scholarly journals Scoping the Line Up: A Comparison of Biomonitoring Methodologies for Surf Zone Fish Communities

2021 ◽  
Author(s):  
Zachary Gold ◽  
McKenzie Q. Koch ◽  
Nicholas K. Schooler ◽  
Kyle A. Emery ◽  
Jennifer E. Dugan ◽  
...  
Keyword(s):  
Surf Zone ◽  
Fish Communities ◽  
Environmental Dna ◽  
Cost Effective ◽  
Abundant Species ◽  
Sandy Beaches ◽  
Marine Biodiversity ◽  
Additional Species ◽  
Multiple Challenges ◽  
Elasmobranch Fishes

Surf zones are highly dynamic marine ecosystems that are subject to increasing anthropogenic and climatic pressures, posing multiple challenges for biomonitoring. Traditional methods such as seines and hook and line surveys are often labor intensive, taxonomically biased, and can be physically hazardous. Emerging techniques, such as baited remote underwater video (BRUV) and environmental DNA (eDNA) are promising nondestructive tools for assessing marine biodiversity in surf zones of sandy beaches. Here we compare the relative performance of beach seines, BRUV, and eDNA in characterizing community composition of bony (teleost) and cartilaginous (elasmobranch) fishes of surf zones at 18 open coast sandy beaches in southern California. Seine and BRUV surveys captured overlapping, but distinct fish communities with 50% (18/36) of detected species shared. BRUV surveys more frequently detected larger species (e.g. sharks and rays) while seines more frequently detected one of the most abundant species, barred surfperch ( Amphistichus argenteus ). In contrast, eDNA metabarcoding captured 83.3% (30/36) of all fishes observed in seine and BRUV surveys plus 59 additional species, including 13 that frequent surf zone habitats. eDNA approaches showed significantly higher sensitivity than seine and BRUV methods and more consistently detected 29 of the 30 (96.7%) jointly observed species across beaches. The six species detected by BRUV/seines, but not eDNA either lacked reference sequences, were only resolved at higher taxonomic ranks (e.g. Embiotocidae surfperches), or were detected below occupancy thresholds. Low site-species overlap between methods limited comparisons of richness and abundance estimates, highlighting the challenge of comparing biomonitoring approaches. Despite potential for improvement, results overall demonstrate that eDNA can provide a cost-effective tool for long-term surf zone monitoring that complements data from seine and BRUV surveys, allowing more comprehensive surveys of vertebrate diversity in surf zone habitats.

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 Cross-shore Mysidacea (Crustacea) distribution in two sandy beaches with contrasting morphodynamics

2007 ◽  
Vol 24 (4) ◽  
pp. 943-949 ◽  
Author(s):  
Carlos A. Borzone ◽  
Luciano Lorenzi ◽  
Patrícia Calil
Keyword(s):  
Competitive Exclusion ◽  
Surf Zone ◽  
Abundant Species ◽  
Sandy Beaches ◽  
Nearshore Zone ◽  
Present Contribution ◽  
Nearshore Circulation ◽  
Abundance And Distribution ◽  
Spatial Resources ◽  
Beach Environment

The order Mysidacea comprises small and very common crustaceans that inhabit most coastal ecosystem. The present contribution describes the composition, abundance and distribution of mysids in two sandy beaches representing the extreme conditions of the morphodynamics spectrum. Six species of mysids were found at the studied beaches. Metamysidopsis neritica Bond-Buckup & Tavares, 1992 was the most abundant species with more than 97% of the total individuals collected at the two beaches. At the dissipative beach was dominant in the swash and surf zone, with the greater abundance in the inner surf zone. At the reflective beach, this species was extremely abundant in the surf zone and backward the breaker. Bowmaniella brasiliensis Bacescu, 1968 occurred in low density at the surf zone of the dissipative beach, with the greater abundance in the outer surf zone, and it was practically absent in the nearshore zone. We suggest that mysids zonation in sandy beaches may be first developed as a response to food availability patterns imposed by the nearshore circulation systems, and in the second place as a result of competitive exclusion. The suggestion of partitioning of food and spatial resources shown by the mysid species is surprising in view of the apparent physical harshness and low spatial heterogeneity that seem to characterise the beach environment.

scholarly journals Environmental DNA metabarcoding as an effective and rapid tool for fish monitoring in canals:

2018 ◽  
Author(s):  
Allan D McDevitt ◽  
Naiara Guimaraes Sales ◽  
Samuel S Browett ◽  
Abbie Sparnenn ◽  
Stefano Mariani ◽  
...  
Keyword(s):  
Fish Assemblages ◽  
Fish Communities ◽  
Environmental Dna ◽  
Cost Effective ◽  
Aquatic Habitats ◽  
Dna Metabarcoding ◽  
Canal Systems ◽  
Rapid Tool ◽  
Fish Monitoring

