Microbiome Composition and Function in Aquatic Vertebrates: Small Organisms Making Big Impacts on Aquatic Animal Health

Climate challenges for fish larvae: Interactive multi-stressor effects impair acclimation potential of Atlantic herring larvae

Fish early life stages are particularly vulnerable and heavily affected by changing environmental factors. The interactive effects of multiple climate change-related stressors on fish larvae remain, however, largely underexplored. As rising temperatures can increase the abundance and virulence of bacteria, we investigated the combination of a spring heat wave and bacterial exposure on the development of Atlantic herring larvae (Clupea harengus). Eggs and larvae of Western Baltic Spring-spawners were reared at a normal and high temperature ramp and exposed to Vibrio alginolyticus and V. anguillarum, respectively. Subsequently, mRNA and miRNA transcriptomes, microbiota composition, growth and survival were assessed. Both high temperature and V. alginolyticus exposure induced a major downregulation of gene expression likely impeding larval cell proliferation. In contrast, interactive effects of elevated temperature and V. alginolyticus resulted in minimal gene expression changes, indicating an impaired plastic response, which may cause cellular damage reducing survival in later larval stages. The heat wave alone or in combination with V. alginolyticus induced a notable shift in miRNA expression leading to the down- but also upregulation of predicted target genes. Moreover, both increased temperature and the Vibrio exposures significantly altered the larval microbiota composition, with warming reducing microbial richness and diversity. The outcomes of this study highlight the high sensitivity of herring early life stages towards multiple climate change-related stressors. Our results indicate that interactive effects of rapidly changing environmental factors may exceed the larval stress threshold impairing essential acclimation responses, which may contribute to the ongoing recruitment decline of Western Baltic Spring-Spawning herring.

Potential of nature-based solutions to reduce antibiotics, antimicrobial resistance, and pathogens in aquatic ecosystems. a critical review

This comprehensive scientific review evaluates the effectiveness of nature-based solutions (NBS) in reducing antibiotics (ABs), combating antimicrobial resistance (AMR), and controlling pathogens in various aquatic environments at different river catchment levels. It covers conventional and innovative treatment wetland configurations for wastewater treatment to reduce pollutant discharge into the aquatic ecosystems as well as exploring how river restoration and saltmarshes can enhance pollutant removal. Through the analysis of experimental studies and case examples, the review shows NBS's potential for providing sustainable and cost-effective solutions to improve the health of aquatic ecosystems. It also evaluates the use of diagnostic indicators to predict NBS effectiveness in removing specific pollutants such as ABs and AMR. The review concludes that NBS are feasible for addressing the new challenges stemming from human activities such as the presence of ABs, AMR and pathogens, contributing to a better understanding of NBS, highlighting success stories, addressing knowledge gaps, and providing recommendations for future research and implementation.

Gill-associated ammonia oxidizers are widespread in teleost fish

Recent advances in sequencing methods have greatly expanded the knowledge of teleost-associated microorganisms. While fish-gut microbiomes are comparatively well studied, less attention has gone toward other, external organ-microbiome associations. Gills are particularly interesting to investigate due to their functions in gas exchange, osmoregulation, and nitrogen excretion. We recently discovered a branchial symbiosis between nitrogen-cycling bacteria and teleosts (zebrafish and carp), in which ammonia-oxidizing Nitrosomonas and denitrifying bacteria together convert toxic ammonia excreted by the fish into harmless dinitrogen (N2) gas. This symbiosis can function as a "natural biofilter" in fish gills and can potentially occur in all ammonotelic fish species, but it remains unknown how widespread this symbiosis is. In this study, we analyzed all publicly available gill microbiome data sets and checked for the presence of Nitrosomonas. We discovered that more than half of the described fish gill microbiomes contain 16S rRNA gene sequences of ammonia-oxidizing bacteria (AOB). The presence of gill-specific AOB was shown in both wild and aquacultured fish, as well as in marine and freshwater fish species. Based on these findings, we propose that ammonia oxidizers are widespread in teleost fish gills. These gill-associated AOB can significantly affect fish nitrogen excretion, and the widespread nature of this association suggests that the gill-associated AOB can have similar impacts on more fish species. Future research should address the contribution of these microorganisms to fish nitrogen metabolism and the fundamental characteristics of this novel symbiosis.IMPORTANCERecent advances in sequencing have increased our knowledge of teleost-associated microbiota, but the gill microbiome has received comparatively little attention. We recently discovered a consortium of nitrogen-cycling bacteria in the gills of common carp and zebrafish, which are able to convert (toxic) ammonia into harmless dinitrogen gas. These microorganisms thus function as a natural nitrogen biofilter. We analyzed all available gill microbiome data sets to determine how widespread gill-associated ammonia-oxidizing bacteria (AOB) are. More than half of the data sets contained AOB, representing both aquacultured and wild fish from freshwater and marine habitats. In total, 182 amplicon sequencing variants were obtained, of which 115 were found specifically in the gills and not the environmental microbiomes. As gill-associated AOB are apparently widespread in teleost fish, it is important to study their impact on host nitrogen excretion and the potential to reduce ammonia accumulation in (recirculating) aquaculture of relevant fish species.

Impact of high temperature and drought stress on the microbial community in wolf spiders

High temperatures and drought present significant abiotic challenges that can limit the survival of many arthropods, including wolf spiders, which are ectothermic and play a crucial role in controlling pest populations. However, the impact of these stress factors on the microbiota of spiders remains poorly understood. In this study, we utilized 16 S rRNA gene sequencing to explore the diversity and composition of bacterial communities within Pardosa pseudoannulata under conditions of high temperature and drought stress. We found that Firmicutes, Bacteroidetes, and Proteobacteria were the predominant bacterial phyla present. Analyses of alpha diversity indicated an increase in bacterial diversity under combined stress conditions, as reflected by various diversity indices such as Ace, Chao1, Shannon, and Simpson. Furthermore, co-occurrence network analysis highlighted intricate interactions among the microbial taxa (e.g., Enterobacter, Chitinophaga, and Eubacterium), revealing the adaptive complexity of the spider's microbiome to environmental stress. Functional prediction analysis suggested that combined stress conditions might enhance key metabolic pathways, particularly those related to oxidative phosphorylation and amino acid metabolism. Using Random Forest analysis, we determined that changes in three heat shock proteins were largely attributed to variations in bacterial communities, with Firmicutes being notably influential. Collectively, this in-depth analysis offers novel insights into the responses of microbial communities within spider microbiomes to combined abiotic stresses, providing valuable information for understanding extreme climate impacts and informing ecological management strategies.

Microbiome and network analysis reveal potential mechanisms underlying Carassius auratus diseases: The interactions between critical environmental and microbial factors

Despite the rapid development of research on aquatic environment microbiota, limited attention has been paid to exploring the complex interactions between microbial communities and aquatic environments. Particularly, the mechanisms underlying fish diseases based on such dynamic interactions remain unknown. This study aimed to address the gap by conducting microbiome and co-occurrence network analyses on the typical freshwater aquaculture systems. High-throughput 16S rRNA gene sequencing results revealed significant differences in the microbiota between the disease and healthy groups. Notably, disease mortality varied consistently with the gradient of relative abundance of Proteobacteria (intestine, R2 = 0.46, p < 0.05) and Cyanobacteria (gill, R2 = 0.67, p < 0.01), indicating their potential use as diagnostic criteria. Furthermore, the elevated hepatosomatic index, NO3-N, COD and TC (sediment) were directly correlated with diseases (r > 0.54, p < 0.01). Mean concentrations of NO3-N, COD and TC were elevated by 78.87%, 25.63% and 44.2%, respectively, in ponds where diseases occurred. Quantitative analysis (qPCR) revealed that Aeromonas sobria infected hosts through a potential pathway of "sediment (4.4 × 105 copy number/g)-water (1.1 × 103 copy number/mL)-intestine (1.2 × 106 copy number/g)". Similarly, the potential route for Aeromonas veronii was sediment (4.9 × 106 copy number/g) to gill (5.1 × 105 copy number/g). Additionally, the complexity of microbial networks in the intestine, water, and sediment was significantly lower in the disease group, although no similar phenomenon was observed in the gill microbial network. In summary, these findings reveal that elevated concentrations of crucial environmental factors disrupt the linkages within microbiota, fostering the growth of opportunistic bacteria capable of colonizing fish gut or gills. This offers new insights into potential mechanisms by which environmental factors cause disease in fish.

Network-based integration of omics, physiological and environmental data in real-world Elbe estuarine Zander

Coastal and estuarine environments are under endogenic and exogenic pressures jeopardizing survival and diversity of inhabiting biota. Information of possible synergistic effects of multiple (a)biotic stressors and holobiont interaction are largely missing in estuaries like the Elbe but are of importance to estimate unforeseen effects on animals' physiology. Here, we seek to leverage host-transcriptional RNA-seq and gill mucus microbial 16S rRNA metabarcoding data coupled with physiological and abiotic measurements in a network analysis approach to decipher the impact of multiple stressors on the health of juvenile Sander lucioperca along one of the largest European estuaries. We find mesohaline areas characterized by gill tissue specific transcriptional responses matching osmosensing and tissue remodeling. Liver transcriptomes instead emphasized that zander from highly turbid areas were undergoing starvation which was supported by compromised body condition. Potential pathogenic bacteria, including Shewanella, Acinetobacter, Aeromonas and Chryseobacterium, dominated the gill microbiome along the freshwater transition and oxygen minimum zone. Their occurrence coincided with a strong adaptive and innate transcriptional immune response in host gill and enhanced energy demand in liver tissue supporting their potential pathogenicity. Taken together, we show physiological responses of a fish species and its microbiome to abiotic factors whose impact is expected to increase with consequences of climate change. We further present a method for the close-meshed detection of the main stressors and bacterial species with disease potential in a highly productive ecosystem.

