Space-time dynamics in monitoring neotropical fish communities using eDNA metabarcoding

ABSTRACTThe biodiverse Neotropical ecoregion remains insufficiently assessed, poorly managed, and threatened by unregulated human activities. Novel, rapid and cost-effective DNA-based approaches are valuable to improve understanding of the biological communities and for biomonitoring in remote areas. Here, we evaluate the potential of environmental DNA (eDNA) metabarcoding for assessing the structure and distribution of fish communities by analysing sediments and water from 11 locations along the Jequitinhonha River catchment (Brazil). Each site was sampled twice, before and after a major rain event in a five-week period and fish diversity was estimated using high-through-put sequencing of 12S rRNA amplicons. In total, 252 Molecular Operational Taxonomic Units (MOTUs) and 34 fish species were recovered, including endemic, introduced, and previously unrecorded species for this basin. Spatio-temporal variation of fish assemblages was detected, richness during the first campaign was nearly twice as high as in the second sampling round; though peaks of diversity were primarily associated with only four locations. No correlation between β-diversity and longitudinal distance or presence of dams was detected, but low species richness observed at sites located near dams indicates that these anthropogenic barriers might have an impact on local fish diversity. Unexpectedly high α-diversity levels recorded at the river mouth suggest that these sections should be further evaluated as putative “eDNA reservoirs” for rapid monitoring. By uncovering spatio-temporal changes, unrecorded biodiversity components, and putative anthropogenic impacts on fish assemblages, we further strengthen the potential of eDNA metabarcoding as a biomonitoring tool, especially in regions often neglected or difficult to access.

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Free-diving underwater fish photography contests: a complementary tool for assessing littoral fish communities

Scientia Marina ◽

10.3989/scimar.04781.14a ◽

2018 ◽

Vol 82 (2) ◽

pp. 95 ◽

Cited By ~ 2

Author(s):

Ana Gordoa ◽

Jordi Boada ◽

Antoni García-Rubies ◽

Oscar Sagué

Keyword(s):

Species Richness ◽

Protected Area ◽

Fish Assemblages ◽

Marine Protected Area ◽

Fish Communities ◽

Cost Effective ◽

Fish Diversity ◽

Littoral Fish ◽

Potential Tool ◽

Image Frequency

Characterizing fish communities must be a priority to safeguard resources and determine critical changes. Here, species richness and the spatial and temporal evolution in the structure of fish assemblages were analysed based on photos taken in underwater free-diving contests. A total of 29 contests held from 2008 to 2015 at four different locations along the northeastern Spanish coast, including a marine protected area were analysed. Contests reward the number of species per participant and photographic quality. Species image frequency from each tournament were standardized to catch image rate. A total of 88 taxa were recorded, including 32 cryptobenthic species, the highest number recorded in the Mediterranean littoral system so far. Cluster analyses yielded four major groups. Catch image rates in the marine protected area were significantly higher for seven species of high commercial interest and for two big labrids of recreational interest, including an endangered species (Labrus viridis). Overall, the study showed that photographic free-diving contest data are a potential tool for determining species richness in littoral systems since contest rules promote competition between participants to obtain maximum fish diversity. We believe that this type of cost-effective data can be applied worldwide as a complementary way of monitoring littoral fish assemblage.

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Mesophotic fish communities of the ancient coastline in Western Australia

PLoS ONE ◽

10.1371/journal.pone.0250427 ◽

2021 ◽

Vol 16 (4) ◽

pp. e0250427

Author(s):

Leanne M. Currey-Randall ◽

Ronen Galaiduk ◽

Marcus Stowar ◽

Brigit I. Vaughan ◽

Karen J. Miller

Keyword(s):

