Monitoring Of Fish Assemblages Research Articles

Fishing in the gene-pool: implementing trawl-associated eDNA metaprobe for large scale monitoring of fish assemblages

Marine biodiversity monitoring in the Mediterranean’s increasingly threatened ecosystems is crucial for effective ecosystem conservation and management. Here, we leveraged the Mediterranean International Trawl Survey program (MEDITS) to implement eDNA sampling through the recently tested ‘metaprobe’ procedure and characterize fish assemblages in three separate areas off the Italian coasts: Northern Adriatic Sea (NoAS), Ligurian and Northern Tyrrhenian Sea (LNTS), and Sardinian Sea (SaS). By combining the information from two homologous mitochondrial 12S metabarcodes––i.e., Elas02 and Tele02 targeting elasmobranchs and teleosts, respectively––we identified 108 species, over 60% of which overlapped with those caught by the trawl net. We produced an accurate reconstruction of fish community composition of the examined sites, reflecting differences in species assemblages linked with both geographic area and depth range. Metaprobe eDNA data consistently returned a biodiversity ‘bonus’ mostly consisting of pelagic taxa not captured through bottom trawl surveys, including rare and endangered taxa (e.g., elasmobranchs). Overall, the spatial characterisation of the assemblages across the surveyed areas was better delineated and more robust using eDNA metabarcoding than trawl data. Our results support the operationalisation of the metaprobe as a simple, inexpensive, versatile sampling tool, in association with pre-existing ship surveys, to overcome many of the limitations of marine data collection and strengthen marine management.

Non‐extractive fish diversity assessment in Mediterranean rhodolith beds

Abstract Rhodolith beds, recognized as biodiversity hotspots with high ecological and conservation importance, face local anthropic pressures, including trawl fishing. However, monitoring the diversity associated with this sensitive biogenic habitat in the deep waters of the Mediterranean Sea is challenging. Traditional monitoring methods, such as experimental trawling and trammel nets, are extractive and have sampling limitations in providing comprehensive diversity inventories. In this work, we explore three alternative techniques (still video cameras, environmental DNA [eDNA] and bioacoustics) to monitor fish assemblages associated with rhodolith beds in the Menorca Channel at 45–80 m depth. Ten sites were surveyed with eDNA, and 66 fish taxa were identified, including endangered sharks and cryptic species. The molecular operational taxonomic units (MOTUs) richness varied significantly according to habitat heterogeneity, being higher in homogeneous bottoms, and to exposure to trawling, with higher richness in non‐exposed areas. Bioacoustics, though limited by a reduced library of fish sounds, detected differences in sound richness between habitat types, and the highest abundance of sounds was recorded in the areas with the greatest small‐scale habitat heterogeneity. Underwater video revealed limitations in species detection but proved effective for characterizing small‐scale habitat types and heterogeneity. In summary, each technique provides valuable information at different spatial scales and levels of detail. To assess the feasibility of these techniques for long‐term monitoring, we explored their capabilities and limitations in terms of costs, survey logistics and data output.

Potential passive acoustic tool for reef fish monitoring: A learning-based method

Visual non destructive methods are widely used for assessing marine biodiversity, but a logistically simpler approach is combining passive acoustic techniques with artificial intelligence (AI). Here, we classified sounds of fish on subtropical rocky reefs in Arraial do Cabo (22°57'S, 41°01'W), RJ, Brazil, using supervised machine learning algorithms. Sound detection and feature extraction were performed manually by inspecting spectrograms using Raven Pro 1.6 software. Five supervised algorithms were implemented for classification: naive Bayes, support vector machine, random forest, decision tree, and multilayer perceptron. A representative subset of samples for each sound class was used to train the supervised algorithms. The accuracy of the algorithms was between 67% and 97%. Four classes of sounds were recognized, consisting of sequences of pulses. In general, temporal features were more important, however high frequency was the most important feature of all. Understanding the contribution of each feature is crucial for sound classification, however it is at an early stage for fishes. The classifier showed promising results, highlighting the effectiveness of applying AI to passive acoustics as a tool for monitoring of fish assemblages.

