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USGS2015

Assessing the components of adaptive capacity to improve conservation and management efforts under global change

Natural-resource managers and other conservation practitioners are under unprecedented pressure to categorize and quantify the vulnerability of natural systems based on assessment of the exposure, sensitivity, and adaptive capacity of species to climate change. Despite the urgent need for these assessments, neither the theoretical basis of adaptive capacity nor the practical issues underlying its quantification has been articulated in a manner that is directly applicable to natural-resource management. Both are critical for researchers, managers, and other conservation practitioners to develop reliable strategies for assessing adaptive capacity. Drawing from principles of classical and contemporary research and examples from terrestrial, marine, plant, and animal systems, we examined broadly the theory behind the concept of adaptive capacity. We then considered how interdisciplinary, trait- and triage-based approaches encompassing the oft-overlooked interactions among components of adaptive capacity can be used to identify species and populations likely to have higher (or lower) adaptive capacity. We identified the challenges and value of such endeavors and argue for a concerted interdisciplinary research approach that combines ecology, ecological genetics, and eco-physiology to reflect the interacting components of adaptive capacity. We aimed to provide a basis for constructive discussion between natural-resource managers and researchers, discussions urgently needed to identify research directions that will deliver answers to real-world questions facing resource managers, other conservation practitioners, and policy makers. Directing research to both seek general patterns and identify ways to facilitate adaptive capacity of key species and populations within species, will enable conservation ecologists and resource managers to maximize returns on research and management investment and arrive at novel and dynamic management and policy decisions.

Conservation Biology↗

USGS2025

Chapter 6: Climate change, wildlife, and wildlife habitats in the Oregon Coast Range

Climate change is likely to have profound effects on wildlife species within the Oregon Coast Adaptation Partnership (OCAP) assessment area, although the direction and magnitude of effects are likely to vary across species. Increased mean and extreme temperatures, especially during summer, may cause shifts in plant and animal species ranges, reduce habitat for some temperature-sensitive wildlife, alter plant phenology and the timing of available food resources, and affect species interactions (e.g., predation, competition). Altered timing of precipitation, summer drought, loss of fog, increased flooding events, earlier snowmelt, and rising sea level may reduce plant productivity, increase tree mortality, shift plant species composition, and lead to reduced wildlife habitat and habitat quality for some forests, riparian areas, wetlands, meadows, estuaries, and beaches. In addition, increasing frequency and extent of wildfire and insect outbreaks may reduce the extent of late-successional forest, reduce habitat connectivity, and increase the spread of invasive species. The biggest change expected for the assessment area is an increase in area where climatic conditions favor coastal mixed forest and a large reduction in area favoring montane conifer forest. Although actual changes in forest types may not necessarily occur by the end of the 21st century, climate change may add physiological and behavioral stress to wildlife. Some wildlife species will be able to persist in place and adapt to new conditions; some may be able to migrate to find suitable habitat; and some may be greatly reduced or extirpated from the assessment area or even go extinct. Shifts in major tree and shrub species will play a major role in food, den, and cover availability for wildlife. Rising sea level will reduce low-elevation habitats along the coast. An increase in the frequency of high-severity weather events will increase frequency and magnitude of flooding, including debris flow events. Coupled with increased temperatures during summer, this may reduce or fragment important ecosystems for aquatic and semi-aquatic species. Evaluation of the vulnerabilities of nine wildlife species based on literature reviews suggests that each species has life-history attributes that can lead to resilience or vulnerability to climate change effects. Depending on long-term objectives, several broad adaptation strategies focus on protecting refugia, establishing redundant wildlife strongholds with large-scale connectivity, and promoting structural and biological complexity.

Oregon↗

USGS2018

Patterns of longer-term climate change effects on CO2 efflux from biocrusted soils differ from those observed in the short term

Biological soil crusts (biocrusts) are predicted to be sensitive to the increased temperature and altered precipitation associated with climate change. We assessed the effects of these factors on soil carbon dioxide (CO 2 ) balance in biocrusted soils using a sequence of manipulations over a 9-year period. We warmed biocrusted soils by 2 and, later, by 4 °C to better capture updated forecasts of future temperature at a site on the Colorado Plateau, USA. We also watered soils to alter monsoon-season precipitation amount and frequency and had plots that received both warming and altered precipitation treatments. Within treatment plots, we used 20 automated flux chambers to monitor net soil exchange (NSE) of CO 2 hourly, first in 2006–2007 and then again in 2013–2014, for a total of 39 months. Net CO 2 efflux from biocrusted soils in the warming treatment increased a year after the experiment began (2006–2007). However, after 9 years and even greater warming (4 °C), results were more mixed, with a reversal of the increase in 2013 (i.e., controls showed higher net CO 2 efflux than treatment plots) and with similarly high rates in all treatments during 2014, a wet year. Over the longer term, we saw evidence of reduced photosynthetic capacity of the biocrusts in response to both the temperature and altered precipitation treatments. Patterns in biocrusted soil CO 2 exchange under experimentally altered climate suggest that (1) warming stimulation of CO 2 efflux was diminished later in the experiment, even in the face of greater warming; and (2) treatment effects on CO 2 flux patterns were likely driven by changes in biocrust species composition and by changes in root respiration due to vascular plant responses.

