A research tool for long-term and continuous analysis of fish assemblage in coral-reefs using underwater camera footage

We present a research tool that supports marine ecologists' research by allowing analysis of long-term and continuous fish monitoring video content. The analysis can be used for instance to discover ecological phenomena such as changes in fish abundance and species composition over time and area. Two characteristics set our system apart from traditional ecological data collecting and processing methods. First, the continuous video recording results in enormous data volumes of monitoring data. Currently around a year of video recordings (containing over the 4 million fish observations) have been processed. Second, different from traditional manual recording and analysing the ecological data, the whole recording, analysing and presentation of results is automated in this system. On one hand, it saves the effort of manually examining every video, which is infeasible. On the other hand, no automatic video analysis method is perfect, so the user interface provides marine ecologists with multiple options to verify the data. Marine ecologists can examine the underlying videos, check results of automatic video analysis at different certainty levels computed by our system, and compare results generated by multiple versions of automatic video analysis software to verify the data in our system. This research tool enables marine ecologists for the first time to analyse long-term and continuous underwater video records

Camera methods for the assessment of coastal biodiversity in low visibility environments

Coastal marine environments are important ecological, economic and social areas providing valuable services such as coastal protection, areas of recreation and tourism, fishing, climate regulation, biotic materials and biofuels. Marine renewable energy developments in the coastal environment are becoming a key objective for many countries globally. Assessing and monitoring the impacts of these developments on features, such as coastal biodiversity, becomes a difficult prospect in these environments due to the complexity of marine process at the locations in which these developments are targeted. This thesis explores the main challenges faced when assessing biodiversity in dynamic coastal environments, in particular those susceptible to high levels of turbidity. Various underwater camera techniques were trialled in reduced visibility environments including baited remote underwater video (BRUV), drop-down video and hydroacoustic methods. This research successfully refined BRUV guidelines in the North-East Atlantic region and identified key methodological and environmental factors influencing data collected BRUV deployments. Key findings included mackerel as the recommended bait type in this region and highlighting the importance of collecting consistent metadata when using these methods. In areas of high turbidity, clear liquid optical chambers (CLOCs) were successfully used to enhance the quality of information gathered using underwater cameras when monitoring benthic fauna and fish assemblages. CLOCs were applied to both conventional BRUV camera systems and benthic drop-down camera systems. Improvements included image quality, species and habitat level identification, and taxonomic richness. Evaluations of the ARIS 3000 imaging sonar and its capability of visualising distinguishing identifying features in low visibility environments for motile fauna showed mixed results with morphologically distinct species such as elasmobranchs much clearer in the footage compared to individuals belonging to finfish families. A combined approach of optical and hydroacoustic camera methods may be most suitable for adequately assessing coastal biodiversity in low visibility environments

An Assessment of Mobile Predator Populations along Shallow and Mesophotic Depth Gradients in the Hawaiian Archipelago.

Large-bodied coral reef roving predators (sharks, jacks, snappers) are largely considered to be depleted around human population centers. In the Hawaiian Archipelago, supporting evidence is primarily derived from underwater visual censuses in shallow waters (=30?m). However, while many roving predators are present or potentially more abundant in deeper strata (30-100?m+), distributional information remains sparse. To partially fill that knowledge gap, we conducted surveys in the remote Northwestern Hawaiian Islands (NWHI) and populated Main Hawaiian Islands (MHI) from 2012-2014 using baited remote underwater stereo-video. Surveys between 0-100?m found considerable roving predator community dissimilarities between regions, marked conspicuous changes in species abundances with increasing depth, and largely corroborated patterns documented during shallow water underwater visual censuses, with up to an order of magnitude more jacks and five times more sharks sampled in the NWHI compared to the MHI. Additionally, several species were significantly more abundant and larger in mesophotic versus shallow depths, which remains particularly suggestive of deep-water refugia effects in the MHI. Stereo-video extends the depth range of current roving predator surveys in a more robust manner than was previously available, and appears to be well-suited for large-scale roving predator work in the Hawaiian Archipelago