Host-associated microbes mitigate the negative impacts of aquatic pollution

Pollution can negatively impact aquatic ecosystems, aquaculture operations, and recreational water quality. Many aquatic microbes can sequester or degrade pollutants and have been utilized for bioremediation. While planktonic and benthic microbes are well-studied, host-associated microbes likely play an important role in mitigating the negative impacts of aquatic pollution and represent an unrealized source of microbial potential. For example, aquatic organisms that thrive in highly polluted environments or concentrate pollutants may have microbiomes adapted to these selective pressures. Understanding microbe-pollutant interactions in sensitive and valuable species could help protect human well-being and improve ecosystem resilience. Investigating these interactions using appropriate experimental systems and overcoming methodological challenges will present novel opportunities to protect and improve aquatic systems. In this perspective, we review examples of how microbes could mitigate negative impacts of aquatic pollution, outline target study systems, discuss challenges of advancing this field, and outline implications in the face of global changes.

Microbial Diversity and Screening for Potential Pathogens and Beneficial Bacteria of Five Jellyfish Species-Associated Microorganisms Based on 16S rRNA Sequencing

Jellyfish, microorganisms, and the marine environment collectively shape a complex ecosystem. This study aimed to analyze the microbial communities associated with five jellyfish species, exploring their composition, diversity, and relationships. Microbial diversity among the species was assessed using 16S rRNA gene sequencing and QIIME analysis. Significant differences in bacterial composition were found, with distinct dominant taxa in each species: Mycoplasmataceae (99.21%) in Aurelia coerulea, Sphingomonadaceae (22.81%) in Cassiopea andromeda, Alphaproteobacteria_unclassified (family level) (64.09%) in Chrysaora quinquecirrha, Parcubacteria_unclassified (family level) (93.11%) in Phacellophora camtschatica, and Chlamydiaceae (35.05%) and Alphaproteobacteria_unclassified (family level) (38.73%) in Rhopilema esculentum. C. andromeda showed the highest diversity, while A. coerulea exhibited the lowest. Correlations among dominant genera varied, including a positive correlation between Parcubacteria_unclassified (genus level) and Chlamydiaceae_unclassified (genus level). Genes were enriched in metabolic pathways and ABC transporters. The most abundant potential pathogens at the phylum level were Proteobacteria, Tenericutes, Chlamydiae, and Epsilonbacteraeota. The differing microbial compositions are likely influenced by species and their habitats. Interactions between jellyfish and microorganisms, as well as among microorganisms, showed interdependency or antagonism. Most microbial gene functions focused on metabolic pathways, warranting further study on the relationship between pathogenic bacteria and these pathways.

Tracing Acinetobacter baumannii's Journey from Hospitals to Aquatic Ecosystems

BACKGROUND

This study provides a comprehensive analysis of Acinetobacter baumannii in aquatic environments and fish microbiota by integrating culture-dependent methods, 16S metagenomics, and antibiotic resistance profiling.

METHODS

A total of 83 A. baumannii isolates were recovered using culture-dependent methods from intra-hospital infections (IHI) and wastewater (WW) and surface water (SW) samples from two southern Romanian cities in August 2022. The antibiotic susceptibility was screened using disc diffusion, microdilution, PCR, and Whole Genome Sequencing assays.

RESULTS

The highest microbial load in the analyzed samples was found in Glina, Bucharest, for both WW and SW samples across all investigated phenotypes. For Bucharest isolates, the resistance levels corresponded to fluoroquinolones > aminoglycosides > β-lactam antibiotics. In contrast, A. baumannii from upstream SW samples in Târgoviște showed the highest resistance to aminoglycosides. The blaOXA-23 gene was frequently detected in IHI, WW, and SW isolates in Bucharest, but was absent in Târgoviște. Molecular phylogeny revealed the presence of ST10 in Târgoviște isolates and ST2 in Bucharest isolates, while other minor STs were not specifically correlated with a sampling point. Using 16S rRNA sequencing, significant differences in microbial populations between the two locations was identified. The low abundance of Alphaproteobacteria and Actinobacteria in both locations suggests environmental pressures or contamination events.

CONCLUSIONS

These findings indicate significant fecal contamination and potential public health risks, emphasizing the need for improved water quality monitoring and management.

Environmentally responsive changes in mucus indicators and microbiota of Chinese sturgeon Acipensersinensis

The impact of environmental factors on the health of the endangered Chinese sturgeon (Acipenser sinensis) and the potential hazards associated with sample collection for health monitoring pose urgent need to its conservation. In this study, Chinese sturgeons were selected from indoor and outdoor environments to evaluate metabolic and tissue damage indicators, along with a non-specific immune enzyme in fish mucus. Additionally, the microbiota of both water bodies and fish mucus were determined using 16S rRNA high-throughput sequencing. The correlation between the indicators and the microbiota was investigated, along with the measurement of multiple environmental factors. The results revealed significantly higher levels of two metabolic indicators, total protein (TP) and cortisol (COR) in indoor fish mucus compared to outdoor fish mucus (p < 0.05). The activities of acid phosphatase (ACP), alkaline phosphatase (ALP), creatine kinase (CK), alanine aminotransferase (ALT), aspartate aminotransferase (AST), and lactate dehydrogenase (LDH) were significantly higher in indoor fish, serving as indicators of tissue damage (p < 0.05). The activity of lysozyme (LZM) was significantly lower in indoor fish (p < 0.01). Biomarker analysis at the phylum and genus levels in outdoor samples revealed that microorganisms were primarily related to the catabolism of organic nutrients. In indoor environments, microorganisms displayed a broader spectrum of functions, including ecological niche establishment, host colonization, potential pathogenicity, and antagonism of pathogens. KEGG functional enrichment corroborated these findings. Dissolved oxygen (DO), electrical conductivity (EC), ammonia nitrogen (NH3-N), turbidity (TU), and chemical oxygen demand (COD) exerted effects on outdoor microbiota. Temperature (TEMP), nitrate (NO3-), total phosphorus (TP), and total nitrogen (TN) influenced indoor microbiota. Changes in mucus indicators, microbial structure, and function in both environments were highly correlated with these factors. Our study provides novel insights into the health impacts of different environments on Chinese sturgeon using a non-invasive method.

Deciphering taxonomic and functional patterns of microbial communities associated with the tiger tail seahorse (Hippocampus comes)

Gaining insight into the diversity, structure, and metabolic functions of microbial communities is essential for understanding their roles in host health and ecosystem dynamics. However, research on the seahorse-associated microbiome remains limited, despite these threatened fish facing increasing human pressures worldwide. Here, we explored the microbial diversity and metabolic functions of the skin and gut of the tiger tail seahorse (Hippocampus comes) and its surrounding environment using shotgun metagenomics and bioinformatics. Members of the Pseudomonadota phylum were dominant in the skin microbiome, whereas Bacteroidota was dominant in the gut. Bacillota, Actinomycetota, and Planctomycetota were also detected in the seahorse-associated microbiome. Statistical analysis revealed significant differences (P < 0.01) in species diversity between skin and gut microbiomes, with members belonging to the Moraxellaceae family being dominant on the skin and the Bacteroidaceae family in the gut. Moreover, the surrounding environment (water or sediment) did not have a direct effect on the seahorse microbiome composition. The skin microbiome exhibited a higher abundance of functional genes related to energy, lipid, and amino acid metabolism as well as terpenoids and polyketides metabolism, xenobiotics biodegradation, and metabolism compared with the gut. Despite differences among classes, the total abundance of bacteriocins was similar in both gut and skin microbiomes, which is significant in shaping microbial communities due to their antimicrobial properties. A better knowledge of seahorse microbiomes benefits conservation and sustainable aquaculture efforts, offering insights into habitat protection, disease management, and optimizing aquaculture environments, thereby promoting seahorse health and welfare while minimizing environmental impact and enhancing aquaculture sustainability.NEW & NOTEWORTHY To the best of our knowledge, this study represents the first comprehensive examination of the taxonomic and functional patterns of the skin and gut microbiome in the tiger tail seahorse. These findings have the potential to significantly enhance our understanding of the seahorse-associated microbiome, thereby contributing to the prediction and control of bacterial infections in seahorses, which are a leading cause of high mass mortality rates in seahorse aquaculture and other fish species.

