Mesohabitat Scale Research Articles

Habitat associations of the Rio Grande Silvery Minnow, an endangered desert river fish, from a retrospective analysis based on a period of high abundance

AbstractObjectiveCharacterizing habitat associations is useful to aid in understanding the habitat requirements of native fishes, particularly those of conservation concern. Our study objective was to characterize mesoscale habitat associations of the only remaining wild population of the Rio Grande Silvery Minnow Hybognathus amarus (a federally endangered desert river fish), and provide comparisons with mesohabitat availability in the middle Rio Grande, New Mexico, from 1994 to 1996.MethodsWe collected fish monthly at two sites (separated by 160 km) near the northern and southern limits of the species' current range, and we recorded depth, velocity, substrate, and mesohabitat type for each habitat surveyed. Mesohabitat availability was recorded across 10 equally spaced and fixed transect lines at both study sites.ResultRio Grande Silvery Minnow most frequently occupied mesohabitats characterized by relatively shallow depths (≤25 cm) and low to near‐zero water velocities (≤15 cm/s). Statistical analyses indicated that mesohabitats occupied by the species were not the most frequently available at the study sites, suggesting a preference for shallow, low‐velocity habitats. Relatively high abundance of Rio Grande Silvery Minnow (n = 10,971), especially compared with post‐2009 abundance, facilitated robust characterization of species‐specific habitat associations.ConclusionComparison of our results with other studies of pelagic broadcast‐spawning leuciscids (pelagophils) endemic to the Great Plains and desert rivers of North America suggested broad overlap in mesohabitat associations among members of this reproductive guild. Our work contributes to a growing body of research aimed at conserving this declining reproductive ecotype of freshwater fishes and suggests that increasing hydraulic diversity through innovative management approaches (e.g., habitat creation, restoration of fluvial processes, and preservation of natural streamflow characteristics) will be crucial for their long‐term recovery and conservation.

From micro to mesoscale: Understanding the influence of macroalgal communities on Ostreopsis Schmidt blooms

Harmful Algal Blooms (HABs) are increasing in temperate areas, and the growth rates of benthic harmful dinoflagellates may be favoured in the context of global climate change. Benthic dinoflagellates, including species belonging to the Ostreopsis Schmidt genus, are known to develop on the surface of macroalgae and different macroalgal morphotypes and communities could host higher or lower cell abundances. The physical structure of the macroalgal substrate at the small scale (cm, microhabitat scale) and the structural complexity of the macroalgal community at the medium scale (few m, mesohabitat scale) could play a relevant role in bloom facilitation: the hypothesis that Ostreopsis species could be associated with macroalgal turfs and shrubs, structurally less complex communities than canopy-forming macroalgae, is especially under discussion and, if confirmed, could link bloom occurrence to regime shifts in temperate ecosystems. The present study, performed in two locations of the Ligurian Sea (Rochambeau, France and Vernazzola, Italy) aimed at understanding marine vegetation's role at the micro and mesohabitat scales in controlling the distribution and abundance of Ostreopsis. The abundance of the microalgal cells was quantified at different spatial scales, from cm to a few m, on different macroalgal species and communities, including artificial substrates, to tease apart the micro and mesohabitat effects. The results obtained show a high spatio-temporal variability, potentially hiding habitat-related patterns. The substrate's preferences diminish when cell abundances are very high, as in the case of Rochambeau, while in presence of moderate cell abundances as in Vernazzola or the first phases of blooms, it is possible to appreciate differences in abundances among substrates (in our study, Dictyota fasciola (Roth) Lamouroux supporting higher abundances). Our results open new research topics such as the study of blooms at a larger scale (macrohabitat) and testing different sampling methods to standardise the cells' abundances independently on the substrate.

