Name and shame: can taxonomists agree on systematic reforms?

The Linnean nomenclatural system dominates in taxonomy, despite various ethical issues being raised regarding the rules applied to this approach. Some recent proposals to adapt the system have been dismissed as destabilizing by many taxonomists. However, simple rule changes and amendments to address these issues could be implemented without excessive disruption.

Synopsis of the Species of Coccidians Reported in Marine Fish.

Eimeriid coccidians represent one of the largest groups of parasitic unicellular organisms and comprise many species of veterinary and medical importance. The aim of this work is to provide information, as complete as possible, concerning the oocyst phase of the species of coccidians (Apicomplexa: Eimeriorina) with four sporocysts, which were reported in marine fish. For each species, the accepted scientific name and respective authorities, its synonyms, reported hosts, site of infection (organ), and geographic distribution have been assembled. Available information on morphology (oocyst, sporocyst, and sporozoite) and GenBank accession numbers were also compiled. A total of 100 species of coccidians were described and reported from 60 families of marine fishes. Most species have been described from marine teleosts, with only 14 of the species described from marine elasmobranchs. Most of the species reported in marine fish belong to the genera Eimeria and Goussia, and only a handful belong to the genera Epieimeria, Calyptospora, and Crystallospora. Although marine coccidians have began to be described for more than one century, the collection of genetic data on marine fish coccidians only started in the 2010s and remains largely disconnected from the morphological analysis of specimens, which is available for only six formally described species.

Disruption of the skin, gill, and gut mucosae microbiome of gilthead seabream fingerlings after bacterial infection and antibiotic treatment.

The activity of the microbiome of fish mucosae provides functions related to immune response, digestion, or metabolism. Several biotic and abiotic factors help maintaining microbial homeostasis, with disruptions leading to dysbiosis. Diseases and antibiotic administration are known to cause dysbiosis in farmed fish. Pathogen infections greatly affect the production of gilthead seabream, and antibiotic treatment is still frequently required. Here, we employed a 16S rRNA high-throughput metataxonomics approach to characterize changes in the gut, skin, and gill microbiomes occurring due to infection with Photobacterium damselae subsp. piscicida and subsequent antibiotic treatment with oxytetracycline (OTC), as well as during recovery. Although microbiota response differed between studied tissues, overall changes in composition, diversity, structure, and predicted function were observed in all mucosae. The skin and gill microbiomes of diseased fish became largely dominated by taxa that have been frequently linked to secondary infections, whereas in the gut the genus Vibrio, known to include pathogenic bacteria, increased with OTC treatment. The study highlights the negative impacts of disease and antibiotic treatment on the microbiome of farmed fish. Our results also suggest that fish transportation operations may have profound effects on the fish microbiome, but further studies are needed to accurately evaluate their impact.

Factors shaping the gut microbiome of five species of lizards from different habitats.

Background: Host-gut microbiota interactions are complex and can have a profound impact on the ecology and evolution of both counterparts. Several host traits such as systematics, diet and social behavior, and external factors such as prey availability and local environment are known to influence the composition and diversity of the gut microbiota. Methods: In this study, we investigate the influence of systematics, sex, host size, and locality/habitat on gut microbiota diversity in five lizard species from two different sites in Portugal: Podarcis bocagei and Podarcis lusitanicus, living in syntopy in a rural area in northern Portugal (Moledo); the invasive Podarcis siculus and the native Podarcis virescens, living in sympatry in an urbanized environment (Lisbon); and the invasive Teira dugesii also living in an urban area (Lisbon). We also infer the potential microbial transmission occurring between species living in sympatry and syntopy. To achieve these goals, we use a metabarcoding approach to characterize the bacterial communities from the cloaca of lizards, sequencing the V4 region of the 16S rRNA. Results: Habitat/locality was an important factor explaining differences in gut bacterial composition and structure, with species from urbanized environments having higher bacterial diversity. Host systematics (i.e., species) influenced gut bacterial community structure only in lizards from the urbanized environment. We also detected a significant positive correlation between lizard size and gut bacterial alpha-diversity in the invasive species P. siculus, which could be due to its higher exploratory behavior. Moreover, estimates of bacterial transmission indicate that P. siculus may have acquired a high proportion of local microbiota after its introduction. These findings confirm that a diverse array of host and environmental factors can influence lizards' gut microbiota.

