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All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Bird Species Use of Bioenergy Croplands in Illinois, USA—Can Advanced Switchgrass Cultivars Provide Suitable Habitats for Breeding Grassland Birds?

Grassland birds have sustained significant population declines in the United States through habitat loss, and replacing lost grasslands with bioenergy production areas could benefit these species and the ecological services they provide. Point count surveys and autonomous acoustic monitoring were used at two field sites in Illinois, USA, to determine if an advanced switchgrass cultivar that is being used for bioenergy feedstock production could provide suitable habitats for grassland and other bird species. At the Brighton site, the bird use of switchgrass plots was compared to that of corn plots during the breeding seasons of 2020–2022. At the Urbana site, the bird use of restored prairie, switchgrass, and Miscanthus × giganteus was studied in the 2022 breeding season. At Brighton, Common Yellowthroat, Dickcissel, Grasshopper Sparrow, and Sedge Wren occurred on switchgrass plots more often than on corn; Common Yellowthroat and Dickcissel increased on experimental plots as the perennial switchgrass increased in height and density over the study period; and the other two species declined over the same period. At Urbana, Dickcissel was most frequent in prairie and switchgrass; Common Yellowthroat was most frequent in miscanthus and switchgrass. These findings suggest that advanced switchgrass cultivars could provide suitable habitats for grassland birds, replace lost habitats, and contribute to the recovery of these vulnerable species.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Existing evidence on the effects of climate variability and climate change on ungulates in North America: a systematic map

Abstract Background Climate is an important driver of ungulate life-histories, population dynamics, and migratory behaviors. Climate conditions can directly impact ungulates via changes in the costs of thermoregulation and locomotion, or indirectly, via changes in habitat and forage availability, predation, and species interactions. Many studies have documented the effects of climate variability and climate change on North America’s ungulates, recording impacts to population demographics, physiology, foraging behavior, migratory patterns, and more. However, ungulate responses are not uniform and vary by species and geography. Here, we present a systematic map describing the abundance and distribution of evidence on the effects of climate variability and climate change on native ungulates in North America. Methods We searched for all evidence documenting or projecting how climate variability and climate change affect the 15 ungulate species native to the U.S., Canada, Mexico, and Greenland. We searched Web of Science, Scopus, and the websites of 62 wildlife management agencies to identify relevant academic and grey literature. We screened English-language documents for inclusion at both the title and abstract and full-text levels. Data from all articles that passed full-text review were extracted and coded in a database. We identified knowledge clusters and gaps related to the species, locations, climate variables, and outcome variables measured in the literature. Review findings We identified a total of 674 relevant articles published from 1947 until September 2020. Caribou ( Rangifer tarandus ), elk ( Cervus canadensis ), and white-tailed deer ( Odocoileus virginianus ) were the most frequently studied species. Geographically, more research has been conducted in the western U.S. and western Canada, though a notable concentration of research is also located in the Great Lakes region. Nearly 75% more articles examined the effects of precipitation on ungulates compared to temperature, with variables related to snow being the most commonly measured climate variables. Most studies examined the effects of climate on ungulate population demographics, habitat and forage, and physiology and condition, with far fewer examining the effects on disturbances, migratory behavior, and seasonal range and corridor habitat. Conclusions The effects of climate change, and its interactions with stressors such as land-use change, predation, and disease, is of increasing concern to wildlife managers. With its broad scope, this systematic map can help ungulate managers identify relevant climate impacts and prepare for future changes to the populations they manage. Decisions regarding population control measures, supplemental feeding, translocation, and the application of habitat treatments are just some of the management decisions that can be informed by an improved understanding of climate impacts. This systematic map also identified several gaps in the literature that would benefit from additional research, including climate effects on ungulate migratory patterns, on species that are relatively understudied yet known to be sensitive to changes in climate, such as pronghorn ( Antilocapra americana ) and mountain goats ( Oreamnos americanus ), and on ungulates in the eastern U.S. and Mexico.

