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Exiguobacterium indicum has often reported from a wide variety of environmental samples, ranging from extreme to common habitats. Here we report the 3.1-Mb draft genome of E. indicum strain LL15, discovered during an investigation of freshwater lakes in residential-urban environments.
The movement ecology of raccoons varies widely across habitats with important implications for the management of zoonotic diseases such as rabies. However, the spatial ecology of raccoons remains poorly understood in many regions of the United States, particularly in the southeast. To better understand the spatial ecology of raccoons in the southeastern US, we investigated the role of sex, season, and habitat on monthly raccoon home range and core area sizes in three common rural habitats (bottomland hardwood, upland pine, and riparian forest) in South Carolina, USA. From 2018–2022, we obtained 264 monthly home ranges from 46 raccoons. Mean monthly 95% utilization distribution (UD) sizes ranged from 1.05 ± 0.48 km 2 (breeding bottomland females) to 5.69 ± 3.37 km 2 (fall riparian males) and mean monthly 60% UD sizes ranged from 0.25 ± 0.15 km 2 (breeding bottomland females) to 1.59 ± 1.02 km 2 (summer riparian males). Males maintained home range and core areas ~2–5 times larger than females in upland pine and riparian habitat throughout the year, whereas those of bottomland males were only larger than females during the breeding season. Home ranges and core areas of females did not vary across habitats, whereas male raccoons had home ranges and core areas ~2–3 times larger in upland pine and riparian compared to bottomland hardwood throughout much of the year. The home ranges of males in upland pine and riparian are among the largest recorded for raccoons in the United States. Such large and variable home ranges likely contribute to elevated risk of zoonotic disease spread by males in these habitats. These results can be used to inform disease mitigation strategies in the southeastern United States.
Abstract Effective species management often requires understanding patterns of movement and habitat use. A common approach in identifying where individuals reside relies upon chemical tracers from the environment that are incorporated into an individual's tissues. For fish, isotopes in their otoliths, specifically the portion of their otolith formed during their larval stage, have been used to identify the natal origin. Complicating this work, however, is the fact that during this life stage, there is a shift in the source of isotopes deposited onto the growing otolith from maternally to environmentally derived. The objective of this study was to identify the portion of the otolith representing this transition to environmentally derived isotopes so as to accurately investigate questions of natal origin for a threatened population of fall Chinook salmon ( Oncorhynchus tshawytscha ). We exposed developing larvae to four treatments that differed in terms of their water strontium isotope ratio ( 87 Sr/ 86 Sr) and used change‐point analysis of otolith 87 Sr/ 86 Sr and strontium to calcium ratio (Sr/Ca) to identify the otolith radius corresponding to the transition to environmentally derived isotopes. Our results indicated this transition occurred, on average, at 132 μm ( 87 Sr/ 86 Sr; ±50 μm standard deviation) and 127 μm (Sr/Ca; ±29 μm) from the otolith core, which corresponded to the developmental time between hatching and exogenous feeding. A substantial proportion of our otoliths (i.e., 61%) did not show convergence between otolith and water 87 Sr/ 86 Sr by the end of the 113‐day experiment, which was likely due to the dietary contribution of marine‐based feed. Therefore, we were unable to recommend an otolith radius to target for the purposes of reconstructing natal origin apart from being beyond approximately 130 μm.
Abstract Establishing robust methods and metrics to evaluate habitat quality is critical for the recovery of endangered Pacific salmonids ( Oncorhynchus spp.). A variety of modeling approaches are used for status and trend monitoring of anadromous species throughout the Pacific Northwest, USA, but current methods may fail to capture the complex relationship between fish and habitat and are often limited in predictive power beyond specific watersheds. Further, the focus on species distribution and abundance is not easily manipulated to predict carrying capacity and traditional stock‐recruitment analyses are reliant on long‐term data which are not always available. In this study, we developed a quantile random forest model to provide estimates of habitat carrying capacity for Chinook salmon ( O. tshawytscha ) parr during the summer months, at both the site and watershed scale. Quantile random forest models allow for the consideration of noisy data, correlated variables, and non‐linear relationships: common features in fish–habitat datasets. We leveraged Columbia Habitat Monitoring Program data to select habitat co‐variates and predict capacity at those sites. We also identified a set of globally available attributes to extrapolate capacity estimate predictions throughout wadeable streams within the Columbia River basin. Total capacity estimates for watersheds closely matched estimates from alternative fish productivity models. Carrying capacity estimates based on quantile random forest models, like those presented here, provide managers a framework to guide the identification, prioritization, and development of habitat rehabilitation actions to recover salmon populations.
