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USGS2014

Habitat prioritization across large landscapes, multiple seasons, and novel areas: an example using greater sage-grouse in Wyoming

Animal habitat selection is an important and expansive area of research in ecology. In particular, the study of habitat selection is critical in habitat prioritization efforts for species of conservation concern. Landscape planning for species is happening at ever-increasing extents because of the appreciation for the role of landscape-scale patterns in species persistence coupled to improved datasets for species and habitats, and the expanding and intensifying footprint of human land uses on the landscape. We present a large-scale collaborative effort to develop habitat selection models across large landscapes and multiple seasons for prioritizing habitat for a species of conservation concern. Greater sage-grouse ( Centrocercus urophasianus , hereafter sage-grouse) occur in western semi-arid landscapes in North America. Range-wide population declines of this species have been documented, and it is currently considered as “warranted but precluded” from listing under the United States Endangered Species Act. Wyoming is predicted to remain a stronghold for sage-grouse populations and contains approximately 37% of remaining birds. We compiled location data from 14 unique radiotelemetry studies (data collected 1994–2010) and habitat data from high-quality, biologically relevant, geographic information system (GIS) layers across Wyoming. We developed habitat selection models for greater sage-grouse across Wyoming for 3 distinct life stages: 1) nesting, 2) summer, and 3) winter. We developed patch and landscape models across 4 extents, producing statewide and regional (southwest, central, northeast) models for Wyoming. Habitat selection varied among regions and seasons, yet preferred habitat attributes generally matched the extensive literature on sage-grouse seasonal habitat requirements. Across seasons and regions, birds preferred areas with greater percentage sagebrush cover and avoided paved roads, agriculture, and forested areas. Birds consistently preferred areas with higher precipitation in the summer and avoided rugged terrain in the winter. Selection for sagebrush cover varied regionally with stronger selection in the Northeast region, likely because of limited availability, whereas avoidance of paved roads was fairly consistent across regions. We chose resource selection function (RSF) thresholds for each model set (seasonal × regional combination) that delineated important seasonal habitats for sage-grouse. Each model set showed good validation and discriminatory capabilities within study-site boundaries. We applied the nesting-season models to a novel area not included in model development. The percentage of independent nest locations that fell directly within identified important habitat was not overly impressive in the novel area (49%); however, including a 500-m buffer around important habitat captured 98% of independent nest locations within the novel area. We also used leks and associated peak male counts as a proxy for nesting habitat outside of the study sites used to develop the models. A 1.5-km buffer around the important nesting habitat boundaries included 77% of males counted at leks in Wyoming outside of the study sites. Data were not available to quantitatively test the performance of the summer and winter models outside our study sites. The collection of models presented here represents large-scale resource-management planning tools that are a significant advancement to previous tools in terms of spatial and temporal resolution.

Wyoming↗

USGS2019

Effect of permafrost thaw on plant and soil fungal community in the boreal forest: Does fungal community change mediate plant productivity response?

Permafrost thaw is leading to rapid shifts in boreal ecosystem function. Permafrost thaw affects soil carbon turnover through changes in soil hydrology, however, the biotic mechanisms regulating plant community response remain elusive. Here, we measured the response of fungal community composition and soil nutrient content in an intact permafrost plateau forest soil and an adjacent thermokarst bog using barcoded amplicon targeting ITS2 and 28S rRNA genes. Next, we used the soils from the permafrost plateau and the thermokarst bog as soil inoculum in a greenhouse experiment to measure whether shifts in fungal community and soil water level regulate plant productivity. Overall, we found that fungal community composition differed significantly between the thawed and intact permafrost sites, but soil nutrient content did not. Relative abundance of mycorrhizal fungal taxa decreased while relative abundance of putative fungal pathogens increased with permafrost thaw. In the greenhouse, we found that ecto- and arbuscular associated host plants had higher productivity in permafrost-intact soils relative to thawed soils. However, productivity of non-mycorrhizal tussock grass was more affected by soil water levels than soil communities. Our results suggest that fungal communities are crucial in mediating plant response to permafrost thaws inducing hydrology changes.