On the underwater visual census of Western Indian Ocean coral reef fishes

This study conducted the first high-resolution investigation of the ichthyofaunal assemblages on a high-latitude coral reef in the Western Indian Ocean (WIO). Two-Mile reef, in South Africa, is a large, accessible patch-reef, and was selected as a candidate study area. Although the effect of season in structuring coral reef fish communities is most-often overlooked, the relationship between these fish communities and their habitat structure has been investigated. In South Africa, however, neither of these potential community-level drivers has been explored. As coral reefs worldwide are faced with high levels of usage pressure, nondestructive underwater visual census (UVC) techniques were identified as the most appropriate survey methods. This study had two primary aims that were; (1) to identify the most suitable technique for the UVC of coral reef fishes, and to test variations of the selected technique for appropriateness to implementation in long-term monitoring programs, and (2) to determine if possible changes to ichthyofaunal community structure could be related to trends in season and/or habitat characteristics. A review of the literature indicated that the most appropriate UVC method for surveying epibenthic coral reef fishes is underwater transecting. To compare the traditional slate-based transects to variations that implement digital image technology, slate transects were compared to a first-attempt digital photographic transect technique, and digital videographic transects. Videographic transects produced the most favourable species richness, abundance, and standard deviations of the three techniques. Diversity was not significantly different between transect techniques. The minimum required sample size was lowest for videographic transects (17 replicates), intermediate for photographic transects (27 replicates) and highest for slate transects (37 replicates). Videographic and photographic transects required greater analysis time to generate counts, but required lower observer training time. While videographic transects produced the lowest proportion of species considered unidentifiable, all three transect techniques showed similar functionality to surveying epibenthic coral reef fishes. Videographic transects were therefore identified as the most appropriate UVC technique for this study. Videographic transects at shallow (6 – 14 m), intermediate (14 – 22 m) and deep (22 – 30 m) depths in mid-winter and mid-summer, sampled a total of 41 families consisting of 209 species and 18172 individuals, dominated by pomacentrids in abundance and labrids in richness. The fish assemblages on Two-Mile Reef were found to be similar in composition to lower-latitude WIO reefs. Overall ichthyofaunal abundance and richness was significantly higher in summer than in winter, and was higher at shallow sites than at intermediate and deep sites. A multivariate approach confirmed differences between seasons at shallow depths but not between seasons at intermediate and deep depths. The fish assemblages on Two-Mile Reef can therefore be described as being comprised of four relatively distinct communities: a shallow, winter community; a shallow, summer community; a year-round intermediate community; and a year-round deep community. The distributions of discriminating species indicated that high abundances of the algal-feeding pomacentrids are observed only at shallow and intermediate sites while high abundances of the zooplanktivorous serranid subfamily, the Anthiinae, are observed predominantly at deep sites. Assessment of all measured supplementary variables indicated that of all factor combinations, observed patterns could be ascribed most strongly to depth. Quantification of reef characteristics indicated that as depth increases, habitat complexity decreases, benthic communities shift from dense coral domination to sparse sponge domination, and algal biomass and cover decreases. The ability of the videographic transect technique to detect changes in community structure with season and depth indicates that season and depth should be accounted for in future high-latitude ichtyofaunal surveys, and that the videographic transect technique is suitable for implementation in long-term monitoring programs on coral reefs. The similarity in fish assemblages between Two-Mile Reef and lower latitude regions suggests that the protocol for surveying epibenthic coral reef fishes, resulting from this study, is relevant throughout the continental WIO

Patterns in reef fish assemblages as determined by baited remote underwater video (BRUV) along the western side of False Bay: effects of site, depth and protection status