Biogeosciences↗

USGS2019

Abundance-occupancy patterns in a riverine fish assemblage

The interspecific relationships between abundance and site occupancy have been widely studied in plants and animals, but principally in terrestrial systems. With few exceptions, a positive abundance–occupancy relationship has been reported. Few publications have included freshwater fish, possibly suggesting a general lack of abundance–occupancy patterns for this taxonomic group. We examined the relationship between abundance and the extent of site occupancy by 145 species of freshwater fish, including nine non-indigenous species, sampled over 85 sites spread across the Duck River Basin, Tennessee, U.S.A. A distinct ( r 2 = 0.79) positive abundance–occupancy curve was observed, with curves differing relative to feeding and size guilds, but not relative to environmental tolerance, conservation status (i.e. listed/non-listed), or origin (i.e. indigenous/non-indigenous). The patterns observed are consistent with those reported in many studies of terrestrial taxa. The existence of positive abundance–occupancy relationships in stream fish has at least two major implications for fish conservation. First, species that decrease in occupancy due to anthropogenic disturbances are likely to decrease in abundance, facing inflated prospects for local extinction. Second, occupancy alone may be used to index community status and the need for, or success of, conservation activities.

Tennessee↗

USGS2022

Spatially explicit management of genetic diversity using ancestry probability surfaces

1. Ecological restoration and conservation efforts are increasing worldwide and the management of intraspecific genetic variation in plants and animals, an important component of biodiversity, is increasingly valued. As a result, tailorable, spatially explicit approaches to map genetic variation are needed to support decision-making and management frameworks related to the recovery of threatened and endangered species and the maintenance of genetic resources in species utilized by humans, such as for restoration or agricultural purposes. 2. Here, we describe and demonstrate a workflow to spatially interpolate patterns of genetic differentiation using novel functions in the R package POPMAPS ( Pop ulation M anagement using A ncestry P robability S urfaces). Our approach uses empirical genetic data to estimate ancestry coefficients across a user-defined landscape correlated with patterns of differentiation in the focal species. The resulting surface, which we term the ancestry probability surface, includes two components: hard population boundaries and estimations of uncertainty that represent confidence in population assignments (i.e., ancestry probabilities). 3. An ancestry probability surface developed for Hilaria jamesii , an important graminoid utilized in restoration across the western United States, demonstrates the functionality of POPMAPS . Genetic distances among empirical sites correlated better with least-cost distances across suitable habitat than with geographic distances, informing the surface over which the interpolation was conducted (i.e., a model indicating habitat suitability). A jackknifing procedure identified parameter values resulting in robust population assignments across the species’ range, which were utilized in downstream analyses to estimate ancestry coefficients from empirical data. Ancestry coefficients were translated into ancestry probabilities, which tended to be low for cells that were intermediate in distance between empirical sampling locations representing different populations or when influenced by empirical sampling locations with mixed genetic ancestry. 4. POPMAPS allows users to tailor parameter values and analytical approaches and thereby incorporate species-specific biological characteristics and desired levels of uncertainty into maps illustrating patterns of genetic differentiation. Ancestry probability surfaces may be used to guide management or investigate further ecological or evolutionary hypotheses. We discuss how maps produced by POPMAPS can inform multiple management challenges including species recovery planning and the utilization of commonly used species in restoration.

Methods in Ecology and Evolution↗

USGS2016

Diversity of fungal endophytes in non-native Phragmites australis in the Great Lakes

