The use of fish parasites as biological indicators of anthropogenic influences in coral-reef lagoons: a case study of Apogonidae parasites in New-Caledonia

A Comprehensive Analysis of the Fowleria variegata (Valenciennes, 1832) Mitochondrial Genome and Its Phylogenetic Implications within the Family Apogonidae

Controversies surrounding the phylogenetic relationships within the family Apogonidae have persisted due to the limited molecular data, obscuring the evolution of these diverse tropical marine fishes. This study presents the first complete mitochondrial genome of Fowleria variegata, a previously unrepresented genus, using high-throughput Illumina sequencing. Through a comparative mitogenomic analysis, F. variegate was shown to exhibit a typical genome architecture and composition, including 13 protein-coding, 22 tRNA and 2 rRNA genes and a control region, consistent with studies of other Apogonidae species. Nearly all protein-coding genes started with ATG, while stop codons TAA/TAG/T were observed, along with evidence of strong functional constraints imposed via purifying selection. Phylogenetic reconstruction based on maximum likelihood and Bayesian approaches provided robust evidence that F. variegata forms a basal lineage closely related to P. trimaculatus within Apogonidae, offering novel perspectives into the molecular evolution of this family. By generating new mitogenomic resources and evolutionary insights, this study makes important headway in elucidating the phylogenetic relationships and mitogenomic characteristics of Apogonidae fishes. The findings provide critical groundwork for future investigations into the drivers of diversification, speciation patterns, and adaptive radiation underlying the extensive ecological diversity and biological success of these marine fishes using phylogenomics and population genomics approaches.

SPATIAL VARIATION IN HELMINTH PARASITE COMMUNITIES OF THE FRENCH GRUNT, HAEMULON FLAVOLINEATUM (TELEOSTEI: HAEMULIDAE), FROM THE YUCATAN PENINSULA

The French grunt, Haemulon flavolineatum, is an abundant fish and a good model for studying parasite communities. Specimens were collected at 4 localities between the Campeche Bank (within the Gulf of Mexico) and the Mexican Caribbean Sea to describe and compare the differences and similarities between localities and regions in the communities of parasitic helminths. Thus, we calculated the Hill numbers associated with species richness (q = 0) and the dominance estimator (q = 2) using rarefaction and extrapolation curves to provide asymptotic estimators of diversity. A 2-way PERMANOVA was used to determine whether there was a significant difference in parasite assemblage structure between localities or regions. A total of 11 helminth taxa (species level) were recorded in 104 individuals of H. flavolineatum, consisting of 8 digenean trematodes species, 2 acanthocephalan species, and 1 nematode species. Our findings include new reports of 7 parasite taxa and new geographical records for some parasites in H. flavolineatum. The highest dissimilarities in parasite composition were observed between the most distant locations (Banco Chinchorro vs. Cayo Arcas) that were each located in different regions. Species richness was similar between regions, although the most dominant helminths were Postmonorchis orthopristis and Dollfustrema sp. in the Mexican Caribbean and Campeche Bank regions, respectively. Future studies should explore how patterns in parasite community structure are affected by currents running south to north by the Yucatan Current through the Yucatan Channel and easterly to Campeche Bank.

Impact assessment of a large river on the sediments and fish from its continental shelf: using Solea solea as sentinel in the Ebro river mouth (NW Mediterranean, Spain)

Many studies have been carried out along mighty rivers with heavily industrialized watersheds to evaluate pollutants and their effects on freshwater organisms. However, their impact on marine organisms is virtually unknown. In order to cover this gap, Solea solea, one of the most important commercial fish species, together with sediments, were sampled during 2013-2015 offshore from the Ebro Delta river mouth. Fish health indicators (condition indices, histological tissue alterations, and parasite descriptors) were used to assess the potential effect of pollutants, an issue of particular interest in the area following the dredging activities taking place in the river upstream in 2013. No major histopathological alterations were detected, but perivascular inflammatory foci (PIF) were frequently observed, especially in 2014. The most prevalent and abundant parasites were acanthocephalans and digeneans within the digestive tract and copepods on the gills. Levels of trace metals from sediments and fish muscle were below the effects range median and reference levels accepted for human consumption, respectively. However, the lower levels of the hepatosomatic index, higher numbers of PIF, and variations in the abundance of parasites in 2014 and 2015 could suggest a pollutant exposure during these years. These results warn signs of toxicity, which could be associated with sediment leaks during the dredging activities.