Species Richness ◽

Western Australia ◽

Fish Assemblages ◽

Spatial Scales ◽

Habitat Type ◽

Fish Communities ◽

Fish Diversity ◽

North West ◽

Fish Biodiversity ◽

Marine Diversity

Marine diversity across the Australian continental shelf is shaped by characteristic benthic habitats which are determined by geomorphic features such as paleoshorelines. In north-western Australia there has been little attention on the fish communities that inhabit an ancient coastline at ~125 m depth (the designated AC125), which is specified as a key ecological feature (KEF) of the region and is thought to comprise hard substrate and support enhanced diversity. We investigated drivers of fish species richness and assemblage composition spanning six degrees of latitude along sections of the ancient coastline, categorised as ‘on’ and ‘off’ the AC125 based on depth, across a range of habitats and seafloor complexity (~60–180 m depth). While some surveyed sections of the AC125 had hard bottom substrate and supported enhanced fish diversity, including over half of the total species observed, species richness and abundance overall were not greater on the AC125 than immediately adjacent to the AC125. Instead, depth, seafloor complexity and habitat type explained patterns in richness and abundance, and structured fish assemblages at both local and broad spatial scales. Fewer fishes were associated with deep sites characterized by negligible complexity and soft-bottom habitats, in contrast to shallower depths that featured benthic biota and pockets of complex substrate. Drivers of abundance of common species were species-specific and primarily related to sampling Areas, depth and substrate. Fishes of the ancient coastline and adjacent habitats are representative of mesophotic fish communities of the region, included species important to fisheries and conservation, and several species were observed deeper than their currently known distribution. This study provides the first assessment of fish biodiversity associated with an ancient coastline feature, improving our understanding of the function it plays in regional spatial patterns in abundance of mesophotic fishes. Management decisions that incorporate the broader variety of depths and habitats surrounding the designated AC125 could enhance the ecological role of this KEF, contributing to effective conservation of fish biodiversity on Australia’s north west shelf.

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Habitat characteristics and environmental parameters influencing fish assemblages of karstic pools in southern Mexico

Neotropical Ichthyology ◽

10.1590/s1679-62252013000400014 ◽

2013 ◽

Vol 11 (4) ◽

pp. 859-870 ◽

Cited By ~ 9

Author(s):

María Eugenia Vega-Cendejas ◽

Mirella Hernandez de Santillana ◽

Steven Norris

Keyword(s):

Fish Assemblages ◽

Anthropogenic Impacts ◽

Conservation Status ◽

Monitoring Program ◽

Biosphere Reserve ◽

Fish Diversity ◽

Fish Assemblage Structure ◽

Southern Mexico ◽

Calakmul Biosphere Reserve ◽

Poecilia Mexicana

Fish assemblage structure was evaluated and compared among 36 karstic pools located within protected areas of the Calakmul Biosphere Reserve (southern Mexico) and unprotected adjacent areas beyond the Reserve. Nonmetric multidimensional scaling (MDS), indicator species analysis (ISA), and canonical correspondence analysis (CCA) were used to identify which environmental factors reflected local influences and to evaluate the correlation of these variables with fish assemblages structure. Thirty-one species were encountered in these karstic pools, some for the first time within the Reserve. These aquatic environments were separated into three groups based on physico-chemical characteristics. Although CCA identified significant associations between several fish species (based on their relative abundance) and environmental variables (K, NH4, NO3, and conductivity), the most abundant species (Astyanax aeneus, Poecilia mexicana, and Gambusia sexradiata ) occur in most pools and under several environmental conditions. Baseline data on fish diversity along with a continued monitoring program are essential in order to evaluate the conservation status of fish assemblages and their habitats, as well as to measure the influence of anthropogenic impacts on pristine habitats such as the karstic pools of the Calakmul Biosphere Reserve.

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Assessing the Drivers behind the Structure and Diversity of Fish Assemblages Associated with Rocky Shores in the Galapagos Archipelago

Journal of Marine Science and Engineering ◽

10.3390/jmse9040375 ◽

2021 ◽

Vol 9 (4) ◽

pp. 375

Author(s):

Stijn Bruneel ◽

Wout Van Echelpoel ◽

Long Ho ◽

Heleen Raat ◽

Amber Schoeters ◽

...

Keyword(s):

Environmental Management ◽

Fish Assemblages ◽

Oceanic Islands ◽

Nutrient Concentrations ◽

Fish Diversity ◽

Rocky Shores ◽

Santa Cruz ◽

Galapagos Archipelago ◽

Pristine Area ◽

Α Diversity

Oceanic islands harbor unique yet fragile marine ecosystems that require evidence-based environmental management. Among these islands, the Galapagos archipelago is well known for its fish diversity, but the factors that structure communities within and between its islands remain poorly understood. In this study, water quality, physical habitats and geographical distance were assessed as potential predictors for the diversity and structure of fish assemblages. Differences in the structure of fish assemblages of the two studied islands (Santa Cruz and Floreana) were most likely driven by temperature and nutrient concentrations. In the relatively highly populated island Santa Cruz, the structure of fish assemblages was more affected by water conditions than physical habitats while the contrary was true for the more pristine area of Floreana. A wide variety of species with different geographical origins were distributed over the different islands, which indicates that most fish species are able to reach the islands of the archipelago. However, temperature gradients and elevated nutrient levels cause large differences in the structure of local fish assemblages. In addition, in Santa Cruz nutrient concentrations were negatively correlated with α diversity. Since pollution is a clear pressure on the fish assemblages of oceanic islands, environmental management of the coastal areas is of paramount importance.

