in plots where plague was detected were up to 20-fold higher or lower compared to associated control plots, and these differences were >2-fold in 22 of 38 comparisons. The results were statistically supported in eight studies involving seven host species in three families and two orders of small mammals. Plague tended to be positively associated with manganese and cobalt, and the plague association was negative for copper, zinc, and molybdenum. In additional studies, these investigators detected similar connections between pasturellosis and concentrations of some chemical elements. A One Health narrative should recognize that the chemistry of soil and water may facilitate or impede epidemics in humans and epizootics in non-human animals.

International Journal of Environmental Research an↗

USGS2013

Spatial and temporal patterns of dust emissions (2004-2012) in semi-arid landscapes, southeastern Utah, USA

Aeolian dust can influence nutrient availability, soil fertility, plant interactions, and water-holding capacity in both source and downwind environments. A network of 85 passive collectors for aeolian sediment spanning numerous plant communities, soil types, and land-use histories covering approximately 4000 square kilometers across southeastern Utah was used to sample horizontal emissions of aeolian sediment. The sample archive dates to 2004 and is currently the largest known record of field-scale dust emissions for the southwestern United States. Sediment flux peaked during the spring months in all plant communities (mean: 38.1 g m −2 d −1 ), related to higher, sustained wind speeds that begin in the early spring. Dust flux was lowest during the winter period (mean: 5 g m−2 d−1) when surface wind speeds are typically low. Sites dominated by blackbrush and sagebrush shrubs had higher sediment flux (mean: 19.4 g m−2 d−1) compared to grasslands (mean: 11.2 g m−2 d−1), saltbush shrublands (mean: 10.3 g m −2 d −1 ), and woodlands (mean: 8.1 g m −2 d −1 ). Contrary to other studies on dust emissions, antecedent precipitation during one, two, and three seasons prior to sample collection did not significantly influence emission rates. Physical site-scale factors controlling dust emissions were complex and varied from one vegetation type to another.

Utah↗

USGS2023

Effects of solar energy development on ants in the Mojave Desert

Land-use change from solar energy development may affect desert ecosystems and the soils, plants, and animals therein, yet our understanding of these interactions is nascent. With their ubiquity, criticality as ecosystem constituents, and sensitivity to environmental variation, ants may be useful study organisms for elucidating ecological effects of solar energy development in deserts. Our objectives were to disentangle the response of a desert ant community to solar energy development decisions and test the efficacy of ants as bioindicators at a solar power facility (392 MW) in the Mojave Desert, USA. We used pitfall traps to collect ants in treatments representing different solar energy development decisions, including variably intense site preparation practices: blading (i.e., bulldozing) and mowing, and establishment of undeveloped patches in solar fields, replicated across three power blocks comprising the facility and in undeveloped control sites surrounding the facility. We determined that ant abundance, species richness, Shannon Diversity Index, and functional richness were lower in bladed treatments than in all other treatments and controls. For most taxonomic and functional ant responses, we detected no difference between nonbladed treatments and controls; these results suggest that less intensive site preparation and increased spatial heterogeneity (i.e., undeveloped patches in solar fields) can reduce the negative effects of solar energy development on desert ants. However, our results indicate that ants may serve as useful bioindicators of the severity of anthropogenic disturbance from solar energy development in deserts, and indicator analysis signifies that solar energy infrastructure may negatively affect some species with high ecological value (e.g., harvester ants). Negative effects of solar energy development on ants can have significant implications for desert ecosystem function and integrity, but conservation-minded solar facility design and construction may lead to avoidance of “bottom-up” ecological ramifications of increased solar production during the renewable energy transition.

