Development of a prototype 16S rRNA gene-based microarray for monitoring planktonic actinobacteria in shrimp ponds

Abstract

Many reports have shown that the composition of the bacterioplankton community can serve as a biological indicator to evaluate the occurrence of shrimp diseases. However, the distribution, diversity, and function of planktonic actinobacteria in shrimp ponds are still poorly understood. In this study, a prototype of a 16S rRNA gene-based taxonomic microarray was developed and evaluated for monitoring of planktonic actinobacteria in shrimp ponds. The prototype microarray is composed of 30 probes that target ten dominant families of planktonic actinobacteria found in shrimp ponds. The specificity of the actinobacterial microarray was validated by a set of control hybridizations with 16S rRNA genes clones. The prototype microarray was subsequently tested with two seawater samples from ponds with diseased shrimp populations (PDS) and ponds with healthy shrimp populations (PHS). The actinobacteria hybridization profiles revealed a lower abundance of Microbacteriaceae and a higher abundance of Mycobacteriaceae in PDS than in PHS. The changes in planktonic actinobacterial communities were validated by pyrosequencing data. These results support the utility of the microarray for monitoring planktonic actinobacteria in shrimp ponds and aquaculture environments.

Comparative analysis of the intestinal bacterial community and expression of gut immunity genes in the Chinese Mitten Crab (Eriocheir sinensis)

“…Subsequent studies showed that Actinobacteria isolated from the intestinal microorganism of two freshwater fish conferred resistance to human and fish pathogens and demonstrated its potential to produce biologically active compounds (Jami et al 2015). Thus, an actinobacterial microarray can reflect the changes in body condition and culture environment (Wang et al 2017). We speculate that Actinobacteria are symbiotic bacteria in the crab intestines and do not increase AMP gene expression.…”

Longitudinal variations in the gastrointestinal microbiome of the white shrimp, Litopenaeus vannamei

“…On the other hand, the Cellulomonadaceae family was mainly found in the shrimp Hindgut, and this family has been reported in shrimp ponds ( Wang et al, 2017a ). A large variety of hydrolytic starch, xylan and cellulose-degrading enzymes, are produced by Cellulomonadaceae, which belongs to the Actinobacteria phylum.…”

Evaluation of a eukaryote phylogenetic microarray for environmental monitoring of marine sediments

“…Microarray technology has previously been proposed as a tool with good potential for environmental monitoring (Rich, 2011;Rivas, 2011;Wang et al, 2017). Here we aimed to assess this by comparing microarray-based results to morpho-taxonomy and metabarcoding results from the same samples.…”

“…Further, microarrays targeting algae that cause toxic blooms have been tested and integrated in environmental monitoring (Diercks et al, 2008;Dittami et al, 2013a;Dittami et al, 2013b;Edvardsen et al, 2013;Galluzzi et al, 2011). Also, microarrays targeting a broader diversity have been designed for the 16S small subunit (SSU) ribosomal RNA (rRNA) gene and tested on environmental samples (DeSantis et al, 2007;Dubinsky et al, 2012;Nemir et al, 2010;Wang et al, 2017;Yergeau et al, 2009;Zhao et al, 2017).…”