Fish Tissue Contamination with Organic Pollutants and Heavy Metals: Link between Land Use and Ecological Health

Under pressure from existing and emerging contaminants, lotic ecosystems are becoming increasingly susceptible to ecological deterioration. Therefore, investigations of the impacts of persistent organic pollutants (POPs) and heavy metals on riverine fish health, water quality, and biotic integrity are critical. We examined the effects of 52 POPs and heavy metals on ecological health and land use, based on the monitoring of fish assemblages and river water quality from 2007 to 2014. Among the 52 chemical species, 35 were present in water and fish tissues, including eight heavy metals. The concentrations of these POPs and heavy metals in 12 fish species are presented. Most POPs were either undetected or present at negligible levels in fish tissues, although a few polycyclic aromatic hydrocarbons (PAHs) and organochlorine pesticides (OCPs; dichlorodiphenyltrichloroethanes and heptachlor epoxide) were detected above the screening values (SVs). Hg, As, and Cd were detected in most water samples and fish species at concentrations above their SVs. Among the fish species in the investigated trophic guild, heavy metal contents were in the order of Zn < Cr < Cu < Pb < Se, while trophic levels were in the order of insectivorous < omnivorous < carnivorous. Agricultural cover showed an association with endosulfan II (R2 = 0.50, r = 0.70), followed by alachlor (R2 = 0.43, r = 0.66). For PAHs, all detected substances showed significant relationships with forest cover. Ecological health assessment revealed that most river sites are in poor condition, indicating the direct impacts of pollutants. In conclusion, of the 28 POPs detected, 16 PAHs and 3 OCPs (hexachlorobenzene, lindane, and heptachlor epoxide) were of significant concern, such that action is needed to curb their inflow to the riverine environment. The studied river basin is under substantial threat from harmful POPs that endanger ecological health and fish biodiversity.

Investigations of Fish Assemblages Using Two Methods in Three Terminal Reservoirs of the East Route of South-to-North Water Transfer Project, China.

The terminal reservoirs of water transfer projects directly supply water for domestic, agricultural, and industrial applications, and the water quality of these reservoirs produce crucial effects on the achievement of project targets. Typically, fish assemblages are monitored as indicators of reservoir water quality, and can also be regulated for its improvement. In the present study, we compared traditional fish landing (TFL) and environmental DNA (eDNA) metabarcoding methods for monitoring fish assemblages in three terminal reservoirs of the East Route of the South-to-North Water Transfer Project, China. Results of TFL and eDNA showed similar assemblage structures and patterns of diversity and spatial distribution with obvious differences in fish composition across three examined reservoirs. Demersal and small fish were dominant in all reservoirs. In addition, a strong association between water transfer distance and assemblages and distribution of non-native fish was found. Our findings highlight the necessity of the fish assemblage monitoring and managing for water quality and revealed the impact of water diversion distance on the structure of fish assemblages and dispersal of alien species along the water transfer project.

Spatio-temporal variability of eDNA signal and its implication for fish monitoring in lakes.

Environmental DNA (eDNA) metabarcoding is revolutionizing the monitoring of aquatic biodiversity. The use of eDNA has the potential to enable non-invasive, cost-effective, time-efficient and high-sensitivity monitoring of fish assemblages. Although the capacity of eDNA metabarcoding to describe fish assemblages is recognised, research efforts are still needed to better assess the spatial and temporal variability of the eDNA signal and to ultimately design an optimal sampling strategy for eDNA monitoring. In this context, we sampled three different lakes (a dam reservoir, a shallow eutrophic lake and a deep oligotrophic lake) every 6 weeks for 1 year. We performed four types of sampling for each lake (integrative sampling of sub-surface water along transects on the left shore, the right shore and above the deepest zone, and point sampling in deeper layers near the lake bottom) to explore the spatial variability of the eDNA signal at the lake scale over a period of 1 year. A metabarcoding approach was applied to analyse the 92 eDNA samples in order to obtain fish species inventories which were compared with traditional fish monitoring methods (standardized gillnet samplings). Several species known to be present in these lakes were only detected by eDNA, confirming the higher sensitivity of this technique in comparison with gillnetting. The eDNA signal varied spatially, with shoreline samples being richer in species than the other samples. Furthermore, deep-water samplings appeared to be non-relevant for regularly mixed lakes, where the eDNA signal was homogeneously distributed. These results also demonstrate a clear temporal variability of the eDNA signal that seems to be related to species phenology, with most of the species detected in spring during the spawning period on shores, but also a peak of detection in winter for salmonid and coregonid species during their reproduction period. These results contribute to our understanding of the spatio-temporal distribution of eDNA in lakes and allow us to provide methodological recommendations regarding where and when to sample eDNA for fish monitoring in lakes.

