Cross-ocean patterns and processes in fish biodiversity on coral reefs through the lens of eDNA metabarcoding.

Increasing speed and magnitude of global change threaten the world's biodiversity and particularly coral reef fishes. A better understanding of large-scale patterns and processes on coral reefs is essential to prevent fish biodiversity decline but it requires new monitoring approaches. Here, we use environmental DNA metabarcoding to reconstruct well-known patterns of fish biodiversity on coral reefs and uncover hidden patterns on these highly diverse and threatened ecosystems. We analysed 226 environmental DNA (eDNA) seawater samples from 100 stations in five tropical regions (Caribbean, Central and Southwest Pacific, Coral Triangle and Western Indian Ocean) and compared those to 2047 underwater visual censuses from the Reef Life Survey in 1224 stations. Environmental DNA reveals a higher (16%) fish biodiversity, with 2650 taxa, and 25% more families than underwater visual surveys. By identifying more pelagic, reef-associated and crypto-benthic species, eDNA offers a fresh view on assembly rules across spatial scales. Nevertheless, the reef life survey identified more species than eDNA in 47 shared families, which can be due to incomplete sequence assignment, possibly combined with incomplete detection in the environment, for some species. Combining eDNA metabarcoding and extensive visual census offers novel insights on the spatial organization of the richest marine ecosystems.

Comparability and complementarity of reef fish measures from underwater visual census (UVC) and baited remote underwater video stations (BRUVS).

The much-publicized threats to coral reef systems necessitate a considered management response based on comprehensive ecological data. However, data from large reef systems commonly originate from multiple monitoring programs that use different methods, each with distinct biases that limit united assessments of ecological status. The effective integration of data from different monitoring methods would allow better assessment of system status and hence, more informed management. Here we examine the scope for comparability and complementarity of fish data from two different methods used on Australia's Great Barrier Reef (GBR): underwater visual census (UVC) and baited remote underwater video stations (BRUVS). We compared commonly reported reef fish measures from UVC and BRUVS on similar reef slope habitats of three central GBR reefs. Both methods recorded similar estimates of total species richness, although ~30% of recorded species were not common to both methods. There were marked differences between methods in sub-group species richness, frequency of species occurrences, relative abundances of taxa and assemblage structure. The magnitude and orientation of inter-method differences were often inconsistent among taxa. However, each method better categorized certain components of fish communities: BRUVS sampled more predatory species in higher numbers while UVC was similarly better at sampling damselfishes (Pomacentridae). Our results suggest limited scope for direct or adjusted comparisons of data from UVC and BRUVS. Conversely, complementary aspects of the two methods confirm that their integration in monitoring programs will provide a more complete and extensive assessment of reef fish status for managers than from either method alone.

A Minimal Metric for the Characterization of Acoustic Noise Emitted by Underwater Vehicles.

Underwater robots emit sound during operations which can deteriorate the quality of acoustic data recorded by on-board sensors or disturb marine fauna during in vivo observations. Notwithstanding this, there have only been a few attempts at characterizing the acoustic emissions of underwater robots in the literature, and the datasheets of commercially available devices do not report information on this topic. This work has a twofold goal. First, we identified a setup consisting of a camera directly mounted on the robot structure to acquire the acoustic data and two indicators (i.e., spectral roll-off point and noise introduced to the environment) to provide a simple and intuitive characterization of the acoustic emissions of underwater robots carrying out specific maneuvers in specific environments. Second, we performed the proposed analysis on three underwater robots belonging to the classes of remotely operated vehicles and underwater legged robots. Our results showed how the legged device produced a clearly different signature compared to remotely operated vehicles which can be an advantage in operations that require low acoustic disturbance. Finally, we argue that the proposed indicators, obtained through a standardized procedure, may be a useful addition to datasheets of existing underwater robots.

Counts of coral reef fishes by an experienced observer are not biased by the number of target species.

