Responses of fishes and lampreys to the re‐creation of meanders in a small English chalk stream

River rehabilitation initiatives have become commonplace in European water courses as a result of European Union Water Framework Directive requirements. However, the short‐term responses of fishes to such work have thus far been varied, with some river rehabilitation efforts resulting in demonstrable improvements in diversity and size structure, whereas others have resulted in little or no change. Electrofishing and channel character surveys were conducted annually between 2009 and 2014 on a reach of the River Glaven (North Norfolk, UK) before and after rehabilitation work (embankment removal in 2009 and re‐meandering in 2010) as well as on a control reach immediately upstream. To assess the effects of rehabilitation work, before‐after‐control‐impact analysis tested for changes in channel character (geomorphology, substratum composition, and mesohabitat structure) and in fish species richness, relative abundance, population density, and size structure (calculated after fish data entry into the UK Environment Agency's National Fisheries Population Database). Following re‐meandering work (i.e., treatment), habitat heterogeneity and depth variation increased in the treatment reach, but fish responses were not significant except for biomass and density increases of brown trout Salmo trutta and abundance decreases of European eel Anguilla anguilla, in the treatment but not the control reach. These results are consistent with comparable river rehabilitation initiatives elsewhere, and they suggest that larger‐scale rehabilitations are probably needed to produce greater increases in fish density and diversity. It is recommended that future rehabilitation initiatives address catchment‐scale factors that can enhance ecosystem recovery, for example, removal of barriers to colonization, and increases in connectivity and water quality issues linked to eutrophication, elevated fine sediment inputs, and various pollutants.     

Identification of Priority Areas for the Conservation of Stream Fish Assemblages: Implications for River Management in France

Financial and human resources allocated to biodiversity conservation are often limited, making it impossible to protect all natural places, and priority areas for protection must be identified. In this study, we applied ecological niche models to predict fish assemblages in the stream network of France. Four non‐correlated conservation objectives were derived from these species assemblages: taxonomic diversity, functional diversity, natural heritage importance and socio‐economic value. We proposed a multi‐objective prioritization method based on the Pareto optimality principle to rank the planning units (i.e. 6097 subcatchments) according to their inherent trade‐offs between the four conservation objectives. Four types of hydrosystems of great conservation importance presenting specific fish assemblages were identified: (i) the most upstream areas of large catchments; (ii) the most downstream areas of large catchments; (iii) the small coastal catchments of the English Channel and the Atlantic Ocean; and (iv) the Mediterranean streams of medium altitude. The fish assemblages characterizing these hydrosystems were complementary and representative of the entire fish fauna of France. Most of these priority subcatchments were found to be practically suitable for the implementation of conservation actions, which is very promising for the protection of river biodiversity. Copyright © 2016 John Wiley & Sons, Ltd.     

The spatial arrangement of Neritina virginea (Gastropoda: Neritidae) during upstream migration in a split‐channel reach

This paper relates differences in flow hydraulics between a main channel (MC) and a side channel (SC) of a river to patterns of upstream migration by Neritina virginea (Neritidae: Gastropoda), a dominant diadromous snail in streams of Puerto Rico (Greater Antilles). Near‐bed water velocity, snail density and shell size were measured on a weekly basis between August and December 2000 along cross‐sections in a main channel (MC) and an adjacent channel (SC) under a bridge crossing of the Río Mameyes of Northeastern Puerto Rico. Near‐bed velocity and water depth were used to compute Reynolds (Re) and Froude (Fr) numbers, and to classify flows within each channel. During base flow conditions (<2 m³ s⁻¹), flow was chaotic and supercritical (Fr > 1) in the MC, and non‐chaotic and subcritical (Fr < 1) in the SC. Higher mean densities (>100 ind m⁻²) of relatively small snails (mean ± s.d., 6.3 ± 2.8 mm) were consistently recorded in the MC. Conversely, the SC had lower mean densities (<20 ind m⁻²) and significantly larger snails (7.6 ± 2.4 mm). Within the MC, migratory groups preferred near‐bed velocities > 0.8 m s⁻¹. Within the SC, they preferred the channel thalweg and depths > 30 cm. The spatial arrangement that was observed between and within the channels may be related to food resources, predation pressure or biomechanics. Characteristics of preferred upstream migration pathways of N. virginea must be accounted when building road crossings in coastal streams with diadromous fauna. Published in 2007 by John Wiley & Sons, Ltd.     

