Bacterial Abundance and Community Composition in Pond Water From Shrimp Aquaculture Systems With Different Stocking Densities

Acute nitrite exposure causes gut microbiota dysbacteriosis and proliferation of pathogenic Photobacterium in shrimp

Nitrite exposure has become a significant concern in the aquaculture industry, posing a severe threat to aquatic animals such as shrimp. While studies have reported the adverse effects of nitrite on shrimp growth, the part played by the gut microbiota in shrimp mortality resulting from nitrite exposure is poorly understood. Here, the effects of nitrite on shrimp gut bacterial community were investigated using 16S rRNA amplicon sequencing, bacterial isolation, genomic analysis, and infection experiments. Compared to the control_healthy group, changes in the bacterial composition of the nitrite_dead group were associated with reduced abundance of specific beneficial bacteria and increased abundance of certain pathogenic bacteria. Notably, members of the Photobacterium genus were found to be significantly enriched in the nitrite_dead group. Genomic analysis of a representative Photobacterium strain (LvS-8n3) revealed a variety of genes encoding bacterial toxins, including hemolysin, adhesin, and phospholipase. Furthermore, it was also found that LvS-8n3 exhibits strong pathogenicity, probably due to its high production of pathogenic factors and the ability to utilize nitrite for proliferation. Therefore, the proliferation of pathogenic Photobacterium species appears pivotal for driving shrimp mortality caused by nitrite exposure. These findings provide novel insights into the disease mechanism in shrimp under conditions of environmental change.

Response of sediment microbial communities to the flow effect of the triangular artificial reef: A simulation-based experimental study

Artificial reefs (ARs), as an important tool for habitat restoration, play significant impacts on benthic microbial ecosystems. This study utilized 16S rRNA gene sequencing technology and computational fluid dynamics (CFD) flow simulation to investigate the effects of flow field distribution around ARs on microbial community structure. The results revealed distinct regional distribution patterns of microbial communities affected by different hydrodynamic conditions. Flow velocity and flow regime of water in sediment-water interface shaped the microbial community structure. The diversity and richness in R-HF were significantly decreased compared to other five regions (p < 0.05). At the phyla and OUT levels, most abundant taxa (1>%) showed an enrichment trend in R-HB. However, more than half of differentially abundant taxa were enriched in R-HB, which was significantly correlated with organic matter (OM). Bugbase phenotypic predictions indicated a low abundance of the anaerobic phenotype in R-HF and a high abundance of the biofilm-forming phenotype in R-HB.

Phycosphere bacterial disturbance of Saccharina japonica caused by white rot disease relates to seawater nutrients

In mid-November 2021, there were large areas of white rot disease on cultivated Saccharina japonica in Rongcheng City, China, and diseases were undetected on Sargassum horneri and Porphyra yezoensis. The disturbance direction of bacterial community in the phycosphere after disease outbreak and the relationship with seawater nutrients remain unclear. Here, in situ studies of bacterial community in the non-diseased and diseased areas (Shawo and Dongchu islands) and seawater nutrient levels were carried out. 16S rRNA sequencing showed that the bacterial richness of the studied seaweeds increased in the diseased area. Only in S. japonica, Algitalea outcompeted abundant primary bacteria with probiotic relationships to the host of the non-diseased area, and dominated in the diseased area (17.6% of the total abundance). Nitrogen and phosphorus levels in seawater were 57.8% and 19.6% higher in the non-diseased area than those in the diseased area, respectively, and were strongly correlated with the phycosphere bacteria at the family level of S. japonica. There was no difference in potential pathogenicity between the two areas, while positive signal communications decreased, and nitrogen cycle, chemoheterotrophy, and cellulolysis increased in the diseased area compared to the non-diseased area. Overall, white rot disease caused a structural disturbance in phycosphere bacterial community of S. japonica that related to seawater nutrient levels. Enriched degraders and altered bacterial community functions may exacerbate the disease. This evaluation will provide information for white rot disease management to prevent and mitigate the occurrence of S. japonica outbreaks.

Effects of Fishery Utilization on the Physicochemical Index and Microbial Community Composition in Saline-Alkaline Water

Fishery utilization of idle saline-alkaline water resources offers various benefits including reducing surrounding soil salinity, improving the ecological environment, increasing arable land area, and providing economic advantages to the fishery industry. However, for decades, the characteristics and regulatory mechanisms of microbial communities that affect fishery utilization have not been clear, which restricts their application. In this study, high-throughput 16S rRNA amplicon sequencing was employed to analyze the bacterial community in these water resources. The sequencing yielded high-quality sequences (2,765,063), resulting in the identification of 18,761 bacterial operational taxonomic units (OTUs). Analysis revealed that the type of saline-alkaline water had a more significant influence on the bacterial community compared to seasonal variations within the aquaculture period. The Chao index for saline-alkaline ponds (ASW) was significantly lower (P < 0.05) than for still saline-alkaline water (SSW) and flowing saline-alkaline water (FSW), while the Shannon index for ASW was also significantly lower (P < 0.05) compared to FSW. When comparing ASW to nonaquaculture saline-alkaline water, a decrease in Proteobacteria to 26.87% was noted, particularly α-proteobacteria and γ-proteobacteria, accompanied by a rapid increase in Actinobacteria and Cyanobacteria to 28.60%. Networkx analysis further revealed that ASW significantly increased competition and amensalism from secondary saline-alkaline water microorganisms, resulting in a more solitary bacterial community composition as an adaptive strategy to cope with intense environmental pressures. Key bacterial species such as Pseudomonas, Hydrogenophaga, and Flavobacterium were found to be involved in hydrogen-cycling, nitrogen-cycling, and carbon-cycling, respectively, with all three exhibiting high abundance in FSW. Consequently, FSW demonstrates significant advantages in biogeochemical cycling, pollutant degradation, and the utilization of indigenous probiotic bacteria. Although the surface of abandoned secondary saline-alkaline land was covered with white salt particles, the fishery utilization of saline-alkaline water with low salinity levels (4.0-5.5), and the presence of nitrate and phosphate were identified as primary determinants of bacterial community composition. Nevertheless, a comparison of coastal high-salinity ponds indicated that salinity still selectively affects bacterial communities to some extent. Overall, our study provides valuable insights into the microbial regulation of nitrite during saline-alkaline water aquaculture, thereby aiding in the efficient utilization of secondary saline-alkaline water resources for fisheries.

