Comparability of macroinvertebrate biomonitoring indices of river health derived from semi-quantitative and quantitative methodologies

Aquatic macroinvertebrates have been the basis for one of the primary indicators and a cornerstone of lotic biomonitoring for over 40 years. Despite the widespread use of lotic invertebrates in statutory biomonitoring networks, scientific research and citizen science projects, the sampling methodologies employed frequently vary between studies. Routine statutory biomonitoring has historically relied on semi-quantitative sampling methods (timed kick sampling), while much academic research has favoured fully quantitative methods (e.g. Surber sampling). There is an untested assumption that data derived using quantitative and semi-quantitative samples are not comparable for biomonitoring purposes. As a result, data derived from the same site, but using different sampling techniques, have typically not been analysed together or directly compared. Here, we test this assumption by comparing a range of biomonitoring metrics derived from data collected using timed semi-quantitative kick samples and quantitative Surber samples from the same sites simultaneously. In total, 39 pairs of samples from 7 rivers in the UK were compared for two seasons (spring and autumn). We found a strong positive correlation (r_s = +0.84) between estimates of taxa richness based on ten Surber sub-samples and a single kick sample. The majority of biomonitoring metrics were comparable between techniques, although only fully quantitative sampling allows the density of the community (individual m⁻²) to be determined. However, this advantage needs to be balanced alongside the greater total sampling time and effort associated with the fully quantitative methodology used here. Kick samples did not provide a good estimate of relative abundance of a number of species/taxa and, therefore, the quantitative method has the potential to provide important additional information which may support the interpretation of the biological metrics.     

Effect of investigator disturbance in experimental forensic entomology: succession and community composition

Carrion insect succession studies have historically used repeated sampling of single or a few carcasses to produce data, either weighing the carcasses, removing a qualitative subsample of the fauna present, or both, on every visit over the course of decomposition and succession. This study, conducted in a set of related experimental hypotheses with two trials in a single season, investigated the effect that repeated sampling has on insect succession, determined by the number of taxa collected on each visit and by community composition. Each trial lasted at least 21 days, with daily visits on the first 14 days. Rat carcasses used in this study were all placed in the field on the same day, but then either sampled qualitatively on every visit (similar to most succession studies) or ignored until a given day of succession, when they were sampled qualitatively (a subsample) and then destructively sampled in their entirety. Carcasses sampled on every visit were in two groups: those from which only a sample of the fauna was taken and those from which a sample of fauna was taken and the carcass was weighed for biomass determination. Of the carcasses visited only once, the number of taxa in subsamples was compared to the actual number of taxa present when the carcass was destructively sampled to determine if the subsamples adequately represented the total carcass fauna. Data from the qualitative subsamples of those carcasses visited only once were also compared to data collected from carcasses that were sampled on every visit to investigate the effect of the repeated sampling. A total of 39 taxa were collected from carcasses during the study and the component taxa are discussed individually in relation to their role in succession. Number of taxa differed on only one visit between the qualitative subsamples and the actual number of taxa present, primarily because the organisms missed by the qualitative sampling were cryptic (hidden deep within body cavities) or rare (only represented by very few specimens). There were no differences discovered between number of taxa in qualitative subsamples from carcasses sampled repeatedly (with or without biomass determinations) and those sampled only a single time. Community composition differed considerably in later stages of decomposition, with disparate communities due primarily to small numbers of rare taxa. These results indicate that the methods used historically for community composition determination in experimental forensic entomology are generally adequate.     

Longitudinal variation in the composition of the benthic macroinvertebrate fauna of a typical North coast Jamaican river

Benthic macroinvertebrate fauna plays a major role in river ecosystems, especially those of tropical islands. Since there is no information on the distribution of benthic invertebrates along a Jamaican river, we report here on the composition of the benthic fauna of the Buff Bay river, on the Northern coast of Jamaica. A total of 14 samples were collected from five sites, using kick nets and a Surber sampler, between May 1997 and October 1998. We also examined the applicability of the rhithron/potamon model, and some of the premises of the River Continuum Concept (RCC) in relation to the distribution of invertebrate taxa. The results showed a total of 38 taxa of identified invertebrates. A group of dominant taxa, composed mainly of immature stages of insects, occurred at all sites. Two notable characteristics of the river were the absence of a true potamonic fauna and the low representation of the shredder functional feeding group in the community We conclude that, while there was minor variation in the composition of the benthic macroinvertebrate fauna among the sites, this was a response to local conditions within the river system. The characteristics of the community did not conform to either of the models.     

