Biological Diversity in Headwater Streams

Targeted eDNA Metabarcoding Reveals New Populations of a Range-Limited Stonefly

Understanding the geographic distributions of rare species can be crucial for conservation management. New environmental DNA (eDNA) technologies offer the potential to efficiently document the distributions of endangered species, but to date, such screening has focused largely on vertebrate taxa. Here we use freshwater eDNA to assess the geographic distribution of the Maungatua stonefly, Zelandoperla maungatuaensis, a flightless insect previously known from only a handful of streams draining a 4-km section of the Maungatua mountain range in southern New Zealand. We analyzed freshwater eDNA from 12 stream localities across the Maungatua range. Screening with commercial eDNA COI primers failed to detect the focal species Z. maungatuaensis. However, newly designed species-specific primers detected this taxon from four adjacent east-flowing streams known to contain Z. maungatuaensis, and two streams from which it had not previously been detected. Subsequent manual surveys confirmed the presence of two newly discovered Z. maungatuaensis populations, with COI barcoding revealing that they together represent a previously unknown, genetically divergent subclade. Our results illustrate the potential of eDNA metabarcoding to help delineate the geographic ranges of rare taxa, and highlight the importance of primer specificity when screening for rare taxa. These findings also have considerable implications for commercial companies offering biodiversity and stream health eDNA services targeting invertebrates.

Seasonal Dynamics and Factors Shaping Aquatic Insect Assemblages in Mountain Streams of the Pannonian Lowland Ecoregion

This study focused on the aquatic insect orders that serve as biological indicators. Ephemeroptera, Plecoptera, Trichoptera, Coleoptera, and Odonata were studied with their relationships to physical, chemical, hydrological and morphological variables in 14 streams on three Croatian mountains: Papuk, Medvednica and Psunj. From 675 samples collected in three dominant sediment microhabitats (e.g., macrolithal and mesolithal) in each stream, we identified 130 macroinvertebrate taxa. The most abundant group was Ephemeroptera (36 taxa). Aquatic insect assemblages between Papuk and Psunj showed higher similarity due to the geographical proximity of these two mountains, which is expressed as spatial connectivity. In spring, greater variability and diversity of investigated aquatic insects were observed due to the phenology of studied insects. The combination of environmental and morphological properties (e.g., oxygen concentration and substrate type) had the most significant influence on shaping the assemblage of aquatic insects of Psunj, while morphological properties were the most important in shaping aquatic insect assemblages on Papuk (e.g., streambed width) and Medvednica (e.g., elevation). Baetis sp. was the dominant taxon in summer, Protonemura montana in spring, and Leuctra sp. in autumn. Seasonal shifts in environmental conditions lead to functionally unique communities that utilize the pool of available seasonal resources. The dominance of feeding groups varied by season, with scrapers and collector-gatherers being most prevalent in summer, while shredders were dominant in spring. The results on the relationships between environmental characteristics and species richness, functional structure, and distribution of aquatic insects in mountain streams provide important clues for future research and conservation strategies in these vulnerable ecosystems.

Nymphs of the Northeastern Nearctic Species of Neoleptophlebia Kluge, 1997 and Paraleptophlebia Lestage, 1917 (Ephemeroptera: Leptophlebiidae)

Although male imagos of the three species of Neoleptophlebia and seven species of Paraleptophlebia known from the northeastern Nearctic region (i.e., eastern Canada and northeastern United States) are reasonably well-known and can be reliably keyed, nymphs are not as well-known and often cannot be reliably identified using the existing keys. Descriptions of nymphs of the northeastern Nearctic species of Neoleptophlebia and Paraleptophlebia vary in completeness and frequently lack important morphological details or information on variation that occurs with development or between different sexes. Thus, all existing keys based on these descriptions have problematic couplets, and some do not treat all 10 species. To address these problems a new key to nymphs of the 10 northeastern Nearctic species of Neoleptophlebia and Paraleptophlebia is presented here based on a reassessment of the morphology of nymphs and exuviae of reared specimens. The new key uses several new characters in combination with previously known diagnostic characters to increase the probability of achieving accurate species determinations. In support of the key each species is discussed regarding key characters, specifically regarding variability that may cause interpretation problems. Regional distribution and habitat also are discussed for each species. Lastly, comments are provided on the apparent vulnerability of each species to large scale changes in its occurrence within the northeast Nearctic region as a result of the predicted effects of climate change on regional aquatic habitats.

