Diversity of autochthonous bacterial communities in the intestinal mucosa of grass carp (Ctenopharyngodon idellus) (Valenciennes) determined by culture‐dependent and culture‐independent techniques

Traditional culture‐based technique and 16S rDNA sequencing method were used to investigate the mucosa‐associated autochthonous microbiota of grass carp (Ctenopharyngodon idellus). Twenty‐one phylotypes were detected from culturable microbiota, with Aeromonas, Shewanella, Lactococcus, Serratia, Brevibacillus, Delftia, Pseudomonas, Pantoea, Enterobacter, Buttiauxella and Yersinia as their closest relatives. Genomic DNA was directly extracted from the gut mucosa of C. idellus originating from six different geographical regions, and used to generate 609 random bacterial clones from six clone libraries and 99 archaeal clones from one library, which were grouped into 67 bacterial and four archaeal phylotypes. Sequence analysis revealed that the intestinal mucosa harboured a diversified bacterial microbiota, where Proteobacteria, Firmicutes and Bacteroidetes were dominant, followed by Actinobacteria, Verrucomicrobia and Deinococcus‐Thermus. The autochthonous bacterial communities in the gut mucosa of fish from different aquatic environments were not similar (C_s < 0.80), but γ‐Proteobacteria was a common bacterial class. In comparison to bacterial communities, the archaeal community obtained from one library consisted of Crenarchaeota and Euryarchaeota. These results demonstrate that molecular methods facilitate culture‐independent studies, and that fish gut mucosa harbours a larger bacterial diversity than previously recognized. The grass carp intestinal habitat selects for specific bacterial taxa despite pronounced differences in host environments.     

Relationships among invasive common carp,native fishes and physicochemical characteristics in upper Midwest (USA) lakes

Abstract – Common carp Cyprinus carpio is a widespread invasive species that, in high abundance, can impose numerous deleterious effects in aquatic ecosystems. Common carp increase turbidity and nutrient availability while reducing invertebrate prey resources and aquatic macrophytes, transforming shallow lakes from the clear‐ to turbid‐water state. However, potential effects of common carp on native fish communities have received limited attention. We evaluated the relationships among relative abundances of nine native fishes and common carp for 81 lakes in eastern South Dakota and their associated physicochemical characteristics. Inverse threshold relationships among relative abundances of native fishes and common carp were identified for black bullhead Ameiurus melas, black crappie Pomoxis nigromaculatus, bluegill Lepomis macrochirus, white bass Morone chrysops and northern pike Esox lucius, while marginally significant relationships were detected for largemouth bass Micropterus salmoides and smallmouth bass M. dolomieu. Lakes where common carp relative abundance exceeded 0.6 fish per net night had low abundance of native fishes, whereas lower abundance of common carp resulted in variable abundance of native fishes. Lakes with abundance of common carp surpassing 0.6 fish per net night were also characterised by larger surface areas and watersheds and impaired water quality (higher dissolved solids and chlorophyll a concentrations and lower secchi depth). Our results are consistent with the biotic‐abiotic constraining hypothesis that proposes biotic factors can regulate fish populations regardless of abiotic conditions. Thus, common carp abundance may need to be reduced and sustained below ecological thresholds to improve water quality and increase abundance of native fishes.     

Factors influencing the abundance of three common nearshore fishes in south‐west Lake Michigan

Variation in the distribution and abundance of nearshore fishes is critical to understand food web processes and fishery management issues in Lake Michigan. This study characterised patterns in abundance of three common nearshore species, yellow perch Perca flavescens (Mitchell), round goby Neogobius melanostomus (Pallas) and alewife Alosa pseudoharengus (Wilson), in relation to spatio‐temporal, abiotic and biotic factors using gillnet sampling conducted across 5 years at multiple locations representing different substrates. Significant variations were observed in alewife and round goby catches between locations. A negative relationship between round goby and age‐0 yellow perch catch was observed, indicating potential competition between the two species. This study demonstrates that variability in nearshore fish communities can be driven by factors including substrate and interspecific interactions. Given the prominent role these species play in Lake Michigan's food web and thus their importance to fishery production, a thorough understanding of these factors is warranted.     

