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USGS2018

Biota connect aquatic habitats throughout freshwater ecosystem mosaics

Freshwater ecosystems are linked at various spatial and temporal scales by movements of biota adapted to life in water. We review the literature on movements of aquatic organisms that connect different types of freshwater habitats, focusing on linkages from streams and wetlands to downstream waters. Here, streams, wetlands, rivers, lakes, ponds, and other freshwater habitats are viewed as dynamic freshwater ecosystem mosaics (FEMs) that collectively provide the resources needed to sustain aquatic life. Based on existing evidence, it is clear that biotic linkages throughout FEMs have important consequences for biological integrity and biodiversity. All aquatic organisms move within and among FEM components, but differ in the mode, frequency, distance, and timing of their movements. These movements allow biota to recolonize habitats, avoid inbreeding, escape stressors, locate mates, and acquire resources. Cumulatively, these individual movements connect populations within and among FEMs and contribute to local and regional diversity, resilience to disturbance, and persistence of aquatic species in the face of environmental change. Thus, the biological connections established by movement of biota among streams, wetlands, and downstream waters are critical to the ecological integrity of these systems. Future research will help advance our understanding of the movements that link FEMs and their cumulative effects on downstream waters.

Journal of the American Water Resources Associatio↗

USGS2003

Application of ecological criteria in selecting marine reserves and developing reserve networks

Marine reserves are being established worldwide in response to a growing recognition of the conservation crisis that is building in the oceans. However, designation of reserves has been largely opportunistic, or protective measures have been implemented (often overlapping and sometimes in conflict) by different entities seeking to achieve different ends. This has created confusion among both users and enforcers, and the proliferation of different measures provides a false sense of protection where little is offered. This paper sets out a procedure grounded in current understanding of ecological processes, that allows the evaluation and selection of reserve sites in order to develop functional, interconnected networks of fully protected reserves that will fulfill multiple objectives. By fully protected we mean permanently closed to fishing and other resource extraction. We provide a framework that unifies the central aims of conservation and fishery management, while also meeting other human needs such as the provision of ecosystem services (e.g., maintenance of coastal water quality, shoreline protection, and recreational opportunities). In our scheme, candidate sites for reserves are evaluated against 12 criteria focused toward sustaining the biological integrity and productivity of marine systems at both local and regional scales. While a limited number of sites will be indispensable in a network, many will be of similar value as reserves, allowing the design of numerous alternative, biologically adequate networks. Devising multiple network designs will help ensure that ecological functionality is preserved throughout the socioeconomic evaluation process. Too often, socioeconomic criteria have dominated the process of reserve selection, potentially undermining their efficacy. We argue that application of biological criteria must precede and inform socioeconomic evaluation, since maintenance of ecosystem functioning is essential for meeting all of the goals for reserves. It is critical that stakeholders are fully involved throughout this process. Application of the proposed criteria will lead to networks whose multifunctionality will help unite the objectives of different management entities, so accelerating progress toward improved stewardship of the oceans.

Ecological Applications↗

USGS2004

Stream salamanders as indicators of stream quality in Maryland, USA

Biological indicators are critical to the protection of small, headwater streams and the ecological values they provide. Maryland and other state monitoring programs have determined that fish indicators are ineffective in small streams, where stream salamanders may replace fish as top predators. Because of their life history, physiology, abundance, and ubiquity, stream salamanders are likely representative of biological integrity in these streams. The goal of this study was to determine whether stream salamanders are effective indicators of ecological conditions across biogeographic regions and gradients of human disturbance. During the summers of 2001 and 2002, we intensively surveyed for stream salamanders at 76 stream sites located west of the Maryland Coastal Plain, sites also monitored by the Maryland Biological Stream Survey (MBSS) and City of Gaithersburg. We found 1,584 stream salamanders, including all eight species known in Maryland, using two 15 ? 2 m transects and two 4 m2 quadrats that spanned both stream bank and channel. We performed removal sampling on transects to estimate salamander species detection probabilities, which ranged from 0.67-0.85. Stepwise regressions identified 15 of 52 non-salamander variables, representing water quality, physical habitat, land use, and biological conditions, which best predicted salamander metrics. Indicator development involved (1) identifying reference (non-degraded) and degraded sites (using percent forest, shading, riparian buffer width, aesthetic rating, and benthic macroinvertebrate and fish indices of biotic integrity); (2) testing 12 candidate salamander metrics (representing species richness and composition, abundance, species tolerance, and reproductive function) for their ability to distinguish reference from degraded sites; and (3) combining metrics into an index that effectively discriminated sites according to known stream conditions. Final indices for Highlands, Piedmont, and Non-Coastal Plain regions comprised four metrics: number of species, number of salamanders, number of intolerant salamanders, and number of adult salamanders, producing classification efficiencies between 87% and 90%. Partial validation of these indices was obtained when a test of the number of salamanders metric produced an 82% correct classification of 618 MBSS sites surveyed in 1995-97. This study supports the use of stream salamander monitoring and a composite stream salamander index of biotic integrity (SS-IBI) to determine stream quality in Maryland.