First Molecular Identification of a Goussia Parasite from a New World Invasive Blenny.

PURPOSE: Introduced or invasive fish are susceptible to new parasites but can simultaneously carry infectious parasites from their native range towards new hosts. Screening these parasites is key to address the health of fish populations and spread of diseases. METHODS: In this study, we sequenced a Coccidia parasite, for the first time from the blenny Omobranchus sewalli, introduced in the northern coast of Brazil with an Indo-Pacific origin. RESULTS: Only one individual was infected, its genetic sequence matched (over 99%) with two lineages of undetermined species, belonging to the genus Goussia, sequenced from three marine fish species (Mulloidichthys flavolineatus, Lutjanus kasmira, and Selar crumenophthalmus) in Hawaii. CONCLUSIONS: Phylogenetic analysis suggests considerable differentiation between the Goussia detected and other Goussia spp. sequenced from North Atlantic marine fish, thus we cannot exclude the possibly that this parasite was carried by O. sewalli from its native Indo-Pacific range.

Reef Location and Client Diversity Influence the Skin Microbiome of the Caribbean Cleaner Goby Elacatinus evelynae.

Fish-associated microorganisms are known to be affected by the environment and other external factors, such as microbial transfer between interacting partners. One of the most iconic mutualistic interactions on coral reefs is the cleaning interactions between cleaner fishes and their clients, during which direct physical contact occurs. Here, we characterized the skin bacteria of the Caribbean cleaner sharknose goby, Elacatinus evelynae, in four coral reefs of the US Virgin Islands using sequencing of the V4 region of the 16S rRNA gene. We specifically tested the relationship between gobies' level of interaction with clients and skin microbiota diversity and composition. Our results showed differences in microbial alpha- and beta-diversity in the skin of gobies from different reef habitats and high inter-individual variation in microbiota diversity and structure. Overall, the results showed that fish-to-fish direct contact and specifically, access to a diverse clientele, influences the bacterial diversity and structure of cleaner gobies' skin. Because of their frequent contact with clients, and therefore, high potential for microbial exchange, cleaner fish may serve as models in future studies aiming to understand the role of social microbial transfer in reef fish communities.

Clarifying the taxonomy of some cryptic blennies (Blenniidae) in their native and introduced range.

Omobranchus punctatus is native to the Indo-Pacific region and invasive in the Atlantic region, currently being considered one of the most widely distributed blenny species. However, recent molecular studies indicated that O. punctatus is a complex of species, with three divergent mtDNA lineages identified to date, stressing the need for a taxonomic revision. In this study, we used an integrative approach, combining morphological and genetic data, to shed light on the taxonomy and distribution of O. punctatus. Moreover, we provide the first genetic records of introduced populations in Brazil and discuss the introduction pattern of this species in this region. Morphological data shows that O. punctatus consists of at least five distinct and geographically restricted species: O. punctatus sensu stricto, O. dispar, O. sewalli, O. cf. kochi, and O. cf. japonicus. Species delimitation analyses performed using the mtDNA data available confirmed that O. punctatus sensu stricto, O. dispar and O. sewalli correspond to different species that started to diverge about 2.6 Mya. Furthermore, O. sewalli was identified as the invasive species colonizing Atlantic shores. The existence of historical oceanographic barriers, such as the emergence of the Sunda Shelf in the Eastern Indian Ocean during the Pleistocene, and the biological traits of these blennies are the most likely factors responsible for their genetic differentiation and subsequent speciation.

Hemolymph Glycemia as an Environmental Stress Biomarker in the Invasive Red Swamp Crayfish (Procambarus clarkii).

