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At least 415 records · Page 23Linked to original sources
USGS2008

Soil texture drives responses of soil respiration to precipitation pulses in the sonoran desert: Implications for climate change

Climate change predictions for the desert southwestern U.S. are for shifts in precipitation patterns. The impacts of climate change may be significant, because desert soil processes are strongly controlled by precipitation inputs ('pulses') via their effect on soil water availability. This study examined the response of soil respiration-an important biological process that affects soil carbon (C) storage-to variation in pulses representative of climate change scenarios for the Sonoran Desert. Because deserts are mosaics of different plant cover types and soil textures-which create patchiness in soil respiration-we examined how these landscape characteristics interact to affect the response of soil respiration to pulses. Pulses were applied to experimental plots of bare and vegetated soil on contrasting soil textures typical of Sonoran Desert grasslands. The data were analyzed within a Bayesian framework to: (1) determine pulse size and antecedent moisture (soil moisture prior to the pulse) effects on soil respiration, (2) quantify soil texture (coarse vs. fine) and cover type (bare vs. vegetated) effects on the response of soil respiration and its components (plant vs. microbial) to pulses, and (3) explore the relationship between long-term variation in pulse regimes and seasonal soil respiration. Regarding objective (1), larger pulses resulted in higher respiration rates, particularly from vegetated fine-textured soil, and dry antecedent conditions amplified respiration responses to pulses (wet antecedent conditions dampened the pulse response). Regarding (2), autotrophic (plant) activity was a significant source (???60%) of respiration and was more sensitive to pulses on coarse- versus fine-textured soils. The sensitivity of heterotrophic (microbial) respiration to pulses was highly dependent on antecedent soil water. Regarding (3), seasonal soil respiration was predicted to increase with both growing season precipitation and mean pulse size (but only for pulses between 7 and 25 mm). Thus, the heterogeneity of the desert landscape and the timing or the number of medium-sized pulses is expected to significantly impact desert soil C loss with climate change. ?? 2008 Springer Science+Business Media, LLC.

Ecosystems↗
USGS2024

Biodiversity loss reduces global terrestrial carbon storage

Natural ecosystems store large amounts of carbon globally, as organisms absorb carbon from the atmosphere to build large, long-lasting, or slow-decaying structures such as tree bark or root systems. An ecosystem’s carbon sequestration potential is tightly linked to its biological diversity. Yet when considering future projections, many carbon sequestration models fail to account for the role biodiversity plays in carbon storage. Here, we assess the consequences of plant biodiversity loss for carbon storage under multiple climate and land-use change scenarios. We link a macroecological model projecting changes in vascular plant richness under different scenarios with empirical data on relationships between biodiversity and biomass. We find that biodiversity declines from climate and land use change could lead to a global loss of between 7.44-103.14 PgC (global sustainability scenario) and 10.87-145.95 PgC (fossil-fueled development scenario). This indicates a self-reinforcing feedback loop, where higher levels of climate change lead to greater biodiversity loss, which in turn leads to greater carbon emissions and ultimately more climate change. Conversely, biodiversity conservation and restoration can help achieve climate change mitigation goals.

Nature Communications↗
USGS2006

Aspects of the biology of Salicornia bigelovii torr. In relation to a proposed restoration of a wind-tidal flat system on the South Texas, USA Coast

Wind-tidal flats are the dominant coastal wetland type in southern Texas USA. Succulent vascular plants are colonizing the flats in some locations, often where past dredge disposal along navigation channels and other activities have interrupted natural water communication between hypersaline bays and large areas of wind-tidal flats. The objective of this study was to test the feasibility of proposed removal of a causeway at Laguna Atascosa National Wildlife Refuge to restore the historic hydrologic regime and eradicate encroaching vascular plants, mostly Salicornia bigelovii, on the assumption that high sediment salt excluded these vascular plants under natural conditions. Assessment in spring 1998 of the density of Salicornia in relation to elevation and sediment salt of bare and vegetated zones on the vegetated flats on one side of the causeway and entirely barren flats with unimpaired connection to Laguna Madre on the other side of the causeway suggested that sediment salt >0.1 g ml-1 excluded vascular plants. However, bimonthly sampling in 1999-2000 revealed that sediment salt concentrations were >0.1 g ml-1 throughout the vegetated zone in July and more locally in the period of winter low water, with little impairment to established plants. This indicates that if control is desired, it must be exerted at germination and early establishment during and after fall high water. Continuous monitoring of water levels on either side of the causeway suggests that, even with removal of the causeway, flooding with hypersaline lagoon water will be too infrequent to counteract the freshening effect of a permanent hydraulic connection to the main agricultural drain of the lower Rio Grande Valley that has developed at the other end of the salt flat. Monitoring Salicornia distribution over six years documented huge variation between years but no trend toward increasing dominance of the flats. The results of this study illustrate that the most obvious alterations to a site may not be the most influential on function and that the scale of analysis may have to extend far beyond the site in space and time to evaluate a proposed restoration properly. ?? 2006, The Society of Wetland Scientists.