Plant–microbial interactions may play a key role in plant invasions. One common microbial interaction takes place between plants and fungal endophytes when fungi asymptomatically colonize host plant tissues. The objectives of this study were to isolate and sequence fungal endophytes colonizing non-native Phragmites australis in the Great Lakes region to evaluate variation in endophyte community composition among three host tissue types and three geographical regions. We collected entire ramets from multiple clones and populations, surface sterilized plant tissues, and plated replicate tissue samples from leaves, stems, and rhizomes on corn meal agar plates to culture and isolate fungal endophytes. Isolates were then subjected to Sanger sequencing of the ITS region of the nuclear ribosomal DNA. Sequences were compared to fungal databases to define operational taxonomic units (OTUs) that were analyzed statistically for community composition. In total, we obtained 173 endophyte isolates corresponding to 55 OTUs, 39 of which were isolated only a single time. The most common OTU corresponded most closely to Sarocladium strictum and comprised 25 % of all fungal isolates. More OTUs were found in stem tissues, but endophyte diversity was greatest in rhizome tissues. PERMANOVA analyses indicated significant differences in endophyte communities among tissue types, geographical regions, and the interaction between those factors, but no differences among individual ramets were detected. The functional role of the isolated endophytes is not yet known, but one genus isolated here ( Stagonospora ) has been reported to enhance Phragmites growth. Understanding the diversity and functions of Phragmites endophytes may provide targets for control measures based on disrupting host plant/endophyte interactions.

Great Lakes region↗

USGS2025

Impacts of flowering rush (Butomus umbellatus L.) on macrophyte diversity and composition in the Upper Mississippi River

Flowering rush ( Butomus umbellatus L.), a perennial plant native to Eurasia, made a widespread appearance in the Upper Mississippi River in the United States in 2020, following extremely high river discharge during the previous year. Flowering rush expanded rapidly and was found at 1–10% of sites (n = 6,630 total sites) across a 400 km river reach within the first 4 years of invasion. Flowering rush invaded at least 12 of 31 wetland vegetation classes, including submersed aquatic, rooted-floating, deep marsh, and shallow marsh. Analysis of long-term macrophyte data and our targeted field study revealed that plant diversity declined with greater abundance of flowering rush over a 4-year early invasion period, suggesting that native species were displaced. Furthermore, species correlation plots showed a significant negative correlation (r < -0.1) between flowering rush and several native species, including wild celery, water stargrass, and wild rice. Non-metric multi-dimensional scaling (NMDS) ordination placed flowering rush near the center of the plot, which may indicate tolerance to a wide range of environmental conditions such as water depth, flow, and substrate. Centering on the NMDS plot also shows that flowering rush invades many types of vegetated aquatic land cover classes, which was also supported by our geographic information systems analysis of land cover invasion. These habitat associations and ecological impacts of the recent, widespread invasion of flowering rush in the Upper Mississippi River can help inform restoration and management actions during early invasion. Continuing long-term data collection can break limitations on modeling cause-effect relationships and provide insights to the future ecological trajectory of the macrophyte community to this non-native invasive species.

Illinois, Iowa, Minnesota, Wisconsin↗

USGS2004

The elusive baseline of marine disease: Are diseases in ocean ecosystems increasing?

Disease outbreaks alter the structure and function of marine ecosystems, directly affecting vertebrates (mammals, turtles, fish), invertebrates (corals, crustaceans, echinoderms), and plants (seagrasses). Previous studies suggest a recent increase in marine disease. However, lack of baseline data in most communities prevents a direct test of this hypothesis. We developed a proxy to evaluate a prediction of the increasing disease hypothesis: the proportion of scientific publications reporting disease increased in recent decades. This represents, to our knowledge, the first quantitative use of normalized trends in the literature to investigate an ecological hypothesis. We searched a literature database for reports of parasites and disease (hereafter “disease”) in nine marine taxonomic groups from 1970 to 2001. Reports, normalized for research effort, increased in turtles, corals, mammals, urchins, and molluscs. No significant trends were detected for seagrasses, decapods, or sharks/rays (though disease occurred in these groups). Counter to the prediction, disease reports decreased in fishes. Formulating effective resource management policy requires understanding the basis and timing of marine disease events. Why disease outbreaks increased in some groups but not in others should be a priority for future investigation. The increase in several groups lends urgency to understanding disease dynamics, particularly since few viable options currently exist to mitigate disease in the oceans.

PLoS Biology↗

USGS2005

Hydrologic, water-quality, and biological assessment of Laguna de las Salinas, Ponce, Puerto Rico, January 2003-September 2004