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Spatio-Temporal Variation of the Bacterial Communities along a Salinity Gradient within a Thalassohaline Environment (Saline di Tarquinia Salterns, Italy)

Molecules ◽

10.3390/molecules26051338 ◽

2021 ◽

Vol 26 (5) ◽

pp. 1338

Author(s):

Susanna Gorrasi ◽

Andrea Franzetti ◽

Roberto Ambrosini ◽

Francesca Pittino ◽

Marcella Pasqualetti ◽

...

Keyword(s):

Bacterial Diversity ◽

Generalized Linear Models ◽

Bacterial Communities ◽

Linear Models ◽

Salinity Gradient ◽

Sampling Site ◽

Α Diversity ◽

Spatio Temporal ◽

Abundance Variation ◽

Microbiological Aspects

The “Saline di Tarquinia” salterns have been scarcely investigated regarding their microbiological aspects. This work studied the structure and composition of their bacterial communities along the salinity gradient (from the nearby sea through different ponds). The communities showed increasing simplification of pond bacterial diversity along the gradient (particularly if compared to those of the sea). Among the 38 assigned phyla, the most represented were Proteobacteria, Actinobacteria and Bacteroidetes. Differently to other marine salterns, where at the highest salinities Bacteroidetes dominated, preponderance of Proteobacteria was observed. At the genus level the most abundant taxa were Pontimonas, Marivita, Spiribacter, Bordetella, GpVII and Lentibacter. The α-diversity analysis showed that the communities were highly uneven, and the Canonical Correspondence Analysis indicated that they were structured by various factors (sampling site, sampling year, salinity, and sampling month). Moreover, the taxa abundance variation in relation to these significant parameters were investigated by Generalized Linear Models. This work represents the first investigation of a marine saltern, carried out by a metabarcoding approach, which permitted a broad vision of the bacterial diversity, covering both a wide temporal span (two years with monthly sampling) and the entire salinity gradient (from the nearby sea up to the crystallisation ponds).

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FISH DIVERSITY IN THE DOWNSTREAM REGION OF CIPANAS RIVER INDRAMAYU, WEST JAVA INDONESIA

Zoo Indonesia ◽

10.52508/zi.v29i1.3978 ◽

2020 ◽

Vol 29 (1) ◽

Author(s):

Titin Herawati ◽

Gema Wahyudewantoro ◽

Yuli Andriani ◽

Heti Herawati ◽

Naomi Masnida Yunisia Siregar

Keyword(s):

Water Quality ◽

Census Data ◽

Fish Assemblages ◽

Survey Methods ◽

Upstream Region ◽

Fish Diversity ◽

West Java ◽

Fish Collection ◽

Java Sea ◽

Downstream Area

Cipanas River is one river in West Java where its upstream region in Tampomas Mountain, Sumedang and it is emptied into the Java Sea, Indramayu. The study was aimed to investigate fish diversity in the downstream area of Cipanas River. The study was conducted by survey methods with census data collection techniques, taken place at 3 stations of Santing, Tempalong, and Cemara of Indramayu Regency. The parameters measured consisted water quality and fish assemblages. Water quality was measured referring to standard laboratory protocol, and fish collection was made by case net with different mesh sizes. The results showed that water quality conditions of the Cipanas River downstream was suitable for inhabiting fishes. There were as many as 548 individual fishes caught belonging to 21 species, 16 genera, and 14 families. Fish diversity was categorized as medium with 1.6 ≤ H ’≤ 2.2 indicating fairly good community structure, and the Evenness index was 0.81 ≤ E ≤ 0.86 to show highly evenly distributed.

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Dredging fundamentally reshapes the ecological significance of 3D terrain features for fish in estuarine seascapes

Landscape Ecology ◽

10.1007/s10980-021-01394-5 ◽

2022 ◽

Author(s):

Hayden P. Borland ◽

Ben L. Gilby ◽

Christopher J. Henderson ◽

Rod M. Connolly ◽

Bob Gorissen ◽

...

Keyword(s):