Wetlands↗
USGS2009

Structural changes in vegetation coincident with annual grass invasion negatively impacts sprint velocity of small vertebrates

Sagebrush ecosystems in the intermountain west of the United States are being threatened by conversion to the non-native grass, cheatgrass ( Bromus tectorum ). The dramatic shift in the physical structure of vegetation coincident with cheatgrass invasion likely has negative impacts on animal communities, yet these structural impacts have not been well-studied. In a previous study, dense cheatgrass stems reduced sprint velocity for the flattened, wide-bodied desert horned lizard ( Phrynosoma platyrhinos ). Here, we asked if a decrease in sprint velocity due to cheatgrass impediment can be generalized to the suite of small vertebrates inhabiting the sagebrush ecosystems of western Utah. We evaluated sprint performance of the common rodent ( n = 3) and lizard ( n = 4) species on two raceway types, cheatgrass and no-cheatgrass, and hypothesized that body size, body shape, and form of movement are important factors influencing sprint velocity through dense cheatgrass stems. All species showed significant reductions in speed on cheatgrass versus no-cheatgrass raceways, with percent reduction greatest for larger, wider, or hopping organisms compared to smaller, more slender, or running organisms. Of concern, surveys for rodents and lizards at our study areas support a common pattern: lower abundances of small vertebrates, as well as a loss of rodent species richness, in areas infested with cheatgrass compared to intact, native sagebrush communities. By extension, we expect a negative impact on animal communities in other semi-arid regions experiencing dramatic shifts in vegetation structure upon invasion by non-native grasses that are capable of forming dense stands in the interspaces of native desert plants [e.g., Sonoran desert invaded by buffelgrass ( Pennisetum ciliare )].

Utah↗
USGS2015

Pollen and spores of terrestrial plants

Pollen and spores are valuable tools in reconstructing past sea level and climate because of their ubiquity, abundance, and durability as well as their reciprocity with source vegetation to environmental change (Cronin, 1999; Traverse, 2007; Willard and Bernhardt, 2011). Pollan is found in many sedimentary environments, from freshwater to saltwater, terrestrial to marine. It can be abundant in a minimal amount of sample material, for example half a gram, as concentrations can be as high as four million grains per gram (Traverse, 2007). The abundance of pollen in a sample lends it to robust statistical analysis for the quantitative reconstruction of environments. The outer cell wall is resistant to decay in sediments and allows palynomorphs (pollen and spores) to record changes in plant communities and sea level over millions of years. These characteristics make pollen and spores a powerful tool to use in sea-level research. This chapter describes the biology of pollen and spores and how they are transported and preserved in sediments. We present a methodology for isolating pollen from sediments and a general language and framework to identify pollen as well as light micrographs of a selection of common pollen grains, We then discuss their utility in sea-level research.

Book chapter↗
USGS2013

Status of exotic grasses and grass-like vegetation and potential impacts on wildlife in New England

The Northeastern section of the United States, known as New England, has seen vast changes in land cover and human population over the past 3 centuries. Much of the region is forested; grasslands and other open-land cover types are less common, but provide habitat for many species that are currently declining in abundance and distribution. New England also consists of some of the most densely populated and developed states in the country. The origin, distribution, and spread of exotic species are highly correlated with human development. As such, exotics are common throughout much of New England, including several species of graminoids (grasses and grass-like plants such as sedges and rushes). Several of the more invasive grass species can form expansive dense mats that exclude native plants, alter ecosystem structure and functions, and are perceived to provide little-to-no value as wildlife food or cover. Although little research has been conducted on direct impacts of exotic graminoids on wildlife populations in New England, several studies on the common reed ( Phragmites australis ) in salt marshes have shown this species to have variable effects as cover for birds and other wildlife, depending on the distribution of the plant (e.g., patches and borders of reeds are used more by wildlife than expansive densely growing stands). Direct impacts of other grasses on wildlife populations are largely unknown. However, many of the invasive graminoid species that are present in New England have the capability of outcompeting native plants and thereby potentially affecting associated fauna. Preservation, protection, and restoration of grassland and open-land cover types are complex but necessary challenges in the region to maintain biological and genetic diversity of grassland, wetland, and other open-land obligate species.