Selected freshwater fish species for assessing the water quality of the lower catchment of the Kelani River, Sri Lanka.

Kelani River is the most polluted river in Sri Lanka and the lower catchment is more polluted than the upper catchment. In the present study, freshwater fish species of the lower catchment of the river were investigated for the use of assessing the water quality. Cast net sampling and identification recorded 34 freshwater fish species from the lower catchment, the majority represented by family Cyprinidae. Fish species richness, diversity indices, distribution, abundance and the regression analysis of fish species with water quality parameters revealed high sensitivity and tolerance of three fish species with certain water quality parameters. Dawkinsia singhala was tolerant to the fluctuations of the chemical parameters of the water, while Rasbora daniconius and Pethia reval were tolerant to the physical parameters. Positive correlations were evident between the ammonium and phosphate concentrations of the water and distribution and abundance of D. singhala, while R. daniconius and P. reval showed positive correlations with turbidity of water and pH value respectively. Furthermore, the study reveals that D. singhala is more suitable for predicting the water quality of urban and peri-urban locations of the river, while P. reval and R. daniconius are more suitable for assessing the water quality of rural locations. Thus, the present study reveals a strong possibility of using D. singhala, R. daniconius and P. reval, as biological indicators for assessing the variation of water quality of the lower catchment of the Kelani River. However, despite the fact that such a study has been conducted for the first time in Sri Lanka, it is restrained by certain limitations, and seasonal variations of water quality parameters with fish parameters, adaptations inherent to fish species and food availability in different locations combined with long-term monitoring of fish assemblages have not been considered. Future studies investigating these aspects will further enhance the value of the study.

Fish assemblage monitoring in Alberta’s Ells River: Baseline fish and habitat variability prior to major development

The collection of sentinel fish species for Environmental Effects Monitoring (EEM) has provided ancillary fish assemblage surveys on several tributaries in the Athabasca Oil Sands Region (AOSR) of Alberta, Canada over the last decade. Using available, comparable data we investigated baseline fish assemblage variability along the Ells River, a tributary of the Athabasca River experiencing increasing proximity to natural bitumen deposits and proposed mining development as it approaches confluence with the mainstem Athabasca. Transect-based electrofishing data from four sites surveyed in September 2013, 2014 and 2018 showed significant spatiotemporal variability in assemblages, where spatial variability was greatest in 2013 and temporal variability was observed in assemblages both upstream (2013–2014) and downstream (2014–2018) of proposed development. Habitat assessments in 2018 revealed significant relationships among pH, algae cover and site slope with fish assemblages of the same year. Due to the complementary nature of assemblage surveys, data challenges (changing methodologies, sampling effort, and limited ancillary physiochemical data) have presented limitations to the multivariate approach applied in the study. Moving forward, employing consistent methods for fish collections and fine-scale habitat assessments will improve the ability to correlate assemblage variability with changes in the physical environment. Ultimately, this will aid in developing potential triggers of change that may be attributed to or confound adjacent, expanding Oil Sands activities. These findings will also inform monitoring programs on the use of fish assemblages as indicators of change, potentially providing an alternative to existing biomonitoring approaches in small streams with small fish populations.