Filling the gaps in stream size spectra: using electroshocking to collect large macroinvertebrates

Studies of stream benthic macroinvertebrate size distributions describe assemblages from random small area samplers or cobbles. Large organisms are often underestimated in these samples because of their mobility or low densities. This study compared the performance of cobble collection and a Hess sampler with electrobugging (using a backpack electroshocker to collect macroinvertebrates) to determine whether electrobugging could improve estimates of the biomass of large organisms. We sampled 12 stream sites, collecting cobbles and Hess samples and conducting 3–4 consecutive electrobugging passes (repeating until attrition was observed, following with kick samples). Electrobugging collected more biomass of mobile taxa than cobble or Hess samples, and collected greater taxonomic richness, particularly at sites with low algal biomass. However, it was less effective at collecting attached and immobile taxa. Electrobugging extended the size distribution range by up to eight size classes by collecting larger macroinvertebrates than the cobble or Hess methods, and collected significantly more taxa per size class. Size distributions created from only cobble or Hess samples clearly do not represent the entire benthic community, but our results indicate that electrobugging provides a means to improve estimates of the biomass of large, mobile taxa, providing a more accurate estimate of body size distributions.     

Variability in stream macroinvertebrates at multiple spatial scales

1. We intensively sampled 16 western Oregon streams to characterize: (1) the variability in macroinvertebrate assemblages at seven spatial scales; and (2) the change in taxon richness with increasing sampling effort. An analysis of variance (ANOVA) model calculated spatial variance components for taxon richness, total density, percent individuals of Ephemeroptera, Plecoptera and Trichoptera (EPT), percent dominance and Shannon diversity.
2. At the landscape level, ecoregion and among‐streams components dominated variance for most metrics, accounting for 43–72% of total variance. However, ecoregion accounted for very little variance in total density and 36% of the variance was attributable to differences between streams. For other metrics, variance components were more evenly divided between stream and ecoregion effects.
3. Within streams, approximately 70% of variance was associated with unstructured local spatial variation and not associated with habitat type or transect position. The remaining variance was typically split about evenly between habitat and transect. Sample position within a transect (left, centre or right) accounted for virtually none of the variance for any metric.
4. New taxa per stream increased rapidly with sampling effort with the first four to eight Surber samples (500–1000 individuals counted), then increased more gradually. After counting more than 50 samples, new taxa continued to be added in stream reaches that were 80 times as long as their mean wetted width. Thus taxon richness was highly dependent on sampling effort, and comparisons between sites or streams must be normalized for sampling effort.
5. Characterization of spatial variance structure is fundamental to designing sampling programmes where spatial comparisons range from local to regional scales. Differences in metric responses across spatial scales demonstrate the importance of designing sampling strategies and analyses capable of discerning differences at the scale of interest.     

Large variation of suction sampling efficiency depending on arthropod groups,species traits,and habitat properties

Suction sampling is widely used to estimate arthropod abundance and diversity. To test the reliability of abundance data derived from suction sampling, we examined sampling efficiency across a wide range of arthropod groups and tested for effects of species traits, vegetation density, and differences between sites. Suction sampling efficiency was quantified by vacuuming an enclosed meadow area and subsequent removal of the turf, which was treated with heat extraction to collect the remaining arthropods. We obtained 250 pairs of suction and turf samples from seven grasslands with variable vegetation density. High suction sampling efficiencies between 49 and 86% were obtained for Auchenorrhyncha, Heteroptera, Araneida, Curculionoidea, Hymenoptera, and Diptera. In contrast, efficiencies were below 30% for Aphidae, Thysanoptera, Staphylinidae and other Coleoptera, and for soil arthropods such as Collembola, Isopoda, Diplopoda, and Formicidae. Efficiency varied significantly among habitats (sites) for most groups, often more than two‐fold. Surprisingly, sampling efficiency for Hymenoptera, Diplopoda, and Collembola increased with vegetation density, probably because aboveground activity of these taxa was higher in dense vegetation. Suction sampling was nearly twice as efficient for spiders living in the vegetation than for spiders living near the soil surface, and cursorial and large‐bodied spider species were more efficiently sampled than web‐builders and small species. Depending on the sampling effort, suction sampling missed between 49% (one sample) and 31% (250 samples) of the spider species present. Suction sampling efficiency varied more strongly among sites and among arthropod groups than previously recognized. Abundance data derived from suction sampling are strongly underestimated, especially for arthropods living near the soil surface. Thus, comparisons of abundance and diversity between sites should be restricted to vegetation‐dwelling species of the most efficiently sampled groups. The positive relationship of sampling efficiency with vegetation density demonstrates that variation in efficiency is mediated by arthropod behaviour.     