Artificial reefs as a reef restoration strategy in sediment‐affected environments: Insights from long‐term monitoring

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Assessment of changes in the ichthyofauna in a tropical reservoir in south-eastern Brazil: Consequences of global warming?

Increases in temperatures over the last century, more intensively after the eighties, were recorded in several databases for the south-eastern Brazil. These increases are likely to change fish communities in aquatic systems by decreasing abundances, biomass and sizes of some species more sensitive to climate change. Reservoirs may be particularly susceptible to the effects of climate change, as they isolate previously connected areas limiting fish dispersal and migration, as well as increasing water temperature and thermal stratification. We assessed temporal changes in the abundance and biomass of the ichthyofauna in an isolate reservoir (inflowing waters from small tributaries in a highland region) aiming to associate changes with climate effects over three decades (1990, 2000, 2010). Two abundant native species, a loricariid Loricariichthys castaneus (Castelnau, 1855) and a cichlid Geophagus brasiliensis (Quoy & Gaimard, 1824), were selected to assess eventual response to climate changes in their geographical distribution in the Southeast Atlantic Hydrographic Region, considering different carbon emission scenarios using ecological niche models. A decrease in the densities and biomass of the ichthyofauna and of the two selected species were observed in both summer and winter over the three decades, coinciding with increases in temperatures. These decreases were correlated with increases in positive anomalies of temperature, which may be an indicator of climatic changes, although with low explanation of the data variation. The mean size of L. castaneus decreased between the nineties and 2010, whereas no significant trend was found for the size of G. brasiliensis. Our predictions of new area for future adequacy indicated a loss in the distribution area for both species (mainly for G. brasiliensis), considering the most pessimistic scenario for 2050 and 2070, possibly due to climatic changes. Both hydroelectric dams and global warming pose threats to freshwater fish diversity, and both will interact. Changes observed in the fish assemblage over the last decades were essential for an assessment of the consequences of global warming in this type of reservoir combining larger scale studies with future projections.     

Effect of tributyrin supplementation in high‐soya bean meal diet on growth performance,body composition,intestine morphology and microbiota of juvenile yellow drum (Nibea albiflora)

Six equal‐protein and equal‐lipid diets were formulated: the fish meal (FM) diet, the soya bean meal (SBM) diet with 40% of FM protein replaced by SBM protein and tributyrin (TB) diets with 0.05% (TB0.05), 0.10% (TB0.1), 0.20% (TB0.2) and 0.40% (TB0.4) tributyrin supplemented in the SBM‐based diet. Each kind of diet was randomly fed to triplicate tanks with 20 fish per tank. Fish were fed apparent satiation twice daily for 56 days. No significant difference in weight gain rate (WGR) and feed efficiency rate (FER) was observed between fish fed the FM, TB0.1 and TB0.2 diets (p > .05). Muscle histidine and arginine proportion of fish fed TB0.1 diet was significantly higher than that of fish fed the SBM diet (p < .05). Intestine morphology results indicated that the supplementation of 0.1% tributyrin significantly improved the mucosal fold height, microvilli length and microvilli density when compared with those of fish fed the SBM diet (p < .05). The supplementation of dietary tributyrin suppressed the pro‐inflammatory gene expression, which may be due to the improvement of physical barrier and modification of microbial communities, such as Acinetobacter, Rhodocyclaceae, Brevundimonas, Sphingopyxis, Hydrogenophaga, Methyloversatilis and Devosia. In conclusion, dietary 0.1% tributyrin supplementation in high‐soya bean meal diet improved growth performance, flesh quality and intestinal morphology structure integrity of yellow drum.     

Cage aquaculture in Neotropical waters promotes attraction and aggregation of fish

The influence of cage aquaculture on the attraction and aggregation of wild fish was evaluated with an experimental tilapia farming structure. The structure was installed in the Corvo River, Rosana Reservoir, Paranapanema River basin, for 140 days. Samples were taken before and after farming began. Gillnets on the surface and near the bottom at different distances from the cages (0, 100 and 400 m) were used for fish sampling. The effects of the food supply at two protein levels were also analysed: Phase 1 = 32% PB and Phase 2 = 28% PB. Changes in species richness and abundance were observed, with the number of individuals and the fish biomass increasing significantly just after the farming began. Some species, such as Iheringichthys labrosus, presented increased abundance near the cages, while others, such as Plagioscion squamosissimus, were more abundant far from the cages. Auchenipterus osteomystax was the most abundant species during the experiment, especially when the protein content of the pellets was higher. It was demonstrated that farming tilapia in cages profoundly altered the abundance and composition of the wild ichthyofauna, suggesting the need to propose effective regulations for such activities, including fisheries restrictions in farmed areas or even the prohibition of cage farming.     

