scholarly journals Beyond traditional biodiversity fish monitoring: environmental DNA metabarcoding and simultaneous underwater visual census detect different sets of a complex fish community at a marine biodiversity hotspot

2019 ◽  
Author(s):  
Tania Valdivia-Carrillo ◽  
Axayácatl Rocha-Olivares ◽  
Héctor Reyes-Bonilla ◽  
José Francisco Domínguez-Contreras ◽  
Adrian Munguia-Vega
Keyword(s):  
Gulf Of California ◽  
High Throughput Sequencing ◽  
Environmental Dna ◽  
Marine Ecology ◽  
Marine Biodiversity ◽  
Rocky Reef ◽  
Monitoring Methods ◽  
Visual Census ◽  
Traditional Methods ◽  
Underwater Visual Census

ABSTRACTSignificant advances in the study of marine fish communities have been achieved with traditional monitoring methods and recently with novel genetic approaches. eDNA metabarcoding is one of them and a powerful tool for the study of biodiversity still in continuous development. Its applicability in marine ecology and conservation studies may be gauged by comparing its results with those of traditional methods. In the present investigation, we compare results from the underwater visual census (UVC) with eDNA metabarcoding (eDNA) carried out simultaneously in 24 rocky reef sites along the Gulf of California. We developed a two-PCR library preparation protocol followed by high throughput sequencing aimed at teleost fish. Our results show that both methods had different detection capabilities, and each registered different sets of fish taxa from rocky reefs, with some overlap. In particular, eDNA identified taxa from pelagic, demersal, and estuarine habitats beyond the rocky reef itself, suggesting differences in detection mainly attributed to the transport and permanence time of the eDNA in the ocean. Overlap in the detection with both methods increased with taxonomic level. We argue that substantial gaps in sequence reference databases for teleost are at the root of major discrepancies. Our results also confirm that PCR-based eDNA metabarcoding of seawater samples does not reflect patterns in abundance and biomass of species estimated from traditional methods. We discuss how to reconcile the results of eDNA metabarcoding and traditional methods in marine hotspots.

scholarly journals eDNA Captures Microhabitat Partitioning in a Kelp Forest Ecosystem

2021 ◽  
Author(s):  
Keira Monuki ◽  
Paul Barber ◽  
Zachary Gold
Keyword(s):  
Southern California ◽  
Surf Zone ◽  
Habitat Preferences ◽  
Kelp Forest ◽  
Environmental Dna ◽  
Marine Biodiversity ◽  
Rocky Reef ◽  
Temporal And Spatial Variability ◽  
Community Assemblages ◽  
Zone Sampling

Environmental DNA (eDNA) metabarcoding is an increasingly important tool for surveying biodiversity in marine ecosystems. However, the scale of temporal and spatial variability in eDNA signatures, and how this variation may impact eDNA-based marine biodiversity assessments, remains uncertain. To address this question, we systematically examined variation in vertebrate eDNA signatures across depth (0 m to 10 m) and horizontal space (nearshore and surf zone) over three successive days in a Southern California kelp forest. Across a broad range of marine vertebrates (teleosts, elasmobranchs, birds, and mammals), results showed significant variation in species richness and community assemblages across 4-5 m depth, reflecting microhabitat depth preferences of common Southern California nearshore rocky reef taxa. We also found significant differences in community assemblages between nearshore and surf zone sampling stations at the same depth, and across three sampling days. Patterns of microhabitat partitioning in eDNA signatures across space and time were largely consistent with known habitat preferences and species behavior. Results highlight the sensitivity of eDNA in capturing fine-scale vertical, horizontal, and temporal variation in marine vertebrate communities, demonstrating the ability of eDNA to capture a highly localized snapshot of marine biodiversity in dynamic coastal environments.

scholarly journals Novel Universal Primers for Metabarcoding eDNA Surveys of Marine Mammals and Other Marine Vertebrates

2019 ◽  
Author(s):  
Elena Valsecchi ◽  
Jonas Bylemans ◽  
Simon J. Goodman ◽  
Roberto Lombardi ◽  
Ian Carr ◽  
...  
Keyword(s):  
Marine Mammals ◽  
High Throughput Sequencing ◽  
Environmental Dna ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Taxonomic Resolution ◽  
Universal Primers ◽  
Marine Biodiversity ◽  
Primer Sets ◽  
Marine Megafauna

