Use of the Index of Biotic Integrity to Assess Water Quality in Forested Streams of the Ouachita Mountains Ecoregion, Arkansas

Trout density and biotic integrity scores are central metrics used to guide trout stream management actions. However, it is unclear whether reach-scale habitat characteristics affect trout density and biotic integrity in a similar fashion. To determine the relative strength of relationships between reach-scale habitat characteristics and important biological metrics, we used artificial neural network models to examine the relationships between 11 reach-scale habitat variables and (1) catch per effort (CPE) for brook trout Salvelinus fontinalis, (2) CPE for brown trout Salmo trutta, and (3) coldwater fish index of biotic integrity (IBI) scores. The trout CPE models generally included habitat features related to physical characteristics; the IBI model generally included physical characteristics as well as those related to water quality. The brook trout CPE model included sinuosity and percent pool area. The brown trout CPE model included gradient and cover. The coldwater IBI model included gradient, percent fine sediments, buffer width, and width : depth ratio. Habitat restoration efforts that seek to maximize brook trout CPE, brown trout CPE, or IBI may benefit from consideration of habitat variables associated with each metric. We also performed quantile regression to evaluate whether any one of the three response metrics of interest was limiting to any of the other variables. Conditions that control IBI scores may also limit brook trout and brown trout densities; 90th-percentile regressions between brook trout or brown trout CPE and IBI score were significant. Although our findings suggest that IBI scores and trout densities can often be increased simultaneously, the fact that different habitat variables were included in each model suggests that the most appropriate habitat restoration efforts may also differ depending on the management goal.

Single-pass electrofishing was used to define the most efficient sampling distance to assess stream condition using the index of biotic integrity (IBI) methodology in headwater (<36 km(2) drainage area), warmwater streams in the Eastern Corn Belt Plain ecoregion. Based on wetted widths (1-3.3 m) of sampled reaches, we defined effort based on increased area (range 50-555 m(2)). Sampled area necessary to capture a representative fish assemblage increased until 167-m(2) distance, which is equivalent to a minimum sampling distance of one habitat cycle. No significant difference in metric actual observed value response was found with increasing habitat cycle. Increased effort is required in smaller streams widths (≤1 m) to achieve the recommended sample area. The effect of rare fish on the IBI was tested using a modified Walford method. A significant decrease in IBI score was observed when 10% of the rare data were removed. The presence of rare fish did not influence individual IBI metrics or scores for either the increased effort or reduced effort calibrations until greater than 3% of the data was removed for number of species, 15% removal of data for number of minnow species, and 5% removal of data for catch per unit effort (CPUE). Increased effort did not affect any metric or IBI score, while reduced effort influenced the number of darter, madtom, and sculpin species and catch per unit effort metric scores but did not affect IBI score.

We characterized the biotic integrity of the sub‐tropical Duero River, Mexico, comparing current and past index of biotic integrity (IBI) scores with results of an environmental quality index (EQI), inventorying abiotic characteristics and human impacts, and documenting ecosystem changes over the last three decades. We sampled the fish community and measured environmental variables during the dry season of 2009 at 19 sites. We compared 2009 findings with fish data obtained in 1986 and 1991 at nine of the sites. The correlation between the IBI and EQI was high (r2 = 0.79, p = 0.0002), indicating that the IBI accurately characterized environmental condition. Thirteen sites were degraded (68%) based on IBI scores, three were fair (16%) and three had good conditions (16%). Based on the EQI, 12 sites were classified as poor (63%), two as fair (11%) and five as good (19%). A cluster analysis of nine abiotic variables and the IBI values yielded three groups: six sites with good integrity and environmental quality, eight with high chemical oxygen demand and four with high total dissolved solids. A discriminant analysis (square canonical correlation: 0.922, and Wilks' lambda significance: 0.001) identified biochemical oxygen demand, distance to vegetation and total dissolved solids as the main predictors. Compared to 1986 and 1991, 2009 IBI values and ratings had declined significantly (multiple response permutation procedure A = 0.16, p = 0.0005), indicating a trend of environmental deterioration, with scores and ratings at 7 of 9 sites lower in 2009. One site had declined from good to fair, one from good to poor, five from fair to poor, one had remained fair and one had remained good. Degradation was related to excessive human water use, reduced river flows, increased wastewater discharge, deforestation, erosion, and invasive species, and mismanagement of preserved sites (springs), all of which highlight an urgent need to reverse declining environmental conditions. Copyright © 2014 John Wiley &amp; Sons, Ltd.