Physical habitat modeling for river macroinvertebrate communities

Habitat models rarely consider macroinvertebrate communities as ecological targets in rivers. Available approaches mainly focus on single macroinvertebrate species, not addressing the ecological needs and functionality of the whole community.This research aimed at providing an approach to model the habitat of the macroinvertebrate communities. The study was carried out in three rivers, located in Italy and characterized by a braiding morphology, gravel riverbeds, and low flows during the summer period. The approach is based on the recently developed Flow-T index, together with a Random Forest (RF) regression, which is employed to apply the Flow-T index at the mesohabitat scale. Using different datasets gathered from field data collection and 2D hydrodynamic simulations, the model was calibrated in the Trebbia River (2019 field campaign) and validated in the Trebbia, Taro, and Enza rivers (2020 field campaign).The RF model selected 12 mesohabitat descriptors as important for the macroinvertebrate community. These descriptors belong to different frequency classes of water depth, flow velocity, substrate grain size, and connectivity to the main river channel. The cross-validation R2 coefficient (R2cv) of the training dataset was 0.71, whereas the R2 coefficient (R2test) for the validation dataset was 0.63. The agreement between the simulated results and the experimental data shows sufficient accuracy and reliability. The outcomes of the study reveal that the model can identify the ecological response of the macroinvertebrate community to possible flow regime alterations and river morphological modifications.Lastly, the proposed approach allowed to extend the MesoHABSIM methodology, widely used for the fish habitat assessment, to a different ecological target community. Further applications of the approach can be related to ecological flows design in both perennial and non-perennial rivers, including river reaches in which fish fauna is absent.

Go with the flow: Impacts of high and low flow conditions on freshwater mussel assemblages and distribution.

Understanding the drivers of distribution and assemblage composition of aquatic organisms is an important aspect of management and conservation, especially in freshwater systems that are inordinately facing increasing anthropogenic pressures and decreasing biodiversity. For stream organisms, habitat conditions during high flows may be impossible to measure in the field, but can be an important factor for their distribution, especially for less mobile organisms like freshwater mussels. Hence, the objective of this study was to use a two dimensional HEC-RAS model to simulate hydraulic conditions during high and baseline flows (flows approx. 10-600 x and 0.7 x median daily flows respectively) in a 20 km segment in the San Saba River, Texas in combination with existing mussel survey data from 200 sites (collected every 100m) to 1) examine whether hydraulic conditions differed between areas of increased mussel richness and diversity (referred to as hotspots) and other sites, and 2) understand how well site occupancy and species abundance could be explained by hydraulic conditions occurring under different flow conditions. The results showed that richness and diversity hotspots occurred in deeper areas with lower shear stress, stream power, and Froude number during both high and low flows. Occupancy could be predicted with 67-79% accuracy at the site scale and 60-70% accuracy at the mesohabitat scale (∼20 to 1200 m long). In addition, hydraulic conditions across flow scenarios explained up to 55% of variation in species abundances, but predictions were less successful for species often observed to occupy micro-scale flow refuges such as bedrock crevices. The results indicate that pools may serve as important refuge for all species during both high and low flow events, which may be relatively unique to bedrock-dominated systems. Understanding hydraulic conditions that occur at extreme flows such as these is important given that the frequency and magnitude of such events are increasing due to climate change.

Application of lidar to assess the habitat selection of an endangered small mammal in an estuarine wetland environment.