Fishes are commercially, recreationally and functionally important inhabitants of coral reefs. Accordingly, accurate assessments of fish abundance and diversity are necessary for effective reef management. While some reef fish monitoring programmes target all fishes, many survey a subset of common and visually obvious species. Changing to counts of all species, while desirable, risks new and unwelcome biases from altered observer swimming speeds and search patterns. Here we test whether substantially increasing the number of target species in an established fish monitoring programme biases counts of the original subset, so precluding ongoing comparisons with historical data. A subset of 141 fish species have been visually surveyed along 50 × 5 m transects over 27 years throughout Australia's Great Barrier Reef. We experimentally compared counts of the subset from standard subset-only surveys and from surveys of all species (excluding small site-attached fishes that are surveyed separately) at three diverse reefs. Subset species richness and abundance, in total and of major families, and assemblage structure did not differ due to survey method. The high-level experience of the one observer appeared to overcome new biases from counting more species and the extra 2 min/transect was not logistically excessive. Surveys of all fishes recorded almost 80% more species than subset-only surveys and >130% higher total abundance on average from >150% more genera that included abundant and functionally important taxa. Overall, fish counts by an experienced observer were not biased by the number of species surveyed and counts of all species markedly improved assessments of reef fish diversity and function.

Biofluorescence as a survey tool for cryptic marine species.

As ecosystems come under increasing anthropogenic pressure, rare species face the highest risk of extinction. Paradoxically, data necessary to evaluate the conservation status of rare species are often lacking because of the challenges of detecting species with low abundance. One group of fishes subject to this undersampling bias are those with cryptic body patterns. Twenty-one percent of cryptic fish species assessed for their extinction risk (International Union for Conservation of Nature [IUCN]) are data deficient. We developed a nondestructive method for surveying cryptically patterned marine fishes based on the presence of biofluorescence (underwater biofluorescence census, UBC). Blue LED torches were used to investigate how widespread biofluorescence was in cryptic reef fishes in the Coral Triangle region. The effectiveness of UBC to generate abundance data was tested on a data-deficient pygmy seahorse species (Hippocampus bargibanti) and compared with data obtained from standard underwater visual census (UVC) surveys. We recorded 95 reef fish species displaying biofluorescence, 73 of which had not been previously described as biofluorescent. Of those fish with cryptic patterns, 87% were biofluorescent compared with 9% for noncryptic fishes. The probability of species displaying biofluorescence was 70.9 times greater for cryptic species than for noncryptic species. Almost twice the number of H. bargibanti was counted using the UBC compared with UVC. For 2 triplefin species (Ucla xenogrammus, Enneapterygius tutuilae), the abundance detected with UBC was triple that detected with UVC. The UBC method was effective at finding cryptic species that would otherwise be difficult to detect and thus will reduce interobserver variability inherent to UVC surveys. Biofluorescence is ubiquitous in cryptic fishes, making this method applicable across a wide range of species. Data collected using UBC could be used with multiple IUCN criteria to assess the extinction risk of cryptic species. Adopting this technique will enhance researchers' ability to survey cryptic species and facilitate management and conservation of cryptic marine species.

Assessing coral health and disease from digital photographs and in situ surveys.

Methods for monitoring the status of marine communities are increasingly adopting the use of images captured in the field. However, it is not always clear how data collected from photographic images relate to historic data collected using traditional underwater visual census methods. Here, we compare coral health and disease data collected in situ by scuba divers with photographic images collected simultaneously at 12 coral reef sites. Five globally relevant coral diseases were detected on 194 colonies from in situ surveys and 79 colonies from photos, whilst 698 colonies from in situ surveys and 535 colonies from photos exhibited signs of compromised health other than disease. Comparisons of in situ surveys with photographic analyses indicated that the number of disease cases occurring in the examined coral populations (prevalence) was six times higher (4.5 vs. 0.8% of colonies), whilst compromised health was three times higher (14 vs. 4% of colonies) from in situ surveys. Skeletal eroding band disease, sponge overgrowth and presence of Waminoa flatworms were not detected in photographs, though they were identified in situ. Estimates of black band disease and abnormally pigmented coral tissues were similar between the two methods. Estimates of the bleached and healthy colonies were also similar between methods and photographic analyses were a strong predictor of bleached (r 2 = 0.8) and healthy (r 2 = 0.5) colony prevalence from in situ surveys. Moreover, when data on disease and compromised health states resulting in white or pale coral colony appearance were pooled, the prevalence of 'white' colonies from in situ (14%) and photographic analyses (11%) were statistically similar. Our results indicate that information on coral disease and health collected by in situ surveys and photographic analyses are not directly comparable, with in situ surveys generally providing higher estimates of prevalence and greater ability to identify some diseases and compromised states. Careful sampling of photographs can however identify signs of coral stress, including some coral diseases, which may be used to trigger early-warning management interventions.