A new western Atlantic member of the ctenochelid genus Paragourretia Sakai, 2004 is described to accommodate a single unique specimen collected by dredge on muddy rubble substrates of the continental shelf in the southwestern Gulf of Mexico. Paragourretia sandrae n. sp. closely resembles Paragourretia biffari, another regionally reported species for which photographs and additional illustrations are herein provided. While P. biffari and P. sandrae n. sp. are similar in habitus and known habitat o the more commonly encountered confamilial Dawsonius latispina, the third maxillipeds in Paragourretia bear distinct exopods that are absent in Dawsonius. As in eight other world congeners, P. sandrae n. sp. differs from both P. biffari and Dawsonius in lacking triangular ventrolateral projections on the sixth pleomere. It is further distinguished from P. biffari by lacking a distinctly incised notch in the anterodistal margin of the uropodal exopod and by absence of a median terminal spine on the telson. Additional sequence-quality specimens of P. sandrae n. sp. are required to clarify its relationships within the polyphyletic genus Paragourretia on a molecular genetic basis.
Abstract The 2011 nuclear accident in Fukushima, Japan caused the evacuation of > 100,000 people and prompted studies on environmental impacts of radiological contamination. However, few researchers have explored how the human evacuation has affected ecosystem processes. Despite contamination, one common scavenger (wild boar, Sus scrofa ) is 2–3× more abundant inside the Fukushima Exclusion Zone (FEZ). Shifts in abundance of some scavenger species can have cascading effects on ecosystems, so our objective was to investigate impacts of the evacuation and the resulting increase in wild boar on vertebrate scavenger communities. We deployed cameras at 300 carcasses in the FEZ and a nearby inhabited area, and quantified carcass fate, scavenger species, and detection/persistence times. We also tested effects of carcass size and habitat on scavenger community composition and efficiency by balancing trials across two carcass sizes and habitats in each zone. Overall scavenger richness and carcass removal rates (73%) were similar in the FEZ and inhabited area, but species-specific carcass removal rates and occurrence differed between zones. Wild boar removed substantially more carcasses inside the FEZ, with implications for nutrient and contaminant distribution. Our results suggest carcass size affects scavenging dynamics more than human activity or habitat, and abundance changes of common scavengers can influence carrion resource allocation.
During prolonged resource limitation, bacterial cells can persist in metabolically active states of non-growth. These maintenance periods, such as those experienced in stationary phase, can include upregulation of secondary metabolism and release of exometabolites into the local environment. As resource limitation is common in many environmental microbial habitats, we hypothesized that neighboring bacterial populations employ exometabolites to compete or cooperate during maintenance and that these exometabolite-facilitated interactions can drive community outcomes. Here, we evaluated the consequences of exometabolite interactions over the stationary phase among three environmental strains: Burkholderia thailandensis E264, Chromobacterium subtsugae ATCC 31532, and Pseudomonas syringae pv. tomato DC3000. We assembled them into synthetic communities that only permitted chemical interactions. We compared the responses (transcripts) and outputs (exometabolites) of each member with and without neighbors. We found that transcriptional dynamics were changed with different neighbors and that some of these changes were coordinated between members. The dominant competitor B. thailandensis consistently upregulated biosynthetic gene clusters to produce bioactive exometabolites for both exploitative and interference competition. These results demonstrate that competition strategies during maintenance can contribute to community-level outcomes. It also suggests that the traditional concept of defining competitiveness by growth outcomes may be narrow and that maintenance competition could be an additional or alternative measure.
Marine energy devices are installed in highly dynamic environments and have the potential to affect benthic and pelagic habitats around them. Regulatory bodies often require baseline characterization and/or post-installation monitoring to determine whether changes in these habitats are being observed. However, a great diversity of technologies is available for surveying and sampling marine habitats. Selecting the most suitable instrument to identify and measure changes in habitats at marine energy sites can become a daunting task. We conducted a thorough review of journal articles, survey reports, and grey literature to extract information about the technologies used, the data collection and processing methods, and the performance and effectiveness of these instruments. We examined documents related to marine energy development, offshore wind farms, oil and gas offshore sites, and other marine industries around the world over the last 20 years, as well as national and international guidelines for surveying habitats around offshore activities. A total of 120 different technologies were identified across six main habitat categories: seafloor, sediment, infauna, epifauna, pelagic, and biofouling. The technologies were organized into 12 broad technology classes: acoustic, corer, dredge, grab, hook and line, net and trawl, plate, remote sensing, scrape samples, trap, visual, and others. Visual was the most common and the most diverse technology class, with applications across all six habitat categories. Sampling designs varied considerably among the reviewed studies but transect was the predominant design for surveying seafloor, epifauna, and pelagic habitats. The most common data analyses were univariate and multivariate statistical analyses aimed at calculating and comparing biodiversity indices, characterizing faunal assemblages or sediment classes, or modeling the distribution of animals related to abiotic parameters. Technologies and sampling methods adaptable and designed to work efficiently in energetic environments have greater success at marine energy sites. In addition, sampling designs and statistical analyses should be carefully thought through to identify differences in faunal assemblages and spatiotemporal changes in habitats.