Wildlife Society Bulletin↗
USGS2018

Fungal loop transfer of nitrogen depends on biocrust constituents and nitrogen form

Besides performing multiple ecosystem services individually and collectively, biocrust constituents may also create biological networks connecting spatially and temporally distinct processes. In the fungal loop hypothesis rainfall variability allows fungi to act as conduits and reservoirs, translocating resources between soils and host plants. To evaluate the extent to which biocrust species composition and nitrogen (N) form influence loops, we created a minor, localized rainfall event containing 15 NH 4 + and 15 NO 3 − . We then measured the resulting δ 15 N in the surrounding dry cyanobacteria- and lichen-dominated crusts and grass, Achnatherum hymenoides , after 24 h. We also estimated the biomass of fungal constituents using quantitative PCR and characterized fungal communities by sequencing the 18S rRNA gene. We found evidence for the initiation of fungal loops in cyanobacteria-dominated crusts where 15 N, from 15 NH 4 + , moved 40 mm h −1 in biocrust soils with the δ 15 N of crusts decreasing as the radial distance from the water addition increased (linear mixed effects model (LMEM)): R 2 = 0.67, F 2,12 = 11, P = 0.002). In cyanobacteria crusts, δ 15 N, from 15 NH 4 + , was diluted as Ascomycota biomass increased (LMEM: R 2 = 0.63, F 2,8 = 6.8, P = 0.02), Ascomycota accounted for 82 % (±2.8) of all fungal sequences, and one order, Pleosporales, comprised 66 % (±6.9) of Ascomycota. The seeming lack of loops in moss-dominated crusts may stem from the relatively large moss biomass effectively absorbing and holding N from our minor wet deposition event. The substantial movement of 15 NH 4 + may indicate a fungal preference for the reduced N form during amino acid transformation and translocation. We found a marginally significant enrichment of δ 15 N in A. hymenoides leaves but only in cyanobacteria biocrusts translocating 15 N, offering evidence of links between biocrust constituents and higher plants. Our results suggest that minor rainfall events may initiate fungal loops potentially allowing constituents, like dark septate Pleosporales, to rapidly translocate N from NH 4 + over NO 3 − through biocrust networks.

Biogeosciences↗
USGS2006

Integrating bioavailability approaches into waste rock evaluations

The presence of toxic metals in soils affected by mining, industry, agriculture and urbanization, presents problems to human health, the establishment and maintenance of plant and animal habitats, and the rehabilitation of affected areas. A key to managing these problems is predicting the fraction of metal in a given soil that will be biologically labile, and potentially harmful ('bioavailable'). The molecular form of metals and metalloids, particularly the uncomplexed (free) form, controls their bioavailability and toxicity in solution. One computational approach for determining bioavailability, the biotic ligand model (BLM), takes into account not only metal complexation by ligands in solution, but also competitive binding of hardness cations (Ca 2+,Mg 2+,) and metal ions to biological receptor sites. The more direct approach to assess bioavailability is to explicitly measure the response of an organism to a contaminant. A number of microbial enzyme tests have been developed to assess the impact of pollution in a rapid and procedurally simple way. These different approaches in making bioavailability predictions may have value in setting landuse priorities, remediation goals, and habitat reclamation strategies.