California↗

USGS2016

Optical properties of dissolved organic matter (DOM): Effects of biological and photolytic degradation

Advances in spectroscopic techniques have led to an increase in the use of optical properties (absorbance and fluorescence) to assess dissolved organic matter (DOM) composition and infer sources and processing. However, little information is available to assess the impact of biological and photolytic processing on the optical properties of original DOM source materials. We measured changes in commonly used optical properties and indices in DOM leached from peat soil, plants, and algae following biological and photochemical degradation to determine whether they provide unique signatures that can be linked to original DOM source. Changes in individual optical parameters varied by source material and process, with biodegradation and photodegradation often causing values to shift in opposite directions. Although values for different source materials overlapped at the end of the 111-day lab experiment, multivariate statistical analyses showed that unique optical signatures could be linked to original DOM source material even after degradation, with 17 optical properties determined by discriminant analysis to be significant (p<0.05) in distinguishing between DOM source and environmental processing. These results demonstrate that inferring the source material from optical properties is possible when parameters are evaluated in combination even after extensive biological and photochemical alteration.

Limnology and Oceanography↗

USGS2011

Cumuilative Effects of Impoundments on the Hydrology of Riparian Wetlands along the Marmaton River, west-central Missouri

The effects of proposed impoundments and resulting streamflow regulation on riparian wetlands in the Marmaton River Basin, Missouri, USA were determined using measurements and numerical simulations of wetland water budgets. Calibrated and validated Soil-Plant-Air-Water (SPAW) models were used to simulate daily water depths of four riparian wetlands for Current (model scenario of existing impoundments) and Proposed (model scenario of existing and proposed impoundments) impoundment conditions. The simulated frequency of flooding decreased 19–65% at the wetlands following the additions of proposed impoundments. The reduced flooding resulted in decreases in wetland water depths at all sites during the 10 simulated growing seasons under Proposed conditions with an average duration of continuous water-depth declines of 289 days at the upstream (most regulated) site. Downstream wetlands within the zone of least regulation had an average duration of water level decreases of about 20 days. Decreased water levels under Proposed conditions resulted in a range of 65–365 additional dry days at the study wetlands during the simulated 10-year period of Proposed conditions. The areas of the four wetlands meeting the hydrologic criteria of a formal jurisdictional wetland definition decreased ranging from zero to 31% under Proposed impoundment conditions.

Wetlands↗

USGS2006

A global perspective on the use, sales, exposure pathways, occurrence, fate and effects of veterinary antibiotics (VAs) in the environment

Veterinary antibiotics (VAs) are widely used in many countries worldwide to treat disease and protect the health of animals. They are also incorporated into animal feed to improve growth rate and feed efficiency. As antibiotics are poorly adsorbed in the gut of the animals, the majority is excreted unchanged in faeces and urine. Given that land application of animal waste as a supplement to fertilizer is often a common practice in many countries, there is a growing international concern about the potential impact of antibiotic residues on the environment. Frequent use of antibiotics has also raised concerns about increased antibiotic resistance of microorganisms. We have attempted in this paper to summarize the latest information available in the literature on the use, sales, exposure pathways, environmental occurrence, fate and effects of veterinary antibiotics in animal agriculture. The review has focused on four important groups of antibiotics (tylosin, tetracycline, sulfonamides and, to a lesser extent, bacitracin) giving a background on their chemical nature, fate processes, occurrence, and effects on plants, soil organisms and bacterial community. Recognising the importance and the growing debate, the issue of antibiotic resistance due to the frequent use of antibiotics in food-producing animals is also briefly covered. The final section highlights some unresolved questions and presents a way forward on issues requiring urgent attention.

Chemosphere↗

USGS2019

Decreased atmospheric nitrogen deposition in eastern North America: Predicted responses of forest ecosystems