Effects of dietary chitosan oligosaccharide on the growth, intestinal microbiota and immunity of juvenile red claw crayfish (Cherax quadricarinatus)

This study aimed to evaluate the potential benefits of chitosan oligosaccharide (COS) on red claw crayfish (Cherax quadricarinatus) and explore its underlying mechanisms. The crayfish were randomly divided into six groups, and the diets were supplemented with COS at levels of 0 (C0), 0.2 (C1), 0.4 (C2), 0.6 (C3), 0.8 (C4), and 1 (C5) g kg-1. Treatment with COS significantly improved the growth performance of the crayfish with a higher weight gain rate (WGR) and specific growth rate (SGR) in the C2 group compared to the C0 group. Additionally, the content of crude protein in the crayfish muscles in the C1 group was significantly higher than that of the C0 group. Regarding non-specific immunity, the activities of superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GSH-Px), and alkaline phosphatase (AKP), and the levels of expression of the genes related to immunity (SOD; anti-lipopolysaccharide factor [ALF]; thioredoxin1 [Trx1]; C-type lysozyme, [C-LZM]; and GSH-Px) in the hepatopancreas and hemolymph increased significantly (P < 0.05) after supplementation with 0.4 g kg-1 of COS, while the content of malondialdehyde (MDA) decreased (P < 0.05). The survival rate of C. quadricarinatus increased (P < 0.05) in the C2, C3, C4, and C5 groups after the challenge with Aeromonas hydrophila. This study found that COS has the potential to modulate the composition of the intestinal microbiota and significantly reduce the abundance of species of the phylum Proteobacteria and the genera Aeromonas and Vibrio in the gut of C. quadricarinatus, while the abundance of bacteria in the phylum Firmicutes and the genus Candidatus_Hepatoplasma improved significantly. This study suggests that the inclusion of COS in the diet of C. quadricarinatus can enhance growth, boost immunity, and increase resistance to infection with A. hydrophila, especially when supplemented at 0.4-0.8 g kg-1.

Acute effects of the environmental probiotics Rhodobacter sphaeroides on intestinal bacteria and transcriptome in shrimp Penaeusvannamei

In recent years, a substantial number of studies have been dedicated to exploring the potential benefits of probiotics in aquaculture. Rhodobacter sphaeroides can be used in aquaculture-related environmental bioremediation, and its protein is also used as a feed additive in Penaeus vannamei culture. To investigate the effects of releasing R. sphaeroides as environmental probiotics on P. vannamei, we employed 16S rRNA gene and mRNA transcriptome sequencing. Our study focused on assessing alterations in intestinal bacteria and intestinal gene expression in P. vannamei, establishing correlations between them. Our findings revealed a significant increase in the relative abundances of Rhodobacter, Paracoccus, Sulfitobacter, and other bacterial OTUs within the intestinal bacterial community. Additionally, we observed enhanced complexity and stability in the intestinal bacterial correlation network, indicating improved synergy among bacteria and reduced competition. Moreover, the introduction of R. sphaeroides resulted in the down-regulation of certain immune genes and the up-regulation of genes linked to growth and metabolism in the intestinal tissues of P. vannamei. Importantly, we identified a noteworthy correlation between the changes in intestinal bacteria and these alterations in intestinal tissue gene expressions. By conducting analyses of the intestinal bacterial community and intestinal tissue transcriptome, this study revealed the effects of releasing R. sphaeroides as sediment probiotics in P. vannamei culture water. These results serve as vital scientific references for the application of R. sphaeroides in P. vannamei aquaculture.

Rhein: A potent immunomodulator empowering largemouth bass against MSRV infection

Micropterus salmoides rhabdovirus (MSRV) is a significant viral pathogen in largemouth bass aquaculture, causing substantial annual economic losses. However, effective prevention methods remain elusive for various reasons. Medicinal plant extracts have emerged as valuable tools in preventing and managing aquatic animal diseases. Thus, the search for immunomodulators with straightforward, safe structures in plant extracts is imperative to ensure the continued health and growth of the largemouth bass industry. In our research, we employed epithelioma papulosum cyprinid (EPC) cells and largemouth bass as models to assess the anti-MSRV properties and immunomodulatory effects of ten plant-derived bioactive compounds. Among them, rhein demonstrated noteworthy potential, exhibiting a 75 % reduction in viral replication in vitro at a concentration of 50 mg/L. Furthermore, rhein pre-treatment significantly inhibited MSRV genome replication in EPC cells, with the highest inhibition rate reaching 64.8 % after 24 h, underscoring rhein's preventive impact against MSRV. Likewise, rhein displayed remarkable therapeutic effects on EPC cells during the early stages of MSRV infection, achieving a maximum inhibition rate of 85.6 % in viral replication. Subsequent investigations unveiled that rhein, with its consistent activity, effectively mitigated cytopathic effects (CPE) and nuclear damage induced by MSRV infection. Moreover, it restrained mitochondrial membrane depolarization and reduced the apoptosis rate by 38.8 %. In vivo experiments reinforced these findings, demonstrating that intraperitoneal injection of rhein enhanced the expression levels of immune related genes in multiple organs, hindered virus replication, and curtailed the mortality rate of MSRV-infected largemouth bass by 29 %. Collectively, our study endorses the utility of rhein as an immunomodulator to combat MSRV infections in largemouth bass. This not only underscores the potential of rhein as a broad-spectrum antiviral and means to bolster the immune response but also highlights the role of apoptosis as an immunological marker, making it an invaluable addition to the armamentarium against aquatic viral pathogens.

Sources and contamination routes of seafood with human pathogenic Vibrio spp.: A Farm-to-Fork approach

Vibrio spp., known human foodborne pathogens, thrive in freshwater, estuaries, and marine settings, causing vibriosis upon ingestion. The rising global vibriosis cases due to climate change necessitate a deeper understanding of Vibrio epidemiology and human transmission. This review delves into Vibrio contamination in seafood, scrutinizing its sources and pathways. We comprehensively assess the contamination of human-pathogenic Vibrio in the seafood chain, covering raw materials to processed products. A "Farm-to-Fork" approach, aligned with the One Health concept, is essential for grasping the complex nature of Vibrio contamination. Vibrio's widespread presence in natural and farmed aquatic environments establishes them as potential entry points into the seafood chain. Environmental factors, including climate, human activities, and wildlife, influence contamination sources and routes, underscoring the need to understand the origin and transmission of pathogens in raw seafood. Once within the seafood chain, the formation of protective biofilms on various surfaces in production and processing poses significant food safety risks, necessitating proper cleaning and disinfection to prevent microbial residue. In addition, inadequate seafood handling, from inappropriate processing procedures to cross-contamination via pests or seafood handlers, significantly contributes to Vibrio food contamination, thus warranting attention to reduce risks. Information presented here support the imperative for proactive measures, robust research, and interdisciplinary collaboration in order to effectively mitigate the risks posed by human pathogenic Vibrio contamination, safeguarding public health and global food security. This review serves as a crucial resource for researchers, industrials, and policymakers, equipping them with the knowledge to develop biosecurity measures associated with Vibrio-contaminated seafood.