Parabacteroides distasonis regulates the infectivity and pathogenicity of SVCV at different water temperatures

BACKGROUND

Spring viremia of carp virus (SVCV) infects a wide range of fish species and causes high mortality rates in aquaculture. This viral infection is characterized by seasonal outbreaks that are temperature-dependent. However, the specific mechanism behind temperature-dependent SVCV infectivity and pathogenicity remains unclear. Given the high sensitivity of the composition of intestinal microbiota to temperature changes, it would be interesting to investigate if the intestinal microbiota of fish could play a role in modulating the infectivity of SVCV at different temperatures.

RESULTS

Our study found that significantly higher infectivity and pathogenicity of SVCV infection in zebrafish occurred at relatively lower temperature. Comparative analysis of the intestinal microbiota in zebrafish exposed to high- and low-temperature conditions revealed that temperature influenced the abundance and diversity of the intestinal microbiota in zebrafish. A significantly higher abundance of Parabacteroides distasonis and its metabolite secondary bile acid (deoxycholic acid, DCA) was detected in the intestine of zebrafish exposed to high temperature. Both colonization of Parabacteroides distasonis and feeding of DCA to zebrafish at low temperature significantly reduced the mortality caused by SVCV. An in vitro assay demonstrated that DCA could inhibit the assembly and release of SVCV. Notably, DCA also showed an inhibitory effect on the infectious hematopoietic necrosis virus, another Rhabdoviridae member known to be more infectious at low temperature.

CONCLUSIONS

This study provides evidence that temperature can be an important factor to influence the composition of intestinal microbiota in zebrafish, consequently impacting the infectivity and pathogenicity of SVCV. The findings highlight the enrichment of Parabacteroides distasonis and its derivative, DCA, in the intestines of zebrafish raised at high temperature, and they possess an important role in preventing the infection of SVCV and other Rhabdoviridae members in host fish. Video Abstract.

One Health Threat of Treated Wastewater Discharge in Urban Ohio Rivers: Implications for Surface Water and Fish Gut Microbiome and Resistome

Wastewater treatment plants (WWTPs) are thought to be a major disseminating source of antibiotic resistance (AR) to the environment, establishing a crucial connection between human and environmental resistome. The objectives of this study were to determine how wastewater effluents impact microbiome and resistome of freshwater and fish, and identify potential AR-carrying clinically relevant pathogens in these matrices. We analyzed wastewater influent and effluent from four WWTPs in three metropolitan areas of Ohio, USA via shotgun metagenomic sequencing. We also sequenced river water and fish guts from three reaches (upstream, at the WWTP outfall, and downstream). Notably, we observed a decline in microbiome diversity and AR gene abundance from wastewater to the receiving river. We also found significant differences by reach and trophic level (diet) in beta-diversity of the fish gut microbiomes. SourceTracker revealed that 0.443 and 0.248 more of the of the fish gut microbiome was sourced from wastewater effluent in fish from the outfall and downstream locations, respectively, compared to upstream fish. Additionally, AR bacteria of public health concern were annotated in effluent and river water samples, indicating potential concern for human exposure. In summary, our findings show the continued role of wastewater as a significant AR reservoir and underscores the considerable impact of wastewater discharge on aquatic wildlife, which highlights the One Health nature of this issue.

Effect of emerging pollutants on the gut microbiota of freshwater animals: Focusing on microplastics and pesticides

In recent years, emerging environmental pollutants have increasingly endangered the health of freshwater organisms. The gut microbiota exhibits sensitivity to medications, dietary factors and environmental pollutants, rendering it a novel target for toxicological studies. The gut microbiota can be a potential exposure route affecting the host's health. Herein, we review the current knowledge on two different but concurrent pollutants, microplastics and pesticides, regarding their impact on the gut microbiota, which includes alterations in microbial composition, gene expression, function, and health effects in the hosts. Moreover, synergetic interactions between microplastics and pesticides can exacerbate dysbiosis and health risks. We discuss health-related implications of gut microbial changes based on the consequences in metabolism, immunity, and physiology function. Further research is needed to discover the mechanisms underlying these effects and develop strategies for mitigating their harmful impacts on freshwater animals.

Exploring BPA alternatives - Environmental levels and toxicity review

Bisphenol A alternatives are manufactured as potentially less harmful substitutes of bisphenol A (BPA) that offer similar functionality. These alternatives are already in the market, entering the environment and thus raising ecological concerns. However, it can be expected that levels of BPA alternatives will dominate in the future, they are limited information on their environmental safety. The EU PARC project highlights BPA alternatives as priority chemicals and consolidates information on BPA alternatives, with a focus on environmental relevance and on the identification of the research gaps. The review highlighted aspects and future perspectives. In brief, an extension of environmental monitoring is crucial, extending it to cover BPA alternatives to track their levels and facilitate the timely implementation of mitigation measures. The biological activity has been studied for BPA alternatives, but in a non-systematic way and prioritized a limited number of chemicals. For several BPA alternatives, the data has already provided substantial evidence regarding their potential harm to the environment. We stress the importance of conducting more comprehensive assessments that go beyond the traditional reproductive studies and focus on overlooked relevant endpoints. Future research should also consider mixture effects, realistic environmental concentrations, and the long-term consequences on biota and ecosystems.

Tolerance to environmental pollution in the freshwater crustacean Asellus aquaticus: A role for the microbiome

Freshwater habitats are frequently contaminated by diverse chemicals of anthropogenic origin, collectively referred to as micropollutants, that can have detrimental effects on aquatic life. The animals' tolerance to micropollutants may be mediated by their microbiome. If polluted aquatic environments select for contaminant-degrading microbes, the acquisition of such microbes by the host may increase its tolerance to pollution. Here we tested for the potential effects of the host microbiome on the growth and survival of juvenile Asellus aquaticus, a widespread freshwater crustacean. Using faecal microbiome transplants, we provided newly hatched juveniles with the microbiome isolated from donor adults reared in either clean or micropollutant-contaminated water and, after transplantation, recipient juveniles were reared in water with and without micropollutants. The experiment revealed a significant negative effect of the micropollutants on the survival of juvenile isopods regardless of the received faecal microbiome. The micropollutants had altered the composition of the bacterial component of the donors' microbiome, which in turn influenced the microbiome of juvenile recipients. Hence, we show that relatively high environmental concentrations of micropollutants reduce survival and alter the microbiome composition of juvenile A. aquaticus, but we have no evidence that tolerance to micropollutants is modulated by their microbiome.

Dual stressors of infection and warming can destabilize host microbiomes

Climate change is causing extreme heating events and intensifying infectious disease outbreaks. Animals harbour microbial communities, which are vital for their survival and fitness under stressful conditions. Understanding how microbiome structures change in response to infection and warming may be important for forecasting host performance under global change. Here, we evaluated alterations in the microbiomes of several wild Caenorhabditis elegans isolates spanning a range of latitudes, upon warming temperatures and infection by the parasite Leucobacter musarum. Using 16S rRNA sequencing, we found that microbiome diversity decreased, and dispersion increased over time, with the former being more prominent in uninfected adults and the latter aggravated by infection. Infection reduced dominance of specific microbial taxa, and increased microbiome dispersion, indicating destabilizing effects on host microbial communities. Exposing infected hosts to warming did not have an additive destabilizing effect on their microbiomes. Moreover, warming during pre-adult development alleviated the destabilizing effects of infection on host microbiomes. These results revealed an opposing interaction between biotic and abiotic factors on microbiome structure. Lastly, we showed that increased microbiome dispersion might be associated with decreased variability in microbial species interaction strength. Overall, these findings improve our understanding of animal microbiome dynamics amidst concurrent climate change and epidemics. This article is part of the theme issue 'Sculpting the microbiome: how host factors determine and respond to microbial colonization'.

Integrated microbiome and metabolome analyses reveal the effects of low pH on intestinal health and homeostasis of crayfish (Procambarus clarkii)

Low pH (LpH) poses a significant challenge to the health, immune response, and growth of aquatic animals worldwide. Crayfish (Procambarus clarkii) is a globally farmed freshwater species with a remarkable adaptability to various environmental stressors. However, the effects of LpH stress on the microbiota and host metabolism in crayfish intestines remain poorly understood. In this study, integrated analyses of antioxidant enzyme activity, histopathological damage, 16S rRNA gene sequencing, and liquid chromatography-mass spectrometry (LC-MS) were performed to investigate the physiology, histopathology, microbiota, and metabolite changes in crayfish intestines exposed to LpH treatment. The results showed that LpH stress induced obvious changes in superoxide dismutase and catalase activities and histopathological alterations in crayfish intestines. Furthermore, 16S rRNA gene sequencing analysis revealed that exposure to LpH caused significant alterations in the diversity and composition of the crayfish intestinal microbiota at the phylum and genus levels. At the genus level, 14 genera including Bacilloplasma, Citrobacter, Shewanella, Vibrio, RsaHf231, Erysipelatoclostridium, Anaerorhabdus, Dysgonomonas, Flavobacterium, Tyzzerella, Brachymonas, Muribaculaceae, Propionivibrio, and Comamonas, exhibited significant differences in their relative abundances. The LC-MS analysis revealed 859 differentially expressed metabolites in crayfish intestines in response to LpH, including 363 and 496 upregulated and downregulated metabolites, respectively. These identified metabolites exhibited significant enrichment in 24 Kyoto Encyclopedia of Genes and Genomes pathways (p < 0.05), including seven and 17 upregulated and downregulated pathways, respectively. These pathways are mainly associated with energy and amino acid metabolism. Correlation analysis revealed a strong correlation between the metabolites and intestinal microbiota of crayfish during LpH treatment. These findings suggest that LpH may induce significant oxidative stress, intestinal tissue damage, disruption of intestinal microbiota homeostasis, and alterations in the metabolism in crayfish. These findings provide valuable insights into how the microbial and metabolic processes of crayfish intestines respond to LpH stress.