Spatial and Temporal Variations in Fish Assemblage in Feitsui Reservoir, in Northern Taiwan, from 2006–2020

Reservoirs are artificial ecosystems that modify the hydrological and environmental components nearby. The long-term monitoring of fish assemblages in reservoirs may provide key information to understand how these artificial ecosystems allow fish population fluctuations and identify proper conservation strategies. A sentinel-site approach method assessed changes in fish assemblages in the Feitsui Reservoir (1024 ha) over 14 years, including the periods 2006–2008, 2010–2011, 2016, 2018, and 2020. Fish assemblages, sampled using gill nets, were composed of 38 species (12 families and 8 orders) with Cyprinidae as the dominant family; the fish fauna were dominated by species of the family Cyprinidae (71%) and Cichlidae (20.3%). Principal component analysis and nonmetric multidimensional scaling categorized the assemblages into two groups (cold and warm seasons), and we identified three parameters that were significantly correlated with the season (p < 0.05): SD (R = −0.04), Chl-a (R = 0.01), and algal count (R = 0.19); the algal count was higher in the warm season than in the cold season. The fish assemblage in the cold and warm seasons contained no exclusive taxa, contributing to the dissimilarity between the groups. The fish assemblage for the years before and after 2010 indicated partial overlap between the two groups; S. macrops contributed greatly to the separation of the two periods (>10% each; SIMPER) and O. mossambicus was dominant in assemblage structures after 2010. Our findings show the importance of long-term fish monitoring for the investigation of the effects of nonnative fish species on native fish species composition.

Performance of a baited underwater video system vs. the underwater visual census technique in assessing the structure of fish assemblages in a Mediterranean marine protected area

Accurate, rapid and cost-effective fish assemblage monitoring is fundamental for marine protected area (MPA) management as a pivotal tool to verify whether and to what extent MPA conservation objectives have been achieved and to redefine these objectives in the framework of an adaptive management. Recently, there has been a sharp increase in the number of video-based methods to study fish fauna, such as baited remote underwater video (BRUV) systems, that, depending on the objectives of the monitoring, can provide complementary or additional data to the more commonly used underwater visual census (UVC). Even though BRUV systems have been widely used in a wide range of geographic contexts and habitats, their use in the Mediterranean basin is still sporadic and the evaluation of the efficiency of BRUV systems and whether they can be used to complement other techniques needs investigation. Thus, the objective of this study was to assess the performance of a BRUV system in a Mediterranean MPA and to evaluate its effectiveness in assessing the structure of fish assemblages (abundance and species richness) by comparing estimates with those obtained by the UVC technique. The fish fauna were monitored by BRUV and UVC in the Capo Caccia – Isola Piana Marine Protected Area (Sardinia, Italy), in July and October-November 2020, at four sampling sites and two areas, hundreds of meters apart, for each site. Overall, 46 taxa and a total of 3620 individuals were observed by BRUV, while 36 taxa and a total of 2995 individuals were observed by UVC. The species first observed in front of the camera’s field of view and able to reach the maximum abundance were the planktivores (Chromis chromis and Oblada melanura) followed by several carnivorous species belonging to the families Labridae, Serranidae and Sparidae, and lastly two carnivores (Mullus surmuletus and Mugilidae spp.) and some high-level predators (Dentex dentex, Seriola dumerili, Sphyraena viridensis, Dicentrarchus labrax). The maximum species richness and abundance were reached between 39 and 50 min. The cumulative species richness increased until around 30 min. Species richness was higher during the BRUV compared to the UVC monitoring. The consistency in findings between BRUV and UVC and a better performance of BRUV in detecting some species (mainly high-level predators), supports BRUV as an additional technique for describing and quantifying species richness and abundance also in the Mediterranean Sea. Based on the results of this study, the advantages/disadvantages, shortcomings, suggestions and resources needed for the two techniques are outlined.

