The Impact of Intensive Fish Farming on Pond Sediment Microbiome and Antibiotic Resistance Gene Composition

Antimicrobial Activity, Genetic Relatedness, and Safety Assessment of Potential Probiotic Lactic Acid Bacteria Isolated from a Rearing Tank of Rotifers (Brachionus plicatilis) Used as Live Feed in Fish Larviculture

Aquaculture is a rapidly expanding agri-food industry that faces substantial economic losses due to infectious disease outbreaks, such as bacterial infections. These outbreaks cause disruptions and high mortalities at various stages of the rearing process, especially in the larval stages. Probiotic bacteria are emerging as promising and sustainable alternative or complementary strategies to vaccination and the use of antibiotics in aquaculture. In this study, potential probiotic candidates for larviculture were isolated from a rotifer-rearing tank used as the first live feed for turbot larvae. Two Lacticaseibacillus paracasei and two Lactiplantibacillus plantarum isolates were selected for further characterization due to their wide and strong antimicrobial activity against several ichthyopathogens, both Gram-positive and Gram-negative. An extensive in vitro safety assessment of these four isolates revealed the absence of harmful traits, such as acquired antimicrobial resistance and other virulence factors (i.e., hemolytic and gelatinase activities, bile salt deconjugation, and mucin degradation, as well as PCR detection of biogenic amine production). Moreover, Enterobacterial Repetitive Intergenic Consensus-PCR (ERIC-PCR) analyses unveiled their genetic relatedness, revealing two divergent clusters within each species. To our knowledge, this work reports for the first time the isolation and characterization of Lactic Acid Bacteria (LAB) with potential use as probiotics in aquaculture from rotifer-rearing tanks, which have the potential to optimize turbot larviculture and to introduce novel microbial management approaches for a sustainable aquaculture.

Dissecting the Genetic Basis of the Technological, Functional, and Safety Characteristics of Lacticaseibacillus paracasei SRX10

Nonstarter lactic acid bacteria (NSLAB) are major contributors to the unique characteristics (e.g., aroma, flavor, texture) of dairy and nondairy fermented products. Lc. paracasei SRX10 is an NSLAB strain originally isolated from a traditional Greek cheese and previously shown to exhibit favorable biotechnological characteristics. More specifically, the strain showed tolerance to simulated gastrointestinal conditions, exopolysaccharide (EPS) biosynthetic capacity, and lack of hemolytic activity and was used in the production of yoghurt and feta cheese with distinct organoleptic characteristics. The aim of the present study was to investigate these traits at the genome level through whole-genome sequencing (WGS), annotation, and comparative genomics. Functional annotation of the genome revealed that Lc. paracasei SRX10 can utilize different carbon sources, leading to the generation of flavor compounds, including lactic acid, acetate, ethanol, and acetoin. Similarly, full clusters for fatty acid biosynthesis, protein and peptide degradation, as well as genes related to survival under extreme temperatures, osmotic shock, and oxidative stress were annotated. Importantly, no transferable antibiotic resistance genes or virulence factors were identified. Finally, strain-specific primers based on genome-wide polymorphisms were designed for the efficient and rapid identification of Lc. paracasei SRX10 via multiplex PCR in fermented products.

In vitro screening and characterization of lactic acid bacteria from Lithuanian fermented food with potential probiotic properties

The present work aimed to identify probiotic candidates from Lithuanian homemade fermented food samples. A total of 23 lactic acid bacteria were isolated from different fermented food samples. Among these, only 12 showed resistance to low pH, tolerance to pepsin, bile salts, and pancreatin. The 12 strains also exhibited antimicrobial activity against Staphylococcus aureus ATCC 29213, Salmonella Typhimurium ATCC 14028, Streptococcus pyogenes ATCC 12384, Streptococcus pyogenes ATCC 19615, and Klebsiella pneumoniae ATCC 13883. Cell-free supernatants of isolate 3A and 55w showed the strongest antioxidant activity of 26.37 μg/mL and 26.06 μg/mL, respectively. Isolate 11w exhibited the strongest auto-aggregation ability of 79.96% as well as the strongest adhesion to HCT116 colon cells (25.671 ± 0.43%). The selected strains were tested for their synbiotic relation in the presence of a prebiotic. The selected candidates showed high proliferation in the presence of 4% as compared to 2% galactooligosaccharides. Among the strains tested for tryptophan production ability, isolate 11w produced the highest L-tryptophan levels of 16.63 ± 2.25 μm, exhibiting psychobiotic ability in the presence of a prebiotic. The safety of these strains was studied by ascertaining their antibiotic susceptibility, mucin degradation, gelatin hydrolysis, and hemolytic activity. In all, isolates 40C and 11w demonstrated the most desirable probiotic potentials and were identified by 16S RNA and later confirmed by whole genome sequencing as Lacticaseibacillus paracasei 11w, and Lactiplantibacillus plantarum 40C: following with the harboring plasmid investigation. Out of all the 23 selected strains, only Lacticaseibacillus paracasei 11w showed the potential and desirable probiotic properties.