AbstractSeveral freshwater crayfish species, including Procambarus clarkii, are both ecologically important and commercially important benthic macroinvertebrates, remarkable for their potential to adapt and reproduce but also for their unique abilities to face distinct abiotic and biotic environments and become successful invaders. While much work has been done to study crayfish introductions, less focus has been given to how crayfish cope with pollution and other environmental stressors, in terms of physiological responses, and whether crayfish responses can be used to assess the effective state of their living environment. Here, we used a mixed approach combining laboratory experiments with field data to validate the use of hemolymph glucose as a relevant biomarker of red swamp crayfish (Procambarus clarkii) stress response. Three meaningful sampling locations were chosen across southern Portugal that are representative of different environments where crayfish live and are frequently captured for human consumption but also correspond to different pollution levels. To reference field measurements of glucose levels, we performed two lab-based experiments: (a) crayfish were exposed to different levels of stress (stress challenge) and (b) crawfish were exposed to a maze dispersal test, with or without water. Crayfish glucose levels were responsive to induced stress but were not correlated with dispersal efforts. Wild crayfish's body condition and stress levels responded differently to environmental conditions, with more challenged individuals showing higher glycemia levels but similar body condition. The glucose levels of the more stressed wild crayfish were visually similar to lab-based crayfish subjected to the higher stress levels (electric shocks), while the levels of glucose of crayfish at the less polluted site corresponded to those measured before the start of the challenge (baseline). The maintenance of high levels of glycemia in crayfish inhabiting more challenging habitats is revealing of their higher energetic demand state. Since P. clarkii ia globally distributed and easily sampled invasive species, quantifying its hemolymph glucose levels can be a particularly useful proxy for assessing environmental quality.

The Terrific Skink bite force suggests insularity as a likely driver to exceptional resource use.

Natural history museum collections hold extremely rare, extinct species often described from a single known specimen. On occasions, rediscoveries open new opportunities to understand selective forces acting on phenotypic traits. Recent rediscovery of few individuals of Bocourt´s Terrific Skink Phoboscincus bocourti, from a small and remote islet in New Caledonia allowed to genetically identify a species of land crab in its diet. To explore this further, we CT- and MRI-scanned the head of the holotype, the only preserved specimen dated to about 1870, segmented the adductor muscles of the jaw and bones, and estimated bite force through biomechanical models. These data were compared with those gathered for 332 specimens belonging to 44 other skink species. Thereafter we recorded the maximum force needed to generate mechanical failure of the exoskeleton of a crab specimen. The bite force is greater than the prey hardness, suggesting that predation on hard-shelled crabs may be an important driver of performance. The high bite force seems crucial to overcome low or seasonal variations in resource availability in these extreme insular environments. Phoboscincus bocourti appears to be an apex predator in a remote and harsh environment and the only skink known to predate on hard-shelled land crabs.

Monitoring Infection and Antibiotic Treatment in the Skin Microbiota of Farmed European Seabass (Dicentrarchus Labrax) Fingerlings.

The microbiota of fish skin, the primary barrier against disease, is highly dynamic and modulated by several factors. In fish aquaculture, disease outbreaks occur mainly during early-life stages, with associated high economic losses. Antibiotic treatments sometimes remain the best option to control bacterial diseases, despite many reported negative impacts of its use on fish and associated microbiota. Notwithstanding, studies monitoring the effects of disease and antibiotic treatment on the microbiota of fingerlings are scarce. We sequenced the bacterial 16S rRNA V4 gene region using a metabarcoding approach to assess the impact of a mixed infection with Photobacterium damselae ssp. piscicida and Vibrio harveyi and subsequent antibiotic treatment with flumequine, on the skin microbiota of farmed seabass (Dicentrarchus labrax) fingerlings. Both infection and antibiotic treatment led to a significant increase in bacterial diversity and core microbial communities and impacted microbiome structure. Dysbiosis was confirmed by changes in the abundance of potential pathogenic and opportunistic bacterial taxa. Skin bacterial metabolic function was also significantly affected by flumequine administration, suggesting a detriment to fish skin health. Our results add to an increasing body of literature, showing how fish microbiome response to infection and antibiotics cannot be easily predicted.

Transcriptomic response of the intertidal limpet Patella vulgata to temperature extremes.