Aggregative Behaviour of Spiny Butterfly Rays (Gymnura altavela, Linnaeus, 1758) in the Shallow Coastal Zones of Gran Canaria in the Eastern Central Atlantic.

The presence of spiny butterfly rays, Gymnura altavela, in waters less than 20 m deep off the Canary Islands shows marked seasonality, with relatively high abundances in the summer and autumn. Large aggregations of sometimes hundreds of individuals, primarily females, appear in specific shallow areas of the archipelago and seem to be associated with the seasonal variation in water temperature. This seasonal pattern of presence or absence in shallow areas suggests that spiny butterfly rays migrate into deeper waters or other unknown areas during the rest of the year. G. altavela shows sexual dimorphism; in our study, females were larger and more abundant than males, with a sex ratio of 1:18.9. The species' estimated asymptotic length, L∞, was 183.75 cm and thus close to the common length reported for the species (200 cm). The von Bertalanffy growth constant (k) oscillated between 0.210 and 0.310 year-1, as similarly described for the species in the Western North Atlantic off the U.S. coast. From June to November, the seawater temperature oscillated between 19 and 24 °C, and massive aggregations of females occurred at 22-24 °C and in a few specific sandy beaches on the islands. Spiny butterfly rays, mostly females, show a preference for aggregating in shallow waters during summertime, probably conditionate to mating or breeding behaviour.

Coral reefs in the northeastern Saudi Arabian Red Sea are resilient to mass coral mortality events.

We conducted an integrated survey combining visual census and baited remote underwater video survey on the coral reefs in the northeastern Red Sea and examined their health by comparing the baseline information from two decades ago. The mean coverage of the corals of all stations was 36 %, including 32 % stony corals and 4.0 % soft corals, significantly higher and lower to previous baseline. Observed high proportion of dead corals indicated the occurrence of the events of mass mortality, and the heating events were the most likely cause. Similar levels of coral coverage compared to two decades ago indicated their resilience to past events with mass coral mortality. Small proportions of macroalgae and sea urchins indicated that they might be controlled by their predators frequently observed in both visual census and underwater video survey. Regular monitoring and careful development plans are needed to safeguard these invaluable reefs.

Does the colors of light matter? Testing different light color in nocturnal underwater visual censuses.

Most methods for assessing reef fish assemblages at night require artificial light, but the use of different colors of light may influence the results. We used data from 135 underwater visual censuses (UVCs) performed with different colors of light (red, blue and white) to evaluate the structure of fish assemblages on subtropical rocky reefs along three depth intervals. We did not detect any effect of the color of light on total density or fish species richness per transect, nor on the structure of the entire assemblage. However, the density of some of the most abundant species varied according to the color used. Red light showed the highest values of frequency of occurrence for most species, while the white light resulted in decreased abundance of some fish species. Our results emphasize the importance of choosing the color of light depending on the type of studies to be conducted. This will depend on the objectives of the research (e.g. inventory, behavior or community dynamics) and the target fish fauna (e.g. mobile or sedentary).

Boosted fish abundance associated with Posidonia oceanica meadows in temperate shallow CO2 vents.