Metagenomic analysis to determine the characteristics of antibiotic resistance genes in typical antibiotic-contaminated sediments

Comprehensive studies of the effects of various physical and chemical variables (including heavy metals), antibiotics, and microorganisms in the environment on antibiotic resistance genes are rare. We collected sediment samples from the Shatian Lake aquaculture area and surrounding lakes and rivers located in Shanghai, China. The spatial distribution of sediment ARGs was assessed by metagenomic analysis that revealed 26 ARG types (510 subtypes), dominated by Multidrug, β-lactam, Aminoglycoside, Glycopeptides, Fluoroquinolone, and Tetracyline. Redundancy discriminant analysis indicated that antibiotics (SAs and MLs) in the aqueous environment and sediment along with water TN and TP were the key variables affecting the abundance distribution of total ARGs. However, the main environmental drivers and key influences differed among the different ARGs. For total ARGs, the environmental subtypes affecting their structural composition and distribution characteristics were mainly antibiotic residues. Procrustes analysis showed a significant correlation between ARGs and microbial communities in the sediment in the survey area. Network analysis revealed that most of the target ARGs were significantly and positively correlated with microorganisms, and a small number of ARGs (e.g., rpoB, mdtC, and efpA) were highly significantly and positively correlated with microorganisms (e.g., Knoellia, Tetrasphaera, and Gemmatirosa). Potential hosts for the major ARGs included Actinobacteria, Proteobacteria, and Gemmatimonadetes. Our study provides new insight and a comprehensive assessment of the distribution and abundance of ARGs and the drivers of ARG occurrence and transmission.

Effect of dietary garlic (Allium sativum) on the zootechnical performance and health indicators of aquatic animals: A mini-review

Considerable efforts have been made by modern aquaculture to mitigate the environmental damages caused by its practices while also attempting to improve the quality of the aquatic organisms by promoting alternatives, such as the use of natural products, like garlic (Allium sativum), and instead of chemical agents. Garlic has multiple properties, including antifungal, antibacterial, antiviral, antitoxic, and anticancer effects. In fish, the antiparasitic activity of garlic is one of the most reported effects in the literature, mainly using immersion baths for aquatic organisms. Using garlic also has an antimicrobial effect on the culture of aquatic organisms. Therefore, this review focuses on the impact of garlic on the health and production of aquatic organisms.

Diversity of enterobacterales in sediments of lagoons with fish farming activity and analysis of antibiotic resistance

The use of antibiotics in fish production can induce bacterial populations to develop resistance to multiple antibiotics and transfer antibiotic resistance genes to other bacteria, including clinically relevant bacteria. This study evaluated the diversity of Enterobacterales in sediment from lagoons with fish farming activity and analyzed antibiotic resistance in the central region of Peru. Sediment samples were collected from four fish-active ponds and transported to the laboratory for analysis. Bacterial diversity was analyzed using DNA sequencing and antibiotic resistance was tested using the disk diffusion method. The results showed variability of bacterial diversity in the ponds with fish farming activity. Simpson's index indicated that the Habascocha lagoon is the most diverse in bacterial species of the order Enterobacterales (0.8), but the least dominant. The Shannon-Wiener index revealed that it is the most diverse (2.93) and the Margalef index revealed that species richness in this lagoon is high (5.72). Similarity percentage analysis (SIMPER) allowed the identification of the main Enterobacterales with the highest percentage contribution in the frequencies of individuals. In general, the Enterobacterales species isolated showed multi-resistance to the antibiotics used and Escherichia coli was the most resistant.