Alaska↗

USGS2018

Amendments fail to hasten biocrust recovery or soil stability at a disturbed dryland sandy site

In most drylands, biological soil crusts (biocrusts), an assemblage of lichens, bryophytes, fungi, green algae, and cyanobacteria, are critical to healthy ecosystem function. However, they are extremely sensitive to disturbance and attempts to facilitate their recovery have had variable success. In this study, we applied soil amendments designed to improve soil surface stability and accelerate biocrust recovery on an area disturbed by oil/gas exploration vehicles. Treatments included: 1) Control (one time water only); 2) Biocrust‐only: biocrust inoculum + nutrients in water; 3) Polyacrylamide gels (PAM; which are known to stabilize soils) + biocrust inoculum + nutrients in water; 4) Gypsum + biocrust inoculum + nutrients in water; and 5) Saline (NaCl) solution + biocrust inoculum + nutrients in water. Only the NaCl treatment showed any effects on soil properties and these were only short‐term. These effects included an increase in soil strength and a reduction in soil aggregate stability, unsaturated hydraulic conductivity (K h ), and cyanobacterial biomass. The inoculated biocrust material failed to develop and even after 10 years, there was only a very low natural recolonization of the plots. These results show that inoculating soils or applying these levels of soil amendments does not guarantee recovery of soil stability or biocrust, and that some sites are unlikely to recover without assistance. Thus, there is a need for more research into ways to enhance soil stability and identify the factors limiting biocrust establishment.

Restoration Ecology↗

USGS2007

Habitat effects on condition of doe mule deer in arid mixed woodland-grassland

Productivity of mule deer (Odocoileus hemionus Raf.) populations is closely linked to individual nutritional condition. We modeled body fat of individual does as a function of vegetation cover, composition, and water characteristics of their annual, summer, and winter home ranges in north-central New Mexico. We also modeled home range size as a function of the same characteristics. Levels of body fat were most closely and negatively related to the amount of pinyon-juniper in an individual deer's annual home range (F1,21 = 7.6; P = 0.012; r2 = 0.26). Pinyon-juniper types provided little (combined ground cover of preferred forbs and shrubs = 5.7%) mule deer forage but were included in home ranges in excess of their availability on the landscape, likely because of security cover attributes. Proportion of grasslands in home ranges was most strongly related to both annual (F1,23 = 4.9; P = 0.037; r2 = 0.18) and summer (F2,25 = 5.7; P = 0.009; r2 = 0.31) home range sizes, and home ranges increased as the grassland component increased, indicating that this habitat type was providing little value to mule deer. Grassland (0.2% combined cover of preferred forb and shrub) and montane conifer (3.2% ground cover of preferred forb and shrub) habitat types similarly lacked preferred mule deer food, and grasslands also lacked cover. Most immediate gains in mule deer habitat in north-central New Mexico may be attained by management of pinyon-juniper communities to increase forage quantity and quality while maintaining cover attributes. Gains can also be realized in grasslands, but here management must establish both cover and forage.

Rangeland Ecology and Management↗

USGS2010

A global overview of drought and heat-induced tree mortality reveals emerging climate change risks for forests

Greenhouse gas emissions have significantly altered global climate, and will continue to do so in the future. Increases in the frequency, duration, and/or severity of drought and heat stress associated with climate change could fundamentally alter the composition, structure, and biogeography of forests in many regions. Of particular concern are potential increases in tree mortality associated with climate-induced physiological stress and interactions with other climate-mediated processes such as insect outbreaks and wildfire. Despite this risk, existing projections of tree mortality are based on models that lack functionally realistic mortality mechanisms, and there has been no attempt to track observations of climate-driven tree mortality globally. Here we present the first global assessment of recent tree mortality attributed to drought and heat stress. Although episodic mortality occurs in the absence of climate change, studies compiled here suggest that at least some of the world's forested ecosystems already may be responding to climate change and raise concern that forests may become increasingly vulnerable to higher background tree mortality rates and die-off in response to future warming and drought, even in environments that are not normally considered water-limited. This further suggests risks to ecosystem services, including the loss of sequestered forest carbon and associated atmospheric feedbacks. Our review also identifies key information gaps and scientific uncertainties that currently hinder our ability to predict tree mortality in response to climate change and emphasizes the need for a globally coordinated observation system. Overall, our review reveals the potential for amplified tree mortality due to drought and heat in forests worldwide.