A New Method for Standardizing Inland Fish Community Surveys: Characterizing Habitat Associated with Small-Bodied Fish Species, Abundance, and Size Distributions in a Highly Modified Estuary

Monitoring fish assemblages in estuary environments is often difficult to standardize due to habitat complexity and gear-specific selectivity. This is further compounded by conventional sampling methods which require fish handling that might cause stress or mortality. To ameliorate these issues, we developed the Single-Platform Aquatic Species and Habitat Sampling System (Platform), an integrated and mobile concentrator net and live box prototype, coupled with a range of physical monitoring equipment. The long-term goal of the Platform is to employ non-invasive sampling techniques such as video and eDNA; however, our aim in this study was to test the Platform’s ability to sample across different habitat types and detect differences in fish assemblages. We investigated the utility of the Platform over a short time period (2 mo) in a relatively small and complex embayment within the highly modified San Francisco Estuary, California. We were able to identify clear physical distinctions among estuary/delta habitat types and detect habitat segregation by ecological groups of sampled fishes with the Platform. The Platform also detected discernable ontogenetic shifts (i.e., size differences) within estuary habitats of commonly observed fish species. These initial results demonstrate the Platform’s ability to contrast fish density, size, and species diversity, which sets the stage to advance more passive monitoring techniques, including video and eDNA methods. The Platform has the potential to fill a methodological gap in non-invasive surveying of small-bodied fish across a range of estuarine habitats, warranting further investigation of potential applications.

Underwater robots provide similar fish biodiversity assessments as divers on coral reefs

AbstractCoral reefs are under increasing threat, and the loss of reef‐associated fishes providing valuable ecosystem services is accelerating. The monitoring of such rapid changes has become a challenge for ecologists and ecosystems managers using traditional approaches like scuba divers performing underwater visual censuses (UVC) or diver operated video recording (DOV). However, the use of small, low‐cost robots could help tackle the challenge of such monitoring, provided that they perform at least as well as diver‐based methods. To address this question, tropical fish assemblages from 13 fringing reefs around Mayotte Island (Indian Ocean) were monitored along 50 m‐long transects using stereo videos recorded by a semi‐autonomous underwater vehicle (SAUV) and by a scuba diver (Diver Operated stereo Video system, DOV). Differences between the methods were tested for complementary fish assemblage metrics (species richness, total biomass, total density, Shannon diversity and Pielou evenness) and for the number and size of nine targeted species. SAUV recorded on average 35% higher biomass than DOV which in turn recorded on average 12% higher species richness. Biomass differences were found to be due to SAUV monitoring larger fishes than DOV, a potential marker of human‐related fish avoidance behaviour. This study demonstrates that SAUV provides accurate metrics of coral reef fish biodiversity compared to diver‐based procedures. Given their ability to conduct video transects at high frequency, 100 m depth range and at a moderate cost, SAUV is a promising tool for monitoring fish assemblages in coral reef ecosystems.

Incorporating costs, thresholds and spatial extents for selecting stream bioindicators in an ecotone between two Brazilian biodiversity hotspots

Biomonitoring is critical for characterizing and monitoring status, spatial patterns, and long-term trends in the ecological condition of freshwater ecosystems. The selection of cost-effective bioindicators is a critical step in establishing such monitoring programs. Key indicator considerations are a reliable response to anthropogenic disturbances, a high benefit-cost-ratio and sensitivity at multiple spatial extents. We evaluated non-linear responses of Ephemeroptera, Plecoptera and Trichoptera (EPT) and fish to the effects of native vegetation loss within buffers of 100 m and 1000 m and assessed the sampling and processing costs involved for each assemblage. We sampled 37 neotropical stream sites in the Formoso River network, a karstic region of the Bodoquena Plateau, midwest Brazil, lying in the ecotone between the Cerrado and Atlantic Forest biological hotspots. We used TITAN (threshold indicator taxa analysis) to identify six indicator taxa, four EPT genera and two fish species. The four EPT genera had low negative thresholds to native vegetation loss, whereas the two fish species had positive thresholds. Thresholds were lower for the 100 m buffers than the 1000 m buffers for EPT. The most sensitive taxon (Macronema, Trichoptera) had a threshold of 0% native vegetation loss in the 100 m buffers and nearly 40% in the 1000 m buffers. For taxa richness, we found no non-linear response to the effects of native vegetation loss for buffer extent nor assemblage. The total cost for EPT biomonitoring was US$ 3,616; whereas for fish, the total was US$ 1,901. Although fish were less expensive than EPT, they did not respond negatively to native vegetation loss and their positive threshold started at 48%, a level of vegetation loss that was highly disruptive of EPT. Therefore, we do not recommend using fish to monitor the effects of native vegetation loss on headwater streams in the Bodoquena Plateau. Although EPT monitoring costs 52% more than fish assemblage monitoring, it detected earlier impacts of the effects of native vegetation loss on stream biota, especially in the 100 m buffer. Therefore, EPT are more cost-effective early warning indicators for monitoring the effects of native vegetation loss in Bodoquena Plateau headwaters.