Dietary Cinnamaldehyde Enhances Growth Performance, Digestion, Immunity, and Lipid Metabolism in Juvenile Fat Greenling (Hexagrammos otakii)

Fat greenling (Hexagrammos otakii) is a kind of economic fish that is widely consumed by human, and its intensive farming technology is making important progress. However, high-density farming may cause the occurrence of diseases in H. otakii. Cinnamaldehyde (CNE) is a new feed additive for aquatic animals and has a positive effect on disease resistance. In the study, dietary CNE was evaluated on the growth performance, digestion, immune response, and lipid metabolism of juvenile H. otakii (6.21 ± 0.19 g). Six experimental diets were formulated containing CNE at levels of 0, 200, 400, 600, 800, and 1000 mg/kg for 8 weeks. The percent weight gain (PWG), specific growth rate (SGR), survival (SR), and feeding rate (FR) were significantly increased by including CNE in fish diets regardless of the inclusion level (P < 0.05). The feed conversion ratio (FCR) was significantly decreased among the groups fed CNE supplemented diets (P < 0.05). A significant decrease in hepatosomatic index (HSI) was observed in fish fed 400 mg/kg-1000 mg/kg CNE compared to the control diet (P < 0.05). Fish-fed diets containing 400 mg/kg and 600 mg/kg CNE had a higher level of crude protein in muscles than the control diet (P < 0.05). Moreover, the activities of lipase (LPS) and pepsin (PEP) in the intestinal were markedly increased in juvenile H. otakii-fed dietary CNE (P < 0.05). Apparent digestibility coefficient (ADC) of dry matter, protein, and lipid was significantly increased with CNE supplement (P < 0.05). The activities of catalase (CAT) and acid phosphatase (ACP) in the liver were markedly enhanced by including CNE in juvenile H. otakii diets compared with the control (P < 0.05). The activities of superoxide dismutase (SOD) and alkaline phosphatase (AKP) in the liver were markedly enhanced in juvenile H. otakii treated with CNE supplements 400 mg/kg-1000 mg/kg (P < 0.05). Additionally, the levels of total protein (TP) in the serum were markedly increased by including CNE in juvenile H. otakii diets compared with the control (P < 0.05). In the CNE200, CNE400, and CNE600 groups, albumin (ALB) levels in the serum were markedly higher compared with that in the control (P < 0.05). In the CNE200 and CNE400 groups, the levels of immunoglobulin G (IgG) in the serum were significantly increased compared with that the control group (P < 0.05). The juvenile H. otakii-fed dietary CNE had lower triglycerides (TG) and total cholesterol (TCHO) levels in the serum than fish-fed CNE-free diets (P < 0.05). The gene expression of peroxisome proliferator-activated receptor alpha (PPAR-α), hormone-sensitive lipase (HSL), and carnitine O-palmitoyltransferase 1 (CPT1) in the liver was significantly increased by including CNE in fish diets regardless of the inclusion level (P < 0.05). However, fatty acid synthase (FAS), peroxisome proliferator-activated receptor gamma (PPAR-γ), and acetyl-CoA carboxylase alpha (ACCα) in the liver were markedly decreased with CNE supplements 400 mg/kg-1000 mg/kg (P < 0.05). The glucose-6-phosphate1-dehydrogenase (G6PD) gene expression levels in the liver were markedly decreased compared with the control (P < 0.05). The optimal supplementation level of CNE was shown by curve equation analysis to be 590.90 mg/kg.

Exploring the interactions between the gut microbiome and the shifting surrounding aquatic environment in fisheries and aquaculture: A review

The rise of "new" sequencing technologies and the development of sophisticated bioinformatics tools have dramatically increased the study of the aquaculture microbiome. Microbial communities exist in complex and dynamic communities that play a vital role in the stability of healthy ecosystems. The gut microbiome contributes to multiple aspects of the host's physiological health status, ranging from nutritional regulation to immune modulation. Although studies of the gut microbiome in aquaculture are growing rapidly, the interrelationships between the aquaculture microbiome and its aquatic environment have not been discussed and summarized. In particular, few reviews have focused on the potential mechanisms driving the alteration of the gut microbiome by surrounding aquatic environmental factors. Here, we review current knowledge on the host gut microbiome and its interrelationship with the microbiome of the surrounding environment, mainly including the main methods for characterizing the gut microbiome, the composition and function of microbial communities, the dynamics of microbial interactions, and the relationship between the gut microbiome and the surrounding water/sediment microbiome. Our review highlights two potential mechanisms for how surrounding aquatic environmental factors drive the gut microbiome. This may deepen the understanding of the interactions between the microbiome and environmental factors. Lastly, we also briefly describe the research gaps in current knowledge and prospects for the future orientation of research. This review provides a framework for studying the complex relationship between the host gut microbiome and environmental stresses to better facilitate the widespread application of microbiome technologies in fisheries and aquaculture.