Forest Ecology and Management↗

USGS2002

Environmental setting and water-quality issues of the Mobile River Basin, Alabama, Georgia, Mississippi, and Tennessee

The Mobile River Basin is one of over 50 river basins and aquifer systems being investigated as part of the U.S. Geological Survey National Water-Quality Assessment (NAWQA) Program. This basin is the sixth largest river basin in the United States, and fourth largest in terms of streamflow, encompassing parts of Alabama, Georgia, Mississippi, and Tennessee. Almost two-thirds of the 44,000-square-mile basin is located in Alabama. Extensive water resources of the Mobile River Basin are influenced by an array of natural and cultural factors. These factors impart unique and variable qualities to the streams, rivers, and aquifers providing abundant habitat to sustain the diverse aquatic life in the basin. Data from Federal, State, and local agencies provide a description of the environmental setting of the Mobile River Basin. Environmental data include natural factors such as physiography, geology, soils, climate, hydrology, ecoregions, and aquatic ecology, and human factors such as reservoirs, land use and population change, water use, and water-quality issues. Characterization of the environmental setting is useful for understanding the physical, chemical, and biological characteristics of surface and ground water in the Mobile River Basin and the possible implications of that environmental setting for water quality. The Mobile River Basin encompasses parts of five physiographic provinces. Fifty-six percent of the basin lies within the East Gulf section of the Coastal Plain Physiographic Province. The remaining northeastern part of the basin lies, from west to east, within the Cumberland Plateau section of the Appalachian Plateaus Physiographic Province, the Valley and Ridge Physiographic Province, the Piedmont Physiographic Province, and the Blue Ridge Physiographic Province. Based on the 1991 land-use data, about 70 percent of the basin is forested, while agriculture, including livestock (poultry, cattle, and swine), row crops (cotton, corn, soybeans, sorghum, and wheat), and pasture land accounts for about 26 percent of the study unit. Agricultural land use is concentrated along the Black Prairie Belt district of the Coastal Plain. Urban areas account for only 3 percent of the total land use; however, the areal extent of the metropolitan statistical areas (MSA) may indicate more urban influences. The MSAs include urban areas outside of the city boundaries and can include adjacent counties. Seven MSAs are delineated in the Mobile River Basin, including Montgomery, Mobile, Tuscaloosa, Birmingham, Gadsden, Anniston, and Atlanta. The total population for the Mobile River Basin was about 3,673,100 in 1990. State water-quality agencies have identified numerous causes and sources of water-body impairment in the Mobile River Basin. In 1996, organic enrichment, dissolved oxygen depletion, elevated nutrient concentrations, and siltation were the most frequently cited causes of impairment, affecting the greatest number of river miles. Bacteria, acidic pH, and elevated metal concentrations also were identified as causes of impairment. The sources for impairment varied among river basins, were largely a function of land use, and were attributed primarily to municipal and industrial sources, mining, and agricultural activities.

Water-Resources Investigations Report↗

USGS2017

Intraspecific functional diversity of common species enhances community stability

Common species are fundamental to the structure and function of their communities and may enhance community stability through intraspecific functional diversity (iFD). We measured among-habitat and within-habitat iFD (i.e., among- and within-plant community types) of two common small mammal species using stable isotopes and functional trait dendrograms, determined whether iFD was related to short-term population stability and small mammal community stability, and tested whether spatially explicit trait filters helped explain observed patterns of iFD. Southern red-backed voles ( Myodes gapperi ) had greater iFD than deer mice ( Peromyscus maniculatus ), both among habitats, and within the plant community in which they were most abundant (their “primary habitat”). Peromyscus maniculatus populations across habitats differed significantly between years and declined 78% in deciduous forests, their primary habitat, as did the overall deciduous forest small mammal community. Myodes gapperi populations were stable across habitats and within coniferous forest, their primary habitat, as was the coniferous forest small mammal community. Generalized linear models representing internal trait filters (e.g., competition), which increase within-habitat type iFD, best explained variation in M. gapperi diet, while models representing internal filters and external filters (e.g., climate), which suppress within-habitat iFD, best explained P. maniculatus diet. This supports the finding that M. gapperi had higher iFD than P. maniculatus and is consistent with the theory that internal trait filters are associated with higher iFD than external filters. Common species with high iFD can impart a stabilizing influence on their communities, information that can be important for conserving biodiversity under environmental change.