An Assessment of Fish Assemblage Structure in a Large River

The Penobscot River drains the largest watershed in Maine and once provided spawning and rearing habitats to 11 species of diadromous fishes. The construction of dams blocked migrations of these fishes and likely changed the structure and function of fish assemblages throughout the river. The proposed removal of two main‐stem dams, improved upstream fish passage at a third dam, and construction of a fish bypass on a dam obstructing a major tributary is anticipated to increase passage of and improve habitat connectivity for both diadromous and resident fishes. We captured 61 837 fish of 35 species in the Penobscot River and major tributaries, through 114 km of boat electrofishing. Patterns of fish assemblage structure did not change considerably during our sampling; relatively few species contributed to seasonal and annual variability within the main‐stem river, including smallmouth bass Micropterus dolomieu, white sucker Catostomus commersonii, pumpkinseed Lepomis gibbosus, and golden shiner Notemigonus crysoleucas. However, distinct fish assemblages were present among river sections bounded by dams. Many diadromous species were restricted to tidal waters downriver of the Veazie Dam; Fundulus species were also abundant within the tidal river section. Smallmouth bass and pumpkinseed were most prevalent within the Veazie Dam impoundment and the free‐flowing river section immediately upriver, suggesting the importance of both types of habitat that supports multiple life stages of these species. Further upriver, brown bullhead Ameiurus nebulosus, yellow perch Perca flavescens, chain pickerel Esox niger, and cyprinid species were more prevalent than within any other river section. Our findings describe baseline spatial patterns of fish assemblages in the Penobscot River in relation to dams with which to compare assessments after dam removal occurs. Copyright © 2014 John Wiley & Sons, Ltd.     

The impact of small and large impoundments on freshwater mussel distribution in the Hawkesbury‐Nepean River,southeastern Australia

The influence of weirs on the distribution of freshwater mussels was investigated in the Hawkesbury‐Nepean River, Australia. Distribution of species and densities of size classes were strongly correlated with catchment level factors (e.g. location around a major impoundment, stream order). At catchment scale, weir height, presence of a fish barrier, fish ladder type and position above or below small weirs did not influence the presence/absence of mussel populations. Lower mussel densities in the upper catchment may therefore reflect inhibition of host fish migration. Where present, weir height and geomorphic reach type were linked to differences in densities among species. Geomorphic reach‐based differences were reflected by the Hyridella species, but not Velesunio ambiguus. When population structure was described by size class distribution, there were significant differences between densities of small and medium mussels from weirs above, compared to weirs below, a major impoundment, but not for large mussels. Upstream populations may therefore be functionally extinct. Distribution of mussel size classes differed among geomorphic reach types with highest densities for each class found in the least human‐impacted reaches. Small mussels were almost invariably found below the major impoundment, most frequently below weirs. Distribution patterns were inconsistent across species, suggesting habitat preference. V. ambiguus and Hyridella australis were most abundant in shale reaches, where assemblages were influenced by fish ladder type. Hyridella depressa and H. australis dominated in sandstone gorges and straights with assemblage density related to weir height. In upper catchment sandstone reaches, mussel assemblages comprising predominantly V. ambiguus were influenced by fish ladder type and weir height. While multiple factors defined localized distribution, large impoundments were linked with reduced population densities. The probable mechanism is the restriction of host fish movement and resulting lack of recruitment. In the Hawkesbury‐Nepean River, smaller weirs also seriously impacted recruitment. Copyright © 2008 John Wiley & Sons, Ltd.     

