Comparative analysis of the bacterial community compositions of the shrimp intestine, surrounding water and sediment

Comparative analysis of crab growth performance, enzyme activity, and microbiota between rice-crab coculture and pond farming systems

Introduction

To support the sustainable development of rice and aquaculture industries, various rice-animal coculture systems have been developed. One such system, the rice-crab coculture system (RCC), has been practiced for decades in northern China. However, studies on the crab physiological status in RCC remain limited. Microorganisms play a crucial role in aquaculture by influencing animal nutrition, health, nutrient cycling, water quality, and environmental impact. Research on the gut and environmental microbiota in RCC is scarce.

Methods

This study compared the growth performance, immune and digestive enzyme activities of crabs between RCC and traditional pond farming system (PF). In addition, the microbiota in crab guts, water, and sediment from both systems was investigated using 16S rRNA gene sequencing.

Results

Crabs in RCC exhibited superior growth performance and higher enzymatic activities, including acid phosphatase (ACP), alkaline phosphatase (AKP), lipase (LPS), and trypsin (TRY). Significant differences were observed in microbiota composition across crab gut, water, and sediment samples, respectively. RCC crabs had a lower abundance of Bacteroidota and a higher abundance of Firmicutes in their gut microbiota. The RCC environment was enriched with beneficial bacteria such as Rhizobiales, Methylococcales, KD4-96, C39, Xanthomonadales, and Nitrosomonadaceae. Microbial function predictions confirmed enhanced methanotrophy and nitrogen fixation in the RCC.

Discussion

The RCC enhances the growth rate and immune capability of crabs. Crabs from RCC consume more animal-based nutrition, which results in distinct differences in gut microbiota composition and higher levels of LPS and TRY compared to those in PF. Additionally, RCC supports environmentally beneficial bacteria that contribute to greenhouse gas reduction, carbon and nitrogen fixation, organic matter decomposition, and ammonia oxidation, benefiting both the crabs and their ecosystem. These findings enhance our understanding of crab physiology and microbial communities in RCC and PF systems.

The diversity, composition, network characteristics and community assembly of intestinal microbiome in sea cucumber reflect the differences in habitats and aquaculture practices

The possible differentiation of microbiomes in various habitats and aquaculture practices has rarely been studied until now. Here, the microbiomes of five different culture systems for sea cucumber Apostichopus japonicus were compared, including outdoor pond, indoor workshop, net cage, suspension cage, marine ranching. Samples of intestinal contents from sea cucumber, surrounding water and sediment were collected from these culture systems. Significant differentiations in microbial diversity, composition, function were found in various culture systems. Microbial source-tracking analysis indicated that intestinal microbiomes of sea cucumber were more similar to sediment than to surrounding water. Totally, 23 shared core operational taxonomic units (OTUs) were identified in intestinal microbiome of sea cucumber in these systems, belong to following orders: Rhodobacterales (15), Rhizobiales (3), Flavobacteriales (2), Verrucomicrobiales (1), Campylobacterales (1), unclassified (1). Meanwhile, unique core OTUs in various systems tended to aggregate toward oligotrophic, potentially beneficial, or pathogenic bacteria. Microbial network characteristics in marine ranching and suspension cage systems were consistent with those in high-stress habitats, exhibiting lower diversity, complexity, modularity, dominated by positive interactions. Conversely, opposite trends were observed in indoor workshop, outdoor pond, net cage systems. Strong diffusion limitations on intestinal microbial community of sea cucumber, particularly in marine ranching system, were elucidated. Distinct characteristics of microbiome in various culture systems reflected differences in habitats and aquaculture practices. These findings provide new insights into impact of aquaculture systems on microbial community in aquatic animals, could contribute to healthy aquaculture practices for sea cucumber industry.

Relations Between Core Taxa and Metabolic Characteristics of Bacterial Communities in Litopenaeus vannamei Ponds and Their Probiotic Potential

Microorganisms play a crucial role in purifying aquaculture water bodies. However, there is limited understanding regarding the core species of bacterial communities in aquaculture ponds and their metabolic functions. Using 16S rRNA gene sequencing technology, network analysis, and Biolog EcoPlates, we identified keystone and core taxa of bacterial communities in Litopenaeus vannamei ponds and investigated their correlations with their community's carbon source utilization abilities based on Biolog EcoPlates. We found that keystone and core taxa in bacterial communities were significantly correlated with the carbon source utilization abilities of bacterial communities. The positively correlated core taxa include (1) Bacillus, Flavobacterium, Brevibacillus, and Paenibacillus, which are used as probiotics in aquaculture, and (2) Candidatus Aquiluna, Dechloromonas, Sulfurifustis, Terrimicrobium, Alsobacter, and Gemmobacter, which have been reported to play a role in nitrogen removal. Furthermore, the positively correlated Tropicimonas (Rhodobacterales: Rhodobacteraceae) in aquaculture has not yet been applied. By nitrogen degradation experiments in aquaculture wastewater, we confirmed the synergistic relationship between the genera Tropicimonas and Bacillus. The co-introduction of Tropicimonas sediminicola SDUM182003 and Priestia aryabhattai HG1802 or Bacillus subtilis XQ1804 into the aquaculture tailwater reduced the time required for the removal rates of nitrite nitrogen and nitrate nitrogen to reach over 90% by 24-48 h. Our research reveals the correlation between core taxa and community carbon source utilization, indicating that the core taxa of bacterial communities play a crucial role in the metabolic functions of the community, and offering a reference for exploring new bacterial genera with probiotic potential.

Insight into the bacterial communities in the sediment-water interface across different salinities of Pacific White shrimp, Penaeus vannamei, by metabarcoding

Microbes play an important role in the food chain by metabolizing organic matter, cycling nutrients, and maintaining a dynamic equilibrium among organisms in water and sediment. The objective is to study the fluctuating taxonomic microbial diversity profile in the sediment-water interface at different days of culture (DOC) of Penaeus vannamei in varying salinities using the Illumina MiSeq platform. Sediment samples were collected in Tamil Nadu, India, from low-saline, brackish water, and high-saline ponds at 30, 60, and 90 DOC. Bacterial richness and diversity in species were high in low-saline ponds. Beta-diversity variation indicated more differences in bacterial composition in high- and low-saline ponds. The predominant phyla observed were Proteobacteria, Actinobacteria, Chloroflexi, Bacteroidetes, Firmicutes, and Cyanobacteria. High-saline ponds accounted for more nitrification bacterial communities, sulfur-reducing bacterial communities, sulfur-oxidizing bacterial communities, and high redox potential, whereas denitrification bacterial communities were high in brackish water ponds.

Intestine bacterial community affects the growth of the Pacific white shrimp (Litopenaeus vannamei)

Increasing evidence suggests that intestine microorganisms are closely related to shrimp growth, but there is no existing experiment to prove this hypothesis. Here, we compared the intestine bacterial community of fast- and slow-growing shrimp at the same developmental stage with a marked difference in body size. Our results showed that the intestine bacterial communities of slow-growing shrimp exhibited less diversity but were more heterogeneous than those of fast-growing shrimp. Uncultured_bacterium_g_Candidatus Bacilloplasma, Tamlana agarivorans, Donghicola tyrosinivorans, and uncultured_bacterium_f_Flavobacteriaceae were overrepresented in the intestines of fast-growing shrimp, while Shimia marina, Vibrio sp., and Vibrio campbellii showed the opposite trends. We further found that the bacterial community composition was significantly correlated with shrimp length, and some bacterial species abundances were found to be significantly correlated with shrimp weight and length, including T. agarivorans and V. campbellii, which were chosen as indicators for a reverse gavage experiment. Finally, T. agarivorans was found to significantly promote shrimp growth after the experiment. Collectively, these results suggest that intestine bacterial community could be important factors in determining the growth of shrimp, indicating that specific bacteria could be tested in further studies against shrimp growth retardation. KEY POINTS: • A close relationship between intestine bacterial community and shrimp growth was proven by controllable experiments. • The bacterial signatures of the intestine were markedly different between slow- and fast-growing shrimp, and the relative abundances of some intestine bacterial species were correlated significantly with shrimp body size. • Reverse gavage by Tamlana agarivorans significantly promoted shrimp growth.

