This study evaluated the role of increasing salinity in brackish-water aquaponics, also defined as haloponics, during an 8-month cycle characterized by two fish monoculture phases in autumn and ...spring and a polyculture phase in winter. The effects of three water salinity levels (low: 0.5‰; medium: 3.0‰; high: 6.0‰) were assessed on the health, growth performance and carcass traits of black bullhead catfish (Ameiurus melas) and rainbow trout (Oncorhynchus mykiss), and the concurrent production of Swiss chard (Beta vulgaris, ssp. vulgaris) and cherry tomato (Solanum lycopersicum). During 268 days, from September to June, a total of 261 catfish (initial weight 147 ± 22 g) were distributed in the nine units of an experimental aquaponic system (three units per treatment; initial stocking density 8.50 kg m−3). In December, 150 trout (initial weight 153 ± 22 g) were added to the system (initial stocking density 5.06 kg m−3) and reared for 103 days with catfish. During the trial, two growing cycles of Swiss chard and one of cherry tomato were carried out. Water microbiota communities were dominated by the phyla of Proteobacteria (60%) and Bacteroidota (19%), followed by Actinobacteriota, Cyanobacteria, Fusobacteriota, Patescibacteria, and Firmicutes. The Shannon entropy index for alpha-diversity decreased when the water salinity increased, where low and high salinities groups significantly differed. As for the 20 most abundant genera, differences according to water salinities were found on their relative abundance. Water salinity did not affect the final weight (348 g, on average), eviscerated carcass yield (87.5%) and fillet (52.0%) yields of trout, as well as the final weight (193 g), eviscerated carcass yield (84.1%) and fillet yield (48.3%) of catfish. Water salinity did not affect the fillet chemical composition in both species. At low salinity, the fillet fatty acid profile of catfish showed lower (−6.5%; P < 0.05) MUFA and higher PUFA (+6.8%; P < 0.05) and n-6 (+5.9%; P < 0.05) proportions compared with high salinity. At high and medium salinity, Swiss chard showed higher total yield (+61%; P < 0.01) in the first production cycle and higher total (+28%; P < 0.01) and marketable (+32%; P < 0.001) yield in the second production cycle compared with low salinity, whereas cherry tomato truss weight was lower (−32%: P < 0.001) at high compared with medium and low salinity.
The use of brackish water until 6‰ proved to be a viable alternative to reduce freshwater consumption, without impairing fish and leafy vegetable growth or the overall balance of the aquaponic system.
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•An 8-month aquaponic cycle was run by exploiting seasonal temperature variations.•Water salinity did not affect fish growth and quality.•Increase in salinity reduced the abundance of bacteria populations in the water.•A polyculture phase with trout and catfish was feasible in a brackish aquaponic system.
The microbiota of recirculating aquaculture systems (RAS) is of major importance for optimal fish health. However, the microbial communities in commercial RAS are highly complex and more knowledge is ...needed to potentially control and maintain beneficial microbial communities for good fish production. In this study we monitored microbial communities in a commercial RAS producing Atlantic salmon fry (Salmo salar) during seven consecutive production batches. The water of rearing tanks and the water sump downstream of the biofilter/upstream of the UV, as well as biofilm of the wall of the rearing tanks and the fixed bed biofilter were analysed using 16S rRNA gene amplicon sequencing to elucidate the spatial-temporal microbial dynamics. The results showed that the microbiota composition of water and biofilm varied within and between the production batches, and that the fallowing periods had a substantial effect on the microbial communities. The correlation of the water and biofilm microbiota to fish presence in the system was confirmed by supervised machine learning. Shifts in the composition of the microbiota were identified in conjunction with variations in organic matter loading both during production and fallowing. In addition, variables like oxygen saturation, biomass, and feed type, showed good correlation with variations in the water microbiota composition. Although microbiota changed at fallowing, the microbiota returned to similar compositions during the production phases and was especially evident for the water microbiota. This indicates that the development of microbiota composition is strongly dictated by the similar selection pressure in the system. Nitrifying communities were dominated by Nitrospira, and the third most abundant Nitrospira OTUs were related to the comammox Nitrospira nitrificans. The microbial communities in the biofilter biofilm and water were significantly different but shared abundant taxa and followed the same temporal microbial dynamics and indicates an interaction between the biofilter biofilm and the suspended bacteria. CFU analysis showed that the fraction of rapid-growing bacteria was significantly higher in the rearing water than in the water sump upstream the UV disinfection, indicating that disinfection upstream the rearing tanks allowed for growth of opportunistic bacteria. A community with considerable potential for opportunistic regrowth can have consequences for the microbial water quality and the resistance against pathogen invasion The absence of an in-line disinfection step or placing the disinfection unit upstream the biofilter might provide better microbial water quality and a more resilient system against pathogen proliferation.