Effects of elevated water temperature on fish and macroinvertebrate communities below small dams

Many studies have investigated the ecological changes that occur below dams that release cold, hypolimnetic water, but very few studies have looked at the effects of the release of warm, surface waters. The effect of small, surface release dams on downstream thermal regimes is a major habitat concern for many cold‐water systems, however. The objective of this study was to examine the effects of summer temperature increases due to impoundment on downstream fish and macroinvertebrate communities in cold‐water streams. We sampled fish, macroinvertebrates and habitat upstream and downstream of dams on ten rivers during the summers of 1998 and 1999. Changes in mean summer temperature downstream varied from a cooling of 1 °C to an increase of more than 5 °C. Increasing temperatures downstream coincided with lower densities of several cold‐water fish species, specifically brown trout (Salmo trutta), brook trout (Salvelinus fontinalis) and slimy sculpin (Cottus cognatus) while overall fish species richness increased downstream. Density of mottled sculpin (Cottus bairdi), another cold‐water species, was not related to temperature changes below the dams. Macroinvertebrates showed shifts in community composition below dams that increased temperature. This study provides information useful for determining the extent of impact of these small, surface release dams, which are abundant across the country. Copyright © 2003 John Wiley & Sons, Ltd.     

Factors affecting recruitment dynamics of Great Lakes sea lamprey (Petromyzon marinus) populations

Knowledge of stock–recruitment dynamics is as important for control of pest species such as the sea lamprey (Petromyzon marinus) as it is for sustainable harvest management of exploited fish species. A better understanding of spatial and temporal variation in recruitment of pest populations may inform managers on where and when to effectively apply different control methods. Sea lamprey stock–recruitment data combined from streams across the Great Lakes basin into a Ricker stock–recruitment model indicated both compensation (density-dependent survival) and a large amount of density-independent recruitment variation. We evaluated the use of a mixed-effects model to look at common year effects and stream-level variables that could affect productivity and growing season length, with the objective of identifying factors that may explain this density-independent variation in recruitment. After selecting the “best model”, we tested factors that might affect recruitment variation, using a Great Lakes dataset comprising 97 stream–years. Lake Superior tributaries, streams with larger numbers of lamprey competitors, and streams regularly requiring lampricide treatment showed significantly higher recruitment. Alkalinity and thermal regulation did not affect the observed recruitment pattern among streams. In four long-term study streams we observed significant variation among streams, tested as a fixed effect, but no evidence suggested a common pattern of variation among years. Differences in recruitment among streams were consistent with evidence of quality of spawning and larval habitat among streams. Our findings suggest that management models should account for differences in recruitment dynamics among sea lamprey-producing streams, but not common year effects.     

The impact of intermediate‐head navigation locks on downstream fish passage

Navigation in inland waterways is increasingly important worldwide and so is inherently the construction and use of navigation locks. However, the impact of navigation locks on downstream migrating fish is rarely documented. In Belgium, the Albert Canal connecting the Meuse River to the Scheldt Estuary may offer migration opportunities for European eel (Anguilla anguilla) and Atlantic salmon (Salmo salar), two critically endangered species. During their downstream migration phase (respectively silver eels and salmon smolts), both species have to pass five intermediate‐head navigation locks before reaching the estuary. Previous research showed that silver eel escapement is largely unsuccessful and that eels are delayed extensively at the navigation lock complexes. To get a better understanding of the mechanisms behind these failures and delays, we tagged and released 62 silver eels and 44 salmon smolts in the vicinity of one navigation lock complex of the canal. This paper reports the mechanisms behind the previously perceived delay, the route choices to pass the complex, and the risks involved. Of the 65% tagged eels and 73% tagged smolts that succeeded to pass the complex, respectively, 20% and 41% needed more than one trial to pass the complex. Moreover, 52% of all trials were via intakes of the lock filling system, at least four smolts (17%) died after intake passing, and about 30% of both intake‐passing smolts and eels stopped migrating after passage. Therefore, intermediate‐head navigation locks are a potential threat to downstream migrating fish, which requires more research to fully investigate its impact.     

