Melding wildlife surveys to improve conservation inference.

Integrated models are a popular tool for analyzing species of conservation concern. Species of conservation concern are often monitored by multiple entities that generate several datasets. Individually, these datasets may be insufficient for guiding management due to low spatio-temporal resolution, biased sampling, or large observational uncertainty. Integrated models provide an approach for assimilating multiple datasets in a coherent framework that can compensate for these deficiencies. While conventional integrated models have been used to assimilate count data with surveys of survival, fecundity, and harvest, they can also assimilate ecological surveys that have differing spatio-temporal regions and observational uncertainties. Motivated by independent aerial and ground surveys of lesser prairie-chicken, we developed an integrated modeling approach that assimilates density estimates derived from surveys with distinct sources of observational error into a joint framework that provides shared inference on spatio-temporal trends. We model these data using a Bayesian Markov melding approach and apply several data augmentation strategies for efficient sampling. In a simulation study, we show that our integrated model improved predictive performance relative to models for analyzing the surveys independently. We use the integrated model to facilitate prediction of lesser prairie-chicken density at unsampled regions and perform a sensitivity analysis to quantify the inferential cost associated with reduced survey effort.

Demographic effects of a megafire on a declining prairie grouse in the mixed-grass prairie.

Recent studies have documented benefits of small, prescribed fire and wildfire for grassland-dependent wildlife, such as lesser prairie-chickens (Tympanuchus pallidicintus), but wildlife demographic response to the scale and intensity of megafire (wildfire >40,000 ha) in modern, fragmented grasslands remains unknown. Limited available grassland habitat makes it imperative to understand if increasing frequency of megafires could further reduce already declining lesser prairie-chicken populations, or if historical evolutionary interactions with fire make lesser prairie-chickens resilient. To evaluate lesser prairie-chicken demographic response to megafires, we compared lek counts, nest density, and survival rates of adults, nests, and chicks before (2014-2016) and after (2018-2020) a 2017 megafire in the mixed-grass prairie of Kansas, USA (Starbuck fire ~254,000 ha). There was a 67% decline in attending males on leks post-fire and a 57% decline in occupied leks post-fire. Despite population declines as indicated by lek counts, adult female breeding season survival ( S ^ ) was similar pre- ( S ^  = 0.65 ± 0.08 [SE]) and post-fire (0.61 ± 0.08), as was chick survival (pre-fire: 0.23 ± 0.07; post-fire: 0.27 ± 0.11). Nest survival appeared lower post-fire (pre-fire: 0.38 ± 0.06; post-fire: 0.20 ± 0.06), but did not differ at the 95% confidence interval. Nest density of marked females declined 73% in areas burned by megafire. Although lesser prairie-chickens persisted in the study area and we documented minimal effects on most demographic rates, reduced lesser prairie-chicken abundance and reproductive output suggests full recovery may take >3 years. Increased propensity for megafire resulting from suppression of smaller fires, compounded by climate change and woody encroachment, may impose a short-term (3-5 year) threat to already declining lesser prairie-chicken populations.

Acute and lagged fitness consequences for a sagebrush obligate in a post mega-wildfire landscape.

Species responses to disturbance influence their extinction risks. Greater sage-grouse (Centrocercus urophasianus) are bioindicators of sagebrush ecosystem health and the loss of sagebrush (Artemisia spp.) due to wildfire, can cause long-term declines in sage-grouse populations and other sagebrush obligate species. We examined the demographic response of a greater sage-grouse population following a mega-wildfire using stochastic age-structured female-based matrix models over 6 years (2013-2018). Notably, chick survival (range = 0.18-0.38) and female survival (yearling range: 0.20-0.68; adult range: 0.27-0.75) were low compared to values reported for greater sage-grouse in other parts of their distribution. Greater sage-grouse displayed variation in demographic tactics after the fire; however, adult female survival explained most of the variation in λ during each year, which reflected a declining population in 3 of 6 years with more uncertainty observed in 2015 when populations may have been increasing, and 2017 and 2018, when populations may have been declining. The continued annual population decline observed since 2016 suggested there were additional strong environmental impacts that may have been compounded by the fire effects, prolonging recovery of greater sage-grouse. Our results support others that reported negative effects to greater sage-grouse demographics from broad-scale fire and provide a baseline for understanding how this species responds to loss of sagebrush cover based on their life history strategy.