Applied Herpetology↗

USGS2008

Occurrence of endocrine active compounds and biological responses in the Mississippi River— Study design and data, June through August 2006

Concern that selected chemicals in the environment may act as endocrine active compounds in aquatic ecosystems is widespread; however, few studies have examined the occurrence of endocrine active compounds and identified biological markers of endocrine disruption such as intersex occurrence in fish longitudinally in a river system. This report presents environmental data collected and analyzed by the U.S. Geological Survey, Minnesota Pollution Control Agency and St. Cloud State University as part of an integrated biological and chemical study of endocrine disruption in fish in the Mississippi River. Data were collected from water, bed sediment, and fish at 43 sites along the river from the headwaters at Lake Itasca to 14 miles downstream from Brownsville, Minnesota during June through August 2006. Twenty-four individual compounds were detected in water samples, with cholesterol, atrazine, N,N-diethyl-meta-toluamide, metolachlor, and hexahydrohexamethylcyclopentabenzopyran detected most frequently (in at least 10 percent of the samples). The number of compounds detected in water per site ranged from 0 to 8. Forty individual compounds were detected in bed-sediment samples. The most commonly detected compounds (in at least 50 percent of the samples) were indole, beta-sitosterol, cholesterol, beta-stigmastanol, 3-methyl-1H-indole, p-cresol, pyrene, phenol, fluoranthene, 3-beta coprostanol, benzo[a]pyrene, acetophenone, and 2,6-dimethylnaphthalene. The total number of detections in bed sediment (at a site) ranged from 3 to 31. The compounds NP1EO, NP2EO, and 4-nonylphenol were detected in greater than 10 percent of the samples. Most (80 percent) female fish collected had measurable concentrations of vitellogenin. Vitellogenin also was detected in 62, 63, and 33 percent of male carp, smallmouth bass, and redhorse, respectively. The one male walleye sample plasma sample analyzed had a vitellogenin detection. Vitellogenin concentrations were lower in male fish (not detected to 10.80 micrograms per milliliter) than female fish (0.04 to 248,079 micrograms per milliliter). Gonadosomatic Index values ranged from 0.02 to 7.49 percent among all male fish and were greater for male carp than for the other three species. No intersex (oocytes present in testes tissue) was found in any male fish sampled.

Minnesota, Wisconsin↗

USGS2021

Seasonal periphyton response to low-level nutrient exposure in a least disturbed mountain stream, the Buffalo River, Arkansas

Like most streams located in the Ozark Plateaus, the Buffalo River in Arkansas generally has excellent water quality. Water-quality conditions in Big Creek, however, a major tributary of the middle Buffalo River, have been less favorable than that of other Buffalo River tributaries. Concerns regarding the influence of water quality in Big Creek on the Buffalo River magnified in 2013 when a large confined animal feeding operation (CAFO) began operating in the watershed. In response to these concerns, the U.S. Geological Survey compared monthly nutrient concentrations and seasonal periphyton assemblage metrics of a site on Big Creek downstream of the CAFO, two Buffalo River control sites upstream of the confluence with Big Creek, and three Buffalo River test sites downstream of the confluence with Big Creek. In addition to identifying potential nutrient patterns and periphyton responses along a low-level nutrient exposure gradient, the study determined how nutrient contributions from Big Creek (and the CAFO) are affecting ecological conditions and consequent ecosystem services in the Buffalo River. Nutrient and periphyton data exhibited more temporal than spatial variability. Nutrient concentrations were generally highest of all sites at the Big Creek site. Concentrations at the five sites on the Buffalo River were typically low (near laboratory reporting limits), and concentrations at the three test sites rarely exceeded those of the two control sites. An index developed with three ecologically relevant periphyton metrics (oligotrophic taxa and Homoeothrix percent relative abundance and mesotrophic diatoms percent taxa richness) suggested that nutrient uptake at sites downstream of the Big Creek-Buffalo River confluence resulted in subtle shifts in downstream periphyton assemblages. The periphyton index of biological integrity at control sites was slightly and generally more favorable compared to test sites. Even so, when periphyton data were considered in conjunction with both hydrology and water-quality data, the negative consequences of antecedent high flows and associated scouring exceeded the potential positive effects that low-level nutrients had on algal productivity. These findings emphasize the importance of comparing biological and chemical data across extended temporal scales, particularly when working with low-level nutrient gradients.

