Metagenomic analysis between free-living and cultured Epinephelus fuscoguttatus under different environmental conditions in Indonesian waters

Philipp, Hennersdorf; Mrotzek, Grit; Abdul-Aziz, Muslihudeen A.; Saluz, Hans Peter

doi:10.1016/j.marpolbul.2016.05.009

Cited by 20 publications

(9 citation statements)

References 38 publications

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“…Captive common snook juveniles harbored decreased bacterial species richness and evenness as compared to acclimated and wild snook. Numerous studies on the gut microbiota of fishes report similar findings [ 8 , 9 , 44 , 45 ]. Captive fish rearing in a recirculating aquaculture system maintains a relatively constant salinity, temperature, and oxygen level, generally buffered by the external environment.…”

Section: Discussionsupporting

confidence: 54%

Shifts in the Skin-Associated Microbiota of Hatchery-Reared Common Snook Centropomus undecimalis During Acclimation to the Wild

et al. 2018

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The skin-associated microbiota of fish competes against pathogens for space and nutrients, preventing colonization by harmful bacteria encountered during environmental transitions such as those faced during stock enhancement. Thus, alterations in bacterial community structure during release of cultured fish have important implications for health of these individuals. This study investigated microbiota structure during acclimation of juvenile hatchery-reared common snook Centropomus undecimalis to the wild by comparing skin-associated microflora among snook in captivity, after 48 h of acclimation at release sites, and from the wild. After two days of acclimation, the microbiota of hatchery-reared snook mirrored that observed on wild snook. Relative abundances of potential pathogens were higher in captive fish, whereas acclimated and wild fish harbored bacterial taxa influenced by geographical factors and water quality at release sites. Predicted microbiota function of acclimated and wild fish showed higher production of protective amino acids and antimicrobials, identifying a mechanism for microbial supplementation of the immune defense of these fish. The two-day transition to wild-type microbiota suggests a temporal scale of hours associated with bacterial succession indicating that the microbiota, whose structure is vital to fish health, aids in acclimation of fish to new environments during stock enhancement efforts.

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Section: Discussionsupporting

confidence: 54%

Shifts in the Skin-Associated Microbiota of Hatchery-Reared Common Snook Centropomus undecimalis During Acclimation to the Wild

et al. 2018

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“…Overall, the fish intestinal microbiome in this study was dominated by the phylum of Proteobacteria, Firmicutes, Fusobacteria, and Plantomycetes, and the order of Clostridiales, Vibrionales, Fusobacteriales, Lactobacillales, and Rhodobacterales, as reported in previous studies (Dehler et al, 2017a(Dehler et al, , 2017bHuang et al, 2017;Hennersdorf et al, 2016;Sullam et al, 2012). Both dry and wet seasons share the same dominant phyla in the intestinal microbiome of Asian seabass, which were Proteobacteria, Firmicutes and Fusobacteria, but they were more abundant in the dry season, when water temperature, ambient temperature, and salinity were significantly higher.…”

Section: Discussionsupporting

confidence: 83%

Diversity, Relative Abundance, and Functional Genes of Intestinal Microbiota of Tiger Grouper (Epinephelus fuscoguttatus) and Asian Seabass (Lates calcarifer) Reared in A Semi-Closed Hatchery in Dry and Wet Seasons

Sutra¹,

Saadu²,

Hashim³

et al. 2021

JTAS

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Grouper and Asian seabass are among the economically important cultured marine fish in Malaysia. However, fry productions in large scale tend to introduce stress that changes the fish microbiota and increases susceptibility to diseases. Currently, high-throughput sequencing is used to study fish microbiota and their respective gene functions. In this study, we investigate the diversity, abundance and functional genes of intestinal microbiota of tiger grouper and Asian seabass that were reared in a semi-closed hatchery during dry and wet seasons. Intestinal samples were collected from tiger grouper and Asian seabass of different sizes before proceeded to DNA extraction. The extracted DNA were then subjected to 16S rRNA gene amplicon sequencing using the Illumina Miseq platform targeting V3 and V4 regions for determination of the bacterial diversity, abundance and functional genes in both seasons. The results revealed that intestinal microbiota of Asian seabass were dominated by the phylum Proteobacteria and order Vibrionales in both seasons. Meanwhile, intestinal microbiome of tiger groupers were shifted from domination of phylum Firmicutes and order Clostridiales in dry season to Proteobacteria and order Lactobacillales in wet season. PICRUSt analysis revealed that the functional genes that were dominantly present were the genes encoded for metabolism, genetic information processing, environmental information processing, cellular process and human diseases. Remarkably, SIMPER analysis showed several potential metagenomics biomarker genes in dry and wet seasons. This study revealed the importance of utilizing amplicon metagenomics approaches in microbiome studies for better identification of the microbial profiling in aquaculture systems.