Scaling up private land conservation to meet recovery goals for grassland birds.

Long-term population declines have elevated recovery of grassland avifauna to among the highest conservation priorities in North America. Because most of the Great Plains is privately owned, recovery of grassland bird populations depends on voluntary conservation with strong partnerships between private landowners and resource professionals. Despite large areas enrolled in voluntary practices through U.S. Department of Agriculture's Lesser Prairie-chicken (Tympanuchus pallidicinctus) Initiative (LPCI), the effectiveness of Farm Bill investments for meeting wildlife conservation goals remains an open question. Our objectives were to evaluate extents to which Conservation Reserve Program (CRP) and LPCI-grazing practices influence population densities of grassland birds; estimate relative contributions of practices to regional bird populations; and evaluate percentages of populations conserved relative to vulnerability of species. We designed a large-scale impact-reference study and used the Integrated Monitoring in Bird Conservation Regions program to evaluate bird population targets of the Playa Lakes Joint Venture. We used point transect distance sampling to estimate density and population size for 35 species of grassland birds on private lands enrolled in native or introduced CRP plantings and LPCI-prescribed grazing. Treatment effects indicated CRP plantings increased densities of three grassland obligates vulnerable to habitat loss, and LPCI grazing increased densities of four species requiring heterogeneity in dense, tall-grass structure (α = 0.1). Population estimates in 2016 indicated the practices conserved breeding habitat for 4.5 million birds (90% CI: 4.0-5.1), and increased population sizes of 16 species , totaling 1.8 million birds (CI: 1.4-2.4). Conservation practices on private land benefited the most vulnerable grassland obligate species (AICc weight = 0.53). By addressing habitat loss and degradation in agricultural landscapes, conservation on private land provides a solution to declining avifauna of North America and scales up to meet population recovery goals for the most imperiled grassland birds.

Ampliación de la Conservación en Terrenos Privados para Cumplir los Objetivos de Recuperación para Aves de Pastizales Resumen La declinación a largo plazo de las poblaciones ha posicionado a la recuperación de la avifauna de los pastizales entre las prioridades de conservación más importantes en América del Norte. Debido a que la mayor parte de las Grandes Planicies es propiedad privada, la recuperación de las poblaciones de aves de los pastizales depende de la conservación voluntaria sumada a la colaboración entre los terratenientes privados y los profesionales de la gestión de recursos. A pesar de que varias áreas se encuentran inscritas en prácticas voluntarias por medio de la Iniciativa de la Gallina de Pradera Menor (Tympanuchus pallidicinctus) (IGPM), la efectividad de la inversión del Proyecto de Ley de Granjas para cumplir con los objetivos de conservación de fauna todavía permanece como una pregunta abierta. Nuestros objetivos se enfocaron en evaluar hasta qué punto el Programa de Reservas de Conservación (PRC) y las prácticas de forrajeo de la IGPM influyen sobre la densidad poblacional de las aves de los pastizales; estimar las contribuciones relativas de las prácticas para las poblaciones de aves regionales; y evaluar el porcentaje de poblaciones conservadas en relación con la vulnerabilidad de la especie. Diseñamos un estudio a gran escala con referencia de impactos y usamos el programa de Monitoreo Integrado en las Regiones de Conservación de Aves para evaluar los objetivos poblacionales de las aves del Proyecto Conjunto de Playa Lakes. Usamos un muestreo de distancia por puntos en transecto para estimar la densidad y el tamaño poblacional de 35 especies de aves de pastizales en los terrenos privados inscritos en plantaciones nativas o introducidas del PRC y en las zonas de forrajeo prescritas por la IGPM. Los efectos del tratamiento indicaron que las plantaciones del PRC incrementaron la densidad de tres especies estrictas de pastizales vulnerables a la pérdida del hábitat, mientras que el forrajeo de la LPCI incrementó la densidad de cuatro especies que requieren heterogeneidad en la estructura de pastos altos y gruesos (α = 0.1). Las estimaciones poblacionales indicaron que las prácticas conservaron el hábitat de reproducción para 4.5 millones de aves (90% IC 4.0 - 5.1) e incrementaron el tamaño poblacional de 16 especies, para un total de 1.8 millones de aves (IC 1.4 - 2.4). Las prácticas de conservación en terrenos privados beneficiaron a las especies estrictas de pastizales más vulnerables (peso AICc = 0.53). Al abordar la pérdida y degradación del hábitat en los paisajes agrícolas, la conservación en terrenos privados proporciona una solución para la avifauna en declinación de América del Norte y se amplía para cumplir con los objetivos de recuperación establecidos para las aves de pastizales que se encuentran en mayor peligro.