An invasive and a native macrophyte species provide similar feeding habitat for fish

Invasive macrophytes usually increase the homogenisation of habitats and can affect local communities with negative effects on the food chain. We evaluated experimentally the composition, density, richness and diversity of the invertebrates in the invasive macrophyte Hydrilla verticillata and assessed the potential effects of this macrophyte on the diet and foraging efficiency of small native fishes. The native macrophyte Egeria najas was used as control, since it has very similar physical structure and physical complexity to H. verticillata. Macrophytes of both species were maintained separately in aquaria with the fishes, and the invertebrates richness and abundance associated with plants and within fish stomach were evaluated. No significant difference was found in the richness and diversity of invertebrates attached to macrophytes; however, the two macrophytes differed in regard to invertebrate composition, and the density was significantly higher in H. verticillata. The fish foraging efficiency was high in both macrophytes, and the difference between them was not significant. The fish diet did not differ significantly between the native and the invasive macrophyte in respect to invertebrate composition, abundance and richness, and trophic niche breadth. We found no evidence that H. verticillata negatively affects the density of associated invertebrates, and as a consequence, fish diet and foraging efficiency. Our results indicate that the replacement of E. najas by a similar biomass of H. verticillata does not affect the feeding behaviour of associated fish species.     

Isolation,molecular characterization and antimicrobial susceptibility of Aeromonas spp. obtained from Tiger Grouper (Epinephelus fuscoguttatus) and Marble Goby (Oxyeleotris marmoratus) fish in Sabah,Malaysia

Aeromonads are ubiquitous in aquatic environments and have been implicated in fish and human infections. In this study, we isolated, studied antimicrobial susceptibility patterns and screened the existence of 15 virulence genes in aeromonads from two famously consumed fish species—seven marine Tiger Grouper (Epinephelus fuscoguttatus) and eight freshwater Marble Goby (Oxyeleotris marmoratus) from the aquaculture hatchery in Sabah, Malaysia. A total of 30 aeromonads (17 A. caviae, 9 A. rivuli, 4 A. dhakensis) were identified using PCR targeting GCAT gene, rpoD‐restriction fragment length polymorphism and multi‐locus phylogenetic analysis. All 30 strains were resistant to amoxicillin and cephalothin and five strains were multidrug‐resistant. Nine virulence genes (lip, ela, eno, fla, aerA, hylA, dam, alt and ser) present in A. dhakensis, suggesting the virulence potential of this species as a fish pathogen. This study offers as a baseline for future studies in monitoring and managing these two fish in aquaculture industry.     

Mycobacteria in aquarium fish: results of a 3‐year survey indicate caution required in handling pet‐shop fish

Fish are commonly infected with non‐tuberculous mycobacteria (NTM), which should be regarded as potential pathogens when handling aquarium fish and equipment. This study examined 107 aquarium fish from pet shops. Cultivation of the fish samples using different selective media was conducted for identification of NTM. Isolates were identified using the GenoType Mycobacterium common mycobacteria and additional species assays, sequencing of the 16S rRNA and rpoB genes, and real‐time PCR assay for identification of Mycobacterium (M.) marinum. Among the investigated fish, 79.4% (85/107) were positive for mycobacteria, with 8.2% (7 of 85) having two mycobacterial species present. Among the positive fish, the common pathogens M. marinum, Mycobacterium fortuitum (M. fortuitum group) and Mycobacterium chelonae were identified in approx. 90% of fish and other NTM species in 10%, including Mycobacterium peregrinum/septicum, Mycobacterium gordonae, Mycobacterium arupense, Mycobacterium kansasii, Mycobacterium ulcerans and Mycobacterium setense. The well‐known human pathogen M. marinum was present in 10.6% of the positive fish (9 of 85). The species of mycobacteria identified in the study are not only recognized as aquarium fish pathogens, but can also cause pathology in humans. Microbiological and clinical communities should therefore be sensitized to the role of NTM in infections associated with exposure to aquarium fish.     