Arkansas↗

USGS2018

Tools for managing hydrologic alteration on a regional scale II: Setting targets to protect stream health

Widespread hydrologic alteration creates a need for tools to assess ecological impacts to streams that can be applied across large geographic scales. A regional framework for biologically based flow management can help catchment managers prioritise streams for protection, evaluate impacts of disturbance or interventions and provide a starting point for causal assessment in degraded streams. However, lack of flow data limit the ability to assess hydrologic conditions across a region. Hydrologic models can address this problem. Regionally calibrated hydrologic models were used to estimate current and reference flows at 572 bioassessment sites in southern and central coastal California. Flow alteration was characterised as the difference in 39 flow metrics calculated from simulations of present‐day and reference flow time‐series, calculated under up to four precipitation conditions. Biological condition was assessed with the California Stream Condition Index (CSCI) and its components. Logistic regressions were used to predict the likelihood of high scores (i.e. ≥10th percentile of the CSCI reference calibration data). Statistically significant relationships between increasing severity of hydrologic alteration and decreasing biological condition were used to set thresholds that reflected tolerance for risk of a stakeholder advisory group. An index of hydrologic alteration was created by selecting flow metrics based on their importance for predicting biological response variables in boosted regression tree models. Metrics were selected in the order of decreasing importance, and no more than two metrics per metric class were selected (i.e. duration, frequency, magnitude, timing and variability). Seven metrics were selected: HighDur (duration of high‐flow events), HighNum (# of high‐flow events), NoDisturb (duration between high‐ or low‐flow events), MaxMonthQ (maximum monthly discharge), Q99 (99th percentile of daily streamflow), QmaxIDR (interdecile range of annual maxima) and RBI (Richards–Baker Index). Applying the index to data from a probabilistic survey, 34% of stream‐miles in southern California were estimated to be hydrologically altered. One of four management priorities were assigned to each site based on biological condition and hydrologic status: protection (healthy and unaltered, 52% of stream‐miles), monitoring (healthy but altered 4%), evaluation of flow management (unhealthy and altered, 30%) and evaluation of other management (unhealthy but unaltered, 14%). Regionally derived biologically based targets for flow alteration allow catchment managers to prioritise activities and conduct screenings for causal assessments across large spatial scales. Furthermore, regional tools pave the way for incorporation of hydrologic management in policies and catchment planning designed to support biological integrity in streams. Development of regional tools should be a priority where hydrologic alteration is pervasive or expected to increase in response to climate change or urbanisation.

Freshwater Biology↗

USGS2016

Evaluating the adequacy of a reference site pool for ecological assessments in environmentally complex regions

Many advances in the field of bioassessment have focused on approaches for objectively selecting the pool of reference sites used to establish expectations for healthy waterbodies, but little emphasis has been placed on ways to evaluate the suitability of the reference-site pool for its intended applications (e.g., compliance assessment vs ambient monitoring). These evaluations are critical because an inadequately evaluated reference pool may bias assessments in some settings. We present an approach for evaluating the adequacy of a reference-site pool for supporting biotic-index development in environmentally heterogeneous and pervasively altered regions. We followed common approaches for selecting sites with low levels of anthropogenic stress to screen 1985 candidate stream reaches to create a pool of 590 reference sites for assessing the biological integrity of streams in California, USA. We assessed the resulting pool of reference sites against 2 performance criteria. First, we evaluated how well the reference-site pool represented the range of natural gradients present in the entire population of streams as estimated by sites sampled through probabilistic surveys. Second, we evaluated the degree to which we were successful in rejecting sites influenced by anthropogenic stress by comparing biological metric scores at reference sites with the most vs fewest potential sources of stress. Using this approach, we established a reference-site pool with low levels of human-associated stress and broad coverage of environmental heterogeneity. This approach should be widely applicable and customizable to particular regional or programmatic needs.