Light detection and ranging (lidar) has emerged as a valuable tool for examining the fine-scale characteristics of vegetation. However, lidar is rarely used to examine coastal wetland vegetation or the habitat selection of small mammals. Extensive anthropogenic modification has threatened the endemic species in the estuarine wetlands of the California coast, such as the endangered salt marsh harvest mouse (Reithrodontomys raviventris; SMHM). A better understanding of SMHM habitat selection could help managers better protect this species. We assessed the ability of airborne topographic lidar imagery in measuring the vegetation structure of SMHM habitats in a coastal wetland with a narrow range of vegetation heights. We also aimed to better understand the role of vegetation structure in habitat selection at different spatial scales. Habitat selection was modeled from data compiled from 15 small mammal trapping grids collected in the highly urbanized San Francisco Estuary in California, USA. Analyses were conducted at three spatial scales: microhabitat (25 m2), mesohabitat (2025 m2), and macrohabitat (~10,000 m2). A suite of structural covariates was derived from raw lidar data to examine vegetation complexity. We found that adding structural covariates to conventional habitat selection variables significantly improved our models. At the microhabitat scale in managed wetlands, SMHM preferred areas with denser and shorter vegetation and selected for proximity to levees and taller vegetation in tidal wetlands. At the mesohabitat scale, SMHM were associated with a lower percentage of bare ground and with pickleweed (Salicornia pacifica) presence. All covariates were insignificant at the macrohabitat scale. Our results suggest that SMHM preferentially selected microhabitats with access to tidal refugia and mesohabitats with consistent food sources. Our findings showed that lidar can contribute to improving our understanding of habitat selection of wildlife in coastal wetlands and help to guide future conservation of an endangered species.

Multiscale analysis predicts native species presence based on habitat and nonnative species abundance

AbstractObjectiveThe loss and degradation of aquatic habitat through fragmentation, water extraction, and climate warming contribute to declining native stream fish diversity. In response to these declines, a large‐scale repatriation program was established in Arizona and New Mexico to expand the distribution and abundance of native fishes. This program has had variable success, with imperiled fish populations establishing and persisting in some streams, while other populations failed to establish.MethodsTo identify factors contributing to the success of repatriation, we conducted a study investigating how biotic and abiotic variables affect native fish presence or absence at differing spatial scales throughout the Gila River basin. We conducted fish and habitat surveys in 29 river reaches at three spatial scales: the 1‐km, 0.1‐km, and mesohabitat scale. We used generalized linear models to identify associations among species presence, habitat characteristics, and nonnative species abundance across spatial scales. Logistic regression models were also used to test associations with heterogeneity of habitat characteristics and species presence.ResultModels indicated strong species‐ and scale‐specific responses to these variables. Nonnative abundance was less influential than other habitat variables in predicting the presence of native fish, although the majority of associations that emerged were negative. Further, we were able to identify that water velocity, depth, and substrate size were the most common variables associated with species' presence across all scales and age‐classes, with most species responding positively to elevated velocities and variable responses for depth and substrate size. Response to variation in habitat was species‐specific, with some associations positive and others negative.ConclusionCollectively, the information from this study will help identify locations with a reasonably high likelihood of supporting native fishes and broaden our understanding of species responses to habitat and nonnative species across multiple scales.

Spatial relationships and mesoscale habitat variance in co-occurring populations of Church’s sideband and Trinity bristle snail in the Greater Trinity Basin, northern California

In resource management, the kind and extent of ecological co-occurrence between closely related species frequently requires assessment of the spatial relationship among taxa. In my study, analysis of inter-species pair-wise distances revealed no syntopic overlap between Church’s sideband (Monadenia churchi) and Trinity bristle snails (M. setosa). No pair of samples had the same geographic coordinates and no parapatric boundary in environmental covariates was evident between species. This “microsympatric” spatial relationship resembled a metapopulation structure with no high degree of overlap, as co-occurrence was rare and small in geographic scope. Fifteen forest cover-types and 82 soil-types were identified between species. The most common forest-type for M. churchi was Sierra Mixed Conifer (39.9%) and Douglas fir (28.9%). In M. setosa the most common forest-types were the same but in much different percentages (78.8% and 14.8%, respectively). Sixty-one and 39 soil-types were associated with samples of M. churchi and M. setosa, respectively. The Hohmann-Neuns family complex was the most common (22.5%) soil-type for M. churchi and the Holland Deep-Hugo family complex was the most (50.6%) dominant for M. setosa. There were significant differences between species in all environmental attributes and in values of monthly temperature and precipitation, which reflected variance in the mesoclimatic regime seasonally. Principal Components Analysis (PCA) accounted for 57.8% of the dispersion contained in environmental variables on the first 3-eigenvectors. Evapotranspiration and Summer and Winter Temperatures loaded positively while Summer and Winter Precipitation and Elevation loaded negatively along PC I (26.2%). Given significant inter-species differences in ecological occupancy, it seems plausible that microsympatry is based in part on both mesoscale habitat variance and subtle differences in mesoclimate defined by seasonal variation in temperature and precipitation. The hypothesis that M. setosa is adapted to cool habitats and M. churchi to warmer more arid environs in microsympatry was substantiated at a macroscale level.