Outbreeding reduces survival during metamorphosis in a headwater stream salamander

Assessing direct fitness effects of individual genetic diversity is challenging due to the intensive and long-term data needed to quantify survival and reproduction in the wild. But resolving these effects is necessary to determine how inbreeding and outbreeding influence eco-evolutionary processes. We used 8 years of capture-recapture data and single nucleotide polymorphism genotypes for 1906 individuals to test for effects of individual heterozygosity on stage-specific survival probabilities in the salamander Gyrinophilus porphyriticus. The life cycle of G. porphyriticus includes an aquatic larval stage followed by metamorphosis into a semi-aquatic adult stage. In our study populations, the larval stage lasts 6-10 years, metamorphosis takes several months, and lifespan can reach 20 years. Previous studies showed that metamorphosis is a sensitive life stage, leading us to predict that fitness effects of individual heterozygosity would occur during metamorphosis. Consistent with this prediction, monthly probability of survival during metamorphosis declined with multi-locus heterozygosity (MLH), from 0.38 at the lowest MLH (0.10) to 0.06 at the highest MLH (0.38), a reduction of 84%. Body condition of larvae also declined significantly with increasing MLH. These relationships were consistent in the three study streams. With evidence of localised inbreeding within streams, these results suggest that outbreeding disrupts adaptations in pre-metamorphic and metamorphic individuals to environmental gradients along streams, adding to evidence that headwater streams are hotspots of microgeographic adaptation. Our results also underscore the importance of incorporating life history in analyses of the fitness effects of individual genetic diversity and suggest that metamorphosis and similar discrete life stage transitions may be critical periods of viability selection.

Ecologically and medically important black flies of the genus Simulium: Identification of biogeographical groups according to similar larval niches

The black fly genus Simulium includes medically and ecologically important species, characterized by a wide variation of ecological niches largely determining their distributional patterns. In a rapidly changing environment, species-specific niche characteristics determine whether a species benefits or not. With aquatic egg, larval and pupal stages followed by a terrestrial adult phase, their spatial arrangements depend upon the interplay of aquatic conditions and climatic-landscape parameters in the terrestrial realm. The aim of this study was to enhance the understanding of the distributional patterns among Simulium species and their ecological drivers. In an ecological niche modelling approach, we focused on 12 common black fly species with different ecological requirements. Our modelling was based on available distribution data along with five stream variables describing the climatic, land-cover, and topographic conditions of river catchments. The modelled freshwater habitat suitability was spatially interpolated to derive an estimate of the adult black flies' probability of occurrence. Based on similarities in the spatial patterns of modelled habitat suitability we were able to identify three biogeographical groups, which allows us to confirm old assessments with current occurrence data: (A) montane species, (B) broad range species and (C) lowland species. The five veterinary and human medical relevant species Simulium equinum, S. erythrocephalum, S. lineatum, S. ornatum and S. reptans are mainly classified in the lowland species group. In the course of climatic changes, it is expected that biocoenosis will slightly shift towards upstream regions, so that the lowland group will presumably emerge as the winner. This is mainly explained by wider ecological niches, including a higher temperature tolerance and tolerance to various pollutants. In conclusion, these findings have significant implications for human and animal health. As exposure to relevant Simulium species increases, it becomes imperative to remain vigilant, particularly in investigating the potential transmission of pathogens.

Recognizing Agricultural Headwaters as Critical Ecosystems

Agricultural headwaters are positioned at the interface between terrestrial and aquatic ecosystems and, therefore, at the margins of scientific disciplines. They are deemed devoid of biodiversity and too polluted by ecologists, overlooked by hydrologists, and are perceived as a nuisance by landowners and water authorities. While agricultural streams are widespread and represent a major habitat in terms of stream length, they remain understudied and thereby undervalued. Agricultural headwater streams are significantly modified and polluted but at the same time are the critical linkages among land, air, and water ecosystems. They exhibit the largest variation in streamflow, water quality, and greenhouse gas emission with cascading effects on the entire stream networks, yet they are underrepresented in monitoring, remediation, and restoration. Therefore, we call for more intense efforts to characterize and understand the inherent variability and sensitivity of these ecosystems to global change drivers through scientific and regulatory monitoring and to improve their ecosystem conditions and functions through purposeful and evidence-based remediation.

Caddisflies (Trichoptera) checklist and a new species of Helicopsyche von Siebold, 1856, from the Brejo de Altitude de Triunfo, a relict rainforest within the Caatinga domain, Northeast Brazil

Brejos de Altitude are evergreen seasonal forests, associated with plateau regions in the middle of the Caatinga domain in Northeast Brazil, which possibly acted as biological corridors between the Atlantic Forest and the Amazon rainforest during the Pleistocene. The first entomological survey in the highest point in the state of Pernambuco, Brazil, the Brejo de Altitude de Triunfo, was implemented and resulted in a checklist of caddisflies with six families, nine genera, and eleven species, including a new species. Helicopsycheralphi sp. nov. is described and illustrated, based on all semaphoronts. A key to Brazilian Helicopsyche (Feropsyche) Johanson, 1998 species is also provided. In addition to the caddisfly survey in the Brejos de Altitude, the results include new records for the state, region, and also for the country. Thus, this study updates the number of species in the Brazilian Northeast region and Pernambuco state to 169 species and 43 species, respectively.