Commercial fish abundance estimation in the Belgian part of the North Sea through eDNA ddPCR analyses

Monitoring of fish assemblages in the Belgian part of the North Sea (BPNS) mainly happens through trawling. While effective, this method is invasive and destructive as it disturbs bottom communities, catches non-target species and removes organisms from the environment. A more sustainable alternative for monitoring marine diversity is the use of environmental DNA (eDNA) which comprises intra- and extracellular genetic material that comes from the shedding of organic material, like scales and mucus in the case of fish. When applying metabarcoding on eDNA, community composition can be inferred simply by analysing a small volume of water. Therefore the technique does not disturb the environment, and the high sensitivity of eDNA allows the detection of rare and transient species that are frequently missed by traditional sampling methods. Next to determining community composition, the amount of eDNA copies in the water could potentially be used to quantify target fish species in the marine environment. Here, we investigate whether eDNA concentrations from marine water samples correlate with local fish abundance estimates obtained via traditional beam trawling. Species specific Droplet Digital Polymerase Chain Reaction (ddPCR) assays were designed and tested for three economically important species: common sole (Solea solea), plaice (Pleuronectes platessa) and whiting (Merlangius merlangus). In march 2020, 12 sites in the BPNS were selected based on absence, low and high abundances of the three target species as observed in epibenthos monitoring data from previous years. In each site, 2L of seawater was collected with a niskin bottle from ca 1m above the sea floor. Subsequently, beam trawl transects of 1 km were conducted and all epibenthos species caught in the trawling net were morphologically identified, counted and weighted. Our results indicate promising correlations between eDNA concentrations obtained with the ddPCR assays and the number of specimens in the net for all three species. Some “false” positive results were obtained with the ddPCR, but these may actually be “true” positive detections because the fish might be present in the area but were not caught in the trawling transects. This warrants further investigation to see how far eDNA signals can be detected in the North Sea system. Next, 50 water samples were collected in Autumn 2020, involving more locations with or without the three fishes. This time samples were taken at the beginning, middle and end of the 1 km transects to investigate small scale horizontal variation in eDNA concentrations. The autumn samples are currently being processed. In March 2021, samples will be taken at different depths (surface, middle of the water column and ca 1m above the seafloor) to investigate whether there are any vertical patterns in eDNA distribution in a very well mixed system such as the BPNS. A DNA shedding experiment will be performed as well to estimate the rate at which the three fishes shed DNA. This will provide important information on how quickly fishes can be detected when they swim by. The information obtained with the field sampling and experimental setting will help to strengthen the correlation to a point that reliable abundance estimations of our target species become possible and will allow us to evaluate the potential of eDNA as a sustainable alternative/addition to traditional monitoring methods.

Conservation bottom-up initiatives in marine recreational spearfishing suggest the emergence of positive attitudes towards conservation

We show that marine recreational spearfishers voluntarily organize bottom-up conservation actions. The main goals of these actions are to provide support to research in monitoring fish assemblages, tracking biological invasions or mitigating impacts on the environment, such as those stemming from pollution and littering. We show that such initiatives started more than 20 years ago and are now facilitated by social media networking. We argue that the emergence of bottom-up conservation actions in marine recreational spearfishers should be encouraged, supported and integrated into participatory management plans. This is important to mitigate the potential negative impacts of marine recreational spearfishing and to catalyse broader civil actions for conservation of marine ecosystems.

