Sediment microbiota in polyculture of shrimp and fish pattern is distinctive from those in monoculture intensive shrimp or fish ponds

Seaweed feed enhance the long-term recovery of bacterial community and carbon-nitrogen sequestration in eutrophic coastal wetland

Seaweed feed offers a promising approach to enhance sustainability in aquaculture. While much research has focused on its effects on aquatic organisms, the impact of seaweed feed residuals on sediment carbon sequestration and bacterial community dynamics remains underexplored. This study aimed to address this gap through a 96-day incubation experiment using sediment from the coastal wetlands of Zhuhai in southern China. We evaluated the effects of seaweed feed derived from the red seaweed Gracilaria lemaneiformis by analyzing temporal changes in sediment physicochemical properties and microbial community dynamics. Our findings reveal that seaweed feed significantly improved sediment organic carbon and nitrogen storage (p < 0.01), enhanced the recovery of dissolved oxygen levels (p < 0.001) and bacterial α-diversity (p < 0.01) compared to normal feed. Additionally, the variability in microbial community structure (p < 0.01) and functional potential (p < 0.05) due to seaweed feed was less pronounced than that caused by normal feed. This reduced variability may result from the role of seaweed feed in stabilizing microbial community assembly, which helps mitigate fluctuations in bacterial structure and function. Overall, this study offers valuable insights for managing aquaculture ponds and coastal wetlands, contributing to the understanding of seaweed carbon sequestration and highlighting the potential of seaweed feed as a significant carbon sink beyond traditional cultivation practices.

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

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

Examining the effect of iron (ferric) on physiological processes: Invertebrate models

Iron is a common and essential element for maintaining life in bacteria, plants and animals and is found in soil, fresh waters and marine waters; however, over exposure is toxic to organisms. Iron is used in electron transport complexes within mitochondria as well as a co-factor in many essential proteins. It is also established that iron accumulation in the central nervous system in mammals is associated with various neurological disorders. Ample studies have investigated the long-term effects of iron overload in the nervous system. However, its acute effects in nervous tissue and additional organ systems warrant further studies. This study investigates the effects of iron overload on development, behavior, survival, cardiac function, and glutamatergic synaptic transmission in the Drosophila melanogaster. Additionally, physiological responses in crayfish were examined following Fe3+ exposure. Fe3+ reduced neuronal excitability in proprioceptive neurons in a crayfish model. Thus, Fe3+ may block stretch activated channels (SACs) as well as voltage-gated Na+ channels. Exposure also rapidly reduces synaptic transmission but does not block ionotropic glutamatergic receptors, suggesting a blockage of pre-synaptic voltage-gated Ca2+ channels in both crustacean and Drosophila models. The effects are partly reversible with acute exposure, indicating the cells are not rapidly damaged. This study is relevant in demonstrating the effects of Fe3+ on various physiological functions in different organisms in order to further understand the acute and long-term consequences of overload.

Community assembly patterns and processes of bacteria in a field-scale aquaculture wastewater treatment system

Microbial communities are responsible for the biological treatment of wastewater, however, our comprehension of their diversity, assembly patterns, and functions remains limited. In this study, we analyzed bacterial communities in both water and sediment samples. These samples were gathered from a novel field-scale aquaculture wastewater treatment system (FAWTS), which employs a multi-stage purification process to eliminate nutrients from pond culture wastewater. Significant variations were observed in bacterial diversity and composition across various ponds within the system and at different stages of the culture. Notably, the bacterial community in the FAWTS displayed a distinct species abundance distribution. The influence of dispersal-driven processes on shaping FAWTS communities was found to be relatively weak. The utilization of neutral and null models unveiled that the assembly of microbial communities was primarily governed by stochastic processes. Moreover, environmental factors variables such as total nitrogen (TN), dissolved oxygen (DO), and temperature were found to be associated with both the composition and assembly of bacterial communities, influencing the relative significance of stochastic processes. Furthermore, we discovered a close relationship between that bacterial community composition and system functionality. These findings hold significant implications for microbial ecologists and environmental engineers, as they can collaboratively refine operational strategies while preserving biodiversity. This, in turn, promotes the stability and efficiency of the FAWTS. In summary, our study contributes to an enhanced mechanistic understanding of microbial community diversity, assembly patterns, and functionality within the FAWTS, offering valuable insights into both microbial ecology and wastewater treatment processes.