Heartworm and seal louse: Trends in prevalence, characterisation of impact and transmission pathways in a unique parasite assembly on seals in the North and Baltic Sea

The ectoparasitic seal louse, Echinophthirius horridus infects harbour (Phoca vitulina) and grey seals (Halichoerus grypus) in the North and Baltic Sea. The endoparasitic heartworm Acanthocheilonema spirocauda parasitizes the right heart and blood vessels of harbour seals. The complete lifecycle of the heartworm is not entirely understood although the seal louse is assumed to serve as vector for its transmission. Knowledge about the impact of both parasite species on host health are scarce. In this study, necropsy data and archived parasites of harbour and grey seals in German waters were analysed to determine long-term seal louse (SLP) and heartworm prevalence (HWP) from 2014 to 2021. Histology, microbiology and scanning electron microscopy (SEM) were applied on seal louse infected and uninfected skin to investigate associated lesions and the health impact. During the study period, HWP in harbour seals was 13%, the SLP in harbour seals was 4% and in grey seals 10%. HWP of harbour seals was significantly higher during the winter months compared to the summer. SLP in adults was significantly higher in comparison to juvenile harbour seals. SLP varied significantly between grey seals from the North and Baltic Sea. Filarial nematodes were detected in the haemocoel, pharynx, and intestine of E. horridus highlighting the seal louse as vector for heartworms. Alopecia and folliculitis were associated with the attachment posture of E. horridus and microbiological investigations isolated bacteria commonly associated with folliculitis.

Lactic Acid Bacteria of Marine Origin as a Tool for Successful Shellfish Farming and Adaptation to Climate Change Conditions

Climate change, especially in the form of temperature increase and sea acidification, poses a serious challenge to the sustainability of aquaculture and shellfish farming. In this context, lactic acid bacteria (LAB) of marine origin have attracted attention due to their ability to improve water quality, stimulate the growth and immunity of organisms, and reduce the impact of stress caused by environmental changes. Through a review of relevant research, this paper summarizes previous knowledge on this group of bacteria, their application as protective probiotic cultures in mollusks, and also highlights their potential in reducing the negative impacts of climate change during shellfish farming. Furthermore, opportunities for further research and implementation of LAB as a sustainable and effective solution for adapting mariculture to changing climate conditions were identified.

Unveiling the underwater threat: Exploring cadmium's adverse effects on tilapia

Prolonged exposure to environmentally relevant amounts of cadmium (Cd) in aquatic environments, even at small doses (0.1 and 1 μg/L), might endanger the health of underwater creatures. This research delved into the impacts of a four-month cadmium exposure on Mozambique tilapia (Oreochromis mossambicus), aiming to uncover the mechanisms behind it. Through close examination, we found that the 4-momth cadmium exposure led to harmful effects on the fish's gills, muscles, brain, and intestines. This exposure also triggered changes in gene expressions in the brain and liver, affected the respiratory system and weakened liver's ability to detoxify and defend against potential infections. Looking deeper into the fish's gut, we noticed alterations in energy-related genes and disruptions in immune pathways, making it more susceptible to illnesses. The exposure to cadmium also had an impact on the fish's gut and water-dwelling microorganisms, reducing diversity and encouraging harmful microbial communities. Interestingly, some gut microbes seemed to assist in breaking down and detoxifying cadmium, which could potentially protect the fish. Taken together, prolonged low-level cadmium exposure impaired gill, muscle, and brain function, suppressed immunity, disrupted intestines, and altered microbial balance, leading to hindered growth. These insights illuminate cadmium's impact on fish, addressing vital environmental concerns.

Increased environmental microbial diversity reduces the disease risk of a mosquitocidal pathogen

IMPORTANCE

The host-specific microbiotas of animals can both reduce and increase disease risks from pathogens. In contrast, how environmental microbial communities affect pathogens is largely unexplored. Aquatic habitats are of interest because water enables environmental microbes to readily interact with animal pathogens. Here, we focused on mosquitoes, which are important disease vectors as terrestrial adults but are strictly aquatic as larvae. We identified a pathogen of mosquito larvae from the field as a strain of Chromobacterium haemolyticum. Comparative genomic analyses and functional assays indicate this strain and other Chromobacterium are mosquitocidal but are also opportunistic pathogens of other animals. We also identify a critical role for diversity of the environmental microbiota in disease risk. Our study characterizes both the virulence mechanisms of a pathogen and the role of the environmental microbiota in disease risk to an aquatic animal of significant importance to human health.

Fecal and skin microbiota of two rescued Mediterranean monk seal pups during rehabilitation

IMPORTANCE

This study showed that during the rehabilitation of two rescued Mediterranean monk seal pups (Monachus monachus), the skin and fecal bacterial communities showed similar succession patterns between the two individuals. This finding means that co-housed pups share their microbiomes, and this needs to be considered in cases of infection outbreaks and their treatment. The housing conditions, along with the feeding scheme and care protocols, including the admission of antibiotics as prophylaxis, probiotics, and essential food supplements, resulted in bacterial communities with no apparent pathogenic bacteria. This is the first contribution to the microbiome of the protected seal species of M. monachus and contributes to the animal's conservation practices through its microbiome.

Effectiveness assessment of using water environmental microHI to predict the health status of wild fish

Aquatic wildlife health assessment is critically important for aquatic wildlife conservation. However, the health assessment of aquatic wildlife (especially aquatic wild animals) is difficult and often accompanied by invasive survey activities and delayed observability. As there is growing evidence that aquatic environmental microbiota could impact the health status of aquatic animals by influencing their symbiotic microbiota, we propose a non-invasive method to monitor the health status of wild aquatic animals using the environmental microbiota health index (microHI). However, it is unknown whether this method is effective for different ecotype groups of aquatic wild animals. To answer this question, we took a case study in the middle Yangtze River and studied the water environmental microbiota and fish gut microbiota at the fish community level, population level, and ecotype level. The results showed that the gut microHI of the healthy group was higher than that of the unhealthy group at the community and population levels, and the overall gut microHI was positively correlated with the water environmental microHI, whereas the baseline gut microHI was species-specific. Integrating these variations in four ecotype groups (filter-feeding, scraper-feeding, omnivorous, and carnivorous), only the gut microHI of the carnivorous group positively correlated with water environmental microHI. Alcaligenaceae, Enterobacteriaceae, and Achromobacter were the most abundant groups with health-negative-impacting phenotypes, had high positive correlations between gut sample group and environment sample group, and had significantly higher abundance in unhealthy groups than in healthy groups of carnivorous, filter-feeding, and scraper-feeding ecotypes. Therefore, using water environmental microHI to indicate the health status of wild fish is effective at the community level, is effective just for carnivorous fish at the ecotype level. In the middle Yangtze River, Alcaligenaceae, Enterobacteriaceae (family level), and Achromobacter (genus level) were the key water environmental microbial groups that potentially impacted wild fish health status. Of course, more data and research that test the current hypothesis and conclusion are encouraged.

Salmo salar Skin and Gill Microbiome during Piscirickettsia salmonis Infection

Maintaining the high overall health of farmed animals is a central tenant of their well-being and care. Intense animal crowding in aquaculture promotes animal morbidity especially in the absence of straightforward methods for monitoring their health. Here, we used bacterial 16S ribosomal RNA gene sequencing to measure bacterial population dynamics during P. salmonis infection. We observed a complex bacterial community consisting of a previously undescribed core pathobiome. Notably, we detected Aliivibrio wodanis and Tenacibaculum dicentrarchi on the skin ulcers of salmon infected with P. salmonis, while Vibrio spp. were enriched on infected gills. The prevalence of these co-occurring networks indicated that coinfection with other pathogens may enhance P. salmonis pathogenicity.

Pathological changes of highly pathogenic Bacillus cereus on Pelodiscus sinensis

An outbreak of a disease with a high mortality rate occurred in a Chinese Softshell Turtle (Pelodiscus sinensis) farm in Hubei Province. This study isolated a highly pathogenic Bacillus cereus strain (Y271) from diseased P. sinensis. Y271 has β hemolysis, containing both Hemolysin BL (hblA, hblC, and hblD), Non-hemolytic enterotoxin, NHE (nheA, nheB, and nheC), and Enterotoxin FM (entFM) genes. Y271 is highly pathogenic against P. sinensis with an LD50 = 6.80 × 103 CFU/g weight. B. cereus was detected in multiple tissues of the infected P. sinensis. Among them, spleen tissue showed the highest copy number density (1.54 ± 0.12 × 104 copies/mg). Multiple tissues and organs of diseased P. sinensis exhibited significant pathological damage, especially the spleen, liver, kidney, and intestine. It showed obvious tissue structure destruction, lesions, necrosis, red blood cells, and inflammatory cell infiltration. B. cereus proliferating in the spleen, liver, and other tissues was observed. The intestinal microbiota of the diseased P. sinensis was altered, with a greater abundance of Firmicutes, Fusobacterium, and Actinomyces than in the healthy group. Allobaculum, Rothia, Aeromonas, and Clostridium abundance were higher in the diseased group than in the healthy group. The number of unique microbial taxa (472) in the disease group was lower than that of the healthy group (705). Y271 was sensitive to multiple drugs, including florfenicol, enrofloxacin, neomycin, and doxycycline. B. cereus is the etiological agent responsible for the massive death of P. sinensis and reveals its potential risks during P. sinensis cultivation.