Fast, Not Furious - Adaptation of the Species List and Fish Size Classes for Fish Assemblage Survey Technique (FAST) for the Adriatic Sea

Abstract Marine Protected Areas and other managed marine sites are designated to improve the status of coastal fish assemblages and protect valuable habitats. The implementation of management practices relies on data collected through monitoring activities. The monitoring of fish assemblages using the standard non-destructive methods requires significant financial resources and time. A new approach to monitoring fish assemblages in the coastal waters was recently implemented in the Mediterranean – Fish Assemblage Survey Technique (FAST). It is based on Citizen Science where trained volunteer divers collect the data following a pre-established protocol. Considering the differences in species presence/absence and their sizes between the Mediterranean and the Adriatic Sea, a modification of the method was necessary. This study presents 23 main fish species and four ‘joker’ species selected for the Croatian FAST list and their respective sizes that will be considered Large (>2/3 of the total size) for implementing the method in the Croatian part of the Adriatic Sea.

Coastal fish assemblages reflect marine habitat connectivity and ontogenetic shifts in an estuary-bay-continental shelf gradient

The success of marine management initiatives and our capability for dealing with environmental change largely depend on our understanding regarding the distribution of species and their habitat preferences. In the present study, we deployed baited remote underwater video systems (BRUVs) in a portion of Brazilian central coast (i.e., Todos os Santos Bay) to describe fish species-habitat associations along an estuary-bay-continental shelf gradient. Significant variation in the fish assemblage was found among three ecosystems, four depth classes, and eight different types of habitat, confirming that the structure and composition of fish assemblages is mediated by a set of habitat characteristics forming an ecological mosaic. The highest species richness and relative abundance were found in the mangroves and reefs. The data demonstrated that some species, such as Lutjanus jocu, Lutjanus synagris, Carangoides bartholomaei, Eucinostomus argenteus and Eucinostomus melanopterus had clear ontogenetic shifts among habitats and across ecosystems. Some species (Sphoeroides greeley, L. synagris, and Eucinostomus gula) were widespread along the ecosystem-level gradient and were observed in a number of different habitats, reflecting more generalist habitat associations. By contrast, a large number of species (54; e.g., Ptereleotris randali, Decapterus macarellus and Mugil curema) were recorded in a single habitat type, indicating they were habitat specialists. Despite this apparent habitat-related pattern, the size-mediated relationships found in many species indicate cross-migration along the ecosystem gradient. Our findings have implications for the conservation and monitoring of fish assemblages highlighting the role of the connectivity of marine habitats as a conservation priority toward to an ecosystem-based management strategy.

A Systematic Review of Remotely Operated Vehicle Surveys for Visually Assessing Fish Assemblages

Anthropogenic activities and greater demands for marine natural resources has led to increases in the spatial extent and duration of pressures on marine ecosystems. Remotely operated vehicles (ROVs) offer a robust survey tool for quantifying these pressures and tracking the success of management intervention while at a range of depths, including those inaccessible to most SCUBA diver-based survey methods (∼>30 m). As the strengths, limitations, and biases of ROVs for visually monitoring fish assemblages remain unclear, this review aims to evaluate ROVs as a survey technique and to suggest optimal sampling strategies for use in typical ROV-based studies. Using the search engines Scopus™ and Google Scholar™, 119 publications were identified that used ROVs for visual surveys of fish assemblages. While the sampling strategies and sampling metrics used to annotate the imagery in these publications varied considerably, the total abundance of fish recorded over strip transects of varying dimensions was the most common sampling design. The choice of ROV system appears to be a strong indicator of both the types of surveys available to studies and the success of ROV deployments. For instance, larger, more powerful working-class systems can complete longer and more complex designs (e.g., swath, cloverleaf, and polygonal transects) at greater depths, whereas observation-class systems are less expensive and easier to deploy, but are more susceptible to delays or cancellations of deployments. In more severe sea state conditions, radial transects, or strip transects that employ live-boating or a weight to anchor the tether to the seafloor, can be used to improve the performance of observation-class systems. As these systems often employ shorter tethers, radial transects can also be used to maximize sampling area at greater depths and on large vessels that may rotate substantially while anchored. For highly mobile species, and in survey designs where individuals are likely to be recounted (e.g., transects along oil and gas pipelines), relative abundance (MaxN) may be a more robust sampling metric. By identifying subtle, yet important, differences in the application of ROVs as a tool for visually surveying deep-water marine ecosystems, we identified key areas for improvement for best practice for future studies.