Global warming is challenging wild species in land and water. In the intertidal zone, species are already living at their thermal limits, being vulnerable even to small increases in maximum habitat temperatures. Knowledge of the mechanisms by which many intertidal zone species cope with elevated temperatures is limited. We analysed the molecular thermal stress response of the limpet Patella vulgata under slight and frequent (one-day), and extreme and rare (three-day) warming events. Using RNA-seq to assess differential gene expression among treatments, differing molecular responses were obtained in the two treatments, with more changes in gene expression after the three-day event; with one-third of the differentially expressed transcripts being down-regulated. However, across treatments we observed shifts in gene expression for common aspects of the heat stress response including intra-cellular communication, protein chaperoning, proteolysis and cell cycle arrest. Of the 71,675 transcripts obtained, only 259 were differentially expressed after both heating events. From these, 218 defined the core group (i.e. genes induced by thermal stress with similar expression patterns irrespective of the magnitude of the warming event). The core group was composed of already well-studied genes in heat stress responses in intertidal organisms (e.g. heat shock proteins), but also genes from less explored metabolic pathways, e.g. the ubiquitin system, which were also fundamental regardless of the magnitude of the imposed warming. Moreover, we have also identified 41 signaling genes (i.e. a set of genes responding to both events and with expression patterns specific to the intensity of thermal stress), principally including genes involved in the maintenance of extracellular structure that have previously not been identified as part of the response to thermal stress in intertidal zone organisms. These signaling genes will be useful heat stress molecular biomarkers for monitoring heat stress in natural populations.

Effects of aging on the skin and gill microbiota of farmed seabass and seabream.

BACKGROUND: Important changes in microbial composition related to sexual maturation have been already reported in the gut of several vertebrates including mammals, amphibians and fish. Such changes in fish are linked to reproduction and growth during developmental stages, diet transitions and critical life events. We used amplicon (16S rRNA) high-throughput sequencing to characterize the skin and gill bacterial microbiota of farmed seabass and seabream belonging to three different developmental age groups: early and late juveniles and mature adults. We also assessed the impact of the surrounding estuarine water microbiota in shaping the fish skin and gill microbiota. RESULTS: Microbial diversity, composition and predicted metabolic functions varied across fish maturity stages. Alpha-diversity in the seabass microbiota varied significantly between age groups and was higher in older fish. Conversely, in the seabream, no significant differences were found in alpha-diversity between age groups. Microbial structure varied significantly across age groups; moreover, high structural variation was also observed within groups. Different bacterial metabolic pathways were predicted to be enriched in the microbiota of both species. Finally, we found that the water microbiota was significantly distinct from the fish microbiota across all the studied age groups, although a high percentage of ASVs was shared with the skin and gill microbiotas. CONCLUSIONS: We report important microbial differences in composition and potential functionality across different ages of farmed seabass and seabream. These differences may be related to somatic growth and the onset of sexual maturation. Importantly, some of the inferred metabolic pathways could enhance the fish coping mechanisms during stressful conditions. Our results provide new evidence suggesting that growth and sexual maturation have an important role in shaping the microbiota of the fish external mucosae and highlight the importance of considering different life stages in microbiota studies.

Phylogenetic Affinities and Infection Patterns of Goussia Infecting Sardina pilchardus from the NE Atlantic.

PURPOSE: European pilchard (Sardina pilchardus) is a highly valued fish in many European countries, particularly in Portugal. Despite current stock declines and the threats coccidia pose to European pilchards (e.g. castration), little is known about coccidian parasites infecting pilchards captured off the Portuguese coast. METHODS: In this study, we analyzed the infection patterns, the morphology of oocysts and the phylogenetic relations of coccidian parasites from European pilchard captured in Northern Portugal. RESULTS: Only Goussia oocysts were detected in infected tissues and prevalence of infection was 64% (n = 61). Oocysts were detected primarily in the liver with fewer infections in the stomach, intestine and gonads. No differences were found in the prevalence between seasons. Phylogenetic analysis showed these parasites are closely related to Goussia clupearum, placing them within a recently described group of Goussia, the clupearum type. CONCLUSIONS: Our study provides more data on Goussia from the clupearum type with phylogenetic analysis indicating that these parasites cluster according to fish host taxonomy, thus suggesting some degree of co-evolution.

