Dynamic and Assembly of Benthic Bacterial Community in an Industrial-Scale In-Pond Raceway Recirculating Culture System

Transformation fate of bisphenol A in aerobic denitrifying cultures and its coercive mechanism on the nitrogen transformation pathway

Bisphenol A (BPA) is a commonly used endocrine-disrupting chemical found in high levels in wastewater worldwide. Aerobic denitrification is a promising alternative to conventional nitrogen removal processes. However, the effects of BPA on this novel nitrogen removal process have rarely been reported. Herein, we investigated the removal and interaction effects of BPA (0, 0.1, 1, and 10 mg/L) in aerobic denitrifying cultures. Our experimental results demonstrated that the aerobic denitrification system could remove 66%-86% of BPA from wastewater. Fourier transform infrared spectroscopy revealed that polysaccharides and amides were the primary sites for adsorption. An increase in the type and number of intermolecular hydrogen bonds might enhance the ability of aerobic denitrifying cultures to adsorb BPA. Adsorption kinetics analysis demonstrated that inhomogeneous multilayer adsorption was the leading cause of BPA removal. Adsorbed BPA decreased the sedimentation, flocculation, and hydrophobicity of aerobic denitrifying cultures, triggering changes in the levels of proteins and polysaccharides in extracellular polymeric substances. As the influent BPA increased from 0 to 10 mg/L, the nitrate-nitrogen and total organic carbon in the reactor effluent increased from 0.4 ± 0.2 and 26 ± 7.9 mg/L to 18.8 ± 9.3 and 116.2 ± 55.6 mg/L, respectively. BPA (initial concentration range: 1-10 mg/L) significantly influenced the abundance of genes involved in the nitrogen transformation pathway, contributing to the increase in the abundance of gaseous NOx-transformed genes and altering the relative abundance of denitrifying bacteria, particularly Thauera. Correlation analyses revealed that Pseudomonas, Thauera, and AKYH767 are important for maintaining systemic nitrogen transformations and BPA adsorption.

Effects of Different River Crab Eriocheir sinensis Polyculture Practices on Bacterial, Fungal and Protist Communities in Pond Water

Microorganisms, including bacteria, fungi, and protists, are key drivers in aquatic ecosystems, maintaining ecological balance and normal material circulation, playing vital roles in ecosystem functions and biogeochemical processes. To evaluate the environmental impact of different river crab polyculture practices, we set up two different river crab (Eriocheir sinensis) polyculture practices: one where river crabs were cultured with mandarin fish (Siniperca chuatsi), silver carp (Hypophthalmichthys molitrix), and freshwater fish stone moroko (Pseudorasbora parva), and another where river crabs were cultured just with mandarin fish and silver carp. These two polyculture practices were referred to as PC and MC, respectively. We analyzed the water bacterial, fungal, and protist communities in the PC and MC groups using 16S, ITS, and 18S ribosomal RNA high-throughput sequencing. We found that the PC group obviously increased the diversity of microbial communities and altered their composition. The bacterial community held the narrowest habitat niche and exhibited the weakest environmental adaption compared to fungal and protist communities. The PC group altered the co-occurrence networks of bacteria, fungi, and protist, leading to more complex and stable communities of fungi and protist. Furthermore, the PC group shifted the assembly mechanism of the bacterial community from being predominantly deterministic to predominantly stochastic processes, with relatively minor impacts on the fungal and protist communities. Environmental factors, especially dissolved oxygen (DO), were significantly associated with the communities of bacteria, fungi, and protists, with DO being the major contributor to changes in the microbial communities. Our results suggest that the polyculture of river crab with mandarin fish, silver carp, and stone moroko was an effective and viable attempt, and it was superior in terms of microbial community diversity and stability.

Variations in the Bacterial, Fungal, and Protist Communities and Their Interactions Within Sediment Affected by the Benthic Organism, Snail Bellamya purificata

In aquatic benthic environments, benthic organisms have been found to regulate important biogeochemical characteristics and perform key ecosystem functions. To further explore the ecological impact of the snail Bellamya purificata's, presence on the benthic environment, we employed high-throughput sequencing technology to investigate its effects on the bacterial, fungal, and protist communities in sediment and their intrinsic interactions. Our findings revealed that B. purificata's presence significantly enhanced the diversity and evenness of the fungal community while simultaneously decreasing the diversity and richness of the protist community, and it also altered the composition and relative abundance of the dominant phyla across the bacterial, fungal, and protist communities. The snail B. purificata considerably altered the co-occurrence networks of the microbial communities, particularly by enhancing the intrinsic complexity of the protist community and by strengthening the interconnections among the protist, bacterial, and fungal communities. Notably, the proportions of specialists within the sediment bacterial, fungal, and protist communities declined due to the snail B. purificata. Its presence also notably expanded the habitat niche breadth for sediment bacteria and protists. In terms of community assembly, B. purificata shifted the fungal community assembly from being dominated by stochastic processes to being dominated by deterministic processes, whereas the protist community assembly shifted from deterministic processes to being dominated by stochastic processes. The mainly altered ecological processes in the fungal and protist assemblies were drift and homogenizing selection. Additionally, the presence of B. purificata resulted in a notable reduction in the sediment ON level and a significant increase in the ammonia, FA, and EN concentrations. Sediment properties, particularly FA and nitrate, were strongly correlated with microbial communities and were key contributors to changes in microbial community dynamics. These research findings not only broadened our understanding of the ecological impacts of B. purificata on benthic microbial communities but also highlighted its substantial potential in enhancing microbial community stability.