California↗

USGS2020

Diatom enumeration method influences biological assessments of southeastern USA streams

Current fixed-count enumeration methods for benthic diatoms are likely inadequate for most research and monitoring objectives. These methods underestimate taxa richness and may fail to detect losses of species caused by human impacts. Consequently, the full potential of diatoms is not realized in current assessments of biological integrity or species diversity. In this study, we hypothesize that alternative enumeration methods differ in their ability to quantify species composition. Furthermore, we hypothesize that an alternative to the traditional fixed-count method will improve both performance of observed/expected (O/E) indices derived from River Inver- tebrate Prediction and Classification System models and the discrimination of reference-quality and human-modified sites by other standard metrics used in biological assessments. To test these hypotheses, we assessed 1) how well 3 counting methods characterized species richness in a subset of 15 samples of stream benthic diatoms and 2) how counting method affected the performance of O/E indices and metrics by comparing the traditional fixed- count method against the best-performing alternative method. These latter comparisons were based on samples collected from 68 reference-quality streams and 20 streams located along an urban disturbance gradient. We dem- onstrate that traditional fixed counts failed to detect >1⁄2 of species present in most of the 68 reference-quality sites. Instead, timed-presence data produced the O/E index with the best performance and a level of precision similar to published invertebrate O/E indices. Furthermore, the O/E index based on the timed-presence data allowed us to determine which species are most often lost with urbanization. We found that traditional fixed-count and alter- native timed-presence data produce metrics that are nearly equally able to discriminate between reference and dis- turbed sites. This study demonstrates that alternative counting methods improve species detection and require up to ∼30% less effort.

Arkansas, Alabama, Georgia, Louisiana, Maryland, M↗

USGS1999

Assessing biological effects from highway-runoff constituents

Increased emphasis on evaluation of nonpoint-source pollution has intensified the need for techniques that can be used to discern the toxicological effects of complex chemical mixtures. In response, the use of biological assessment techniques is receiving increased regulatory emphasis. When applied with documented habitat assessment and chemical analysis, these techniques can increase our understanding of the influence of environmental contaminants on the biological integrity and ecological function of aquatic communities. The contaminants of greatest potential concern in highway runoff are those that arise from highway construction, maintenance, and use. The major contaminants of interest are deicers; nutrients; metals; petroleum-related organic compounds, such as polycyclic aromatic hydrocarbons (PAHs), benzene, toluene, ethylbenzene, and xylene (BTEX), and methyl tert -butyl ether (MTBE); sediment washed off the road surface; and agricultural chemicals used in highway maintenance. Hundreds, if not thousands, of biological endpoints (measurable responses of living organisms) may be either directly or associatively affected by contaminant exposure. Measurable effects can occur throughout ecosystem processes across the wide range of biological complexity, ranging from responses at the biochemical level to the community level. The challenge to the environmental scientist is to develop an understanding of the relationship of effects at various levels of biological organization in order to determine whether a causal relationship exists between chemical exposure and substantial ecological impairment. This report provides a brief history of the evolution of biological assessment techniques, a description of the major classes of contaminants that are of particular interest in highway runoff, an overview of representative biological assessment techniques, and a discussion of data-quality considerations. Published reports with a focus on the effects of highway runoff on the local ecosystem were reviewed to provide information on (1) the suitability of the existing data for a quantitative national synthesis, (2) the methods available to study the effects of highway runoff on local ecosystems, and (3) the potential for adverse effects on the roadside environment and receiving waters. Although many biological studies have been done, the use of different methods and a general lack of sufficient documentation precludes a quantitative national synthesis on the basis of the existing data. The Federal Highway Administration, the U.S. Environmental Protection Agency, the U.S. Geological Survey, the Intergovernmental Task Force on Monitoring Water Quality, and the National Resources Conservation Service all have developed and documented methods for assessing the effects of contaminants on ecosystems in receiving waters. These published methods can be used to formulate a set of protocols to provide consistent information from highway-runoff studies. Review of the literature indicates (qualitatively) that highway runoff (even from highways with high traffic volume) may not usually be acutely toxic. Tissue analysis and community assessments, however, indicate effects from highway- runoff sediments near discharge points (even from sites near highways with relatively low traffic volumes). At many sites, elevated concentrations of highway-runoff constituents were measured in tissues of species associated with aquatic sediments. Community assessments also indicate decreases in the diversity and productivity of aquatic ecosystems at some sites receiving highway runoff. These results are not definitive, however, and depend on many site-specific criteria that were not sufficiently documented in most of the studies reviewed.