Native brook trout Salvelinus fontinalis and introduced brown trout Salmo trutta support important recreational fisheries in Wisconsin, and coldwater index of biotic integrity (IBI) scores are often used to determine the quality of stream environments for these trout. To successfully manage biotic communities and fish populations, it is important to understand the relationships among metrics of interest. We quantified the relationships among the catch per linear meter (CPE) of brook trout and brown trout, their mean total lengths, and the coldwater fish IBI scores in second‐order and third‐order streams in Wisconsin. Brook trout CPE increased as coldwater IBI score increased, but there was no significant relationship between brown trout CPE and IBI score. The mean length of brown trout decreased as coldwater IBI score increased; the mean length of brook trout and IBI score were not significantly related. The mean lengths of both brook and brown trout decreased with increasing CPE. Balancing the management of trout density, length, and biotic integrity may be difficult in wadeable streams in Wisconsin. Our findings suggest that the increased abundance of brook trout is compatible with high IBI scores but that the increased abundance of brown trout and greater mean lengths are not.

&lt;em&gt;Abstract.&lt;/em&gt;—The Snake River is the tenth longest river in the United States, extending 1,667 km from its origin in Yellowstone National Park in western Wyoming to its union with the Columbia River at Pasco, Washington. Historically, the main-stem Snake River upstream from the Hells Canyon Complex supported at least 26 native fish species, including anadromous stocks of Chinook salmon &lt;em&gt;Oncorhynchus tshawytscha&lt;/em&gt;, steelhead &lt;em&gt;O. mykiss&lt;/em&gt;, Pacific lamprey &lt;em&gt;Lampetra tridentata&lt;/em&gt;, and white sturgeon &lt;em&gt;Acipenser transmontanus&lt;/em&gt;. Of these anadromous species, only the white sturgeon remains in the Snake River between the Hells Canyon Complex and Shoshone Falls. Today, much of the Snake River has been transformed into a river with numerous impoundments and flow diversions, increased pollutant loads, and elevated water temperatures. Current (1993–2002) fish assemblage collections from 15 sites along the Snake River and Henrys Fork contained 35 fish species, including 16 alien species. Many of these alien species such as catfish (Ictaluridae), carp (Cyprinidae), and sunfish (Centrarchidae) are adapted for warmwater impounded habitats. Currently, the Snake River supports 19 native species. An index of biotic integrity (IBI), developed to evaluate large rivers in the Northwest, was used to evaluate recent (1993– 2002) fish collections from the Snake River and Henrys Fork in southern Idaho and western Wyoming. Index of biotic integrity site scores and component metrics revealed a decline in biotic integrity from upstream to downstream in both the Snake River and Henrys Fork. Two distinct groups of sites were evident that correspond to a range of IBI scores—an upper Snake River and Henrys Fork group with relatively high biotic integrity (mean IBI scores of 46–84) and a lower Snake River group with low biotic integrity (mean IBI scores of 10–29). Sites located in the lower Snake River exhibited fish assemblages that reflect poor-quality habitat where coldwater and sensitive species are rare or absent, and where tolerant, less desirable species predominate. Increases in percentages of agricultural land, total number of diversions, and number of constructed channels were strongly associated with these decreasing IBI scores.

Indices of biotic integrity (IBIs) are used to assess ecosystem health of streams and rivers. Streams and rivers with high IBI scores should support abundant and healthy populations of recreationally important sport fishes. However, the fundamental assumption that IBI scores and sport fish populations are associated needs to be examined. To verify this assumption, we tested associations between IBI scores and relative abundance of all sport fishes targeted by anglers, with emphasis on relative abundance of four size groups of smallmouth bass Micropterus dolomieu at 54 stream and river reaches in 2012 and 2013. We also tested for associations with smallmouth bass body condition and growth. A total of 13,708 fishes representing 85 species were captured including 11 sport fish species that included 571 smallmouth bass. We found that the maximum potential relative abundance of sport fishes and smallmouth bass size classes, as well as body condition of bass between 180 and 279 mm, could be predicted by IBI scores. We did not observe significant relationships with body condition of other bass size classes or with growth. Whereas abundance patterns were variable at reaches with higher IBI scores, abundance of larger, quality-sized sport fishes were more limited at reaches with IBI scores <30 that were classified as having poor biotic integrity. Maximum potential body condition was predicted to exceed 95, a condition value indicative of healthy fish, at IBI scores exceeding 50, reflective of reaches being classified as either fair, good, or excellent. These results confirm that management activities that enhance or maintain biotic integrity also support high-quality habitat for sport fish. While our findings support using IBIs as an indicator of the fishable goal specified in the United States Clean Water Act, managers should recognize that other factors not necessarily represented by the index can also limit sport fish populations.