DYNAMICS OF IN‐STREAM WOOD AND ITS IMPORTANCE AS FISH HABITAT IN A LARGE TROPICAL FLOODPLAIN RIVER

The recruitment of wood from the riparian zone to rivers and streams provides a complex habitat for aquatic organisms and can influence both aquatic biodiversity and ecosystem function. The Daly River in the wet–dry tropics of northern Australia is a highly seasonal, perennially flowing sand‐bed river where surveys of river wood aggregations at the reach scale (~2 km) in 2008 and 2009 recorded densities of 37–78 km^?1 and identified distinct types of river wood aggregations: key pieces, standing trees, fallen trees, wrack and single pieces. After larger than average flows in the 2008/2009 wet season, between 46% and 51% of the surveyed river wood had moved. The distribution of wood age classes indicated continual recruitment and slow turnover of wood within the river. Surveys of fish and habitat characteristics at the mesohabitat scale (~100 m) showed fish species richness; diversity and fish abundance were not correlated to the proportion of wood present. Fish assemblage structure was associated with wood cover as well as other environmental variables such as stream width and depth. The importance of in‐stream wood also varied for different species and age classes of fish. This study documents the dynamic nature of river wood aggregations and their complex and variable distribution and suggests their importance as fish habitat in this tropical river. Copyright © 2012 John Wiley & Sons, Ltd.     

Linking ecological science with management outcomes on New Zealand's longest river

New Zealand's Waikato River has had a short but intense history of development, primarily through land‐use change and flow regulation in the upper river, and in the lower river through flood control works, non‐native species invasion, and land‐use intensification. The river undergoes sharp transitions across montane‐flood plain‐coastal environments over a short distance and under similar climate. Together with specialized life‐history requirements of many native fish, these features provide valuable insights into large river ecology and management. Testing approaches to determine outcomes of water quality changes have highlighted the value of functional indicators over traditional biotic measures for monitoring anthropogenic impacts. Initiatives to enhance native fish populations in the lower river have included remediation of migration barriers to improve access to tributary habitat, enhancement of tidal spawning habitat, and traps and gates to limit movement of large pest fish into flood plain lakes for spawning. This example of a southern temperate large river system highlights the importance of recruitment habitat and connectivity for native fish communities dominated by migratory species. Their slender bodies provide opportunities to create semipermeable barriers that enable access to flood plain habitats while restricting larger invasive fish. Recent initiatives have increased momentum to restore the ecological health of this river, but the underpinning science to guide priority actions is often lacking, and there is limited monitoring over the scales and time frames required to evaluate effectiveness.     

Impoverishment of YOY‐fish assemblages by intense commercial navigation in a large Lowland river

Navigation‐induced physical forces have been suggested to modify the structure of riverine fish assemblages by impeding especially the recruitment of littoral bound species. To investigate the effect of vessel frequency on fish, we compared the composition and seasonal succession of young‐of‐the‐year (YOY) fish assemblages in three similarly degraded river reaches differing in average vessel passages (2, 6 and 41 per day). Fish were caught by electrofishing biweekly between May and September. Multivariate tests were used to analyse differences between YOY‐fish assemblages and hurdle regression models applied to determine abiotic factors predicting fish occurrence and abundance. Roach (Rutilus rutilus) and perch (Perca fluviatilis) densities were compared. Roach larvae remain in the littoral zone while perch larvae shift to the pelagic zone immediately after hatch. YOY‐fish assemblage structure substantially changed along the traffic intensity gradient. In the high traffic intensity reach, species number and total fish density were markedly reduced compared to the other reaches. Roach densities were lowest in the high traffic intensity reach whereas perch densities did not decline along the gradient. Hurdle regressions confirmed a stronger effect of commercial navigation traffic intensity on roach than on perch. The total zooplankton biomass was highest in the high traffic intensity reach. Our results provide empirical evidence that intensive commercial navigation impoverishes fish assemblages in width‐restricted waterways. They underlined that in particular those species that have their first nursery habitats in shoreline areas were more affected by intensive commercial navigation than species whose larvae live predominantly pelagic. The results indicate that the negative effect of intensive navigation on riverine fish results primarily from the navigation‐induced hydraulic disturbances along the banks. Therefore, mitigation of navigation‐induced hydraulic forces is required to prevent degradation of fish communities in waterways. Copyright © 2010 John Wiley & Sons, Ltd.     