Environmental DNA (eDNA) metabarcoding has revolutionized biomonitoring of aquatic habitats. Man-made canal systems are among the least-studied environments in terms of biodiversity in Britain. Here we focus on a case study along an English canal comparing eDNA metabarcoding with two types of electrofishing techniques (wade-and-reach and boom-boat). In addition to corroborating data obtained by electrofishing, eDNA provided a wider snapshot of fish assemblages. Given the semi-lotic nature of canals, we encourage the use of eDNA as a fast and cost-effective tool to detect and monitor whole fish communities.

scholarly journals The effect of silica desiccation under different storage conditions on filter-immobilized environmental DNA

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Michael J. Allison ◽  
Jessica M. Round ◽  
Lauren C. Bergman ◽  
Ali Mirabzadeh ◽  
Heather Allen ◽  
...  
Keyword(s):  
Silica Gel ◽  
Storage Temperature ◽  
Environmental Dna ◽  
Cost Effective ◽  
Storage Conditions ◽  
Systematic Evaluation ◽  
Silica Bead ◽  
Gel Beads ◽  
Polymerase Chain

Abstract Objective Silica gel beads have promise as a non-toxic, cost-effective, portable method for storing environmental DNA (eDNA) immobilized on filter membranes. Consequently, many ecological surveys are turning to silica bead filter desiccation rather than ethanol preservation. However, no systematic evaluation of silica bead storage conditions or duration past 1 week has been published. The present study evaluates the quality of filter-immobilized eDNA desiccated with silica gel under different storage conditions for over a year using targeted quantitative real-time polymerase chain reaction (qPCR)-based assays. Results While the detection of relatively abundant eDNA target was stable over 15 months from either ethanol- or silica gel-preserved filters at − 20 and 4 °C, silica gel out-performed ethanol preservation at 23 °C by preventing a progressive decrease in eDNA sample quality. Silica gel filter desiccation preserved low abundance eDNA equally well up to 1 month regardless of storage temperature (18, 4, or − 20 °C). However only storage at − 20 °C prevented a noticeable decrease in detectability at 5 and 12 months. The results indicate that brief storage of eDNA filters with silica gel beads up to 1 month can be successfully accomplished at a range of temperatures. However, longer-term storage should be at − 20 °C to maximize sample integrity.

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

2021 ◽  
Author(s):  
Tania Valdivia‐Carrillo ◽  
Axayácatl Rocha‐Olivares ◽  
Héctor Reyes‐Bonilla ◽  
José Francisco Domínguez‐Contreras ◽  
Adrian Munguia‐Vega
Keyword(s):  
Fish Communities ◽  
Biodiversity Hotspot ◽  
Marine Biodiversity

scholarly journals Environmental DNA metabarcoding uncovers environmental correlates of fish communities in spatially heterogeneous freshwater habitats

2021 ◽  
Vol 126 ◽  
pp. 107698
Author(s):  
Petr Blabolil ◽  
Lynsey R. Harper ◽  
Štěpánka Říčanová ◽  
Graham Sellers ◽  
Cristina Di Muri ◽  
...  
Keyword(s):  
Fish Communities ◽  
Environmental Dna ◽  
Environmental Correlates ◽  
Dna Metabarcoding ◽  
Freshwater Habitats

Temporal and spatial variability in the community structure of the fauna of four sandy beaches in south-eastern New South Wales.

1984 ◽  
Vol 35 (6) ◽  
pp. 663 ◽  
Author(s):  
DM Dexter
Keyword(s):  
Community Structure ◽  
Diversity Index ◽  
Abundant Species ◽  
Sandy Beaches ◽  
Sampling Procedure ◽  
Wave Action ◽  
Physical Factors ◽  
Faunal Composition ◽  
South Wales ◽  
Temporal And Spatial

Four intertidal sandy beaches with different exposures, La Perouse, Ocean Beach, Dolls Point, and Towra Point, were studied for temporal and spatial changes in faunal composition and community structure. Each of these beaches was sampled from 6 to 12 times between July 1980 and July 1981 using a 500 �m sieve. A stratified random sampling procedure across the intertidal zone isolated 40 660 individuals representing 85 species. Distribution and abundance of species were strongly influenced by tidal level. Densities changed during the year but no seasonal changes in intertidal zonation patterns were found. Changes in density were correlated with the reproductive activities of the abundant species, especially Pseudolana concinna and Exoediceros maculosus at La Perouse, and Spio pacifica at Dolls Point and Towra Point. The number of species increased from high to low tide, and also increased with decreasing exposure to wave action. Crustaceans dominated the fauna in the most exposed site and decreased in abundance with increasing protection. Ocean Beach experienced the least fluctuation in physical factors such as wave action, salinity, and temperature, and its fauna exhibited the highest diversity index (H') and evenness (J'), the most stable density, and the greatest stability in faunal composition through time. The highest densities and the most species were found at Towra Point, which also was the most protected site.