The Laguna de Las Salinas is a shallow, 35-hectare, hypersaline lagoon (depth less than 1 meter) in the municipio of Ponce, located on the southern coastal plain of Puerto Rico. Hydrologic, water-quality, and biological data in the lagoon were collected between January 2003 and September 2004 to establish baseline conditions. During the study period, rainfall was about 1,130 millimeters, with much of the rain recorded during three distinct intense events. The lagoon is connected to the sea by a shallow, narrow channel. Subtle tidal changes, combined with low rainfall and high evaporation rates, kept the lagoon at salinities above that of the sea throughout most of the study. Water-quality properties measured on-site (temperature, pH, dissolved oxygen, specific conductance, and Secchi disk transparency) exhibited temporal rather than spatial variations and distribution. Although all physical parameters were in compliance with current regulatory standards for Puerto Rico, hyperthermic and hypoxic conditions were recorded during isolated occasions. Nutrient concentrations were relatively low and in compliance with current regulatory standards (less than 5.0 and 1.0 milligrams per liter for total nitrogen and total phosphorus, respectively). The average total nitrogen concentration was 1.9 milligrams per liter and the average total phosphorus concentration was 0.4 milligram per liter. Total organic carbon concentrations ranged from 12.0 to 19.0 milligrams per liter. Chlorophyll a was the predominant form of photosynthetic pigment in the water. The average chlorophyll a concentration was 13.4 micrograms per liter. Chlorophyll b was detected (detection limits 0.10 microgram per liter) only twice during the study. About 90 percent of the primary productivity in the Laguna de Las Salinas was generated by periphyton such as algal mats and macrophytes such as seagrasses. Of the average net productivity of 13.6 grams of oxygen per cubic meter per day derived from the diel study, the periphyton and macrophyes produced 12.3 grams per cubic meter per day; about 1.3 grams (about 10 percent) were produced by the phytoplankton (plant and algae component of plankton). The total respiration rate was 59.2 grams of oxygen per cubic meter per day. The respiration rate ascribed to the plankton (all organisms floating through the water column) averaged about 6.2 grams of oxygen per cubic meter per day (about 10 percent), whereas the respiration rate by all other organisms averaged 53.0 grams of oxygen per cubic meter per day (about 90 percent). Plankton gross productivity was 7.5 grams per cubic meter per day; the gross productivity of the entire community averaged 72.8 grams per cubic meter per day. Fecal coliform bacteria counts were generally less than 200 colonies per 100 milliliters; the highest concentration was 600 colonies per 100 milliliters.

Scientific Investigations Report↗

USGS2010

Mg isotope constraints on soil pore-fluid chemistry: Evidence from Santa Cruz, California

Mg isotope ratios ( 26 Mg/ 24 Mg) are reported in soil pore-fluids, rain and seawater, grass and smectite from a 90 kyr old soil, developed on an uplifted marine terrace from Santa Cruz, California. Rain water has an invariant 26 Mg/ 24 Mg ratio (expressed as δ26 Mg> δ26 Mg ) at −0.79 ± 0.05‰, identical to seawater δ26 Mg> δ26 Mg . Detrital smectite (from the base of the soil profile, and therefore unweathered) has a δ26Mg"> δ26Mg value of 0.11‰, potentially enriched in 26 Mg by up to 0.3‰ compared to the bulk silicate Earth Mg isotope composition (although within the range of all terrestrial silicates). The soil pore-waters show a continuous profile with depth for δ26 Mg> δ26 Mg , ranging from −0.99‰ near the surface to −0.43‰ at the base of the profile. Shallow pore-waters (<1 m) have δ26 Mg> δ26 Mg values that are similar to, or slightly lower than the rain waters. This implies that the degree of biological cycling of Mg in the pore-waters is relatively small and is quantified as <32%, calculated using the average Mg isotope enrichment factor between grass and rain ( δ26 Mggrass- δ26 Mgrain> δ26 Mggrass- δ26 Mgrain ) of 0.21‰. The deep pore-waters (1–15 m deep) have δ26 Mg> δ26 Mg values that are intermediate between the smectite and rain, ranging from −0.76‰ to −0.43‰, and show a similar trend with depth compared to Sr isotope ratios. The similarity between Sr and Mg isotope ratios confirms that the Mg in the pore-waters can be explained by a mixture between rain and smectite derived Mg, despite the fact that Mg and Sr concentrations may be buffered by the exchangeable reservoir. However, whilst Sr isotope ratios in the pore-waters span almost the complete range between mineral and rain inputs, Mg isotopes compositions are much closer to the rain inputs. If Mg and Sr isotope ratios are controlled uniquely by a mixture, the data can be used to estimate the mineral weathering inputs to the pore-waters, by correcting for the rain inputs. This isotopic correction is compared to the commonly used chloride correction for precipitation inputs. A consistent interpretation is only possible if Mg isotope ratios are fractionated either by the precipitation of a secondary Mg bearing phase, not detected by conventional methods, or selective leaching of 24 Mg from smectite. There is therefore dual control on the Mg isotopic composition of the pore-waters, mixing of two inputs with distinct isotopic compositions, modified by fractionation. The data provide (1) further evidence for Mg isotope fractionation at the surface of the Earth and (2) the first field evidence of Mg isotope fractionation during uptake by natural plants. The coherent behaviour of Mg isotope ratios in soil environments is encouraging for the development of Mg isotope ratios as a quantitative tracer of both weathering inputs of Mg to waters, and the physicochemical processes that cycle Mg, a major cation linked to the carbon cycle, during continental weathering.