African tropical rainforests, and especially their freshwater biodiversity, are seriously threatened by ongoing industrial deforestation. Sound ecological management is needed to ensure the sustainability of these resources. For this purpose, an index of biotic integrity (IBI), based on fish assemblage characteristics, is developed in this paper. It is used to quantify the impact of industrial deforestation on freshwater biodiversity. Data from 30 non-impacted sites were used to develop a series of compositional, structural and functional metrics that reflect sites with a high biotic integrity, i.e. what a stream-fish community should look like in the absence of human perturbation. These data were compared to data collected from sites subjected to substantial forest watershed loss, in order to identify those IBI metrics that best distinguish streams with high and low biotic integrity. The overall IBI scores reflected the quality of the watershed conditions. In addition, there was a close agreement between an index of environmental quality, based on water and habitat quality and the IBI scores, suggesting that the different biological responses of the fish assemblages (observed differences in the IBI scores) were indicative of differences in physico-chemical quality of the streams. The ability of the proposed IBI to index water resource degradation, due to deforestation, suggests that it can be used as a tool for biological monitoring. However, more consistent and comprehensive data are needed to further refine the IBI, especially the assignment of integrity classes and metric threshold values.

In comparison with traditional species identification techniques, environmental DNA (eDNA) metabarcoding technology markedly enhances the resolution and precision of species classification, while simultaneously facilitating the efficiency and accuracy of data collection. However, the majority of extant methods for assessing biological integrity concentrate on monitoring at a single trophic level, and there is a paucity of systematic studies that consider multi-trophic level biomes in an integrated manner. Accordingly, the aim of this study was to conduct a comprehensive assessment of the multi-trophic biotic communities in the downstream section of the Gezhou Dam in the Yangtze River mainstem, which formerly constituted Chinese sturgeon spawning grounds, utilizing eDNA metabarcoding technology. Furthermore, the objective was to establish a multi-trophic Index of Biotic Integrity (IBI) assessment system. In this study, we sampled 18 sampling sites in three time periods, and reference sites were selected based on a number of factors, including the distance between the sampling site and the outfall, the extent of vegetation cover, and the degree of anthropogenic disturbance. The biological integrity of the sampling sites was then compared over different time periods (before, during, and after spawning season). The eDNA analysis enabled the construction of comprehensive biological integrity indicators, which considered fish, benthic invertebrates, zooplankton, phytoplankton, fungi, and microbial communities (It should be noted that due to the overlap of information and the weak indication of integrity of the indicators, the final indicator system will not include all taxa, but only some of them). The results demonstrated that the Index of Biotic Integrity (IBI) scores of the reference and disturbance sites exhibited notable differences in both individual and whole time periods (p &lt; 0.05), with an observed tendency for increased integrity with distance from the dam. Positive linear correlation was observed between IBI scores and sturgeon eDNA concentrations at all sampling sites. The assessment outcomes exhibited satisfactory indicative capacity and spatial and temporal consistency, providing a reliable foundation for an ecosystem health assessment. Furthermore, the successful application of this assessment method offers novel insights and tools for future ecosystem monitoring and assessment.

We evaluated the performance of an index of biotic integrity (IBI) based on 16 fish population metrics of three types: species richness, community assemblage, and trophic composition. Two sets of central Minnesota lakes independent from the original set of lakes used to develop the IBI model were used to validate it. One set of lakes (n = 15) had physical features similar to those used to develop the IBI, while the other set (n = 22) averaged 9 m shallower with 28% more littoral area. We used general linear models to test whether the relationships between IBI or individual metric score and indicators of lake quality (trophic state, floristic quality, or surrounding land use) were the same or differed for the original IBI data set and each new data set. Responses were similar among all data sets, lake IBI scores and individual metrics reflecting differences in land use, trophic state, and aquatic habitat. Sensitivity of individual metrics to different measures of stress varied, supporting the need for a multimetric approach when assessing the biotic integrity of lakes. Index of biotic integrity scores were most highly correlated with trophic state (rho = −0.80). Our results support the validity of the original fish-based IBI as a standardized method for quantitatively measuring the condition of fish assemblages and implied overall biotic integrity of small central Minnesota lakes. As with any model, however, continued evaluation is recommended, especially when applying this IBI to lakes with different physical, chemical, or biological characteristics.