Amazon River plume habitats shape planktonic cnidarian assemblages in the Western Atlantic.

The impact of the Amazon River freshwater plume on planktonic cnidarians over neritic and oceanic provinces is unknown. To provide further knowledge we took advantage of an oceanographic cruise performed in October 2012 in the Western Atlantic off the North Brazilian coast (8°N, 51°W-3.5°S, 37°W). A complex and dynamic system was observed, with strong currents and eddies dispersing the plume over a large area. Our results show that the Amazon River shapes marine habitats with a thin highly productive surface layer compressed by a deeper oxygen minimum zone both over the shelf and in the open ocean. We hypothesized that such habitat structure is particularly advantageous to planktonic cnidarians, which have low metabolic rates, being able to survive in hypoxic zones, resulting in high species richness and abundance. Over the shelf, distinctions were sharp and the area under the influence of the plume presented a diverse assemblage occurring in large abundance, while outside the plume, the hydromedusa Liriope tetraphylla was dominant and occurred almost alone. Divergences in the oceanic province were less pronounced, but still expressive being mostly related to the abundance of dominant species. We concluded that Amazon River plume is a paramount physical feature that profoundly affects the dynamics of the mesoscale habitat structure in the Western Equatorial Atlantic Ocean and that such habitat structure is responsible for shaping planktonic cnidarian assemblages both in neritic and oceanic provinces.

Mesoscale habitat use by St. Lawrence estuary beluga over the annual cycle from an acoustic recording network.

The spatial-temporal distribution pattern of St. Lawrence Estuary (SLE) beluga is examined with a passive acoustic monitoring network of 13 stations from June 2018 to October 2021. A beluga calling index, correlated with beluga density, is used as a proxy for habitat use by the population at weekly, monthly, and yearly scales. The seasonal pattern along SLE upstream-downstream axis was repeated annually. In summer, beluga habitat was confined to a 150 km segment of the SLE, with higher occurrences in its ∼20 km central portion, including the head of the Laurentian Channel and Saguenay Fjord mouth. During fall, the distribution gradually shifted to the downstream portion of the SLE and into the Northwestern Gulf, leaving low to no occurrences upstream in winter, until the spring return, characterized by the highest upstream occurrences. Occurrences off Ste. Marguerite Bay, 25 km upstream in Saguenay Fjord, were essentially from June to October. This multi-year continuous habitat use pattern provides a baseline for year-round SLE beluga distribution dynamics for assessing and mitigating anthropogenic threats to this endangered population, such as shipping noise. It also provides insights for optimizing the assessments of population size from aerial line transect surveys.

Freshwater Invertebrate Assemblage Composition and Water Quality Assessment of an Urban Coastal Watershed in the Context of Land-Use Land-Cover and Reach-Scale Physical Habitat