Nutrient enrichment drives the sediment microbial communities in Chinese mitten crab Eriocheir sinensis culture

Microbial communities play a critical role in aquaculture ecosystems. To identify the influence of sediment nutrient levels on microbial communities, sediment and water samples were collected from Chinese mitten crab Eriocheir sinensis culture ponds with different nutrient enrichment levels. Relevant physicochemical properties were measured, and 16 S rRNA gene sequencing was applied to identify relevant bacterial communities in the sediments. The results showed that the diversity and composition of microbial communities in sediments with different levels of nutrient enrichment varied considerably. Proteobacteria was the most abundant phylum in all samples, followed by Bacteroidetes, and Desulfobacterota with relative abundances of 23.5-40.9%, 9.8-21.5%, and 9.6-18.1%, respectively. Notably, total nitrogen (TN), organic matter (OM), and pH were important factors driving sediment bacterial community aggregation, the TN concentration explaining 61.5% of the microbial community variation. This study highlights that long-term culture activities alter the degree of sediment nutrient enrichment, which in turn affects microbial community composition and may ultimately have an impact on culture efficiency.

Exploring the variation of bacterial community and nitrogen transformation functional genes under the pressure of heavy metals in different coastal mariculture patterns

Equilibrium in microbial dynamics and nitrogen transformation in the sediment is critical for maintaining healthy mariculture environment. However, our understanding about the impact of heavy metals on the bacterial community and nitrogen transformation functional genes in different mariculture patterns is still limited. Here, we analyzed 30 sediment samples in the vertical distribution from three different mariculture patterns mainly include open mariculture zone (K), closed mariculture pond (F) and pristine marine area (Q). Illumina MiSeq Sequencing was applied to investigate the bacterial community and structure in the sediment. Quantitative polymerase chain reaction (qPCR) was used to determine the effect of heavy metals on nitrogen transformation functional genes. Results showed that bacterial community and structure varied greatly in different mariculture patterns. Chloroflexi, Proteobacteria and Desulfobacterota were predominant phyla in the coastal mariculture area. High concentrations of heavy metals mainly enriched in the up layer (5-40 cm) of the sediment in the mariculture zone. The abundance of functional genes in the closed mariculture pond was much higher than the open mariculture zone and pristine marine area. And the high abundance of nitrification and denitrification functional genes mainly accumulated at the depth from 5 cm to 40 cm. Heavy metals content such as Fe, Cr, Mn, Ni, As, Cd, Pb and nutrient content NH₄⁺-N, NO₃^--N and NO₂^--N were highly associated with bacterial community and nitrogen transformation functional genes. This study comprehensively elaborated the effect of heavy metals on the bacterial community and nitrogen transformation functional genes in different coastal mariculture patterns, indicating the possible role of closed mariculture pond in reducing nitrogen transformation efficiency, which will provide useful information for preventing pollution risk in the mariculture area.

Viral diversity and biogeochemical potential revealed in different prawn-culture sediments by virus-enriched metagenome analysis

As the most numerous biological entities on Earth, viruses affect the microbial dynamics, metabolism and biogeochemical cycles in the aquatic ecosystems. Viral diversity and functions in ocean have been relatively well studied, but our understanding of viruses in mariculture systems is limited. To fill this knowledge gap, we studied viral diversity and potential biogeochemical impacts of sediments from four different prawn-mariculture ecosystems (mono-culture of prawn and poly-culture of prawn with jellyfish, sea cucumber, and clam) using a metagenomic approach with prior virus-like particles (VLPs) separation. We found that the order Caudovirales was the predominant viral category and accounted for the most volume (78.39% of classified viruses). Sediment viruses were verified to have a high diversity by using the construct phylogenetic tree of terL gene, with three potential novel clades being identified. Meanwhile, compared with viruses inhabiting other ecosystems based on gene-sharing network, our results revealed that mariculture sediments harbored considerable unexplored viral diversity and that maricultural species were potentially important drivers of the viral community structure. Notably, viral auxiliary metabolic genes were identified and suggested that viruses influence carbon and sulfur cycling, as well as cofactors/vitamins and amino acid metabolism, which indirectly participate in biogeochemical cycling. Overall, our findings revealed the genomic diversity and ecological function of viral communities in prawn mariculture sediments, and suggested the role of viruses in microbial ecology and biogeochemistry.

Bait input altered microbial community structure and increased greenhouse gases production in coastal wetland sediment

Coastal wetland reclamation contributed to development of aquaculture industry, and the residual bait accumulation in aquaculture processes could influence biogeochemical elements cycling, which threaten ecological functions and services in aquaculture and adjacent ecosystems. However, systematic studies for changes in sediment microbial community structure and greenhouse gasses (GHGs) production, as well as environmental parameters following bait input at time scale are still rare. A 90-day incubation experiment was conducted using sediment collected from coastal wetland in Qi'ao Island in southern China, followed by the observations of temporal variations of physicochemical properties, sediment microbial community, and GHGs production in response to different amounts of bait input (0, 20, and 40 mg bait g^-1 wet sediment). The results showed that dissolved oxygen of overlying water was profoundly decreased owing to bait input, while dissolved organic carbon of overlying water and several sediment properties (e.g., organic matter, sulfide, and ammonium) varied in reverse patterns. Meanwhile, bait input led to significant loss of microbial community richness and diversity, and strongly altered microbial compositions from aerobic, slow-growing, and oligotrophic (Actinobacteriota, Chloroflexi, and Acidobacteriota) to anaerobic, fast-growing, and copiotrophic (Firmicutes and Bacteroidota). Moreover, both GHGs production and global warming potential were significantly enhanced by bait input, implying that aquaculture ecosystem is an important hotspot for global GHGs emission. Overall, bait input triggered quick responses of physicochemical properties, sediment microbial community, and GHGs production, followed by long-term resilience of the ecosystem. This study could provide new insight into temporal interactive effects of bait input on physicochemical properties, microbial community, and GHGs production, which can enhance the understanding of the temporal dynamics and ecological impacts of coastal aquaculture activities and emphasize the necessity of sustainable assessment and management in aquaculture ecosystems.