Longitudinal sampling of external mucosae in farmed European seabass reveals the impact of water temperature on bacterial dynamics.

Fish microbiota are intrinsically linked to health and fitness, but they are highly variable and influenced by both biotic and abiotic factors. Water temperature particularly limits bacterial adhesion and growth, impacting microbial diversity and bacterial infections on the skin and gills. Aquaculture is heavily affected by infectious diseases, especially in warmer months, and industry practices often promote stress and microbial dysbiosis, leading to an increased abundance of potentially pathogenic bacteria. In this regard, fish mucosa health is extremely important because it provides a primary barrier against pathogens. We used 16 rRNA V4 metataxonomics to characterize the skin and gill microbiota of the European seabass, Dicentrarchus labrax, and the surrounding water over 12 months, assessing the impact of water temperature on microbial diversity and function. We show that the microbiota of external mucosae are highly dynamic with consistent longitudinal trends in taxon diversity. Several potentially pathogenic genera (Aliivibrio, Photobacterium, Pseudomonas, and Vibrio) were highly abundant, showing complex interactions with other bacterial genera, some of which with recognized probiotic activity, and were also significantly impacted by changes in temperature. The surrounding water temperature influenced fish microbial composition, structure and function over time (days and months). Additionally, dysbiosis was more frequent in warmer months and during transitions between cold/warm months. We also detected a strong seasonal effect in the fish microbiota, which is likely to result from the compound action of several unmeasured environmental factors (e.g., pH, nutrient availability) beyond temperature. Our results highlight the importance of performing longitudinal studies to assess the impact of environmental factors on fish microbiotas.

Effects of Goussia infecting the blue whiting and phylogenetic placement of Goussia infecting marine fish off Northern Portugal.

Coccidian parasites of fish have received considerably less attention than their terrestrial counterparts, and within piscine hosts, most studies have focused on freshwater fish. The present study aimed to describe oocyst morphology, phylogenetic affinities, and the impacts of coccidian parasites infecting the internal organs of a commercially valuable marine fish, the blue whiting (Micromesistius poutassou), captured off the Portuguese coast. As part of the phylogenetic analysis, sequences from coccidians infecting the pout (Trisopterus luscus) and the Atlantic chub mackerel (Scomber colias) were included, and the oocyst morphology of the coccidians infecting the former was also reported. Results showed that the prevalence of coccidiosis in the blue whiting was very high (> 82%), occurring in all analyzed organs, despite being more abundant in the liver. A significant negative correlation was found between the abundance of the parasites in the liver and host condition index (p < 0.05), which indicates a negative effect on the fitness of this host. Phylogenetic analyses of the parasites found in all three species examined identified three different species of Goussia, closely related to Goussia clupearum. Adding to previous research, we propose the existence of a fourth group of Goussia, the clupearum type, able to infect multiple organs and phylogenetic related with G. clupearum.

Hurricane-induced disturbance increases genetic diversity and population admixture of the direct-brooding isopod, Gnathia marleyi.

Severe disturbances can substantially alter eco-evolutionary processes and dynamics. While the impacts of catastrophic events on the biophysical attributes of communities are sometimes assessed, their effects on the genetic patterns of species remain poorly understood. To characterize how severe disturbances impact species at the molecular level, we examined the effects of the most energetic North Atlantic hurricane season in 50 years on the genetic diversity and structure of a dispersal-limited isopod, Gnathia marleyi. We sequenced a portion of the cytochrome oxidase I gene for 432 gnathiids, collected from six localities, ranging from western Puerto Rico to St John, US Virgin Islands. Importantly, multiple years of pre-hurricane sample collection allowed us to characterize temporal genetic patterns under undisturbed conditions and detect the changes subsequent to the 2017 hurricanes. Our results revealed no change to genetic diversity or structure for the years prior to the 2017 hurricanes, with genetic structure occurring at the local and regional levels, with three main clusters corresponding to Southwest Puerto Rico, East Puerto Rico, and the US Virgin Islands. However, directly following the 2017 hurricanes, genetic diversity increased at five of the six sampled localities. Additionally, we found a clear homogenizing effect prompted by increased shared genetic diversity among geographically distant regions and sites that resulted in substantially decreased among-region and among-site differentiation. Our work shows that severe disturbances caused by major tropical hurricanes facilitate gene-flow and increase overall genetic diversity and population admixture of dispersal limited coral reef species, potentially impacting the ecology and evolution of a key regional endemic.

