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Ecogenomics of groundwater viruses suggests niche differentiation linked to specific environmental tolerance. This Narrative contains data for the 261 ENIGMA isolates described in the paper. See Table S2 for a complete list.
The deep subsurface is estimated to host the majority of Earth’s microbial biomass yet remains one of the most challenging environments to access and study. One common approach to investigate these microbial communities is through the analysis of produced water from subsurface reservoirs, where researchers can assess water and gas chemistry along with molecular (DNA/RNA) sequence data. Advances in high-throughput sequencing have greatly expanded our understanding of these environments and their biotechnological potential. However, further progress requires large-scale, integrative meta-analyses across diverse datasets. To address this need, we developed the Produced Water-DNA (PW-DNA) Database, a curated, publicly available resource that consolidates microbial DNA/RNA sequences, geochemical data, and relevant metadata from in situ hydrocarbon environments such as coal beds, oil reservoirs, and natural gas systems. The PW-DNA database delivers three core benefits to the research community: (1) it improves data sharing by linking environmental microbial datasets with corresponding geochemical parameters, enabling more robust filtering and analysis; (2) it connects with complementary research databases to promote broader dissemination and interoperability; and (3) it supports technological innovation by serving as a resource for identifying microbial trends and exploring genetic potential. While individual studies have highlighted basin-specific microbial communities and functional redundancy in biogeochemical cycling, a comprehensive, system-wide perspective is needed to better understand connectivity and novelty across subsurface ecosystems. By designing the PW-DNA in the KBase platform, we provide a reproducible, visual framework for integrating large-scale genomic and geochemical data, enabling researchers to perform more informed analyses and experimental design. Ultimately, this resource enhances the ability to identify, characterize, and interpret microbial functions across diverse subsurface environments, thereby accelerating discovery in subsurface microbiology and biotechnology.
Abstract not provided.
To our knowledge, this is the first study to identify the bacteriophage distribution in a groundwater ecosystem shedding light on their prevalence and distribution across metal-contaminated and background sites. Our study is uniquely based on selective sequencing of solely the extrachromosomal elements of a microbiome followed by analysis for viral signatures, thus establishing a more focused approach for phage identifications.
Abstract not provided.
Abstract not provided.
Environmental flows represent a legal mechanism to balance existing and future water uses and sustain non-use values. Here, we identify current challenges, provide examples where they are important, and suggest research advances that would benefit environmental flow science. Specifically, environmental flow science would benefit by (1) developing approaches to address streamflow needs in highly modified landscapes where historic flows do not provide reasonable comparisons, (2) integrating water quality needs where interactions are apparent with quantity but not necessarily the proximate factor of the ecological degradation, especially as frequency and magnitudes of inflows to bays and estuaries, (3) providing a better understanding of the ecological needs of native species to offset the often unintended consequences of benefiting non-native species or their impact on flows, (4) improving our understanding of the non-use economic value to balance consumptive economic values, and (5) increasing our understanding of the stakeholder socioeconomic spatial distribution of attitudes and perceptions across the landscape. Environmental flow science is still an emerging interdisciplinary field and by integrating socioeconomic disciplines and developing new frameworks to accommodate our altered landscapes, we should help advance environmental flow science and likely increase successful implementation of flow standards.
This study investigates the impact of specific environmental conditions on the formation of colloidal U(IV) nanoparticles by the sulfate reducing bacteria (SRB, Desulfovibrio alaskensis G20). The reduction of soluble U(VI) to less soluble U(IV) was quantitatively investigated under growth and non-growth conditions in bicarbonate or 1,4-piperazinediethanesulfonic acid (PIPES) buffered environments. Here, the results showed that under non-growth conditions, the majority of the reduced U nanoparticles aggregated and precipitated out of solution. High resolution transmission electron microscopy revealed that only a very small fraction of cells had reduced U precipitates in the periplasmic spaces in the presence of PIPES buffer, whereas in the presence of bicarbonate buffer, reduced U was also observed in the cytoplasm with greater aggregation of biogenic U(IV) particles at higher initial U(VI) concentrations. The same experiments were repeated under growth conditions using two different electron donors (lactate and pyruvate) and three electron acceptors (sulfate, fumarate, and thiosulfate). In contrast to the results of the non-growth experiments, even after 0.2 μm filtration, the majority of biogenic U(IV) remained in the aqueous phase resulting in potentially mobile biogenic U(IV) nanoparticles. Size fractionation results showed that U(IV) aggregates were between 18 and 200 nm in diameter, and thus could be very mobile. The findings of this study are helpful to assess the size and potential mobility of reduced U nanoparticles under different environmental conditions, and would provide insights on their potential impact affecting U(VI) bioremediation efforts at subsurface contaminated sites.