Stream ecosystems provide invaluable ecosystem services but are highly impacted ecosystems in need of water quality monitoring for habitat change impacts. Freshwater macroinvertebrate (FWI) assemblages have been shown to be good indicators of water quality and are known to be vulnerable to land-use land cover (LULC) and other habitat changes. The goal of this case study was to use an existing dominant LULC analysis in the Neponset River watershed, Massachusetts, USA, as LULC sampling treatment groups to deliberately capture the influence of these LULC effects on meso-scale habitat quality, FWI assemblages, and FWI water quality indices at eight sampling reaches. To achieve this goal, we collected physical habitat measurements and FWI samples in the summers of 2010 and 2012 at eight reach-scale stations spread across four previously determined LULC sub-watershed types (forest, residential, industrial, and golf) in the watershed. We expected that LULC change would influence the habitat quality, which would influence the FWI assemblage water quality scores and composition. We also expected that the water quality at these LULC sub-watershed types would be reflected in the FWI assemblage composition. We identified five major findings from our study. Our first finding was that the habitat quality in the Neponset River watershed was somewhat degraded relative to pristine conditions. Our second finding was that our habitat characterization analysis reflected some separation of our reach-scale macrohabitat types at land-use land-cover treatment stations with some correlations with microhabitat variables. Our third finding was that the water quality base on FWI assemblages was generally degraded in reference to pristine conditions. Our fourth finding was that, contrary to our expectations, there was no significant correlation between our reach-scale EPA habitat quality scores and FWI water quality scores. Our fifth finding was that our FWI assemblage NMS showed separation of land-use land-cover sampling stations and that that low pollution-tolerant taxa dominated some of our LULC sampling treatment stations and influenced NMS groupings.

A novel unsupervised method for assessing mesoscale river habitat structure and suitability from 2D hydraulic models in gravel‐bed rivers

AbstractApplication of mesoscale habitat models in gravel‐bed rivers is increasingly common for a variety of purposes, from ecological flow design, impact assessment and conservation programmes. Integration with 2D hydraulic modelling offers the potential for broader applicability of mesoscale habitat models, extending applications to larger streams and nonwadable flow conditions, when on‐the‐ground and in‐stream surveys are challenging or even prohibitive. In this work, a novel fully unsupervised procedure that allows the segmentation of the river channel area at a given flow condition at a scale that is consistent with the mesoscale is presented. Further, it defines an objective methodology to choose segmentation parameters and thus an optimal segmentation, based on intrinsic spatial properties of the resulting regions. Segmentation parameters are objectively selected by minimising a Global Score, which is based on three metrics representing intrasegment homogeneity, intersegment heterogeneity and an optimal range of segment numbers based on an empirically defined mesoscale. Applications of the model are tested on two reaches of the multithread Mareta and meandering Aurino Rivers in South Tyrol (NE, Italy). Model outcomes are compared with ground mesohabitat surveys, and habitat suitability is then assessed for three fish species (marble trout, grayling and European bullhead). A high level of agreement is found when comparing model‐ and survey‐based habitat suitability estimates, with an overall value of . The proposed approach shows potential for application of the mesohabitat concept for large gravel‐bed rivers and nonwadable flow conditions. By allowing habitat estimates at flow ranges that could not be surveyed in‐stream, the approach facilitates applicability of mesoscale habitat models to nonwadable conditions and large streams. The workflow is river‐independent and fully unsupervised, as it does not require calibration or subjective choices of segmentation parameters.Significance statementQuantifying suitable habitat for riverine fauna is increasingly used for ecological flows assessment, with the use of mesoscale habitat modelling approaches becoming more common in the past few decades. Existing mesoscale habitat modelling approaches often rely on field surveys, which, however, become prohibitive at nonwadable flow conditions and in large streams. Here we develop and test against field data a fully unsupervised approach able to extract mesohabitats and their hydraulic characteristics from the outputs of 2D hydraulic models. Compared with existing approaches, our approach allows an automated segmentation of the wetted reach into mesoscale units through the implementation of an unsupervised optimality step in which optimal segmentation parameters are defined, and a final mesohabitat mosaic is selected. The methodology makes it easier to expand the applicability of mesoscale habitat modelling to a broader range of river sizes and conditions.