California↗

USGS2005

North American Brant: Effects of changes in habitat and climate on population dynamics

We describe the importance of key habitats used by four nesting populations of nearctic brant (Branta bernicla) and discuss the potential relationship between changes in these habitats and population dynamics of brant. Nearctic brant, in contrast to most geese, rely on marine habitats and native intertidal plants during the non-breeding season, particularly the seagrass, Zostera, and the macroalgae, Ulva. Atlantic and Eastern High Arctic brant have experienced the greatest degradation of their winter habitats (northeastern United States and Ireland, respectively) and have also shown the most plasticity in feeding behavior. Black and Western High Arctic brant of the Pacific Flyway are the most dependent on Zostera, and are undergoing a shift in winter distribution that is likely related to climate change and its associated effects on Zostera dynamics. Variation in breeding propensity of Black Brant associated with winter location and climate strongly suggests that food abundance on the wintering grounds directly affects reproductive performance in these geese. In summer, salt marshes, especially those containing Carex and Puccinellia, are key habitats for raising young, while lake shorelines with fine freshwater grasses and sedges are important for molting birds. Availability and abundance of salt marshes has a direct effect on growth and recruitment of goslings and ultimately, plays an important role in regulating size of local brant populations. ?? 2005 Blackwell Publishing Ltd.

Global Change Biology↗

USGS2023

Ecosystem resilience to invasion and drought: Insights after 24 years in a rare never-grazed grassland

Understanding the resilience of ecosystems globally is hampered by the complex and interacting drivers of change characteristic of the Anthropocene. This is true for drylands of the western US, where widespread alteration of disturbance regimes and spread of invasive non-native species occurred with westward expansion during the 1800s, including the introduction of domestic livestock and spread of Bromus tectorum , an invasive non-native annual grass. In addition, this region has experienced a multi-decadal drought not seen for at least 1200 years with potentially large and interacting impacts on native plant communities. Here, we present 24 years of twice-annual plant cover monitoring (1997–2021) from a semiarid grassland never grazed by domestic livestock but subject to a patchy invasion of B. tectorum beginning in ~1994, compare our findings to surveys done in 1967, and examine potential climate drivers of plant community changes. We found a significant warming trend in the study area, with more than 75% of study year temperatures being warmer than average (1966–2021). We observed a native perennial grass community with high resilience to climate forcings with cover values like those in 1967. In invaded patches, B. tectorum cover was greatest in the early years of this study (1997–2001; ~20%–40%) but was subsequently constrained by climate and subtle variation in soils, with limited evidence of long-term impacts to native vegetation, contradicting earlier studies. Our ability to predict year-to-year variation in functional group and species cover with climate metrics varied, with a 12-month integrated index and fall and winter patterns appearing most important. However, declines to near zero live cover in recent years in response to regional drought intensification leave questions regarding the resiliency of intact grasslands to ongoing aridification and whether the vegetation observations reported here may be a leading indicator of impending change in this protected ecosystem.

Utah↗

USGS2021

A framework for allocating conservation resources among multiple threats and actions

Land managers decide how to allocate resources among multiple threats that can be addressed through multiple possible actions. Additionally, these actions vary in feasibility, effectiveness, and cost. We sought to provide a way to optimize resource allocation to address multiple threats when multiple management options are available, including mutually exclusive options. Formulating the decision as a combinatorial optimization problem, our framework takes as inputs the expected impact and cost of each threat for each action (including do nothing) and for each overall budget identifies the optimal action to take for each threat. We compared the optimal solution to an easy to calculate greedy algorithm approximation and a variety of plausible ranking schemes. We applied the framework to management of multiple introduced plant species in Australian alpine areas. We developed a model of invasion to predict the expected impact in 50 years for each species‐action combination that accounted for each species’ current invasion state (absent, localized, widespread); arrival probability; spread rate; impact, if present, of each species; and management effectiveness of each species‐action combination. We found that the recommended action for a threat changed with budget; there was no single optimal management action for each species; and considering more than one candidate action can substantially increase the management plan's overall efficiency. The approximate solution (solution ranked by marginal cost‐effectiveness) performed well when the budget matched the cost of the prioritized actions, indicating that this approach would be effective if the budget was set as part of the prioritization process. The ranking schemes varied in performance, and achieving a close to optimal solution was not guaranteed. Global sensitivity analysis revealed a threat's expected impact and, to a lesser extent, management effectiveness were the most influential parameters, emphasizing the need to focus research and monitoring efforts on their quantification.