Metagenomic insights into the spatiotemporal responses of antibiotic resistance genes and microbial communities in aquaculture sediments

The dissemination of antibiotic resistance genes (ARGs) in aquaculture systems is a potential threat to environmental safety and human health. However, the spatiotemporal distribution pattern of ARGs and key factors associated with their dissemination in aquaculture sediments remain unclear. In this study, ARGs, mobile genetic elements, microbial community composition, heavy metal contents, and nutrient contents of samples collected from a whole culture cycle of fish in a representative aquaculture farm were characterized. The distribution patterns of nine subtypes of ARGs (tetW, tetM, tetA, ermC, ermB, sul1, sul2, floR, and qnrS) showed clear spatiotemporal differences. The absolute abundance of ARGs in aquaculture sediments was higher in winter and in rivers of the aquaculture farm. Proteobacteria was the dominant phylum in all sediment samples. The results of network and redundancy analyses confirmed that the Dechloromonas, Candidatus Accumulibacter, Smithella, Geobacter, and Anaeromyxobacter belonging to Proteobacteria were positively correlated with ARGs, suggesting that these microbial species are potential hosts of corresponding ARGs. Our study highlights that the microbial community is the determining factor for ARG dissemination. Strategies for inhibiting these potential hosts of ARGs should be developed based on controllable factors.

Antibiotic resistance genes and their links with bacteria and environmental factors in three predominant freshwater aquaculture modes

Rapid development of aquaculture industry and increasing demand of various inputs (especially antibiotics), are suspected to promote the occurrence and spread of ARGs in aquaculture related environments. However, the occurrences of ARGs under different freshwater aquaculture practices are rarely known. Here, we investigated the seasonal profiles of the main ARGs, intI1 and bacteria in waters from three kinds of predominant freshwater aquaculture practices around the Honghu Lake (China), as well as their co-occurrences and interrelationships with antibiotics, heavy metals and general water quality. The results indicate that quinolone resistance genes (qnrB), tetracycline resistance genes (tetB and tetX) and sulfonamide resistance genes (sul1 and sul2) were the top five predominant ARGs with seasonal variations of abundance. Fish ponds were of the highest absolute abundances of tested ARGs than the other two modes. Crayfish ponds and their adjacent ditches shared similar ARGs profile. Different subtypes of ARGs belonging to the same class of resistance were varied in abundances. Some bacteria were predicted to carry different ARGs, which indicating multi-antibiotic resistances. Moreover, the combined environmental factors (antibiotics, heavy metals and water quality) partially shaped the profiles of ARGs and bacteria composition. Overall, this study provides new comprehensive understanding on the characterization of ARGs contamination in different freshwater aquaculture practices from the perspectives of environmental chemistry, microbiology and ecology. The results would benefit the optimization of aquaculture practices toward environmental integrity and sustainability.

Functional and Seasonal Changes in the Structure of Microbiome Inhabiting Bottom Sediments of a Pond Intended for Ecological King Carp Farming

Simple Summary

Bottom sediments are usually classified as extreme habitats for microorganisms. They are defined as matter deposited on the bottom of water bodies through the sedimentation process. The quality of sediments is extremely important for the good environmental status of water, because they are an integral part of the surface water environment. Microorganisms living in sediments are involved in biogeochemical transformations and play a fundamental role in maintaining water purity, decomposition of organic matter, and primary production. As a rule, studies on bottom sediments focus on monitoring their chemistry and pollution, while little is known about the structure of bacterial communities inhabiting this extreme environment. In this study, Next-Generation Sequencing (NGS) was combined with the Community-Level Physiological Profiling (CLPP) technique to obtain a holistic picture of bacterial biodiversity in the bottom sediments from Cardinal Pond intended for ecological king carp farming. It was evident that the bottom sediments of the studied pond were characterized by a rich microbiota composition, whose structure and activity depended on the season, and the most extensive modifications of the biodiversity and functionality of microorganisms were noted in summer.

Abstract

The main goal of the study was to determine changes in the bacterial structure in bottom sediments occurring over the seasons of the year and to estimate microbial metabolic activity. Bottom sediments were collected four times in the year (spring, summer, autumn, and winter) from 10 different measurement points in Cardinal Pond (Ślesin, NW Poland). The Next-Generation Sequencing (MiSeq Illumina) and Community-Level Physiological Profiling techniques were used for identification of the bacterial diversity structure and bacterial metabolic and functional activities over the four seasons. It was evident that Proteobacteria, Acidobacteria, and Bacteroidetes were the dominant phyla, while representatives of Betaproteobacteria, Gammaproteobacteria, and Deltaproteobacteria predominated at the class level in the bottom sediments. An impact of the season on biodiversity and metabolic activity was revealed with the emphasis that the environmental conditions in summer modified the studied parameters most strongly. Carboxylic and acetic acids and carbohydrates were metabolized most frequently, whereas aerobic respiration I with the use of cytochrome C was the main pathway used by the microbiome of the studied bottom sediments.