Environmental factors and potential probiotic lineages shape the active prokaryotic communities associated with healthy Penaeus stylirostris larvae and their rearing water

Microbial dysbiosis is hypothesized to cause larval mass mortalities in New Caledonian shrimp hatcheries. In order to confirm this hypothesis and allow further microbial comparisons, we studied the active prokaryotic communities of healthy Penaeus stylirostris larvae and their surrounding environment during the first 10 days of larval rearing. Using daily nutrient concentration quantitative analyses and spectrophotometric organic matter analyses, we highlighted a global eutrophication of the rearing environment. We also evidenced drastic bacterial community modifications in the water and the larvae samples using Illumina HiSeq sequencing of the V4 region of the 16S rRNA gene. We confirmed that Alteromonadales, Rhodobacterales, Flavobacteriales, Oceanospirillales, and Vibrionales members formed the core bacteriota of shrimp larvae. We also identified, in the water and the larvae samples, several potential probiotic bacterial strains that could lead to rethink probiotic use in aquaculture (AEGEAN 169 marine group, OM27 clade, Ruegeria, Leisingera, Pseudoalteromonas, and Roseobacter). Finally, investigating the existing correlations between the environmental factors and the major bacterial taxa of the water and the larvae samples, we suggested that deterministic and stochastic processes were involved in the assembly of prokaryotic communities during the larval rearing of P. stylirostris. Overall, our results showed that drastic changes mostly occurred during the zoea stages suggesting that this larval phase is crucial during shrimp larval development.

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.

Dietary β-1,3-Glucan Promotes Growth Performance and Enhances Non-Specific Immunity by Modulating Pattern Recognition Receptors in Juvenile Oriental River Prawn (Macrobrachium nipponense)

As a typical pathogen-associated molecular pattern (PAMP), β-1,3-glucan can engage with pattern recognition receptors (PRRs) to initiate an immune response. In this study, we investigated the effects of dietary β-1,3-glucan on growth performance, antioxidant capacity, immune response, intestinal health, and bacterial resistance in juvenile Macrobrachium nipponense. Prawns were fed with five experimental diets containing 0%, 0.05%, 0.1%, 0.2%, and 0.4% β-1,3-glucan for eight weeks. The findings demonstrated that the inclusion of β-1,3-glucan improved weight gain and survival rate in prawns. Prawns fed with β-1,3-glucan exhibited elevated activities of hepatopancreatic ACP (acid phosphatase), AKP (alkaline phosphatase), and SOD (superoxide dismutase), while MDA (malondialdehyde) content was reduced. Expression levels of PRRs related genes including LGBP (lipopolysaccharide and β-1,3-glucan binding protein), lectin, and LBP (lipopolysaccharide-binding protein) were significantly increased in prawns fed with β-1,3-glucan. Intestinal flora analysis revealed suppression of Cyanobacteria abundance at the Phylum level and enhancement in Rhodobacter abundance at the genus level in prawns fed with a 0.2% β-1,3-glucan diet. Furthermore, prawns fed with 0.1%, 0.2%, and 0.4% β-1,3-glucan demonstrated significantly higher survival rates following Aeromonas hydrophila infection. In conclusion, β-1,3-glucan can activate PRRs to improve immune responses in M. nipponese. Within the range of β-1,3-glucan concentrations set in this experiment, it is recommended to add 0.18% of β-1,3-glucan to the diet, taking into account the positive effect of β-1,3-glucan on the survival rate of M. nipponensecu.

Novel indigenous probiotic isolated from the healthy Pacific white shrimp Litopenaeus vannamei intestine in differing stages based on metagenomic and screening approaches

The healthy intestinal microbiota of shrimp can be used as an indicator sustainable shrimp production. In this study, the integrated of metagenomic and screening probiotic approach from healthy Litopenaeus vannamei intestines in differing stages was studied to find novel indigenous probiotics. The microbiota from intestine of naupli, post larva (PL-10), juvenile (40 days), and adult (80 days) of Pacific white shrimp were characterized using a high-quality sequence of V3-V4 of 16S rRNA gene as the hypervariable region. The classifiable sequence number was detected in 54 phyla. Several core intestine bacteria, 35 of these 557 genera, have a prevalence >10 sequences across all samples. We found microbiota were different taxa in the difference stages, such as Proteobacteria, Firmicutes, and Bacteriodetes. The top 10 most abundant genera were Vibrio, Pseudoalteromonas, Spingomonas, Marinibacterium, Klebsiella, Alteromonas, Aestuaribacter, Shimia, Stenotrophomonas, and Ruegeria. Microbiota profiling based on a metagenomic approach was integrated with screening assessment for pathogenicity, antagonistic activity with Vibrio parahaemolyticus Vp5, antibiotic resistance, and digestive enzyme activities. As their assessment activity, several screened culturable bacteria were 19 of these 84 isolates. Three isolates with high activities (P < 0.05) found as novel indigenous probiotics were Shewanella algae A1, Shewanella algae A3, and Vibrio diabolicus UB3. Integrating metagenomic and screening methods was a new signature for the isolating novel indigenous probiotics in Pacific white shrimp.

Unveiling the Bacterial Community across the Stomach, Hepatopancreas, Anterior Intestine, and Posterior Intestine of Pacific Whiteleg Shrimp

The gastrointestinal (GI) tract of shrimp, which is comprised of the stomach, hepatopancreas, and intestine, houses microbial communities that play crucial roles in immune defense, nutrient absorption, and overall health. While the intestine's microbiome has been well-studied, there has been limited research investigating the stomach and hepatopancreas. The present study addresses this gap by profiling the bacterial community in these interconnected GI segments of Pacific whiteleg shrimp. To this end, shrimp samples were collected from a local aquaculture farm in South Korea, and 16S rRNA gene amplicon sequencing was performed. The results revealed significant variations in bacterial diversity and composition among GI segments. The stomach and hepatopancreas exhibited higher Proteobacteria abundance, while the intestine showed a more diverse microbiome, including Cyanobacteria, Actinobacteria, Bacteroidetes, Firmicutes, Chloroflexi, and Verrucomicrobia. Genera such as Oceaniovalibus, Streptococcus, Actibacter, Ilumatobacter, and Litorilinea dominated the intestine, while Salinarimonas, Sphingomonas, and Oceaniovalibus prevailed in the stomach and hepatopancreas. It is particularly notable that Salinarimonas, which is associated with nitrate reduction and pollutant degradation, was prominent in the hepatopancreas. Overall, this study provides insights into the microbial ecology of the Pacific whiteleg shrimp's GI tract, thus enhancing our understanding of shrimp health with the aim of supporting sustainable aquaculture practices.

The intestine microbiota of shrimp and its impact on cultivation

Intestinal microbiome contains several times of functional genes compared to the host and mediates the generation of multiple metabolic products, and therefore it is called "second genome" for host. Crustaceans rank second among the largest subphylum of aquaculture animals that are considered potentially satisfy global substantial food and nutrition security, among which the Pacific white shrimp (Litopenaeus vannamei) ranks the first in the production. Currently, increasing evidences show that outbreaks of some most devastating diseases in shrimp, including white feces syndrome (WFS) and acute hepatopancreatic necrosis disease (AHPND), are related to intestinal microbiota dysbiosis. Importantly, the intestine microbial composition can be altered by environmental stress, diet, and age. In this review, we overview the progress of intestinal microbiota dysbiosis and WFS or ANPHD in shrimp, and how the microbial composition is altered by external factors. Hence, developing suitable microbial micro-ecological prevention and control strategy to maintain intestinal balance may be a feasible solution to reduce the risk of disease outbreaks. Moreover, we highlight that defining the "healthy intestine microbiota" and evaluating the causality of intestinal microbiota dysbiosis and diseases following the logic of "Microecological Koch's postulates" should be the key goal in future shrimp intestinal field, which help to guide disease diagnosis and prevent disease outbreaks in shrimp farming. KEY POINTS: • Intestinal microbiota dysbiosis is relevant to multiple shrimp diseases. • Microecological Koch's postulates help to evaluate the causality of shrimp diseases.

Responses of growth performance, immunity, disease resistance of shrimp and microbiota in Penaeus vannamei culture system to Bacillus subtilis BSXE-1601 administration: Dietary supplementation versus water addition

This study evaluated the effects of Bacillus subtilis BSXE-1601, applied either as dietary supplementation or water addition, on growth performance, immune responses, disease resistance of Penaeus vannamei, and microbiota in shrimp gut and rearing water. During the 42-day feeding experiment, shrimp were fed with basal diet (CO and BW group), basal diet supplemented with live strain BSXE-1601 at the dose of 1 × 109 CFU kg-1 feed (BD group) and 15 mg kg-1 florfenicol (FL group), and basal diet with strain BSXE-1601 added to water at the concentration of 1 × 107 CFU L-1 every five days (BW group). Results showed that dietary supplementation of strain BSXE-1601 significantly promoted growth performance of shrimp, both in the diet and water, enhanced disease resistance against Vibrio parahaemolyticus (P < 0.05). The BD and BW groups exhibited significant increases in acid phosphatase, alkaline phosphatase, lysozyme, peroxidase, superoxide dismutase activities, phenonoloxidase content in the serum of shrimp compared to the control (P < 0.05). Meanwhile, the expression of immune-related genes proPO, LZM, SOD, LGBP, HSP70, Imd, Toll, Relish, TOR, 4E-BP, eIF4E1α, eIF4E2 were significantly up-regulated compared to the control (P < 0.05). When added in rearing water, strain BSXE-1601 induced greater immune responses in shrimp than the dietary supplement (P < 0.05). Chao1 and Shannon indices of microbiota in rearing water were significantly lower in BD group than in the control. The microbiota in rearing water were significantly altered in BD, BW and FL groups compared to the control, while no significant impacts were observed on the microbiota of shrimp gut. When supplemented into the feed, strain BSXE-1601 obviously reduced the number of nodes, edges, modules in the ecological network of rearing water. The results suggested that dietary supplementation of BSXE-1601 could be more suitable than water addition in the practice of shrimp rearing when growth performance, non-specific immunity, disease resistance against V. parahaemolyticus in shrimp were collectively considered.