Ecology and Evolution↗

USGS2002

Effects of vegetation management in constructed wetland treatment cells on water quality and mosquito production

The impact of three vegetation management strategies on wetland treatment function and mosquito production was assessed in eight free water surface wetland test cells in southern California during 1998–1999. The effectiveness of the strategies to limit bulrush Schoenoplectus californicus culm density within the cells was also investigated. Removing accumulated emergent biomass and physically limiting the area in which vegetation could reestablish, significantly improved the ammonia–nitrogen removal efficiency of the wetland cells, which received an ammonia-dominated municipal wastewater effluent (average loading rate=9.88 kg/ha per day NH 4 -N). We determined that interspersing open water with emergent vegetation is critical for maintaining the wetland's treatment capability, particularly for systems high in NH 4 -N. Burning aboveground plant parts and thinning rhizomes only temporarily curtailed vegetation proliferation in shallow zones, whereas creating hummocks surrounded by deeper water successfully restricted the emergent vegetation to the shallower hummock areas. Since the hummock configuration kept open water areas interspersed throughout the stands of emergent vegetation, the strategy was also effective in reducing mosquito production. Decreasing vegetation biomass reduced mosquito refuge areas while increasing mosquito predator habitat. Therefore, the combined goals of water quality improvement and mosquito management were achieved by managing the spatial pattern of emergent vegetation to mimic an early successional growth stage, i.e. actively growing plants interspersed with open water.

California↗

USGS2016

Host contact and shedding patterns clarify variation in pathogen exposure and transmission in threatened tortoise Gopherus agassizii : implications for disease modelling and management

Summary Most directly transmitted infections require some form of close contact between infectious and susceptible hosts to spread. Often disease models assume contacts are equal and use mean field estimates of transmission probability for all interactions with infectious hosts. Such methods may inaccurately describe transmission when interactions differ substantially in their ability to cause infection. Understanding this variation in transmission risk may be critical to properly model and manage some infectious diseases. In this study, we investigate how varying exposure and transmission may be key to understanding disease dynamics in the threatened desert tortoise Gopherus agassizii . We created heterogeneity in Mycoplasma agassizii exposure (the putative bacterial agent of a respiratory disease) by varying the duration of interactions between naturally infected and uninfected captive desert tortoises. Using qPCR, we identified new infections and compared models of transmission probability as a function of contact duration and pathogen load. We then examined the contact patterns of a wild tortoise population using proximity loggers to identify heterogeneity in contact duration. The top-ranked model predicting M. agassizii transmission included a dose term defined as the product of the number of days in proximity to an infected host and the infection level of that host. Models predicted low transmission probability for short interactions, unless the infectious host had a high load of M. agassizii : such hosts were predicted to transmit infection at higher rates with any amount of contact. We observed predominantly short-lived interactions in a free-ranging tortoise population and thus, expect transmission patterns in this population to vary considerably with the frequency and duration of high infection levels. Mean field models may misrepresent natural transmission patterns in this and other populations depending on the distribution of high-risk contact and shedding events. Rapid outbreaks in generally solitary species may result from changes to their naturally low-risk contact patterns or due to increases in the frequency of severe infections or super-shedding events – population characteristics that should be further investigated to develop effective management strategies.

Nevada↗

USGS2014

Plant diversity predicts beta but not alpha diversity of soil microbes across grasslands worldwide

Aboveground–belowground interactions exert critical controls on the composition and function of terrestrial ecosystems, yet the fundamental relationships between plant diversity and soil microbial diversity remain elusive. Theory predicts predominantly positive associations but tests within single sites have shown variable relationships, and associations between plant and microbial diversity across broad spatial scales remain largely unexplored. We compared the diversity of plant, bacterial, archaeal and fungal communities in one hundred and forty-five 1 m 2 plots across 25 temperate grassland sites from four continents. Across sites, the plant alpha diversity patterns were poorly related to those observed for any soil microbial group. However, plant beta diversity (compositional dissimilarity between sites) was significantly correlated with the beta diversity of bacterial and fungal communities, even after controlling for environmental factors. Thus, across a global range of temperate grasslands, plant diversity can predict patterns in the composition of soil microbial communities, but not patterns in alpha diversity.

