Contrasting patterns of bacterial communities in the rearing water and gut of Penaeus vannamei in response to exogenous glucose addition

Noctiluca scintillans bloom alters the composition and carbohydrate utilization of associated bacterial community and enriches potential pathogenic bacterium Vibrio anguillarum

Noctiluca scintillans (red) is a widely distributed heterotrophic dinoflagellate and a prominent red tide forming species. This study investigated the effects of Noctiluca blooms on marine microbial diversity and functionality using multi-omics approaches. Our findings revealed significant differences in the community composition of Noctiluca-associated bacteria compared to those associated with autotrophic plankton and free-living bacteria in the surrounding seawater. The dominant bacterial groups within the Noctiluca-associated community shifted at various bloom stages, which could be attributed to changes in prey composition of Noctiluca. During the non-bloom stage, Burkholderiaceae, Carnobacteriaceae, and Pseudomonadaceae dominated the community, while Vibrionaceae became dominant during the bloom stage, and Saprospiraceae, Crocinitomicaceae, and Pirellulaceae thrived during the post-bloom stage. Compared to the non-bloom stage, Noctiluca-associated bacterial community at the bloom stage exhibited significant down-regulation of genes related to complex carbohydrate metabolism, while up-regulation of genes related to glucose transportation and utilization. Furthermore, we identified Vibrio anguillarum, a potential pathogenic bacterium to marine fish, as a major component of the Vibrionaceae family during the bloom stage. The occurrence of V. anguillarum associated with Noctiluca blooms may be attributed to the increased availability of its preferred carbon sources and its high capabilities in glucose transportation, motility and chemotaxis. Moreover, the presence of Vibrio infection genes (hap, hlyA, rtxA) encoding vibriolysin, hemolysin, and RTX (Repeats-in-toxin) toxin in the V. anguillarum genome, with the hap gene showing high expression levels during Noctiluca blooms, indicates an elevated risk of infection. This study underscores the unique composition of the bacterial community associated with red tide forming heterotrophic dinoflagellates and suggests that Noctiluca cells may serve as reservoirs and vectors for pathogenic bacteria, potentially posing a threat to fish-farming and the health of other marine organisms.

Gut bacterial consortium enriched in a biofloc system protects shrimp against Vibrio parahaemolyticus infection

BACKGROUND

Shrimp cultured in a biofloc system (BFS) have a lower disease incidence than those farmed in a water exchange system (WES). Although a number of studies have reported that the gut bacterial community induced by BFS is highly associated with shrimp disease resistance, the causal relationship remains unknown. Here, the promotive roles of gut bacterial community induced by BFS in pathogenic Vibrio infection resistance and its potential micro-ecological and physiological mechanisms were investigated by gut bacterial consortium transplantation and synthetic community (SynCom) construction.

RESULTS

The BFS induced a more stable and resistant gut bacterial community, and significantly enriched some beneficial bacterial taxa, such as Paracoccus, Ruegeria, Microbacterium, Demequina, and Tenacibaculum. Transplantation of a gut bacterial consortium from BFS shrimp (EnrichBFS) greatly enhanced the stability of the bacterial community and resistance against pathogenic V. parahaemolyticus infection in WES shrimp, while transplantation of a gut bacterial consortium from WES shrimp significantly disrupted the bacterial community and increased pathogen susceptibility in both WES and BFS shrimp. The addition of EnrichBFS in shrimp postlarvae also improved the pathogen resistance through increasing the relative abundances of beneficial bacterial taxa and stability of bacterial community. The corresponding strains of five beneficial bacterial taxa enriched in BFS shrimp were isolated to construct a SynComBFS. The addition of SynComBFS could not only suppress disease development, but also improve shrimp growth, boost the digestive and immune activities, and restore health in diseased shrimp. Furthermore, the strains of SynComBFS well colonized shrimp gut to maintain a high stability of bacterial community.

CONCLUSIONS

Our study reveals an important role for native microbiota in protecting shrimp from bacterial pathogens and provides a micro-ecological regulation strategy towards the development of probiotics to ameliorate aquatic animal diseases. Video Abstract.

Naturally occurring beneficial bacteria Vibrio alginolyticus X-2 protects seaweed from bleaching disease

Microbiome manipulation is gaining fresh attention as a way to mitigate diseases in aquaculture. The commercially farmed seaweed Saccharina japonica suffers from a bacterial-induced bleaching disease, which has major implications for the reliable supply of healthy sporelings. Here, we identify a beneficial bacterium, Vibrio alginolyticus X-2 that significantly reduces the risk of bleaching disease. By combining infection assays and multi-omic analyses, we provide evidence to suggest that the underlying protective mechanisms of V. alginolyticus X-2 involve maintaining epibacterial communities, increasing the gene expression of S. japonica related to immune and stress protection pathways, and stimulating betaine concentrations in S. japonica holobionts. Thus, V. alginolyticus X-2 can elicit a suite of microbial and host responses to mitigate the bleaching disease. Our study provides insights into disease control in farmed S. japonica through the application of beneficial bacteria. IMPORTANCE Beneficial bacteria can elicit a suite of microbial and host responses to enhance the resistance to bleaching disease.