Comparison of several techniques for sampling macroinvertebrates in different habitats of a North Iberian pond

Several habitats of a Mediterranean pond were sampled for macroinvertebrates using different techniques: quantitative methods, semiquantitative hand-net sweep sampling and a qualitative protocol based on hand-net sweeps with fixed counts of individuals. The taxonomic composition was analyzed by DCA and several indices based on taxon composition or percentage of individuals were calculated. The aim of the study was to compare the results provided by these techniques and, in particular, to check if the qualitative approach could be an appropriate low-cost methodology for use in biomonitoring. The results provided by the three sampling methods in relation to submerged macrophytes were very similar. In soft sediment, certain differences were found between the quantitative and semiquantitative techniques. The qualitative protocol applied to single habitats collected fewer taxa than the corresponding quantitative or semiquantitative techniques. However, the overall protocol, consisting of samples from three habitats, provided higher richness values than all the quantitative and semiquantitative methods together, with 59 taxa out of the 70 collected during the study. It is concluded that this qualitative methodology performed reasonably well since it offers a reliable view of the community and it misses few taxa. Moreover, it is not so time consuming as other techniques and can be applied in a variety of habitats. It, therefore, seems to be an efficient method for bioassessment of the macroinvertebrate communities of ponds or the littoral zone of lakes.     

Use of both benthic and drift sampling techniques to assess tropical stream invertebrate communities along an altitudinal gradient, Costa Rica

1. Two sampling techniques were used to characterize invertebrate communities in eight, low-order streams along an altitudinal gradient in Costa Rica that represents the last continuous tract of primary forest spanning such extremes in elevation (i.e. near sea level to 2900 m a.s.l.) along the Caribbean Slope of Central America. A standard Surber sampler was used to sample invertebrates on the stream bottom, and drift sampling nets were used to sample invertebrates drifting in the stream flow. 2. Sites were established at 30, 50, 700 1800 and 2700 m a.s.l. In one to two streams per site, six Surber samples were collected, and drift was sampled every 3 h over one 24-h period between April and August 1994. All sites were in primary forest, with the exception of the lowest elevation site (30 m) which was located in banana plantations. 3. Both sampling techniques indicated that Diptera (Chironomidae) and Ephemeroptera were the dominant insect groups at all sites. Disturbed streams draining banana plantations were dominated by Chironomidae and had lower taxon richness and diversity than other sites. 4. While data from benthic samples indicated that insects were the major faunal component (> 90%) at all sites, drift samples were dominated by larval shrimps (> 50%) at the 30 m and 50 m sites. 5. Drift periodicity of invertebrates was observed at those sites characterized by predaceous fishes: nocturnal drift densities were higher than diurnal densities at 30, 50 and 700 m a.s.l., however, no periodicity was observed at 1800 and 2700 m a.s.l. where fish were absent. 6. This study shows the importance of measuring invertebrate drift, in addition to directly sampling the benthos. Drift sampling provided data on a major community component (shrimps) of lowland tropical streams, that would have been overlooked using traditional benthic sampling techniques, and in some cases provided additional information on taxon richness. 7. Based on results of the present study, it is recommended that drift sampling be included as a standard complementary tool to benthic sampling in biological assessments (e.g. bioassessment protocols) of tropical streams, which are often characterized by migratory invertebrate species such as shrimps. Drift samples provide critical information on the presence or absence of shrimps and also on the timing and magnitude of their migration which is an important link between many tropical rivers and their estuaries.     