Includes bibliographical references.By protecting ecosystems from exploitation, no-take zones are considered the principal means by which marine species and their populations can be conserved for future generations. To be successful, no-take zones require continuous monitoring of the fish community to evaluate the response of marine ecosystems to anthropogenic impacts and environmental change. Obtaining an understanding of the patterns of species composition, abundance, and distribution, allows monitoring efforts to be focused, efficient, and properly interpreted. Baited remote underwater video (BRUV) was used to examine the effects of site, depth, andlevel of protection, on the diversity and relative abundance of temperate reef fish within the Table Mountain National Park (TMNP) Marine Protected Area (MPA). Four notake zones and adjacent exploited areas, subject to conventional management restrictions, were sampled monthly over a four-month period. A total of 36 species from three marine classes and 18 families was recorded. Species diversity (Shannon-Wiener index) was found to increase with sites closest to the mouth of the bay, whilst species abundance was found to increase with depth. Results indicated no consistent response to protection status among the sites at either the community or individual species level. However, the oldest no-take zone proclaimed for the purposes of reef conservation was found to harbour higher species diversity and a higher relative abundance of fish compared to its respective exploited area. Furthermore, the similar frequencies in which hottentot (Pachymetopon blochii) and roman (Chrysoblephus laticeps) were observed across the four study sites, suggests that these two commercially-important species are successfully recruiting inside and outside the no-take zones. These results indicate that physical factors, rather than protection status, within False Bay influence patterns of fish assemblage composition, abundance, and distribution. In future, and to improve comparability, assessments within the TMNP MPA should be designed to target similar locations and depth ranges within the bay. The success of no-take zones must be evaluated according to their individual design and management goals

Spatial ecology and ontogeny: incorporating fish size-classes into species distribution models

I use spatial modelling to investigate how relative abundance and body-length can be used to identify niche requirements and habitat partitioning between conspecific fishes. The models identified specific areas associated with juveniles and adults of same or multiple fish species. I investigate the performance of models using data collected from towed and baited video systems. The towed video models detected fine-scale environmental niche associations of fish, which could be missed by commonly used baited systems

The effect of bait on fine-scale habitat associations of reef fish investigated with remote underwater video systems

Establishing the associations between fish and their habitats can aid in the monitoring of fish stocks and the design of effective marine protected areas (MPAs). Baited remote underwater stereo-video systems (stereo-BRUVs) are now commonly used to asses fish populations. The habitats seen in the video footage of stereo-BRUVs can be used to link fish fauna to preferred habitat types. However, the application of bait potentially attracts fish from surrounding habitats, and might result in a biased understanding of fish–habitat associations. A field study was conducted in the Tsitsikamma National Park MPA to determine the effect of bait on fine-scale fish–habitat associations, using remote photographic and video methods. The study was conducted over the summer season of 2015 and 2016. Data were collected within a 1x1 km shallow (9–44 m) reef complex. Within the sampling area, 944 photo-quadrats of the macrobenthos were taken 30 m apart by means of a drop camera. By separating the macrobenthos into broad taxonomic groups, five habitat types were identified, namely Shallow Sand, Shallow Reef, Deep Reef, Deep Sand and Patch Reef. The results show that even on a fine scale, depth is an important predictor of macrobenthic distribution and assemblage structure. Baited (stereo-BRUVs) and unbaited (stereo-RUVs) surveys were then conducted to sample the fish community in the same area during the period under study. Higher abundances of fish were observed in reef than in sandy habitats, and bait was seen to have a positive effect on species richness and fish abundance. When comparing habitats, fish abundance and composition on reef habitats were significantly different from sand habitats. This was observed in both the stereo-RUVs and stereo-BRUVs methods. High counts of roman (Chrysoblephus laticeps), fransmadam (Boopsoidea inornata) and steentjie (Spondyliosoma emarginatum) in reef habitats were contrasted by high counts of white sea catfish (Galeichthys feliceps), evil-eye puffer (Amblyrhynchotes honckenii) and lesser guitarfish (Rhinecanthus annulatus) in sandy habitats. Overall, the underlying patterns in fish diversity recorded with the two video methods were generally comparable. However, stereo-RUVs appeared to be unable to detect species that were present in sand habitats, while stereo-BRUVs increased the number and abundance of species recorded in all habitat types. In the stereo-RUVs footage, differences between reef habitats were dampened by the presence of highly abundant fish species. In the stereo-BRUVs footage, although bait appeared to have an effect on the observed fish assemblage, this manifested in an increase in species richness, higher fish abundances and a better overall ability to detect fish–habitat relationships. As such, stereo-BRUVs are considered a robust, effective and recommended method for detecting fish–habitat relationships, even over a fine scale