Malpeli, Katherine C. (ORCID:000000030780918X)↗
DOE OSTI2024

Tracking animal movements via collaborative acoustic telemetry networks: Multiscale habitat use, phenology, and management insights

Abstract Estuaries support diverse fish and invertebrate communities, including resident species that rely on estuarine habitats year‐round and transient migratory species. The unique movement patterns of these animals connect habitats within and far beyond the estuary and are integrally linked to fisheries management objectives. With a focus on Chesapeake Bay, this study leveraged data from collaborative acoustic telemetry networks in the northwest Atlantic to assess habitat use and phenology of movements for seven species of fish (cownose rays, dusky sharks, smooth dogfish, alewife, striped bass, common carp, and blue catfish) and one invertebrate (horseshoe crabs). A total of 288 acoustically tagged individuals were detected >3.2 million times (6,743 to 2,095,717 detections per species) on receivers across ~20.5 degrees of latitude spanning the North American Atlantic seaboard from Florida, USA, to New Brunswick, Canada. Common metrics of movement and phenology grouped these species as resident (common carp, blue catfish, horseshoe crabs), primarily resident in estuaries (juvenile striped bass), and coastal migrant (cownose rays, dusky sharks, smooth dogfish, alewife); maximum distance traveled varied by three orders of magnitude among these species. Further analysis of phenology for coastal migrants elucidated the timing and duration of these species' use of Chesapeake Bay. Collectively, movements linked habitats within Chesapeake Bay and connected the estuary to coastal ecosystems both to the north (e.g., alewife) and south (e.g., cownose rays), creating networks of fisheries management jurisdictions that varied in complexity and identified opportunities for enhancement to current management or co‐management of some species. Our results elucidate the importance of estuaries to species with diverse movement behaviors, identify scales and pathways of habitat connectivity via animal movements, and highlight the utility of collaborative acoustic telemetry networks for quantifying movements relevant to both ecological research and fisheries management.

Livernois, Mariah C.↗
DOE OSTI2022

Use of a Black-Tailed Prairie Dog Burrow by Honey Bees in the Texas Panhandle

Cynomys ludovicianus Baird (Black-Tailed Prairie Dog) is considered to be a keystone species in the prairie, providing food and habitat for a diversity of wildlife. In October of 2020, we observed an active Apis mellifera Linnaeus (European Honey Bee) hive visible within the entrance of a burrow made by Black-Tailed Prairie Dogs in the treeless plains of the Texas Panhandle. Furthermore, this observation suggests that prairie dogs could provide habitat for this economically important pollinator and in landscapes otherwise devoid of cavities such as are commonly found in trees, buildings, and other structures.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Brown watersnakes (Nerodia taxispilota) as bioindicators of mercury contamination in a riverine system

Herein, mercury (Hg) is a contaminant that enters the environment through natural or anthropogenic means. Ecological risk assessments have examined Hg bioaccumulation and effects in many taxa, but little is known about Hg dynamics in reptiles, or their potential use as bioindicator species for monitoring Hg in aquatic systems. Numerous snake species, like North American watersnakes (Nerodia spp.), are piscivorous and are exposed to Hg through their diet. The purpose of this study was to identify factors associated with Hg accumulation in a common watersnake species and compare Hg concentrations of the snakes to those in fish occupying the same habitats. To this end, we sampled brown watersnakes (Nerodia taxispilota) from the Savannah River, a major river system in the southeastern U.S., and compared N. taxispilota Hg accumulation trends to those of bass (Micropterus salmoides), catfish (Ictalurus and Ameiurus spp.), and panfish (Lepomis and Pomoxis spp.) collected from the same reach. Total Hg (THg) in N. taxispilota tail tips ranged from 0.020 to 0.431 mg/kg (wet weight; mean: 0.104 ± 0.008). Snake tail THg was significantly correlated with blood THg, which ranged from 0.003 to 1.140 mg/kg (0.154 ± 0.019). Snake size and site of capture were significantly associated with tail THg. Snake tail THg increased at sites along and downstream of the area of historic Hg pollution, consistent with fish THg. Snake muscle THg was predicted based on tail THg and ranged from 0.095 to 1.160 (0.352 ± 0.022). To gauge Hg biomagnification in N. taxispilota, we compared predicted snake muscle THg concentrations to THg in fish of consumable size. Average biomagnification factors for THg in N. taxispilota were 3.1 (panfish) and 5.4 (catfish), demonstrating N. taxispilota likely biomagnify Hg through their diet. These results reveal N. taxispilota to be an effective bioindicator species for monitoring Hg in aquatic environments.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Ventenata dubia projected to expand in the western United States despite future novel conditions

