Fish growth enhances microbial sulfur cycling in aquaculture pond sediments

Exploring the variations in molecular characteristics of dissolved organic matter driven by aquaculture types

In recent decades, global aquaculture has expanded rapidly, raising concerns about coastal environmental degradation due to unregulated or poorly regulated discharge of aquaculture tailwater. Despite the crucial role of dissolved organic matter (DOM) in biogeochemical processes and aquatic biodiversity, the influence of aquaculture type on the molecular characteristics of DOM remains largely unexplored. Herein, this study investigated the variations in chemical and spectroscopic properties as well as molecular characteristics and composition of DOM across different aquaculture types including crustacean, fish and shellfish. Our findings revealed notable differences in DOM quantities among different aquaculture types, with crustacean and fish aquaculture water containing higher DOM amount compared to shellfish aquaculture water. This disparity can be attributed to the more frequent formulated feeds of crustacean and fish in contrast to shellfish aquaculture. Furthermore, distinct differences were also observed in the characteristics and composition of DOM among the different aquaculture waters. Specifically, DOM in shellfish aquaculture water exhibited a higher abundance of unsaturated and reduced molecules as well as increased aromaticity compared to the other two aquaculture waters. Conversely, DOM from fish aquaculture water showed a greater contribution from terrestrial origin characterized by elevated levels of plant-based components such as lignin-like and tannin-like compounds. Interestingly, DOM from shellfish aquaculture water contained lower levels of microbial-derived components such as lipid-like and protein-like compounds, likely due to reduced microorganism populations resulting from lower nutrients availability and higher salinity. Overall, these significant variations in characteristics and composition of DOM underscore the potential impacts of aquaculture type on the DOM biogeochemical cycle and the environmental quality in aquatic ecosystems.

Characteristics of Water Environment and Intestinal Microbial Community of Largemouth Bass (Micropterus salmoides) Cultured Under Biofloc Model

To investigate the effects of biofloc mode on the water environment and intestinal microbial community structure of largemouth bass, a 60-day culture experiment was conducted without water replacement in 300-L glass tanks. The experiment included a control group and a biofloc group, each with three replicates. The results showed the following: (i) the richness and diversity of the water environment and fish intestinal microbial community increased under the biofloc model; (ii) Proteobacteria, Patescibacteria, and Bacteroidota were the dominant phyla in the water environment of largemouth bass, while Proteobacteria, Firmicutes, Bacteroidota, Patescibacteria, and Actinobacteriota were the dominant phyla in the gut of largemouth bass. However, differences in the relative abundance and community structure of microorganisms were observed between the two groups, suggesting that the biofloc system impacts both the water environment and intestinal microbial community structure in largemouth bass culture. (iii) A correlation analysis between water quality indices and enzyme activity with microbial abundance revealed that microbial community composition could effectively reflect water quality and fish physiological health. Based on the analysis of microbial community structure, this study offers a theoretical foundation for integrating largemouth bass culture with the biofloc system, and provides valuable data for future health management and water quality control in largemouth bass production.

Recovery of nutrients from fish sludge to enhance the growth of microalga Chlorella sorokiniana CMBB276

Intensive aquaculture production generates large amounts of sludge. This waste could be considered as a potential source of nutrients that can be recovered and utilized. Little attention has been paid to nutrient recovery from fish sludge. In this study, bioconversion of sludge was evaluated in lab scale under anaerobic (AN), facultative anaerobic (FA) and aerobic (AE) conditions. After 40 days of fermentation, AN recovered the highest values of dissolved total nitrogen (82.7 mg L-1), while AE showed the highest dissolved total phosphorus (11.8 mg L-1) and the highest reduction of total suspended solids (36.0 %). Microbial analysis showed that AN exhibited a distinct bacterial community than that of FA and AE. Furthermore, C. sorokiniana grown in AN effluents collected after 12 days of fermentation achieved the highest biomass production (1.96 g L-1). These results suggest that AN has the best potential to recover nutrients from sludge for production of C. sorokiniana.