Quantitative biological assessment protocols are needed for monitoring river status and evaluating river rehabilitation efforts. We conducted a standardized macroinvertebrate survey at 100 sites on 38 nonwadeable rivers in Wisconsin to construct, test, and apply an index of biotic integrity (IBI) intended to be such a bioassessment tool. We assigned independent samples to IBI development (n = 75) and IBI validation (n = 25) data sets. We placed Hester–Dendy artificial substrates at the sites for 6 wk and processed the samples of colonizing macroinvertebrates in the laboratory with a 500-target subsampling procedure plus a large–rare taxon search. Independent of the biota, we assigned an environmental disturbance score to each site based upon water chemistry, land cover, flow modification, and point-source pollution. Ten metrics that represent macroinvertebrate assemblage structure, composition, and function constitute the IBI: the number of taxa in: 1) Insecta or 2) Ephemeroptera, Plecoptera, Trichoptera (EPT); % individuals that were: 3) Insecta, 4) intolerant EPT, 5) tolerant chironomids, 6) gatherers, 7) scrapers, or from 8) the dominant 3 taxa; 9) the mean pollution tolerance value; and 10) the number of unique ecological functional trait niches. Analyses on both the validation subset of sites and all sites inclusive confirmed that least-disturbed sites had the highest IBI scores, severely disturbed sites had the lowest scores, and moderately disturbed sites had intermediate scores. Chironominae and Hydropsychidae taxa known to tolerate nutrient enrichment and overall degraded conditions dominated samples with low IBI scores. In contrast, a diverse assemblage that thrives in relatively undisturbed conditions was present in samples with high IBI scores. Comparison of the new macroinvertebrate IBI with an existing fish IBI suggested that the indices respond to different environmental stressors and illustrated the limitations of using only one taxonomic group for bioassessment. We discuss new macroinvertebrate methods, an IBI development process, and the refinement of metrics that may be useful in tailoring assessment tools for large rivers or wadeable streams in other regions. We also present applications of the IBI, including its potential use in comprehensive large river monitoring programs and for evaluating management efforts.

We analyzed relationships between watershed land use and habitat quality, and between watershed land use and biotic integrity for 134 sites on 103 streams located throughout Wisconsin. Habitat quality and index of biotic integrity (IBI) scores were significantly positively correlated with the amount of forested land and negatively correlated with the amount of agricultural land in the entire watershed and in a 100-m-wide buffer along the stream. Correlations were generally stronger for the entire watershed than for the buffer. Relationships between forested land and habitat and biotic integrity were linear, although there were several outlying sites with lower-than-expected IBI scores. Relationships with agricultural land use were more complex, with an obvious decline in habitat quality and IBI scores apparent only when agricultural land use exceeded 50%. Even when agricultural land use exceeded 80%, some sites maintained relatively good habitat quality and biotic integrity. These “good” sites te...

The objective of this study was to relate the quality of the fish community with habitat using the Index of Biotic Integrity (IBI) and Qualitative Habitat Evaluation Index (QHEI) in four agriculturally influenced streams in east central, Indiana. A total of 48 species was collected from 42 sites. IBI scores ranged from 14 to 48, and QHEI scores ranged from 29 to 83. There was a significant positive correlation between IBI and QHEI scores. Furthermore, we found significant positive correlations between IBI scores and four individual QHEI metrics (channel morphology, substrate, poollglide and riffletrun quality, and in-stream cover). Habitat influenced the fish assemblages with channelization and substrate being the primary structuring factors. The land use in this area is 70% agriculture, which has heavily influenced lotic character through anthropogenic practices.

Application of neural networks to quantify the utility of indices of biotic integrity for biological monitoring

Cryptic tolerant fish species and their potential effect on index of biotic integrity (IBI) scores

The Maryland Department of Natural Resources is conducting the Maryland Biological Stream Survey, a probability-based sampling program, stratified by river basin and stream order, to assess water quality, physical habitat, and biological conditions in first through third order, non-tidal streams. These streams comprise about 90% of all lotic water miles in the state. About 300 sites (75 m segments) are being sampled during spring and summer each year. All basins in the state will be sampled over a three-year period, 1995-97. MBSS developments in 1995-96 included (1) an electrofishing capture efficiency correction method to improve the accuracy of fish population estimates, (2) two indices of biotic integrity (IBI) for fish assemblages to identify degraded streams, and (3) land use information for catchments upstream of sampled sites to investigate associations between stream condition and anthropogenic stresses. Based on fish IBI scores at 270 stream sites in six basins sampled in 1995, 11% of non-tidal stream miles in Maryland were classified as very poor, 15% as poor, 24% as fair, and 27% as good. IBIs have not yet been developed for stream sites with catchment areas less than 120 hectares (23% of non-tidal stream miles). IBI scores declined with stream acid neutralizing capacity (ANC) and pH, an association that was also evident for fish species richness, biomass, and density. Low IBI scores were associated with several measures of degraded stream habitat, but not with local riparian buffer width. There was a significant negative association between IBI scores and urban land use upstream of sampled sites in the only extensively urbanized basin assessed in 1995. Future plans for the MBSS include (1) identifying all benthic macroinvertebrate samples to genus, (2) developing benthic macroinvertebrate, herpetofaunal, and physical habitat indicators, and (3) enhancing the analysis of stream condition-stressor associations by refining landscape metrics and using multi-variate techniques.