Abstract Distributions of both native and invasive species are expected to shift under future climate. Species distribution models (SDMs) are often used to explore future habitats, but sources of uncertainty including novel climate conditions may reduce the reliability of future projections. We explore the potential spread of the invasive annual grass ventenata ( Ventenata dubia ) in the western United States under both current and future climate scenarios using boosted regression tree models and 30 global climate models (GCMs). We quantify novel climate conditions, prediction variability arising from both the SDMs and GCMs, and the agreement among GCMs. Results demonstrate that currently suitable habitat is concentrated inside the invaded range of the northwest, but substantial habitat exists outside the invaded range in the Southern Rockies and southwestern US mountains. Future suitability projections vary greatly among GCMs, but GCMs commonly projected decreased suitability in the invaded range and increased suitability along higher elevations of interior mountainous areas. Climate novelty did not appear to undermine the prediction reliability in many cases where the climate–species relationship was fully represented by the occurrence data. GCM‐derived variability resulting from variation in future cool season precipitation and temperature seasonality was greatest in the Rocky Mountains. SDM‐derived variability was higher in currently suitable habitat, and few GCMs projections agreed that these areas would contain future suitable habitat. However, while prediction variability was high, many GCM projections agreed that parts of the Rocky, Wasatch, and Uinta Mountains would contain highly suitable habitat in the future. As disturbances in the interior mountains occur in coming decades, reducing some natural barriers to invasion, land managers, and conservationists will need to monitor for ventenata in post‐disturbance environments. Changes to invasion potential may not play out for several decades, but results related to current potential may have applications for early detection and rapid response planning.

Environmental Sciences & Ecology↗
DOE OSTI2022

Selection and development of aptamers for pyoverdine

The rhizosphere is a small region surrounding plant roots that is enriched in biochemicals from root exudates and populated with fungi, nematode, and bacteria. Interaction of rhizosphere organisms with plants is mainly promoted by exudates from the roots. Root exudates contain biochemicals that come from primary and secondary metabolisms of plants. These biochemicals attract microbes, which influence plant nutrition. The rhizosphere bacteria (microbiome) are vital to plant nutrient uptake and influence biotic and abiotic stress and pathogenesis. Pseudomonas is a genus of gammaproteobacteria known for its ubiquitous presence in natural habitats and its striking ecological, metabolic, and biochemical diversity. Within the genus, members of the Pseudomonas fluorescens group are common inhabitants of soil and plant surfaces, and certain strains function in the biological control of plant disease, protecting plants from infection by soilborne and aerial plant pathogens. The soil bacterium Pseudomonas protegens Pf-5 (also known as Pseudomonas fluorescensPf-5) is a well-characterized biological strain, which is distinguished by its prolific production of the secondary metabolite, pyoverdine. Knowledge of the distribution of P. fluorescens secretory activity around plant roots is very important for understanding the interaction between P. fluorescens and plants and can be achieved by real time tracking of pyoverdine. To achieve the capability of real-time tracking in soil, we have used a structure-switching SELEX strategy to select high affinity ssDNA and 2’ F-Y-RNA aptamers with specificity for pyoverdine over other siderophores. Pyoverdines from various strains possess a conserved chromophore along with strain-specific peptide chain. Some of the isolated aptamers bind to chromophore of pyoverdine. These will identify pyoverdines from a variety of pseudomonads. Identification of aptamers that selectively bind the peptide portion of pyoverdine Pf-5 is underway. The identified aptamers that are broadly and narrowly specific for pyoverdines or Pf-5 will be optimized for integration into an electrochemical biosensor to track, in real time, P fluorescens activity and other pseudomonads in and around the rhizosphere.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Microbial community dynamics and coexistence in a sulfide-driven phototrophic bloom