Determining how risk effects predator-prey interactions of marine communities in the nearshore environment of South Bimini, The Bahamas

Predators often have strong top-down effects on ecosystems and are considered a priority for conservation and management. Predator activity can influence prey distribution, abundance, and foraging behaviors and are likely to influence habitat by impacting ecological and environmental characteristics as well as presence of competitor species. There are knowledge gaps of the functional diversity of fish assemblages, non-consumptive predator effects, and environmental effects on fish assemblages. With this study, effects of top marine predators, such as sharks and great barracuda, on diversity and abundance of prey communities were examined in putative low (north side of South Bimini = lagoon) and high-risk (south side of South Bimini = flat) areas around South Bimini, The Bahamas. Baited remote underwater video surveys (BRUVs) deployed in the nearshore habitat captured abundance and potential predator-prey interactions. Predator and prey abundances at each site were compared to determine potential risk affect within high and low risk environments. A general baseline of predator and prey species was established throughout six months of observation (January- June 2018). Results showed a difference in prey communities between high and low risk habitats. Teleost abundance was highest on the south side of South Bimini. There were no differences in flight behavior of prey from predator (sharks vs barracuda). Longitude, depth, temperature, salinity, and dissolved oxygen were significantly linked to biotic assemblages. The identification of significant factors influencing predator-prey interaction is important in understanding community composition and for future implementation of conservation and management practices pertaining to nearby mangrove and seagrass habitats

Mesophotic Animal Forests of the Ligurian Sea (NW Mediterranean Sea): biodiversity, distribution and vulnerability