Ocean acidification (OA) may induce major shifts in the structure and function of coastal marine ecosystems. Studies in volcanic CO2 vents, where seawater is naturally acidified, have reported an overall simplification of fish assemblages structure, while some primary producers are likely to increase their biomass under elevated concentration of CO2. Here we used temperate shallow CO2 vents located around the coast of Ischia island (Italy) to assess the effects of OA on necto-benthic fish assemblages associated with the foundation seagrass species Posidonia oceanica in the Mediterranean Sea. We compared P. oceanica meadow structure, its epiphytic community and the associated fish assemblage structure and diversity at vents with low pH sites and reference sites with ambient pH using underwater visual census strip transects, in two seasons (fall 2018 and summer 2019). Data were analysed using both univariate and multivariate statistical techniques. Results showed greater P. oceanica habitat complexity (i.e. shoot density) and lower abundance of epiphytic calcareous species (e.g. coralline algae) at the vents than reference sites. Total abundance of adult and juvenile fish was higher at vents than reference sites, while no differences were found for species richness and composition. Overall, the herbivore Sarpa salpa stands out among the species contributing the most to dissimilarity between vents and reference sites, showing higher abundances under OA conditions. This pattern could be explained by the combined effect of a positive response to the higher structural meadows complexity and the greater seagrasses palatability/nutritional value occurring at the vents, which may help herbivores to withstand the higher energetic cost to live under high pCO2/low pH conditions. Our results indicate that necto-benthic fish assemblages associated with the Mediterranean P. oceanica ecosystem may cope with OA under the CO2 emission scenarios forecasted for the end of this century.

Integrating eDNA metabarcoding and simultaneous underwater visual surveys to describe complex fish communities in a marine biodiversity hotspot.

Marine biodiversity can be surveyed using underwater visual censuses and recently with eDNA metabarcoding. Although a promising tool, eDNA studies have shown contrasting results related to its detection scale and the number of species identified compared to other survey methods. Also, its accuracy relies on complete reference databases used for taxonomic assignment and, as other survey methods, species detection may show false-negative and false-positive errors. Here, we compared results from underwater visual censuses and simultaneous eDNA metabarcoding fish surveys in terms of observed species and community composition. We also assess the effect of a custom reference database in the taxonomic assignment, and evaluate occupancy, capture and detection probabilities, as well as error rates of eDNA survey data. We amplified a 12S rRNA fish barcode from 24 sampling sites in the gulf of California. More species were detected with eDNA metabarcoding than with UVC. Because each survey method largely detected different sets of species, the combined approach doubled the number of species registered. Both survey methods recovered a known biodiversity gradient and a biogeographic break, but eDNA captured diversity over a broader geographic and bathymetric scale. Furthermore, the use of a modest-sized custom reference database significantly increased taxonomic assignment. In a subset of species, occupancy models revealed eDNA surveys provided similar or higher detection probabilities compared to UVC. The occupancy value of each species had a large influence on eDNA detectability, and in the false positive and negative error. Overall, these results highlight the potential of eDNA metabarcoding in complementing other established ecological methods for studies of marine fishes.

Fish assemblages cope with ocean acidification in a shallow volcanic CO2 vent benefiting from an adjacent recovery area.

Shallow CO2 vents are used to test ecological hypotheses about the effects of ocean acidification (OA). Here, we studied fish assemblages associated with Cymodocea nodosa meadows exposed to high pCO2/low pH conditions at a natural CO2 vent in the Mediterranean Sea. Using underwater visual census, we assessed fish community structure and biodiversity in a low pH site (close to the CO2 vent), a close control site and a far control site, hypothesising a decline in biodiversity and a homogenization of fish assemblages under OA conditions. Our findings revealed that fish diversity did not show a unique spatial pattern, or even significant relationships with pH, but correlated with seagrass leaf canopy. Among-site similarity was found in the abundance of juveniles, contrary to the expected impacts of OA on early life stages. However, pH seems an important driver in structuring fish assemblage in the low pH site, despite its high similarity with the close control site. This unexpected pattern may represent a combined response of fish mobility, enhanced food resources in the acidified site, and a 'recovery area' effect of the adjacent control site.

Point-Combination Transect (PCT): Incorporation of small underwater cameras to study fish communities.

Available underwater visual census (UVC) methods such as line transects or point count observations are widely used to obtain community data of underwater species assemblages, despite their known pit-falls. As interest in the community structure of aquatic life is growing, there is need for more standardized and replicable methods for acquiring underwater census data.Here, we propose a novel approach, Point-Combination Transect (PCT), which makes use of automated image recording by small digital cameras to eliminate observer and identification biases associated with available UVC methods. We conducted a pilot study at Lake Tanganyika, demonstrating the applicability of PCT on a taxonomically and phenotypically highly diverse assemblage of fishes, the Tanganyikan cichlid species-flock.We conducted 17 PCTs consisting of five GoPro cameras each and identified 22,867 individual cichlids belonging to 61 species on the recorded images. These data were then used to evaluate our method and to compare it to traditional line transect studies conducted in close proximity to our study site at Lake Tanganyika.We show that the analysis of the second hour of PCT image recordings (equivalent to 360 images per camera) leads to reliable estimates of the benthic cichlid community composition in Lake Tanganyika according to species accumulation curves, while minimizing the effect of disturbance of the fish through SCUBA divers. We further show that PCT is robust against observer biases and outperforms traditional line transect methods.