Prediction of ammonia contaminants in the aquaculture ponds using soft computing coupled with wavelet analysis

Intensive aquaculture practices generate highly polluted organic effluents such as biological oxygen demand (BOD), alkalinity, total ammonia, nitrates, calcium, potassium, sodium, iron, and chlorides. In recent years, Inland aquaculture ponds in the western delta region of Andhra Pradesh have been intensively expanding and are more concerned about negative environmental impact. This paper presents the water quality analysis of aquaculture waters in 64 random locations in the western delta region of Andhra Pradesh. The average water quality index (WQI) was 126, with WQI values ranging from 21 to 456. Approximately 78% of the water samples were very poor and unsafe for drinking and domestic usage. The mean ammonia content in aquaculture water was 0.15 mg/L, and 78% of the samples were above the acceptable limit set by the World Health Organization (WHO) of 0.5 mg/L. The quantity of ammonia in the water ranged from 0.05 to 2.8 mg/L. The results show that ammonia levels exceed the permissible limits and are a significant concern in aquaculture waters due to toxicity. This paper also presents an intelligent soft computing approach to predicting ammonia levels in aquaculture ponds, using two novel approaches, such as the pelican optimization algorithm (POA) and POA coupled with discrete wavelet analysis (DWT-POA). The modified and enhanced POA with DWT can converge to higher performance when compared to standard POA, with an average percentage error of 1.964 and a coefficient of determination (R²) value of 0.822. Moreover, it was found that prediction models were reliable with good accuracy and simple to execute. Furthermore, these prediction models could help stakeholders and policymakers to make a real-time prediction of ammonia levels in intensive farming inland aquaculture ponds.

Bacteria of Zoonotic Interest Identified on Edible Freshwater Fish Imported to Australia

Previous research has shown that freshwater edible fish imported into Australia are not compliant with Australian importation guidelines and as a result may be high risk for bacterial contamination. In the present study, the outer surface of imported freshwater fish were swabbed, cultured, confirmatory tests performed and antimicrobial patterns investigated. Channidae fish (Sp. A/n = 66) were contaminated with zoonotic Salmonella sp./Staphylococcus aureus (n = 1/66) and other bacteria implicated in cases of opportunistic human infection, these being Pseudomonas sp. (including P. mendocina and P. pseudoalcaligenes (n = 34/66)); Micrococcus sp. (n = 32/66); Comamonas testosteroni (n = 27/66) and Rhizobium radiobacter (n = 3/66). Pangasiidae fish (Species B/n = 47) were contaminated with zoonotic Vibrio fluvialis (n = 10/47); Salmonella sp. (n = 6/47) and environmental bacteria Micrococcus sp. (n = 3/47). One sample was resistant to all antimicrobials tested and is considered to be Methicillin Resistant S. aureus. Mud, natural diet, or vegetation identified in Sp. A fish/or packaging were significantly associated with the presence of Pseudomonas spp. The study also showed that visibly clean fish (Sp. B) may harbour zoonotic bacteria and that certain types of bacteria are common to fish groups, preparations, and contaminants. Further investigations are required to support the development of appropriate food safety recommendations in Australia.

Presence and distribution of triazine herbicides and their effects on microbial communities in the Laizhou Bay, Northern China

This study investigated the distribution of triazine herbicides in the Laizhou Bay, China and found that the total concentrations of triazine herbicides in the seawater and sediments were 111.15-234.85 ng/L and 0.902-4.661 μg/kg, respectively. Triazine herbicides especially ametryn, atrazine, and simazine were negatively correlated with prokaryote diversity in the seawater. While ametryn, desethylatrazine and desisopropylatrazine had positively significant effects on eukaryotes Dinophyceae, Bacillariophyta, and Cercozoa in the sediments. Moreover, the degree of fragmentation of eukaryotic networks increased dramatically with the increasing numbers of removed nodes, but prokaryotic networks did not change with the decrease of nodes. In addition, the stability analysis and neutral community models revealed that eukaryotes were more sensitive to triazine herbicides than prokaryotes. These results suggest that triazine herbicides might affect the structure and interactions of microbial communities. Therefore, more attentions should be paid to the ecological risk of triazine herbicides in marine ecosystems.

Exploring bacterioplankton communities and their temporal dynamics in the rearing water of a biofloc-based shrimp (Litopenaeus vannamei) aquaculture system

Biofloc technology (BFT) has recently gained considerable attention as a sustainable method in shrimp aquaculture. In a successful BFT system, microbial communities are considered a crucial component in their ability to both improve water quality and control microbial pathogens. Yet, bacterioplankton diversity in rearing water and how bacterioplankton community composition changes with shrimp growth are rarely documented. In this study, the Pacific white shrimp, Litopenaeus vannamei was cultivated in a greenhouse-enclosed BFT system. Rearing water samples were collected on a weekly basis for 5 months (152 days) and water quality variables such as physicochemical parameters and inorganic nutrients were monitored. In parallel, 16S rRNA gene pyrosequencing was employed to investigate the temporal patterns of rearing-water microbiota. The productivity, survival rate, and feed conversion ratio were 3.2-4.4 kg/m3, 74%-89%, and 1.2-1.3, respectively, representing successful super-intensive cultures. The metataxonomic results indicated a highly dynamic bacterioplankton community, with two major shifts over the culture. Members of the phylum Planctomycetes dominated in rearing water during the early stages, while Actinobacteria dominated during the middle stages, and Chloroflexi and TM7 dominated during the late stages of culture. The bacterioplankton community fluctuated more in the beginning but stabilized as the culture progressed. Intriguingly, we observed that certain bacterioplankton groups dominated in a culture-stage-specific manner; these groups include Rhodobacteraceae, Flavobacteriaceae, Actinobacteria, and Chloroflexi, which either contribute to water quality regulation or possess probiotic potential. Altogether, our results indicate that an operationally successful BFT-based aquaculture system favors the growth and dynamics of specific microbial communities in rearing water. Our study expands the scientific understanding of the practical utilization of microbes in sustainable aquaculture. A thorough understanding of rearing-water microbiota and factors influencing their dynamics will help to establish effective management strategies.