Do metapopulations and management matter for relict headwater bull trout populations in a warming climate?

Mountain headwater streams have emerged as important climate refuges for native cold-water species due to their slow climate velocities and extreme physical conditions that inhibit non-native invasions. Species persisting in refuges often do so as fragmented, relict populations from broader historical distributions that are subject to ongoing habitat reductions and increasing isolation as climate change progresses. Key for conservation planning is determining where remaining populations will persist and how habitat restoration strategies can improve biological resilience to enhance the long-term prospects for species of concern. Studying bull trout, a headwater species in the northwestern USA, we developed habitat occupancy models using a data set of population occurrence in 991 natal habitat patches with a suite of novel geospatial covariates derived from high-resolution hydroclimatic scenarios and other sources representing watershed and instream habitat conditions, patch geometry, disturbance, and biological interactions. The best model correctly predicted bull trout occupancy status in 82.6% of the patches and included effects for: patch size estimated as habitat volume, extent of within-patch reaches <9°C mean August temperature, distance to nearest occupied patch, road density, invasive brook trout prevalence, patch slope, and frequency of high winter flows. The model was used to assess 16 scenarios of bull trout occurrence within the study streams that represented a range of restoration strategies under three climatic conditions (baseline, moderate change, and extreme change). Results suggested that regional improvements in bull trout status were difficult to achieve in realistic restoration strategies due to the pervasive nature of climate change and the limited extent of restoration actions given their high costs. However, occurrence probabilities in a subset of patches were highly responsive to restoration actions, suggesting that targeted investments to improve the resilience of some populations may be contextually beneficial. A possible strategy, therefore, is focusing effort on responsive populations near more robust population strongholds, thereby contributing to local enclaves where dispersal among populations further enhances resilience. Equally important, strongholds constituted a small numerical percentage of patches (5%-21%), yet encompassed the large majority of occupied habitat by volume (72%-89%) and their protection could have significant conservation benefits for bull trout.

DNA metabarcoding reveals human impacts on macroinvertebrate communities in polluted headwater streams: Evidence from the Liao River in northeast China

Headwater streams are a hotspot of freshwater biodiversity, carrying indispensable resource pools of aquatic species. However, up to now, there remain many challenges to accurately and efficiently characterize the responses of this vulnerable ecosystem to human-induced changes. Here, we collected macroinvertebrate data from 12 different headwater streams in the Liao River of northeast China by DNA metabarcoding approach, to reveal biodiversity changes and ecological thresholds affected by human beings. Our data showed that the community composition and structure of headwater streams had unique and significant differences under human impacts, and 5-day biological oxygen demand (BOD₅) and ammonia nitrogen (NH₃-N) were the key variables explaining the variation in community structure. Although α diversity had a unimodal relationship with nutrients and organic loads, β diversity and its turnover component (species replacement) increased significantly. In addition, 22 and 33 indicative taxa were identified to have significant negative responses to BOD₅ and NH₃-N, respectively, and the change points derived from Threshold Indicator Taxa Analysis (TITAN) for the negative response of their frequency and abundance were BOD₅ >3.42 mg/L and NH₃-N >0.14 mg/L. Overall, this study reveals the biodiversity changes in headwater streams from the aspects of α and β diversity, and also determines the thresholds of BOD₅ and NH₃-N pollutants for one reach at one date from 12 headwater streams, suggesting the potential of DNA metabarcoding approach for threshold analyses in headwater streams.

Characterisation of Benthic Macroinvertebrate Communities in Small Watercourses of the European Central Plains Ecoregion and the Effect of Different Environmental Factors

Most publications on the influence of environmental factors on macroinvertebrate communities focus on large rivers, whereas relatively few examine small watercourses in agricultural areas, which, due to their size and pressure from intensive agricultural production, are much more susceptible to the effects of unfavourable environmental conditions or anthropopressure. The aim of our study was to compare the biodiversity of macrozoobenthos assemblages and to determine the effects of physicochemical and hydrological conditions on their abundance and density in 10 small rivers in agricultural areas located in northwest (53°23' N 15°14' E) and central (52°11' N 20°48' E) Poland. In total, 105 taxa were recorded, with the majority being euryoecious. Among the assessed physicochemical parameters, oxygenation was found to affect the density and number of taxa; another important factor was the content of nitrate nitrogen. Sensitivity to changes in water temperature was observed in some macrozoobenthos taxa (especially Decapoda). Of the examined hydrological parameters, the greatest effects were exerted by speed, flow, and depth.