Background: Lagoons are common along coastlines worldwide and are important for biogeochemical element cycling, coastal biodiversity, coastal erosion protection and blue carbon sequestration. These ecosystems are frequently disturbed by weather, tides, and human activities. Here, we investigated a shallow lagoon in New England. The brackish ecosystem releases hydrogen sulfide particularly upon physical disturbance, causing blooms of anoxygenic sulfur-oxidizing phototrophs. To study the habitat, microbial community structure, assembly and function we carried out in situ experiments investigating the bloom dynamics over time. Results: Phototrophic microbial mats and permanently or seasonally stratified water columns commonly contain multiple phototrophic lineages that coexist based on their light, oxygen and nutrient preferences. We describe similar coexistence patterns and ecological niches in estuarine planktonic blooms of phototrophs. The water column showed steep gradients of oxygen, pH, sulfate, sulfide, and salinity. The upper part of the bloom was dominated by aerobic phototrophic Cyanobacteria, the middle and lower parts by anoxygenic purple sulfur bacteria (Chromatiales) and green sulfur bacteria (Chlorobiales), respectively. We show stable coexistence of phototrophic lineages from five bacterial phyla and present metagenome-assembled genomes (MAGs) of two uncultured Chlorobaculum and Prosthecochloris species. In addition to genes involved in sulfur oxidation and photopigment biosynthesis the MAGs contained complete operons encoding for terminal oxidases. The metagenomes also contained numerous contigs affiliating with Microviridae viruses, potentially affecting Chlorobi. Our data suggest a short sulfur cycle within the bloom in which elemental sulfur produced by sulfide-oxidizing phototrophs is most likely reduced back to sulfide by Desulfuromonas sp. Conclusions: The release of sulfide creates a habitat selecting for anoxygenic sulfur-oxidizing phototrophs, which in turn create a niche for sulfur reducers. Strong syntrophism between these guilds apparently drives a short sulfur cycle that may explain the rapid development of the bloom. The fast growth and high biomass yield of Chlorobi-affiliated organisms implies that the studied lineages of green sulfur bacteria can thrive in hypoxic habitats. This oxygen tolerance is corroborated by oxidases found in MAGs of uncultured Chlorobi. The findings improve our understanding of the ecology and ecophysiology of anoxygenic phototrophs and their impact on the coupled biogeochemical cycles of sulfur and carbon.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Phoresy in animals: review and synthesis of a common but understudied mode of dispersal

Phoresy is a type of interaction in which one species, the phoront, uses another species, the dispersal host, for transportation to new habitats or resources. Despite being a widespread behaviour, little is known about the ecology and evolution of phoresy. Our goal is to provide a comprehensive review of phoretic dispersal in animals and to bring renewed attention to this subject. We surveyed literature published between 1900 and 2020 to understand the extent of known higher-level taxonomic diversity (phyla, classes, and orders) and functional aspects of animals that use phoretic dispersal. Species dispersing phoretically have been observed in at least 13 animal phyla, 25 classes, and 60 orders. The majority of known phoronts are arthropods (Phylum Euarthropoda) in terrestrial habitats, but phoronts also occur in freshwater and marine environments. Marine phoronts may be severely under-represented in the literature due to the relative difficulty of studying these systems. Phoronts are generally small with low mobility and use habitats or resources that are ephemeral and/or widely dispersed. Many phoronts are also parasites. In general, animals that engage in phoresy use a wide variety of morphological and behavioural traits for locating, attaching to, and detaching from dispersal hosts, but the exact mechanisms behind these activities are largely unknown. In addition to diversity, we discuss the evolution of phoresy including the long-standing idea that it can be a precursor to parasitism and other forms of symbioses. To conclude, we suggest several areas of future research to improve our understanding of phoresy and its ecological and evolutionary significance.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Mercury bioaccumulation and Hepatozoon spp. infections in two syntopic watersnakes in South Carolina