Fish Habitat Reclamation Based on Geographical Morphology Heterogeneity in the Yangtze River and the Short-Term Effects on Fish Community Structure

Human alterations, such as hydropower development, are intensive and have negative impacts on fish and ecological environment. However, fish habitat restoration projects based on geographical morphology have not yet been reported in the Yangtze River. To explore engineering measures used to restore fish habitat structure and function, a mesoscale fish habitat restoration project was designed and constructed, which included restructuring of habitat topography in the fluctuating area. Three-dimensional computational fluid dynamics (CFD) models were used to simulate and predict the project’s effect on the hydromorphology prior to construction, and an Acoustic Doppler current profiler (ADCP) was deployed to test and verify actual flow field improvement. Short-term effects on fish species sorting and their main ecological traits were examined. The results showed that vorticity and flow heterogeneity in the river reach increased, suggesting that the restoration projects created flow conditions favourable to indigenous fishes. Thus, pre-optimization using computer simulation is an essential and scientific procedure that could be used to increase the probability of river restoration success. The promotion of habitat diversity had strong effects on fish aggregation, especially for the rare and endemic fish species targeted. Fish abundance, catch biomass and species richness increased by 98.1%, 62.7% and 22.5%, respectively. There were significant differences (p < 0.05) in species number and catch abundance before and after the project. The number of rare and endemic fish species increased from four to nine species. Overall, this research provides evidence that the promotion of habitat hydraulic morphology heterogeneity accelerates the recovery of fish diversity and biomass.

Summer stream habitat preferences of Nunavik anadromous Arctic char (Salvelinus alpinus) fry and parr

Arctic char (Salvelinus alpinus) is a fish species known to occupy diverse habitats within the Arctic region. However, summer habitat use during the juvenile stage of the anadromous form is largely unknown. The present study aims to characterize fry and parr summer habitat preferences. Surveys were conducted by electrofishing, associated with physical habitat characterization on several rivers of the Ungava Bay, Nunavik, Canada. At the microhabitat and station scales (group of microhabitats), fry showed significant habitat preferences for shallow water and slow velocity. At the mesohabitat scale, fry showed a significant habitat selectivity for riffles. This habitat selectivity implies that habitat models can be built to evaluate the potential of habitat suitability for Arctic char fry. However, no significant habitat selectivity was found for parr. Parr size was nonetheless positively correlated with velocity, which was found to be a limitative factor for juvenile habitat use. This first attempt at modeling juvenile anadromous Arctic char habitat in rivers emphasizes the importance of selecting an appropriate spatial scale and reiterates the fact that parr showed relatively high plasticity in stream habitat selection.

Considering mesohabitat scale in ecological impact assessment of sediment flushing

Benthic macroinvertebrates respond to several factors characterizing the physical habitats, as water depth, current and streambed substrate. Thus, anthropogenic disturbances altering these factors may have different effects on benthos, also depending on mesohabitats. These disturbances include sediment flushing operations, commonly carried out to recover reservoir capacity, and investigating their effects at mesohabitat scale could be relevant for an adequate ecological impact assessment of these operations. Here, we compared benthic macroinvertebrate communities sampled before and after a controlled sediment flushing operation in three different mesohabitats (a pool, a riffle and a step-pool) of an Alpine stream. Contrary from expectations, the composition of macroinvertebrate assemblages was not significantly different among mesohabitats. Moreover, the impact of sediment flushing was more significant in terms of density rather than in richness. Two stressor-specific indices were tested, but only one (the Siltation Index for LoTic EcoSystems − SILTES) clearly detected the impact of sediment flushing on the macroinvertebrate community structure. Finally, some differences in the temporal trajectories and recovery times to pre-flushing conditions were observed among mesohabitats, both if the three mesohabitats were considered separately and if all their possible combinations were accounted for. Particularly, riffle was the most sensitive mesohabitat, not fully recovering one year after the sediment disturbance.