Impact of disturbance and dietary shift on gastrointestinal bacterial community and its invertebrate host system

The gut microbiome is one of the most important sites of host-microbe interactions, however, mechanisms governing the responses of host-associated microbes to changing environmental conditions are poorly understood. To address this, we investigated individual and combined effects of dietary changes and increase in salinity (from freshwater to salinity 3) or antibiotic concentration on the gastrointestinal bacterial community of the aquatic snail Ampullaceana balthica. In parallel, the energy reserves of the host were quantified. A change of natural food source to biofilm forming green algae Scenedesmus obliquus as well as the combined treatment of salinity and S. obliquus decreased the richness and changed the composition of the A. balthica gastrointestinal bacterial community. In these treatments Pseudomonas became the dominant bacterium. However, energy reserves of the host were higher in these treatments compared to the reference aquaria specimens and the combined treatment of antibiotics with S. obliquus. The presence of antibiotics inhibited the dominance of Pseudomonas and resulted in lower energy reserves despite S. obliquus feeding. Therefore the host seems to be able to adapt and replace its bacterial community composition to respond to mild changes in salinity and food source. Antibiotics in the water can disturb this self-regulating mechanism. Our study underlines the ability of aquatic macroinvertebrates to respond to sudden changes in food source and mild shifts in salinity. Moreover, it emphasizes the strong impact of the food source on the gastrointestinal microbiome and the importance of generalists during disturbance.

Host-microbiome interaction in fish and shellfish: An overview

The importance of the gut microbiome in the management of various physiological activities including healthy growth and performance of fish and shellfish is now widely considered and being studied in detail for potential applications in aquaculture farming and the future growth of the fish industry. The gut microbiome in all animals including fish is associated with a number of beneficial functions for the host, such as stimulating optimal gastrointestinal development, producing and supplying vitamins to the host, and improving the host's nutrient uptake by providing additional enzymatic activities. Besides nutrient uptake, the gut microbiome is involved in strengthening the immune system and maintaining mucosal tolerance, enhancing the host's resilience against infectious diseases, and the production of anticarcinogenic and anti-inflammatory compounds. Because of its significant role, the gut microbiome is very often considered an "extra organ," as it plays a key role in intestinal development and regulation of other physiological functions. Recent studies suggest that the gut microbiome is involved in energy homeostasis by regulating feeding, digestive and metabolic processes, as well as the immune response. Consequently, deciphering gut microbiome dynamics in cultured fish and shellfish species will play an indispensable role in promoting animal health and aquaculture productivity. It is mentioned that the microbiome community available in the gut tract, particularly in the intestine acts as an innovative source of natural product discovery. The microbial communities that are associated with several marine organisms are the source of natural products with a diverse array of biological activities and as of today, more than 1000 new compounds have been reported from such microbial species. Exploration of such new ingredients from microbial species would create more opportunities for the development of the bio-pharma/aquaculture industries. Considering the important role of the microbiome in the whole life span of fish and shellfish, it is necessary to understand the interaction process between the host and microbial community. However, information pertaining to host-microbiome interaction, particularly at the cellular level, gene expression, metabolic pathways, and immunomodulation mechanisms, the available literature is scanty. It has been reported that there are three ways of interaction involving the host-microbe-environment operates to maintain homeostasis in the fish and shellfish gut i.e. host intrinsic factors, the environment that shapes the gut microbiome composition, and the core microbial community present in the gut system itself has equal influence on the host biology. In the present review, efforts have been made to collect comprehensive information on various aspects of host-microbiome interaction, particularly on the immune system and health maintenance, management of diseases, nutrient uptake, digestion and absorption, gene expression, and metabolism in fish and shellfish.

Metagenomic analysis reveals diverse microbial community and potential functional roles in Baner rivulet, India

BACKGROUND

The health index of any population is directly correlated with the water quality, which in turn depends upon physicochemical characteristics and the microbiome of that aquatic source. For maintaining the water quality, knowledge of microbial diversity is a must. The present investigation attempts to evaluate the microflora of Baner. Metagenomics has been proven to be the technique for examining the genetic diversity of unculturable microbiota without using traditional culturing techniques. The microbial profile of Baner is analyzed using metagenomics for the first time to the best of our knowledge.

RESULTS

To explore the microbial diversity of Baner, metagenomics analysis from 3 different sites was done. Data analysis identified 29 phyla, 62 classes, 131 orders, 268 families, and 741 genera. Proteobacteria was found to be the most abundant phylum in all the sampling sites, with the highest abundance at S3 sampling site (94%). Bacteroidetes phylum was found to be second abundant in S1 and S2 site, whereas Actinobacteria was second dominant in sampling site S3. Enterobacteriaceae family was dominant in site S1, whereas Comamonadaceae and Pseudomonadaceae was abundant in sites S2 and S3 respectively. The Baner possesses an abundant bacterial profile that holds great promise for developing bioremediation tactics against a variety of harmful substances.

CONCLUSION

Baner river's metagenomic analysis offers the first insight into the microbial profile of this hilly stream. Proteobacteria was found to be the most abundant phylum in all the sampling sites indicating anthropogenic interference and sewage contamination. The highest abundance of proteobacteria at S3 reveals it to be the most polluted site, as it is the last sampling site downstream of the area under investigation, and falls after crossing the main city, so more human intervention and pollution were observed. Despite some pathogens, a rich profile of bacteria involved in bioremediation, xenobiotic degradation, and beneficial fish probiotics was observed, reflecting their potential applications for improving water quality and establishing a healthy aquaculture and fishery section.

Insights in Pharmaceutical Pollution: The Prospective Role of eDNA Metabarcoding

Environmental pollution is a growing threat to natural ecosystems and one of the world's most pressing concerns. The increasing worldwide use of pharmaceuticals has elevated their status as significant emerging contaminants. Pharmaceuticals enter aquatic environments through multiple pathways related to anthropogenic activity. Their high consumption, insufficient waste treatment, and the incapacity of organisms to completely metabolize them contribute to their accumulation in aquatic environments, posing a threat to all life forms. Various analytical methods have been used to quantify pharmaceuticals. Biotechnology advancements based on next-generation sequencing (NGS) techniques, like eDNA metabarcoding, have enabled the development of new methods for assessing and monitoring the ecotoxicological effects of pharmaceuticals. eDNA metabarcoding is a valuable biomonitoring tool for pharmaceutical pollution because it (a) provides an efficient method to assess and predict pollution status, (b) identifies pollution sources, (c) tracks changes in pharmaceutical pollution levels over time, (d) assesses the ecological impact of pharmaceutical pollution, (e) helps prioritize cleanup and mitigation efforts, and (f) offers insights into the diversity and composition of microbial and other bioindicator communities. This review highlights the issue of aquatic pharmaceutical pollution while emphasizing the importance of using modern NGS-based biomonitoring actions to assess its environmental effects more consistently and effectively.

The Role of Biogeography in Shaping Intestinal Flora and Influence on Fatty Acid Composition in Red Swamp Crayfish (Procambarus clarkii)

Intestinal microbiota plays an important role in promoting digestion, metabolism, and immunity. Intestinal microbiota and fatty acids are important indicators to evaluate the health and nutritional composition of Procambarus clarkii. They have been shown to be strongly influence by environmental and genetic factors. However, it is not clear whether environmental factors have a greater impact on the intestinal microbiota and fatty acid composition of crayfish. The link between the intestinal microbial communities and fatty acid (FA) compositions of red swamp crayfish from different geographical has not yet been studied. Thus, the current paper focuses on the influence of different environments on the fatty acids in muscles of crayfish and the possible existence between gut microbiota and fatty acids. Therefore, in this study, we compared the fatty acid compositions and intestinal microbiota of five crayfish populations from different geographical locations. The results were further analyzed to determine whether there is a relationship between geographical location, fatty acid compositions and intestinal microbiota. The gut microbial communities of the crayfish populations were characterized using 16S rRNA high-throughput gene sequencing. The results showed that there were significant differences in FA compositions of crayfish populations from different geographical locations. A similar trend was observed in the gut microbiome, which also varied significantly according to geographic location. Interestingly, the analysis revealed that there was a relationship between fatty acid compositions and intestinal microbes, revealed by alpha diversity analysis and cluster analysis. However, further studies of the interactions between the P. clarkii gut microbiota and biochemical composition are needed, which will ultimately reveal the complexity of microbial ecosystems with potential applications in aquaculture and species conservation.