Role of the thermal environment in scaled quail (Callipepla squamata) nest site selection and survival.

Temperature is increasingly recognized as an important component of wildlife habitat. Temperature is particularly important for avian nest sites, where extreme temperatures can influence adult behavior, embryonic development, and survival. For species inhabiting arid and semiarid climates, such as the scaled quail (Callipepla squamata), frequent exposure to extreme temperatures may increase the importance of the nest microclimate. Limited data suggest that scaled quail respond to temperature when selecting nest sites, and they are also known to respond to the presence of surface water and shrub cover on the landscape, two resources which may mitigate thermal stress. To better understand the role of temperature in nest site selection and survival, and to evaluate how other landscape resources may benefit nesting quail, we investigated nest site characteristics of scaled quail in southeastern New Mexico, USA. During the breeding seasons of 2018 and 2019 we located nests, monitored nest fate, and recorded thermal and vegetation characteristics at three spatial scales: the nest bowl, the nest microsite (area within 10 m of the nest bowl), and the landscape. We found that nest bowls moderated temperature relative to both the surrounding microsite and the broader landscape, remaining almost 5 °C cooler on average than the surrounding microsite at mid-day. Nest bowls also had taller, greater cover of vegetation compared to both the surrounding microsites and the landscape. Despite apparent selection for cooler temperatures and taller vegetation, these characteristics demonstrated a weak relationship with nest survival. Rather, nest survival was positively influenced by proximity to surface water and honey mesquite (Prosopis glandulosa), with survival decreasing with increasing distance from these features. Although the mechanism for this relationship is unclear, our results support the importance of temperature for nest site selection of ground-nesting birds in semiarid landscapes, and suggest further exploration of landscape-level sources of thermal mitigation.

The 5,6,7,8-Tetrahydro-2-Naphthoyl-Coenzyme A Reductase Reaction in the Anaerobic Degradation of Naphthalene and Identification of Downstream Metabolites.

Anaerobic degradation of polycyclic aromatic hydrocarbons has been investigated mostly with naphthalene as a model compound. Naphthalene degradation by sulfate-reducing bacteria proceeds via carboxylation to 2-naphthoic acid, formation of a coenzyme A thioester, and subsequent reduction to 5,6,7,8-tetrahydro-2-naphthoyl-coenzyme A (THNCoA), which is further reduced to hexahydro-2-naphthoyl-CoA (HHNCoA) by tetrahydronaphthoyl-CoA reductase (THNCoA reductase), an enzyme similar to class I benzoyl-CoA reductases. When analyzing THNCoA reductase assays with crude cell extracts and NADH as electron donor via liquid chromatography-mass spectrometry (LC-MS), scanning for putative metabolites, we found that small amounts of the product of an HHNCoA hydratase were formed in the assays, but the downstream conversion by an NAD+-dependent ß-hydroxyacyl-CoA dehydrogenase was prevented by the excess of NADH in those assays. Experiments with alternative electron donors indicated that 2-oxoglutarate can serve as an indirect electron donor for the THNCoA-reducing system via a 2-oxoglutarate:ferredoxin oxidoreductase. With 2-oxoglutarate as electron donor, THNCoA was completely converted and further metabolites resulting from subsequent ß-oxidation-like reactions and hydrolytic ring cleavage were detected. These metabolites indicate a downstream pathway with water addition to HHNCoA and ring fission via a hydrolase acting on a ß'-hydroxy-ß-oxo-decahydro-2-naphthoyl-CoA intermediate. Formation of the downstream intermediate cis-2-carboxycyclohexylacetyl-CoA, which is the substrate for the previously described lower degradation pathway leading to the central metabolism, completes the anaerobic degradation pathway of naphthalene.IMPORTANCE Anaerobic degradation of polycyclic aromatic hydrocarbons is poorly investigated despite its significance in anoxic sediments. Using alternative electron donors for the 5,6,7,8-tetrahydro-2-naphthoyl-CoA reductase reaction, we observed intermediary metabolites of anaerobic naphthalene degradation via in vitro enzyme assays with cell extracts of anaerobic naphthalene degraders. The identified metabolites provide evidence that ring reduction terminates at the stage of hexahydro-2-naphthoyl-CoA and a sequence of ß-oxidation-like degradation reactions starts with a hydratase acting on this intermediate. The final product of this reaction sequence was identified as cis-2-carboxycyclohexylacetyl-CoA, a compound for which a further downstream degradation pathway has recently been published (P. Weyrauch, A. V. Zaytsev, S. Stephan, L. Kocks, et al., Environ Microbiol 19:2819-2830, 2017, https://doi.org/10.1111/1462-2920.13806). Our study reveals the first ring-cleaving reaction in the anaerobic naphthalene degradation pathway. It closes the gap between the reduction of the first ring of 2-naphthoyl-CoA by 2-napthoyl-CoA reductase and the lower degradation pathway starting from cis-2-carboxycyclohexylacetyl-CoA, where the second ring cleavage takes place.