Conservation Biology↗

USGS2021

Divergent climate change effects on widespread dryland plant communities driven by climatic and ecohydrological gradients

Plant community response to climate change will be influenced by individual plant responses that emerge from competition for limiting resources that fluctuate through time and vary across space. Projecting these responses requires an approach that integrates environmental conditions and species interactions that result from future climatic variability. Dryland plant communities are being substantially affected by climate change because their structure and function are closely tied to precipitation and temperature, yet impacts vary substantially due to environmental heterogeneity, especially in topographically complex regions. Here, we quantified the effects of climate change on big sagebrush ( Artemisia tridentata Nutt.) plant communities that span 76 million ha in the western United States. We used an individual-based plant simulation model that represents intra- and inter-specific competition for water availability, which is represented by a process-based soil water balance model. For dominant plant functional types, we quantified changes in biomass and characterized agreement among 52 future climate scenarios. We then used a multivariate matching algorithm to generate fine-scale interpolated surfaces of functional type biomass for our study area. Results suggest geographically divergent responses of big sagebrush to climate change (changes in biomass of −20% to +27%), declines in perennial C 3 grass and perennial forb biomass in most sites, and widespread, consistent, and sometimes large increases in perennial C 4 grasses. The largest declines in big sagebrush, perennial C 3 grass and perennial forb biomass were simulated in warm, dry sites. In contrast, we simulated no change or increases in functional type biomass in cold, moist sites. There was high agreement among climate scenarios on climate change impacts to functional type biomass, except for big sagebrush. Collectively, these results suggest divergent responses to warming in moisture-limited versus temperature-limited sites and potential shifts in the relative importance of some of the dominant functional types that result from competition for limiting resources.

Global Change Biology↗

USGS2010

Selected Hydrologic, Water-Quality, Biological, and Sedimentation Characteristics of Laguna Grande, Fajardo, Puerto Rico, March 2007-February 2009

Laguna Grande is a 50-hectare lagoon in the municipio of Fajardo, located in the northeasternmost part of Puerto Rico. Hydrologic, water-quality, and biological data were collected in the lagoon between March 2007 and February 2009 to establish baseline conditions and determine the health of Laguna Grande on the basis of preestablished standards. In addition, a core of bottom material was obtained at one site within the lagoon to establish sediment depositional rates. Water-quality properties measured onsite (temperature, pH, dissolved oxygen, specific conductance, and water transparency) varied temporally rather than areally. All physical properties were in compliance with current regulatory standards established for Puerto Rico. Nutrient concentrations were very low and in compliance with current regulatory standards (less than 5.0 and 1.0 milligrams per liter for total nitrogen and total phosphorus, respectively). The average total nitrogen concentration was 0.28 milligram per liter, and the average total phosphorus concentration was 0.02 milligram per liter. Chlorophyll a was the predominant form of photosynthetic pigment in the water. The average chlorophyll-a concentration was 6.2 micrograms per liter. Bottom sediment accumulation rates were determined in sediment cores by modeling the downcore activities of lead-210 and cesium-137. Results indicated a sediment depositional rate of about 0.44 centimeter per year. At this rate of sediment accretion, the lagoon may become a marshland in about 700 to 900 years. About 86 percent of the community primary productivity in Laguna Grande was generated by periphyton, primarily algal mats and seagrasses, and the remaining 14 percent was generated by phytoplankton in the water column. Based on the diel studies the total average net community productivity equaled 5.7 grams of oxygen per cubic meter per day (2.1 grams of carbon per cubic meter per day). Most of this productivity was ascribed to periphyton and macrophytes, which produced 4.9 grams of oxygen per cubic meter per day (1.8 grams of carbon per cubic meter per day). Phytoplankton, the plant and algal component of plankton, produced about 0.8 gram of oxygen per cubic meter per day (0.3 gram of carbon per cubic meter per day). The total diel community respiration rate was 23.4 grams of oxygen per cubic meter per day. The respiration rate ascribed to plankton, which consists of all free floating and swimming organisms in the water column, composed 10 percent of this rate (2.9 grams of oxygen per cubic meter per day); respiration by all other organisms composed the remaining 90 percent (20.5 grams of oxygen per cubic meter per day). Plankton gross productivity was 3.7 grams of oxygen per cubic meter per day, equivalent to about 13 percent of the average gross productivity for the entire community (29.1 grams of oxygen per cubic meter per day). The average phytoplankton biomass values in Laguna Grande ranged from 6.0 to 13.6 milligrams per liter. During the study, Laguna Grande contained a phytoplankton standing crop of approximately 5.8 metric tons. Phytoplankton community had a turnover (renewal) rate of about 153 times per year, or roughly about once every 2.5 days. Fecal indicator bacteria concentrations ranged from 160 to 60,000 colonies per 100 milliliters. Concentrations generally were greatest in areas near residential and commercial establishments, and frequently exceeded current regulatory standards established for Puerto Rico.