Conference Paper↗
USGS1979

Reconnaissance evaluation of surface-water quality in Eagle, Grand, Jackson, Pitkin, Routt, and Summit Counties, Colorado

Water-quality data were collected from streams in a six-county area to determine if the streams were polluted and, if so, to determine the sources of the pollution. Eighty-three stream sites were selected for sampling in Eagle, Grand, Jackson, Pitkin, Routt, and Summit Counties. Also included are data from 28 sites in Routt County collected for a U.S. Geological Survey cooperative study on the Yampa River basin. A summary of data collected prior to this study, results of current chemical and biological sampling, and needs for future water-quality monitoring are reported for each county. The kinds of data collected were site specific depending upon land-use activities. Data collected at selected sites included temperature, pH, specific conductance, dissolved oxygen, and stream discharge. Chemical data collected included nutrients, inorganics, organics, and trace elements. Biological data collected included counts and species composition of total and fecal-coliform bacteria, fecal-streptococcus bacteria, benthic invertebrates, and phytoplankton. Most of the sites were sampled three times: in April-June 1976, August 1976, and January 1977. The major water-quality problems at the 17 sites sampled in Eagle County are related to mining, recreation, and geology. The Eagle River and Cross Creek in the vicinity of Minturn have concentrations of trace elements that exceed water-quality standards. Gore Creek is influenced by winter recreational use and the water during the winter has total bacteria counts as great as 72,000 per 100 milliliters and concentrations of un-ionized ammonia greater than 0.02 milligrams per liter downstream from the sewage-treatment plant. Mineralized water in the downstream reaches of the Eagle River results from natural chemical processes. The water-quality problems in Grand County, especially on the Fraser River, are related to recreation and urban activities. Chemical and biological indications of water-quality degradation exist for the Fraser River downstream from Winter Park.

Colorado↗
USGS2005

Biology and invasive species in the western U.S

The diversity of environments that characterizes the West is responsible for the region's rich biological heritage. This ecological diversity also means that opportunities for invasive species are many, varied, and complex. Island ecosystems are notoriously vulnerable to invaders as demonstrated in Hawaii and West Coast offshore islands. Aquatic invaders impose high economic and environmental costs in systems as varied as San Francisco Bay and desert springs in the Great Basin. Although the West's arid and montane ecosystems may seem resistant to plant and animal invaders, we now know that ex-otic species have altered physical processes related to fire and hydrology in a manner favoring further expansion and persis-tence of invaders. Natural resource managers value analytical, mapping, and genetics tools developed by USGS scientists to monitor invasive species and help conserve biological systems. USGS biologists conduct research to assist land and water managers' efforts to control invasive species and restore natural systems. Throughout the West, the USGS carries out studies for early detection and rapid assessment of invaders. The following are some examples of how the USGS is making a difference in the western United States.

Fact Sheet↗
USGS2010

Moisture and vegetation controls on decadal-scale accrual of soil organic carbon and total nitrogen in restored grasslands

Revitalization of degraded landscapes may provide sinks for rising atmospheric CO2, especially in reconstructed prairies where substantial belowground productivity is coupled with large soil organic carbon (SOC) deficits after many decades of cultivation. The restoration process also provides opportunities to study the often-elusive factors that regulate soil processes. Although the precise mechanisms that govern the rate of SOC accrual are unclear, factors such as soil moisture or vegetation type may influence the net accrual rate by affecting the balance between organic matter inputs and decomposition. A resampling approach was used to assess the control that soil moisture and plant community type each exert on SOC and total nitrogen (TN) accumulation in restored grasslands. Five plots that varied in drainage were sampled at least four times over two decades to assess SOC, TN, and C4- and C3-derived C. We found that higher long-term soil moisture, characterized by low soil magnetic susceptibility, promoted SOC and TN accrual, with twice the SOC and three times the TN gain in seasonally saturated prairies compared with mesic prairies. Vegetation also influenced SOC and TN recovery, as accrual was faster in the prairies compared with C3-only grassland, and C4-derived C accrual correlated strongly to total SOC accrual but C3-C did not. High SOC accumulation at the surface (0-10 cm) combined with losses at depth (10-20 cm) suggested these soils are recovering the highly stratified profiles typical of remnant prairies. Our results suggest that local hydrology and plant community are critical drivers of SOC and TN recovery in restored grasslands. Because these factors and the way they affect SOC are susceptible to modification by climate change, we contend that predictions of the C-sequestration performance of restored grasslands must account for projected climatic changes on both soil moisture and the seasonal productivity of C4 and C3 plants. ?? 2009 Blackwell Publishing Ltd.