The effects of fire on the thermal environment of sagebrush communities.

Thermal heterogeneity provides options for organisms during extreme temperatures that can contribute to their fitness. Sagebrush (Artemisia spp.) communities exhibit vegetation heterogeneity that creates thermal variation at fine spatial scales. However, fire can change vegetation and thereby variation within the thermal environment of sagebrush communities. To describe spatial and temporal thermal variation of sagebrush communities following wildfire, we measured black bulb temperature (Tbb) at 144 random points dispersed within unburned and burned communities, for 24-h at each random point. We observed a wide thermal gradient in unburned (-7.3° to 63.3 °C) and burned (-4.6° to 64.8 °C) sagebrush communities. Moreover, unburned and burned sagebrush communities displayed high thermal heterogeneity relative to ambient temperature (Tair). Notably, Tbb varied by 47 °C in both unburned and burned communities when Tair was 20 °C. However, fire greatly reduced the buffering capacity and thermal refuge of Wyoming big sagebrush (A. tridentata wyomingensis) communities during low and high Tair. Furthermore, fire increased Tbb in Wyoming big sagebrush and mountain big sagebrush (A. t. vaseyana) during the mid-day hours. These results demonstrate how fire changes the thermal environment of big sagebrush communities and the importance of shrub structure which can provide thermal refuge for organisms in burned communities during extreme low and high Tair.

A multispecies approach to manage effects of land cover and weather on upland game birds.

Loss and degradation of grasslands in the Great Plains region have resulted in major declines in abundance of grassland bird species. To ensure future viability of grassland bird populations, it is crucial to evaluate specific effects of environmental factors among species to determine drivers of population decline and develop effective conservation strategies. We used threshold models to quantify the effects of land cover and weather changes in "lesser prairie-chicken" and "greater prairie-chicken" (Tympanuchus pallidicinctus and T. cupido, respectively), northern bobwhites (Colinus virginianus), and ring-necked pheasants (Phasianus colchicus). We demonstrated a novel approach for estimating landscape conditions needed to optimize abundance across multiple species at a variety of spatial scales. Abundance of all four species was highest following wet summers and dry winters. Prairie chicken and ring-necked pheasant abundance was highest following cool winters, while northern bobwhite abundance was highest following warm winters. Greater prairie chicken and northern bobwhite abundance was also highest following cooler summers. Optimal abundance of each species occurred in landscapes that represented a grassland and cropland mosaic, though prairie chicken abundance was optimized in landscapes with more grassland and less edge habitat than northern bobwhites and ring-necked pheasants. Because these effects differed among species, managing for an optimal landscape for multiple species may not be the optimal scenario for any one species.

Saccharibacteria as Organic Carbon Sinks in Hydrocarbon-Fueled Communities.