Ecology Letters↗

USGS2016

Seasonal sediment dynamics shape temperate bedrock reef communities

Mobilized seafloor sediment can impact benthic reef communities through burial, scour, and turbidity. These processes are ubiquitous in coastal oceans and, through their influence on the survival, fitness, and interactions of species, can alter the structure and function of benthic communities. In northern Monterey Bay, California, USA, as much as 30% of the seafloor is buried or exposed seasonally, making this an ideal location to test how subtidal temperate rocky reef communities vary in the presence and absence of chronic sediment-based disturbances. Designated dynamic plots were naturally inundated by sediment in summer (50 to 100% cover) and swept clean in winter, whereas designated stable plots remained free of sediment during our study. Multivariate analyses indicated significant differences in the structure of sessile and mobile communities between dynamic and stable reef habitats. For sessile species, community structure in disturbed plots was less variable in space and time than in stable plots due to the maintenance of an early successional state. In contrast, community structure of mobile species varied more in disturbed plots than in stable plots, reflecting how mobile species distribute in response to sediment dynamics. Some species were found only in these disturbed areas, suggesting that the spatial mosaic of disturbance could increase regional diversity. We discuss how the relative ability of species to tolerate disturbance at different life history stages and their ability to colonize habitat translate into community-level differences among habitats, and how this response varies between mobile and sessile communities.

California↗

USGS2025

Optimizing control of a freshwater invader in time and space

The global spread of invasive species in aquatic ecosystems has prompted population control efforts to mitigate negative impacts on native species and ecosystem functions. Removal programs that optimally allocate removal effort across space and time offer promise for improving invader suppression or eradication, especially given the limited resources available to these programs. However, science-based guidance to inform such programs remains limited. This study leverages two intensive fish removal programs for nonnative green sunfish (Lepomis cyanellus) in intermittent streams of the Bill Williams River basin in Arizona, USA, to explore alternative management strategies involving variable allocation of removal effort in time and space and compare static versus dynamic decision rules. We used Bayesian hierarchical modeling to estimate demographic parameters using existing removal data, with evidence that both removal programs led to at least a 0.39 probability of eradication. Simulated alternative management strategies revealed that population suppression, but not eradication, could be achieved with reduced effort, and that dynamic management practices that respond to species abundance in real time can improve the efficiency of removal efforts. High removal frequency and program duration, including continued monitoring after zero fish were captured, contributed to successful population control. With management efforts struggling to keep pace with the rising spread and impacts of invasive species, this research demonstrates the utility of quantitative removal models to help improve invasive removal programs and robustly evaluate the success of population suppression and eradication.

Arizona↗

USGS2017

An integrated population model for bird monitoring in North America

Integrated population models (IPMs) provide a unified framework for simultaneously analyzing data sets of different types to estimate vital rates, population size, and dynamics; assess contributions of demographic parameters to population changes; and assess population viability. Strengths of an IPM include the ability to estimate latent parameters and improve the precision of parameter estimates. We present a hierarchical IPM that combines two broad‐scale avian monitoring data sets: count data from the North American Breeding Bird Survey (BBS) and capture–recapture data from the Monitoring Avian Productivity and Survivorship (MAPS) program. These data sets are characterized by large numbers of sample sites and observers, factors capable of inducing error in the sampling and observation processes. The IPM integrates the data sets by modeling the population abundance as a first‐order autoregressive function of the previous year's population abundance and vital rates. BBS counts were modeled as a log‐linear function of the annual index of population abundance, observation effects (observer identity and first survey year), and overdispersion. Vital rates modeled included adult apparent survival, estimated from a transient Cormack‐Jolly‐Seber model using MAPS data, and recruitment (surviving hatched birds from the previous season + dispersing adults) estimated as a latent parameter. An assessment of the IPM demonstrated it could recover true parameter values from 200 simulated data sets. The IPM was applied to data sets (1992–2008) of two bird species, Gray Catbird ( Dumetella carolinensis ) and Wood Thrush ( Hylocichla mustelina ) in the New England/Mid‐Atlantic coastal Bird Conservation Region of the United States. The Gray Catbird population was relatively stable (trend +0.4% per yr), while the Wood Thrush population nearly halved (trend −4.5% per yr) over the 17‐yr study period. IPM estimates of population growth rates, adult survival, and detection and residency probabilities were similar and as precise as estimates from the stand‐alone BBS and CJS models. A benefit of using the IPM was its ability to estimate the latent recruitment parameter. Annual growth rates for both species correlated more with recruitment than survival, and the relationship for Wood Thrush was stronger than for Gray Catbird. The IPM's unified modeling framework facilitates integration of these important data sets.