Global Change Biology↗
USGS2015

Ground-survey and water-quality data for selected wetlands on or near the Lower Brule Indian Reservation in South Dakota, 2012-13

Numerous lakes, ponds, and wetlands are located within the Lower Brule Indian Reservation. Wetlands are an important resource providing aquatic habitat for plants and animals, and acting as a natural water filtration system. Several of the wetlands on or near the reservation are of particular interest, but information on the physical and biological integrity of these wetlands was needed to provide a base-line reference when planning for future water management needs. A reconnaissance-level study of selected wetlands on and near the Lower Brule Indian Reservation was completed in 2012–13 by the U.S. Geological Survey in cooperation with the Lower Brule Sioux Tribe using ground surveys and water-quality analyses. Ground surveys of six wetland areas (Dorman Slough, Little Bend Wetlands, Miller Pond, Potter Slough, an unnamed slough, and West Brule Community wetlands) were completed to map land, water, vegetation, and man-made features of the selected wetland areas using real-time kinematic global navigation satellite systems equipment. Water samples were collected from four of the selected wetlands. Two separate waterbodies were sampled at one of the wetlands for a total of five sampling locations. Water samples were analyzed for physical properties, selected inorganics, metals, nutrients, and suspended sediment. Concentrations of calcium, sodium, and sulfate were greater at the two wetland sites fed by ground water, compared to the wetland sites fed by surface runoff.

South Dakota↗
USGS2019

Ecological and management implications of climate change induced shifts in phenology of coastal fish and wildlife species in the Northeast CASC region

Climate change is causing species to shift their phenology, or the timing of recurring life events such as migration and reproduction, in variable and complex ways. This can potentially result in mismatches or asynchronies in food and habitat resources that negatively impact individual fitness, population dynamics, and ecosystem function. Numerous studies have evaluated phenological shifts in terrestrial species, particularly birds and plants, yet far fewer evaluations have been conducted for marine animals. This project seeks to improve our understanding of shifts in the timing of seasonal migration, spawning or breeding, and biological development (i.e. life stages present, dominant) of coastal fishes, marine mammals,and migratory shore and seabirds along the U.S Atlantic coast. Ideally the suite of species selected will allow us to compare whether fish, marine mammals, shore and seabird predators are shifting their phenology at different rates than their primary prey and optimal habitat conditions, thus influencing trophic interactions and population dynamics. A comprehensive literature review will be conducted simultaneous to data collection and synthesis to determine what is known, and what knowledge/information/data gaps exist regarding regional phenological responses of coastal species to climate change. Project results will help managers assess the vulnerability of coastal species to climate change by providing information on how they are responding to impacts in the region.