Scientific Investigations Report↗

USGS2023

Near-field receiving-water monitoring of trace metals and a benthic community near the Palo Alto Regional Water Quality Control Plant in south San Francisco Bay, California—2020

Trace-metal concentrations in sediment and in the clam Limecola petalum (World Register of Marine Species, 2020; formerly reported as Macoma balthica and M. petalum ), clam reproductive activity, and benthic macroinvertebrate community structure were investigated in a mudflat 1 kilometer (km) south of the discharge of the Palo Alto Regional Water Quality Control Plant (PARWQCP) in south San Francisco Bay, California. This report includes the data collected by the U.S. Geological Survey (USGS) for January 2020–December 2020 (Cain and others, 2022). These data append to long-term datasets extending back to 1974. A major focus of the report is an integrated description of the 2020 data within the context of the longer, multidecadal dataset. This dataset supports the City of Palo Alto’s Near-Field Receiving- Water Monitoring Program, initiated in 1994. Silver and copper contamination substantially decreased at the site in the 1980s following the implementation by PARWQCP of advanced wastewater-treatment and source-control measures. Since the 1990s, concentrations of these elements in surface sediments have continued to decrease, although more slowly. For example, from 1994 to 2020, the minimum annual mean silver concentration—0.20 milligram per kilogram (mg/kg)—was observed in multiple years. In 2020, silver concentrations ranged from 0.18 to 0.28 mg/kg. These concentrations are 2 to 3 times higher than the regional background concentration. Presently (2020), sediment-copper concentrations appear to be near the regional background level. Over the same period (1994–2020), sedimentary iron and zinc exhibited modest decreases. Sedimentary aluminum, chromium, mercury, nickel, and selenium have not exhibited any trend. Since 1994, silver and copper concentrations in L. petalum have varied seasonally, apparently in response to a combination of site-specific metal exposures and cyclic growth and reproduction, as reported previously. Seasonal patterns for other elements, including chromium, mercury, nickel, selenium, and zinc, generally were similar in timing and magnitude as those for silver and copper. Downward trends in the silver and zinc concentrations in L. petalum during 1994–2020 were evident and appeared to be related to the general physiological condition of the clam, indicated by a condition index. Biological effects of elevated silver and copper contamination at the Palo Alto site have been interpreted from data collected during and after the recession of these contaminants. Concentrations of both elements in the soft tissues of L. petalum decreased with sedimentary copper and silver. This pattern was associated with changes in the reproductive activity of L. petalum , as well as the structure of the benthic invertebrate community. Reproductive activity of L. petalum increased as metal concentrations in L. petalum decreased (Hornberger and others, 2000), and presently is stable with almost all animals initiating reproduction in the fall and spawning the following spring. Analyses of the benthic community structure indicate that the infaunal invertebrate community has shifted from one dominated by several opportunistic species when silver and copper exposures were highest to one in which the species abundance is more evenly distributed, a pattern that indicates a more stable community that is subjected to fewer stressors. Importantly, this long-term change is unrelated to other metals and other measured environmental factors, including salinity and sediment composition. In addition, two of the opportunistic species ( Ampelisca abdita and Streblospio benedicti ) that brood their young and live on the surface of the sediment in tubes have shown a continual decrease in dominance coincident with the decrease in metals. Both species had short-lived rebounds in abundance in 2008, 2009, and 2010 and showed signs of increasing abundance in 2020. Heteromastus filiformis (a subsurface polychaete worm that lives in the sediment, consumes sediment and organic particles residing in the sediment, and reproduces by laying its eggs on or in the sediment) showed a concurrent increase in dominance and, in the last several years before 2008, showed a stable population. H. filiformis abundance increased slightly from 2011 to 2012 and returned to pre-2011 numbers in 2020. The reproductive mode of most species that were present in 2020 was indicative of species that were capable of movement either as pelagic larvae or as mobile adults. Although oviparous species were lower in number in this group, the authors hypothesize that these species will return slowly as more species move back into the area. The use of functional ecology was highlighted in the 2020 benthic community data, which showed that the animals that have now returned to the mudflat are those that can respond successfully to a physical, nontoxic disturbance. Today, community data show a mix of species that consume the sediment, or filter feed, those that have pelagic larvae that must survive landing on the sediment, and those that brood their young. The long-term recovery observed after the 1970s can be ascribed to the decrease in sediment pollutants.