Bivalve δ15N isoscapes provide a baseline for urban nitrogen footprint at the edge of a World Heritage coral reef

Eutrophication is a major threat to world's coral reefs. Here, we mapped the distribution of the anthropogenic nitrogen footprint around Nouméa, a coastal city surrounded by 15,743 km² of UNESCO listed reefs. We measured the δ¹⁵N signature of 348 long-lived benthic bivalves from 12 species at 27 sites and interpolated these to generate a δ¹⁵N isoscape. We evaluated the influence of water residence times on nitrogen enrichment and predicted an eutrophication risk at the UNESCO core area. Nitrogen isoscapes revealed a strong spatial gradient (4.3 to 11.7‰) from the outer lagoon to three highly exposed bays of Nouméa. Several protected reefs would benefit from an improved management of wastewater outputs, while one bay in the UNESCO core area may suffer a high eutrophication risk in the future. Our study reinforces the usefulness of using benthic animals to characterize the anthropogenic N-footprint and provide a necessary baseline for both ecologists and policy makers.

Metazoan parasite communities of two deep-sea elasmobranchs: the southern lanternshark, Etmopterus granulosus, and the largenose catshark, Apristurus nasutus, in the Southeastern Pacific Ocean

Two deep-sea shark species were obtained as by-catch of the local fishery of the Patagonian toothfish, Dissostichus eleginoides, at depths ranging from 1000 to 2200 m off central and northern Chile. A total of 19 parasite taxa were found in 133 specimens of the southern lanternshark, Etmopterus granulosus, (n = 120) and largenose catshark, Apristurus nasutus, (n = 13). Fourteen taxa (four Monogenea, one Digenea, four Cestoda, one Nematoda, two Copepoda, one Annelida and one Thecostraca) were found in E. granulosus, whereas five taxa (one Monogenea, two Cestoda and two Nematoda) were found in A. nasutus. Representatives of Cestoda showed higher values of prevalence and a greater intensity of infection; this pattern is consistent with reports for elasmobranchs, but the monogenean richness was higher than that previously reported for related deep-sea sharks. Regarding E. granulosus, a positive and significant correlation between host length and abundance was found for six (four ectoparasites, one mesoparasite, and one endoparasite) of the 14 taxa recorded, but prevalence was significantly correlated with host length only for the monogenean Asthenocotyle sp. Although the sample size for A. nasutus was limited, we compared richness, abundance, diversity and evenness at the infracommunity and component community levels. All of these variables were higher for E. granulosus, but at the infracommunity level, abundance was higher for A. nasutus. All the parasite taxa (except two) represent new host and geographical records.

Parasite fauna of Epinephelus coioides (Hamilton, 1822) (Epinephelidae) as environmental indicator under heavily polluted conditions in Jakarta Bay, Indonesia

The objective of this study was to assess the environmental conditions of a heavily polluted marine habitat using descriptors of fish parasites. Epinephelus coioides from Jakarta Bay as well as off Jakarta Bay was studied for metazoan parasites. Based on 70 fish and considering previous studies (230 fish), an environmental indicator system was designed. Including the recent study, a total of 51 parasite species have been recorded for E. coioides in Indonesian waters. Seven of them combined with five parasitological indices are useful descriptors for the environmental status of marine ecosystems. The results are visualized in a star graph. A significant different parasite infection between nine analyzed localities demonstrates the negative influence of the megacity Jakarta onto the coastal environment. We herewith complete a parasite based indicator system for Indonesian coastal waters, and suggest that it can be used in other marine habitats as well as for further epinephelids.

Helmintofauna of turbot Scophthalmus maximus (Linnaeus, 1758) from the southern Baltic Sea including new data

Turbot Scophthalmus maximus (Linnaeus, 1758) is a fish belonging to the Pleuronectiformes order. It is commonly observed in waters of the northern Atlantic, and also in the Baltic Sea. As an economically significant species, it is fished on an industrial scale, and also farmed in some European countries. Seventy-two turbots from the Gulf of Gdańsk (26th ICES zone) were examined for parasite presence in the years 2010-2012. The study revealed the presence of the tapeworm Bothriocephalus scorpii (Müller, 1776) and acanthocephalan Corynosoma semerme (Forssell, 1904). The overall (both parasites) prevalence of turbot infection was 100% with a mean intensity of 18.7. C. semerme is a parasite which has not been noted so far in turbot from the southern Baltic. The presence of C. semerme in turbot was emphasized in the context of possible infection of terrestrial mammals, including humans.