Conference Paper↗
USGS2001

Green fluorescent protein is lighting up fungal biology

Prasher ( 42 ) cloned a cDNA for the green fluorescent protein (GFP) gene from the jellyfish Aequorea victoria in 1992. Shortly thereafter, to the amazement of many investigators, this gene or derivatives thereof were successfully expressed and conferred fluorescence to bacteria and Caenorhabditis elegans cells in culture ( 10 , 31 ), followed by yeast ( 24 , 39 ), mammals ( 40 ), Drosophila ( 66 ), Dictyostelium ( 23 , 30 ), plants ( 28 , 49 ), and filamentous fungi ( 54 ). The tremendous success of GFP as a reporter can be attributed to unique qualities of this 238-amino-acid, 27-kDa protein which absorbs light at maxima of 395 and 475 nm and emits light at a maximum of 508 nm. The fluorescence of GFP requires only UV or blue light and oxygen, and therefore, unlike the case with other reporters (β-glucuronidase, β-galacturonidase, chloramphenicol acetyltransferase, and firefly luciferase) that rely on cofactors or substrates for activity, in vivo observation of gfp expression is possible with individual cells, with cell populations, or in whole organisms interacting with symbionts or environments in real time. Complications caused by destructive sampling, cell permeablization for substrates, or leakage of products do not occur. Furthermore, the GFP protein is extremely stable in vivo and has been fused to the C or N terminus of many cellular and extracellular proteins without a loss of activity, thereby permitting the tagging of proteins for gene regulation analysis, protein localization, or specific organelle labeling. The mature protein resists many proteases and is stable up to 65°C and at pH 5 to 11, in 1% sodium dodecyl sulfate or 6 M guanidinium chloride (reviewed in references 17 and 67 ), and in tissue fixed with formaldehyde, methanol, or glutaraldehyde. However, GFP loses fluorescence in methanol-acetic acid (3:1) and can be masked by autofluorescent aldehyde groups in tissue fixed with glutaraldehyde. Fluorescence is optimal at pH 7.2 to 8.0 ( 67 ). Limitations on GFP as a reporter for some applications are its low turnover rate, 2-h lag time for autoactivation of its chromophore, improper folding at high temperatures (37°C), which results in nonfluorescent and insoluble forms of the protein, and requirement for oxygen, which is not present in equal concentrations in all subcellular locations or cell types (reviewed in references 17 and 67 ). These characteristics of GFP, however, have not posed a problem for many applications, and mutant forms of GFP that have an ability to fold properly at high temperatures, increased solubility and fluorescence, reduced photobleaching ( 16 , 17 , 51 ), and reduced half-lives ( 1 ) have been developed. Coupled with fluorescence-activated cell sorting, confocal microscopy or quantitative image analysis techniques, GFP technology can be used to isolate transformed cells or specific cell types from populations of cells ( 14 ), to quantify gene expression of individual cells within whole organisms ( 8 ), or to assess the dispersal and biomass of organisms in complex environments, such as in animal or plant hosts ( 38 , 59 ), in biofilms ( 55 ), in fermentors ( 41 ), on leaf surfaces ( 53 , 61 ), or in soils ( 2 ). The vast majority of studies utilizing GFP expression in fungi have been with yeast (reviewed in reference 13 ). Ustilago maydis was the first filamentous fungus for which successful expression of gfp was reported ( 54 ), followed closely by Aspergillus nidulans ( 22 , 57 ) and Aureobasidium pullulans ( 61 ). Presently, gfp expression has been reported for 16 species comprising 12 genera of filamentous fungi, including Colletotrichum ( 21 , 44 ), Mycosphaerella ( 52 ), Magnaporthe ( 32 , 35 ), Cochliobolus ( 38 ), Trichoderma ( 2 , 70 ), Podospora ( 5 ), Sclerotinia ( 63 ), Schizophyllum ( 37 ), Aspergillus ( 20 , 47 , 50 ) and Phytophthora ( 7 , 62 ). In this review we draw on published reports, with the goal of providing an overview of GFP technology as it applies to the biology of filamentous fungi. These reports are not exhaustive of potential applications of GFP technology, as examples of genomic approaches to utilizing GFP in bacterial and yeast systems attest ( 4 , 46 , 60 , 65 ). Expression of gfp in filamentous fungi requires a gfp variant that is efficiently translated in fungi, a transformation system, and a fungal promoter that satisfies the requirements of a given experimental objective. Transformation of fungi has recently been reviewed by Gold et al. ( 26 ). Robinson and Sharon ( 44 ) suggest that GFP can actually be used to optimize transformation protocols. In addition to reporting the construction of a new fungal transformation vector that expresses SGFP under the control of the ToxA gene promoter from Pyrenophora tritici-repentis ( 12 ) and demonstrating its use in plant pathogens belonging to eight different genera of filamentous fungi ( Fusarium, Botrytis, Pyrenophora, Alternaria, Cochliobolus, Sclerotinia, Colletotrichum , and Verticillium ), in this review we also enumerate and describe a comprehensive list of vectors for expressing GFP in fungi.

Applied and Environmental Microbiology↗
USGS2011

Predicting phenology by integrating ecology, evolution and climate science

Forecasting how species and ecosystems will respond to climate change has been a major aim of ecology in recent years. Much of this research has focused on phenology – the timing of life‐history events. Phenology has well‐demonstrated links to climate, from genetic to landscape scales; yet our ability to explain and predict variation in phenology across species, habitats and time remains poor. Here, we outline how merging approaches from ecology, climate science and evolutionary biology can advance research on phenological responses to climate variability. Using insight into seasonal and interannual climate variability combined with niche theory and community phylogenetics, we develop a predictive approach for species’ reponses to changing climate. Our approach predicts that species occupying higher latitudes or the early growing season should be most sensitive to climate and have the most phylogenetically conserved phenologies. We further predict that temperate species will respond to climate change by shifting in time, while tropical species will respond by shifting space, or by evolving. Although we focus here on plant phenology, our approach is broadly applicable to ecological research of plant responses to climate variability.