Performance enhancement, bacterial communities optimization and emerging pollutants elimination by microalgal-bacterial consortium for treating aquaculture pond sediments

Aquaculture pond sediments have a notable influence on the ecosystem balance and farmed animal health. In this study, microalgal-bacterial immobilization (MBI) was designed to improve aquaculture pond sediments via synergistic interactions. The physicochemical characteristics, bacterial communities, and the removal efficiencies of emerging pollutants were systematically investigated. The consortium containing diatom Navicula seminulum and Alcaligenes faecalis was cultivated and established in the free and immobilized forms for evaluating the treatment performance. The results indicated that the immobilized group exhibited superior performance in controlling nutrient pollutants, shaping and optimizing the bacterial community compositions with the enrichment of functional bacteria. Additionally, it showed a stronger positive correlation between the bacterial community shifts and nutrient pollutants removal compared to free cells. Furthermore, the immobilized system maintained the higher removal performance of emerging pollutants (heavy metals, antibiotics, and pathogenic Vibrios) than free group. These findings confirmed that the employment of immobilized N. seminulum and A. faecalis produced more synergistic benefits and exerted more improvements than free cells in ameliorating aquaculture pond sediments, suggesting the potential for engineering application of functional microalgal-bacterial consortium in aquaculture.

Seasonal changes driving shifts in microbial community assembly and species coexistence in an urban river

Microbial communities play a vital role in urban river biogeochemical cycles. However, the seasonal variations in microbial community characteristics, particularly phylogenetic group-based community assembly and species coexistence, have not been extensively investigated. Here, we systematically explored the microbiome characteristics and assembly mechanisms of urban rivers in different seasons using 16S rRNA gene sequencing and multivariate statistical methods. The results indicated that the microbial community presented significant temporal heterogeneity in different seasons, and the diversity decreased from spring to winter. The phylogenetic group-based microbial community assembly was governed by dispersal limitation and drift in spring, summer, and autumn but was structured by homogeneous selection in winter. Moreover, the main functions of nitrification, denitrification, and methanol oxidation were susceptible to dispersal limitation and drift processes, whereas sulfate respiration and aromatic compound degradation were controlled by dispersal limitation and homogeneous selection. Network analyses indicated that network complexity decreased and then increased with seasonal changes, while network stability showed the opposite trend, suggesting that higher complexity and diversity reduced community stability. Temperature was determined to be the primary driver of microbial community structure and assembly processes in different seasons based on canonical correspondence analysis and linear regression analysis. In conclusion, seasonal variation drives the dynamics of microbial community assembly and species coexistence patterns in urban rivers. This study provides new insights into the generation and maintenance of microbial community diversity in urban rivers under seasonal change conditions.

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.

Microbiota composition and correlations with environmental factors in grass carp (Ctenopharyngodon idella) culture ponds in South China

To maintain the health of aquaculture fish, it is critical to understand the composition of microorganisms in aquaculture water and sediment and the factors affecting them. This study examined the water and sediment microbiota compositions of four different types of ponds in South China that were used to culture grass carp (Ctenopharyngodon idella) of different sizes through high-throughput sequencing of the 16S rRNA gene, and analyzed their correlations with environmental factors. The results showed that ponds with cultured grass carp of different sizes exhibited significant differences in terms of water physicochemical properties and composition of water and sediment microbiota. Furthermore, the exchange of microorganisms between water and sediment microbiota was lowest in ponds with the smallest grass carp and highest in ponds with the largest grass carp. All detected environmental factors except water temperature were significantly correlated with the water microbiota, and all detected environmental factors in the sediment were correlated with sediment microbiota. Moreover, Aeromonas hydrophila and Vibrio were significantly increased in the water microbiota, especially in ponds with small juvenile grass carp, implying an increased risk of A. hydrophila and Vibrio infections in these environments. Our results provide useful information for the management of grass carp aquaculture ponds.

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.