Mercury (Hg) is a ubiquitous environmental contaminant known to bioaccumulate in biota and biomagnify in food webs. Parasites occur in nearly every ecosystem and often interact in complex ways with other stressors that their hosts experience. Hepatozoon spp. are intraerythrocytic parasites common in snakes. The Florida green watersnake (Nerodia floridana) and the banded watersnake (Nerodia fasciata) occur syntopically in certain aquatic habitats in the Southeastern United States. The purpose of this study was to investigate relationships among total mercury (THg) concentrations, body size, species,habitat type and prevalence and parasitemia of Hepatozoon spp. infections in snakes. In the present study, we sampled N. floridana and N. fasciata from former nuclear cooling reservoirs and isolated wetlands of the Savannah River Site in South Carolina. We used snake tail clips to quantify THg and collected blood samples for hemoparasite counts. Our results indicate a significant, positive relationship between THg and snake body size in N. floridana and N. fasciata in both habitats. Average THg was significantly higher for N. fasciata compared to N. floridana in bays (0.22 ± 0.02 and 0.08 ± 0.006 mg/kg, respectively; p < 0.01), but not in reservoirs (0.17 ± 0.02 and 0.17 ± 0.03 mg/kg, respectively; p = 0.29). Sex did not appear to be related to THg concentration or Hepatozoon spp. infections in either species. In conclusion, we found no association between Hg and Hepatozoon spp. prevalence or parasitemia; however, our results suggest that species and habitat type play a role in susceptibility to Hepatozoon spp. infection.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗
DOE OSTI2024

2024 OES-Environmental 2024 State of the Science Report, Chapter 3: Marine Renewable Energy: Stressor-Receptor Interactions

Determining the potential effects of marine renewable energy (MRE) development on the ocean requires consideration of how each component of a tidal, wave, riverine, or other MRE system might affect marine animals, habitats that support marine communities, or processes that make up essential oceanographic and ecological systems. Researchers around the world have been assessing the potential effects of MRE deployments and operations using a variety of instruments, models, analytical methods, and approaches. The most common approach, and the one followed throughout this report, is the framework of stressor-receptor interactions (Boehlert & Gill 2010), where stressors are the components of an MRE device and associated system that may cause stress, injury, or death to a marine animal, habitat, or ecosystem. The receptors are the species, their habitats, and the oceanographic and ecological processes that support them.

16 TIDAL AND WAVE POWER↗
DOE OSTI2020

A comparison of cost and quality of three methods for estimating density for wild pig (Sus scrofa)

A critical element in efective wildlife management is monitoring the status of wildlife populations; however, resources to monitor wildlife populations are typically limited. We compared cost efectiveness of three common population estimation methods (i.e. non-invasive DNA sampling, camera sampling, and sampling from trapping) by applying them to wild pigs (Sus scrofa) across three habitats in South Carolina, U.S.A where they are invasive. We used mark-recapture analyses for fecal DNA sampling data, spatially-explicit capture-recapture analyses for camera sampling data, and a removal analysis for removal sampling from trap data. Density estimates were similar across methods. Camera sampling was the least expensive, but had large variances. Fecal DNA sampling was the most expensive, although this technique generally performed well. We examined how reductions in efort by method related to increases in relative bias or imprecision. For removal sampling, the largest cost savings while maintaining unbiased density estimates was from reducing the number of traps. For fecal DNA sampling, a reduction in efort only minimally reduced costs due to the need for increased lab replicates while maintaining high quality estimates. For camera sampling, efort could only be marginally reduced before inducing bias. We provide a decision tree for researchers to help make monitoring decisions.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Genome‐enabled exploration of microbial ecology and evolution in the sea: a rising tide lifts all boats