Barrier removal and dynamics of intermittent stream habitat regulate persistence and structure of fish community

Barrier effects observed in the presence of weirs are exacerbated by low water levels. We conducted a 10-year study to assess the ecological effects of stream restoration while analysing the possibility of a seasonal lack of hydrological continuity, with multiple measurements before and after restoring stream structural continuity. The research hypothesis assumes that in intermittent streams, there would be little or no change in the fish community downstream the barrier before vs. after barrier removal, and a significant change upstream the barrier before vs. after. Our results indicate, that by removing small barriers, their detrimental effects on the longitudinal passage of riverine fishes and fish assemblages can be rehabilitated. In the wet season, fish migrants from the mainstem river appeared in the downstream section of the stream. Stream intermittency, however, placed a habitat filter over the assemblage. Thus, after barrier removal, only two small-bodied fish species that tolerate periodic oxygen deficiencies and rising water temperatures gradually shifted upstream and formed stable populations. We emphasize, that we should not refrain from restoring the longitudinal continuity of intermittent streams, because they periodically provide fish valuable refugia and can also be a source of new generations and strengthen fish populations in mainstem river.

Aquatic Biological Diversity Responses to Flood Disturbance and Forest Management in Small, Forested Watersheds

We examined riparian system responses to an extreme rainfall event on 1–4 December 2007, in eleven small watersheds (mean area—13.2 km2) from 2008–2016 at debris flow, high flood, and low flood reaches (all extended overbank flows). Macroinvertebrate responses followed expected outcomes after extreme disturbance including increasing chironomids and other multi-voltine species. A core assemblage of twenty abundant and common species-maintained populations even after debris flow (likely by recolonizing quickly) with total richness during project of 253 including 183 rare species (<0.01 total abundance) supporting an annual turnover of species from 22 to 33%. Primary disturbance changes to habitat were declines in shade and in-channel wood at all reaches, more strongly at debris flow reaches. Macroinvertebrate communities across disturbance intensities became increasingly similar after the storm. Combined effects of the flood reducing channel complexity and previous logging decreasing in-channel wood recruitment from riparian systems, limits habitat complexity. Until this feature of forested watershed streams returns, there appears to be a ceiling on reach scale aquatic biological diversity.

Land Use Change Influences Ecosystem Function in Headwater Streams of the Lowland Amazon Basin

Intensive agriculture alters headwater streams, but our understanding of its effects is limited in tropical regions where rates of agricultural expansion and intensification are currently greatest. Riparian forest protections are an important conservation tool, but whether they provide adequate protection of stream function in these areas of rapid tropical agricultural development has not been well studied. To address these gaps, we conducted a study in the lowland Brazilian Amazon, an area undergoing rapid cropland expansion, to assess the effects of land use change on organic matter dynamics (OM), ecosystem metabolism, and nutrient concentrations and uptake (nitrate and phosphate) in 11 first order streams draining forested (n = 4) or cropland (n = 7) watersheds with intact riparian forests. We found that streams had similar terrestrial litter inputs, but OM biomass was lower in cropland streams. Gross primary productivity was low and not different between land uses, but ecosystem respiration and net ecosystem production showed greater seasonality in cropland streams. Although we found no difference in stream concentrations of dissolved nutrients, phosphate uptake exceeded nitrate uptake in all streams and was higher in cropland than forested streams. This indicates that streams will be more retentive of phosphorus than nitrogen and that if fertilizer nitrogen reaches streams, it will be exported in stream networks. Overall, we found relatively subtle differences in stream function, indicating that riparian buffers have thus far provided protection against major functional shifts seen in other systems. However, the changes we did observe were linked to watershed scale shifts in hydrology, water temperature, and light availability resulting from watershed deforestation. This has implications for the conservation of tens of thousands of stream kilometers across the expanding Amazon cropland region.