Macroinvertebrate community in the lower Ebro river (NE Spain)

We examine the macroinvertebrate community composition and dynamics in the last 60 km of the Ebro river (NE Spain). Different sampling methods (individual stones, Surber, kick samplers and artificial substrate) were used depending on the characteristics of the sites chosen (substrate, current velocity, saline influence).The high nutrient content and the abundance of UFPOM is the origin of a high density in stones although no clear pattern exists between stone surface area and density or species richness. The high spatial heterogeneity and moderate disturbance intensity and frequency because of river regulation explains the relatively rich macroinvertebrate community and the low temporal changes in the community.     

Application of Rapid Bioassessment Protocols (RBP) for benthic macroinvertebrates in Brazil: comparison between sampling techniques and mesh sizes

This study is part of the effort to test and to establish Rapid Bioassessment Protocols (RBP) using benthic macroinvertebrates as indicators of the water quality of wadeable streams in south-east Brazil. We compared the cost-effectiveness of sampling devices frequently used in RBPs, Surber and Kick-net samplers, and of three mesh sizes (125, 250 and 500 microm). A total of 126,815 benthic macroinvertebrates were collected, representing 57 families. Samples collected with Kick method had significantly higher richness and BMWP scores in relation to Surber, but no significant increase in the effort, measured by the necessary time to process samples. No significant differences were found between samplers considering the cost/effectiveness ratio. Considering mesh sizes, significantly higher abundance and time for processing samples were necessary for finer meshes, but no significant difference were found considering taxa richness or BMWP scores. As a consequence, the 500 microm mesh had better cost/effectiveness ratios. Therefore, we support the use of a kick-net with a mesh size of 500 microm for macroinvertebrate sampling in RBPs using family level in streams of similar characteristics in Brazil.     

Effectiveness of an artificial substrate for sampling macroinvertebrates in small streams

SUMMARY. Factors affecting invertebrate colonization of samplers consisting of twenty-five 5-cm diameter porcelain balls were studied in small northern California streams. Peaks in diversity, in number of individuals and in taxa, occurred after 2—4 weeks in each of four 10-week colonization runs. Most variation in number of organisms was correlated with increases in organic detritus. Time was the second most important variable.
The average coefficient of variation in total numbers collected from the artificial sampler was 0.40, slightly less than the average 0.56 for the Surber sampler. Published coefficients of variation for artificial substrates range from 0.109 to 0.849, which are similar to values reported from work with the Surber sampler. We had several practical difficulties with the artificial substrates. Samplers were lost, became clogged or buried, supported vertebrate predators and were costly. The samplers also collected some organisms in greater proportion than their occurrences in the natural substrate. In sampling small streams these disadvantages (compared to a Surber sampler) outweigh the slight reduction in sampling variability.     

Molecular diversity and distribution of marine fungi across 130 European environmental samples

Environmental DNA and culture-based analyses have suggested that fungi are present in low diversity and in low abundance in many marine environments, especially in the upper water column. Here, we use a dual approach involving high-throughput diversity tag sequencing from both DNA and RNA templates and fluorescent cell counts to evaluate the diversity and relative abundance of fungi across marine samples taken from six European near-shore sites. We removed very rare fungal operational taxonomic units (OTUs) selecting only OTUs recovered from multiple samples for a detailed analysis. This approach identified a set of 71 fungal ‘OTU clusters'' that account for 66% of all the sequences assigned to the Fungi. Phylogenetic analyses demonstrated that this diversity includes a significant number of chytrid-like lineages that had not been previously described, indicating that the marine environment encompasses a number of zoosporic fungi that are new to taxonomic inventories. Using the sequence datasets, we identified cases where fungal OTUs were sampled across multiple geographical sites and between different sampling depths. This was especially clear in one relatively abundant and diverse phylogroup tentatively named Novel Chytrid-Like-Clade 1 (NCLC1). For comparison, a subset of the water column samples was also investigated using fluorescent microscopy to examine the abundance of eukaryotes with chitin cell walls. Comparisons of relative abundance of RNA-derived fungal tag sequences and chitin cell-wall counts demonstrate that fungi constitute a low fraction of the eukaryotic community in these water column samples. Taken together, these results demonstrate the phylogenetic position and environmental distribution of 71 lineages, improving our understanding of the diversity and abundance of fungi in marine environments.     