Comparison of the gill and gut microbiomes of common carp (Cyprinus carpio) and zebrafish (Danio rerio) and their RAS environment

Recirculating aquaculture systems (RAS) are increasingly being used to grow fish, as intensive water reuse reduces water consumption and environmental impact. RAS use biofilters containing nitrogen-cycling microorganisms that remove ammonia from the aquaculture water. Knowledge of how RAS microbial communities relate to the fish-associated microbiome is limited, as is knowledge of fish-associated microbiota in general. Recently, nitrogen-cycling bacteria have been discovered in zebrafish and carp gills and shown to detoxify ammonia in a manner similar to the RAS biofilter. Here, we compared RAS water and biofilter microbiomes with fish-associated gut and gill microbial communities in laboratory RAS housing either zebrafish (Danio rerio) or common carp (Cyprinus carpio) using 16S rRNA gene amplicon sequencing. The phylogeny of ammonia-oxidizing bacteria in the gills and the RAS environment was investigated in more detail by phylogenetic analysis of the ammonia monooxygenase subunit A (amoA). The location from which the microbiome was sampled (RAS compartments and gills or gut) had a stronger effect on community composition than the fish species, but species-specific differences were also observed. We found that carp- and zebrafish-associated microbiomes were highly distinct from their respective RAS microbiomes, characterized by lower overall diversity and a small core microbiome consisting of taxa specifically adapted to the respective organ. The gill microbiome was also defined by a high proportion of unique taxa. Finally, we found that amoA sequences from the gills were distinct from those from the RAS biofilter and water. Our results showed that the gut and gill microbiomes of carp and zebrafish share a common and species-specific core microbiome that is distinct from the microbially-rich RAS environment.

The shared microbiome in mud crab (Scylla paramamosain) of Sanmen Bay, China: core gut microbiome

Introduction

The mud crab, Scylla paramamosain, holds great commercial significance as a marine crustacean widely cultivated in the Indo-Pacific region. Understanding the core gut microbiota of aquatic animals is crucial for their overall health and growth, yet the core gut microbiota of mud crab remains poorly characterized.

Methods

In this study, we gathered gut samples from mud crabs across five locations within Sanmen Bay, China. Through the utilization of high-throughput sequencing, we delved into the composition of the gut microbial community and identified the core gut microbiome of mud crab.

Results

Our results demonstrate that the gut microbial diversity of mud crab did not exhibit significant variation among the five sampling sites, although there were some differences in community richness. At the phylum level, we identified 35 representative phyla, with Firmicutes, Proteobacteria, Bacteroidota, and Campilobacterota as the dominant phyla. Among the 815 representative genera, we discovered 19 core genera, which accounted for 65.45% of the total sequences. These core genera were distributed across 6 phyla, and among them, Photobacterium exhibited the highest average relative abundance.

Discussion

Photobacterium has probiotic activity and may play a crucial role in enhancing the immune response of the host and maintaining the diversity of the gut microbiota. Moreover, we observed a positive correlation between the relative abundance of core genera and the stability of the gut microbial community. Furthermore, our findings revealed distinct differences in gut microbial composition and specific taxa between the sexes of mud crab. These differences subsequently influenced the functionality of the gut microbial community. Overall, our investigation sheds light on the core gut microbiota of mud crab, emphasizing the importance of core gut microbial communities in maintaining the health and growth of these commercially significant marine crustaceans.

Thermal Effect on Algae, Biofilm and Their Composition Towards Membrane Distillation Unit: A Mini-review

Membrane distillation (MD) has lower operating temperature and potential to recycle waste heat for desalination which catches much attention of the researchers in the recent years. However, the biofouling is still a challenging hurdle to be overcome for such applications. The microbial growth rate, secretion and biofilm formation are sensitive to heat. Membrane distillation is a thermally driven separation, so the increase of temperature in the seawater feed could influence the extent of biofouling on the unit parts. In this review, we present the effect of temperature on algal growth, the range of temperature the microbes, marine algae and planktons able to survive and the changes to those planktons once exceed the critical temperature. Thermal effect on the biofilm, its composition and properties are discussed as well, with association of the biofilm secreting microbes, but the study related to membrane distillation unit seems to be lacking and MD biofouling factors are not fully understood. Characterization of the algae, biofilm and EPS that govern biofouling are discussed. This information not only will help in designing future studies to fill up the knowledge gaps in biofouling of membrane distillation, but also to some extent, assist in pointing out possible fouling factors and predicting the degree of biofouling in the membrane distillation unit.

Direct and gut microbiota-mediated toxicities of environmental antibiotics to fish and aquatic invertebrates

The accumulation of antibiotics in the environment has ecological impacts that have received less attention than the human health risks of antibiotics, although the effects could be far-reaching. This review discusses the effects of antibiotics on the health of fish and zooplankton, manifesting in direct or dysbiosis-mediated physiological impairment. Acute effects of antibiotics in these organism groups are usually induced at high concentrations (LC₅₀ at ∼100-1000 mg/L) that are not commonly present in aquatic environments. However, when exposed to sub-lethal, environmentally relevant levels of antibiotics (ng/L-μg/L) disruption of physiological homeostasis, development, and fecundity can occur. Antibiotics at similar or lower concentrations can induce dysbiosis of gut microbiota which can affect the health of fish and invertebrates. We show that the data about molecular-level effects of antibiotics at low exposure concentrations are limited, hindering environmental risk assessment and species sensitivity analysis. Fish and crustaceans (Daphnia sp.) were the two groups of aquatic organisms used most often for antibiotic toxicity testing, including microbiota analysis. While low levels of antibiotics impact the composition and function of gut microbiota in aquatic organisms, the correlation and causality of these changes to host physiology are not straightforward. In some cases, negative or lack of correlation have occurred, and, unexpectedly, gut microbial diversity has been unaffected or increased upon exposure to environmental levels of antibiotics. Efforts to incorporate functional analyses of gut microbiota are beginning to provide valuable mechanistic information, but more data is needed for ecological risk assessment of antibiotics.

Anthropogenic Neighborhood Impact on Bacterial and Fungal Communities in Polar Bear Feces

Climate changes cause a dramatical increase in the ice-free season in the Arctic, forcing polar bears ashore, closer to human settlements associated with new and non-natural food objects. Such a diet may crucially transform the intestinal microbiome and metabolism of polar bears. The aim of this study was to characterize changes in the gut bacterial and fungal communities resulting from the transition to anthropogenic food objects by the means of 16S and ITS metabarcoding. Thus, rectal samples from 16 wild polar bears from the Kara-Barents subpopulation were studied. Human waste consuming resulted in a significant increase in the relative abundance of fermentative bacteria (Lactobacillaceae, Leuconostocaceae, and Streptococcaceae) and a decrease in proteolytic Enterobacteriaceae. However, the alpha-diversity parameters remained similar. Also, for the first time, the composition of the fungal community of the polar bear intestine was determined. Diet change is associated with the displacement of eurybiontic fungi (Thelebolus, Dipodascus, Candida (sake), and Geotrichum) by opportunistic Candida (tropicalis), Kazachstania, and Trichosporon. Feeding on human waste does not cause any signs of dysbiosis and probably leads to adaptive changes in the bacterial microbiome. However, the emergence of fungal facultative pathogens increases the risk of infections.

Vibrio cholerae Invasion Dynamics of the Chironomid Host Are Strongly Influenced by Aquatic Cell Density and Can Vary by Strain

Cholera has been a human scourge since the early 1800s and remains a global public health challenge, caused by the toxigenic strains of the bacterium Vibrio cholerae. In its aquatic reservoirs, V. cholerae has been shown to live in association with various arthropod hosts, including the chironomids, a diverse insect family commonly found in wet and semiwet habitats. The association between V. cholerae and chironomids may shield the bacterium from environmental stressors and amplify its dissemination. However, the interaction dynamics between V. cholerae and chironomids remain largely unknown.  In this study, we developed freshwater microcosms with chironomid larvae to test the effects of cell density and strain on V. cholerae-chironomid interactions. Our results show that chironomid larvae can be exposed to V. cholerae up to a high inoculation dose (109 cells/mL) without observable detrimental effects. Meanwhile, interstrain variability in host invasion, including prevalence, bacterial load, and effects on host survival, was highly cell density-dependent. Microbiome analysis of the chironomid samples by 16S rRNA gene amplicon sequencing revealed a general effect of V. cholerae exposure on microbiome species evenness. Taken together, our results provide novel insights into V. cholerae invasion dynamics of the chironomid larvae with respect to various doses and strains. The findings suggest that aquatic cell density is a crucial driver of V. cholerae invasion success in chironomid larvae and pave the way for future work examining the effects of a broader dose range and environmental variables (e.g., temperature) on V. cholerae-chironomid interactions. IMPORTANCE Vibrio cholerae is the causative agent of cholera, a significant diarrheal disease affecting millions of people worldwide. Increasing evidence suggests that the environmental facets of the V. cholerae life cycle involve symbiotic associations with aquatic arthropods, which may facilitate its environmental persistence and dissemination. However, the dynamics of interactions between V. cholerae and aquatic arthropods remain unexplored. This study capitalized on using freshwater microcosms with chironomid larvae to investigate the effects of bacterial cell density and strain on V. cholerae-chironomid interactions. Our results suggest that aquatic cell density is the primary determinant of V. cholerae invasion success in chironomid larvae, while interstrain variability in invasion outcomes can be observed under specific cell density conditions. We also determined that V. cholerae exposure generally reduces species evenness of the chironomid-associated microbiome. Collectively, these findings provide novel insights into V. cholerae-arthropod interactions using a newly developed experimental host system.

