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. 2022 May 9:13:838640.
doi: 10.3389/fmicb.2022.838640. eCollection 2022.

Microbiome of Penaeus vannamei Larvae and Potential Biomarkers Associated With High and Low Survival in Shrimp Hatchery Tanks Affected by Acute Hepatopancreatic Necrosis Disease

Guillermo Reyes  1   2 , Irma Betancourt  1 , Betsy Andrade  1 , Fanny Panchana  1 , Rubén Román  1 , Lita Sorroza  3 , Luis E Trujillo  4 , Bonny Bayot  1   5
Affiliations

Microbiome of Penaeus vannamei Larvae and Potential Biomarkers Associated With High and Low Survival in Shrimp Hatchery Tanks Affected by Acute Hepatopancreatic Necrosis Disease

Guillermo Reyes et al. Front Microbiol. .

Abstract

Acute hepatopancreatic necrosis disease (AHPND) is an emerging bacterial disease of cultured shrimp caused mainly by Vibrio parahaemolyticus, which harbors the lethal PirAB toxin genes. Although Penaeus vannamei (P. vannamei) postlarvae are susceptible to AHPND, the changes in the bacterial communities through the larval stages affected by the disease are unknown. We characterized, through high-throughput sequencing, the microbiome of P. vannamei larvae infected with AHPND-causing bacteria through the larval stages and compared the microbiome of larvae collected from high- and low-survival tanks. A total of 64 tanks from a commercial hatchery were sampled at mysis 3, postlarvae 4, postlarvae 7, and postlarvae 10 stages. PirAB toxin genes were detected by PCR and confirmed by histopathology analysis in 58 tanks. Seven from the 58 AHPND-positive tanks exhibited a survival rate higher than 60% at harvest, despite the AHPND affectation, being selected for further analysis, whereas 51 tanks exhibited survival rates lower than 60%. A random sample of 7 out of these 51 AHPND-positive tanks was also selected. Samples collected from the selected tanks were processed for the microbiome analysis. The V3-V4 hypervariable regions of the 16S ribosomal RNA (rRNA) gene of the samples collected from both the groups were sequenced. The Shannon diversity index was significantly lower at the low-survival tanks. The microbiomes were significantly different between high- and low-survival tanks at M3, PL4, PL7, but not at PL10. Differential abundance analysis determined that biomarkers associated with high and low survival in shrimp hatchery tanks affected with AHPND. The genera Bacillus, Vibrio, Yangia, Roseobacter, Tenacibaculum, Bdellovibrio, Mameliella, and Cognatishimia, among others, were enriched in the high-survival tanks. On the other hand, Gilvibacter, Marinibacterium, Spongiimonas, Catenococcus, and Sneathiella, among others, were enriched in the low-survival tanks. The results can be used to develop applications to prevent losses in shrimp hatchery tanks affected by AHPND.

Keywords: 16S rRNA gene; AHPND; Penaeus vannamei larvae; biomarkers; differential abundance; microbiome.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

FIGURE 1
FIGURE 1
Experimental design for the microbiome characterization of Penaeus vannamei (P. vannamei) larvae affected with acute hepatopancreatic necrosis disease (AHPND) and identification of potential biomarkers associated with high and low survival in shrimp hatchery tanks through high-throughput sequencing. *Only 56 and 49 samples were collected at PL7 and PL10 as the population of 8 and 7 tanks died at PL6 and PL9 stages, respectively.
FIGURE 2
FIGURE 2
Samples selected for the microbiome characterization of P. vannamei larvae affected by AHPND. (A) High-survival tanks. (B) Low-survival tanks. †Sample did not pass the DNA quality control. ¥Sample not collected as the tank population died at PL9.
FIGURE 3
FIGURE 3
Alpha-diversity of the larval microbiome at amplicon sequence variant (ASV) level in the high- and low-survival tanks affected by AHPND. (A) Shannon index for the high-survival tanks. (B) ACE index for the high-survival tanks. (C) Shannon index for the low-survival tanks. (D) ACE index for the low-survival tanks. At each survival condition, pair of larval stages with different letters indicates alpha-diversity indices significantly different at p < 0.05, based on the Tukey’s honestly significant difference test.
FIGURE 4
FIGURE 4
Relative abundance of the larval microbiome in the high- and low-survival tanks affected with AHPND. (A) Phylum level. (B) Family level. (C) Genus level.
FIGURE 5
FIGURE 5
Principal coordinate analysis (PCoA) of the Bray–Curtis dissimilarity index from larvae collected at the high- and low-survival tanks affected with AHPND. (A) Mysis 3. (B) Postlarvae 4. (C) Postlarvae 7. (D) Postlarvae 10.
FIGURE 6
FIGURE 6
Results of the differential abundance analysis using a linear discriminant analysis (LDA) effect size (LEfSe) of larvae collected from the high- and low-survival tanks affected with AHPND. The length of the bar represents the effect size (LDA cutoff = 2) of all the bacterial lineages at the genus level.
FIGURE 7
FIGURE 7
Absolute abundance of ASV biomarkers at the genus level at the high- and low-survival tanks affected with AHPND.
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