Abstract Invasive black and pale swallow-worts (Vincetoxicum nigrum (L.) Moench, and Vincetoxicum rossicum Kelopow), which are related to milkweeds, can act as ecological traps for monarch butterflies (Danaus plexippus L. (Lepidoptera: Nymphalidae)) as they lay eggs on them that fail to develop. A recently approved biological control agent against swallow-worts, Hypena opulenta Christoph, occupies the same feeding guild on swallow-worts as monarch larvae and could be perceived as a competitor to monarchs. We tested how the presence of this defoliating moth on swallow-worts may influence monarch host selection. In a two-year field experiment, we placed pale swallow-wort plants that were either infested with H. opulenta or noninfested as well as common milkweed (Asclepias syriaca L.), into monarch habitats to assess oviposition rates. In the laboratory, monarchs were either given a choice or not between milkweeds and black swallow-worts with or without H. opulenta. While monarchs strongly preferred common milkweed in the field, up to 25% of the eggs we observed were laid on pale swallow-wort, without preference for swallow-wort with (10.7%) or without (14.3%) H. opulenta. In laboratory choice and no-choice tests, monarchs did not lay any eggs on black swallow-wort, likely because of the long-term laboratory rearing on common milkweeds. Our results confirm that pale swallow-wort may act as an oviposition sink to monarchs in Michigan as well. Since the biological control program is still in its infancy, the nature of interactions between monarchs and H. opulenta may change as the biocontrol agent becomes more widespread.
The coexistence of competing species is a long-lasting puzzle in evolutionary ecology research. Despite abundant experimental evidence showing that the opportunity for coexistence decreases as niche overlap increases between species, bacterial species and strains competing for the same resources are commonly found across diverse spatially heterogeneous habitats. We thus hypothesized that the spatial scale of competition may play a key role in determining bacterial coexistence, and interact with other mechanisms that promote coexistence, including a growth–motility trade-off. To test this hypothesis, we let two Pseudomonas putida strains compete at local and regional scales by inoculating them either in a mixed droplet or in separate droplets in the same Petri dish, respectively. We also created conditions that allow the bacterial strains to disperse across abiotic or fungal hyphae networks. We found that competition at the local scale led to competitive exclusion while regional competition promoted coexistence. When competing in the presence of dispersal networks, the growth–motility trade-off promoted coexistence only when the strains were inoculated in separate droplets. Our results provide a mechanism by which existing laboratory data suggesting competitive exclusion at a local scale is reconciled with the widespread coexistence of competing bacterial strains in complex natural environments with dispersal.
Plant adaptation to terrestrial life started 450 million years ago and has played a major role in the evolution of life on Earth. The genetic mechanisms allowing this adaptation to a diversity of terrestrial constraints have been mostly studied by focusing on flowering plants. Here, we gathered a collection of 133 accessions of the model bryophyte Marchantia polymorpha and studied its intraspecific diversity using selection signature analyses, a genome-environment association study and a pangenome. We identified adaptive features, such as peroxidases or nucleotide-binding and leucine-rich repeats (NLRs), also observed in flowering plants, likely inherited from the first land plants. The M. polymorpha pangenome also harbors lineage-specific accessory genes absent from seed plants. We conclude that different land plant lineages still share many elements from the genetic toolkit evolved by their most recent common ancestor to adapt to the terrestrial habitat, refined by lineage-specific polymorphisms and gene family evolution.