Past research on plant-soil feedbacks (PSF), largely undertaken in highly controlled greenhouse conditions, has established that plant species differentially alter abiotic and biotic soil conditions that in turn affect growth of other conspecific and heterospecific individuals in that soil. Yet, whether feedbacks under controlled greenhouse conditions reflect feedbacks in natural environments where plants are exposed to a range of abiotic and biotic pressures is still unresolved. To address how environmental context affects PSF, we conducted a meta-analysis of previously published studies that examined plant growth responses to multiple forms of competition, stress, and disturbance across various PSF methodology. We asked the following questions: (1) Can competition, stress, and disturbance alter the direction and/or strength of PSF? (2) Do particular types of competition, stress, or disturbance affect the direction and/or strength of PSF more than others? and (3) Do methods of conducting PSF research (i.e., greenhouse vs. field experiments and whether the source of soil inoculum conditioning is from the field vs. greenhouse) affect plant growth responses to PSF or competition, stress, and disturbance, or their interactions? We discovered four patterns that may be predictive of what future PSF studies conducted under more realistic conditions might reveal. First, relatively little is known about how PSF responds to environmental stress and disturbance compared to plant-plant competition. Second, specific types of competition enhanced negative effects of soil microbes on plant growth, and specific environmental stressors enhanced positive effects of soil microbes on plant growth. Third, whether PSF experiments are conducted in the field or greenhouse can change plant growth responses. And, fourth, how the soil conditioning phase is conducted can change plant growth responses. With more detail than previously shown, these results confirm that environmental context writ large can change plant growth responses in PSF experiments. These data should aid theory and predictions for conservation and restoration applications by showing the relative importance of competition, stress, and disturbance in PSF studies over time. Lastly, these data demonstrate how variation in experimental methods can alter interpretation and conclusions of PSF studies.
In this paper specific environmental remediation examples of method applications are given. Radiological contaminated site was created by non-nuclear industry in Turkey. This is designated as a contaminated site and can ultimately lead to undesired health effects for residents. Appropriate actions have been taken to protect human and environment from contaminated site. As every site has its own characteristics, contaminated area was examined by sampling and surveying works. Before taken into action, remediation actions need to be justified and optimized. Radiation levels and homogeneity of contamination was investigated. Remediation program was established and taken into action in parallel two main works. First one covers all actions to the contamination itself. The site was isolated properly and all equipment was deployed. Working methods for segregation of contaminated material from the soil were determined. Besides, risk evaluation was carried out. Pathways between the contaminated soil and people were taken into account. Groundwater samples were taken and analyzed. According to these results, evacuation, area isolation or changing land use options were evaluated. Isolation of the site and removal of radioactive materials were determined as appropriate actions. (authors)
Secondary metabolites are compounds not essential for an organism’s development, but provide significant ecological and physiological benefits. These compounds have applications in medicine, biotechnology and agriculture. Their production is encoded in biosynthetic gene clusters (BGCs), groups of genes collectively directing their biosynthesis. The advent of metagenomics has allowed researchers to study BGCs directly from environmental samples, identifying numerous previously unknown BGCs encoding unprecedented chemistry. Here, we present the BGC Atlas (https://bgc-atlas.cs.uni-tuebingen.de), a web resource that facilitates the exploration and analysis of BGC diversity in metagenomes. The BGC Atlas identifies and clusters BGCs from publicly available datasets, offering a centralized database and a web interface for metadata-aware exploration of BGCs and gene cluster families (GCFs). We analyzed over 35 000 datasets from MGnify, identifying nearly 1.8 million BGCs, which were clustered into GCFs. The analysis showed that ribosomally synthesized and post-translationally modified peptides are the most abundant compound class, with most GCFs exhibiting high environmental specificity. We believe that our tool will enable researchers to easily explore and analyze the BGC diversity in environmental samples, significantly enhancing our understanding of bacterial secondary metabolites, and promote the identification of ecological and evolutionary factors shaping the biosynthetic potential of microbial communities.