Microscale and Mesoscale Aeolian Processes of Sandy Coastal Foredunes from Background to Extreme Conditions

Aeolian transport affects beach and foredune pre-storm morphologies, which directly contribute to storm responses. However, significant spatiotemporal variation exists within beach-dune systems regarding how biotic and abiotic factors affect topography. There are multiple metrics for quantifying topographic change, with varying pros and cons, but understanding how a system changes across spatiotemporal scales relative to varying forcings is necessary to accurately model and more effectively manage these systems. Beach and foredune micro- and mesoscale elevation changes (Δz) were quantified remotely and in situ across a mid-Atlantic coastal system. The microscale field collections consisted of 27 repeat measurements of 73 elevation pins located in vegetated, transitional, and unvegetated foredune microhabitats over three years (2015 to 2018) during seasonal, event-based, and background wind-condition collections. Unoccupied aerial System (UAS) surveys were collected to link microscale point Δz to mesoscale topographic change. Microscale measurements highlight how Δz varies more pre- to post-event than seasonally or monthly, but regardless of collection type (i.e., seasonal, monthly, or event-based), there was lower Δz in the vegetated areas than in the associated unvegetated and partially vegetated microhabitats. Despite lower Δz values per pin measurement, over the study duration, vegetated pins had a net elevation increase of ≈20 cm, whereas transitional and unvegetated microhabitats had much lower change, near-zero net gain. These results support vegetated microhabitats being more stable and having better sediment retention than unvegetated and transitional areas. Comparatively, mesoscale UAS surfaces typically overestimated Δz, such that variation stemming from vegetation across microhabitats was obscured. However, these data highlight larger mesoscale habitat impacts that cannot be determined from point measurements regarding volumetric change and feature mapping. Changes in features, such as beach access paths, that are associated with increased dynamism are quantifiable using mesoscale remote sensing methods rather than microscale methods. Regardless of the metric, maintaining baseline data is critical for assessing what is captured and missed across spatiotemporal scales and is necessary for understanding the contributors to heterogeneous topographic change in sandy coastal foredunes.

2D vs. 3D Numerical Approaches for Fish Habitat Evaluation of a Large River — Is 2D Modeling Sufficient?

Computational Fluid Dynamics is an effective tool for assessing non-present conditions, thus also in habitat evaluation within ecohydraulics. Deciding whether to apply a one-, two- or three-dimensional numerical approach, is an optimization that needs to be performed by every task, given the capability and the demands of specific approaches. In this paper we compare the utility of two-dimensional (2D) versus three-dimensional (3D) hydrodynamical simulations for ecohydraulic purposes. The basis of the comparation were 1) three simulated abiotic variables: water depth, depth averaged flow velocity and bed material composition, and 2) an overall performance in a meso-scale fish habitat evaluation, based on the simulated three variables. The biotic parameters for the models were the habitat suitability curves of three fish species, the Danube streber (Zingel streber), the round goby (Neogobius melanostomus) and the white bream (Blicca bjoerkna). We found that in terms of ecohydraulic utilization, the 2D approach performed sufficiently to simulate the hydrodynamics of a large river. The errors originating from the 3D-2D simplification yielded negligible differences in habitat evaluation, and the agreement in the habitat suitability indices calculated from the simulated metrics was satisfactory. Henceforth, the theory was turned into an application as we performed habitat mapping on a 100 km long, Hungarian reach of the Danube River, with the abiotic parameters resulting from a 2D hydrodynamical simulation. The possibility of simplifying the approach from 3D to 2D provides a cost-efficient numerical tool at larger scales for ecohydraulic studies, and especially for evaluating habitat suitability of riverine fish.