Bacterial community structure and bacterial isolates having antimicrobial potential in shrimp pond aquaculture

Diseases outbreaks in pond aquaculture have resulted in huge losses to the aquaculture industry. The emergence of non-antimicrobial and environment friendly agents (probiotics) is the potential consideration for the healthy shrimp aquaculture. The present study was aimed to compare the bacterial community compositions in shrimp ponds and surrounding seawater, as well as isolate probiotic bacteria from the shrimp ponds. Based on the high-throughput of 16S rRNA gene sequencing, all sequences were assigned to 3584 unique operational taxonomic units (OTUs) at 97% similarity levels, which were affiliated with 24 phyla, 54 classes, 235 families, and 367 genera. The 10 most abundant phyla were Bacteroidota, Proteobacteria, Actinobacteriota, Planctomycetota, Cyanobacteria, Chloroflexi, Firmicutes, Desulfobacterota, Patescibacteria and Verrucomicrobiota. Notably, the alpha diversity (Shannon diversity) of shrimp ponds was significantly differences (P < 0.05) with that of surrounding seawater. There were 2498 and 791 unique OTUs in shrimp ponds and surrounding seawater, respectively. A total of 15 isolates were obtained in the culturable bacterial diversity, and the antibacterial activities were recorded for potential probiotic bacterial isolates against different tested bacterial isolates including pathogenic bacteria. An isolate Hallobacillusmarinus HMALI004 showed strong inhibitory effects against three pathogenic bacteria, Vibrio cholerae CECT 514, non AHPND V. parahaemolyticus BCRC12959 and AHPND V. parahaemolyticus PD-2. The isolates Algophigussanaruensis AGALI005, Algoriphagus taiwanensis ATALI009 and Bacillusaequororis BAALI008 were also identified as potential probiotics strains.

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.

Applicability of bio-synthesized nanoparticles in fungal secondary metabolites products and plant extracts for eliminating antibiotic-resistant bacteria risks in non-clinical environments

The abundance of antibiotic-resistant bacteria in the prawn pond effluents can substantially impact the natural environment. The settlement ponds, which are the most common treatment method for farms wastewater, might effectively reduce the suspended solids and organic matter. However, the method is insufficient for bacterial inactivation. The current paper seeks to highlight the environmental issue associated with the distribution of antibiotic resistant bacteria (ARB) from prawn farm wastewater and their impact on the microbial complex community in the surface water which receiving these wastes. The inactivation of antibiotic-resistant bacteria in prawn wastewater is strongly recommended because the presence of antibiotic-resistant bacteria in the environment causes water pollution and public health issues. The nanoparticles are more efficient for bacterial inactivation. They are widely accepted due to their high chemical and mechanical stability, broad spectrum of radiation absorption, high catalytic activity, and high antimicrobial activity. Many studies have examined the use of fungi or plants extract to synthesis zinc oxide nanoparticles (ZnO NPs). It is evident from recent papers in the literature that green synthesized ZnO NPs from microbes and plant extracts are non-toxic and effective. ZnO NPs inactivate the bacterial cells as a function for releasing reactive oxygen species (ROS) and zinc ions. The inactivation of antibiotic-resistant bacteria tends to be more than 90% which exhibit strong antimicrobial behavior against bacterial species.

Sustainability of the rice-crayfish co-culture aquaculture model: microbiome profiles based on multi-kingdom analyses

While the rice-crayfish culture (RCFP) model, an important aquaculture model in Asia, is generally considered a sustainable model, its sustainability in terms of microbial community profiles has not been evaluated. In this study, multi-kingdom analyses of microbiome profiles (i.e., bacteria, archaea, viruses, and eukaryotes) were performed using environmental (i.e., water and sediment) and animal gut (i.e., crayfish and crab gut) microbial samples from the RCFP and other aquaculture models, including the crab-crayfish co-culture, crayfish culture, and crab culture models, to evaluate the sustainability of the RCFP systematically. Results showed that RCFP samples are enriched with a distinct set of microbes, including Shewanella, Ferroplasma, Leishmania, and Siphoviridae, when compared with other aquaculture models. Additionally, most microbes in the RCFP samples, especially microbes from different kingdoms, were densely and positively connected, which indicates their robustness against environmental stress. Whereas microbes in different aquaculture models demonstrated moderate levels of horizontal gene transfer (HGT) across kingdoms, the RCFP showed relatively lower frequencies of HGT events, especially those involving antibiotic resistance genes. Finally, environmental factors, including pH, oxidation-reduction potential, temperature, and total nitrogen, contributed profoundly to shaping the microbial communities in these aquaculture models. Interestingly, compared with other models, the microbial communities of the RCFP model were less influenced by these environmental factors, which suggests that microbes in the latter have stronger ability to resist environmental stress. The findings collectively reflect the unique multi-kingdom microbial patterns of the RCFP model and suggest that this model is a sustainable model from the perspective of microbiome profiles.

Optimizing Hydraulic Retention Time and Area of Biological Settling Ponds for Super-Intensive Shrimp Wastewater Treatment Systems

Biological settling ponds are a practicable approach for treating super-intensive shrimp aquaculture wastewater for almost all shrimp producers in the Vietnamese Mekong Delta (VMD). The optimization of the hydraulic retention time (HRT) of biological settling ponds plays a crucial role in establishing the stability of outflow wastewater quality and suitability of the settling pond area (SPA). This study aims to suggest appropriate HRT and SPA for super-intensive shrimp wastewater treatment systems based on the National Standard (QCVN 02-19:2014/BNNPTNT) and the best aquaculture practices (BAP) standards and guidelines. We investigated 20 typical super-intensive shrimp farms in the VMD and collected effluent samples from siphoning process, daily water exchange, and outflow of biological effluent-treatment settling ponds. The results showed that the average of each super-intensive shrimp farm produced wastewater at approximately 218 m3 ha−1 day−1. The contaminant loads of TSS, COD, TKN, and TP were commensurate to 177, 113, 9.86, and 4.19 kg ha−1 day−1, respectively. Based on the relationship between outflow COD, TSS concentrations, and HRT of biological-surveyed settling ponds, a 13.4-day HRT and 1934-m2 SPA were suggested to optimize the super-intensive shrimp wastewater treatment systems. Our recommendation for further work is to continuously optimize the HRT and SPA rates of functional ponds (anaerobic, facultative, and maturation) to ameliorate the engineering configuration of the recommended biological settling pond.