Open-File Report↗

USGS2015

Empirical evaluation of the conceptual model underpinning a regional aquatic long-term monitoring program using causal modelling

Conceptual models are an integral facet of long-term monitoring programs. Proposed linkages between drivers, stressors, and ecological indicators are identified within the conceptual model of most mandated programs. We empirically evaluate a conceptual model developed for a regional aquatic and riparian monitoring program using causal models (i.e., Bayesian path analysis). We assess whether data gathered for regional status and trend estimation can also provide insights on why a stream may deviate from reference conditions. We target the hypothesized causal pathways for how anthropogenic drivers of road density, percent grazing, and percent forest within a catchment affect instream biological condition. We found instream temperature and fine sediments in arid sites and only fine sediments in mesic sites accounted for a significant portion of the maximum possible variation explainable in biological condition among managed sites. However, the biological significance of the direct effects of anthropogenic drivers on instream temperature and fine sediments were minimal or not detected. Consequently, there was weak to no biological support for causal pathways related to anthropogenic drivers’ impact on biological condition. With weak biological and statistical effect sizes, ignoring environmental contextual variables and covariates that explain natural heterogeneity would have resulted in no evidence of human impacts on biological integrity in some instances. For programs targeting the effects of anthropogenic activities, it is imperative to identify both land use practices and mechanisms that have led to degraded conditions (i.e., moving beyond simple status and trend estimation). Our empirical evaluation of the conceptual model underpinning the long-term monitoring program provided an opportunity for learning and, consequently, we discuss survey design elements that require modification to achieve question driven monitoring, a necessary step in the practice of adaptive monitoring. We suspect our situation is not unique and many programs may suffer from the same inferential disconnect. Commonly, the survey design is optimized for robust estimates of regional status and trend detection and not necessarily to provide statistical inferences on the causal mechanisms outlined in the conceptual model, even though these relationships are typically used to justify and promote the long-term monitoring of a chosen ecological indicator. Our application demonstrates a process for empirical evaluation of conceptual models and exemplifies the need for such interim assessments in order for programs to evolve and persist.

California, Colorado, Idaho, Montana, Nevada, Oreg↗

USGS2000

Bioassessment of Hollis Creek, Oktibbeha County, Mississippi

Physical, chemical and biological components at five stations on Hollis Creek, Oktibbeha County, Mississippi were evaluated using Rapid Bioassessment Protocols (RBP) and the Sediment Quality Triad (SQT) on August 24-26, 1999, in order to assess potential biological impacts from the Starkville Waste Water Treatment Facility (WWTF) on downstream resources. Two stations were selected above the WWTF and three below. The WWTF discharges treated effluent into Hollis Creek, but during storm events raw sewage may be released. Hollis Creek is a tributary of the Noxubee River that traverses the northern portion of Noxubee National Wildlife Refuge, which is managed as bottomland hardwood forest land for the protection of fish and wildlife resources. Hollis Creek was channelized throughout most of its length, resulting in high, unstable banks, degraded stream channel and unstable substratum. The RBP scores for the habitat evaluations from each station indicated that Stations 1 and 2 had degraded habitat compared to the reference site, Station 5. Benthic macroinvertebrate and fish assemblages also indicated that the biological integrity at Stations 1 and 2 was less than that of the downstream stations. The SQT showed that Stations 1 and 2 were degraded and the most likely causes of the impairment were the elevated concentrations of polycylclic aromatic hydrocarbons and metals in the sediments; Hyalella azteca survival in pore water and growth in solid-phase sediment exposures were reduced at these upstream sites. The source of contaminants to the upper reaches appears to be storm-water runoff. The close concordance between the RBP and SQT in identifying site degradation provided a preponderance of evidence indicating that the upper reaches (Stations 1 and 2) of Hollis Creek were impacted. Biological conditions improved downstream of the WWTF, even though physical degradation steinming from channelization activities were still evident. The increased discharge and stabilized base flow provided by the WWTF appeared to benefit the physically-altered stream system. Impairment attributable to releases from the WWTF on downstream biological resources was not evident from this evaluation, and the potential for degradation in the Noxubee River and National Wildlife Refuge appears minimal.