Diversity, community structure, and abundance of nirS-type denitrifying bacteria on suspended particulate matter in coastal high-altitude aquaculture pond water

Denitrifying bacteria harboring the nitrate reductase S (nirS) gene convert active nitrogen into molecular nitrogen, and alleviate eutrophication in aquaculture water. Suspended particulate matter (SPM) is an important component of aquaculture water and a carrier for denitrification. SPM with different particle sizes were collected from a coastal high-altitude aquaculture pond in Maoming City, China. Diversity, community structure, abundance of nirS-type denitrifying bacteria on SPM and environmental influencing factors were studied using high-throughput sequencing, fluorescence quantitative PCR, and statistical analysis. Pseudomonas, Halomonas, and Wenzhouxiangella were the dominant genera of nirS-type denitrifying bacteria on SPM from the ponds. Network analysis revealed Pseudomonas and Halomonas as the key genera involved in the interaction of nirS-type denitrifying bacteria on SPM in the ponds. qPCR indicated a trend toward greater nirS gene abundance in progressively larger SPM. Dissolved oxygen, pH, temperature, and SPM particle size were the main environmental factors influencing changes in the nirS-type denitrifying bacterial community on SPM in coastal high-altitude aquaculture pond water. These findings increase our understanding of the microbiology of nitrogen cycle processes in aquaculture ecosystem, and will help optimize aquatic tailwater treatment strategies.

Profile of the gut microbiota of Pacific white shrimp under industrial indoor farming system

The gut microbial communities interact with the host immunity and physiological functions. In this study, we investigated the bacterial composition in Litopenaeus vannamei shrimp's gut and rearing water under different host (developmental stage: juvenile and adult; health status: healthy and diseased) and environmental factors (temperature 25 °C and 28 °C; and light intensity: low and high). The PCoA analysis showed that all water samples were clustered together in a quarter, whereas the gut samples spread among three quarters. In terms of functional bacteria, gut samples of adult shrimp, healthy adult shrimp, adult shrimp raised at 28 °C, and juvenile shrimp under high light intensity exhibited a higher abundance of Vibrionaceae compared to each other opposite group. Gut samples of juvenile shrimp, infected adult shrimp, juvenile shrimp with low light intensity, and adult shrimp with a water temperature of 25 °C showed a higher abundance of Pseudoaltromonadaceae bacteria compared to each other opposite group. Gut samples of juvenile shrimp, healthy adult shrimp, adult shrimp raised at a water temperature of 28 °C, and juvenile shrimp with high light intensity showed the higher abundance of Firmicutes/Bacteroidota ratio compared to each other opposite group. Our results showed that L. vannamei juveniles are more sensitive to bacterial infections; besides, water temperature of 28 °C and high light intensity groups were both important conditions improving the shrimp gut bacterial composition under industrial indoor farming systems. KEY POINTS: • Bacteria diversity was higher among shrimp intestinal microbiota compared to the rearing water. • Shrimp juveniles are more sensitive to bacterial infection compared to adults. • Water temperature of 28 °C and high light intensity are recommended conditions for white shrimp aquaculture.

Effects of water ammonia nitrogen on hemolymph and intestinal microbiota of Litopenaeus vannamei

Ammonia stress was detrimental to shrimp, but how water ammonia nitrogen (ammonia-N) influences the shrimp's health remains unclear. Thus, this study was designed to investigate the effects of water ammonia-N on hemolymph ammonia-N concentration, hepatopancreas structure, and the intestinal microbiota of Litopenaeus vannamei with four experiments. We found that the concentration of ammonia-N in shrimp hemolymph was significantly higher than that in pond water, indicating that water ammonia-N stimulates the accumulation of hemolymph ammonia-N. Results also indicated that the hemolymph ammonia-N accumulation would disrupt the hepatopancreas structure and alter the intestinal microbial composition. The concentration of hemolymph ammonia-N and severity of hepatopancreas damage positively correlated with water ammonia-N concentration. However, though the diversity of intestinal microbiota was varied by ammonia-N, there were no significant differences between groups, suggesting that the variation was relatively minimal. Furthermore, returning shrimp to pristine water after ammonia-N exposure could reduce the hemolymph ammonia-N concentration and the mortality rate. This study provides evidence of temporal variations in hemolymph ammonia-N concentration, hepatopancreatic structure, and intestinal microbiota under different water ammonia-N levels, which might shed insights into ecological cognition on scientific management of shrimp culture and microecological prevention of shrimp health.

Host-microbiome interaction in fish and shellfish: An overview

The importance of the gut microbiome in the management of various physiological activities including healthy growth and performance of fish and shellfish is now widely considered and being studied in detail for potential applications in aquaculture farming and the future growth of the fish industry. The gut microbiome in all animals including fish is associated with a number of beneficial functions for the host, such as stimulating optimal gastrointestinal development, producing and supplying vitamins to the host, and improving the host's nutrient uptake by providing additional enzymatic activities. Besides nutrient uptake, the gut microbiome is involved in strengthening the immune system and maintaining mucosal tolerance, enhancing the host's resilience against infectious diseases, and the production of anticarcinogenic and anti-inflammatory compounds. Because of its significant role, the gut microbiome is very often considered an "extra organ," as it plays a key role in intestinal development and regulation of other physiological functions. Recent studies suggest that the gut microbiome is involved in energy homeostasis by regulating feeding, digestive and metabolic processes, as well as the immune response. Consequently, deciphering gut microbiome dynamics in cultured fish and shellfish species will play an indispensable role in promoting animal health and aquaculture productivity. It is mentioned that the microbiome community available in the gut tract, particularly in the intestine acts as an innovative source of natural product discovery. The microbial communities that are associated with several marine organisms are the source of natural products with a diverse array of biological activities and as of today, more than 1000 new compounds have been reported from such microbial species. Exploration of such new ingredients from microbial species would create more opportunities for the development of the bio-pharma/aquaculture industries. Considering the important role of the microbiome in the whole life span of fish and shellfish, it is necessary to understand the interaction process between the host and microbial community. However, information pertaining to host-microbiome interaction, particularly at the cellular level, gene expression, metabolic pathways, and immunomodulation mechanisms, the available literature is scanty. It has been reported that there are three ways of interaction involving the host-microbe-environment operates to maintain homeostasis in the fish and shellfish gut i.e. host intrinsic factors, the environment that shapes the gut microbiome composition, and the core microbial community present in the gut system itself has equal influence on the host biology. In the present review, efforts have been made to collect comprehensive information on various aspects of host-microbiome interaction, particularly on the immune system and health maintenance, management of diseases, nutrient uptake, digestion and absorption, gene expression, and metabolism in fish and shellfish.

Microbial biomarker detection in shrimp larvae rearing water as putative bio-surveillance proxies in shrimp aquaculture

Background

Aquacultured animals are reared in water hosting various microorganisms with which they are in close relationships during their whole lifecycle as some of these microorganisms can be involved in their host's health or physiology. In aquaculture hatcheries, understanding the interactions existing between the natural seawater microbiota, the rearing water microbiota, the larval stage and the larval health status, may allow the establishment of microbial proxies to monitor the rearing ecosystems. Indeed, these proxies could help to define the optimal microbiota for shrimp larval development and could ultimately help microbial management.

Methods

In this context, we monitored the daily composition of the active microbiota of the rearing water in a hatchery of the Pacific blue shrimp Penaeus stylirostris. Two distinct rearing conditions were analyzed; one with antibiotics added to the rearing water and one without antibiotics. During this rearing, healthy larvae with a high survival rate and unhealthy larvae with a high mortality rate were observed. Using HiSeq sequencing of the V4 region of the 16S rRNA gene of the water microbiota, coupled with zootechnical and statistical analysis, we aimed to distinguish the microbial taxa related to high mortality rates at a given larval stage.