ABSTRACTMetabarcoding studies using environmental DNA (eDNA) and high throughput sequencing (HTS) are rapidly becoming an important tool for assessing and monitoring marine biodiversity, detecting invasive species, and supporting basic ecological research. Several barcode loci targeting teleost fish and elasmobranchs have previously been developed, but to date primer sets focusing on other marine megafauna, such as marine mammals have received less attention. Similarly, there have been few attempts to identify potentially ‘universal’ barcode loci which may be informative across multiple marine vertebrate Orders. Here we describe the design and validation of four new sets of primers targeting hypervariable regions of the vertebrate mitochondrial 12S and 16S rRNA genes, which have conserved priming sites across virtually all cetaceans, pinnipeds, elasmobranchs, boney fish, sea turtles and birds, and amplify fragments with consistently high levels of taxonomically diagnostic sequence variation. ‘In silico’ validation using the OBITOOLS software showed our new barcode loci outperformed most existing vertebrate barcode loci for taxon detection and resolution. We also evaluated sequence diversity and taxonomic resolution of the new barcode loci in 680 complete marine mammal mitochondrial genomes demonstrating that they are effective at resolving amplicons for most taxa to the species level. Finally, we evaluated the performance of the primer sets with eDNA samples from aquarium communities with known species composition. These new primers will potentially allow surveys of complete marine vertebrate communities in single HTS metabarcoding assessments, simplifying workflows, reducing costs, and increasing accessibility to a wider range of investigators.

scholarly journals Seasonal changes in fish assemblage structure at a shallow seamount in the Gulf of California

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2357 ◽  
Author(s):  
Salvador J. Jorgensen ◽  
A. Peter Klimley ◽  
Arturo Muhlia-Melo ◽  
Steven G. Morgan
Keyword(s):  
Species Richness ◽  
Gulf Of California ◽  
Individual Species ◽  
Fish Assemblage Structure ◽  
Visual Census ◽  
Underwater Visual Census ◽  
Thermal Habitat ◽  
Definition Of ◽  
Surrounding Areas ◽  
Response To Temperature

Seamounts have generally been identified as locations that can promote elevated productivity, biomass and predator biodiversity. These properties attract seamount-associated fisheries where elevated harvests can be obtained relative to surrounding areas. There exists large variation in the geological and oceanographic environment among the thousands of locations that fall within the broad definition of seamount. Global seamount surveys have revealed that not all seamounts are hotspots of biodiversity, and there remains a strong need to understand the mechanisms that underlie variation in species richness observed. We examined the process of fish species assembly at El Bajo Espiritu Santo (EBES) seamount in the Gulf of California over a five-year study period. To effectively quantify the relative abundance of fast-moving and schooling fishes in a ‘blue water’ habitat, we developed a simplified underwater visual census (UVC) methodology and analysis framework suitable for this setting and applicable to future studies in similar environments. We found correlations between seasonally changing community structure and variability in oceanographic conditions. Individual species responses to thermal habitat at EBES revealed three distinct assemblages, a ‘fall assemblage’ tracking warmer overall temperature, a ‘spring assemblage’ correlated with cooler temperature, and a ‘year-round assemblage’ with no significant response to temperature. Species richness was greatest in spring, when cool and warm water masses stratified the water column and a greater number of species from all three assemblages co-occurred. We discuss our findings in the context of potential mechanisms that could account for predator biodiversity at shallow seamounts.

scholarly journals Scanning ferry routes: looking for eDNA traces of marine mammals and their preys

2021 ◽  
Vol 4 ◽  
Author(s):  
Elena Valsecchi
Keyword(s):  
Marine Mammals ◽  
High Throughput Sequencing ◽  
Simultaneous Detection ◽  
Environmental Dna ◽  
Trophic Levels ◽  
Systematic Sampling ◽  
Marine Biodiversity ◽  
Tyrrhenian Sea ◽  
Night Time ◽  
Species Specific