Stream Temperature Response to 50% Strip-Thinning in a Temperate Forested Headwater Catchment

Stream temperature is a critical parameter for understanding hydrological and biological processes in stream ecosystems. Although a large body of research has addressed the effects of forest harvesting on stream temperature, less is known about the responses of stream temperature to the practice of strip-thinning, which produces more coherent patches of shade and sunlight areas. In this study, we examined stream temperature response to 50% strip-thinning in a 17 ha headwater catchment. The thinning lines extended through the riparian zone. Paired-catchment analysis was applied to estimate changes in daily maximum, mean, and minimum stream temperatures for the first year following treatment. Significant effects on daily maximum stream temperature were found for April to August, ranging from 0.6 °C to 3.9 °C, similar to the magnitude of effect found in previous studies involving 50% random thinning. We conducted further analysis to identify the thermal response variability in relation to hydrometeorological drivers. Multiple regression analysis revealed that treatment effects for maximum daily stream temperature were positively related to solar radiation and negatively related to discharge. Frequent precipitation during the summer monsoon season produced moderate increases in discharge (from 1 to 5 mm day−1), mitigating stream temperature increases associated with solar radiation. Catchment hydrologic response to rain events can play an important role in controlling stream thermal response to forest management practices.

The geography of metapopulation synchrony in dendritic river networks

Dendritic habitats, such as river ecosystems, promote the persistence of species by favouring spatial asynchronous dynamics among branches. Yet, our understanding of how network topology influences metapopulation synchrony in these ecosystems remains limited. Here, we introduce the concept of fluvial synchrogram to formulate and test expectations regarding the geography of metapopulation synchrony across watersheds. By combining theoretical simulations and an extensive fish population time‐series dataset across Europe, we provide evidence that fish metapopulations can be buffered against synchronous dynamics as a direct consequence of network connectivity and branching complexity. Synchrony was higher between populations connected by direct water flow and decayed faster with distance over the Euclidean than the watercourse dimension. Likewise, synchrony decayed faster with distance in headwater than mainstem populations of the same basin. As network topology and flow directionality generate fundamental spatial patterns of synchrony in fish metapopulations, empirical synchrograms can aid knowledge advancement and inform conservation strategies in complex habitats.

Multiple stressors in small streams in the forestry context of Fennoscandia: The effects in time and space

In this paper we describe how forest management practices in Fennoscandian countries, namely Sweden and Finland, expose streams to multiple stressors over space and time. In this region, forestry includes several different management actions and we explore how these may successively disturb the same location over 60-100 year long rotation periods. Of these actions, final harvest and associated road construction, soil scarification, and/or ditch network maintenance are the most obvious sources of stressors to aquatic ecosystems. Yet, more subtle actions such as planting, thinning of competing saplings and trees, and removing logging residues also represent disturbances around waterways in these landscapes. We review literature about how these different forestry practices may introduce a combination of physicochemical stressors, including hydrological change, increased sediment transport, altered thermal and light regimes, and water quality deterioration. We further elaborate on how the single stressors may combine and interact and we consequently hypothesise how these interactions may affect aquatic communities and processes. Because production forestry is practiced on a large area in both countries, the various stressors appear multiple times during the rotation cycles and potentially affect the majority of the stream network length within most catchments. We concluded that forestry practices have traditionally not been the focus of multiple stressor studies and should be investigated further in both observational and experimental fashion. Stressors accumulate across time and space in forestry dominated landscapes, and may interact in unpredictable ways, limiting our current understanding of what forested stream networks are exposed to and how we can design and apply best management practices.

Characteristics, Main Impacts, and Stewardship of Natural and Artificial Freshwater Environments: Consequences for Biodiversity Conservation

In this overview (introductory article to a special issue including 14 papers), we consider all main types of natural and artificial inland freshwater habitas (fwh). For each type, we identify the main biodiversity patterns and ecological features, human impacts on the system and environmental issues, and discuss ways to use this information to improve stewardship. Examples of selected key biodiversity/ecological features (habitat type): narrow endemics, sensitive (groundwater and GDEs); crenobionts, LIHRes (springs); unidirectional flow, nutrient spiraling (streams); naturally turbid, floodplains, large-bodied species (large rivers); depth-variation in benthic communities (lakes); endemism and diversity (ancient lakes); threatened, sensitive species (oxbow lakes, SWE); diverse, reduced littoral (reservoirs); cold-adapted species (Boreal and Arctic fwh); endemism, depauperate (Antarctic fwh); flood pulse, intermittent wetlands, biggest river basins (tropical fwh); variable hydrologic regime—periods of drying, flash floods (arid-climate fwh). Selected impacts: eutrophication and other pollution, hydrologic modifications, overexploitation, habitat destruction, invasive species, salinization. Climate change is a threat multiplier, and it is important to quantify resistance, resilience, and recovery to assess the strategic role of the different types of freshwater ecosystems and their value for biodiversity conservation. Effective conservation solutions are dependent on an understanding of connectivity between different freshwater ecosystems (including related terrestrial, coastal and marine systems).