Organisms of the candidate phylum Saccharibacteria have frequently been detected as active members of hydrocarbon degrading communities, yet their actual role in hydrocarbon degradation remained unclear. Here, we analyzed three enrichment cultures of hydrocarbon-amended groundwater samples using genome-resolved metagenomics to unravel the metabolic potential of indigenous Saccharibacteria. Community profiling based on ribosomal proteins revealed high variation in the enrichment cultures suggesting little reproducibility although identical cultivation conditions were applied. Only 17.5 and 12.5% of the community members were shared between the three enrichment cultures based on ribosomal protein clustering and read mapping of reconstructed genomes, respectively. In one enrichment, two Saccharibacteria strains dominated the community with 16.6% in relative abundance and we were able to recover near-complete genomes for each of them. A detailed analysis of their limited metabolism revealed the capacity for peptide degradation, lactate fermentation from various hexoses, and suggests a scavenging lifestyle with external retrieval of molecular building blocks. In contrast to previous studies suggesting that Saccharibacteria are directly involved in hydrocarbon degradation, our analyses provide evidence that these organisms can be highly abundant scavengers acting rather as organic carbon sinks than hydrocarbon degraders in these communities.

Interactive effects of severe drought and grazing on the life history cycle of a bioindicator species.

We used the lesser prairie-chicken (Tympanuchus pallidicinctus), an iconic grouse species that exhibits a boom-bust life history strategy, on the Southern High Plains, USA, as a bioindicator of main and interactive effects of severe drought and grazing. This region experienced the worst drought on record in 2011. We surveyed lesser prairie-chicken leks (i.e., communal breeding grounds) across 12 years that represented 7 years before the 2011 drought (predrought) and 4 years during and following the 2011 drought (postdrought). Grazing was annually managed with the objective of achieving ≤50% utilization of aboveground vegetation biomass. We used lek (n = 49) count data and covariates of weather and managed grazing to: (a) estimate long-term lesser prairie-chicken abundance and compare abundance predrought and postdrought; (b) examine the influence of annual and seasonal drought (modified Palmer drought index), temperature, and precipitation on long-term lesser prairie-chicken survival and recruitment; and (c) assess and compare the influence of grazing on lesser prairie-chicken population predrought and postdrought. Lesser prairie-chicken abundance was nearly seven times greater predrought than postdrought, and population declines were attributed to decreased survival and recruitment. The number of days with temperature >90th percentile had the greatest effect, particularly on recruitment. The population exhibited a substantial bust during 2011 and 2012 without a boom to recover in four postdrought years. Adaptive grazing positively influenced the population predrought, but had no effects postdrought. Results suggest that the severe drought in 2011 may have been beyond the range of environmental conditions to which lesser prairie-chickens, and likely other species, have adapted. Land management practices, such as grazing, should remain adaptive to ensure potential negative influences to all species are avoided. Increasing habitat quantity and quality by reducing habitat loss and fragmentation likely will increase resiliency of the ecosystem and individual species.

Better living through conifer removal: A demographic analysis of sage-grouse vital rates.

Sagebrush (Artemisia spp.) obligate wildlife species such as the imperiled greater sage-grouse (Centrocercus urophasianus) face numerous threats including altered ecosystem processes that have led to conifer expansion into shrub-steppe. Conifer removal is accelerating despite a lack of empirical evidence on grouse population response. Using a before-after-control-impact design at the landscape scale, we evaluated effects of conifer removal on two important demographic parameters, annual survival of females and nest survival, by monitoring 219 female sage-grouse and 225 nests in the northern Great Basin from 2010 to 2014. Estimates from the best treatment models showed positive trends in the treatment area relative to the control area resulting in an increase of 6.6% annual female survival and 18.8% nest survival relative to the control area by 2014. Using stochastic simulations of our estimates and published demographics, we estimated a 25% increase in the population growth rate in the treatment area relative to the control area. This is the first study to link sage-grouse demographics with conifer removal and supports recommendations to actively manage conifer expansion for sage-grouse conservation. Sage-grouse have become a primary catalyst for conservation funding to address conifer expansion in the West, and these findings have important implications for other ecosystem services being generated on the wings of species conservation.

Wildfire, climate, and invasive grass interactions negatively impact an indicator species by reshaping sagebrush ecosystems.