Integrated rice-yellow catfish farming resulting in variations in the agricultural environment, rice growth performance, and soil bacterial communities

Different rice production patterns exert varying comprehensive impacts on the agricultural environment. Integrated rice-fish farming, an advanced and rapidly developing agricultural production pattern, aims to improve resource utilization efficiency and enhance food productivity. To unravel the responses and internal interactions of the agricultural ecological environment to integrated rice-fish farming, we assessed and compared environmental factor, rice growth performance, and soil microbiome in both integrated rice-yellow catfish farming (IRYF) and rice monoculture (RM) systems. Our results revealed significant increases in the total nitrogen and ammonia concentrations in the paddy water and soil induced by the IRYF. Rice growth performance in the IRYF group surpassed that in the RM group. IRYF obviously impacted almost all dominant bacterial phyla, genera, and functional groups (top ten most abundant), enhancing the ability of bacteria to degrade and utilize organic matter. Additionally, IRYF led to noticeable reductions in the Shannon, Simpson, Chao 1, and Pielou_J indices. IRYF strengthened the interconnections between various taxonomic units in bacterial co-occurrence network, resulting in increased complexity, stability, and disturbance resistance in the soil bacterial community. IRYF notably facilitated the transition from a community assembly dominated by stochastic processes to one dominated by deterministic processes for the soil bacterial community. The deterministic process driving this transition was variable selection. All the environmental factors, except for soil nitrate, demonstrated relatively high contributions to alterations in soil bacterial communities, with environmental variables significantly positively correlated with the soil bacterial community in the IRYF group. Alterations in functionality, composition, and diversity of the soil bacterial community were clearly associated with most environmental variables and rice growth performance indices. Our research contributed to understanding the comprehensive impacts of integrated rice-fish farming on agricultural ecosystems and provide theoretical support for achieving the sustainable agricultural production and optimizing the rice production patterns.

Influences of the Integrated Rice-Crayfish Farming System with Different Stocking Densities on the Paddy Soil Microbiomes

Integrated rice-fish farming has emerged as a novel agricultural production pattern to address global food security challenges. Aiming to determine the optimal, scientifically sound, and sustainable stocking density of red claw crayfish (Cherax quadricarinatus) in an integrated rice-crayfish farming system, we employed Illumina high-throughput 16S rRNA gene sequencing to evaluate the impact of different stocking densities of red claw crayfish on the composition, diversity, function, and co-occurrence network patterns of soil bacterial communities. The high stocking density of red claw crayfish reduced the diversity and evenness of the soil bacterial community during the mid-culture stage. Proteobacteria, Actinobacteria, and Chloroflexi emerged as the most prevalent phyla throughout the experimental period. Low stocking densities initially boosted the relative abundance of Actinobacteria in the paddy soil, while high densities did so during the middle and final stages. There were 90 distinct functional groups identified across all the paddy soil samples, with chemoheterotrophy and aerobic chemoheterotrophy being the most abundant. Low stocking densities initially favored these functional groups, whereas high densities enhanced their relative abundances in the later stages of cultivation. Medium stocking density of red claw crayfish led to a more complex bacterial community during the mid- and final culture stages. The experimental period showed significant correlations with soil bacterial communities, with total nitrogen (TN) and total phosphorus (TP) concentrations emerging as primary factors contributing to the alterations in soil bacterial communities. In summary, our findings demonstrated that integrated rice-crayfish farming significantly impacted the soil microbiomes and environmental factors at varying stocking densities. Our study contributed to theoretical insights into the profound impact of integrated rice-crayfish farming with various stocking densities on bacterial communities in paddy soils.

Similarity of Chinese and Pakistani oral microbiome

Oral microbiota is vital for human health and can be affected by various factors (i.e. diets, ethnicity). However, few studies have compared oral microbiota of individuals from different nationalities in the same environment. Here, we explored the assembly and interaction of oral microbial communities of Chinese and Pakistanis in one university. Firmicutes and Proteobacteria were the predominant microorganisms in the oral cavity of Chinese and Pakistanis. Streptococcus and Neisseria were the dominant genera of China, while Streptococcus and Haemophilus were the dominant genera of Pakistanis. In addition, the oral community membership and structure were not influenced by season, Chinese/Pakistani student and gender, reflecting the stability of the human oral microbiome. The beta diversity of oral microbiomes between Chinese and Pakistanis significantly differed in winter, but not in spring. The alpha diversity of Chinese students and Pakistani students was similar. Moreover, oral microbial community of both Chinese and Pakistani students was mainly driven by stochastic processes. The microbial network of Chinese was more complexity and stability than that of Pakistanis. Our study uncovers the characteristics of human oral microbiota, which is of great significance for oral and human health.