Executive Order 13653, Preparing the United States for the Impacts of Climate Change, was issued in 2013. The President emphasized the importance for federal agencies to take action to enhance climate preparedness and resilience. The U.S. Department of Energy released the DOE Climate Change Adaptation Plan in 2014 to build resilience and mitigation across the Department, and to assure inclusion of climate change adaptation as part of its planning and operations. DOE's Office of Environmental Management has an important mission to manage safe cleanup of environmental legacy contamination brought about from five decades of nuclear weapons development and government sponsored nuclear energy research. Specifically, Environmental Management is responsible for remediation of soil and groundwater, deactivation and decommissioning of facilities, and disposal of hazardous and radioactive waste. Three case studies are discussed in this paper that demonstrate the cost benefit and importance for Environmental Management to assess climate change vulnerability and implement planning procedures: 1. Los Alamos National Laboratory in New Mexico has experienced $0.5 billion in unanticipated costs as a result of climate-related events including: extreme drought, wildfires, deluge rains, and historic flooding over the past 15 years. 2. The U.S. Environmental Protection Agency American Cyanamid Superfund Site, situated on the New Jersey coast was hit by Hurricane Irene in 2011. Three major contaminated, solvent impoundment berms were breached within the 100-year flood plain, causing major damage to the facility. 3. For radioactive waste disposal facilities in low-lying areas in proximity to groundwater, climate change vulnerability and assessment is prudent for operational management. One such Superfund hazardous and radioactive waste disposal facility, the Environmental Management Waste Management Facility located at the DOE Oak Ridge Reservation in Tennessee, has documented surface and ground water management challenges since construction began in 2001, driven by changing regional weather patterns. (authors)
The purpose of environmental monitoring is to promote the early identification of, and response to, potential adverse environmental impacts associated with Lawrence Livermore National Laboratory (LLNL) operations. Environmental monitoring supports the Integrated Safety Management System (ISMS), International Organization for Standardization (ISO) 14001 Environmental Management Systems standard, and U. S. Department of Energy (DOE) Order 458.1, Radiation Protection oft/ic Pubile and the Environment. Specifically, environmental monitoring enables LLNL to detect, characterize, and respond to releases from LLNL activities; assess impacts; estimate dispersal patterns in the environment; characterize the pathways of exposure to members of the public; characterize the exposures and doses to individuals and to the population; and to evaluate the potential impacts to the hiota in the vicinity of LLNL. Environmental monitoring is also a major component of compliance demonstration for permits and other regulatory requirements.
Activities from this DOE sponsored project can be divided into three broad areas: (1) Isolation, characterization and sequencing of genomes of novel model organisms representing species active in methane oxidation, as judged from prior functional metagenomics-based experiments; (2) Manipulation of natural communities consuming methane, followed by observation on community dynamics and species succession, under specific environmental pressures such as variable O 2 and methane concentrations; and (3) Development of synthetic community models, from simple to complex, followed by observations on community dynamics and transcript and metabolite patterns. From these efforts, we have established several dozen novel model organisms representing different types of methane-utilizing species, different types of methylotrophic non-methane-utilizing guilds, as well as non-methylotrophic heterotrophs of different types, all with sequenced and manually curated genome annotations. From manipulation of natural sediment communities under controlled environmental conditions, we have deduced prominent species dynamics patterns and identified most important players in methane metabolism. We have also observed specific patterns in functional partnerships. Based on the discoveries from natural community manipulations, we have established model synthetic communities, ranging from simple, two-species, to complex, 50-species synthetic communities. The patterns from manipulation of synthetic communities were compared to the ones from natural communities. Synthetic communities were also characterized in terms of differential gene expression in response to community living, highlighting the role of alternative methanol dehydrogenases in community function. These observations were further validated through targeted metabolomics, identifying methanol as one major metabolite shared among community members.