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.

Improving the assessment of ecosystem and wildlife health: microbiome as an early indicator

Human activities are causing dramatic declines in ecosystem health, compromising the functioning of the life-support system, economic activity, and animal and human health. In this context, monitoring the health of ecosystems and wildlife populations is crucial for determining ecological dynamics and assessing management interventions. A growing body of evidence indicates that microbiome provides a meaningful early indicator of ecosystem and wildlife health. Microbiome is ubiquitous and both environmental and host-associated microbiomes rapidly reflect anthropogenic disturbances. However, we still need to overcome current limitations such as nucleic acid degradation, sequencing depth, and the establishment of baseline data to maximize the potential of microbiome studies.

Probiotics, Prebiotics, and Synbiotics Utilization in Crayfish Aquaculture and Factors Affecting Gut Microbiota

Aquaculture is affected by numerous factors that may cause various health threats that have to be controlled by the most environmentally friendly approaches. In this context, prebiotics, probiotics, and synbiotics are frequently incorporated into organisms' feeding rations to ameliorate the health status of the host's intestine, enhancing its functionality and physiological performance, and to confront increasing antimicrobial resistance. The first step in this direction is the understanding of the complex microbiome system of the organism in order to administer the optimal supplement, in the best concentration, and in the correct way. In the present review, pre-, pro-, and synbiotics as aquaculture additives, together with the factors affecting gut microbiome in crayfish, are discussed, combined with their future prospective outcomes. Probiotics constitute non-pathogenic bacteria, mainly focused on organisms' energy production and efficient immune response; prebiotics constitute fiber indigestible by the host organism, which promote the preferred gastrointestinal tract microorganisms' growth and activity towards the optimum balance between the gastrointestinal and immune system's microbiota; whereas synbiotics constitute their combination as a blend. Among pro-, pre-, and synbiotics' multiple benefits are boosted immunity, increased resistance towards pathogens, and overall welfare promotion. Furthermore, we reviewed the intestinal microbiota abundance and composition, which are found to be influenced by a plethora of factors, including the organism's developmental stage, infection by pathogens, diet, environmental conditions, culture methods, and exposure to toxins. Intestinal microbial communities in crayfish exhibit high plasticity, with infections leading to reduced diversity and abundance. The addition of synbiotic supplementation seems to provide better results than probiotics and prebiotics separately; however, there are still conflicting results regarding the optimal concentration.

Mediterranean Sea heatwaves jeopardize greater amberjack's (Seriola dumerili) aquaculture productivity through impacts on the fish microbiota

Climate change is dramatically increasing the frequency and severity of marine heatwaves (MHWs) in the Mediterranean basin, strongly affecting marine food production systems. However, how it will shape the ecology of aquaculture systems, and the cascading effects on productivity, is still a major knowledge gap. The present work aims to increase our understanding of future impacts, caused by raising water temperatures, on the interaction between water and fish microbiotas, and consequential effects upon fish growth. Thus, the bacterial communities present in the water tanks, and mucosal tissues (skin, gills and gut), of greater amberjack farmed in recirculatory aquaculture systems (RAS), at three different temperatures (24, 29 and 33 °C), were characterized in a longitudinal study. The greater amberjack (Seriola dumerili) is a teleost species with high potential for EU aquaculture diversification due to its fast growth, excellent flesh quality and global market. We show that higher water temperatures disrupt the greater amberjack's microbiota. Our results demonstrate the causal mediation exerted by this bacterial community shifts on the reduction of fish growth. The abundance of members of the Pseudoalteromonas is positively correlated with fish performance, whereas members of the Psychrobacter, Chryseomicrobium, Paracoccus and Enterovibrio are suggested as biomarkers for dysbiosis, at higher water temperatures. Hence, opening new evidence-based avenues for the development of targeted microbiota-based biotechnological tools, designed to increase the resilience and adaptation to climate change of the Mediterranean aquaculture industry.

Intestinal bacteria diversity of suckermouth catfish (Pterygoplichthys pardalis) in the Cd, Hg, and Pb contaminated Ciliwung River, Indonesia

The contamination of aquatic environments with heavy metals poses a serious threat to fish, potentially leading to diseases or even death. Therefore, there is an urgent need for studies to investigate the adaptability of fish in heavy metal-contaminated environments. Several studies have explored the adaptability of suckermouth catfish (P. pardalis) to survive in the contaminated Ciliwung River. The findings obtained showed that the presence of intestinal bacteria helped these fish overcome the heavy metals in their intestines, thereby enabling the fish to survive. Analysis using the Next Generation Sequencing (NGS) technology has succeeded in identifying diversity of these bacteria in P. pardalis living in the Ciliwung River, which contaminated with Cd (0.3-1.6 ppm in the water & 0.9-1.6 ppm in the sediment), Hg (0.6-2 ppm in the water & 0.6-1.8 ppm in the sediment), and Pb (59.9-73.8 ppm in the water & 26.1-58.6 ppm in the sediment). Diversity index of intestinal bacteria in P. pardalis was relatively high, but it had a negative correlation with the presence of these contaminants. Actinobacteria, Firmicutes, and Proteobacteria were abundant in the intestines of P. pardalis from the upstream to downstream of the river, with an overall abundance range of 15-48%. Furthermore, Mycobacterium along with 6 other genera were identified as core intestinal bacteria. The presence of these bacterial communities in all the samples affected their survival in heavy metals-contaminated rivers. The fish's adaptability to live in this harsh environment indicated that it has the potential to be utilized as a bioremediator of heavy metals in river sediments.

Intestinal microbiome in crayfish: Its role upon growth and disease presentation

The intestine-associated microbiota in crustaceans are considered a key element for maintaining homeostasis and health within the organisms. Recently, efforts have been made to characterize bacterial communities of freshwater crustaceans, including crayfish, and their interplay with the host's physiology and the aquatic environments. As a result, it has become evident that crayfish intestinal microbial communities display high plasticity, which is strongly influenced by both the diet, especially in aquaculture, and the environment. Moreover, studies regarding the characterization and distribution of the microbiota along the gut portions led to the discovery of bacteria with probiotic potential. The addition of these microorganisms to their food has shown a limited positive correlation with the growth and development of crayfish freshwater species. Finally, there is evidence that infections, particularly those from viral etiology, lead to low diversity and abundance of the intestinal microbial communities. In the present article, we have reviewed data on the crayfish' intestinal microbiota, highlighting the most frequently observed taxa and emphasizing the dominance of phylum within this community. In addition, we have also searched for evidence of microbiome manipulation and its potential impact on productive parameters, and discussed the role of the microbiome in the regulation of diseases presentation, and environmental perturbations.

Core and conditionally rare taxa as indicators of agricultural drainage ditch and stream health and function

BACKGROUND

The freshwater microbiome regulates aquatic ecological functionality, nutrient cycling, pathogenicity, and has the capacity to dissipate and regulate pollutants. Agricultural drainage ditches are ubiquitous in regions where field drainage is necessary for crop productivity, and as such, are first-line receptors of agricultural drainage and runoff. How bacterial communities in these systems respond to environmental and anthropogenic stressors are not well understood. In this study, we carried out a three year study in an agriculturally dominated river basin in eastern Ontario, Canada to explore the spatial and temporal dynamics of the core and conditionally rare taxa (CRT) of the instream bacterial communities using a 16S rRNA gene amplicon sequencing approach. Water samples were collected from nine stream and drainage ditch sites that represented the influence of a range of upstream land uses.

RESULTS

The cross-site core and CRT accounted for 5.6% of the total number of amplicon sequence variants (ASVs), yet represented, on average, over 60% of the heterogeneity of the overall bacterial community; hence, well reflected the spatial and temporal microbial dynamics in the water courses. The contribution of core microbiome to the overall community heterogeneity represented the community stability across all sampling sites. CRT was primarily composed of functional taxa involved in nitrogen (N) cycling and was linked to nutrient loading, water levels, and flow, particularly in the smaller agricultural drainage ditches. Both the core and the CRT were sensitive responders to changes in hydrological conditions.

CONCLUSIONS

We demonstrate that core and CRT can be considered as holistic tools to explore the temporal and spatial variations of the aquatic microbial community and can be used as sensitive indicators of the health and function of agriculturally dominated water courses. This approach also reduces computational complexity in relation to analyzing the entire microbial community for such purposes.

Vaccines for a sustainable planet

The health of the planet is one objective of the United Nations' Sustainable Development Goals. Vaccines can affect not only human health but also planet health by reducing poverty, preserving microbial diversity, reducing antimicrobial resistance, and preventing an increase in pandemics that is fueled partly by climate change.

