Predictive functional profiles using metagenomic 16S rRNA data: a novel approach to understanding the microbial ecology of aquaculture systems

Abstract

Micro‐organisms are an essential component of natural marine ecosystems, but also play important roles in anthropogenically modified ecosystems, including aquaculture. Although metagenomics is currently used to explore microbial communities, its application has not been as extensive in aquaculture. Although some taxonomic profiles and phylogenetic studies have been deciphered using biomarker genes, the functional potential of microbial communities associated with aquaculture systems is still unknown in most cases. Predicting functional profiles through 16S rRNA gene‐based metagenomics analysis is perhaps the most promising tool to elucidate the metabolic capabilities of microbial communities because there is no need to perform shotgun sequencing to have an idea of these capabilities. Moreover, robust bioinformatics background is not required to assess this information, and so the same data (16S rRNA sequences) are used to estimate both taxonomic and functional profiles, therefore providing deeper insights into these kinds of communities. In this review, we suggest the need to major use of novel bioinformatics tools that construct functional profiles from metagenomic 16S rRNA data, as strategy to obtain a preliminary approach about metabolic capacities of microbes that coexist in aquaculture systems.

Effects of Hydraulic Retention Time and Influent Nitrate-N Concentration on Nitrogen Removal and the Microbial Community of an Aerobic Denitrification Reactor Treating Recirculating Marine Aquaculture System Effluent

“…The microbiota active within biofilms attached to the media within biofilters mediate the denitrification process. Our understanding of the functional dynamics of the microbial communities, while still incomplete, is advancing with the application of molecular microbial identification techniques [35]. Due to its presence in most microbes and its slow rate of evolution [36], the 16S rRNA gene is widely used for the classification and molecular identification of microbes.…”

“…Brailo et al [41] showed distinct, diverse microbial communities in a commercial inoculant and in nitrifying and denitrifying biofilters. Reviewing the literature, Ortiz-Estrada et al [35] suggested the use of metagenomic 16s rRNA data to gain a deeper understanding of the functional profiles of microbial communities in aquaculture systems. With the ongoing development of biofiltration technology and increased knowledge of microbial diversity, there have been reports of new microbes utilizing different nitrogen removal pathways, including nitratation, nitrifier denitrification, anaerobic ammonium oxidation (anammox), and combined pathways [42], including aerobic denitrification [15][16][17][18][19][20].…”

Metagenome gene prediction of naturally fermented milk products of India using PICRUSt2 and Piphillin

“…Microbial functional gene prediction has been popularly studied using metagenomic gene prediction tools in recent years [1]. Recently, PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States version 2) has been improved for metagenomic gene prediction overcoming some of the limitations of its predecessor, PICRUSt and other similar pipelines [2].…”

Microbial Communities of Culture Water and African Catfish Reared in Different Aquaculture Systems in Nigeria Analyzed Using Culture Dependent Techniques

“…The authors did not find any significant difference between microbiota of tilapia from replicates of similar culture system. So far studies investigating microbial communities in fish culture system like RAS [33,34] and the culture fish is yet novel [35]. However it has been noted that the composition of the gastrointestinal microbiome of rainbow trout reared in different aquaculture systems like raceways, earthen ponds and inshore tank systems can be rearing system influenced [14,36,37].…”