Marine environmental DNA (eDNA) surveys are becoming a promising approach to monitor biodiversity status and its variation over time. However, monitoring offshore areas could be extremely costly when using dedicated vessels, beside the impossibility to sample simultaneously geographically distant (even if adjacent) areas. The unexplored possibility of availing on operating ferries as an opportunistic platform for eDNA sampling offers several advantages besides opening limitless opportunities for systematic surveys on marine biodiversity.We present the results of both metabarcoding and barcoding approaches obtained from the analysis of water samples collected on board of a ferry boat along a pilot Mediterranean route crossing the Pelagos Sanctuary for Mediterranean Marine Mammals. The recently described MarVer primer sets (12SrDNA and 16SrDNA regions), specifically designed for the simultaneous detection of marine mammals and other marine vertebrates, were employed. The High Throughput Sequencing (HTS) outcome showed that the markers successfully detected most trophic levels of vertebrate marine communities, and classes, including bony fish, rays, cetaceans and birds. Ferry-based sampling allow to collect sample at any time of the day, and we indeed found diel differences in both quantitative and qualitative distribution of read counts. For instances, we observed an increased abundance of lantern fish amplicons in night-time collect samples (50%), reflecting nocturnal migration through the water column. In general, the number of read counts was significantly higher in nocturnal samples. Such diel differences within our sample indirectly provides evidence of the efficiency of the eDNA approach to detect contemporary signals in the sampled environment. Similarly, cetaceans were detected in correspondence of visual sightings (when these occurred, supplementary samples were collected). Rare species, such as the monk seal, are difficult to be detected in metabarcoding surveys, thus we opted to side the screening of the ferry-samples with a panel of species-specific qPCR assays, which were able to detect DNA traces of the endangered pinniped in the Tuscany archipelago (Tyrrhenian Sea) long before visual observations witnessed its presence in the same area. The study demonstrates the feasibility of using commercial shipping as a platform for eDNA marine sampling without dedicated survey cruises. Commercial shipping routes have potential to act as regular systematic sampling transects which can contribute to evaluating and monitoring marine biodiversity.

scholarly journals Seasonal changes in fish assemblage structure at a shallow seamount in the Gulf of California

2016 ◽  
Author(s):  
Salvador J Jorgensen ◽  
A. Peter Klimley ◽  
Arturo Muhlia-Melo ◽  
Steven G Morgan
Keyword(s):  
Species Richness ◽  
Gulf Of California ◽  
Individual Species ◽  
Fish Assemblage Structure ◽  
Visual Census ◽  
Underwater Visual Census ◽  
Thermal Habitat ◽  
Definition Of ◽  
Surrounding Areas ◽  
Response To Temperature

Seamounts have generally been identified as locations that can promote elevated productivity, biomass and predator biodiversity. These properties attract seamount-associated fisheries where elevated harvests can be obtained relative to surrounding areas. There exists large variation in the geological and oceanographic environment among the thousands of locations that fall within the broad definition of seamount. Global seamount surveys have revealed that not all seamounts are hotspots of biodiversity, and there remains a strong need to understand the mechanisms that underlie variation in species richness observed. We examined the process of fish species assembly at El Bajo Espiritu Santo (EBES) seamount in the Gulf of California over a five-year study period. To effectively quantify the relative abundance of fast-moving and schooling fishes in a ‘blue water’ habitat, we developed a simplified underwater visual census (UVC) methodology and analysis framework suitable for this setting and applicable to future studies in similar environments. We found correlations between seasonally changing community structure and variability in oceanographic conditions. Individual species responses to thermal habitat at EBES revealed three distinct assemblages, a ‘summer assemblage’ tracking warmer overall temperature, a ‘winter assemblage’ correlated with cooler temperature, and a ‘year-round assemblage’ with no significant response to temperature. Species richness was greatest in spring, when cool and warm water masses stratified the water column and a greater number of species from all three assemblages co-occurred. We discuss our findings in the context of potential mechanisms that could account for predator biodiversity at shallow seamounts.

scholarly journals Comparing environmental DNA metabarcoding and underwater visual census to monitor tropical reef fishes

2020 ◽  
Author(s):  
Andrea Polanco Fernández ◽  
Virginie Marques ◽  
Fabian Fopp ◽  
Jean‐Baptiste Juhel ◽  
Giomar Helena Borrero‐Pérez ◽  
...  
Keyword(s):  
Environmental Dna ◽  
Reef Fishes ◽  
Visual Census ◽  
Underwater Visual Census ◽  
Dna Metabarcoding ◽  
Tropical Reef

scholarly journals Seasonal changes in fish assemblage structure at a shallow seamount in the Gulf of California

2016 ◽  
Author(s):  
Salvador J Jorgensen ◽  
A. Peter Klimley ◽  
Arturo Muhlia-Melo ◽  
Steven G Morgan
Keyword(s):  
Species Richness ◽  
Gulf Of California ◽  
Individual Species ◽  
Fish Assemblage Structure ◽  
Visual Census ◽  
Underwater Visual Census ◽  
Thermal Habitat ◽  
Definition Of ◽  
Surrounding Areas ◽  
Response To Temperature