Pollution and Release Characteristics of Nitrogen, Phosphorus and Organic Carbon in Pond Sediments in a Typical Polder Area of the Lake Taihu Basin

There is currently a lack of knowledge on the release characteristics of nutrients from artificial pond sediments in polder areas, resulting in problems in future management of such environments, including converting polders to lakes. In this study, sediment samples were taken from a fish pond and a lotus pond in a typical polder area of the Lake Taihu Basin in China. The total nitrogen (TN, 1760–1810 mg/kg), total phosphorus (TP, 1370–1463 mg/kg) and total organic carbon (TOC, 10.1–21.2 g/kg) contents were significantly higher than those found in sediments from the adjacent aquatic system, which indicates that the legacy of agricultural activities has had an obvious cumulative effect on pond sediment nutrients. The release behavior of TN, TP and TOC varied significantly, not only under disturbed and static conditions, but also from sediments sampled at different ponds and depths. During the disturbing condition, there were continuous releases of carbon and nutrients in the lotus pond sediments, while the fish pond sediments showed a higher release at the beginning. Under static release conditions, the release of TP in the surface and bottom sediments of the fish pond increased first, then decreased and stabilized within 24 h, while the release of the lotus pond showed a slow upward trend. Despite the lower concentration of nutrients and TOC, the lotus pond sediment showed a higher release rate. The results suggested that it is necessary to adopt different strategies for different types of ponds in the project of returning polders to lakes; it is especially important to pay attention to the release of nutrients from the bottom sediments of lotus ponds in the project management.

Advantage of Species Diversification to Facilitate Sustainable Development of Aquaculture Sector

Intensified agrochemical-based monoculture systems worldwide are under adoption to meet the challenge of human population growth and the ever-growing global demand for food. However, this path has been opposed and criticized because it involves overexploitation of land, monoculture of few species, excessive input of agrochemicals, and adverse impacts on human health and the environment. The wide diversity among polyculture systems practiced across the globe has created confusion over the priority of a single strategy towards sustainable aquaculture development and safer products. Herein, we highlight the significance of polyculture and integrated aquaculture practices in conveying the successful transition of the aquaculture industry towards sustainable development. So far, the established thought is that the precise selection of aquatic species and a focus on compatible and complementary species combinations are supposed to facilitate rapid progress in food production with more profitability and sustainability. Therefore, the advantages of species diversification are discussed from an ecological perspective to enforce aquaculture expansion. This account asserts that a diverse range of aquaculture practices can promote synergies among farmed species, enhance system resilience, enable conservation, decrease ecological footprints, and provide social benefits such as diversified income and local food security.

The response of sediment microbial communities to temporal and site-specific variations of pollution in interconnected aquaculture pond and ditch systems

Sediment microbial communities play critical roles in the health of fish and the biogeochemical cycling of elements in aquaculture ecosystems. However, the response of microbial communities to temporal and spatial variations in interconnected aquaculture pond and ditch systems remains unclear. In this study, 61 sediment bacterial samples were collected over one year from 11 sites (including five ponds and six ditches) in a 30-year-old fish aquaculture farm. The 16S rRNA approach was used to determine the relative abundances of microbial communities in the sediment samples. The relationships among nutrients, heavy metals, and abundant microorganisms were analyzed. Our results showed that Proteobacteria, Bacteroides and Chloroflexi were the predominant phyla in the sediments of aquaculture pond, with average abundances of 36.33%, 18.60%, and 14.58%, respectively. The microbial diversity in aquaculture sediments was negatively correlated (P < 0.05) with the concentrations of total nitrogen and total phosphorus in sediments, indicating that the microbial diversity is highly associated with the remediation of nutrients in sediments. The sediment samples with high similarities were discovered by the t-distributed stochastic neighbor embedding (t-SNE) method. The site-specific correlations between specific microorganisms and heavy metals were explored. The network analysis revealed that the microbial diversities in aquaculture ponds were more stable than that in aquaculture ditches. The network analysis also illustrated that the microbial genera with low relative abundances may become key groups of microbial communities in sediment ecosystems. Our work deepens the understanding of the relationships between microbial communities and the spatiotemporal characteristics of surface water and sediments in aquaculture farms.