Molecular detection of apicomplexan blood parasites of coral reef fishes from free-living stages of ectoparasitic gnathiid isopods.

Gnathiid isopods are marine ectoparasites that feed on the blood of fishes that have been implicated as vectors of blood parasites, with transmission possibly occurring through biting during their parasitic life-stages, or through ingestion by fishes. However, evidence for their role as vectors is limited, reflecting the small number of research groups working on them. Here, we used a molecular barcode approach to identify fish hosts and apicomplexan parasites in free-living gnathiids from the eastern Caribbean Sea, with the goal of further evaluating their potential role as reservoirs and/or vectors for these parasites. Apicomplexa were only identified in 8% of the Gnathia analyzed, and in four cases we could identify both Apicomplexa and fish host DNA. The results further suggest that Gnathia spp. in this region may serve as reservoirs for Apicomplexa, but whether they are vectors for this parasite remains uncertain.

First genetic record of the non-native muzzled blenny Omobranchus punctatus (Teleostei: Blenniidae) in the Atlantic Coast of Central and South America.

In this study we sequenced two mitochondrial (COI and 16S rRNA) and one nuclear (18S rRNA) gene fragment of an introduced muzzled blenny (Omobranchus punctatus) specimen collected from the Orinoco Delta (Gulf of Paria estuary) in Venezuela. This is the first genetic data generated for this species' introduced range in Central and South America, suggesting an introduction from the Indian Ocean.

Effects of disease, antibiotic treatment and recovery trajectory on the microbiome of farmed seabass (Dicentrarchus labrax).

The mucosal surfaces of fish harbour microbial communities that can act as the first-line of defense against pathogens. Infectious diseases are one of the main constraints to aquaculture growth leading to huge economic losses. Despite their negative impacts on microbial diversity and overall fish health, antibiotics are still the method of choice to treat many such diseases. Here, we use 16 rRNA V4 metataxonomics to study over a 6 week period the dynamics of the gill and skin microbiomes of farmed seabass before, during and after a natural disease outbreak and subsequent antibiotic treatment with oxytetracycline. Photobacterium damselae was identified as the most probable causative agent of disease. Both infection and antibiotic treatment caused significant, although asymmetrical, changes in the microbiome composition of the gills and skin. The most dramatic changes in microbial taxonomic abundance occurred between healthy and diseased fish. Disease led to a decrease in the bacterial core diversity in the skin, whereas in the gills there was both an increase and a shift in core diversity. Oxytetracycline caused a decrease in core diversity in the gill and an increase in the skin. Severe loss of core diversity in fish mucosae demonstrates the disruptive impact of disease and antibiotic treatment on the microbial communities of healthy fish.

Genetic diversity of Hepatozoon (Apicomplexa) from domestic cats in South Africa, with a global reassessment of Hepatozoon felis diversity.

Genetic diversity within partial 18S rRNA sequences from Hepatozoon protozoan parasites from domestic cats in South Africa was assessed and compared against published data to assess global biogeographic patterns. Multiple distinct haplotypes of Hepatozoon felis were identified, as well as an unrelated Hepatozoon lineage. Hepatozoon felis genetic diversity globally is very high, indicating a likely complex of species. The recently described Hepatozoon apri from wild boars is closely related to some lineages of H. felis. Sarcocystis and Babesia parasites were also detected. Since Hepatozoon felis is apparently a species complex, potential differences between genetically distinct forms need to be assessed. The finding of an unrelated Hepatozoon indicates that felids can be infected by more species of Hepatozoonthan currently known, and that trophic interactions may increase the number of Hepatozoon species found in carnivores. Genetic screening again is demonstrated to identify previously unrecognised parasites from vertebrate hosts.