Composition and abundance of benthic marine litter in a coastal area of the central Mediterranean Sea.

Abundance and qualitative composition of benthic marine litter were investigated in a coastal area of the central Mediterranean Sea. Almost 30 km of video footage, collected by a Remotely Operated Vehicle between 5 and 30 m depth, were analyzed. Litter density ranged from 0 to 0.64 items/m2 with a mean of 0.11 (±0.16) items/m2. General wastes, made up almost entirely of plastic objects, were the dominant sources of debris representing 68% of the overall litter. The remaining 32% consisted of lost or abandoned fishing gears. Synthetic polymers, considering both fishing gears and general waste, represented 73% of total debris items. Our results are comparable with litter amounts reported in other Mediterranean sites at similar depths. Overall, the results are discussed in terms of monitoring strategy, to support the implementation of the Marine Strategy Framework Directive (2008/56/EC) for descriptor 10 and the Mediterranean UN Environment (UNEP/MAP) regional Plan on Marine Litter.

How many fish? Comparison of two underwater visual sampling methods for monitoring fish communities.

BACKGROUND: Underwater visual surveys (UVSs) for monitoring fish communities are preferred over fishing surveys in certain habitats, such as rocky or coral reefs and seagrass beds and are the standard monitoring tool in many cases, especially in protected areas. However, despite their wide application there are potential biases, mainly due to imperfect detectability and the behavioral responses of fish to the observers. METHODS: The performance of two methods of UVSs were compared to test whether they give similar results in terms of fish population density, occupancy, species richness, and community composition. Distance sampling (line transects) and plot sampling (strip transects) were conducted at 31 rocky reef sites in the Aegean Sea (Greece) using SCUBA diving. RESULTS: Line transects generated significantly higher values of occupancy, species richness, and total fish density compared to strip transects. For most species, density estimates differed significantly between the two sampling methods. For secretive species and species avoiding the observers, the line transect method yielded higher estimates, as it accounted for imperfect detectability and utilized a larger survey area compared to the strip transect method. On the other hand, large-scale spatial patterns of species composition were similar for both methods. DISCUSSION: Overall, both methods presented a number of advantages and limitations, which should be considered in survey design. Line transects appear to be more suitable for surveying secretive species, while strip transects should be preferred at high fish densities and for species of high mobility.

Effect of underwater visual survey methodology on bias and precision of fish counts: a simulation approach.

Bias in underwater visual census has always been elusive. In fact, the choice of sampling method and the behavioural traits of fish are two of the most important factors affecting bias, but they are still treated separately, which leads to arbitrarily chosen sampling methods. FishCensus, a two-dimensional agent-based model with realistic fish movement, was used to simulate problematic behavioural traits in SCUBA diving visual census methods and understand how sampling methodology affects the precision and bias of counts. Using a fixed true density of 0.3 fish/m2 and a fixed visibility of 6 m, 10 counts were simulated for several combinations of parameters for transects (length, width, speed) and point counts (radius, rotation speed, time), generating trait-specific heatmaps for bias and precision. In general, point counts had higher bias and were less precise than transects. Fish attracted to divers led to the highest bias, while cryptic fish had the most accurate counts. For point counts, increasing survey time increased bias and variability, increasing radius reduced bias for most traits but increased bias in the case of fish that avoid divers. Rotation speed did not have a significant effect in general, but it increased bias for fish that avoid divers. Wider and longer transects and a faster swim speed are beneficial when sampling mobile species, but a narrower, shorter transect with a slow swim is beneficial for cryptic fish.

"How" and "what" matters: Sampling method affects biodiversity estimates of reef fishes.