Stochastic Assembly Increases the Complexity and Stability of Shrimp Gut Microbiota During Aquaculture Progression

The gut microbiota of aquaculture species contributes to their food metabolism and regulates their health, which has been shown to vary during aquaculture progression of their hosts. However, limited research has examined the outcomes and mechanisms of these changes in the gut microbiota of hosts. Here, Kuruma shrimps from the beginning, middle, and late stages of aquaculture progression (about a time duration of 2 months between each stage) were collected and variations in the gut microbiota of Kuruma shrimp during the whole aquaculture process were examined. High-throughput sequencing demonstrated increases in the diversity and richness of the shrimp gut microbiota with aquaculture progression. In addition, the gut microbiota composition differed among cultural stages, with enrichment of Firmicutes, RF39, and Megamonas and a reduction in Proteobacteria in the mid-stage. Notably, only very few taxa were persistent in the shrimp gut microbiota during the whole aquaculture progression, while the number of taxa that specific to the end of aquaculture was high. Network analysis revealed increasing complexity of the shrimp gut microbiota during aquaculture progression. Moreover, the shrimp gut microbiota became significantly more stable towards the end of aquaculture. According to the results of neutral community model, contribution of stochastic processes for shaping the shrimp gut microbiota was elevated along the aquaculture progression. This study showed substantial variations in shrimp gut microbiota during aquaculture progression and explored the underlying mechanisms regulating these changes.

Effects of Bellamya purificata Cultivation at Different Stocking Densities on the Dynamics and Assembly of Bacterial Communities in Sediment

To optimize the integrated multi-trophic aquaculture (IMTA) model, improve the efficiency of resource utilization, and reduce environmental pollution, Bellamya purificata, as a potential bioremediation species, was studied to investigate the effect of B. purificata culture on the dynamics and assembly of bacterial communities in sediment. Four experimental groups were established at four different densities: 0, 234.38, 468.75, and 937.5 g/m² (represented as CON, LD, MD, and HD, respectively). Each group was with three replicates. The 16S ribosomal RNA (rRNA) high-throughput sequencing was used to evaluate the composition, function, and assembly of bacterial communities in sediment. B. purificata cultivation significantly altered the composition and function of the bacterial communities in sediment; at high stocking density, it significantly decreased anaerobic and increased aerobic organic matter decomposition, whereas at low stocking density, it decreased the number of bacteria involved in sulfate reduction and inhibited the denitrification process. B. purificata decreased direct competition and promoted collaboration or niche sharing in bacterial communities, especially at the high stocking density. Moreover, B. purificata cultivation resulted in greater changes in the environmental factors. Variations in dissolved oxygen, pH, total nitrogen, nitrate, and nitrite levels were closely related to the altered composition and function of the bacterial communities. Stochastic processes dominated the bacterial community assembly in the sediment and B. purificata cultivation had limited impacts on the bacterial community assembly. The study provided a reference for the dynamics and assembly of bacterial communities in sediment with different densities of B. purificata cultivation and we hope that the findings will provide a theoretical reference for the optimization of IMTA and improve management strategies for B. purificata polyculture.

Apex Predators Enhance Environmental Adaptation but Reduce Community Stability of Bacterioplankton in Crustacean Aquaculture Ponds

Aquaculture environments harbor complex bacterial communities that are critical for the growth and health of culture species. Apex predators are frequently added to aquaculture ponds to improve ecosystem stability. However, limited research has explored the effects of apex predators on the composition and function of bacterioplankton communities, as well as the underlying mechanisms of community assembly. Using 16S ribosomal RNA (rRNA) high-throughput sequencing, we investigated bacterioplankton communities of crustacean aquaculture ponds with and without apex predators (mandarin fish, Siniperca chuatsi) throughout the culture process. In addition to investigating differences in bacterioplankton communities, we also explored variations in environmental adaptation, functional redundancy, and community stability. Significant differences were observed in bacterioplankton composition among different cultural stages; there was an increase in Bacteriobota and fermentation-related bacteria, but a decrease in Firmicutes and pathogens in the middle stages of aquaculture. Apex predators increased the abundance of organic matter degradation bacteria and decreased pathogens. Bacterioplankton communities under apex predator disturbances had a wider environmental breadth, indicating broader environmental adaptation. Moreover, functional prediction and network analyses revealed that communities under apex predator disturbances were less functionally redundant and unstable. Based on the null model, stochastic processes drove community assembly during aquaculture, whereas apex predators elevated the contribution of deterministic processes. Greater changes in nitrate in culture ponds caused by apex predator disturbances were decisive in controlling the balance between stochasticity and determinism in community assembly. Our study provided insight into the mechanisms underlying bacterioplankton community assembly in aquaculture systems in response to apex predator disturbances.

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

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