Results

We highlight that the active microbiota of the rearing water is highly dynamic whatever the larval survival rate. A clear distinction of the microbial composition is shown between the water harboring heathy larvae reared with antibiotics versus the unhealthy larvae reared without antibiotics. However, it is hard to untangle the effects of the antibiotic addition and of the larval death on the active microbiota of the rearing water. Various active taxa of the rearing water are specific to a given larval stage and survival rate except for the zoea with a good survival rate. Comparing these communities to those of the lagoon, it appears that many taxa were originally detected in the natural seawater. This highlights the great importance of the microbial composition of the lagoon on the rearing water microbiota. Considering the larval stage and larval survival we highlight that several genera: Nautella, Leisingera, Ruegerira, Alconivorax, Marinobacter and Tenacibaculum, could be beneficial for the larval survival and may, in the rearing water, overcome the r-strategist microorganisms and/or putative pathogens. Members of these genera might also act as probiotics for the larvae. Marivita, Aestuariicocccus, HIMB11 and Nioella, appeared to be unfavorable for the larval survival and could be associated with upcoming and occurring larval mortalities. All these specific biomarkers of healthy or unhealthy larvae, could be used as early routine detection proxies in the natural seawater and then during the first days of larval rearing, and might help to manage the rearing water microbiota and to select beneficial microorganisms for the larvae.

The characteristics of the intestinal bacterial community from Oreochromis mossambicus and its interaction with microbiota from artificial fishery habitats

BACKGROUND

Artificial habitats can allow many fish to flock together and interact and have been widely used to restore and protect fishery resources. The piece of research intends to elucidate the relationship of microbial communities between tilapia (Oreochromis mossambicus) intestines and artificial fishery habitats (water and sediments). Hence, 16 S rDNA sequencing technology was used to study the bacterial communities from intestines, water, and sediments.

RESULTS

The results showed that the tilapia intestines had the lowest richness of Operational Taxonomic Units (OTUs) and the lowest diversity of the bacterial community compared to water and sediments. The intestine, water, and sediment microbial communities shared many OTUs. Overall, 663 shared OTUs were identified from the tilapia intestines (76.20%), the surrounding water (71.14%), and sediment (56.86%) in artificial habitats. However, there were unique OTUs that were detected in different sample types. There were 81, 77 and 112 unique OTUs observed in tilapia intestines, the surrounding water and sediment, respectively. Proteobacteria, Cyanobacteria, Actinobacteria, Firmicutes, Fusobacteria, and Bacteroidetes were the most common and dominant bacterial phyla between the tilapia intestines and habitats. In the two groups, the microbial communities were similar in the taxonomic composition but different in the abundance of bacterial phyla. Interestingly, Firmicutes increased, while Fusobacteria decreased in artificial habitats. These findings indicated that the artificial habitats had fewer effects on the water environment and indicated that the mode of artificial habitats could have an effect on the enriched bacteria in the tilapia intestines.

CONCLUSIONS

This study analysed the bacterial communities of artificial habitats from the intestines, water, and sediments, which can explain the relationship between the tilapia intestines and habitats and strengthen the value of ecological services provided by artificial habitats.

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.

A multi-omics-based investigation into the flavor formation mechanisms during the fermentation of traditional Chinese shrimp paste

The fermentation process of traditional shrimp paste is closely associated with the production of flavor substances, but the formation mechanism of key aroma components is still unclear. In this study, a comprehensively flavor profile analysis of traditional fermented shrimp paste was carried out by E-nose and SPME-GC-MS. A total of 17 key volatile aroma components with OAV > 1 contributed greatly to the overall flavor formation of shrimp paste. In addition, high-throughput sequencing (HTS) analysis revealed that Tetragenococcus was the dominant genera in the whole fermentation process. Moreover, metabolomics analysis showed that the oxidation and degradation of lipids, protein, organic acids and amino acids produced a large number of flavor substances and intermediates, which laid the foundation for the Maillard reaction in term of generating the distinct aroma of the traditional shrimp paste. This work will provide theoretical support for the realization of flavor regulation and quality control in traditional fermented foods.

Intestinal Microbiota Differences in Litopenaeus vannamei Shrimp between Greenhouse and Aquaponic Rearing

The sustainability of shrimp aquaculture can be achieved through the development of greenhouse and aquaponic rearing modes, which are classified as heterotrophic and autotrophic bacterial aquaculture systems. However, there have been few investigations into the discrepancies between the intestinal and water microbiota of these two rearing methods. In this study, we collected shrimp samples from greenhouse-rearing (WG) and aquaponic-rearing (YG) ponds, and water samples (WE, YE), and investigated the intestinal and water microbiota between the two rearing modes. The results, through alpha and beta diversity analyses, reveal that there was basically no significant difference between shrimp intestine WG and YG (p > 0.05) or between rearing water WE and YE (p > 0.05). At the phylum and genus levels, the common bacteria between WE and WG differed significantly from those of YE and YG. The analysis of the top six phyla shows that Proteobacteria and Patescibacteria were significantly more abundant in the WG group than those in the YG group (p < 0.05). Conversely, Actinobacteriota, Firmicutes, and Verrucomicrobiota were significantly more abundant in the YG group than those in the WG group (p < 0.05). Venn analysis between WE and WG shows that Amaricoccus, Micrococcales, Flavobacteriaceae, and Paracoccus were the dominant bacteria genera, while Acinetobacter, Demequina, and Rheinheimera were the dominant bacteria genera between YE and YG. Pathways such as the biosynthesis of secondary metabolites, microbial metabolism in different environments, and carbon metabolism were significantly more upregulated in WG than those in YG (p < 0.05). In addition, pathways such as sulfate, chloroplast, phototrophy, and the nitrogen metabolism were significantly different between the WE and YE samples. These findings suggest that the greenhouse mode, a typical heterotrophic bacterial model, contains bacterial flora consisting of Amaricoccus, Micrococcales, Flavobacteriaceae, and other bacteria, which is indicative of the biological sludge process. Conversely, the aquaponic mode, an autotrophic bacterial model, was characterized by Acinetobacter, Demequina, Rheinheimera, and other bacteria, signifying the autotrophic biological process. This research provides an extensive understanding of heterotrophic and autotrophic bacterial aquaculture systems.

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.

Phage-prokaryote coexistence strategy mediates microbial community diversity in the intestine and sediment microhabitats of shrimp culture pond ecosystem

Emerging evidence supports that the phage-prokaryote interaction drives ecological processes in various environments with different phage life strategies. However, the knowledge of phage-prokaryote interaction in the shrimp culture pond ecosystem (SCPE) is still limited. Here, the viral and prokaryotic community profiles at four culture stages in the intestine of Litopenaeus vannamei and cultural sediment microhabitats of SCPE were explored to elucidate the contribution of phage-prokaryote interaction in modulating microbial communities. The results demonstrated that the most abundant viral families in the shrimp intestine and sediment were Microviridae, Circoviridae, Inoviridae, Siphoviridae, Podoviridae, Myoviridae, Parvoviridae, Herelleviridae, Mimiviridae, and Genomoviridae, while phages dominated the viral community. The dominant prokaryotic genera were Vibrio, Formosa, Aurantisolimonas, and Shewanella in the shrimp intestine, and Formosa, Aurantisolimonas, Algoriphagus, and Flavobacterium in the sediment. The viral and prokaryotic composition of the shrimp intestine and sediment were significantly different at four culture stages, and the phage communities were closely related to the prokaryotic communities. Moreover, the phage-prokaryote interactions can directly or indirectly modulate the microbial community composition and function, including auxiliary metabolic genes and closed toxin genes. The interactional analysis revealed that phages and prokaryotes had diverse coexistence strategies in the shrimp intestine and sediment microhabitats of SCPE. Collectively, our findings characterized the composition of viral communities in the shrimp intestine and cultural sediment and revealed the distinct pattern of phage-prokaryote interaction in modulating microbial community diversity, which expanded our cognization of the phage-prokaryote coexistence strategy in aquatic ecosystems from the microecological perspective and provided theoretical support for microecological prevention and control of shrimp culture health management.

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.