Summary As a young bacteriologist just launching my career during the early days of the ‘microbial revolution’ in the 1980s, I was fortunate to participate in some early discoveries, and collaborate in the development of cross‐disciplinary methods now commonly referred to as "metagenomics". My early scientific career focused on applying phylogenetic and genomic approaches to characterize ‘wild’ bacteria, archaea and viruses in their natural habitats, with an emphasis on marine systems. These central interests have not changed very much for me over the past three decades, but knowledge, methodological advances and new theoretical perspectives about the microbial world certainly have. In this invited ‘How we did it’ perspective, I trace some of the trajectories of my lab's collective efforts over the years, including phylogenetic surveys of microbial assemblages in marine plankton and sediments, development of microbial community gene‐ and genome‐enabled surveys, and application of genome‐guided, cultivation‐independent functional characterization of novel enzymes, pathways and their relationships to in situ biogeochemistry. Throughout this short review, I attempt to acknowledge, all the mentors, students, postdocs and collaborators who enabled this research. Inevitably, a brief autobiographical review like this cannot be fully comprehensive, so sincere apologies to any of my great colleagues who are not explicitly mentioned herein. I salute you all as well!

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

White-tailed deer responses to acoustic predator cues are contingent upon past land use and contemporary fire regime

Prey can assess the immediate risk of predation by detecting cues of predator presence, and it is expected that prey should invest in costly antipredator behaviors when a cue of predator presence is detected. Features of the habitat in which the cue is detected, such as vegetative concealment, serve as indirect cues of risk and can mediate how prey respond to direct cues of predator presence. Past agricultural land use and contemporary fire regimes are common disturbances that may modify prey perceptions of risk and could, therefore, alter prey responses to direct cues of predator presence. Here we examined whether the overlap of these two disturbances affected white-tailed deer (Odocoileus virginianus) responses to cues of predator presence by measuring deer vigilance and foraging bout duration in response to coyote (Canis latrans) vocalizations across 20 woodlands that varied in past land use and contemporary fire regime. Frequent fire regimes consistently increased deer visibility to predators across both land-use history contexts. Deer exhibited no behavioral response to the predator cue in habitats containing infrequent fire regimes or agricultural legacies. Deer responded to the cue in frequently burned woodlands without agricultural legacies through increased vigilance and time spent at a foraging location. These findings reveal that land-use legacies and contemporary fire regimes can mediate how prey respond to direct cues of risk. They also suggest that prey may balance the uncertainty associated with cues of predation risk with the urgency of responding to a potential attack by being vigilant and remaining in place.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

A comparative genome analysis of the Bacillota ( Firmicutes ) class Dehalobacteriia

Dehalobacterium formicoaceticum is recognized for its ability to anaerobically ferment dichloromethane (DCM), and a catabolic model has recently been proposed. D. formicoaceticum is currently the only axenic representative of its class, the Dehalobacteriia, according to the Genome Taxonomy Database. However, substantial additional diversity has been revealed in this lineage through culture-independent exploration of anoxic habitats. Here we performed a comparative analysis of 10 members of the Dehalobacteriia, representing three orders, and infer that anaerobic DCM degradation appears to be a recently acquired trait only present in some members of the order Dehalobacteriales. Inferred traits common to the class include the use of amino acids as carbon and energy sources for growth, energy generation via a remarkable range of putative electron-bifurcating protein complexes and the presence of S-layers. The ability of D. formicoaceticum to grow on serine without DCM was experimentally confirmed and a high abundance of the electron-bifurcating protein complexes and S-layer proteins was noted when this organism was grown on DCM. We suggest that members of the Dehalobacteriia are low-abundance fermentative scavengers in anoxic habitats.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