The solar industry is responding to demand for building a clean energy future. At the same time, pollinator declines and habitat losses are resulting in listing consideration for once-common species like monarch butterflies, plus petitions to list bees and other species. How can projects responsibly co-locate pollinator plantings at solar facilities? What ecological and performance benefits can be realized from pollinator plantings? How do developers and owners weigh the costs and challenges of maintaining pollinator plantings and determine the effects it has on power generation, community acceptance, and operations? The Pollinator Habitat Aligned with Solar Energy (PHASE) project is a four-year research project that aims to answer these questions and better support the solar industry in successfully implementing pollinator plantings. This project is funded by the U.S. Department of Energy's Solar Energy Technologies Office. In collaboration with an advisory group composed of industry and technical professionals, the PHASE team developed methodologies to evaluate the impacts of plantings on both biodiversity and the facility operations, including the diversity of plant and insect communities, pollinator services being provided by the site, and the effects of pollinator vegetation on panel temperature and efficiency. The PHASE team also used data to develop tools designed to better support solar industry decision-making on pollinator vegetation including a Pollinator Planting Implementation Manual, a Cost Comparison Tool, a Seed Selection Tool, and Habitat Assessment Module Guidance. Final versions of the four tools will be released this year.
Abstract Larval source management has gained renewed interest as a malaria control strategy in Africa but the widespread and transient nature of larval breeding sites poses a challenge to its implementation. To address this problem, we propose combining an integrated high resolution (50 m) distributed hydrological model and remotely sensed data to simulate potential malaria vector aquatic habitats. The novelty of our approach lies in its consideration of irrigation practices and its ability to resolve complex ponding processes that contribute to potential larval habitats. The simulation was performed for the year of 2018 using ParFlow-Common Land Model (CLM) in a sugarcane plantation in the Oromia region, Ethiopia to examine the effects of rainfall and irrigation. The model was calibrated using field observations of larval habitats to successfully predict ponding at all surveyed locations from the validation dataset. Results show that without irrigation, at least half of the area inside the farms had a 40% probability of potential larval habitat occurrence. With irrigation, the probability increased to 56%. Irrigation dampened the seasonality of the potential larval habitats such that the peak larval habitat occurrence window during the rainy season was extended into the dry season. Furthermore, the stability of the habitats was prolonged, with a significant shift from semi-permanent to permanent habitats. Our study provides a hydrological perspective on the impact of environmental modification on malaria vector ecology, which can potentially inform malaria control strategies through better water management.
Marine energy devices are installed in highly dynamic environments and have the potential to affect the benthic and pelagic habitats around them. Regulatory bodies often require baseline characterization and/or post-installation monitoring to determine whether changes in these habitats are being observed. However, a great diversity of technologies is available for surveying and sampling marine habitats, and selecting the most suitable instrument to identify and measure changes in habitats at marine energy sites can become a daunting task. We conducted a thorough review of journal articles, survey reports, and grey literature to extract information about the technologies used, the data collection and processing methods, and the performance and effectiveness of these instruments. We examined documents related to marine energy development, offshore wind farms, oil and gas offshore sites, and other marine industries around the world over the last 20 years. A total of 120 different technologies were identified across six main habitat categories: seafloor, sediment, infauna, epifauna, pelagic, and biofouling. The technologies were organized into 12 broad technology classes: acoustic, corer, dredge, grab, hook and line, net and trawl, plate, remote sensing, scrape samples, trap, visual, and others. Visual was the most common and the most diverse technology class, with applications across all six habitat categories. Technologies and sampling methods that are designed for working efficiently in energetic environments have greater success at marine energy sites. In addition, sampling designs and statistical analyses should be carefully thought through to identify differences in faunal assemblages and spatiotemporal changes in habitats.
Ecosystem restoration is a common tool for re-establishing ecosystem processes, structures, and functions to improve biodiversity and services in coastal and estuarine ecosystems. In the Salish Sea, salmon habitats have been fragmented, reduced in size, and diminished in quality, and the ecosystem processes that form and sustain these habitats have been degraded and disrupted as well. This loss is especially prevalent in estuaries, where up to 90% of former salmon habitat has been lost or compromised. Salmon species are integral to the identities and cultures of people in the Pacific Northwest, yet salmon abundances remain at historic lows, especially in urbanized areas. Recent investments in restoration are creating rearing habitat and repairing lost ecosystem function. However, restoration efforts in this region have largely proceeded at the site scale, with less attention to big-picture thinking regarding how restoration will effectively recover degraded or lost habitats for target species. As a result, no landscape-scale evaluation program exists, and the cumulative benefits of multiple interventions are unknown. We describe innovative methods for science synthesis related to the evaluation of cumulative effects of ecosystem restoration for Pacific salmon, using years of existing, but disparate data. Building from previous work on cumulative effects evaluation and incorporating a hierarchy of hypotheses approach, we propose using causal inference across numerous hypotheses in a framework to assess the cumulative benefits to Pacific salmon from multiple estuarine restoration projects. We present the framework as a method that can be used to address many complex questions and provide examples from the Salish Sea where the approach is being implemented. The framework draws on science synthesis from numerous fields and uses a hierarchy of hypotheses, causal analysis at multiple scales, and a new hierarchy of synthesis for assessing multiple lines of evidence documenting restoration effects on Pacific salmon. We propose causal inference to synthesize dissimilar data streams, in our case, to identify various manifestations of cumulative effects of restoration and benefits to salmon, and to further inform restoration and recovery planning. A unifying framework would allow for the detection of thresholds at which restoration provides measurable improvement and would greatly advance understanding of the effects of restoration on ecosystems.