Salt marsh sediment diversity: a test of the variability of the rare biosphere among environmental replicates

Much of the phylogenetic diversity in microbial systems arises from rare taxa that comprise the long tail of taxon rank distribution curves. This vast diversity presents a challenge to testing hypotheses about the effects of perturbations on microbial community composition because variability of rare taxa among environmental replicates may be sufficiently large that it would require a prohibitive degree of sequencing to discern differences between samples. In this study we used pyrosequencing of 16S rRNA tags to examine the diversity and within-site variability of salt marsh sediment bacteria. Our goal was to determine whether pyrosequencing could produce similar patterns in community composition among replicate environmental samples from the same location. We hypothesized that repeated sampling from the same location would produce different snapshots of the rare community due to incomplete sequencing of the taxonomically rich rare biosphere. We demonstrate that the salt marsh sediments we sampled contain a remarkably diverse array of bacterial taxa and, in contrast to our hypothesis, repeated sampling from within the same site produces reliably similar patterns in bacterial community composition, even among rare organisms. These results demonstrate that deep sequencing of 16s tags is well suited to distinguish site-specific similarities and differences among rare taxa and is a valuable tool for hypothesis testing in microbial ecology.     

Native and alien macroinvertebrate richness in a remnant of the former river Rhine: a source for recolonisation of restored habitats?

Rivers are among the most endangered ecosystems of the world with dramatically decreasing biodiversity. Rehabilitation programmes aiming at restoration of riverine ecosystems rely on the recolonisation of native macroinvertebrates from refuges. We examined whether a relatively natural remnant of the former river Rhine (Altrhein) harbours a higher richness of benthic macroinvertebrates than two sites of the modified Rhine with artificial and semi-natural embankments near Basel. All three sites were bimonthly sampled between May 2007 and May 2008 using three techniques: Kick and Sweep, drifting animals collected from pieces of stone turned by hand, and animals collected from stone surfaces. Taxa richness was higher in the Altrhein than in the two sampling sites in the river Rhine, but it was mainly a result of the large number of individuals sampled at this site. Despite 17% of taxa recorded were alien, the three sampling sites differed neither in the number of alien taxa nor in their abundances. However, lower percentages of both alien taxa and individuals were recorded in the Altrhein than at the other two sites in the Rhine. Indicator value analysis showed that the macroinvertebrate community of the Altrhein maintains several native and specific taxa. Multivariate analyses supported the separation of the communities collected at different sampling sites and also the uniqueness of the community in the Altrhein. The observed patterns, however, strongly depended on the sampling method applied, thereby calling the attention to the application of standard sampling methods and also to the restriction of result comparisons on projects using identical sampling methodology. Our study shows that the remnant of the former river Rhine serves as a refuge for macroinvertebrates which may facilitate future restoration of the river embankment.     

Structure of bacterial communities in diverse freshwater habitats

The structures and dynamics of bacterial communities from raw source water, groundwater, and drinking water before and after filtration were studied in four seasons of a year, with culture-independent methods. Genomic DNA from water samples was analyzed by the polymerase chain reaction?- denaturing gradient gel electrophoresis system and by cloning of the 16S rRNA gene. Water samples exhibited complex denaturing gradient gel electrophoresis genetic profiles composed of many bands, corresponding to a great variety of bacterial taxa. The bacterial communities of different seasons from the four sampling sites clustered into two major groups: (i) water before and after filtration, and (ii) source water and groundwater. Phylogenetic analyses of the clones from the autumn sampling revealed 13 phyla, 19 classes, and 155 operational taxonomic units. Of the clones, 66% showed less than 97% similarities to known bacterial species. Representatives of the phyla Proteobacteria, Bacteroidetes, and Actinobacteria were found at all four sampling sites. Species belonging to the phylum Firmicutes were an important component of the microbial community in filtered water. Representatives of Enterobacteriaceae were not detected, indicating the absence of fecal pollution in the drinking water. Differences were found in the bacterial populations that were sampled from the same sites in different seasons. Each water habitat had a unique bacterial profile. Drinking water harbors diverse and dynamic microbial communities, part of which may be active and resilient to chlorine disinfection. This study provides, for the first time, basic data for uncultivable drinking water bacteria in Israel.     