Seamounts have generally been identified as locations that can promote elevated productivity, biomass and predator biodiversity. These properties attract seamount-associated fisheries where elevated harvests can be obtained relative to surrounding areas. There exists large variation in the geological and oceanographic environment among the thousands of locations that fall within the broad definition of seamount. Global seamount surveys have revealed that not all seamounts are hotspots of biodiversity, and there remains a strong need to understand the mechanisms that underlie variation in species richness observed. We examined the process of fish species assembly at El Bajo Espiritu Santo (EBES) seamount in the Gulf of California over a five-year study period. To effectively quantify the relative abundance of fast-moving and schooling fishes in a ‘blue water’ habitat, we developed a simplified underwater visual census (UVC) methodology and analysis framework suitable for this setting and applicable to future studies in similar environments. We found correlations between seasonally changing community structure and variability in oceanographic conditions. Individual species responses to thermal habitat at EBES revealed three distinct assemblages, a ‘summer assemblage’ tracking warmer overall temperature, a ‘winter assemblage’ correlated with cooler temperature, and a ‘year-round assemblage’ with no significant response to temperature. Species richness was greatest in spring, when cool and warm water masses stratified the water column and a greater number of species from all three assemblages co-occurred. We discuss our findings in the context of potential mechanisms that could account for predator biodiversity at shallow seamounts.

Evaluation and optimisation of underwater visual census monitoring for quantifying change in rocky-reef fish abundance

2015 ◽  
Vol 186 ◽  
pp. 326-336 ◽  
Author(s):  
Timothy Jones ◽  
Robert J. Davidson ◽  
Jonathan P.A. Gardner ◽  
James J. Bell
Keyword(s):  
Reef Fish ◽  
Fish Abundance ◽  
Rocky Reef ◽  
Visual Census ◽  
Underwater Visual Census ◽  
Rocky Reef Fish

scholarly journals New Distributional Record of Twelve Scleractinian Corals From Saint Martin’s Island, Bangladesh

2021 ◽  
Vol 49 (1) ◽  
pp. 3-18
Author(s):  
Kazi Ahsan Habib ◽  
Md Jayedul Islam
Keyword(s):  
Scleractinian Coral ◽  
Coral Species ◽  
New Records ◽  
Scleractinian Corals ◽  
Marine Biodiversity ◽  
Biodiversity Monitoring ◽  
Visual Census ◽  
Underwater Visual Census ◽  
Coral Communities ◽  
First Time

Saint Martin's Island is the only island in Bangladesh where coral communities are found. An expedition on marine biodiversity monitoring of Saint Martin’s Island through underwater visual census method was carried out from December 2017 to March 2018. In this study, a total of 25 scleractinian coral species of 8 families and 14 genera were identified, of which 12 species, Dipsastraea lizardensis, Dipsastraea maritima, Dipsastraea veroni, Favites acuticollis, Favites melicerum, Favites pentagona, Goniastrea stelligera, Goniopora albiconus, Goniopora norfolkensis, Pavona clavus, Plesiastrea versipora, and Psammocora exesa were recorded for the first time in Bangladeshi marine water. These new records exemplify gaps in sampling and recording of coral species in Bangladesh, and suggest the need of extensive research on coral ecosystem in the country. Assessment of different valid reports and publications including the present study revealed that a total of 98 species of hard corals of 18 families and 37 genera have been reported until now in Saint Martin’s Island as well as Bangladesh. Bangladesh J. Zool. 49(1): 03-18, 2021

scholarly journals Underwater Visual Census of Deeper Vertical Rocky Reefs

2020 ◽  
Vol 20 (11) ◽  
pp. 785-794
Author(s):  
Alen Soldo ◽  
Igor Glavičić
Keyword(s):  
Fish Assemblages ◽  
Scuba Diving ◽  
Marine Biodiversity ◽  
Biodiversity Hotspots ◽  
Visual Census ◽  
Underwater Visual Census ◽  
Video Cameras ◽  
Rocky Reefs ◽  
Temperate Fish ◽  
Vertical Transect

Diver-based underwater visual census (UVC), particularly transect-based survey, is a widely used method for the study of tropical and temperate fish assemblages. However, due to logistical constraints associated with conventional SCUBA diving, deeper habitats, such as vertical rocky reefs, are rarely studied and poorly known. This paper describes the Deep Vertical Transect (DVT) method as a safe and effective method for assessing fish in waters up to 50 m of depth. It is based on sampling of vertical transects browsing within it (S-type transect) by divers using Full HD video cameras. The diving profile includes the use of deep decompression stops and Nitrox 50 as a decompression gas. Hence, the study yields information on fish assemblages associated with deeper vertical coralligenous reefs. The results of 51 recorded species, yielded 41 considered as reef-associated and 10 as occasional. This suggests that underwater steep coralligenous reefs are marine biodiversity hotspots. They may be considered to represent a distinctive marine subecosystem, possessing its own food chain, with the depth, in relation to temperature, as the most important factor responsible for the diversity of fish assemblages within this habitat.

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