Return of adult anadromous allis shad (Alosa alosa L.) in the river Seine,France: A sign of river recovery?

In the past, the diadromous fish fauna of the river Seine comprised 11 native species. From the second part of the 19th century, the progressive modification of the river for navigation purposes and the increase of domestic and industrial pollution led to a general decline of migratory stocks and the extinction of several species. Among them, allis shad (Alosa alosa) was previously widespread in the Seine basin, but disappeared at the beginning of the 20th century. In July 2004, several individuals of shad were observed in the river Seine upstream of Paris (410 km from the sea), one of them was identified as an allis shad that had clearly spawned (thin fish and large scale erosion). A second allis shad was caught in a more downstream location (180 km from the sea) in November 2007 and a spawning mark was found on scales demonstrating clear evidence of reproduction. Recent occurrences of this species are discussed in relation to the present conditions of water quality and migration in the Seine watershed and recent evolution of the species' distribution in the northwestern part of France. Copyright © 2009 John Wiley & Sons, Ltd.     

Fish zonation and indicator species for the evaluation of the ecological status of rivers: example of the Loire basin (France)

In the context of river alteration, ecologists are asked to develop tools for the assessment of river integrity. Fish are known to be good bioindicators of the ecological condition of rivers. The Loire basin (France) is often considered as relatively little impacted compared to most other large European systems. But curiously, no study clearly addressed the question of fish assemblages patterns in this system in order to assess this status. Thus, we studied fish assemblages along the river network in the Loire basin using self‐organizing maps (SOMs) and we built a fish typology. Four basic assemblages were described and indicator species were identified. These assemblages varied in terms of individual species patterns as well as in terms of flow preference guilds and species richness. A discriminant analysis carried out on environmental variables revealed that they could be mainly determined by the slope, temperature and depth. Finally, fish assemblages were arrayed along a longitudinal gradient and roughly fitted the theoretical zonation expected in European rivers with the succession of brown trout (Salmo trutta fario), grayling (Thymallus thymallus), barbel (Barbus barbus) and bream (Abramis brama) zones in a downstream direction. Such patterns are still rarely observed in large European systems. However, the fish assemblage characteristic of the bream zone occurred more frequently than predicted on the basis of environmental variables. Such deviations between field data and theory suggest lotic‐to‐lentic shifts probably due to anthropogenic disturbances, especially in the grayling and barbel zones. In these river sectors, eurytopic and limnophilic species tend to replace rheophilic ones. Finally, the method used in this study to investigate fish patterns may be helpful to detect disturbances and may serve as a tool for the establishment of management plans. Copyright © 2007 John Wiley & Sons, Ltd.     

Mechanically reshaping stream banks alters fish community composition

Mechanically reshaping stream banks is a common practice to mitigate bank erosion in streams that have been extensively channelised and lowered for land drainage. A common perception regarding this activity is that fish populations will be largely unaffected, at least in the short term, because the low‐flow wetted channel remains undisturbed. However, the response of fish populations to this practice has rarely been quantitatively evaluated. Using a Before‐After‐Control‐Impact design, we assessed fish community responses to a catchment‐scale bank reshaping event in a fourth‐order low‐gradient stream that drains an intensive agricultural landscape. Quantitative electric fishing and fish habitat data were collected 2 months before and annually for 3 years after the reshaping event. After reshaping, deposited fine sediment levels increased in impact reaches, and there was a significant reduction in anguillid eel biomass (by 49%). In contrast, densities of obligate benthic gobiid bully species increased significantly in impact reaches—potentially due to reduced predation pressure from eels. Three years after bank reshaping, fish community structure had largely returned to its preimpact state in the reshaped areas. Our results suggest that, even in highly modified stream channels, further bank modification can reduce instream habitat quality and displace eels for at least 1 year. Managers should endeavour to use bank erosion control measures that conserve bank‐edge cover, especially in streams with populations of anguillid eels, because these fish are declining globally.     