Aquamimicry system: a sutiable strategy for shrimp aquaculture – a review

Shrimp culture is the most lucrative sector in aquaculture industry; however, for its sustainable development the environment conservation should be concerned. New developed technologies are required to achieve aquaculture to its sustainable goals. Among the different novel sustainable technologies, the biofloc technology (BFT) and more recently the aquamimicry system are considered as reliable methods in burgeoning development of shrimp culture. The establishment of the BFT needs a certain carbon to nitrogen (C: N) ratio so that heterotrophic bacteria able to utilize nitrogenous metabolites, and preserve the water quality in the standard ranges suitable for shrimp culture. In addition, the produced floc can be used as supplementary food for shrimp. On the other hand, the establishment of the aquamimicry system relies on organic carbon without providing a specific C: N ratio. In this system, a synergistic relationship between a prebiotic source, which usually consists of an oligosaccharide derived from the fermentation of a carbon source (e.g., rice bran), and a probiotic source such as Bacillus sp. can provide natural conditions by blooming phytoplankton and zooplankton organisms, especially copepods. These live foods can be used as complementary foods for shrimp. Furthermore, the proliferation of beneficial bacteria in the aquamimicry system can provide stable culture condition for growth and welfare of shrimp. Based on the findings of recent literature, using the aquamimicry system for shrimp production is a more sustainable, eco-friendly, and greener than the conventional systems.

The Active Microbiota of the Eggs and the Nauplii of the Pacific Blue Shrimp Litopenaeus stylirostris Partially Shaped by a Potential Vertical Transmission

The many ecological niches present in an organism harbor distinct microorganisms called microbiota. Different factors can influence the establishment of these commensal microbial communities. In a previous article, we have concluded that some bacterial lineages associated with the early larval stages of the Pacific blue shrimp Litopenaeus stylirostris could be acquired from the breeders via a potential vertical transmission. The present study was conducted in order to investigate this hypothesis. Using HiSeq sequencing of the V4 region of 16S rRNA gene, we analyzed the active microbiota associated with the eggs and the nauplii of L. stylirsotris as well as with the reproductive organs of their breeders. Microbial communities associated with the rearing water were also considered to discriminate environmental microbial lineages. Using these analyses, we highlight a set of core bacterial families present in all samples and composed of members of Colwelliaceae, Alteromonadaceae, Pseudoalteromonadaceae, Saccharospirillaceae, Oceanospirillaceae, Vibrionaceae, Burkholderiaceae, Rhodobacteraceae, Flavobacteraceae, and Corynebacteriaceae; showing the importance of the environment in the establishment of the larval microbiota. We also present specific bacteria affiliated to the Arcobacteraceae, Rhodobacteraceae, Comamonadaceae, and Colwelliaceae families, which were only found in the breeders and their offspring strengthening the hypothesis of a potential vertical transmission shaping the active microbiota of the eggs and the nauplii of L. stylirostris.

Sedimentary Nitrogen and Sulfur Reduction Functional-Couplings Interplay With the Microbial Community of Anthropogenic Shrimp Culture Pond Ecosystem

Sediment nitrogen and sulfur cycles are essential biogeochemical processes that regulate the microbial communities of environmental ecosystems, which have closely linked to environment ecological health. However, their functional couplings in anthropogenic aquaculture sedimentary ecosystems remain poorly understood. Here, we explored the sediment functional genes in shrimp culture pond ecosystems (SCPEs) at different culture stages using the GeoChip gene array approach with 16S amplicon sequencing. Dissimilarity analysis showed that the compositions of both functional genes and bacterial communities differed at different phases of shrimp culture with the appearance of temporal distance decay (p < 0.05). During shrimp culture, the abundances of nitrite and sulfite reduction functional genes decreased (p < 0.05), while those of nitrate and sulfate reduction genes were enriched (p < 0.05) in sediments, implying the enrichment of nitrites and sulfites from microbial metabolism. Meanwhile, nitrogen and sulfur reduction genes were found to be linked with carbon degradation and phosphorous metabolism (p < 0.05). The influence pathways of nutrients were demonstrated by structural equation modeling through environmental factors and the bacterial community on the nitrogen and sulfur reduction functions, indicating that the bacterial community response to environmental factors was facilitated by nutrients, and led to the shifts of functional genes (p < 0.05). These results indicate that sediment nitrogen and sulfur reduction functions in SCPEs were coupled, which are interconnected with the SCPEs bacterial community. Our findings will be helpful for understanding biogeochemical cycles in anthropogenic aquaculture ecosystems and promoting sustainable management of sediment environments through the framework of an ecological perspective.

Environmental Water and Sediment Microbial Communities Shape Intestine Microbiota for Host Health: The Central Dogma in an Anthropogenic Aquaculture Ecosystem

From increasing evidence has emerged a tight link among the environment, intestine microbiota, and host health status; moreover, the microbial interaction in different habitats is crucial for ecosystems. However, how the environmental microbial community assembly governs the intestinal microbiota and microbial communities of multiple habitats contribute to the metacommunity remain elusive. Here, we designed two delicate experiments from temporal and spatial scales in a shrimp culture pond ecosystem (SCPE). Of the SCPE metacommunity, the microbial diversity was mainly contributed to by the diversity of^–β_{IntraHabitats} and β_{InterHabitats}, and water and sediment communities had a large contribution to the shrimp intestine community as shown by SourceTracker and Sloan neutral community model analyses. Also, phylogenetic bin-based null model results show that microbial assembly of three habitats in the SCPE appeared to be largely driven by stochastic processes. These results enrich our understanding of the environment–intestinal microbiota–host health closely linked relationship, making it possible to be the central dogma for an anthropogenic aquaculture ecosystem. Our findings enhance the mechanistic understanding of microbial assembly in the SCPE for further analyzing metacommunities, which has important implications for microbial ecology and animal health.

Profiling intestinal microbiota of Metaplax longipes and Helice japonica and their co-occurrence relationships with habitat microbes

Intestinal microbiota plays key roles in maintaining the health and homeostasis of the host. However, information about whether the formation of intestinal microbiota of wild aquatic animals is associated with habitat microbes is not fully understood. Here, intestine samples were collected from two wild crab species and sediment samples were collected from the habitat environment. The total DNA of each sample was extracted, and the V3–V4 regions of 16S rRNA were sequenced using the MiSeq platform. The purpose of this study was to investigate the composition and diversity of intestinal microbiota and habitat microbes, and bacterial community relationships between wild crab intestine and habitat sediment. In the present study, the composition and diversity of intestinal microbiota of the two crab species were different from the habitat microbes. In contrast, a similar composition and diversity of the intestinal microbiota were observed between two crab species. Moreover, the bacterial community relationships between crab intestine and habitat sediment were associated with intestinal regions. Further network analysis revealed that the network structure of the intestinal microbiota was not only associated with intestinal regions, but also with the crab species. Additionally, although the compositions of bacterial functions were similar between crab intestine and sediment, no significant correlation in bacterial functions was observed between crab intestine and sediment. The findings of the present study would contribute to understanding the relationship between intestinal microbiota of wild aquatic animal and habitat microbes, and providing new insights into the intestinal microbiota of wild aquatic animals.

The Characteristics of Intestinal Bacterial Community in Three Omnivorous Fishes and Their Interaction with Microbiota from Habitats

Artificial fishery habitats have been extensively used for fishery resource protection and water habitat restoration, and they could attract a large number of omnivorous fishes to gather together. This study intended to reveal the relationship between bacterial communities in the habitats (water and sediment) and intestines of omnivorous fishes (Oreochromis mossambicus, Toxabramis houdemeri and Hemiculter leucisculus). Therefore, we investigated the bacterial communities of samples collected from intestines, water, and sediments in artificial fishery habitats via 16S rRNA metabarcoding high-throughput sequencing technology. The results showed that there were significant differences in the composition, core indicators, diversity and prediction functions in water, sediments, and intestinal microbial communities of the three omnivorous fish. The microbial diversities were significantly higher in habitats than in intestines. The analysis of similarity (ANOSIM) and nonmetric multidimensional scaling (NMDS) results indicated that the intestine microbial communities (T. houdemeri and H. leucisculus) were more similar to the water microbiota, but the intestine microbial communities (O. mossambicus) were more similar to the sediments. Source tracking analysis also confirmed that the contribution of habitat characteristics to omnivorous fish intestinal microorganisms was different; the sediment had a greater contribution than water to the intestinal microbiota of O. mossambicus, which was consistent with their benthic habit. Moreover, the functional prediction results showed that there were unique core indicators and functions between the bacterial community of habitats and intestines. Altogether, these results can enhance our understanding of the bacterial composition and functions about omnivorous fish intestines and their living with habitats, which have provided new information for the ecological benefits of artificial fishery habitats from the perspective of bacterial ecology and contributed to apply artificial fishery habitats in more rivers.