Regime shift in fish assemblage structure in the Yangtze River following construction of the Three Gorges Dam

Dams have well-documented ecological impacts on downstream river segments; however, long-term impacts of river impoundment have rarely been investigated in upstream reaches. Using data from long-term standardized surveys, we analyzed temporal changes in fish assemblages in the Yangtze River upstream of the Three Gorges Dam (TGD) before, during and after its construction. Our analysis indicated fish assemblage regime shifts in the two closer reaches in 2008, in accordance with the filling to 172.5 m in 2008; and in the other reach, farthest from the TGD, in 2011, indicating timing of the effects being related to distance. These shifts were evident in relative abundance of native fish species rather than non-native species and have altered community structures and functional groups. Relative abundance of the lotic guilds declined in the two closer reaches, but increased in the farthest. Invertivores declined, but piscivores and opportunistic life-history strategists increased in all reaches. We conclude that construction of TGD had led to significant changes in species distributions influenced by species functional traits. Our findings emphasize the need for long-term monitoring of fish assemblages before and after dam construction in order to understand ecological responses to hydrological changes for effective resource management in regulated rivers.

Assessing Fish Species Tolerance in the Huntai River Basin, China: Biological Traits versus Weighted Averaging Approaches

Fish species tolerance used as a component of fish-index of biological integrity (F-IBI) can be problematic as it is usually classified using the historical data, data from literature or expert judgments. In this study, fish assemblages, water quality parameters and physical habitat factors from 206 sampling sites in the Huntai River Basin were analyzed to develop tolerance indicator values (TIVs) of fish based on a (Fb-TIVs) and the weighted averaging (WA) method (FW-TIVs). The two quantitative methods for fish tolerance were then compared. The FW-TIVs and Fb-TIVs of fish species were calculated separately using a WA inference model based on ten water quality parameters (WT, pH, DO, SC, TDS, NH3, NO2−, NO3−, TP, Cl−, and SO42−), and six biological traits (lithophilic spawning, benthic invertivores, cold water species, equilibrium or periodic life history strategies, families of Cottidae, and species distribution range). Fish species were then classified into biological traits approach three categories (tolerant species, moderately tolerant species, and sensitive species). The results indicated that only 30.3% fish species have the same classification based on FW-TIVs and Fb-TIVs. However, the proportion of tolerant species based on two methods had a similar response to environmental stress, and these tolerant species were correlated with PCA axes 1 site scores obtained by (FW-TIVs, p < 0.05, R2 = 0.434; Fb-TIVs, p < 0.05, R2 = 0.334) and not correlated with PCA axis 2 site scores (FW-TIVs, p > 0.05, R2 = 0.001; Fb-TIVs, p > 0.05, R2 = 0.012) and PCA axis 3 site scores (FW-TIVs, p > 0.05, R2 = 0.000; Fb-TIVs, p > 0.05, R2 = 0.013). The results of linear regression analyses indicated that Fb-TIVs can be used for the study of fish tolerance. Fish tolerance assessments based on FW-TIVs requires long-term monitoring of fish assemblages and water quality parameters to provide sufficient data for quantitative studies. The Fb-TIV method relies on the accurate identification of fish traits by an ichthyologist. The two methods used in this study can provide methodological references for quantitative studies of fish tolerance in other regions, and are of great significance for the development of biological assessment tools.