Multi-biomarker approach using the blue mussel (Mytilus edulis L.) to assess the quality of marine environments: season and habitat-related impacts

Using a comprehensive approach, intertidal, near- and offshore sites in the German Bight were analysed for their environmental quality by assessing the health of blue mussels (Mytilus edulis). During a ten month sampling period mussels were studied with a set of biomarkers comprising lysosomal membrane stability and accumulation of lipofuscin, supplemented by biomarkers indicating nutritional status such as neutral lipids and glycogen in the cells of the digestive gland. Data were analysed in relation to sex, gonadal status, condition index and for the presence of parasites, to determine the overall health status of mussels at the respective sites. Mussels from all sites showed clear signs of stress, indicating an inferior environmental quality throughout the southern German Bight. Further, habitat characteristics such as inundation time and growing on- or off-bottom, as well as seasonal factors, can clearly influence the response of biomarkers in mussels exposed to similar levels of chemical environmental stress.

Neglected wild life: Parasitic biodiversity as a conservation target

Parasites appropriate host resources to feed and/or to reproduce, and lower host fitness to varying degrees. As a consequence, they can negatively impact human and animal health, food production, economic trade, and biodiversity conservation. They can also be difficult to study and have historically been regarded as having little influence on ecosystem organization and function. Not surprisingly, parasitic biodiversity has to date not been the focus of much positive attention from the conservation community. However, a growing body of evidence demonstrates that parasites are extremely diverse, have key roles in ecological and evolutionary processes, and that infection may paradoxically result in ecosystem services of direct human relevance. Here we argue that wildlife parasites should be considered meaningful conservation targets no less relevant than their hosts. We discuss their numerical and functional importance, current conservation status, and outline a series of non-trivial challenges to consider before incorporating parasite biodiversity in conservation strategies. We also suggest that addressing the key knowledge gaps and communication deficiencies that currently impede broad discussions about parasite conservation requires input from wildlife parasitologists.

Parasites of the grouper fish Epinephelus coioides (Serranidae) as potential environmental indicators in Indonesian coastal ecosystems

A total of 195 Epinephelus coioides (Hamilton, 1822) were studied for fish parasites from Javanese (Segara Anakan lagoon) and Balinese waters. Up to 25 different parasite species belonging to the following taxa: one Ciliata, one Microsporea, five Digenea, one Monogenea, four Cestoda, four Nematoda, one Acanthocephala, one Hirudinea and seven Crustacea were identified with four new host and locality records. The dominant parasites included the monogenean Pseudorhabdosynochus lantauensis (53.3-97.1%), the nematode Spirophilometra endangae (23.3-42.9%), the digenean Didymodiclinus sp. (2.9-40.0%), the nematodes Philometra sp. (22.6-34.3%) and Raphidascaris sp. (2.9-28.6%), and the isopod Alcirona sp. (6.7-31.4%). Regional differences for E. coioides were found in terms of endoparasite diversity, total diversity according to Shannon-Wiener, Simpson index and Evenness. A comparison with published data from Sumatera revealed highest endoparasite diversity (Shannon-Wiener: 1.86/1.67-2.04) and lowest ectoparasite/endoparasite ratio (0.73/0.57-0.88) off the Balinese coast, followed by Lampung Bay, Sumatera (1.84; 0.67), off the coast of Segara Anakan lagoon (1.71; 0.71), and in the lagoon (0.30/0.19-0.66; 0.85/0.67-1.00). The presented data demonstrate the natural range of these parameters and parasite prevalences according to habitat and region, allowing adjustment of the scale that has been used in the visual integration of the parasite parameters into a star graph. The parasite fauna of E. coioides in Segara Anakan lagoon 'improved' from 2004 until 2008/09, possibly related to earlier oil spill events in 2002 and 2004. The use of grouper fish parasites as an early warning system for environmental change in Indonesian coastal ecosystems is discussed.

Use of cestodes as indicator of heavy-metal pollution

Thirty snakehead fish, Channa micropeltes (Cuvier, 1831) were collected at Lake Kenyir, Malaysia. Muscle, liver, intestine and kidney tissues were removed from each fish and the intestine was opened to reveal cestodes. In order to assess the concentration of heavy metal in the environment, samples of water in the surface layer and sediment were also collected. Tissues were digested and the concentrations of manganese (Mn), zinc (Zn), copper (Cu), cadmium (Cd) and lead (Pb) were analysed by using inductively-coupled plasma mass-spectrometry (ICP-MS) equipment. The results demonstrated that the cestode Senga parva (Fernando and Furtado, 1964) from fish hosts accumulated some heavy metals to a greater extent than the water and some fish tissues, but less than the sediment. In three (Pb, Zn and Mn) of the five elements measured, cestodes accumulated the highest metal concentrations, and in remaining two (Cu and Cd), the second highest metal accumulation was recorded in the cestodes when compared to host tissues. Therefore, the present study indicated that Senga parva accumulated metals and might have potential as a bioindicator of heavy-metal pollution.