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“…RAS decreased bacterial diversity and evenness in the snook external microbiota compared to Wild environments, a trend that is commonly reported [4,[44][45][46][47]. It is clear that conditions in captivity influence hostassociated microbial communities, in part from increased nutrient input and water disinfection as described previously, but also from altered diets which can influence both the gut and skin microbiota [48].…”

Section: Discussionsupporting

confidence: 53%

Effect of copper sulfate on the external microbiota of adult common snook (Centropomus undecimalis)

et al. 2021

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Background The environment exerts a strong influence on the fish external microbiota, with lower diversity and increased abundances of opportunistic bacterial groups characterizing cultured fish compared to their wild counterparts. Deviation from a healthy external microbiota structure has been associated with increased susceptibility to bacterial pathogens. Treatment of wild-caught broodstock with copper sulfate for the removal of external parasites is a common aquaculture practice. Despite the microbiota’s importance to fish health, the effects of copper sulfate on mucosal bacterial communities and their ability to recover following this chemical treatment have not been examined. The skin microbiota of adult common snook was characterized from wild individuals (Wild), and wild-caught fish maintained in recirculating aquaculture systems (RAS) immediately following a month-long copper sulfate treatment (Captive-1), and then two-weeks (Captive-2) and 2 years (Captive-3) after cessation of copper treatment. Results The skin microbiota of wild fish were characterized by high diversity and taxa including Synechocococcus, SAR11, and a member of the Roseobacter clade. Bacterial diversity decreased in Captive individuals during the 2-year sampling period. Captive fish harbored greater abundances of Firmicutes, which may reflect glycan differences between aquaculture and natural feeds. Bacterial taxa with copper resistance mechanisms and indicative of metal contamination were enriched in Captive-1 and Captive-2 fish. Vibrionaceae were dominant in Captive fish, particularly immediately and 2 weeks following copper treatment. Based on our observations and previous literature, our results suggest putatively beneficial taxa amass over time in captivity. Within 2 years, Captive individuals harbored Bacillus which contains numerous probiotic candidates and the complex carbon degraders of the family Saprospiraceae. Predicted butanoate metabolism exceeded that of Wild fish, and its reported roles in immunity and energy provision suggest a prebiotic effect for fishes. Conclusions The mucosal microbiota contains bacterial taxa that may act as bioindicators of environmental pollution. Increases in mutualistic groups indicate a return to a beneficial skin microbiota following copper sulfate treatment. Our data also suggests that vastly different taxa, influenced by environmental conditions, can be associated with adult fish without noticeable health impairment, perhaps due to establishment of various mutualists to maintain fish mucosal health.

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Metagenomic analysis between free-living and cultured Epinephelus fuscoguttatus under different environmental conditions in Indonesian waters

Cited by 20 publications

References 38 publications

Shifts in the Skin-Associated Microbiota of Hatchery-Reared Common Snook Centropomus undecimalis During Acclimation to the Wild

Shifts in the Skin-Associated Microbiota of Hatchery-Reared Common Snook Centropomus undecimalis During Acclimation to the Wild

Diversity, Relative Abundance, and Functional Genes of Intestinal Microbiota of Tiger Grouper (Epinephelus fuscoguttatus) and Asian Seabass (Lates calcarifer) Reared in A Semi-Closed Hatchery in Dry and Wet Seasons

Effect of copper sulfate on the external microbiota of adult common snook (Centropomus undecimalis)

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