Interaction of Microbiota between Fish and the Environment of an In-Pond Raceway System in a Lake

Due to its ability to collect and remove aquaculture waste, an in-pond raceway system (IPRS) has been used to decrease the uncontrolled waste discharge in the traditional cage aquaculture method in large water bodies. However, when applied to large water bodies, its environmental performance is still lacking. This study focused on analyzing the microbial characteristics and the interaction between largemouth bass (gill and gut) microbiota and the environment (water and sediment) microbiota of an IPRS. Further, it revealed the primary relationship from the perspective of microbiota in the IPRS. The results show that (1) the alpha diversity of microbiota in the water is significantly lower than that of fish and sediment. The relationship between water microbiota and fish microbiota is limited. (2) The water microbiota inside and outside the tank showed high similarity and were not significantly affected by environmental factors. (3) The SourceTrack analysis showed that fish microbiota is one of the primary sources of sediment microbiota, and more than 15% of the sediment microbiota come from fish. Microbes such as Faecalibacterium, Escherichia-Shigella, and Bacteroides can significantly enrich the sediment. Our study revealed the characteristics and preliminary interaction of fish and environmental microbiota in the IPRS. It provided a reference for evaluating microbial health status in the application of IPRS in large water bodies’ aquaculture.

Contaminants of emerging concern (CECs) in aquaculture effluent: Insight into breeding and rearing activities, alarming impacts, regulations, performance of wastewater treatment unit and future approaches

The contamination of aquaculture products and effluents by contaminants of emerging concern (CECs) from the direct chemical use in aquaculture activities or surrounding industries is currently an issue of increasing concern as these CECs exert acute and chronic effects on living organisms. CECs have been detected in aquaculture water, sediment, and culture species, and antibiotics, antifoulants, and disinfectants are the commonly detected groups. Through accumulation, CECs can reside in the tissue of aquaculture products and eventually consumed by humans. Currently, effluents containing CECs are discharged to the surrounding environment while producing sediments that eventually contaminate rivers as receiving bodies. The rearing (grow-out) stages of aquaculture activities are issues regarding CECs-contamination in aquaculture covering water, sediment, and aquaculture products. Proper regulations should be imposed on all aquaculturists to control chemical usage and ensure compliance to guidelines for appropriate effluent treatment. Several techniques for treating aquaculture effluents contaminated by CECs have been explored, including adsorption, wetland construction, photocatalysis, filtration, sludge activation, and sedimentation. The challenges imposed by CECs on aquaculture activities are discussed for the purpose of obtaining insights into current issues and providing future approaches for resolving associated problems. Stakeholders, such as researchers focusing on environment and aquaculture, are expected to benefit from the presented results in this article. In addition, the results may be useful in establishing aquaculture-related CECs regulations, assessing toxicity to living biota, and preventing pollution.

Microbial diversity in intensively farmed lake sediment contaminated by heavy metals and identification of microbial taxa bioindicators of environmental quality

The cumulative effects of anthropogenic stress on freshwater ecosystems are becoming increasingly evident and worrisome. In lake sediments contaminated by heavy metals, the composition and structure of microbial communities can change and affect nutrient transformation and biogeochemical cycling of sediments. In this study, bacterial and archaeal communities of lake sediments under fish pressure contaminated with heavy metals were investigated by the Illumina MiSeq platform. Despite the similar content of most of the heavy metals in the lagoon sediments, we found that their microbial communities were different in diversity and composition. This difference would be determined by the resilience or tolerance of the microbial communities to the heavy metal enrichment gradient. Thirty-two different phyla and 66 different microbial classes were identified in sediment from the three lagoons studied. The highest percentages of contribution in the differentiation of microbial communities were presented by the classes Alphaproteobacteria (19.08%), Cyanophyceae (14.96%), Betaproteobacteria (9.01%) y Actinobacteria (7.55%). The bacteria that predominated in sediments with high levels of Cd and As were Deltaproteobacteria, Actinobacteria, Coriobacteriia, Nitrososphaeria and Acidobacteria (Pomacocha), Alphaproteobacteria, Chitinophagia, Nitrospira and Clostridia (Tipicocha) and Betaproteobacteria (Tranca Grande). Finally, the results allow us to expand the current knowledge of microbial diversity in lake sediments contaminated with heavy metals and to identify bioindicators taxa of environmental quality that can be used in the monitoring and control of heavy metal contamination.