Understanding changes in biodiversity requires the implementation of monitoring programs encompassing different dimensions of biodiversity through varying sampling techniques. In this work, fish assemblages associated with the "outer" and "inner" sides of four marinas, two at the Canary Islands and two at southern Portugal, were investigated using three complementary sampling techniques: underwater visual censuses (UVCs), baited cameras (BCs), and fish traps (FTs). We firstly investigated the complementarity of these sampling methods to describe species composition. Then, we investigated differences in taxonomic (TD), phylogenetic (PD) and functional diversity (FD) between sides of the marinas according to each sampling method. Finally, we explored the applicability/reproducibility of each sampling technique to characterize fish assemblages according to these metrics of diversity. UVCs and BCs provided complementary information, in terms of the number and abundances of species, while FTs sampled a particular assemblage. Patterns of TD, PD, and FD between sides of the marinas varied depending on the sampling method. UVC was the most cost-efficient technique, in terms of personnel hours, and it is recommended for local studies. However, for large-scale studies, BCs are recommended, as it covers greater spatio-temporal scales by a lower cost. Our study highlights the need to implement complementary sampling techniques to monitor ecological change, at various dimensions of biodiversity. The results presented here will be useful for optimizing future monitoring programs.

Considerations on the effects of tidal regimes in the movement of floating litter in an estuarine environment: Case study of the estuarine system of Santos-São Vicente, Brazil.

Floating litter in the estuarine system of Santos-São Vicente is common and is part of day-to-day activities of various users of the area. The objective of the present study was to carry out a quali-quantitative evaluation of the occurrence of floating litter, to infer their sources, and to identify environmental factors that are likely to control occurrence and distribution, with particular emphasis on the effects of tidal regimes. Six sampling stations were selected along the aforementioned estuary and visited monthly between July 2010 and January 2012. Floating litter was counted from a fixed sampling station. Plastics prevailed (89.64%) and their main source was domestic activities (55.41%). More litter was found during ebb spring tides, with higher concentrations obeying confluence patterns of the estuary's channels. Results indicated that occurrence can be attributed to the deficiency in basic sewage system in the area and the deliberate disposal into the estuary by the local population.

New Approaches to Marine Conservation Through the Scaling Up of Ecological Data.

In an era of rapid global change, conservation managers urgently need improved tools to track and counter declining ecosystem conditions. This need is particularly acute in the marine realm, where threats are out of sight, inadequately mapped, cumulative, and often poorly understood, thereby generating impacts that are inefficiently managed. Recent advances in macroecology, statistical analysis, and the compilation of global data will play a central role in improving conservation outcomes, provided that global, regional, and local data streams can be integrated to produce locally relevant and interpretable outputs. Progress will be assisted by (a) expanded rollout of systematic surveys that quantify species patterns, including some carried out with help from citizen scientists; (b) coordinated experimental research networks that utilize large-scale manipulations to identify mechanisms underlying these patterns;

Comparative analysis of different survey methods for monitoring fish assemblages in coastal habitats.

Coastal ecosystems are among the most productive yet increasingly threatened marine ecosystems worldwide. Particularly vegetated habitats, such as eelgrass (Zostera marina) beds, play important roles in providing key spawning, nursery and foraging habitats for a wide range of fauna. To properly assess changes in coastal ecosystems and manage these critical habitats, it is essential to develop sound monitoring programs for foundation species and associated assemblages. Several survey methods exist, thus understanding how different methods perform is important for survey selection. We compared two common methods for surveying macrofaunal assemblages: beach seine netting and underwater visual census (UVC). We also tested whether assemblages in shallow nearshore habitats commonly sampled by beach seines are similar to those of nearby eelgrass beds often sampled by UVC. Among five estuaries along the Southern Gulf of St. Lawrence, Canada, our results suggest that the two survey methods yield comparable results for species richness, diversity and evenness, yet beach seines yield significantly higher abundance and different species composition. However, sampling nearshore assemblages does not represent those in eelgrass beds despite considerable overlap and close proximity. These results have important implications for how and where macrofaunal assemblages are monitored in coastal ecosystems. Ideally, multiple survey methods and locations should be combined to complement each other in assessing the entire assemblage and full range of changes in coastal ecosystems, thereby better informing coastal zone management.