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

Sediment microbial community plays a crucial role in aquaculture ecosystem. In aquaculture practice, rather than monoculture intensive shrimp (IS) or intensive fish (IF) patterns, polyculture of shrimp and fish (PolySF) pattern leads to a more reliable production. However, knowledge is still limited about the characteristics of sediment microbiota and its potential functions in the PolySF ponds compared to monoculture patterns (IS and IF). Herein, we collected sediment samples from these three patterns in seven cities to evaluate microbial variations among patterns. The highest oxidation reduction potential (ORP), total phosphate (TP) and total organic carbon (TOC) were detected in the PolySF pattern, representing a relatively less anoxic environment, while the highest iron (Fe) was detected in IS pattern. Proteobacteria was the most abundant phylum among three patterns, followed by Bacteroidetes and Chloroflexi. The microbial alpha diversity in the PolySF was higher than those in the IF, but lower than those in the IS. Microbial communities of these three patterns were significantly distinct from each other, and 23 distinguished taxa for each pattern were further characterized. In additional, the relative abundances of genes involved in nitrogen metabolism, fatty acid biosynthesis and carbon fixation pathways were markedly shifted. Moreover, ORP, TOC and Fe were the shaping factors for sediment microbiota, which significantly varied among three patterns. Collectively, these findings demonstrated that sediment microbial communities in the PolySF were distinctive from those in the IS and IF, which enlarged our understanding for the underlying mechanism of advances in the PolySF pattern from ecological perspective.

The Intestinal Bacterial Community and Functional Potential of Litopenaeus vannamei in the Coastal Areas of China

Intestinal bacteria are crucial for the healthy aquaculture of Litopenaeus vannamei, and the coastal areas of China are important areas for concentrated L. vannamei cultivation. In this study, we evaluated different compositions and structures, key roles, and functional potentials of the intestinal bacterial community of L. vannamei shrimp collected in 12 Chinese coastal cities and investigated the correlation between the intestinal bacteria and functional potentials. The dominant bacteria in the shrimp intestines included Proteobacteria, Bacteroidetes, Tenericutes, Firmicutes, and Actinobacteria, and the main potential functions were metabolism, genetic information processing, and environmental information processing. Although the composition and structure of the intestinal bacterial community, potential pathogenic bacteria, and spoilage organisms varied from region to region, the functional potentials were homeostatic and significantly (p < 0.05) correlated with intestinal bacteria (at the family level) to different degrees. The correlation between intestinal bacteria and functional potentials further suggested that L. vannamei had sufficient functional redundancy to maintain its own health. These findings help us understand differences among the intestinal bacterial communities of L. vannamei cultivated in different regions and provide a basis for the disease management and healthy aquaculture of L. vannamei.

Aquaculture industry prospective from gut microbiome of fish and shellfish: An overview

The microbiome actually deals with micro-organisms that are associated with indigenous body parts and the entire gut system in all animals, including human beings. These microbes are linked with roles involving hereditary traits, defence against diseases and strengthening overall immunity, which determines the health status of an organism. Considerable efforts have been made to find out the microbiome diversity and their taxonomic identification in finfish and shellfish and its importance has been correlated with various physiological functions and activities. In recent past due to the availability of advanced molecular tools, some efforts have also been made on DNA sequencing of these microbes to understand the environmental impact and other stress factors on their genomic structural profile. There are reports on the use of next-generation sequencing (NGS) technology, including amplicon and shot-gun approaches, and associated bioinformatics tools to count and classify commensal microbiome at the species level. The microbiome present in the whole body, particularly in the gut systems of finfish and shellfish, not only contributes to digestion but also has an impact on nutrition, growth, reproduction, immune system and vulnerability of the host fish to diseases. Therefore, the study of such microbial communities is highly relevant for the development of new and innovative bio-products which will be a vital source to build bio and pharmaceutical industries, including aquaculture. In recent years, attempts have been made to discover the chemical ingredients present in these microbes in the form of biomolecules/bioactive compounds with their functions and usefulness for various health benefits, particularly for the treatment of different types of disorders in animals. Therefore, it has been speculated that microbiomes hold great promise not only as a cure for ailments but also as a preventive measure for the number of infectious diseases. This kind of exploration of new breeds of microbes with their miraculous ingredients will definitely help to accelerate the development of the drugs, pharmaceutical and other biological related industries. Probiotic research and bioinformatics skills will further escalate these opportunities in the sector. In the present review, efforts have been made to collect comprehensive information on the finfish and shellfish microbiome, their diversity and functional properties, relationship with diseases, health status, data on species-specific metagenomics, probiotic research and bioinformatics skills. Further, emphasis has also been made to carry out microbiome research on priority basis not only to keep healthy environment of the fish farming sector but also for the sustainable growth of biological related industries, including aquaculture.

Microbiome Analysis Reveals Microecological Balance in the Emerging Rice-Crayfish Integrated Breeding Mode

The interaction between the microbial communities in aquatic animals and those in the ambient environment is important for both healthy aquatic animals and the ecological balance of aquatic environment. Crayfish (Procambarus clarkii), with their high commercial value, have become the highest-yield freshwater shrimp in China. The traditional cultivation in ponds (i.e., monoculture, MC) and emerging cultivation in rice co-culture fields (i.e., rice–crayfish co-culture, RC) are the two main breeding modes for crayfish, and the integrated RC is considered to be a successful rice-livestock integration practice in eco-agricultural systems. This study explored the ecological interactions between the microbial communities in crayfish intestine and the ambient environment, which have not been fully described to date. The bacterial communities in crayfish intestine, the surrounding water, and sediment in the two main crayfish breeding modes were analyzed with MiSeq sequencing and genetic networks. In total, 53 phyla and 1,206 genera were identified, among which Proteobacteria, Actinobacteria, Tenericutes, Firmicutes, Cyanobacteria, Chloroflexi, Bacteroidetes, Acidobacteria, RsaHF231, and Nitrospirae were the dominant phyla. The microbiota composition significantly differed between the water, sediment, and crayfish intestine, while it did not between the two breeding modes. We also generated a co-occurrence correlation network based on the high-confidence interactions with Spearman correlation ρ ≥ 0.75. In the genera co-correlation network, 95 nodes and 1,158 edges were identified, indicating significant genera interactions between crayfish intestine and the environment. Furthermore, the genera clustered into three modules, based on the different environments. Additionally, Candidatus_Bacilloplasma, g_norank_f_Steroidobacteraceae, Dinghuibacter, Hydrogenophaga, Methyloparacoccus, and Defluviicoccus had the highest betweenness centrality and might be important in the interaction between crayfish and the ambient environment. Overall, this study enhances our understanding of the characteristics of the microbiota in crayfish and their surrounding environment. Moreover, our findings provide insights into the microecological balance in crayfish eco-agricultural systems and theoretical reference for the development of such systems.

Stochastic processes shape the bacterial community assembly in shrimp cultural pond sediments

Sediment environments harbor a repertoire of microorganisms that contribute to animal health and the microecosystem in aquaculture ecosystems, but their community diversity and the potential factors that control it remain unclear. Here, we applied 16S rRNA gene amplicon sequencing to investigate bacterial diversity and assembly mechanisms in the sediments of shrimp cultural ponds at the mesoscale. Our results showed that sediment bacterial communities contained 10,333 operational taxonomic units (OTUs) but had only 34 core OTUs and that the relative abundances of these core OTUs were significantly correlated with the physicochemical properties of the sediments. Proteobacteria, Bacteroidetes, Chloroflexi, Cyanobacteria, Acidobacteria, Firmicutes, Actinobacteria, Ignavibacteriae, Spirochaetae and Planctomycetes were the ten most abundant bacterial phyla. Notably, some opportunistic pathogens (e.g. Vibrio and Photobacterium) and potential functional microbes (e.g. Nitrospira, Nitrosomonas, Desulfobulbus and Desulfuromusa) were widely distributed in shrimp cultural pond sediments. More importantly, we found that there was a significant negative but weak distance-decay relationship among bacterial communities in shrimp culture pond sediments at the mesoscale, and that the spatial turnover of these bacterial communities appeared to be largely driven by stochastic processes. Additionally, environmental factors, such as pH and total nitrogen, also played important roles in influencing the sediment bacterial structure. Our findings enhance our understanding of microbial ecology in aquatic ecosystems and facilitate sediment microbiota management in aquaculture. KEY POINTS: • Core bacterial taxa in cultural pond sediments contributed to the shrimp health and element cycling. • There was a significant negative distance-decay relationship among bacterial communities in shrimp culture pond sediments at the mesoscale, and its spatial turnover appeared to be largely driven by stochastic processes. • Environmental factors (e.g. pH and total nitrogen) played important roles in influencing bacterial structure in shrimp cultural pond sediments.