•Monitoring of microbial communities in a commercial RAS producing Atlantic salmon•The microbial communities of water and biofilm underwent large changes over time•Microbial communities in biofilm and water were different, but shared many taxa•Nitrospira OTUs were related to the comammox Nitrospira nitrificans
The environmental pathways for the dissemination of antibiotic resistance have recently received increased attention. Aquatic environments act as reservoirs or sources of antimicrobial-resistant ...bacteria, antimicrobial residues, and antimicrobial resistance genes (ARGs). Therefore, it is imperative to identify the role of polluted water in the dissemination of antimicrobial resistance. The aim of this study was to evaluate the antimicrobial residues, ARGs, and microbiota in the freshwater systems of the Mekong Delta. We selected 12 freshwater sites from aquacultures and rivers in Can Tho, Vietnam and analyzed them for 45 antimicrobial residues and 8 ARGs by LC/MS/MS and real-time PCR, respectively. A 16S rDNA-based metagenomic analysis was conducted to characterize the water microbiota. Residues of sulfamethoxazole (10/12) and sulfadimidine (7/12) were widely detected, together with the sulfa-resistance genes sul1 (11/12) and sul2 (9/12). Additionally, sulfamethoxazole residues and the β-lactamase-resistance gene blaCTX-M-1 were detected in eight freshwater systems (8/12), suggesting that these freshwater systems may have been polluted by human activity. The metagenomic analysis showed that all the tested freshwater systems contained the phyla Proteobacteria, Actinobacteria, and Bacteroidetes, representing 64% of the total microbiota. Moreover, the Cai Rang River site (Ri-E), which is located at the merge point of wastewaters from backyard-based aquacultures, contained the genera Polynucleobacter, Variovorax, and Limnohabitans, representing more than 78.4% of the total microbiota. Bacterial diversity analysis showed that the Ri-E exhibited the lowest diversity compared with other regions. Principal coordinate analysis showed that the differences among water microbiotas in backyard-based aquacultures could be explained by the farmers' aquaculture techniques.
In conclusion, this study demonstrated a collapse of bacterial diversity at the merge point of wastewaters from backyard-based aquacultures in the Mekong Delta.
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•SMX and SDD residues were widely detected with the sul1 sulfa-resistance gene.•Nine out of twelve sites had blaCTX-M, blaTEM, and blaSHV.•Wastewater merge point of backyard-based aquacultures (Ri-E) had low diversity.•Three genera of Polynucleobacter, Varivorax and Limnohabitans predominated at Ri-E.•Aquaculture management may affect the diversity of backyard-based aquaculture.
•The major findings in this study were:•The microbial community of the water was similar between the compartments in each RAS.•The microbial communities of the water underwent large changes over time ...within each system.•The biofilm microbiota differed significantly from the water microbiota within each system.•Biofilm community profiles were more stable over time and between systems than the water communities.•Salinity appeared to structure the microbial communities.
Fish live in close contact with microbes in their surrounding water. For cultivated marine fish larvae, stable microbial environments, characterized by slow-growing, K-selected bacteria, have been found to improve growth and survival. Compared to flow-through systems, recirculating aquaculture systems (RAS) offer a better possibility for obtaining microbial stability in the rearing water. However, the microbial ecology in RAS is complex and little studied, and to optimize the microbial water quality more knowledge is needed on microbial community dynamics and interactions between microbes and fish. In the present study we investigated microbial community dynamics in three large-scale RAS, operated with different salinities (12, 22 and 32ppt), for production of Atlantic salmon post-smolts. We focused on the stability of microbial communities over time in the bioreactors and the fish tanks, and compared the microbial communities within and between the three RAS. The study showed that: 1) The microbial community of the water was similar between the compartments of each RAS at the same time point, 2) The microbial communities of the water (and to a lesser extent the biofilm) within each system underwent large changes over time, 3) The microbiota of biofilm and water differed significantly within each system, 4) Biofilm community profiles were more similar between RAS than the water community profiles, and 5) Salinity structured the microbial community composition. The present study provides new knowledge on how the microbiota in RAS varies with time and how it is influenced by environmental factors.
Being part of fish's natural diets, insects have become a practical alternative feed ingredient for aquaculture. While nutritional values of insects have been extensively studied in various fish ...species, their impact on the fish microbiota remains to be fully explored. In an 8-week freshwater feeding trial, Atlantic salmon (Salmo salar) were fed either a commercially relevant reference diet or an insect meal diet wherein black soldier fly (Hermetia illucens) larvae meal comprised 60% of total ingredients. Microbiota of digesta and mucosa origin from the proximal and distal intestine were collected and profiled along with feed and water samples.
The insect meal diet markedly modulated the salmon intestinal microbiota. Salmon fed the insect meal diet showed similar or lower alpha-diversity indices in the digesta but higher alpha-diversity indices in the mucosa. A group of bacterial genera, dominated by members of the Bacillaceae family, was enriched in salmon fed the insect meal diet, which confirms our previous findings in a seawater feeding trial. We also found that microbiota in the intestine closely resembled that of the feeds but was distinct from the water microbiota. Notably, bacterial genera associated with the diet effects were also present in the feeds.