Composition and functionality of bacterioplankton communities in marine coastal zones adjacent to finfish aquaculture

Finfish aquaculture is a fast-growing primary industry and is increasingly common in coastal ecosystems. Bacterioplankton is ubiquitous in marine environment and respond rapidly to environmental changes. Changes in bacterioplankton community are not well understood in semi-enclosed stratified embayments. This study aims to examine aquaculture effects in the composition and functional profiles of the bacterioplankton community using amplicon sequencing along a distance gradient from two finfish leases in a marine embayment. Results revealed natural stratification in bacterioplankton associated to NOx, conductivity, salinity, temperature and PO₄. Among the differentially abundant bacteria in leases, we found members associated with nutrient enrichment and aquaculture activities. Abundant predicted functions near leases were assigned to organic matter degradation, fermentation, and antibiotic resistance. This study provides a first effort to describe changes in the bacterioplankton community composition and function due to finfish aquaculture in a semi-enclosed and highly stratified embayment with a significant freshwater input.

Effects of cadmium exposure on intestinal microflora of Cipangopaludina cathayensis

As one of the most environmentally toxic heavy metals, cadmium (Cd) has attracted the attention of researchers globally. In particular, Guangxi, a province in southwestern China, has been subjected to severe Cd pollution due to geogenic processes and anthropogenic activities. Cd can be accumulated in aquatic animals and transferred to the human body through the food chain, with potential health risks. The aim of the present study was to explore the effects of waterborne Cd exposure (0.5 mg/L and 1.5 mg/L) on the intestinal microbiota of mudsnail, Cipangopaludina cathayensis, which is favored by farmers and consumers in Guangxi. Gut bacterial community composition was investigated using high-throughput sequencing of the V3–V4 segment of the bacterial 16S rRNA gene. Our results indicated that C. cathayensis could tolerate low Cd (0.5 mg/L) stress, while Cd exposure at high doses (1.5 mg/L) exerted considerable effects on microbiota composition. At the phylum level, Proteobacteria, Bacteroidetes, and Firmicutes were the dominant phyla in the mudsnail gut microbiota. The relative abundances of Bacteroidetes increased significantly under high Cd exposure (H14) (p < 0.01), with no significant change in the low Cd exposure (L14) treatment. The dominant genera with significant differences in relative abundance were Pseudomonas, Cloacibacterium, Acinetobacter, Dechloromonas, and Rhodobacter. In addition, Cd exposure could significantly alter the pathways associated with metabolism, cellular processes, environmental information processing, genetic information processing, human diseases, and organismal systems. Notably, compared to the L14 treatment, some disease-related pathways were enriched, while some xenobiotic and organic compound biodegradation and metabolism pathways were significantly inhibited in the H14 group. Overall, Cd exposure profoundly influenced community structure and function of gut microbiota, which may in turn influence C. cathayensis gut homeostasis and health.

Response of gut microbiota to feed-borne bacteria depends on fish growth rate: a snapshot survey of farmed juvenile Takifugu obscurus

Environmental bacteria have a great impact on fish gut microbiota, yet little is known as to where fish acquire their gut symbionts, and how gut microbiota response to the disturbance from environmental bacteria. Through the integrative analysis by community profiling and source tracking, we show that feed-associated bacteria can impose a strong disturbance upon the hindgut microbiota of cultured fugu. Consequently, marked alterations in the composition and function of gut microbiota in slow growth fugu were observed, implying a reduced stability upon bacterial disturbance from feed. Moreover, quantitative ecological analyses indicated that homogeneous selection and dispersal limitation largely contribute to the community stability and partial variations among hosts in the context of lower degree of disturbance. While the disturbance peaked, variable selection leads to an augmented interaction within gut microbiota, entailing community unstability and shift. Our findings emphasized the intricate linkage between feed and gut microbiota and highlighted the importance of resolving the feed source signal before the conclusion of comparative analysis of microbiota can be drawn. Our results provide a deeper insight into aquaculture of fugu and other economically important fishes and have further implications for an improved understanding of host-microbe interactions in the vertebrate gastrointestinal tract.