The purpose of environmental monitoring is to promote the early identification of, and response to, potential adverse environmental impacts associated with Lawrence Livermore National Laboratory (LLNL) operations. Environmental monitoring supports the Integrated Safety Management System (ISMS), International Organization for Standardization (ISO) 14001 Environmental Management Systems standard, and U. S. Department of Energy (DOE) Order 458.1, Radiation Protection of the Public and the Environment. Specifically, environmental monitoring enables LLNL to detect, characterize, and respond to releases from LLNL activities; assess impacts; estimate dispersal patterns in the environment; characterize the pathways of exposure to members of the public; characterize the exposures and doses to individuals and to the population; and to evaluate the potential impacts to the biota in the vicinity of LLNL. Environmental monitoring is also a major component of compliance demonstration for permits and other regulatory requirements.
Background: Bacterial small RNAs (sRNAs) regulate gene expression by base-pairing with downstream target mRNAs to attenuate translation of mRNA into protein at the post-transcriptional level. In response to specific environmental changes, sRNAs can modulate the expression levels of target genes, thus enabling adaptation of cellular physiology. Results: We profiled sRNA expression in the Gram-negative bacteria Burkholderia thailandensis cultured under 54 distinct growth conditions using a Burkholderia-specific microarray that contains probe sets to all intergenic regions greater than 90 bases. We identified 38 novel sRNAs and performed experimental validation on five sRNAs that play a role in adaptation of Burkholderia to cell stressors. In particular, the trans-encoded BTH_s1 and s39 exhibited differential expression profiles dependent on growth phase and cell stimuli, such as antibiotics and serum. Furthermore, knockdown of the highly-expressed BTH_s39 by antisense transcripts reduced B. thailandensis cell growth and attenuated host immune response upon infection, indicating that BTH_s39 functions in bacterial metabolism and adaptation to the host. In addition, expression of cis-encoded BTH_s13 and s19 found in the 5' untranslated regions of their cognate genes correlated with tight regulation of gene transcript levels. This sRNA-mediated downregulation of gene expression may be a conserved mechanism of post-transcriptional gene dosage control. Conclusions: These studies provide a broad analysis of differential Burkholderia sRNA expression profiles and illustrate the complexity of bacterial gene regulation in response to different environmental stress conditions.
The Early Site Permit (ESP) process offered under Title 10 Code of Federal Regulations (CFR) Part 52, Subpart A, was promulgated by the Nuclear Regulatory Commission (NRC) in 1989 to address industry concerns with the former licensing process under 10 CFR Part 50. Previously, the licensing process required large expenditures of time and money by applicants well before key site specific environmental, safety, and emergency planning issues could be resolved. As envisioned, the ESP process is meant to resolve these issues well in advance of when a decision is made to build a nuclear power facility and before substantial capital is invested in the construction of a new nuclear facility. The ESP application is required to provide design information pertaining to structures, systems, and components along with site-specific parameters (such as meteorology, demographics, and hydrology) and address site safety, environmental protection, and emergency planning. Although an ESP applicant does not need to specify a particular nuclear plant design, as in construction permit applications, it does need to provide sufficient surrogate design information (developed to bound the nuclear plant design(s) that are being considered by the applicant) so that the NRC can make a determination on the acceptability of the site and the environmental impacts, and determine whether designs bounded by the surrogate design information provided by the applicant can be qualified for the proposed site.
Sustainability analysis requires a joint assessment of environmental, social and economic aspects of production processes. Here we propose the use of Life Cycle Analysis (LCA), a metafrontier (MF) directional distance function (DDF) approach, and Data Envelopment Analysis (DEA), to assess technological and managerial differences in eco-efficiency between production systems. We use LCA to compute six environmental and health impacts associated with the production processes of nearly 200 Spanish citrus farms belonging to organic and conventional farming systems. DEA is then employed to obtain joint economic-environmental farm's scores that we refer to as eco-efficiency. DDF allows us to determine farms' global eco-efficiency scores, as well as eco-efficiency scores with respect to specific environmental impacts. Furthermore, the use of an MF helps us to disentangle technological and managerial eco-inefficiencies by comparing the eco-efficiency of both farming systems with regards to a common benchmark. Our core results suggest that the shift from conventional to organic farming technology would allow a potential reduction in environmental impacts of 80% without resulting in any decline in economic performance. In contrast, as regards farmers' managerial capacities, both systems display quite similar mean scores.