An environmental assessment of the parasite fauna of the reef-associated grouper Epinephelus areolatus from Indonesian waters

Sixty Epinephelus areolatus were examined for metazoan fish parasites in Indonesia, off Segara Anakan lagoon, Java and in Balinese waters. The study revealed 21 different parasite species, and 14 new host and locality records. The anisakid nematodes Anisakis typica and, for the first time in Indonesia, Anisakis sp. HC-2005 were identified by using molecular methods. Ecological parameters were calculated for both sites off the anthropogenically influenced Segara Anakan lagoon and the relatively undisturbed reference site at the southern Balinese coast. The fish from Segara Anakan demonstrated a significantly higher enzymatic activity (Hepatosomatic index) and a significantly reduced number of heteroxenous gut helminths (e.g. the digenean Didymodiclinus sp., the nematode Raphidascaris sp. and the acanthocephalan Serrasentis sagittifer). Other regional differences for E. areolatus included ecto-/endoparasite ratio, endoparasite diversity, the parasite species composition and prevalence of infection of the respective parasite species. We applied the stargraph method to visualize observed regional differences using grouper parasites as biological indicators for the sampled coastal ecosystems at both sampling sites.

Digenean species diversity in teleost fishes from the Gulf of Gabes, Tunisia (Western Mediterranean)

This study is the first attempt to survey the diversity of fish digeneans in the Gulf of Gabes (southern coast of Tunisia). A total of 779 fishes belonging to 32 species were sampled. 53 species of Digenea belonging to 15 families were recorded. Among these species, 24 are reported for the first time from the coast of Tunisia. We report one new host record, Lecithochirium sp. from Sardinella aurita. The Hemiuridae is the dominant family. A host-parasite list is presented with the information on the prevalence, abundance and mean intensity of each species collected. The diversity of Digenea is compared with other localities in the Mediterranean Sea and the northern east of Tunisia. The Gulf of Gabes shows the lowest diversity linked to the anthropogenic activities and impact of exotic species. The use of Digenea as indicators of the state of the ecosystem is discussed.

Parasite diversity as an indicator of environmental change? An example from tropical grouper (Epinephelus fuscoguttatus) mariculture in Indonesia

Fish parasites are used to monitor long-term change in finfish grouper mariculture in Indonesia. A total of 210Epinephelus fuscoguttatuswere sampled in six consecutive years between 2003/04 and 2008/09 and examined for parasites. The fish were obtained from floating net cages of a commercially run mariculture facility that opened in 2001. The fauna was species rich, consisting of ten ecto- and 18 endoparasite species. The ectoparasite diversity and composition was relatively stable, with the monogeneansPseudorhabdosynochusspp. (83–100% prevalence, Berger-Parker Index of 0·82–0·97) being the predominant taxon. Tetraphyllidean larvaeScolex pleuronectisand the nematodesTerranovasp. andRaphidascarissp. 1 were highly abundant in 2003/04–2005/06 (max. prevalenceS. pleuronectis40%,Terranovasp. 57%,Raphidascarissp. 1 100%), and drastically reduced until 2008/09. These parasites together with the prevalence ofTrichodinaspp., ecto-/endoparasite ratio and endoparasite diversity illustrate a significant change in holding conditions over the years. This can be either referred to a definite change in management methods such as feed use and fish treatment, or a possible transition of a relatively undisturbed marine environment into a more affected habitat. By visualizing all parameters within a single diagram, we demonstrate that fish parasites are useful bioindicators to monitor long-term change in Indonesian grouper mariculture. This also indicates that groupers can be used to monitor environmental change in the wild. Further taxonomic and systematic efforts in less sampled regions significantly contributes to this new application, supporting fish culture and environmental impact monitoring also in other tropical marine habitats.