Distinct bacterial communities in the environmental water, sediment and intestine between two crayfish-plant coculture ecosystems

Microorganisms are an important part of productivity, water quality, and biogeochemical cycles in an aquaculture ecosystems and play a key role in determining the growth and fitness of aquaculture animals. Coculture ecosystems are widely applied with great significance in agricultural production worldwide. The crayfish-rice coculture ecosystem (CRCE) and crayfish-waterweed coculture ecosystem (CWCE) are two high-profile artificial ecosystems for crayfish culture. However, the bacterial communities of the environmental water, sediment, and intestine in the CRCE and CWCE remain elusive. In this study, we investigated the diversity, composition, and function of bacterial communities in water, sediment, and intestine samples from the CRCE to CWCE. The physicochemical factors of water [such as ORP (oxidation-reduction potential), TC (total carbon), TOC (total oxygen carbon), and NO₃^--N] and sediment [such as TC, TOC, TN (total nitrogen), and TP (total phosphate)] were significantly different in the CRCE and CWCE. The abundances of Proteobacteria, Actinobacteria, Verrucomicrobia, Cyanobacteria, Chlorobi, Chloroflexi, and Firmicutes were significantly different in the water bacterial communities of the CRCE and CWCE. The abundance of Vibrio in the crayfish intestine was higher in the CRCE than in the CWCE. The most abundant phyla in the CRCE and CWCE sediment were Proteobacteria and Bacteroidetes. The abundances of genes involved in transporters and ABC transporters were different in water of CRCE and CWCE. The abundances of genes involved in oxidative phosphorylation were significantly higher in the crayfish intestine of the CRCE than in that of the CWCE. Furthermore, the functional genes associated with carbon metabolism were significantly more abundant in the sediment of the CRCE than in that of the CWCE. Spearman correlation analysis and redundancy analysis (RDA) showed that the bacterial communities of the water and sediment in the CRCE and CWCE were correlated with environmental factors (pH, total carbon (TC), total oxygen carbon (TOC), total nitrogen (TN), and total phosphorus (TP)). Our findings showed that the composition, diversity and function of the bacterial communities were distinct in the environmental water, sediment, and intestine of the CRCE and CWCE crayfish coculture ecosystems due to their different ecological patterns. These results can help guide healthy farming practices and deepen the understanding of bacterial communities in crayfish-plant coculture ecosystems from the perspective of bacterial ecology. KEY POINTS: • The composition of bacterial communities in the environmental water, sediment, and intestine of the CRCE and CWCE were distinct. ̉• The abundances of genes involved in transporters and ABC transporters were different in the water of the CRCE and CWCE. • The bacterial communities of the water and sediment in the CRCE and CWCE were correlated with some environmental factors.

Bacterial Communities and Enzymatic Activities in Sediments of Long-Term Fish and Crab Aquaculture Ponds

Aquaculture is among the most important and fastest growing agriculture sectors worldwide; however, it generates environmental impacts by introducing nutrient accumulations in ponds, which are possibly different and further result in complex biological processes in the sediments based on diverse farming practices. In this study, we investigated the effects of long-term farming practices of representative aquatic animals dominated by grass carp (GC, Ctenopharyngodon idella) or Chinese mitten crab (CMC, Eriocheir sinensis) on the bacterial community and enzyme activity of sediments from more than 15 years of aquaculture ponds, and the differences associated with sediment properties were explored in the two farming practices. Compared to CMC ponds, GC ponds had lower contents of TC, TN, and TP in sediments, and similar trends for sediment pH and moisture content. Sediment bacterial communities were significantly different between GC and CMC ponds, with higher bacterial richness and diversity in GC ponds. The bacterial communities among the pond sediments were closely associated with sediment pH, TC, and TN. Additionally, the results showed profoundly lower activities of β-1,4-glucosidase, leucine aminopeptidase, and phosphatase in the sediments of GC ponds than CMC ponds. Pearson’s correlation analysis further revealed strong positive correlations between the hydrolytic enzyme activities and nutrient concentrations among the aquaculture ponds, indicating microbial enzyme regulation response to sediment nutrient dynamics. Our study herein reveals that farming practices of fish and crab differently affect bacterial communities and enzymatic activities in pond sediments, suggesting nutrient-driven sediment biological processes in aquaculture ponds for different farming practices.

Host development overwhelms environmental dispersal in governing the ecological succession of zebrafish gut microbiota

Clarifying mechanisms underlying the ecological succession of gut microbiota is a central theme of gut ecology. Under experimental manipulations of zebrafish hatching and rearing environments, we test our core hypothesis that the host development will overwhelm environmental dispersal in governing fish gut microbial community succession due to host genetics, immunology, and gut nutrient niches. We find that zebrafish developmental stage substantially explains the gut microbial community succession, whereas the environmental effects do not significantly affect the gut microbiota succession from larvae to adult fish. The gut microbiotas of zebrafish are clearly separated according to fish developmental stages, and the degree of homogeneous selection governing gut microbiota succession is increasing with host development. This study advances our mechanistic understanding of the gut microbiota assembly and succession by integrating the host and environmental effects, which also provides new insights into the gut ecology of other aquatic animals.

Comparable Ecological Processes Govern the Temporal Succession of Gut Bacteria and Microeukaryotes as Shrimp Aged

Understanding the rules that govern the successions of gut microbiota is prerequisite for testing general ecological theories and sustaining a desirable microbiota. However, the ignorance of microeukaryotes raises the question of whether gut microeukaryotes are assembled according to the same rules as bacteria. We tracked the shrimp gut bacterial and microeukaryotic communities by a longitudinal dense sampling. The successions of both domains were significantly correlated with host age, with relatively stable microeukaryotic communities in adult shrimp. Gut microeukaryotes exhibited significantly higher turnover rate, but fewer transient species, lower proportion of temporal generalists, and narrower habitat niche breadth than bacteria. The γ-diversity partitioning analysis revealed that the successions of gut microbiotas were primarily ascribed to the high dissimilarity as shrimp aged ([Formula: see text]_IntraTimes), whereas the relative importance of [Formula: see text]_IntraTimes was significantly higher for microeukaryotes than that for bacteria. Compared with contrasting ecological processes in governing free-living bacteria and microeukaryotes, the ecological patterns were comparable between host-associated gut counterparts. However, the gut microeukaryotes were governed more strongly by deterministic selection relative to nestedness compared with the gut bacteria, which supports the "size-plasticity" hypothesis. Our results highlight the importance of independently interpreting free-living and host-associated meta-communities for a comprehensive understanding of the processes that govern microbial successions.

Community diversity and abundance of ammonia-oxidizing archaea and bacteria in shrimp pond sediment at different culture stages

AIMS

Ammonia oxidation is a significant process of nitrogen cycles in a lot of ecosystems sediments while there are few studies in shrimp culture pond (SCP) sediments. This paper attempted to explore the community diversity and abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in SCP sediments at different culture stages.

METHODS AND RESULTS

We collected SCP sediments and analysed the community diversity and abundance of AOA and bacteria in shrimp pond sediment at different culture stages using the ammonia monooxygenase (amoA) gene with quantitative PCR (qPCR) and 16S rRNA gene sequencing. The AOB-amoA gene abundance was showed higher than AOA-amoA gene abundance in SCP sediments on Day 50 and Day 60 after shrimp larvae introducing into the pond, and the diversity of AOA in SCP sediments was higher than that of AOB. The phylogenetic tree revealed that the most of AOA were the member of Nitrosopumilus and Nitrososphaera, and the majority of AOB sequences were clustered into Nitrosospira, Nitrosomonas clusters 6a and 7. The AOA community has close relationship with total organic carbon (TOC), pH, total phosphorus (TP), nitrate reductase, urease, acid phosphatase and β-glucosidase. The AOB community was related to TOC, C/N and nitrate reductase.

CONCLUSIONS

AOA and AOB play the different ecological roles in SCP sediments at different culture stages.

SIGNIFICANCE AND IMPACT OF THE STUDY

Our results suggested that the different community diversity and abundance of AOA and AOB in SCP sediments, which may improve our ecological cognition of shrimp culture stages in SCP ecosystems.

Dissimilarity of microbial diversity of pond water, shrimp intestine and sediment in Aquamimicry system

The Pacific white shrimp, with the largest production in shrimp industry, has suffered from multiple severe viral and bacterial diseases, which calls for a more reliable and environmentally friendly system to promote shrimp culture. The "Aquamimicry system", mimicking the nature of aquatic ecosystems for the well-being of aquatic animals, has effectively increased shrimp production and been adapted in many countries. However, the microbial communities in the shrimp intestine and surrounding environment that act as an essential component in Aquamimicry remain largely unknown. In this study, the microbial composition and diversity alteration in shrimp intestine, surrounding water and sediment at different culture stages were investigated by high throughput sequencing of 16S rRNA gene, obtaining 13,562 operational taxonomic units (OTUs). Results showed that the microbial communities in shrimp intestine and surrounding environment were significantly distinct from each other, and 23 distinguished taxa for each habitat were further characterized. The microbial communities differed significantly at different culture stages, confirmed by a great number of OTUs dramatically altered during the culture period. A small part of these altered OTUs were shared between shrimp intestine and surrounding environment, suggesting that the microbial alteration of intestine was not consistent with that of water and sediment. Regarding the high production of Aquamimicry farm used as a case in this study, the dissimilarity between intestinal and surrounding microbiota might be considered as a potential indicator for healthy status of shrimp farming, which provided hints on the appropriate culture practices to improve shrimp production.