Benthic invertebrates play critical ecosystem roles including the breakdown of organic matter, sediment mixing, and nutrient cycling. In the lower Columbia River and estuary, benthic invertebrates provide a foraging resource for threatened and endangered juvenile salmon. Driven by the goal to create low velocity, shallow water, and riparian shrub habitats to benefit juvenile salmon, the USACE placed 237,000 CY of dredged material, resulting in the deposition of 13.5 acres of sand on the off-channel margins at Woodland Islands. The Pacific Northwest National Laboratory (PNNL) designed and implemented an action effectiveness research study to understand how dredged material placement at Woodland Islands affected sediment conditions and benthic invertebrate assemblages. A Before-After-Control-Impact, or BACI, study design was used to evaluate the response of environmental conditions and benthic invertebrates to dredged material placement. The design included one impact site and two control sites. Sampling occurred for two years prior to dredged material placement and two years after. Our study found that spatial variation was a significant factor for both environmental and biological response variables which suggests local conditions are important considerations for mechanisms affecting benthic assemblages. We found that off-channel habitats across all locations sampled were producing benthic invertebrates, many of which are common prey items for juvenile salmon and steelhead—e.g., insects, chironomids, crustaceans, and corophium. There was a significant BACI effect (i.e., an effect at the dredged material placement site, relative to conditions at the control sites) for concentration of carbon and ammonium in sediment, but not for phosphorous concentrations or for percent sand. The estimated abundance for the three invertebrate response variables—total abundance, total chironomid abundance, and total corophium abundance—was significantly lower at the impact site after dredged material placement, compared to the control sites. At Woodland Island, the estimated mean abundance for all invertebrates combined decreased 28% after dredged material placement. Estimated mean abundances of chironomid and corophium decreased by 8% and 88%, respectively. While invertebrate abundances were lower after dredged placement, the composition of benthic invertebrates was similar before and after placement suggesting that as the new habitat feature evolves recolonization will likely follow. These findings provide a foundation for understanding potential benefits and consequences of repurposing dredged material for habitat creation in the LCRE.
Ammonia-oxidizing archaea (AOA) are among the most abundant and ubiquitous microorganisms in the ocean, exerting primary control on nitrification and nitrogen oxides emission. Although united by a common physiology of chemoautotrophic growth on ammonia, a corresponding high genomic and habitat variability suggests tremendous adaptive capacity. Here, we compared 44 diverse AOA genomes, 37 from species cultivated from samples collected across diverse geographic locations and seven assembled from metagenomic sequences from the mesopelagic to hadopelagic zones of the deep ocean. Comparative analysis identified seven major marine AOA genotypic groups having gene content correlated with their distinctive biogeographies. Phosphorus and ammonia availabilities as well as hydrostatic pressure were identified as selective forces driving marine AOA genotypic and gene content variability in different oceanic regions. Notably, AOA methylphosphonate biosynthetic genes span diverse oceanic provinces, reinforcing their importance for methane production in the ocean. Together, our combined comparative physiological, genomic, and metagenomic analyses provide a comprehensive view of the biogeography of globally abundant AOA and their adaptive radiation into a vast range of marine and terrestrial habitats.
Species occupying broad geographic regions have evolved multiple mechanisms to regulate phenological characteristics, enabling adaptations to diverse native habitats. By developing computer vision AI to process citizen science observations across native habitats over North America, we uncovered a consistent latitudinal trend of earlier flowering at higher latitudes in warm-season perennial grasses. To explore the underlying mechanisms of adaptation, we conducted common garden experiments with one species (switchgrass) and discovered the opposite latitudinal flowering-time trend. Integration of differential plasticity of GI-Hd1-FTL1 haplotypes of flowering time regulatory genes, haplotype range, and local environmental profiles found that observations from native habitats capture only part of the genotype-environment-phenotype spectrum established in common garden experiments, therefore reconciling the discrepancy. Two mechanisms emerged as key forces shaping current haplotype ranges and influencing future shifts. Our study highlights the power of combining citizen science observations with designed experiments to uncover mechanisms of adaptation across spatiotemporal scales.