California↗

USGS2000

Cassin's Sparrow (Aimophila cassinii) status assessment and conservation plan

Executive Summary Cassin’s Sparrow ( Aimophila cassinii ) is a grassland species endemic to the southwestern U.S. and northern Mexico. Its behavior and ecology have been shaped by these arid ecosystems and the health of its populations is dependent on the availability of grasslands that contain a shrub component. Populations of many grassland birds have experienced dramatic declines due to the loss and deterioration of grassland habitats, and there has been concern about the trends in Cassin’s Sparrow populations. Without better information about population trends, ecology, and effects of management activities, and without a stronger emphasis on grassland management, Cassin’s Sparrows and other grassland species may continue to experience declines. Little information exists about historic Cassin’s Sparrow population levels, and current population estimates for states in the breeding range are unknown. Significant survey-wide declines are documented by the Breeding Bird Survey (BBS) between 1966 and 1996. However, closer examination of these data suggest that the survey-wide trends are driven by population declines in the Edwards Plateau and South Texas Brushlands in Texas. No other areas within the core of its range or on the periphery show consistent, significant trends. In fact, there is consensus that in the core of its range in New Mexico Cassin’s Sparrow remains the most abundant breeding bird in grasslands with a shrub component. Understanding of population patterns in this species is complicated by large yearly fluctuations in distribution and numbers at any particular location, apparently in response to precipitation. This is particularly obvious in the periphery of its range. These dramatic fluctuations have hampered a clear assessment of population status, and our understanding has been confounded by the fact that the timing of BBS data collection does not always coincide with the peak breeding season of this species. The lack of information about the Cassin’s Sparrow’s status, ecology, and response to management activities, and the apparent declines indicated by BBS data, have been cause for concern. Habitat disturbance and degradation, mainly due to grazing and rangeland management practices such as shrub control, fire management, and planting of exotics, pose threats to Cassin’s Sparrow populations, as does habitat conversion through suburban development and agriculture. There is evidence that heavy grazing negatively affects populations, but the information is primarily available from the southwestern portion of its range (Arizona) and may not be applicable throughout the Cassin’s Sparrow’s entire range. Any management practice that results in complete removal of the shrub component, or loss of grass cover and an increase in shrub density beyond a threshold preferred by the species, also poses a threat. Lack of standardized or coordinated studies of Cassin’s Sparrow ecology and response to management practices in different geographic portions of its range has made it difficult to assess its status and make specific management recommendations. Limited data are available from the wintering grounds, and from its range (both breeding and wintering) in Mexico. The greatest needs are for determining of the causes of significant declines where they occur, determining of the effects of various management activities on Cassin’s Sparrow throughout its range, improved assessments of population and trends, and a better understanding of the annual population and distribution dynamics of this species, which shows such dramatic annual distributional fluctuations.

Wyoming, Nebraska, Kansas, Oklahoma,Texas, New Mex↗

USGS2020

Ultra‐high‐resolution mapping of biocrusts with Unmanned Aerial Systems

Biological soil crusts (biocrusts) occur in drylands globally where they support ecosystem functioning by increasing soil stability, reducing dust emissions and modifying soil resource availability (e.g. water, nutrients). Determining biocrust condition and extent across landscapes continues to present considerable challenges to scientists and land managers. Biocrusts grow in patches, cover vast expanses of rugged terrain and are vulnerable to physical disturbance associated with ground‐based mapping techniques. As such, remote sensing offers promising opportunities to map and monitor biocrusts. While satellite‐based remote sensing has been used to detect biocrusts at relatively large spatial scales, few studies have used high‐resolution imagery from Unmanned Aerial Systems (UAS) to map fine‐scale patterns of biocrusts. We collected sub‐centimeter, true color 3‐band imagery at 10 plots in sagebrush and pinyon‐juniper woodland communities in a semiarid ecosystem in the southwestern US and used object‐based image analysis (OBIA) to segment and classify the imagery into maps of light and dark biocrusts, bare soil, rock and various vegetation covers. We used field data to validate the classifications and assessed the spatial distribution and configuration of different classes using fragmentation metrics. Map accuracies ranged from 46 to 77% (average 65%) and were higher in pinyon‐juniper (average 70%) versus sagebrush (average 60%) plots. Biocrust classes showed generally high accuracies at both pinyon‐juniper plots (average dark crust = 70%; light crust = 80%) and sagebrush plots (average dark crust = 69%; light crust = 77%). Point cloud density, sun elevation and spectral confusion between vegetation cover explained some differences in accuracy across plots. Spatial analyses of classified maps showed that biocrust patches in pinyon‐juniper plots were generally larger, more aggregated and contiguous than in sagebrush plots. Pinyon‐juniper plots also had greater patch richness and a lower Shannon evenness index than sagebrush plots, suggesting greater soil cover heterogeneity in this plant community type.

Utah↗