Studies of aquatic insects in the Atna River 1987–2002

River Atna is situated in south-eastern Norway and stretches from approx. 1400 m a.s.l. in the Rondane Mountains, through Lake Atnsjøen, at 701 m a.s.l.; to the confluence with River Glomma at 338 m a.s.l. The catchment area is 1323 km², oligotrophic and very susceptible to acid precipitation. The river water is very poor in nutrients and ions, and pH varies from 5.0 to 7.2. Samples were taken each year from 1987 to 2002 at three to five localities from 1280 to 380 m a.s.l. Insect larvae were collected by Surber sampling and by kick sampling. Malaise traps were used to collect adults of Plecoptera, Trichoptera, Chironomidae and Limoniidae. A total of 16 taxa of Ephemeroptera, 24 taxa of Plecoptera, 39 taxa of Trichoptera, 125 taxa of Chironomidae and 52 taxa of Limoniidae, were identified. Our results from Atna provide some support for a zonation of the river based on zoobenthos. The occurrence and abundance of functional groups among the Plecoptera, Trichoptera, and Chironomidae are discussed in relation to the River Continuum Concept (RCC). Our conclusion is that grazers dominate in the zoobenthos in streams in the treeless alpine region in Norway. Natural lakes, which occur in most watercourses in Norway, appear to cause a disturbance in relation to the original RCC concept, as the zoobenthos community in and below the lake outlet is dominated by collectors (filter feeders). The pattern found in the Atna watercourse is probably a general pattern for a northern watercourse in the Holarctic, where the glacial periods created lakes in most watercourses. The results of the long term sampling in Atna are discussed in relation to the practicalities and the cost-benefit of zoobenthos in efficient bio-monitoring in rivers.     

Immediate impact of piscicide operations on a Cape Floristic Region aquatic insect assemblage: a lesser of two evils?

The piscicide rotenone is used as a conservation tool to remove alien fishes from rivers, though there is controversy over its effects on aquatic insects. An alien fish removal operation in the Rondegat River, Cape Floristic Region, South Africa, allowed the immediate impact of rotenone on an aquatic insect community in a region with high conservation values to be quantified. The insect community within the treated river was sampled in February 2011 (1 year before rotenone operations), February 2012 (1 week before) and March 2012 (1 week after). Insects were collected using kick sampling across multiple biotopes, together with samples from individual stones. We considered rotenone-precipitated losses to be those taxa captured a week before treatment but absent after, and assessed the endemism of lost species to determine the conservation impact of the rotenone. Species richness decreased significantly following treatment, even though many rare taxa were not recorded immediately prior to treatment. Of the 85 taxa identified, 18 were lost including five endemic to the mountain range which the river drains. Ephemeroptera were most severely affected, with a significant loss of density on stones post-rotenone and six out of 20 species missing. Since half the missing taxa were recorded upstream of the treatment area, recovery of diversity is likely to be relatively rapid. Given that alien invasive fish negatively affect both fish and aquatic insect communities in South Africa, the long-term positive conservation impact of removing these fish is likely to outweigh the short-term negative effects of the piscicide.     

A comparison of diversity estimators applied to a database of host–parasite associations

Understanding the drivers of biodiversity is important for forecasting changes in the distribution of life on earth. However, most studies of biodiversity are limited by uneven sampling effort, with some regions or taxa better sampled than others. Numerous methods have been developed to account for differences in sampling effort, but most methods were developed for systematic surveys in which all study units are sampled using the same design and assemblages are sampled randomly. Databases compiled from multiple sources, such as from the literature, often violate these assumptions because they are composed of studies that vary widely in their goals and methods. Here, we compared the performance of several popular methods for estimating parasite diversity based on a large and widely used parasite database, the Global Mammal Parasite Database (GMPD). We created artificial datasets of host–parasite interactions based on the structure of the GMPD, then used these datasets to evaluate which methods best control for differential sampling effort. We evaluated the precision and bias of seven methods, including species accumulation and nonparametric diversity estimators, compared to analyzing the raw data without controlling for sampling variation. We find that nonparametric estimators, and particularly the Chao2 and second-order jackknife estimators, perform better than other methods. However, these estimators still perform poorly relative to systematic sampling, and effect sizes should be interpreted with caution because they tend to be lower than actual effect sizes. Overall, these estimators are more effective in comparative studies than for producing true estimates of diversity. We make recommendations for future sampling strategies and statistical methods that would improve estimates of global parasite diversity.