Phytoremediation of cadmium-polluted soil assisted by D-gluconate-enhanced Enterobacter cloacae colonization in the Solanum nigrum L. rhizosphere

Microbe-assisted phytoremediation for Cd-polluted soil is being regarded increasingly. However, the availability of microbes that can collaborate with Cd-hyperaccumulators effectively has become one of bottlenecks restricting the remediation efficiency. A siderophore-producing bacterium (Y16; Enterobacter cloacae) isolated from the rhizospheric soil of Cd-hyperaccumulator Solanum nigrum L. was identified by 16S rRNA gene sequencing and biochemical analysis, and then used for analyzing microbial chemotaxis, carbon source utilization, and insoluble P/Cd mobilization capacities. Besides, a soil-pot trial was performed to underlie the phytoremediation mechanism of Cd-polluted soil assisted by D-gluconate-enhanced Enterobacter cloacae colonization (DEYC) in the Solanum nigrum L. rhizosphere. Results displayed that D-gluconate was an effective chemoattractant and carbon source strengthening Y16 colonization, and Y16 exhibited strong abilities to mobilize insoluble P/Cd in shake flask by extracellular acidification (p < 0.05). In the soil-pot trial, DEYC observably enhanced soil Cd phytoextraction by Solanum nigrum L., and increased microbial diversity according to alpha- and beta-diversity analysis (p < 0.05). Taxonomic distribution and co-occurrence network analysis suggested that DEYC increased relative abundances of dominant microbial taxa associated with soil acidification (Acidobacteria-6), indoleacetic acid secretion (Ensifer adhaerens), soil fertility improvement (Flavisolibacter, Bdellovibrio bacteriovorus, and Candidatus nitrososphaera), and insoluble Cd mobilization (Massilia timonae) at different classification levels. Importantly, COGs analysis further shown that DEYC aroused the up-regulation of key genes related to chemotactic motility, carbon fixation, TCA cycle, and propanoate metabolism. These results indicated that DEYC drove the rhizospheric enrichment of pivotal microbial taxa directly or indirectly involved in soil Cd mobilization, meanwhile distinctly promoted plant growth for accumulating more mobilizable Cd. Therefore, Y16 could be used as bio-inoculants for assisting phytoremediation of Cd-polluted soil.

Identifying Potential Polymicrobial Pathogens: Moving Beyond Differential Abundance to Driver Taxa

It is now recognized that some diseases of aquatic animals are attributed to polymicrobial pathogens infection. Thus, the traditional view of "one pathogen, one disease" might mislead the identification of multiple pathogens, which in turn impedes the design of probiotics. To address this gap, we explored polymicrobial pathogens based on the origin and timing of increased abundance over shrimp white feces syndrome (WFS) progression. OTU70848 Vibrio fluvialis, OTU35090 V. coralliilyticus, and OTU28721 V. tubiashii were identified as the primary colonizers, whose abundances increased only in individuals that eventually showed disease signs but were stable in healthy subjects over the same timeframe. Notably, the random Forest model revealed that the profiles of the three primary colonizers contributed an overall 91.4% of diagnosing accuracy of shrimp health status. Additionally, NetShift analysis quantified that the three primary colonizers were important "drivers" in the gut microbiotas from healthy to WFS shrimp. For these reasons, the primary colonizers were potential pathogens that contributed to the exacerbation of WFS. By this logic, we further identified a few "drivers" commensals in healthy individuals, such as OUT50531 Demequina sediminicola and OTU_74495 Ruegeria lacuscaerulensis, which directly antagonized the three primary colonizers. The predicted functional pathways involved in energy metabolism, genetic information processing, terpenoids and polyketides metabolism, lipid and amino acid metabolism significantly decreased in diseased shrimp compared with those in healthy cohorts, in concordant with the knowledge that the attenuations of these functional pathways increase shrimp sensitivity to pathogen infection. Collectively, we provide an ecological framework for inferring polymicrobial pathogens and designing antagonized probiotics by quantifying their changed "driver" feature that intimately links shrimp WFS progression. This approach might generalize to the exploring disease etiology for other aquatic animals.

The implication of metabolically active Vibrio spp. in the digestive tract of Litopenaeus vannamei for its post-larval development

This work aimed to evaluate the link between the occurrence/abundance of Vibrio populations and bacterial composition in shrimp’s intestine (Litopenaeus vannamei) during post-larval ontogenetic development and in its culture water, and the correlation of these with environmental parameters. The total and metabolically active populations of Vibrio in the digestive tract of shrimp during its post-larval development were analysed using quantitative PCR (qPCR) and reverse transcription qPCR targeting the 16S rRNA gene sequence. A lab-scale shrimp bioassay was performed for 80 days in a recirculating aquarium under strictly controlled conditions. The results indicate that the Vibrio population from shrimp’s gut is associated with its developmental stage and the environment. Multivariate analyses revealed that the presence of Vibrio spp. drove the studied system, but their metabolically active performance was related to earlier developmental stages in an aqueous environment. Also, the samples taken from water of culture units to compare the influence of the aquatic environment on the intestinal microbial community during shrimp’s ontogenetic development showed significant differences. Finally, our results revealed that Vibrio is an important member of shrimp’s gut microbiota; however, its metabolic activity seems to be highly regulated, possibly by the host and by the rest of the microbiota.

Understanding the role of the shrimp gut microbiome in health and disease

With rapid increases in the global shrimp aquaculture sector, a focus on animal health during production becomes ever more important. Animal productivity is intimately linked to health, and the gut microbiome is becoming increasingly recognised as an important driver of cultivation success. The microbes that colonise the gut, commonly referred to as the gut microbiota or the gut microbiome, interact with their host and contribute to a number of key host processes, including digestion and immunity. Gut microbiome manipulation therefore represents an attractive proposition for aquaculture and has been suggested as a possible alternative to the use of broad-spectrum antibiotics in the management of disease, which is a major limitation of growth in this sector. Microbiota supplementation has also demonstrated positive effects on growth and survival of several different commercial species, including shrimp. Development of appropriate gut supplements, however, requires prior knowledge of the host microbiome. Little is known about the gut microbiota of the aquatic invertebrates, but penaeid shrimp are perhaps more studied than most. Here, we review current knowledge of information reported on the shrimp gut microbiota, highlighting the most frequently observed taxa and emphasizing the dominance of Proteobacteria within this community. We discuss involvement of the microbiome in the regulation of shrimp health and disease and describe how the gut microbiota changes with the introduction of several economically important shrimp pathogens. Finally, we explore evidence of microbiome supplementation and consider its role in the future of penaeid shrimp production.

Microbiota comparison of Pacific white shrimp intestine and sediment at freshwater and marine cultured environment

Environmental microbiota plays important roles in the intestinal microbiota of aquatic animals. The Pacific white shrimp with high commercial value and euryhaline property has become the most important commercial species of shrimp in the world. However, the association between shrimp intestine and sediment at freshwater and marine cultured environment should be investigated to reveal the microbiota differences. In the present study, Miseq sequencing technology and bioinformatics were used to comprehensively compare the bacterial communities and all samples' V3-V4 regions of 16S rRNA gene were sequenced. Results showed that 55 phyla and 789 genera were identified due to the classifiable sequence. Sequencing data demonstrated statistically significant diverse microbiota compositions in the shrimp intestine and sediment at freshwater and marine cultured environment at the phylum and genus level. At the phylum level, the dominant phyla in all groups were Proteobacteria, Chloroflexi, Actinobacteria, Firmicutes, Cyanobacteria, Bacteroidetes, Acidobacteria, Verrucomicrobia, Saccharibacteria. Proteobacteria were the most abundant and largest phylum except in the intestine of marine cultured shrimp and Actinobacteria may be enriched in the shrimp intestine from sediment. At the genus level, nine out of the twelve dominant genera exhibited statistically significant differences among all groups. Moreover, Lactobacillus tend to be enriched in the freshwater cultured shrimp intestine, while Synechococcus and Vibrio extremely abundance in the marine cultured shrimp intestine. These results showed that the bacterial compositions are mostly the same in shrimp intestine and sediment, while with different relative abundances of the bacterial communities. In conclusion, this study may greatly enhance our understanding of the microbiota characteristics between shrimp and sediment. Moreover, it provided guidance for the healthy aquaculture at freshwater and marine cultured environment.