Combining green LiDAR bathymetry, aerial images and telemetry data to derive mesoscale habitat characteristics for European grayling and brown trout in a Norwegian river

While many studies provide microscale relationships between fish and habitat characteristics, studies covering longer river reaches are scarce. Modern remote sensing techniques may enable new and effective ways of mapping and assessing mesoscale habitat characteristics. Using green LIDAR-derived bathymetry and hydraulic modelling, we tested how mesoscale depth and velocity were related to fish counts of adult European grayling (Thymallus thymallus L.) and brown trout (Salmo trutta L.) in 500 m river sections in three separate periods during the year. Using riverbank sinuosity from aerial images and a Froude number-based index from the hydraulic model as proxies for mesoscale spatial and hydraulic heterogeneity, we tested for temporal correlations with river section fish counts of adult European grayling and brown trout. Results showed that mesoscale mean depth and velocity were correlated to period fish counts of adult European grayling. Using mixed model analysis we found that riverbank sinuosity and the Froude number-based index were significantly correlated with river section occurrence of adult European grayling during spawning. The results can be used to assess how flow-induced changes and channel adjustments at the mesoscale level can influence access to and use of relevant habitats in rivers occupied by European grayling and brown trout.

Impacts of fine sediment input on river macroinvertebrates: the role of the abiotic characteristics at mesohabitat scale

Impacts of fine sediment input on river macroinvertebrates: the role of the abiotic characteristics at mesohabitat scale

Spatial variability of epi- and mesopelagic 38 kHz backscatter from nekton and macrozooplankton across the southeastern US shelf break

Acoustic echosounders collect detailed information on the location of patchily distributed pelagic organisms over varying spatial scales. This study measured the spatial variability of epi- and mesopelagic 38 kHz backscatter along the US Mid- and South Atlantic continental shelf and slope. We used variogram analysis to estimate the horizontal spatial structure of backscatter measurements, examined whether environmental variables might affect these estimates, and assessed potential impacts of acoustic survey design. Backscatter data were collected during ship-based surveys (50-100 km2) at 7 sites during 4 cruises between November 2017 and November 2019. Average patch size estimates were consistently between 2 and 4 km among locations. Modeled variogram range varied significantly with the depth of the backscatter layer, but linear effect sizes were negligible (<1 m). Chlorophyll a (chl a) concentration had a significant positive effect on range (95 m), suggesting that patch sizes are slightly larger in the epipelagic where chl a concentration is higher. Incorporating variogram parameters of range, sill, and nugget produced some clustering of spatial correlation parameters with scattering layer depth, particularly for the deepest sites assessed (700-900 m depth). Spatial characteristics of a given location were not significantly different between surveys of the same size, but sometimes differed with smaller (25% of area) survey sizes. These results offer insight into nekton and macrozooplankton backscatter patterns in important shelf break and slope systems across horizontal and vertical dimensions, and provide needed information for monitoring fine- to mesoscale offshore marine habitat areas.

Enhancing an unsupervised clustering algorithm with a spatial contiguity constraint for river habitat analysis

AbstractThe spread of two‐dimensional numerical hydrodynamic tools for ecohydraulic applications allowed for the development of automatic habitat detection methods, adopted as predicting tools for river habitat analysis. These automatic approaches differ for the employed identification rules, such as preference curves, fuzzy rules and clustering methods. Previous research has shown promising results in the automatic identification of mesoscale habitat patches by using clustering algorithms together with numerical hydrodynamic model results. These algorithms attempt to implement and simulate some of the expert‐based requirements adopted in the field to delineate habitat patches. Spatial contiguity is one of such expert‐based requirements that has not been enforced and exploited in automatic mesohabitat identification so far. In this work, we propose a novel tool (BASEmeso) based on an agglomerative hierarchical clustering algorithm where we enforced a spatial contiguity criteria. We compare our approach with a more established method without spatial constraints, considering a synthetic river reach where the composition of mesohabitat patches is known a priori, and on three experimental river reaches, to investigate the effects of different river morphologies. Our results show that when employing a contiguity constraint, a patch's extent is better captured, different patches can be distinguished better and the distribution of patch characteristics is smoother. This holds for all investigated morphologies. Together, it suggests that including a spatial contiguity constraint can improve the automatic delineation of river mesohabitat patches. The proposed methodology could positively contribute in the development of automatic, objective and predictive meso‐scale habitat assessment workflows.