We conclude that salmon fed the insect meal diets show consistent changes in the intestinal microbiota. The next challenge is to evaluate the extent to which these alterations are attributable to feed microbiota and dietary nutrients, and what these changes mean for fish physiology and health.
The individual Probiotic application has become increasingly widespread in aquaculture and has been extensively studied. However, investigating probiotics as water additives in the grouper culture is ...still lacking. This study evaluated the functional efficacy of the Bacillus subtilis CICC 10071 (3 × 1011 CFU / g) and Lactobacillus sp. (8 × 1011 CFU / g) combination in a 1:1 ratio on the rearing water quality, water microbial community structure, and growth performance of hybrid grouper. Depending on the additive concentrations of probiotics, we designed four groups, each in triplicate: control (WT, 0g/m3), low concentration (WL, 0.038g/m3), middle concentration (WM, 0.075g/m3), and high concentration (WH, 0.113g/m3). The result shows that throughout the 22-day feeding period, the water supplementation of probiotics significantly decreased Ammonia (NH3) and nitrite (NO2-) in culture water. Final weight (FW), Specific growth rate (SGR), and Weight gain rate (WGR) in treated groups were higher than that in the control group (P<0.05). Analysis of water microbiota revealed that the dominant phylum Bacteroidetes, Proteobacteria, Cyanobacteria, and Actinobacteria enriched in the culture water. Furthermore, we found that the Probiotics combination could significantly reduce the abundance of Cetobacterium (phyla Fusobacteria) related to ammonia and nitrite. The Phylogenetic Investigation of Communities by Reconstruction of Unobserved States 2 (PICRUSt2) also shows that the 'metabolism of other amino acids and ‘Fatty acid biosynthesis’ functions of water microbiota were reinforced by the addition of the probiotic combination. Thus, the probiotic combination exhibited a range of advantages in the grouper culture environment, and further in-depth studies are needed.
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.
In this context, we monitored the daily composition of the active microbiota of the rearing water in a hatchery of the Pacific blue shrimp
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.
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
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:
,
,
and
, 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.
,
HIMB11 and
, 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.
By their nature and geographical location, estuaries shape different marine habitats via freshwater and seawater interactions. Thus, fish intestinal microbiota, as mediated by estuary habitat ...fluctuations, are fundamentally important but rarely studied. Similarly, it is unclear how, and to what extent, water microbiota influences fish intestinal microbiota in different estuary habitats. In this study, the euryhaline fish species,
Collichthys lucidus
from three different habitats in the Pearl River estuary (PRE) was investigated to determine the influence of habitat fluctuation on intestinal microbiota. The three water environments selected for sample collection were very different, particularly for chlorophyll-a, suspended solid, and nutrient constituents. Using high-throughput sequencing of 16S rRNA gene amplicons, we observed that dominant microbial genera in surrounding estuary waters or fish intestines were seldom shared. The most dominant genera in water samples were Candidatus
Actinomarina
and HIMB11, while
Bifidobacterium
,
Stenotrophomonas
,
Escherichia-Shigella
and
Rhodopseudomonas
were more abundant in fish intestines. Fish hosts can shape fish intestinal microbiota. However, microbial exchange was also found between fish intestines and water samples. The frequency of microbial exchange between fish intestines and water samples was increased from upstream to downstream estuary points, and was influenced by changes in seawater salinity in the estuary. Finally, core intestinal microbiota from
C
.
lucidus
was analyzed, and showed that
Bifidobacterium
,
Rhodopseudomonas
,
Escherichia
-
Shigella
,
Acinetobacter,
and
Stenotrophomonas
were highly abundant. These microbiota were theoretically implicated in immune responses, nutrient metabolism, probiotics, and potential pathogen behaviors. Overall, these data highlighted the composition of
C
.
lucidus
intestinal microbiota in different habitats across the PRE.
Healthy longevity is associated with many factors, however, the potential correlation between longevity and microbiota remains elusive. To address this, we explored environmental microbiota from one ...of the world’s longevity townships in China. We used 16S rRNA gene high-throughput sequencing to analyze the composition and function of water microbiota. The composition and diversity of water microbiota significantly differed between the towns. Lactobacillus, Streptococcus, Bacteroides, Faecalibacterium, and Stenotrophomonas were only dominant in Xinpu, a town with an exceptionally high centenarian population. Several biomarkers were identified, including Flavobacterium, Acinetobacter, Paracoccus, Lactobacillales, Psychrobacter, Bacteroides, Ruminococcaceae, and Faecalibacterium, and these shown to be responsible for the significant differences between towns. The main species contributing to the differences between towns were Cyanobacteria, Cupriavidus and Ralstonia. Based on KEGG pathways showed that the predicted metabolic characteristics of the water microbiota in Xinpu towns were significantly different to those of the other towns. The results revealed significant differences in the composition and diversity of water microbiota in the longevity township. These findings provide a foundation for further research on the role of water microbiota in healthy longevity.
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