Ecological Applications↗

USGS2024

The cost of self-defense: Browsing effects in the rare plant species Salix arizonica

Coevolution between plants and their animal predators has led to diverse defensive adaptations. Multiple theories of defense propose that there are resource allocation costs associated with producing chemical defenses. One leading hypothesis, optimal defense theory (ODT), suggests that natural selection will result in the allocation of resources to defenses that optimize the cost-to-benefit ratio between defense and other functional processes. The population decline of the rare subalpine wetland species, Arizona willow ( Salix arizonica ), has been attributed to various biotic and abiotic factors, with browsing from wild and domestic ungulates as a significant concern for at least three decades. In a field experiment using natural populations, we compare the relationship between phytochemical defense and height in Arizona willows with and without long-term protection from browsing via browse exclosures. Consistent with the predictions of ODT, individuals with physical protection from ungulate browsing for multiple years had significantly lower phenolic glycoside (PG) concentrations and increased plant height compared to unprotected individuals. A similar pattern was found across all individuals, whereby total PG concentration and height were negatively correlated. In a short-term experiment in natural populations, changes in levels of defense were not observed when plants received protection for only one growing season. The contrasting pattern of defense plasticity in response to long-term versus short-term physical protection suggests a differential plastic response in this long-lived species. Delayed reduction in PG concentration may serve as a benefit to avoid mismatches between environmental cues and responses. Our research sheds light on the intricate dynamics between plant-defense strategies, environmental pressures, and evolutionary adaptations in shaping plant–browser interactions.

Arizona, Colorado, New Mexico, Utah↗

USGS2013

Integrating resource selection information with spatial capture--recapture

1. Understanding space usage and resource selection is a primary focus of many studies of animal populations. Usually, such studies are based on location data obtained from telemetry, and resource selection functions (RSFs) are used for inference. Another important focus of wildlife research is estimation and modeling population size and density. Recently developed spatial capture–recapture (SCR) models accomplish this objective using individual encounter history data with auxiliary spatial information on location of capture. SCR models include encounter probability functions that are intuitively related to RSFs, but to date, no one has extended SCR models to allow for explicit inference about space usage and resource selection. 2. In this paper we develop the first statistical framework for jointly modeling space usage, resource selection, and population density by integrating SCR data, such as from camera traps, mist-nets, or conventional catch traps, with resource selection data from telemetered individuals. We provide a framework for estimation based on marginal likelihood, wherein we estimate simultaneously the parameters of the SCR and RSF models. 3. Our method leads to increases in precision for estimating parameters of ordinary SCR models. Importantly, we also find that SCR models alone can estimate parameters of RSFs and, as such, SCR methods can be used as the sole source for studying space-usage; however, precision will be higher when telemetry data are available. 4. Finally, we find that SCR models using standard symmetric and stationary encounter probability models may not fully explain variation in encounter probability due to space usage, and therefore produce biased estimates of density when animal space usage is related to resource selection. Consequently, it is important that space usage be taken into consideration, if possible, in studies focused on estimating density using capture–recapture methods.

Methods in Ecology and Evolution↗

USGS2009

Species richness and occupancy estimation in communities subject to temporary emigration

Species richness is the most common biodiversity metric, although typically some species remain unobserved. Therefore, estimates of species richness and related quantities should account for imperfect detectability. Community dynamics can often be represented as superposition of species-specific phenologies (e. g., in taxa with well-defined flight [insects], activity [rodents], or vegetation periods [plants]). We develop a model for such predictably open communities wherein species richness is expressed as the sum over observed and unobserved species of estimated species-specific and site-specific occurrence indicators and where seasonal occurrence is modeled as a species-specific function of time. Our model is a multispecies extension of a multistate model with one unobservable state and represents a parsimonious way of dealing with a widespread form of 'temporary emigration.'' For illustration we use Swiss butterfly monitoring data collected under a robust design (RD); species were recorded on 13 transects during two secondary periods within <= 7 primary sampling periods. We compare estimates with those under a variation of the model applied to standard data, where secondary samples are pooled. The latter model yielded unrealistically high estimates of total community size of 274 species. In contrast, estimates were similar under models applied to RD data with constant (122) or seasonally varying (126) detectability for each species, but the former was more parsimonious and therefore used for inference. Per transect, 6 44 (mean 21.1) species were detected. Species richness estimates averaged 29.3; therefore only 71% (range 32-92%) of all species present were ever detected. In any primary period, 0.4-5.6 species present were overlooked. Detectability varied by species and averaged 0.88 per primary sampling period. Our modeling framework is extremely flexible; extensions such as covariates for the occurrence or detectability of individual species are easy. It should be useful for communities with a predictable form of temporary emigration where rigorous estimation of community metrics has proved challenging so far.