scholarly journals Emergence and Migration of a Nearshore Bar: Sediment Flux and Morphological Change on a Multi-Barred Beach in the Great Lakes

2007 ◽  
Vol 60 (1) ◽  
pp. 31-47 ◽  
Author(s):  
Brian Greenwood ◽  
Allana Permanand-Schwartz ◽  
Christopher A. Houser
Keyword(s):  
Great Lakes ◽  
Suspended Sediment ◽  
Surf Zone ◽  
Sandy Beaches ◽  
Sediment Flux ◽  
Accommodation Space ◽  
Longshore Transport ◽  
Sediment Balance ◽  
And Migration ◽  
Equilibrium Morphology

Abstract Burley Beach (southeastern Lake Huron) exhibits a multi-barred shoreface, the long-term equilibrium morphology characteristic of many low angle, sandy beaches in the Canadian Great Lakes. During a single major storm, a new bar emerged 50-60 m offshore as an irregular trough-crest form, through differential erosion of an existing shore terrace. Emergence, bar growth and offshore migration were associated with: (a) an overall negative sediment balance in the inner surf zone initially (‑2.30 m3>/m beach width), but with a large positive sediment balance (+5.10 m3/m) subsequent to the storm peak and during the storm decay; (b) progradation of the beach step to produce a new shore terrace; and (c) offshore migration of the two outer bars to provide the accommodation space necessary for the new bar. The primary transport mechanisms accounting for emergence of the new bar, its growth and migration were: (a) the mean cross-shore currents (undertow), which always transported suspended sediment offshore; and (b) the onshore transport of suspended sediment by incident gravity wave frequencies early in the storm and subsequently by infragravity waves (at the storm peak and the decay period). The longshore transport of sediment was significant in terms of the gross transport, although the net result was only a small transport to the south-west (historic littoral transport direction). It did not cause bar initiation, but it may have supplied some of the sediment for bar growth. The primary mechanism for bar initiation and growth was the cross-shore displacement of sediment by wave-driven (oscillatory) transport and cross-shore mean currents (undertow).

scholarly journals Towards environmental DNA-based bioassessment of freshwater reservoirs with small volumes of water: robust molecular protocols

2021 ◽  
Author(s):  
Rebecca Ker Loh ◽  
Sujatha Narayanan Kutty ◽  
Darren Chong Jinn Yeo ◽  
Rudolf Meier
Keyword(s):  
Water Sample ◽  
Environmental Dna ◽  
Cost Effective ◽  
Sampling Time ◽  
Small Water ◽  
Tropical Reservoirs ◽  
Frequent Monitoring ◽  
Planktonic Crustaceans ◽  
Water Volumes ◽  
Dna Template

Bioassessment of freshwater quality via eDNA is rapidly developing into a powerful alternative to traditional methods involving collecting, sorting, and identifying macroinvertebrates based on morphology. Particularly attractive would be methods that can use remote-controlled boats for sampling because it would allow for cost-effective, and frequent monitoring at multiple sites. The latter will be particularly important for tropical reservoirs that require year-around surveillance. We here optimize molecular protocols for capturing reservoir-specific differences in metazoan communities based on small water volumes (15 mL). The optimization is based on samples from two freshwater reservoirs with very different water qualities ("reservoir signal"). Each reservoir was sampled at three sites ("biological replicates"). For each water sample, the DNA was extracted twice ("technical replicates"). We then tested how much DNA template (0.1 ng to 15 ng) and how many PCR cycles (25 or 35) minimized variance between technical replicates. We find that 15 mL is sufficient for capturing the reservoir signal regardless of sampling time, template amounts, or PCR cycle numbers. Indeed, extrapolation from our results suggests that <1 mL would be sufficient because only 17 of 59 metazoan mOTUs (mainly planktonic crustaceans and rotifers) detected with a 313bp COI minibarcode were shared. We find that the use of 35 PCR cycles significantly lowered the number of detected species and that template amounts <0.5 ng yielded somewhat higher variance between technical replicates. Despite extensive trials, the variance between technical replicates remained high (Bray-Curtis: 5-20%; Jaccard: 10-40%) and we predict that it will be difficult to reduce this variance further. However, the overall reservoir differences are so strong that all biological and technical replicates can be correctly assigned.

Sign in / Sign up

Export Citation Format

Share Document