Preparation and characterization of glucose-conjugated super-paramagnetic iron oxide nanoparticles (G-SPIONs) for removal of Edwardsiella tarda and Aeromonas hydrophila from water

The present research was conducted to prepare efficient G-SPIONs by co-precipitation to remove Edwardsiella tarda and Aeromonas hydrophila from the aqueous solution. The synthesized G-SPIONs were characterized by UV-Vis spectrophotometer, DLS, FEG-TEM, FT-IR, XRD, and VSM analysis. The results showed that the synthesized G-SPIONs had super-paramagnetic properties (58.31 emu/g) and spherical shape (16 ± 3 nm). The antibacterial activity was assessed in sterilized distilled water at different G-SPIONs concentrations viz. 0, 1.5, 3, 6, 12, 24, 48, 120, and 240 mg/L against E. tarda and A. hydrophila with various bacterial loads viz. 1 × 10³ , 1 × 10⁴ , 1 × 10⁵ , 1 × 10⁶ , and 1 × 10⁷  CFU/ml at different time intervals 15, 30, 45, and 60 min. At a lower bacterial load of E. tarda and A. hydrophila 1 × 10³ -1 × 10⁴  CFU/ml, 100% bacterial load was removed by 15 min exposure with NPs concentration 6-48 mg/L and 1.5-6 mg/L, respectively. Cent percent bacterial removal was observed in both the bacterial species even at higher bacterial load (1 × 10⁵ -1 × 10⁷  CFU/ml) by increasing exposure time (15-60 min) and nanoparticle concentration as well (24-240 mg/L). At an initial bacterial load of E. tarda and A. hydrophila (1 × 10³ -1 × 10⁷  CFU/ml), the EC₅₀ ranged between 0.01-6.51 mg/L and 0.02-3.84 mg/L, respectively, after 15-60 min exposure. Thus, it is concluded that the antibacterial effect of G-SPIONs depends on concentration and exposure time. Hence, G-SPIONs can be used as an antibacterial/biocidal agent to treat Edwardsiellosis and Aeromonosis disease in aquaculture.

The effect of piscidin antimicrobial peptides on the formation of Gram-negative bacterial biofilms

Fish-derived antimicrobial peptides are an important part of the innate immune system due to their potent antimicrobial properties. Piscidins are a class of antimicrobial peptides first described in hybrid striped bass (Morone chrysops x Morone saxatilis) but have also been identified in many other fish species. Previous work demonstrated the broad antimicrobial activity of piscidins against Gram-negative and Gram-positive bacterial species. This study sought to determine the extent to which class I (striped bass piscidin 1, white bass piscidin 1 and striped bass/white bass piscidin 3) and class II (striped bass piscidin 4 and white bass piscidin 5) piscidins inhibit biofilm formation of different Gram-negative bacteria. In general, the class I and II piscidins demonstrate potent activity against Escherichia coli and Flavobacterium columnare biofilms. The class II piscidins showed more activity against E. coli and F. columnare isolates than did the class I piscidins. The piscidins in general were much less effective against inhibiting Aeromonas hydrophila and A. veronii biofilm growth. Only the class I piscidins showed significant growth inhibition among the Aeromonas spp. examined.

Comparative analysis of microbial communities between water and sediment in Laoshan Bay marine ranching with varied aquaculture activities

We profiled and compared the bacterial and protist community compositions and dynamics in the Laoshan Bay marine ranching involving varied aquaculture activities. The dominant species, differential species and community compositions among the five aquaculture areas, two habitats and two periods were significantly different. The relationships between microbial communities and environmental factors were analyzed. We found that microbial communities in the water were more sensitive to the environmental changes than sediment, and the responses of bacterial and protist communities to the disturbances were varied. To meet the challenges of higher aquaculture density, the proportion of the positive correlations among co-occurrence networks in the water increased markedly from July to November; while the positive proportion in the sediment was stable. Potential ecological interactions and keystone taxa between bacteria and protists were studied. These results advanced our understanding of how mariculture stressors affect microbial communities in marine ranching.

Development of top-dressing automation technology for sustainable shrimp aquaculture in India

Globally, the shrimp farming industry faces increasing challenges and pressure to reduce the broken shrimps and maintain a healthier pond environment. Shrimps lack an adaptive immune system to combat invading pathogens due to an imbalance in beneficial gut microbiota. The use of top-dressing agents like probiotics and pond optimizes is an alternative strategy to improve the innate immune system leading produce disease-free shrimp in international markets. The cost of top-dressing agents is accounted for 20% of the production cost and therefore, the development of top-dressing automation technology is important to maintain and improve the financial and environmental viability of shrimp sustainable farming. This perspective described several sensor-based aquaculture technologies for on-farm management systems but sustainability in the aquaculture industry is not yet achieved in practice. The present technology is a new invention to reduce labor and production costs required for reducing bacterial and organic loads in Biofloc shrimp cultures. Aquaculture automation system disperses the top-dressing agents to the shrimp ponds based on the signals received from microbial and environmental sensors. Continuous monitoring of shrimp growth, mortality, immune responses, diseases, and pond water quality parameters will fetch larger profits with additional savings on labor and production costs for sustainable shrimp aquaculture in India.

Recent advances in Shrimp aquaculture wastewater management

Aquaculture has been celebrated globally and believed to usher in a viable alternative to capture fisheries. It is most welcomed especially now that the world population explosion has pushed the demand on fisheries products to worrisome limits. Shrimp farming is an area of aquaculture that has witnessed significant growth in recent years, contributing substantially to the global aquaculture production. However, intensification of shrimp aquaculture has come with unintended consequences such as wastewater management and other problems emanating from environmental impact of the wastewater. This study identified excess feed and fertilizer application, metabolite wastes, shrimp mortalities, oil spillage from farm machines, drug and chemical abuse as some of the activities contributing to wastewater generation in shrimp aquaculture farming. The impact of shrimp effluent water discharged has been observed to be socio-economic with both positive and negative dimensions. In attempt to overcome the overwhelming problems associated with shrimp effluent water and bring reassurances to its sustainability, a good number of new technological approaches have been identified including caviation, high-rate algal pond system, use of nanomaterials, biofloc technology, nanoadsorbent and polymeric nanoadsorbents. Although all have been proven to be useful, none could boast of a complete and integrated approach that considers all the technological, legal, social, environmental, public health and institutional concerns.

In Silico Prediction of Novel Probiotic Species Limiting Pathogenic Vibrio Growth Using Constraint-Based Genome Scale Metabolic Modeling

The prevalence of bacterial diseases and the application of probiotics to prevent them is a common practice in shrimp aquaculture. A wide range of bacterial species/strains is utilized in probiotic formulations, with proven beneficial effects. However, knowledge of their role in inhibiting the growth of a specific pathogen is restricted. In this study, we employed constraint-based genome-scale metabolic modeling approach to screen and identify the beneficial bacteria capable of limiting the growth of V. harveyi, a common pathogen in shrimp culture. Genome-scale models were built for 194 species (including strains from the genera Bacillus, Lactobacillus, and Lactococcus and the pathogenic strain V. harveyi) to explore the metabolic potential of these strains under different nutrient conditions in a consortium. In silico-based phenotypic analysis on 193 paired models predicted six candidate strains with growth enhancement and pathogen suppression. Growth simulations reveal that mannitol and glucoronate environments mediate parasitic interactions in a pairwise community. Furthermore, in a mannitol environment, the shortlisted six strains were purely metabolite consumers without donating metabolites to V. harveyi. The production of acetate by the screened species in a paired community suggests the natural metabolic end product's role in limiting pathogen survival. Our study employing in silico approach successfully predicted three novel candidate strains for probiotic applications, namely, Bacillus sp 1 (identified as B. licheniformis in this study), Bacillus weihaiensis Alg07, and Lactobacillus lindneri TMW 1.1993. The study is the first to apply genomic-scale metabolic models for aquaculture applications to detect bacterial species limiting Vibrio harveyi growth.