Gambusia holbrooki,the ‘tadpolefish’: The impact of its predatory behaviour on four protected species of European amphibians

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大陈洋产卵场保护区鱼类群落结构特征及其与环境因子的关系

为了解大陈洋产卵场保护区的保护效果,基于2018年4月(春季)和11月(秋季)在大陈洋产卵场保护区的渔业资源调查数据,利用相对重要性指数(IRI)、多样性分析、聚类分析和典范对应分析(CCA)等方法,对该海域鱼类群落结构特征及其与环境因子的关系进行了相关分析。结果显示,共捕获鱼类83种,隶属于9目51科,其中优势种鱼类2种,重要种18种,隶属于5目11科,优势种为六丝钝尾虾虎鱼和龙头鱼。等级聚类(CLUSTER)和非度量多维测度(NMDS)分析表明,春、秋季鱼类群落在空间上均可分为3组,且群落组间差异显著,龙头鱼、七星底灯鱼、赤鼻棱鳀等是影响群落结构季节变化的主要分歧种。ABC曲线分析表明,春季鱼类群落受到中度干扰(W=0.027);秋季鱼类群落处于较为严重干扰状态(W=-0.185)。典范对应(CCA)分析表明,水深、温度和盐度为影响该海域鱼类种类组成及群落结构时空变化的重要海洋理化因子。与2015年和2017年同期资源量相比,2018年11月生物量和丰度均大幅增加。研究表明,保护区的建立对渔业资源恢复起到了一定的保护作用,但想要将海洋资源恢复到理想状态,需要进行长久的资源保护。     

Bonga shad (Ethmalosa fimbriata) spawning tactics in an upwelling environment

Successful recruitment in small pelagic fish populations inhabiting upwelling zones is subject to variation in fecundity and is driven by spatial and temporal fluctuations in environmental conditions, that is, mainly sea surface temperature, salinity and food availability. These fluctuations in abiotic factors have stimulated small pelagic fish populations to exhibit specifically adapted spawning tactics. To better understand to what extent a short‐lived exploited fish species such as bonga shad Ethmalosa fimbriata has adapted to an upwelling environment, we have investigated the interrelationship between upwelling intensity as a proxy for productivity and population fecundity by means of a virtual population analysis. We found that females of intermediate size contributed significantly more eggs to the population's fecundity than smaller or larger ones. Our model results further indicate that E. fimbriata exhibits a spawning preference at water temperatures of around 25°C and upwelling intensities of around 2.5 m³ s^?1 m^?1. Hence, we hypothesize that climate change‐driven increases in sea temperatures and modifications of upwelling‐favourable winds could significantly impact the species’ reproductive biology. To understand how climate change might impact fisheries, spawning tactics of small pelagic fishes are important to assess as well as their recruitment success. Such information is particularly relevant in countries where the fishery is critical at socio‐economic level, to better implement fisheries management addressing multiple stressors.     

Spatial and temporal variation in otolith chemistry and its relationship with water chemistry: Stock discrimination of Sperata aor

Long‐whiskered catfish, Sperata aor (Hamilton 1822), is commercially important in food, ornamental and sport fisheries. The fish is mainly caught from the wild populations because its aquaculture practices are not commercialised. Inland fishery in the Ganga basin is mostly unorganised; hence, no published report is available on the trend of S. aor production from the selected habitat. In India, S. aor has been categorised vulnerable mainly due to natural and anthropogenic threats. Otolith chemistry shows variation with changing physico‐chemical conditions of the fish habitat. Therefore, the present study was conducted with the objective to analyse spatio‐temporal variations in water chemistry in relation to environmental factors; relationship between water and otolith chemistry; and spatio‐temporal variations in otolith chemistry to discriminate the stocks of S. aor inhabiting the River Ganga. Most of the element: Ca ratios in water samples did not show significant correlations with environmental factors, viz. temperature and conductivity. Only few element: Ca concentrations in otoliths were positively correlated to their corresponding ratios in the ambient water. In the selected study area, the S. aor populations were discriminated into four stocks possibly because of heterogeneous water chemistry at the sampling sites, and physical barriers. In the present study, otolith chemistry showed relatively low temporal variability as compared to spatial variability; thus, the classification accuracy of individuals to their original populations remained consistent over the selected time period. The findings could be useful in devising scientifically sound management strategies and/or any conservation plans for the vulnerable S. aor populations inhabiting the River Ganga.     