Knowledge about deep-sea megabenthic communities has greatly increased during the last two decades thanks to the improvement of technical diving equipment, submersibles, remotely operated and autonomous vehicles. In the last 10 years, several studies, targeting the Mediterranean deep continental shelf or mesophotic zone (40-200 m), have reported the occurrence of rich hotspots of biodiversity, namely marine animal forests, dominated by habitat-forming species such as corals and sponges thriving in dim light conditions. This bathymetric range hosts the deepest extension of shallow-water animal forests as well as proper mesophotic assemblages thriving on the so-called roche du large ecosystems. These complex aggregations play a fundamental ecological role in the marine ecosystems (refuge effect, nursery area, benthic-pelagic coupling, biogeochemical cycles) and the characterization of their diversity and distribution is considered of primary interest worldwide. Explorations have depicted not only the diversity of these forests but also their vulnerability towards mechanical impacts inflicted by demersal fishing activities, especially in the overexploited Mediterranean basin. This leads to an urgent need to quantify the damages burdening on these sensitive ecosystems and to develop easy-to-apply tools to evaluate and monitor their environmental status, in order to provide effective conservation measures. This thesis aims to address these topics focusing on the marine animal forests of the Ligurian deep continental shelf. The Ligurian Sea represents one of the most studied Mediterranean basins due to several extensive researches, which have characterized the benthic and pelagic fauna mainly through SCUBA diving (shallow waters) and trawl surveys (bathyal waters) since the beginning of the last century. On the other hand, a large knowledge gap still exists for this region regarding the deep circalittoral megabenthic communities and, overall, on the anthropic threats insisting on deep-sea communities. Indeed, considering the significant amount of professional and recreational fishermen operating at these depths in the Ligurian region, it was crucial to carry out an extensive investigation in this area. In the present study, about 80 sites have been investigated during a four-years ROV survey conducted along the Ligurian deep continental shelf representing the most comprehensive study so far for the Italian waters. ROV footage was used to characterize the benthic biocoenoses thriving on soft and hard bottoms, determine the most relevant environmental factors driving their spatial distribution, and quantify the anthropogenic disturbance. Twelve major assemblages have been identified by means of community analysis, including gorgonian and hydrozoan forests, dense keratose sponge grounds, a Dendrophyllia cornigera facies, bryozoan beds and soft-bottom meadows of sabellids and alcyonaceans, some of them reported for the first time. Forests of black corals and Paramuricea macrospina aggregations have also been reported from the video footage, although with a more scattered distribution. The distribution of these assemblages is determined by different environmental parameters, namely depth, substrate type and inclination. The abundance of marine litter herein observed is among the highest ever recorded in Europe, with maximum values up to 7900 items ha-1. Abandoned, lost or discarded fishing gears represent the 81% of the total sightings, with the highest abundance recorded on the deep rocky shoals facing the largest fishing harbors and fleets. The majority of the fishing gears observed is attributable to artisanal and recreational fishing activities, suggesting that these represent the main source of litter in the Ligurian Sea. Urban litter, mainly represented by plastic, has also been observed, generally with higher abundances nearby large cities and river mouths. A multidisciplinary approach based on ROV explorations, background fishermen interviews and on-board bycatch monitoring has also been applied to obtain quantitative data on the impact of different fishing methods adopted within two Ligurian case studies. The study areas have been selected following a bathymetric point of view to study two different deep-sea ecosystems (a deep circalittoral coralligenous shoal exploited by a small-scale fishery and a trawling ground located nearby a cold-water coral thanatocoenoses), and the investigated parameters were designed to fulfil the criteria proposed by FAO for the identification of Vulnerable Marine Ecosystems (VMEs). A fine characterisation of the megabenthic assemblages and the fishing effort was obtained, as well as the quantification of no-target catches rates (with particular attention to structuring megabenthic invertebrates and rare species), and the frequency of gear entanglement and loss. This information allowed to initiate the process to delineate Fisheries Restricted Areas (FRAs), over these sensitive deep areas. Finally, to evaluate the environmental status of megabenthic assemblages thriving on mesophotic coralligenous or rocky reefs at temperate latitudes, a multiparametric index (MACS) integrating all possible sources of ROV-based information regarding community structure and impacts has been developed and validated. This practical tool was thought to have a large-scale application within the on-going Marine Strategy monitoring programs of these ecosystems. In conclusion, a georeferenced database of the location of diversity hotspots and sites of litter accumulation has been created, in order to set the baseline for the monitoring of Ligurian mesophotic sensitive animal forests. This dataset will provide managers and stakeholders the scientific information and the tools for the creation of an extensive network of deep-sea marine protected areas in the Ligurian basin

Untangling coastal diversity: how habitat complexity shapes demersal and benthopelagic assemblages in NW Iberia

Understanding species–habitat relationships is essential for ecosystem-based conservation. This study explores the significance of habitat characteristics and complexity for demersal and benthopelagic communities within a patchwork of coastal habitats, including rocky seabed, macroalgae formations, sandy bottoms, and a combination of rock and sand areas. Species and habitats were surveyed along the north-west (NW) Iberian continental shelf area of Viana do Castelo using baited remote underwater video stations (BRUVS). We found significant differences (p < 0.05) in species assemblages across habitats, with rocky substrates showing the highest diversity and abundance. Sand habitats showed the lowest species richness and abundance, underscoring the importance of habitat complexity to support marine life. Our study also emphasises the role of specific species in shaping the communities, identifying key species such as Trisopterus luscus, Diplodus vulgaris, and Ctenolabrus rupestris as the three most abundant in the region and significant contributors to the observed dissimilarities between habitats. By elucidating the impact of habitat complexity on marine life, our results offer essential baseline data, which serve as a kick-start point to inform sustainable management and conservation strategies for the long-term health and productivity of these vital ecological systems in the North-East Atlantic.Fundação para a Ciência e a Tecnologia | Ref. UIDB/04050/2020Fundação para a Ciência e a Tecnologia | Ref. LA/P/0069/2020Fundação para a Ciência e a Tecnologia | Ref. PD/BD/143088/2018Fundação para a Ciência e a Tecnologia | Ref. COVID/BD/153031/2022Fundação para a Ciência e a Tecnologia | Ref. PD/BD/150365/201