The Effect of Two Dietary Protein Sources on Water Quality and the Aquatic Microbial Communities in Marron (Cherax cainii) Culture

Feeding freshwater crayfish species with different diets not only affects the water quality but also induces the abundance of various microbial communities in their digestive tracts. In this context, very limited research has been undertaken to understand the impacts of various protein incorporated aqua-diets on the characteristics of water and its microbial communities. In this study, we have critically analysed the water quality parameters including pH, dissolved oxygen, nitrate, nitrite, ammonia and phosphorus, as well as bacterial communities under marron (Cherax cainii) aquaculture, fed fishmeal (FM) and poultry by-product meal (PBM)-based diets for 60 days. The results unveiled that over the time, feeding has significant impacts on organic waste accumulation, especially ammonia, nitrate, nitrite and phosphate, while no effects were observed on pH and dissolved oxygen. Analysis of 16S rRNA sequence data of water sample indicated significant (P < 0.05) shift of microbial abundance in post-fed FM and PBM water with the evidence of microbial transmission from the gut of marron. Post-fed marron resulted in a significant correlation of Hafnia, Enterobacter, Candidatus Bacilloplasma and Aquitella with the quality and microbial population of water. The results of this study generated valuable knowledge database of microbes-water relationship for better health management practices and production of marron aquaculture fed with FM and PBM diets in under restricted feeding regime with the feeding ratios provided.

Changes in the gut microbial community of the eastern newt (Notophthalmus viridescens) across its three distinct life stages

Understanding the forces that shape vertebrate gut microbial community assembly and composition throughout development is a major focus of the microbiome field. Here, we utilize the complex life cycle of the eastern newt (Notophthalmus viridescens) as a natural wild model to compare the effects of host and environmental factors on gut microbiome development. We compared bacterial inventories of each of the newt's three physiologically distinct developmental stages to determine if each hosted a unique community, or if the two stages which share an aquatic habitat (larvae and adults) harbored more similar communities than those of the third stage, the terrestrial juvenile eft. Additionally, we assessed how the contribution of selective processes to gut microbial assembly changed through development. We found that structurally, each life stage harbored a distinct community, which may be attributable to host factors. Further, across development, we found that community assembly processes shifted from a predominance of neutral to selective forces. However, habitat may also be important in determining community membership and diversity due the uniqueness of eft communities based on these metrics. Our results are similar to those in other vertebrate taxa, suggesting that gut microbiota assembly processes may be conserved across diverse lineages.

Assessment of selected trace metals in fish feeds, pond water and edible muscles of Oreochromis mossambicus and the evaluation of human health risk associated with its consumption in Vhembe district of Limpopo Province, South Africa

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Fish from Luvuvhu River recorded lower levels of trace metals than those from commercial fish ponds.

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Edible muscles of Oreochromis mossambicus had higher concentrations of trace metals than pond water.

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Low and moderate bioaccumulation factor (BF<5000) was recorded for most of the metals.

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There is no potential non-carcinogenic health risks from consumption of Oreochromis mossambicus in the study area.

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Cancer risk is more likely to occur in children than in adult consuming fish from the study area.

Fish is a rich source of proteins for humans and is widely consumed in various places in the world. This study assessed the levels of twenty trace metals (B, Al, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, As, Se, Sr, Mo, Cd, Sn, Sb, Ba, Hg and Pb) in fish feeds (n = 2), water (n = 27), and edible muscles of Oreochromis mossambicus (n = 20 from 8 ponds) from fish farms and Luvuvhu River (n = 3 from 1 river site) in Vhembe district of Limpopo Province, South Africa. Physicochemical parameters of water in the study area were analysed. Temperature ranged between 21.4–30.47 °C, pH: 5.59–7.28, electrical conductivity: 608–1216 μS/cm, total dissolved solids: 156–675 mg/l, dissolved oxygen: 0.28 - 0.56 mg/l, turbidity: 3.92–356.7 NTU, respectively. Levels of most trace metals such as Cr (2 μg/l and 1000 μg/kg), Mn (100 μg/l and 500 μg/kg), Fe (10 μg/l and 300 μg/kg), Ni (20 μg/l and 100 μg/kg), As (50 μg/l and 3 μg/kg), Pb (10 μg/l and 300 μg/kg) and Cu (2 μg/l and 2250 μg/kg) in water and O. mossambicus muscles were mostly below the World Health Organization (WHO), Food and Agricultural Organization (FAO)/WHO and European Commission (EC) recommended limit in the collected samples (Tshifulalani site and Duthuni site). However, Cu and Fe recorded concentration above the recommended limit at the control site (Luvuvhu River) in water and O. mossambicus muscles, respectively. Results from the bioaccumulation factor (BF), suggests the presence of metals in the water which can bioaccumulate in the fish muscles. Most of the metals (As, Cd, Hg, Mo, Sr, Sb and Sn) that recorded no possible bioaccumulation also recorded levels that complied with their maximum permissible limit (MPL) of WHO, FAO/WHO and EC guideline values in the fish feeds except for Se and Co. Moderate bioaccumulation was recorded for Cr, Mn, Fe and Zn in some of the sampling sites. Pb and Ni showed extreme bioaccumulation (BF > 5000) in one of the sampling sites and also recorded elevated levels in the fish feeds. Average daily dose (ADD), hazard quotient (HQ) and total hazard quotient (THQ) computed were less than 1. The Cancer risk (CR) evaluated were all below 10⁻⁴ except in one site for children (Tshifulanani 2) but the overall average result showed no carcinogenic health risk to the consumers of the O. mossambicus. Therefore, O. mossambicus intake in the study area should be constantly monitored to prevent future health implications.