Gut microbiota impairment following graphene oxide exposure is associated to physiological alterations in Xenopus laevis tadpoles

Graphene-based nanomaterials such as graphene oxide (GO) possess unique properties triggering high expectations for the development of technological applications. Thus, GO is likely to be released in aquatic ecosystems. It is essential to evaluate its ecotoxicological potential to ensure a safe use of these nanomaterials. In amphibians, previous studies highlighted X. laevis tadpole growth inhibitions together with metabolic disturbances and genotoxic effects following GO exposure. As GO is known to exert bactericidal effects whereas the gut microbiota constitutes a compartment involved in host homeostasis regulation, it is important to determine if this microbial compartment constitutes a toxicological pathway involved in known GO-induced host physiological impairments. This study investigates the potential link between gut microbial communities and host physiological alterations. For this purpose, X. laevis tadpoles were exposed during 12 days to GO. Growth rate was monitored every 2 days and genotoxicity was assessed through enumeration of micronucleated erythrocytes. Genomic DNA was also extracted from the whole intestine to quantify gut bacteria and to analyze the community composition. GO exposure led to a dose dependent growth inhibition and genotoxic effects were detected following exposure to low doses. A transient decrease of the total bacteria was noticed with a persistent shift in the gut microbiota structure in exposed animals. Genotoxic effects were associated to gut microbiota remodeling characterized by an increase of the relative abundance of Bacteroides fragilis. The growth inhibitory effects would be associated to a shift in the Firmicutes/Bacteroidetes ratio while metagenome inference suggested changes in metabolic pathways and upregulation of detoxification processes. This work indicates that the gut microbiota compartment is a biological compartment of interest as it is integrative of host physiological alterations and should be considered for ecotoxicological studies as structural or functional impairments could lead to later life host fitness loss.

Genotype-environment interactions determine microbiota plasticity in the sea anemone Nematostella vectensis

Most multicellular organisms harbor microbial colonizers that provide various benefits to their hosts. Although these microbial communities may be host species- or even genotype-specific, the associated bacterial communities can respond plastically to environmental changes. In this study, we estimated the relative contribution of environment and host genotype to bacterial community composition in Nematostella vectensis, an estuarine cnidarian. We sampled N. vectensis polyps from 5 different populations along a north-south gradient on the Atlantic coast of the United States and Canada. In addition, we sampled 3 populations at 3 different times of the year. While half of the polyps were immediately analyzed for their bacterial composition by 16S rRNA gene sequencing, the remaining polyps were cultured under laboratory conditions for 1 month. Bacterial community comparison analyses revealed that laboratory maintenance reduced bacterial diversity by 4-fold, but maintained a population-specific bacterial colonization. Interestingly, the differences between bacterial communities correlated strongly with seasonal variations, especially with ambient water temperature. To decipher the contribution of both ambient temperature and host genotype to bacterial colonization, we generated 12 clonal lines from 6 different populations in order to maintain each genotype at 3 different temperatures for 3 months. The bacterial community composition of the same N. vectensis clone differed greatly between the 3 different temperatures, highlighting the contribution of ambient temperature to bacterial community composition. To a lesser extent, bacterial community composition varied between different genotypes under identical conditions, indicating the influence of host genotype. In addition, we identified a significant genotype x environment interaction determining microbiota plasticity in N. vectensis. From our results we can conclude that N. vectensis-associated bacterial communities respond plastically to changes in ambient temperature, with the association of different bacterial taxa depending in part on the host genotype. Future research will reveal how this genotype-specific microbiota plasticity affects the ability to cope with changing environmental conditions.

Comparison of environmental microbiomes in an antibiotic resistance-polluted urban river highlights periphyton and fish gut communities as reservoirs of concern

Natural waterways near urban areas are heavily impacted by anthropogenic activities, including their microbial communities. A contaminant of growing public health concern in rivers is antibiotic resistant genes (ARGs), which can spread between neighboring bacteria and increase the potential for transmission of AR bacteria to animals and humans. To identify the matrices of most concern for AR, we compared ARG burdens and microbial community structures between sample types from the Scioto River Watershed, Ohio, the United States, from 2017 to 2018. Five environmental matrices (water, sediment, periphyton, detritus, and fish gut) were collected from 26 river sites. Due to our focus on clinically relevant ARGs, three carbapenem resistance genes (bla_KPC, bla_NDM, and bla_OXA-48) were quantified via DropletDigital™ PCR. At a subset of nine urbanized sites, we conducted16S rRNA gene sequencing and functional gene predictions. Carbapenem resistance genes were quantified from all matrices, with bla_KPC being the most detected (88 % of samples), followed by bla_NDM (64 %) and bla_OXA-48 (23 %). Fish gut samples showed higher concentrations of bla_KPC and bla_NDM than any other matrix, indicating potential ARG bioaccumulation, and risk of broader dissemination through aquatic and nearshore food webs. Periphyton had higher concentrations of bla_NDM than water, sediment, or detritus. Microbial community analysis identified differences by sample type in community diversity and structure. Sediment samples had the most diverse microbial communities, and detritus, the least. Spearman correlations did not reveal significant relationships between the concentrations of the monitored ARGs and microbial community diversity. However, several differentially abundant taxa and microbial functions were identified by sample type that is definitive of these matrices' roles in the river ecosystem and habitat type. In summary, the fish gut and periphyton are a concern as AR reservoirs due to their relatively high concentration of carbapenem resistance genes, diverse microbial communities, and natural functions that promote AR.

Hatchery tanks induce intense reduction in microbiota diversity associated with gills and guts of two endemic species of the São Francisco River

The São Francisco River (SFR), one of the main Brazilian rivers, has suffered cumulative anthropogenic impacts, leading to ever-decreasing fish stocks and environmental, economic, and social consequences. Rhinelepis aspera and Prochilodus argenteus are medium-sized, bottom-feeding, and rheophilic fishes from the SFR that suffer from these actions. Both species are targeted for spawning and restocking operations due to their relevance in artisanal fisheries, commercial activities, and conservation concerns. Using high-throughput sequencing of the 16S rRNA gene, we characterized the microbiome present in the gills and guts of these species recruited from an impacted SFR region and hatchery tanks (HT). Our results showed that bacterial diversity from the gill and gut at the genera level in both fish species from HT is 87% smaller than in species from the SFR. Furthermore, only 15 and 29% of bacterial genera are shared between gills and guts in R. aspera and P. argenteus from SFR, respectively, showing an intimate relationship between functional differences in organs. In both species from SFR, pathogenic, xenobiont-degrading, and cyanotoxin-producer bacterial genera were found, indicating the critical pollution scenario in which the river finds itself. This study allowed us to conclude that the conditions imposed on fish in the HT act as important modulators of microbial diversity in the analyzed tissues. It also raises questions regarding the effects of these conditions on hatchery spawn fish and their suitability for restocking activities, aggravated by the narrow genetic diversity associated with such freshwater systems.

Supplementing artemisinin positively influences growth, antioxidant capacity, immune response, gut health and disease resistance against Vibrio parahaemolyticus in Litopenaeus vannamei fed cottonseed protein concentrate meal diets

Artemisinin (ART) is a kind of Chinese herbal medicine worth exploring, which obtains various physiological activities. In order to study the prebiotic effect of ART on Litopenaeus vannamei fed cottonseed protein concentrate meal diets, six groups of isonitrogenous and isolipid diets were prepared (including the fish meal control group, FM; cottonseed protein concentrate replacing 30% fishmeal protein and supplementing ART groups: ART0, ART0.3, ART0.6, ART0.9, and ART1.2). The feeding trials was lasted for 56 days. The results showed that the final body weight, weight gain and specific growth rate of the ART0.6 group were the highest, yet the feed coefficient rate of the ART0.6 group was the lowest significantly (P < 0.05). There was no significant difference in survival rate among treatments (P > 0.05). In serum, the content of malondialdehyde in ART0 group was the highest (P < 0.05); the activities of superoxide dismutase, catalase, phenol oxidase and lysozyme increased firstly and then decreased among the ARTs groups (P < 0.05). The activities of intestinal digestive enzymes (including the trypsin, lipase and amylase) showed an upward trend among the ARTs groups (P < 0.05). The histological sections showed that the intestinal muscle thickness, fold height and fold width in the FM group were significantly better than those in the ART0 group; while the mentioned above morphological indexes in the ART0 group were significantly lowest among the ARTs groups (P < 0.05). Sequencing of intestinal microbiota suggested that the microbial richness indexes firstly increased and then decreased (P < 0.05); the bacterial community structure of each treatment group was almost close; the relative abundance of pathogenic bacteria decreased significantly (P < 0.05), such as the Proteobacteria and Cyanobacteria at phylum level, besides the Vibrio and Candidatus Bacilloplasma at genus level. In intestinal tissue, the relative expression levels of TOLL1, TRAF6 and Pehaeidih3 showed up-regulated trends, while the expression of Crustin and LZM firstly up-regulated and then down-regulated (P < 0.05). The challenge experiment suggested that the cumulative mortality of FM group was significantly lower than that of ART0 group; besides the cumulative mortality firstly increased and then decreased between the ARTs groups (P < 0.05). In conclusion, the dietary supplementation of ART can improve the growth, antioxidant capacity, immune response, gut health and disease resistance of the shrimp. To be considered as a dietary immune enhancer, the recommended supplementation level of ART in shrimp's cottonseed protein concentrate meal diets is 0.43%.