Ecology↗

USGS1999

Dietary assimilation of cadmium associated with bacterial exopolymer sediment coatings by the estuarine amphipod Leptocheirus plumulosus: Effects of Cd concentration and salinity

Bacterial extracellular substances (also known as exopolysaccharides, or EPS) may serve as vectors for trophic transfer of metals in benthic systems because these ubiquitous sediment coatings can sorb high concentrations of toxic metals, and because many benthic invertebrates assimilate EPS sediment coatings upon ingestion. We conducted 3 sets of experiments to determine the assimilative bioavailability of EPS-associated Cd to the benthic amphipod Leptocheirus plumulosus as a function of Cd concentration and salinity. Bioavailability was measured as L. plumulosus Cd assimilation efficiency (AE) from EPS-coated silica (EPS-Si) and from uncoated silica (NC-Si) using modified pulse-chase methods with the gamma-emitting radioisotope 109 Cd. Cd AE was significantly greater from NC-Si than from EPS-Si at 7.5‰, but not at 2.5 or 25‰. Overall, Cd AE from EPS-Si was between 15.1 and 21.5%. Because EPS-Si sorbed more Cd than NC-Si, EPS coatings magnified the amount of Cd amphipods accumulated at each salinity by up to a factor of 10. Salinity did not directly affect Cd AE from EPS-Si, but because Cd-EPS partitioning increased with decreasing salinity, amphipods accumulated more Cd from EPS at the lowest Cd-EPS incubation salinity (2.5‰) than at higher salinities (7.5 and 25‰). Finally, Cd concentration in EPS exhibited an inverse relationship with Cd AE at 2.5‰, but not at 25‰. Specifically, Cd AE was 12 times greater at 1 compared with 10 µg Cd µg -1 EPS. Together, these results show that estuarine benthos can accumulate Cd from EPS sediment coatings, but that the degree to which this phenomenon occurs is dependent upon seawater salinity and Cd concentration in EPS.

Marine Ecology Progress Series↗

USGS2016

Functional role of bacteria from invasive Phragmites australis in promotion of host growth

We hypothesize that bacterial endophytes may enhance the competitiveness and invasiveness of Phragmites australis. To evaluate this hypothesis, endophytic bacteria were isolated from P. australis. The majority of the shoot meristem isolates represent species from phyla Firmicutes, Proteobacteria, and Actinobacteria. We chose one species from each phylum to characterize further and to conduct growth promotion experiments in Phragmites. Bacteria tested include Bacillus amyloliquefaciens A9a, Achromobacter spanius B1, and Microbacterium oxydans B2. Isolates were characterized for known growth promotional traits, including indole acetic acid (IAA) production, secretion of hydrolytic enzymes, phosphate solubilization, and antibiosis activity. Potentially defensive antimicrobial lipopeptides were assayed for through application of co-culturing experiments and mass spectrometer analysis. B. amyloliquefaciens A9a and M. oxydans B2 produced IAA. B. amyloliquefaciens A9a secreted antifungal lipopeptides. Capability to promote growth of P. australis under low nitrogen conditions was evaluated in greenhouse experiments. All three isolates were found to increase the growth of P. australis under low soil nitrogen conditions and showed increased absorption of isotopic nitrogen into plants. This suggests that the Phragmites microbes we evaluated most likely promote growth of Phragmites by enhanced scavenging of nitrogenous compounds from the rhizosphere and transfer to host roots. Collectively, our results support the hypothesis that endophytic bacteria play a role in enhancing growth of P. australis in natural populations. Gaining a better understanding of the precise contributions and mechanisms of endophytes in enabling P. australis to develop high densities rapidly could lead to new symbiosis-based strategies for management and control of the host.

New Jersey↗