A global perspective on bacterial diversity in the terrestrial deep subsurface

While recent efforts to catalogue Earth’s microbial diversity have focused upon surface and marine habitats, 12–20% of Earth’s biomass is suggested to exist in the terrestrial deep subsurface, compared to ~1.8% in the deep subseafloor. Metagenomic studies of the terrestrial deep subsurface have yielded a trove of divergent and functionally important microbiomes from a range of localities. However, a wider perspective of microbial diversity and its relationship to environmental conditions within the terrestrial deep subsurface is still required. Our meta-analysis reveals that terrestrial deep subsurface microbiota are dominated by Betaproteobacteria, Gammaproteobacteria and Firmicutes, probably as a function of the diverse metabolic strategies of these taxa. Evidence was also found for a common small consortium of prevalent Betaproteobacteria and Gammaproteobacteria operational taxonomic units across the localities. This implies a core terrestrial deep subsurface community, irrespective of aquifer lithology, depth and other variables, that may play an important role in colonizing and sustaining microbial habitats in the deep terrestrial subsurface. An in silico contamination-aware approach to analysing this dataset underscores the importance of downstream methods for assuring that robust conclusions can be reached from deep subsurface-derived sequencing data. Understanding the global panorama of microbial diversity and ecological dynamics in the deep terrestrial subsurface provides a first step towards understanding the role of microbes in global subsurface element and nutrient cycling.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Unraveling the ecological success of Iodidimonas in a bioreactor treating oil and gas produced water

Iodidimonas sp., a bacterium found in bioreactors treating oil and gas produced water as well as iodide-rich brines, has garnered attention for its unique ability to oxidize iodine. However, little is known about the metabolic capabilities that enable Iodidimonas sp. to thrive in certain unique ecological niches. In this study, we isolated, characterized, and sequenced three strains belonging to the Iodidimonas genus from the sludge of a membrane bioreactor used for produced water treatment. We investigated the genomic features of these isolates and compared them with the four publicly available isolate genomes from this genus, as well as a metagenome-assembled genome from the source bioreactor. Our Iodidimonas isolates had several genes associated with mitigating salinity, heavy metal, and organic compound stress, which likely help these bacteria to survive in produced water. Phenotyping tests revealed that while the isolates could utilize a wide variety of simple carbon substrates, they failed to degrade aliphatic or aromatic hydrocarbons, consistent with the lack of genes associated with common hydrocarbon degradation pathways in their genomes. We hypothesize that these microbes may lead a scavenging lifestyle in the bioreactor and similar iodide-rich brines. IMPORTANCE: Occupying a niche habitat and having few representative isolates, the genus Iodidimonas is a relatively understudied alphaproteobacterial group. Its ability to corrode pipes in iodine production facilities has economic implications, and its ability to generate potentially carcinogenic iodinated organic compounds during treatment of oil and gas produced water may cause environmental and health concerns with the recycling of treated water. Therefore, detailed characterization of the metabolic potential of the Iodidimonas isolates in this study both sheds light on their adaptation to the environmental conditions they inhabit and has environmental and economic significance.

Acharya, Shwetha M↗
DOE OSTI2024

Deep learning models map rapid plant species changes from citizen science and remote sensing data

Anthropogenic habitat destruction and climate change are reshaping the geographic distribution of plants worldwide. However, we are still unable to map species shifts at high spatial, temporal, and taxonomic resolution. Here, we develop a deep learning model trained using remote sensing images from California paired with half a million citizen science observations that can map the distribution of over 2,000 plant species. Our model— Deepbiosphere— not only outperforms many common species distribution modeling approaches (AUC 0.95 vs. 0.88) but can map species at up to a few meters resolution and finely delineate plant communities with high accuracy, including the pristine and clear-cut forests of Redwood National Park. These fine-scale predictions can further be used to map the intensity of habitat fragmentation and sharp ecosystem transitions across human-altered landscapes. In addition, from frequent collections of remote sensing data, Deepbiosphere can detect the rapid effects of severe wildfire on plant community composition across a 2-y time period. These findings demonstrate that integrating public earth observations and citizen science with deep learning can pave the way toward automated systems for monitoring biodiversity change in real-time worldwide.

Gillespie, Lauren E.↗