Global Change Biology↗
USGS2016

Extending ordinal regression with a latent zero-augmented beta distribution

Ecological abundance data are often recorded on an ordinal scale in which the lowest category represents species absence. One common example is when plant species cover is visually assessedwithin bounded quadrats and then assigned to pre-defined cover class categories.We present an ordinal beta hurdle model that directly models ordinal category probabilitieswith a biologically realistic beta-distributed latent variable.Ahurdle-at-zero model allows ecologists to explore distribution (absence) and abundance processes in an integrated framework. This provides an alternative to cumulative link models when data are inconsistent with the assumption that the odds ofmoving into a higher category are the same for all categories (proportional odds). Graphical tools and a deviance information criterion were developed to assess whether a hurdle-at-zero model should be used for inferences rather than standard ordinal methods. Hurdle-at-zero and non-hurdle ordinal models fit to vegetation cover class data produced substantially different conclusions.The ordinal beta hurdle model yielded more precise parameter estimates than cumulative logit models, although out-of-sample predictions were similar. The ordinal beta hurdle model provides inferences directly on the latent biological variable of interest, percent cover, and supports exploration of more realistic ecological patterns and processes through the hurdle-at-zero or two-part specification.We provide JAGS code as an on-line supplement. Supplementary materials accompanying this paper appear on-line.

Journal of Agricultural, Biological, and Environme↗
USGS2015

Science foundation Chapter 5 Appendix 5.1: Case study marsh macroinvertebrates

This case study includes representative macroinvertebrates that live in the marsh plain, its associated channels and pannes (ponds), and the marsh-upland transition zone. While less visible than animals such as birds, invertebrates play important roles in physical and biological processes (e.g., burrowing activity and channel bank erosion, and detritivores breaking down organic matter) and are important food resources for higher trophic animals. Common invertebrates in these habitats include plant-hopper ( Prokelisia marginata ), beach hopper ( Traskorchestia traskiana ), pygmy blue butterfly ( Brephidium exilis ), inchworm moth ( Perizoma custodiata ), western tanarthus beetle ( Tanarthus occidentalis ), salt marsh mosquitoes ( Aedes spp.; Maffei 2000a, Maffei 2000b, Maffei 2000c), crabs (native Hemigrapsus oregonensis and introduced Carcinus maenas ), copepods, snails (e.g. native California horn snail Cerithidea californica and introduced Ilyanassa obsoleta , Myosotella myosotis ), polychaetes (e.g. Capitella spp., Eteone californica , Neanthes brandti ), small clams ( Macoma petalum / M. balthica ), and corophiid amphipods (Cohen 2011, Race 1982, Robinson et al. 2011). Some common species were described in detail in the San Francisco Bay Goals Project Species and Community Profiles (Goals Project 2000).

California↗
USGS2025

Pesticide contamination detected across five wildlife refuges in the Sacramento Valley of California

An important goal for the applied ecological sciences is to understand the extent to which the biodiversity on conserved or managed lands is exposed to anthropogenic stressors. Among the various categories of conserved lands in the United States, the National Wildlife Refuge System is focused on the protection and management of native wildlife and plant populations. Refuge lands can be associated with wetlands and, especially in California, tend to be near areas of intense human use, including agriculture. The proximity of refuges to cultivated lands results in potential exposure to pesticide drift, which increases the possibility of non-target effects on plants and wildlife. We used a passive sampler approach to quantify aerial pesticide deposition during 28 days in spring of 2023, across five refuges in the Sacramento Valley of California. Pesticides were detected across all refuges and plots within the study area, with 36 individual compounds identified, including insecticides, herbicides, and fungicides, from 176 silicone bands from 49 plots. Distance to agriculture was not an important predictor in our models for most indices of contamination. However, our models revealed that the nearest crop type was an important mediator of the importance of distance to agriculture, as fungicide contamination decreased with distance to agriculture only when orchards were the nearest crop type. The overall lack of distance effects suggests that the interior of refuges in the study area do not necessarily provide more protection from pesticides than refuge edges, although larger refuges could offer more protection. We currently lack information on how the level of contamination found herein is biologically relevant to wildlife, and ongoing monitoring efforts have found productive communities of insects in the study area. The results of this study provide a foundation for future investigations on refuges to analyze impacts of specific pesticide compounds on plants and wildlife.

California↗