Iconic sagebrush ecosystems of the American West are threatened by larger and more frequent wildfires that can kill sagebrush and facilitate invasion by annual grasses, creating a cycle that alters sagebrush ecosystem recovery post disturbance. Thwarting this accelerated grass-fire cycle is at the forefront of current national conservation efforts, yet its impacts on wildlife populations inhabiting these ecosystems have not been quantified rigorously. Within a Bayesian framework, we modeled 30 y of wildfire and climatic effects on population rates of change of a sagebrush-obligate species, the greater sage-grouse, across the Great Basin of western North America. Importantly, our modeling also accounted for variation in sagebrush recovery time post fire as determined by underlying soil properties that influence ecosystem resilience to disturbance and resistance to invasion. Our results demonstrate that the cumulative loss of sagebrush to direct and indirect effects of wildfire has contributed strongly to declining sage-grouse populations over the past 30 y at large spatial scales. Moreover, long-lasting effects from wildfire nullified pulses of sage-grouse population growth that typically follow years of higher precipitation. If wildfire trends continue unabated, model projections indicate sage-grouse populations will be reduced to 43% of their current numbers over the next three decades. Our results provide a timely example of how altered fire regimes are disrupting recovery of sagebrush ecosystems and leading to substantial declines of a widespread indicator species. Accordingly, we present scenario-based stochastic projections to inform conservation actions that may help offset the adverse effects of wildfire on sage-grouse and other wildlife populations.

An observation of Clostridium perfringens in Greater Sage-Grouse.

Mortality due to infectious diseases is seldom reported in the Greater Sage-Grouse (Centrocercus urophasianus). A case of necrotic enteritis associated with Clostridium perfringens type A is described in a free-ranging adult male sage-grouse in eastern Oregon. Clostridial enteritis is known to cause outbreaks of mortality in various domestic and wild birds, and should be considered as a potential cause of mortality in sage-grouse populations.

Guidelines for managing lesser prairie-chicken populations and their habitats.

Lesser prairie-chicken (Tympanuchus pallidicinctus) populations have declined by >90% since the 1800s. These declines have concerned both biologists and private conservation groups and led to a petition to list the lesser prairie-chicken as threatened under the Endangered Species Act. Most of the land in the current range of the lesser prairie-chicken is privately owned, and declines have been primarily attributed to anthropogenic factors. Conversion of native rangeland to cropland and excessive grazing have been implicated as leading causes in the species' decline. Periodic drought probably has exacerbated these problems. Little research on habitat requirements was conducted prior to 1970. Despite recent advances in the knowledge of lesser prairie-chicken ecology, no comprehensive guidelines for management of the species have been published. In these guidelines, we provide a synopsis of our current knowledge of lesser prairie-chicken habitat requirements and suggest management strategies to monitor, maintain, and enhance lesser prairie-chicken populations.

Prevalence of mycoplasma antibodies in lesser prairie-chicken sera.

Serologic testing by the serum plate agglutination (SPA) procedure was performed to detect the presence of cross-reacting antibodies to Mycoplasma meleagridis, Mycoplasma synoviae, and Mycoplasma gallisepticum in lesser prairie-chickens (Tympanuchus pallidicinctus) trapped over a 2-yr period in Finney and Kearny counties of southwestern Kansas. Sera examined from birds (n = 50) obtained in March-April 2000 tested positive for M meleagridis, M. synoviae, and M. gallisepticum at levels of 6%, 10%, and 10%, respectively, for the population examined. Mycoplasma meleagridis antibodies were detected in 3 samples (2.7%), M. synoviae antibodies in 2 samples (1.7%), and M. gallisepticum antibodies in 3 samples (2.7%) from birds (n = 112) collected in March-April 2001. Data obtained by SPA can result in false positives and should be verified by additional procedures such as the hemagglutination-inhibition test. Low amounts of sera prohibited this additional testing. Thus, the positive SPA results should be considered presumptive for the presence of Mycoplasma antibodies. Although Mycoplasma antibodies have been detected in wild turkeys (Meleagris gallopavo) from Kingman and Butler counties in Kansas, this report is the first of possible mycoplasmosis in Finney and Kearny counties, Kansas. All birds testing positive by this procedure should be considered as potential carriers of Mycoplasma and should not be used in relocation efforts.