Book↗

USGS2016

Moss and vascular plant indices in Ohio wetlands have similar environmental predictors

Mosses and vascular plants have been shown to be reliable indicators of wetland habitat delineation and environmental quality. Knowledge of the best ecological predictors of the quality of wetland moss and vascular plant communities may determine if similar management practices would simultaneously enhance both populations. We used Akaike's Information Criterion to identify models predicting a moss quality assessment index (MQAI) and a vascular plant index of biological integrity based on floristic quality (VIBI-FQ) from 27 emergent and 13 forested wetlands in Ohio, USA. The set of predictors included the six metrics from a wetlands disturbance index (ORAM) and two landscape development intensity indices (LDIs). The best single predictor of MQAI and one of the predictors of VIBI-FQ was an ORAM metric that assesses habitat alteration and disturbance within the wetland, such as mowing, grazing, and agricultural practices. However, the best single predictor of VIBI-FQ was an ORAM metric that assessed wetland vascular plant communities, interspersion, and microtopography. LDIs better predicted MQAI than VIBI-FQ, suggesting that mosses may either respond more rapidly to, or recover more slowly from, anthropogenic disturbance in the surrounding landscape than vascular plants. These results supported previous predictive studies on amphibian indices and metrics and a separate vegetation index, indicating that similar wetland management practices may result in qualitatively the same ecological response for three vastly different wetland biological communities (amphibians, vascular plants, and mosses).

Ohio↗

USGS2007

A comparison of macroinvertebrate and habitat methods of data collection in the Little Colorado River Watershed, Arizona 2007

The Arizona Department of Environmental Quality (ADEQ) and the U.S. Environmental Protection Agency (USEPA) Ecological Monitoring and Assessment Program (EMAP), use different field methods for collecting macroinvertebrate samples and habitat data for bioassessment purposes. Arizona’s Biocriteria index was developed using a riffle habitat sampling methodology, whereas the EMAP method employs a multi-habitat sampling protocol. There was a need to demonstrate comparability of these different bioassessment methodologies to allow use of the EMAP multi-habitat protocol for both statewide probabilistic assessments for integration of the EMAP data into the national (305b) assessment and for targeted in-state bioassessments for 303d determinations of standards violations and impaired aquatic life conditions. The purpose of this study was to evaluate whether the two methods yield similar bioassessment results, such that the data could be used interchangeably in water quality assessments. In this Regional EMAP grant funded project, a probabilistic survey of 30 sites in the Little Colorado River basin was conducted in the spring of 2007. Macroinvertebrate and habitat data were collected using both ADEQ and EMAP sampling methods, from adjacent reaches within these stream channels. All analyses indicated that the two macroinvertebrate sampling methods were significantly correlated. ADEQ and EMAP samples were classified into the same scoring categories (meeting, inconclusive, violating the biocriteria standard) 82% of the time. When the ADEQ-IBI was applied to both the ADEQ and EMAP taxa lists, the resulting IBI scores were significantly correlated (r=0.91), even though only 4 of the 7 metrics in the IBI were significantly correlated. The IBI scores from both methods were significantly correlated to the percent of riffle habitat, even though the average percent riffle habitat was only 30% of the stream reach. Multivariate analyses found that the percent riffle was an important attribute for both datasets in classifying IBI scores into assessment categories. Habitat measurements generated from EMAP and ADEQ methods were also significantly correlated; 13 of 16 habitat measures were significantly correlated (p<0.01). The visual-based percentage estimates of percent riffle and pool habitats, vegetative cover and percent canopy cover, and substrate measurements of percent fine substrate and embeddedness were all remarkably similar, given the different field methods used. A multivariate analysis identified substrate and flow conditions, as well as canopy cover as important combinations of habitat attributes affecting both IBI scores. These results indicate that similar habitat measures can be obtained using two different field sampling protocols. In addition, similar combinations of these habitat parameters were important to macroinvertebrate community condition in multivariate analyses of both ADEQ and EMAP datasets. These results indicate the two sampling methods for macroinvertebrates and habitat data were very similar in terms of bioassessment results and stressors. While the bioassessment category was not identical for all sites, overall the assessments were significantly correlated, providing similar bioassessment results for the cold water streams used in this study. The findings of this study indicate that ADEQ can utilize either a riffle-based sampling methodology or a multi-habitat sampling approach in cold water streams as both yield similar results relative to the macroinvertebrate assemblage. These results will allow for use of either macroinvertebrate dataset to determine water quality standards compliance with the ADEQ Indexes of Biological Integrity, for which threshold values were just recently placed into the Arizona Surface Water Quality Standards. While this survey did not include warm water desert streams of Arizona, we would predict that EMAP and ADEQ sampling methodologies would provide similar bioassessment results and would not be significantly different, as we have found that the percent riffle habitat in cold and warm water perennial, wadeable streams is not significantly different. However, a comparison study of sampling methodologies in warm water streams should be conducted to confirm the predicted similarity of bioassessment results. ADEQ will continue to implement a monitoring strategy that includes probabilistic monitoring for a statewide ecological assessment of stream conditions. Conclusions from this study will guide decisions regarding the most appropriate sampling methods for future probabilistic monitoring sample plans.