Outer membrane protein A (OmpA) is a potential virulence factor of Vibrio alginolyticus strains isolated from diseased fish

Vibrio alginolyticus is one of the most serious causative agents of diseases in cultured marine fish and shellfish. However, the characteristics of virulence factors in pathogenic V. alginolyticus are poorly known. To gain insight into fish diseases caused by V. alginolyticus, we carried out two-dimensional gel electrophoresis (2-DE) combined with MALDI-TOF mass spectrometry to identify uniquely expressed proteins in the disease-causing V. alginolyticus. V. alginolyticus strains were isolated from marine environments and diseased fish obtained from southern Thailand. We identified seven unique proteins in the disease-causing V. alginolyticus strain. Among those, the outer membrane protein A (OmpA) had the strongest expression. Therefore, the function of this protein was further analysed. To investigate the role of OmpA protein, an in-frame deletion mutant of ompA was constructed using the homologous recombination method. Although the ompA mutant V. alginolyticus strain (ΔompA) grew normally, the mutant exhibited a significant defect in the swarming ability and the biofilm formation. Furthermore, Galleria mellonella larvae injected with the mutant bacteria had a significantly greater survival percentage than those injected with the wild-type strain, demonstrating that OmpA protein is required for the pathogenicity of V. alginolyticus. Together, this study suggests a potential target for vaccine development against pathogenic V. alginolyticus strain.     

Assessment of a channel catfish population in a large open river system

Estimates of dynamic rate functions for riverine channel catfish, Ictalurus punctatus (Rafinesque), populations are limited. The open nature and inherent difficulty in sampling riverine environments and the propensity for dispersal of channel catfish impede estimation of population variables. However, contemporary population models (i.e. robust design models) can incorporate the open nature of these systems. The purpose of this study was to determine channel catfish population abundance, survival and size structure and to characterise growth in the lower Platte River, Nebraska, USA. Annual survival estimates of adult channel catfish were 13%–49%, and channel catfish abundance estimates ranged from 8,281 to 24,261 fish within a 10‐km sampling reach. Channel catfish were predominantly (90%) <age 5 and <400 mm total length, and adult growth was similar to other populations across the species’ range. The channel catfish population characteristics in the lower Platte River are likely a result of a combination of factors including recreational harvest and potential shifts in habitat during different life stages. A multifaceted sampling and analytical approach provided additional information such as movement and abundance estimates and may also help to decipher abiotic and biotic factors that interact when managing fish populations in riverine environments.     

Evidence for the facultative intracellular behaviour of the fish pathogen Vibrio ordalii

Vibrio ordalii is an extracellular, Gram‐negative bacterium that produces vibriosis in salmonids. While pathogenesis is not fully understood, this bacterium has numerous likely genes for adhesion, colonization, invasion factors and, as recently suggested, intracellular behaviour. Therefore, this study aimed to clarify possible intracellular behaviour for V. ordalii Vo‐LM‐18 and ATCC 33509^T in the fish‐cell lines SHK‐1 and CHSE‐214. Confocal microscopy revealed Vo‐LM‐18 and ATCC 33509^T inside cytoplasm in both fish‐cell lines at 4 hr post‐inoculation (hpi). At 8 and 16 hpi, the proportion of fish cells invaded by both strains increased. Moreover, intracellular V. ordalii were observed after 8 hpi inside mouse embryonic fibroblasts (MEF), demonstrating that entry was not due to a cellular phagocytosis process. Flow cytometry confirmed immunocytochemistry results, with both V. ordalii evidencing statistically significant differences in the number of infected cells between 8 and 16 hpi. Interestingly, V. ordalii infection did not significantly damage fish cells, as determined by LDH liberation. Viable counts at 8 hpi detected, on average for both lines, 176 ± 47 CFU/ml of culturable intracellular Vo‐LM‐18 and ATCC 33509^T cells. These in vitro findings support the facultative intracellular behaviour of V. ordalii and may be of importance for understanding pathogenicity and survival in aquatic environments.     