Fish Assemblages ◽

Three Dimensional ◽

Ecological Impacts ◽

Fish Diversity ◽

Urban Landscapes ◽

Ecological Significance ◽

Landscape Modification ◽

Eastern Australia ◽

Coastal Landscapes ◽

Terrain Features

Abstract Context Landscape modification alters the condition of ecosystems and the structure of terrain, with widespread impacts on biodiversity and ecosystem functioning. Seafloor dredging impacts a diversity of flora and fauna in many coastal landscapes, and these processes also transform three-dimensional terrain features. The potential ecological significance of these terrain changes in urban seascapes has, however, not been investigated. Objectives We examined the effects of terrain variation on fish assemblages in 29 estuaries in eastern Australia, and tested whether dredging changes how fish associate with terrain features. Methods We surveyed fish assemblages with baited remote underwater video stations and quantified terrain variation with nine complementary metrics (e.g. depth, aspect, curvature, slope, roughness), extracted from bathymetry maps created with multi-beam sonar. Results Fish diversity and abundance were strongly linked to seafloor terrain in both natural and dredged estuaries, and were highest in shallow waters and near features with high curvature. Dredging, however, significantly altered the terrain of dredged estuaries and transformed the significance of terrain features for fish assemblages. Abundance and diversity switched from being correlated with lower roughness and steeper slopes in natural estuaries to being linked to features with higher roughness and gentler slopes in dredged estuaries. Conclusions Contrasting fish-terrain relationships highlight previously unrecognised ecological impacts of dredging, but indicate that plasticity in terrain use might be characteristic of assemblages in urban landscapes. Incorporating terrain features into spatial conservation planning might help to improve management outcomes, but we suggest that different approaches would be needed in natural and modified landscapes.

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Anthropogenic impacts on Keshalia River, Eastern Nepal

Nepalese Journal of Biosciences ◽

10.3126/njbs.v7i1.41796 ◽

2017 ◽

Vol 7 (1) ◽

pp. 105-111

Author(s):

Jay Narayan Shrestha

Keyword(s):

Anthropogenic Impact ◽

Anthropogenic Impacts ◽

Industrial Effluents ◽

Fish Diversity ◽

Dam Construction ◽

Fish Ladder ◽

Very High

The anthropogenic impact on Keshalia river, especially on fish diversity, is very high. Over fishing with unconventional fishing methods, disposal of domestic and industrial effluents, excess use of pesticides, dumping sites of municipalities, dam construction without fish ladder across the river and mining of sands and gravels are major anthropogenic impacts on the river.

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Ichthyoplankton metabarcoding as a tool for studying fish reproductive dynamics

ARPHA Conference Abstracts ◽

10.3897/aca.4.e65404 ◽

2021 ◽

Vol 4 ◽

Author(s):

Daniel Teixeira ◽

Heron Hilário ◽

Gustavo Rosa ◽

Guilherme Santos ◽

Gilmar Santos ◽

...

Keyword(s):

Fish Assemblages ◽

Fish Larvae ◽

Reference Sequence ◽

12S Rrna ◽

Morphological Identification ◽

Rrna Gene ◽

Fish Eggs ◽

Migration Routes ◽

Dna Metabarcoding ◽

Primer Sets

The study of ichthyoplankton composition, abundance and distribution is paramount to understand the reproductive dynamics of local fish assemblages. The analysis of these parameters allows the identification of spawning sites, nursery areas and migration routes. However, due to the lack of characters in early life stages, the morphological identification of ichthyoplankton is often impractical and many studies identify only fish larvae. Additionally, its accuracy shows great variation between taxonomists and laboratories according to their experience and specialty. DNA barcoding emerged as an alternative to provide assertive identification of fish eggs and larvae, but it becomes too expensive and laborious when the study demands the processing of huge amounts of organisms. DNA metabarcoding can overcome these limitations as a rapid, cost-effective, broad and accurate taxonomy tool, allowing the identification of multiple individuals simultaneously. Here, we present the identification of a sample containing 68 fish eggs and another containing 293 fish larvae from a single site in the São Francisco River Basin, Eastern Brazil, through DNA metabarcoding. We used a low-cost saline DNA extraction followed by PCR amplification with three primer sets targeting the 12S rRNA gene: MiFish (~170bp), Teleo_1 (~60bp), and NeoFish (~190bp). The latter was recently developed by our research group specifically for the identification of Neotropical fishes. All the amplified samples were sequenced in a single multiplexed Illumina MiniSeq run. We performed the filtering steps and assigned Amplicon Sequence Variants (ASVs) using a DADA2/Phyloseq based pipeline and a custom 12S reference sequence database including 101 species and 70 genera from the Jequitinhonha and São Francisco basins. The species Cyphocharax gilbert, Leporinus taeniatus, Megaleporinus elongatus, Prochilodus argenteus, P. costatus and Psalidodon fasciatus were detected by all three primer sets in the larva pool, while Pterygoplichthys etentaculatus was detected solely by NeoFish (Fig. 1). Within the egg pool, all three markers detected the species Characidium zebra, Curimatella lepidura, M. elongatus, Pimelodus fur and P. costatus, but Brycon orthotaenia was detected only by NeoFish, P. maculatus only by Teleo, and P. pohli by MiFish and Teleo (Fig. 1). The consistency in species detection among all three markers underpins the credibility of this method to accurately describe the sample composition. Considering that most of species were exclusive to the larvae or egg pool, our experiment highlights the importance of including the identification of fish eggs in reproduction studies, as it can provide additional information about which species are spawning in an area. Furthermore, the application of DNA metabarcoding to the study of ichthyoplankton can help decision makers create more informed guidelines for conservation of economically and ecologically important fish species.

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