Arizona↗

USGS1986

Biomonitors of stream quality on agricultural areas: fish versus invertebrates

Although the utility of using either fish or benthic invertebrates as biomonitors of stream quality has been clearly shown, there is little comparative information on the usefulness of the groups in any particular situation. We compared fish to invertebrate assemblages in their ability to reflect habitat quality of sediment-impacted streams in agricultural regions of northeast Missouri, USA. Habitat quality was measured by a combination of substrate composition, riparian type, buffer strip width, and land use. Invertebrates were more sensitive to habitat differences when structural measurements, species diversity and ordination, were used. Incorporating ecological measurements, by using the Index of Biological Integrity, increased the information obtained from the fish assemblage. The differential response of the two groups was attributed to the more direct impact of sediments on invertebrate life requisites; the impact of sedimentation on fish is considered more indirect and complex, affecting feeding and reproductive mechanisms.

Environmental Management↗

USGS2013

Euryhalinity in an evolutionary context

This chapter focuses on the evolutionary importance and taxonomic distribution of euryhalinity. Euryhalinity refers to broad halotolerance and broad halohabitat distribution. Salinity exposure experiments have demonstrated that species vary tenfold in their range of tolerable salinity levels, primarily because of differences in upper limits. Halotolerance breadth varies with the species’ evolutionary history, as represented by its ordinal classification, and with the species’ halohabitat. Freshwater and seawater species tolerate brackish water; their empirically-determined fundamental haloniche is broader than their realized haloniche, as revealed by the halohabitats they occupy. With respect to halohabitat distribution, a minority of species (<10%) are euryhaline. Habitat-euryhalinity is prevalent among basal actinopterygian fishes, is largely absent from orders arising from intermediate nodes, and reappears in the most derived taxa. There is pronounced family-level variability in the tendency to be halohabitat-euryhaline, which may have arisen during a burst of diversification following the Cretaceous-Palaeogene extinction. Low prevalence notwithstanding, euryhaline species are potent sources of evolutionary diversity. Euryhalinity is regarded as a key innovation trait whose evolution enables exploitation of new adaptive zone, triggering cladogenesis. We review phylogenetically-informed studies that demonstrate freshwater species diversifying from euryhaline ancestors through processes such as landlocking. These studies indicate that some euryhaline taxa are particularly susceptible to changes in halohabitat and subsequent diversification, and some geographic regions have been hotspots for transitions to freshwater. Comparative studies on mechanisms among multiple taxa and at multiple levels of biological integration are needed to clarify evolutionary pathways to, and from, euryhalinity.

Book chapter↗

USGS2009

Alligators and crocodiles as indicators for restoration of Everglades ecosystems

Alligators and crocodiles integrate biological impacts of hydrological operations, affecting them at all life stages through three key aspects of Everglades ecology: (1) food webs, (2) diversity and productivity, and (3) freshwater flow. Responses of crocodilians are directly related to suitability of environmental conditions and hydrologic change. Correlations between biological responses and environmental conditions contribute to an understanding of species' status and trends over time. Positive or negative trends of crocodilian populations relative to hydrologic changes permit assessment of positive or negative trends in restoration. The crocodilian indicator uses monitoring parameters (performance measures) that have been shown to be both effective and efficient in tracking trends. The alligator component uses relative density (reported as an encounter rate), body condition, and occupancy rates of alligator holes; the crocodile component uses juvenile growth and hatchling survival. We hypothesize that these parameters are correlated with hydrologic conditions including depth, duration, timing, spatial extent and water quality. Salinity is a critical parameter in estuarine habitats. Assessments of parameters defined for crocodilian performance measures support these hypotheses. Alligators and crocodiles are the charismatic megafauna of the Everglades. They are both keystone and flagship species to which the public can relate. In addition, the parameters used to track trends are easy to understand. They provide answers to the following questions: How has the number of alligators or crocodiles changed? Are the animals fatter or thinner than they should be? Are the animals in the places (in terms of habitat and geography) where they should be? As surely as there is no other Everglades, no other single species defines the Everglades as does the American alligator. The Everglades is the only place in the world where both alligators and crocodiles exist. Crocodilians clearly respond to changes in hydrologic parameters of management interest. These relationships are easy to communicate and mean something to managers, decision makers, and the public. Having crocodilians on the list of system-wide, general indicators provides us with one of the most powerful tools we have to communicate progress of ecosystem restoration in Greater Everglades ecosystems to diverse audiences.