Long-term effects of three compound probiotics on water quality, growth performances, microbiota distributions and resistance to Aeromonas veronii in crucian carp Carassius auratus gibelio

Probiotics could promote the healthy growth of aquatic animals and have been widely used in aquaculture. However, the influence of high concentration compound probiotics on the aquatic animals has not been reported. In the present study, a compound probiotics was used in high-density culture of crucian carps under the condition of micro-water exchange. During nearly 7-weeks feeding experiment, the aquaculture water quality, growth performances, disease resistance and microbiota distributions of crucian carps were tested. Under the high concentrations of compound probiotics, the content of total ammonia nitrogen and nitrite were finally in a state of dynamic equilibrium. The body length and weight of crucian carps in the experimental group (E) was significantly higher than that in the recirculating group (R). The antioxidant enzymes in the intestines and gills of the E group including SOD, CAT, GSH and MDA, were significantly higher than those in R group. The mortality of crucian carps in E group was significantly lower after the immersion infection of Aeromonas veronii. The addition of compound probiotics significantly increased the number of microorganisms detected in the intestines and gills of crucian carps in E group. The bacteria including Firmicutes, Planctomycetes, Verrucomicrobiota at the phylum level in E group were higher than those in R group. At the genus level, these bacteria (Pirellula, Roseimicrobium, Malikia) were not only higher in E group water, but also significantly higher in the intestines and gills than R group. The results of present study systematically analyzed the impact of high-concentration probiotics on crucian carps breeding, and speculated genus Pirellula, Roseimicrobium, Malikia may be used as aquatic probiotics. The present study will provide a new idea for the green and sustainable development of aquaculture.

Characteristics of bacterial community structure and function associated with nutrients and heavy metals in coastal aquaculture area

Coastal aquaculture area has become one of the critical zones that are more susceptible to the influence of human activity. Many aquaculture operations invariably result in the accumulation of nutrients and heavy metals in the coastal ecosystem. Our study investigated sediment bacterial community structure and function across 23 sites under the influence of nutrients and heavy metals in the coastal aquaculture area. The habitat environment of the sediment was described by analyzing physicochemical characteristics. Sediment bacterial community structure and diversity were investigated by 16S rRNA sequencing. The sequencing data presented that Proteobacteria, Bacteroidetes, Planctomycetes, Acidobacteria and Chloroflexi were predominant at phylum level. Variations in the bacterial community composition and diversity were significant (P < 0.01) among different groups (according to the distance from the bank side) which indicated that specific environmental conditions had shaped distinct bacterial community. Specifically, bacterial diversity and composition were significantly influenced by the temperature, salinity, pH, dissolved oxygen (DO), TOC, TON, nitrite, nitrate and heavy metals (P < 0.05). Results related to functional prediction demonstrated that carbon, nitrogen and sulfur metabolism were the dominant processes in the coastal aquaculture area. In the meantime, the potential pathogens such as Arcobacter was found in site S3, which indicated the possible threat to the cultured species in this area. Overall, variations in bacterial communities caused by nutrients and heavy metals can affect biogeochemical cycles, which may provide an indication for the protection of coastal aquaculture environments.

Impact of Marine Aquaculture on the Microbiome Associated with Nearby Holobionts: The Case of Patella caerulea Living in Proximity of Sea Bream Aquaculture Cages

Aquaculture plays a major role in the coastal economy of the Mediterranean Sea. This raises the issue of the impact of fish cages on the surrounding environment. Here, we explore the impact of aquaculture on the composition of the digestive gland microbiome of a representative locally dwelling wild holobiont, the grazer gastropod Patella caerulea, at an aquaculture facility located in Southern Sicily, Italy. The microbiome was assessed in individuals collected on sea bream aquaculture cages and on a rocky coastal tract located about 1.2 km from the cages, as the control site. Patella caerulea microbiome variations were explained in the broad marine metacommunity context, assessing the water and sediment microbiome composition at both sites, and characterizing the microbiome associated with the farmed sea bream. The P. caerulea digestive gland microbiome at the aquaculture site was characterized by a lower diversity, the loss of microorganisms sensitive to heavy metal contamination, and by the acquisition of fish pathogens and parasites. However, we also observed possible adaptive responses of the P. caerulea digestive gland microbiome at the aquaculture site, including the acquisition of putative bacteria able to deal with metal and sulfide accumulation, highlighting the inherent microbiome potential to drive the host acclimation to stressful conditions.