Biogeochemical typology and temporal variability of lagoon waters in a coral reef ecosystem subject to terrigeneous and anthropogenic inputs (New Caledonia)

Considering the growing concern about the impact of anthropogenic inputs on coral reefs and coral reef lagoons, surprisingly little attention has been given to the relationship between those inputs and the trophic status of lagoon waters. The present paper describes the distribution of biogeochemical parameters in the coral reef lagoon of New Caledonia where environmental conditions allegedly range from pristine oligotrophic to anthropogenically influenced. The study objectives were to: (i) identify terrigeneous and anthropogenic inputs and propose a typology of lagoon waters, (ii) determine temporal variability of water biogeochemical parameters at time-scales ranging from hours to seasons. Combined ACP-cluster analyses revealed that over the 2000 km(2) lagoon area around the city of Nouméa, "natural" terrigeneous versus oceanic influences affecting all stations only accounted for less than 20% of the spatial variability whereas 60% of that spatial variability could be attributed to significant eutrophication of a limited number of inshore stations. ACP analysis allowed to unambiguously discriminating between the natural trophic enrichment along the offshore-inshore gradient and anthropogenically induced eutrophication. High temporal variability in dissolved inorganic nutrients concentrations strongly hindered their use as indicators of environmental status. Due to longer turn over time, particulate organic material and more specifically chlorophyll a appeared as more reliable nonconservative tracer of trophic status. Results further provided evidence that ENSO occurrences might temporarily lower the trophic status of the New Caledonia lagoon. It is concluded that, due to such high frequency temporal variability, the use of biogeochemical parameters in environmental surveys require adapted sampling strategies, data management and environmental alert methods.

Circulation and suspended sediment transport in a coral reef lagoon: the south-west lagoon of New Caledonia

The south-west lagoon of New Caledonia is a wide semi-open coral reef lagoon bounded by an intertidal barrier reef and bisected by numerous deep inlets. This paper synthesizes findings from the 2000-2008 French National Program EC2CO-PNEC relative to the circulation and the transport of suspended particles in this lagoon. Numerical model development (hydrodynamic, fine suspended sediment transport, wind-wave, small-scale atmospheric circulation) allowed the determination of circulation patterns in the lagoon and the charting of residence time, the later of which has been recently used in a series of ecological studies. Topical studies based on field measurements permitted the parameterisation of wave set-up induced by the swell breaking on the reef barrier and the validation of a wind-wave model in a fetch-limited environment. The analysis of spatial and temporal variability of suspended matter concentration over short and long time-scales, the measurement of grain size distribution and the density of suspended matter (1.27 kg l(-1)), and the estimation of erodibility of heterogeneous (sand/mud, terrigenous/biogenic) soft bottoms was also conducted. Aggregates were shown to be more abundant near or around reefs and a possible biological influence on this aggregation is discussed. Optical measurements enabled the quantification of suspended matter either in situ (monochromatic measurements) or remotely (surface spectral measurements and satellite observations) and provided indirect calibration and validation of a suspended sediment transport model. The processes that warrant further investigation in order to improve our knowledge of circulation and suspended sediment transport in the New Caledonia lagoon as well as in other coral reef areas are discussed, as are the relevance and reliability of the numerical models for this endeavour.

A new approach to visualize ecosystem health by using parasites

A new approach is chosen to visualize ecosystem health by using parasite bioindicators in Segara Anakan Lagoon, a brackish water ecosystem at the southern Java coast, Indonesia. Three fish species (Mugil cephalus, Scatophagus argus, Epinephelus coioides) were collected in two different years and sampling sites and studied for ecto- and endoparasites. Additional data were taken for E. coioides from two further sites in Lampung Bay, Sumatra, and for E. fucoguttatus out of floating cages from a mariculture facility in the Thousand Islands, Jakarta Bay, North Java. The parasite fauna of fishes inside the lagoon was characterized by a high number of ecto- and a low number of endoparasites, the endoparasite diversity was relatively low and the prevalence of ectocommensalistic trichodinid ciliates was high. These parameters were chosen to indicate the biological conditions inside the lagoon. In E. coioides during rainy season, the prevalence of trichodinid ciliates was highest inside the lagoon (55%) compared with 27% in an open-net-cage mariculture and 5.7% in free-living specimens in Lampung Bay. The endoparasite diversity (Shannon-Wiener) was lowest in fish from Segara Anakan lagoon (0.66) compared with fish from an open-net-cage mariculture (0.71) and free-living specimens (1.39). Results for E. fuscoguttatus from the mariculture site in the Thousand Islands, a relatively undisturbed marine environment, demonstrated high parasite diversity (1.58) in the cultivated fish, a high number of endoparasites, and no trichodinids. A star graph is used to visualize the parasite composition for the different fishes, sampling sites, and conditions, using (1) the prevalence of trichodinid ciliates, (2) the ecto/endoparasite ratio and (3) the endoparasite diversity as bioindicators. The application of the star graph is suggested to be a suitable tool to visualize and monitor environmental health under high parasite biodiversity conditions within tropical ecosystems. It can also support a better communication to stake holders and decision makers in order to monitor environmental impact and change.