Historical increases in emissions and atmospheric deposition of oxidized and reduced nitrogen (N) provided the impetus for extensive, global-scale research investigating the effects of excess N in terrestrial and aquatic ecosystems, with several regions within the Eastern Deciduous Forest of the United States found to be susceptible to negative effects of excess N. The Clean Air Act and associated rules have led to decreases in emissions and deposition of oxidized N, especially in eastern U.S., representing a research challenge and opportunity for ecosystem ecologists and biogeochemists. The purpose of this paper is to predict changes in the structure and function of North American forest ecosystems in a future of decreased N deposition. Hysteresis is a property of a system wherein output is not a strict function of corresponding input, incorporating lag, delay, or history dependence, particularly when the response to decreasing input is different from the response to increasing input. We suggest a conceptual hysteretic model predicting varying lag times in recovery of soil acidification, plant biodiversity, soil microbial communities, forest carbon (C) and N cycling, and surface water chemistry toward pre-N impact conditions. Nearly all of these can potentially respond strongly to reductions in N deposition. Most responses are expected to show some degree of hysteresis, with the greatest delays in response occurring in processes most tightly linked to “slow pools” of N in wood and soil organic matter. Because experimental studies of declines in N loads in forests of North America are lacking and because of the expected hysteresis, it is difficult to generalize from experimental results to patterns expected from declining N deposition. These will likely be long-term phenomena, difficult to distinguish from other, concurrent environmental changes, including elevated atmospheric CO 2 , climate change, reductions in acidity, invasions of new species, and long-term vegetation responses to past disturbance.

Environmental Pollution↗

USGS2016

Online induction heating for determination of isotope composition of woody stem water with laser spectrometry: A methods assessment

Application of stable isotopes of water to studies of plant–soil interactions often requires a substantial preparatory step of extracting water from samples without fractionating isotopes. Online heating is an emerging approach for this need, but is relatively untested and major questions of how to best deliver standards and assess interference by organics have not been evaluated. We examined these issues in our application of measuring woody stem xylem of sagebrush using a Picarro laser spectrometer with online induction heating. We determined (1) effects of cryogenic compared to induction-heating extraction, (2) effects of delivery of standards on filter media compared to on woody stem sections, and (3) spectral interference from organic compounds for these approaches (and developed a technique to do so). Our results suggest that matching sample and standard media improves accuracy, but that isotopic values differ with the extraction method in ways that are not due to spectral interference from organics.

Isotopes in Environmental and Health Studies↗

USGS1970

Minor metals of the geochemical environment, health and disease

The possibility of causal relationships between environmental factors and the occurrence of many degenerative diseases is slowly being recognized. One aspect of the environment -- that concerned with the geochemistry of the rocks, soils, plants, and water -- should be studied carefully and the distribution of minor elements be compared with geographic patterns of animal and human health and disease.

Science↗

USGS2018

UZIG research: Measurement and characterization of unsaturated zone processes under wide-ranging climates and changing conditions

Unsaturated zone properties and processes are central to understanding the interacting effects of land-use change, contamination, and hydroclimate on our ability to grow food, sustain clean water supplies, and minimize loss of life and property. Advances in unsaturated zone science are being achieved through collaborations across traditional boundaries where information from biological, physical, and chemical disciplines is combined for new insights. The Unsaturated Zone Interest Group (UZIG) is an organization that exists principally to promote multidisciplinary collaborations and the sharing of ideas, expertise, and technical assets. Here we summarize key findings from 14 papers, several of which originated from a meeting convened by UZIG in 2017 at the University of Florida in Gainesville titled “Land-Use Change, Climate Change, and Hydrologic Extremes: Unsaturated Zone Responses and Feedbacks.” This special section of Vadose Zone Journal contains multidisciplinary research in three general categories relevant to measuring and understanding unsaturated zone responses to changing land uses and climate: (i) unsaturated zone properties and processes; (ii) soil–plant–atmosphere interactions; and (iii) novel field sampling devices. A strong cross-cutting theme in these papers is the value of continuous monitoring data and ways of utilizing them to discover novel hydrologic, biologic, and pedologic information. As climatic and land-use conditions change and demands for resources and stresses on ecosystems continue to intensify, it is vital to improve our fundamental understanding of the processes at work in the unsaturated zone. Toward that goal, we discuss the need for improved ground-based unsaturated zone monitoring networks.

Vadose Zone Journal↗