Potential climate change impacts on Arctic char Salvelinus alpinus L. in Ireland

Climate change has been identified as a global threat to Arctic char Salvelinus alpinus L. populations. Bayesian statistical models were used to identify important physical and ecological factors explaining Arctic char presence and persistence in Irish lakes. Maximum lake depth and the presence of mixed fish communities (i.e. including non‐salmonid fish species) were the most important drivers of Arctic char presence. There was a 75% probability that an Irish lake would contain Arctic char when maximum depth exceeded 40 m, if only a salmonid community was present. However, the required depth increased to 57 m when a mixed fish community (e.g. pike, perch or roach) was present. Similar variables explained char persistence, with surviving Arctic char populations being more likely in lakes with greater maximum depth and fewer non‐salmonid fish species. Tested temperature covariates were not important in explaining Arctic char presence or persistence in Irish lakes. A risk analysis was undertaken to identify which Arctic char lakes are vulnerable to colonisation by thermally plastic mixed fish communities due to flooding. Results indicated that 32 out of 45 lakes were not at any risk from the colonisation of thermally plastic mixed fish communities and 13 lakes had some level of risk.     

Effects of fisheries zoning and environmental characteristics on population parameters of the tambaqui (Colossoma macropomum) in managed floodplain lakes in the Central Amazon

Fisheries zoning and the influence of biotic and abiotic factors in the spatial distribution of Colossoma macropomum (Cuvier) in the Piagaçu‐Purus Sustainable Development Reserve, Central Amazon, during 2012–2013 were evaluated. The relative abundance and population parameters of the C. macropomum were compared between conservation (no‐take zone) and fishing (open to fishing zone) lakes. The fish were collected by experimental fishing in 2012 and 2013. A total of 296 individuals were captured, most of which were from the conservation lakes (62.8%). Higher proportions of larger adults and individuals were found in the conservation lakes, although no significant difference in the average C. macropomum catch‐per‐unit‐effort was found between the lake categories. Abundance was positively influenced by zooplankton density (r² = 0.53, P < 0.03). Therefore, it is hypothesised that conservation lakes may serve as refugia for juveniles due to the high availability of planktonic food available during the dry season. Although there were environmental differences between the two lake types, the relative success of management models that use no‐take zones in freshwater habitats was highlighted. Finally, the importance of zooplankton as a factor in the distribution of C. macropomum among floodplain lakes was emphasised.     

DNA barcoding reveals blend of silver catfish Rhamdia species from fish farms in Southern Brazil

Rhamdia quelen is the most produced native freshwater fish in fish farms in South Brazil. Until recently, Rhamdia branneri and Rhamdia voulezi were synonyms of R. quelen, and all the species are commercialized as silver catfish (locally called jundiá or bagre sapo) by the aquaculture industry. In fact, because these species are morphologically very similar, interspecific crosses easily might occur in fish farming. We employed standard DNA barcoding to identify jundiá molecular operational taxonomic units (MOTUs) in fish cultivated and commercialized in the industry and in possible escapees in the natural environment in southern Brazil. We analysed 48 individuals from six fish farms and 48 individuals from three rivers (Uruguay, Benedito Novo and Itapocu Rivers) using the mitochondrial cytochrome oxidase subunit I (COI). Four MOTUs were identified based on the estimated optimum threshold (OT = 0.77), and these MOTUs were concordant with Bayesian Inferece (BI) and Neighbour‐Joining (NJ) trees. Our results support the existence of at least three species in our dataset: R. branneri, R. voulezi, and R. quelen 1 and R. quelen 2. The interspecific genetic divergence ranged from 1.1% to 5.1% (mean = 3.5%), and the intraspecific distance ranged from 0% to 1.4% (mean = 0.24%). The presence of cultivated fish in the Uruguay and Benedito Novo Rivers provides evidence of genetic contamination in native populations. These results show the need to regulate aquaculture activities and to characterize the species and commercial lineages of silver catfish that are cultivated in South Brazil.