Florida↗

USGS2016

Fluctuating water depths affect American alligator ( Alligator mississippiensis ) body condition in the Everglades, Florida, USA

Successful restoration of wetland ecosystems requires knowledge of wetland hydrologic patterns and an understanding of how those patterns affect wetland plant and animal populations.Within the Everglades, Florida, USA restoration, an applied science strategy including conceptual ecological models linking drivers to indicators is being used to organize current scientific understanding to support restoration efforts. A key driver of the ecosystem affecting the distribution and abundance of organisms is the timing, distribution, and volume of water flows that result in water depth patterns across the landscape. American alligators (Alligator mississippiensis) are one of the ecological indicators being used to assess Everglades restoration because they are a keystone species and integrate biological impacts of hydrological operations through all life stages. Alligator body condition (the relative fatness of an animal) is one of the metrics being used and targets have been set to allow us to track progress. We examined trends in alligator body condition using Fulton’s K over a 15 year period (2000–2014) at seven different wetland areas within the Everglades ecosystem, assessed patterns and trends relative to restoration targets, and related those trends to hydrologic variables. We developed a series of 17 a priori hypotheses that we tested with an information theoretic approach to identify which hydrologic factors affect alligator body condition. Alligator body condition was highest throughout the Everglades during the early 2000s and is approximately 5–10% lower now (2014). Values have varied by year, area, and hydrology. Body condition was positively correlated with range in water depth and fall water depth. Our top model was the “Current” model and included variables that describe current year hydrology (spring depth, fall depth, hydroperiod, range, interaction of range and fall depth, interaction of range and hydroperiod). Across all models, interaction between range and fall water depth was the most important variable (relative weight of 1.0) followed by spring and fall water depths (0.99), range (0.96), hydroperiod (0.95) and interaction between range and hydroperiod (0.95). Our work provides additional evidence that restoring a greater range in annual water depths is important for improvement of alligator body condition and ecosystem function. This information can be incorporated into both planning and operations to assist in reaching Everglades restoration goals.

Florida↗

USGS2022

A biological condition gradient for Caribbean coral reefs: Part II. Numeric rules using sessile benthic organisms

The Biological Condition Gradient (BCG) is a conceptual model used to describe incremental changes in biological condition along a gradient of increasing anthropogenic stress. As coral reefs collapse globally, scientists and managers are focused on how to sustain the crucial structure and functions, and the benefits that healthy coral reef ecosystems provide for many economies and societies. We developed a numeric (quantitative) BGC model for the coral reefs of Puerto Rico and the US Virgin Islands to transparently facilitate ecologically meaningful management decisions regarding these fragile resources. Here, reef conditions range from natural, undisturbed conditions to severely altered or degraded conditions. Numeric decision rules were developed by an expert panel for scleractinian corals and other benthic assemblages using multiple attributes to apply in shallow-water tropical fore reefs with depths <30 m. The numeric model employed decision rules based on metrics (e.g., % live coral cover, coral species richness, pollution-sensitive coral species, unproductive and sediment substrates, % cover by Orbicella spp.) used to assess coral reef condition. Model confirmation showed the numeric BCG model predicted the panel’s median site ratings for 84% of the sites used to calibrate the model and 89% of independent validation sites. The numeric BCG model is suitable for adaptive management applications and supports bioassessment and criteria development. It is a robust assessment tool that could be used to establish ecosystem condition that would aid resource managers in evaluating and communicating current or changing conditions, protect water and habitat quality in areas of high biological integrity, or develop restoration goals with stakeholders and other public beneficiaries.

Ecological Indicators↗