Nature‐like fishways as compensatory lotic habitats

Damming of rivers disrupts migration of fish and results in lotic habitats being both scarcer and spaced further apart, ultimately affecting riverine fish communities. Nature‐like fishways are often designed as bypass channels, constructed with natural materials that reroute part of the water around weirs and dams, restoring longitudinal connectivity as well as forming nature‐mimicking habitats. We evaluated the potential of such bypasses to function as compensatory lotic habitats by comparing fish fauna in 23 bypasses to adjacent lotic stream habitats in a same‐river pairwise design. Bypasses were narrower, shallower, and less shaded than adjacent stream habitats, but very few significant differences could be detected in the fish communities, indicating the potential of such nature‐like fishways to constitute compensatory lotic habitats for fish. Analyses also indicated how bypass design may be altered to favour or disfavour certain target species. Generally, narrower and shallower bypasses with high gradient favoured brown trout (Salmo trutta), whereas European eel (Anguilla anguilla) were more abundant at sites with lower gradient. Finally, to increase the impact of these compensatory habitats on running water ecosystems, we suggest that the size of bypasses should be maximized in areas where natural stream habitats have been lost.     

The response of anguilliform fish to underwater sound under an experimental setting

Traditional physical screens designed to prevent fish entering dangerous areas (e.g., turbine intakes) can have negative impacts due to impingement or mechanical abrasion at high velocities. Behavioural deterrents may provide an alternative approach to screening. This study investigated the potential for a continuous broadband sound to modify the behaviour of two endangered species of anguilliform fish: European eel (Anguilla anguilla) and river lamprey (Lampetra fluviatilis). Experiments were conducted in an experimental channel. Eel and lamprey were, respectively, released upstream and downstream of an “acoustic maze”. A single individual released per trial encountered two successive chambers that offered a choice of passage through either an ensonified or a control (ambient noise only) corridor with a speaker turned off. Two possible configurations were tested to control for any lateral bias with positions of the activated speakers reversed. The influence of treatment, chamber, and configuration on route selection, rejection, and time to pass were tested. No influence of any of the three factors on route selection was observed for eel. River lamprey tended to pass through the ensonified corridor more often under Configuration 2 but only in the first chamber. Both species were more likely to reject the ensonified corridors than the controls, and the time taken to pass these routes was greater for those that did so. For eel, the variation in time to pass was greater for the non‐migratory (yellow phase) life stage. Although the acoustic signal used in this study influenced fish behaviour, the response observed would likely be insufficient to induce a strong deterrent effect in the field if used in isolation.     

Influence of a high‐head dam as a dispersal barrier to fish community structure of the Upper Mississippi River

In river systems, high‐head dams may increase the distance‐decay of fish community similarity by creating nearly impermeable dispersal barriers to certain species from upstream reaches. Substantial evidence suggests that migratory species are impacted by dams, and most previous studies in stream/river networks have focused on small streams and headwaters. Here, we assess whether a high‐head dam (Lock and Dam 19; LD 19) on a large river, the Upper Mississippi River (UMR), substantially alters fish community structure relative to variability expected to occur independent of the dam's effect as a fish dispersal barrier. Using fish catch per unit effort data, we modelled the distance‐decay function for the UMR fish community and then estimated the similarity that would be expected to occur across LD19 and compared it with measured similarity. Measured similarity in the fish community above and below LD19 was close to the expected value based on the distance‐decay function, suggesting LD19 does not create an abrupt transition in the fish community. Although some migratory fish species no longer occur above LD19 (e.g., skipjack herring, Alosa chrysochloris), these species do not occur in high abundance below the dam and so do not drive variation in fish community structure. Instead, much of the variation in species structure is driven by the loss/gain of species across the latitudinal gradient. Lock and Dam 19 does not appear to be a clear transition point in the river's fish community, although it may function as a meaningful barrier for particular species (e.g., invasive species) and warrant future attention from a management perspective.     