Assessing the efficacy of bleaching powder in disinfecting marine water: Insights from the rapid recovery of microbiomes

Single-bleaching powder disinfection is a highly prevalent practice to disinfect source water for marine aquaculture to prevent diseases. However, due to the decay of active chlorine and the presence of disinfectant resistance bacteria (DRB), the effects of bleaching powder on prokaryotic community compositions (PCCs) and function in marine water remain unknown. In the present study, the source water in a canvas pond was treated with the normal dose of bleaching powder, and the impact on PCCs and functional profiles was investigated using 16S rRNA gene amplicon sequencing. The bleaching powder strongly altered the PCCs within 0.5 h, but they began to recover at 16 h, eventually achieving 76% similarity with the initial time at 72 h. This extremely rapid recovery was primarily driven by the decay of Bacillus and the regrowth of Pseudoalteromonas, both of which are DRB. Abundant community not only help PCCs recover but also provide larger functional redundancy than rare community. During the recovery of PCCs, stochastic processes drove the community assembly. After 72 h, five out of seven identified disinfectant resistance genes related to efflux pump systems were highly enriched, primarily in Staphylococcus and Bacillus. However, 15 out of the 16 identified antibiotic resistance genes (ARGs) remained unchanged compared to the initial time, indicating that bleaching powder does not contribute to ARGs removal. Overall, the findings demonstrate that single-bleaching powder disinfection cannot successfully meet the objective of disease prevention in marine aquaculture water due to the extremely rapid recovery of PCCs. Hence, secondary disinfection or novel disinfection strategies should be explored for source water disinfection.

Freshwater mussels and host fish gut microbe community composition shifts after agricultural contaminant exposure

AIMS

We examined the effects of a mixture of contaminants found in agricultural watersheds on the gut microbiota and physiology of both the freshwater mussel Lampsilis cardium, and L. cardium host fish Micropterus salmoides.

METHODS AND RESULTS

Lampsilis cardium and M. salmoides were exposed to three concentrations of agricultural contaminants for 60 days (observing behaviour daily) before being sampled for gut microbiota analyses. DNA was extracted from the gut samples, amplified via PCR, and sequenced using the Illumina Mi-Seq platform. Only L. cardium guts had differing microbiota across treatments, with an increase in potentially pathogenic Aeromonas. We also provide novel evidence of a core microbiota within L. cardium and M. salmoides. In terms of physiology, female L. cardium exhibited a decrease in movement and marsupial gill display in contaminant exposures.

CONCLUSIONS

Exposure to contaminants from agricultural watersheds may affect population recruitment within freshwater mussel communities over time. Specifically, increased pathogenic micro-organisms and altered behaviour can reduce the likelihood of glochidia dispersal.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study supports emerging research that contaminants found in agricultural watersheds may be a factor in freshwater mussel population declines. It also provides novel evidence that unionids have a core gut microbiota.

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.

Sucrose addition directionally enhances bacterial community convergence and network stability of the shrimp culture system

Sucrose is an effective carbon source for creating more reliable and environmentally friendly conditions for shrimp growth by regulating bacteria in biofloc-based culture systems. However, the influence of sucrose addition on the interaction, co-occurrence networks, and assembly mechanisms of bacterial communities in biofloc-based culture systems remains largely unknown. Here, we comprehensively investigated the effects of sucrose addition on bacterial communities in three habitats (water, bioflocs, and gut). The bacterial community structures and compositions of these three habitats became more similar in groups with sucrose addition, compared with those in controls. More than 50% gut bacterial communities were mainly derived from water and biofloc communities in the sucrose addition groups, but only about 33% bacterial communities migrated from water and biofloc to the gut in the control culture system. Sucrose addition accordantly enriched core taxa belonging to the phylum Actinobacteria and the families Rhodobacteraceae and Flavobacteriaceae in water, biofloc, and gut habitats. These core taxa were important for maintaining bacterial network stability in the sucrose addition culture systems and some were identified as keystone taxa for improving shrimp growth. Furthermore, after sucrose addition, gut bacterial community assembly from water and biofloc was dominated by the heterogeneous select with the ratios of 55–91% and 67–83%, respectively, indicating that sucrose addition can directionally shape the bacterial assembly of the shrimp culture system. These results provide a basis for selectively regulating certain beneficial taxa to improve shrimp growth in culture systems.