Evaluation of the Physiological Bacterial Groups in a Tropical Biosecured, Zero-Exchange System Growing Whiteleg Shrimp, Litopenaeus vannamei

To elucidate the individual and multiple roles of physiological bacterial groups involved in biogeochemical cycles of carbon, nitrogen, phosphorus and sulfur, the changes in the abundance of aerobic bacteria (heterotrophs, methane oxidizers, ammonia oxidizers, sulfur oxidizers, phosphate solubilizers, phosphate accumulators) and anaerobic bacteria (total anaerobes, nitrate reducers, denitrifiers and sulfate reducers) were investigated in a biosecured, zero-exchange system stocked with whiteleg shrimp, Litopenaeus vannamei for one production cycle. Key water quality parameters during the 96-day production cycle fell within the normal range for L. vannamei culture. Results of Spearman's correlation matrix revealed that different sets of variables correlated at varying levels of significance of the interrelationships between bacterial abundances and water quality parameters. The three nitrogenous species (ammonia, nitrite and nitrate) strongly influenced the physiological bacterial groups' abundance. The strong relationship of bacterial groups with phytoplankton biomass and abundance clearly showed the trophic interconnections in nutrient exchange/recycling. Canonical correspondence analysis performed to assess the total variation revealed that the three dissolved nitrogen species followed by salinity, temperature, phytoplankton biomass and pH collectively accounted for as much as 82% of the total variation. In conclusion, the results of the study revealed that the major drivers that interweaved biogeochemical cycles are the three dissolved nitrogen species, which microbially mediated various aerobic-anaerobic assimilation/dissimilation processes in the pond ecosystem. Considering the pond microbial ecology becoming an important management tool where applied research could improve the economic and environmental sustainability of the aquaculture industry, the findings of the present study are practically relevant.

Non-surface Attached Bacterial Aggregates: A Ubiquitous Third Lifestyle

Bacteria are now generally believed to adopt two main lifestyles: planktonic individuals, or surface-attached biofilms. However, in recent years medical microbiologists started to stress that suspended bacterial aggregates are a major form of bacterial communities in chronic infection sites. Despite sharing many similarities with surface-attached biofilms and are thus generally defined as biofilm-like aggregates, these non-attached clumps of cells in vivo show much smaller sizes and different formation mechanisms. Furthermore, ex vivo clinical isolates were frequently reported to be less attached to abiotic surfaces when compared to standard type strains. While this third lifestyle is starting to draw heavy attention in clinical studies, it has a long history in natural and environmental sciences. For example, marine gel particles formed by bacteria attachment to phytoplankton exopolymers have been well documented in oceans; large river and lake snows loaded with bacterial aggregates are frequently found in freshwater systems; multispecies bacterial "flocs" have long been used in wastewater treatment. This review focuses on non-attached aggregates found in a variety of natural and clinical settings, as well as some recent technical developments facilitating aggregate research. The aim is to summarise the characteristics of different types of bacterial aggregates, bridging the knowledge gap, provoking new perspectives for researchers from different fields, and highlighting the importance of more research input in this third lifestyle of bacteria closely relevant to our daily life.

Metabolically-active bacteria in reclaimed water and ponds revealed using bromodeoxyuridine DNA labeling coupled with 16S rRNA and shotgun sequencing

Understanding the complex microbiota of agricultural irrigation water is vital to multiple sectors of sustainable agriculture and public health. To date, microbiome characterization methods have provided comprehensive profiles of aquatic microbiotas, but have not described which taxa are likely metabolically-active. Here, we combined 5‑bromo‑2'-deoxyuridine (BrdU) labeling with 16S rRNA and shotgun sequencing to identify metabolically-active bacteria in reclaimed and agricultural pond water samples (n = 28) recovered from the Mid-Atlantic United States between March 2017 and January 2018. BrdU-treated samples were significantly less diverse (alpha diversity) compared to non-BrdU-treated samples. The most abundant taxa in the metabolically-active fraction of water samples (BrdU-treated samples) were unclassified Actinobacteria, Flavobacterium spp., Pseudomonas spp. and Aeromonas spp. Interestingly, we also observed that antimicrobial resistance and virulence gene profiles seemed to be more diverse and more abundant in non-BrdU-treated water samples compared to BrdU-treated samples. These findings raise the possibility that these genes may be associated more with relic (inactive) DNA present in the tested water types rather than viable, metabolically-active microorganisms. Our study demonstrates that the coupled use of BrdU labeling and sequencing can enhance understanding of the metabolically-active fraction of bacterial communities in alternative irrigation water sources. Agricultural pond and reclaimed waters are vital to the future of sustainable agriculture, and thus, the full understanding of the pathogenic potential of these waters is important to guide mitigation strategies that ensure appropriate water quality for intended purposes.

Effects of Chitosan-Gentamicin Conjugate Supplement on Non-Specific Immunity, Aquaculture Water, Intestinal Histology and Microbiota of Pacific White Shrimp (Litopenaeus vannamei)

When the aquaculture water environment deteriorates or the temperature rises, shrimp are susceptible to viral or bacterial infections, causing a large number of deaths. This study comprehensively evaluated the effects of the oral administration of a chitosan-gentamicin conjugate (CS-GT) after Litopenaeus vannamei were infected with Vibrio parahaemolyticus, through nonspecific immunity parameter detection, intestinal morphology observation, and the assessment of microbial flora diversification by 16S rRNA gene sequencing. The results showed that the oral administration of CS-GT significantly increased total hemocyte counts and reduced hemocyte apoptosis in shrimp (p < 0.05). The parameters (including superoxide dismutase, glutathione peroxidase, glutathione, lysozyme, acid phosphatase, alkaline phosphatase, and phenoloxidase) were significantly increased (p < 0.05). The integrity of the intestinal epithelial cells and basement membrane were enhanced, which correspondingly alleviated intestinal injury. In terms of the microbiome, the abundances of Vibrio (Gram-negative bacteria and food-borne pathogens) in the water and gut were significantly reduced. The canonical correspondence analysis (CCA) showed that the abundances of Vibrio both in the water and gut were negatively correlated with CS-GT dosage. In conclusion, the oral administration of CS-GT can improve the immunity of shrimp against pathogenic bacteria and significantly reduce the relative abundances of Vibrio in aquaculture water and the gut of Litopenaeus vannamei.

Structure and co-occurrence patterns of bacterial communities associated with white faeces disease outbreaks in Pacific white-leg shrimp Penaeus vannamei aquaculture

Bacterial diseases cause production failures in shrimp aquacultures. To understand environmental conditions and bacterial community dynamics contributing to white faeces disease (WFD) events, we analysed water quality and compared bacterial communities in water as well as in intestines and faeces of healthy and diseased shrimps, respectively, via 16S rRNA gene sequencing and qPCR of transmembrane regulatory protein (toxR), thermolabile haemolysin (tlh), and thermostable direct haemolysin genes of pathogenic Vibrio parahaemolyticus as a proxy for virulence. WFD occurred when pH decreased to 7.71–7.84, and Alteromonas, Pseudoalteromonas and Vibrio dominated the aquatic bacterial communities. The disease severity further correlated with increased proportions of Alteromonas, Photobacterium, Pseudoalteromonas and Vibrio in shrimp faeces. These opportunistic pathogenic bacteria constituted up to 60% and 80% of the sequences in samples from the early and advances stages of the disease outbreak, respectively, and exhibited a high degree of co-occurrence. Furthermore, toxR and tlh were detected in water at the disease event only. Notably, bacterial community resilience in water occurred when pH was adjusted to 8. Then WFD ceased without a mortality event. In conclusion, pH was a reliable indicator of the WFD outbreak risk. Dissolved oxygen and compositions of water and intestinal bacteria may also serve as indicators for better prevention of WFD events.