Downstream Swimming Behaviour of Catadromous and Potamodromous Fish Over Spillways

Flow characteristics associated with spillways are important to restore ecological connectivity because spillways can either constrain or offer safe routes for downstream passage of fish. We studied the hydrodynamics of flow and downstream movement behaviour of the catadromous European eel (Anguilla anguilla) and the potamodromous Iberian barbel (Luciobarbus bocagei) in spillways with upstream face inclinations of θ = 90° (standard) 45° and 30° (modified). The standard spillway was tested for two water depths (H = 32 and 42 cm). Modified spillways facilitated downstream passage and reduced delay times of passage of the European eel. Upstream of the 90° spillway, distinct recirculation areas were observed, and associated turbulence strongly hampered downstream passage of fish. Both species were found to avoid turbulence, but barbel displayed stronger avoidance for areas of rapid changes in flow velocity when comparing to eels. Overall, eels were faster in passing the spillway and had a higher downstream passage success (80%) than barbel (32%). Eels were predominantly thigmotactic in contrast to barbel, which showed limited contact with structures. The results suggest that modified spillways may enhance passage survival. Copyright © 2015 John Wiley & Sons, Ltd.     

INVERTEBRATE AND FISH ASSEMBLAGE RELATIONS TO DISSOLVED OXYGEN MINIMA IN LOWLAND STREAMS OF SOUTHWESTERN LOUISIANA

Dissolved oxygen (DO) concentrations in lowland streams are naturally lower than those in upland streams; however, in some regions where monitoring data are lacking, DO criteria originally established for upland streams have been applied to lowland streams. This study investigated the DO concentrations at which fish and invertebrate assemblages at 35 sites located on lowland streams in southwestern Louisiana began to demonstrate biological thresholds. Average threshold values for taxa richness, diversity and abundance metrics were 2.6 and 2.3 mg/L for the invertebrate and fish assemblages, respectively. These thresholds are approximately twice the DO concentration that some native fish species are capable of tolerating and are comparable with DO criteria that have been recently applied to some coastal streams in Louisiana and Texas. DO minima >2.5 mg/L were favoured for all but extremely tolerant taxa. Extremely tolerant taxa had respiratory adaptations that gave them a competitive advantage, and their success when DO minima were <2 mg/L could be related more to reductions in competition or predation than to DO concentration directly. DO generally had an inverse relation to the amount of agriculture in the buffer area; however, DO concentrations at sites with both low and high amounts of agriculture (including three least‐disturbed sites) declined to <2.5 mg/L. Thus, although DO fell below a concentration that was identified as an approximate biological threshold, sources of this condition were sometimes natural (allochthonous material) and had little relation to anthropogenic activity. Copyright © 2012 John Wiley & Sons, Ltd.     

Reference databases,primer choice,and assay sensitivity for environmental metabarcoding: Lessons learnt from a re‐evaluation of an eDNA fish assessment in the Volga headwaters

Biodiversity monitoring via environmental DNA, particularly metabarcoding, is evolving into a powerful assessment tool for riverine systems. However, for metabarcoding to be fully integrated into standardized monitoring programmes, some current challenges concerning sampling design, laboratory workflow, and data analysis need to be overcome. Here, we review some of these major challenges and potential solutions. We further illustrate three potential pitfalls, namely the choice of suitable metabarcoding primers, the necessity of complete reference databases, and varying assay sensitivities, by a reappraisal of our‐own recently carried out metabarcoding study in the Volga headwaters. TaqMan qPCRs had detected catfish (Silurus glanis) and European eel (Anguilla anguilla), whereas metabarcoding had not, in the same samples. Furthermore, after extending the genetic reference database by 12 additional species and re‐analysing the metabarcoding data, we additionally detected the Siberian spiny loach (Cobitis sibirica) and Ukrainian brook lamprey (Eudontomyzon mariae) and reassigned the operational taxonomic units previously assigned to Misgurnus fossilis to Cobitis sibirica. In silico analysis of metabarcoding primer efficiencies revealed considerable variability among primer pairs and among target species, which could lead to strong primer bias and potential false‐negatives in metabarcoding studies if not properly compensated for. These results highlight some of the pitfalls of eDNA‐metabarcoding as a means of monitoring fish biodiversity in large rivers, which need to be considered in order to fully unleash the full potential of these approaches for freshwater biodiversity monitoring.