BALOs Improved Gut Microbiota Health in Postlarval Shrimp (Litopenaeus vannamei) After Being Subjected to Salinity Reduction Treatment

White shrimp, Litopenaeus vannamei, is a widely farmed species. In China, shrimp postlarvae (PL) are frequently subjected to salinity reduction treatment to meet end growers' needs. However, although this treatment effectively reduces vibrio counts, its impact on gut microbiota health is still unknown. In this study, we applied a euryhaline strain of BALOs, BDN-1F2 (BD), and Bacillus subtilis (SD) to the rearing of second-generation shrimp PL after salinity reduction treatment so as to determine if they could impact PL gut microbiota by using high-throughput sequencing analysis. Results show that PL gut microbiota, both compositionally and functionally, have been badly wrecked after salinity reduction treatment with the generally recognized as opportunistic pathogens Gammaproteobacteria being the only dominant class at day 1 of test, viz., 99.43, 85.61, and 83.28% in BD, SD, and control (CD) groups, respectively. At day 7, Gammaproteobacteria was still the only dominant class in the SD and CD groups with relative abundance of 99.77 and 99.87% correspondingly, whereas in the BD group, its value dropped to 8.44%. Regarding biodiversity parameter the Shannon index, over the 7-day test period, while the SD group was unchanged (0.98-0.93), the CD group dropped to 0.94 from 2.94, and the BD group was raised to 7.14 from 0.93. Functionally, compared to control, the SD group displayed similar strength of various predicted community functions, but the BD group had hugely enhanced its various capabilities (p < 0.05). These results demonstrated that the addition of BDN-1F2 had exceedingly improved PL gut microbiota health by raising its biodiversities and strengthening its functionalities. On reviewing data derived from this as well as relevant studies, a Shannon index cutoff value was tentatively suggested so as to differentiate microbiota-healthy PL7-15 from the unhealthy ones. Furthermore, a conceptual mechanism of BALOs in the rectification/improvement of the microbial community health has also been proposed.

A Definition of Aquaculture Intensity Based on Production Functions—The Aquaculture Production Intensity Scale (APIS)

Aquaculture intensity has been used for years as a means to gauge how much production a site makes using three terms: extensive, semi-intensive and intensive aquaculture production systems. The industry has a relatively coordinated understanding of these terms, but an explicit general definition does not seem to exist. This paper aims to use three kinds of production function groups; the input, treatment and output functions to describe and define the terms extensive, semi-intensive and intensive explicitly. This is done with extensive literature review to find the meaning of the terms. The terms are then mapped onto the three production function groups. The resulting framework accomplishes two things. Firstly, it defines extensive, semi-intensive and intensive aquaculture in terms of production functions. Secondly, it creates an eight level scale, the aquaculture production intensity scale (APIS), that provides three levels of extensive systems, two level of semi-intensive systems and three level of intensive systems. APIS allows mapping of all uses of the terms in current literature to an APIS score, though some results might differ from current usage.

Microbial community structure associated with submarine groundwater discharge in northern Java (Indonesia)

Submarine groundwater discharge (SGD) can be an important pathway for chemical or biological pollutants from land to the ocean around the world. However, studies on the microbial communities associated with SGD in Southeast Asia, which has been hypothesized as SGD hotspot, remain scarce. In this study, we examined the microbial community composition with 16S rRNA gene sequencing along the hydrological continuum of an SGD site in a tropical urban area of Indonesia. Of the observed parameters in this study, salinity and temperature were the most determinant variables explaining patterns in microbial community composition. The bacterial taxon Burkholderiaceae was predominantly found in low salinity samples, including those from terrestrial groundwater and brackish pore water, while cyanobacteria of the genus Synechococcus sp. CC9902 were indicative of saline SGD and seawater samples. The composition of microbial taxa in each sample pointed to the influence of shallow terrestrial groundwater in the beach pore water, while seawater recirculation dominated the SGD sampling points situated further offshore. We identified taxa containing fecal indicators and potential pathogens at the SGD compartments; however, while a likely explanation, we could not conclude with certainty that SGD was a conduit for these bacteria. Overall, the results from this study show that microbial community analysis can highlight hydrological processes and water quality at the SGD site; thus, they could be useful for environmental policymakers to formulate water management strategies in coastal areas.

Comparative diversity of microbiomes and Resistomes in beef feedlots, downstream environments and urban sewage influent

Background

Comparative knowledge of microbiomes and resistomes across environmental interfaces between animal production systems and urban settings is lacking. In this study, we executed a comparative analysis of the microbiota and resistomes of metagenomes from cattle feces, catch basin water, manured agricultural soil and urban sewage.

Results

Metagenomic DNA from composite fecal samples (FC; n = 12) collected from penned cattle at four feedlots in Alberta, Canada, along with water from adjacent catchment basins (CB; n = 13), soil (n = 4) from fields in the vicinity of one of the feedlots and urban sewage influent (SI; n = 6) from two municipalities were subjected to Illumina HiSeq2000 sequencing. Firmicutes exhibited the highest prevalence (40%) in FC, whereas Proteobacteria were most abundant in CB (64%), soil (60%) and SI (83%). Among sample types, SI had the highest diversity of antimicrobial resistance (AMR), and metal and biocide resistance (MBR) classes (13 & 15) followed by FC (10 & 8), CB (8 & 4), and soil (6 & 1). The highest antimicrobial resistant (AMR) gene (ARG) abundance was harboured by FC, whereas soil samples had a very small, but unique resistome which did not overlap with FC & CB resistomes. In the beef production system, tetracycline resistance predominated followed by macrolide resistance. The SI resistome harboured β-lactam, macrolide, tetracycline, aminoglycoside, fluoroquinolone and fosfomycin resistance determinants. Metal and biocide resistance accounted for 26% of the SI resistome with a predominance of mercury resistance.

Conclusions

This study demonstrates an increasing divergence in the nature of the microbiome and resistome as the distance from the feedlot increases. Consistent with antimicrobial use, tetracycline and macrolide resistance genes were predominant in the beef production system. One of the feedlots contributed both conventional (raised with antibiotics) and natural (raised without antibiotics) pens samples. Although natural pen samples exhibited a microbiota composition that was similar to samples from conventional pens, their resistome was less complex. Similarly, the SI resistome was indicative of drug classes used in humans and the greater abundance of mercury resistance may be associated with contamination of municipal water with household and industrial products.

Electronic supplementary material

The online version of this article (10.1186/s12866-019-1548-x) contains supplementary material, which is available to authorized users.