Functional and taxonomic classification of a greenhouse water drain metagenome

Abstract

Microbiome sequencing has become the standard procedure in the study of new ecological and human-constructed niches. To our knowledge, this is the first report of a metagenome from the water of a greenhouse drain. We found that the greenhouse is not a diverse niche, mainly dominated by Rhizobiales and Rodobacterales. The analysis of the functions encoded in the metagenome showed enrichment of characteristic features of soil and root-associated bacteria such as ABC-transporters and hydrolase enzymes. Additionally, we found antibiotic resistances genes principally for spectinomycin, tetracycline, and aminoglycosides. This study aimed to identify the bacteria and functional gene composition of a greenhouse water drain sample and also provide a genomic resource to search novel proteins from a previously unexplored niche. All the metagenome proteins and their annotations are available to the scientific community via http://microbiomics.ibt.unam.mx/tools/metagreenhouse/.

Water Microbiota in Greenhouses With Soilless Cultures of Tomato by Metabarcoding and Culture-Dependent Approaches

“…In line with our results, relatively high levels of bacterial richness, yielding 88 bacterial orders (vs. 141 in our case) were found in a study aiming at comparing microbiota between groundwater collected from aquifer and well ecosystems, as determined by Illumina MiSeq metabarcoding of 16S rRNA (Korbel et al, 2017). Burkholderiales, Actinomycetales, and Sphingomonadales bacterial orders were found as dominant in wells and aquifers (Korbel et al, 2017); Rhizobiales and Rhodobacterales in a water drain greenhouse (López-Leal et al, 2018) and Mycobacterium bacterial genus and Phoma fungal genus in a water reuse system facility (Stamps et al, 2018). All of them were found in our study among the top 20 fungal and/or bacterial taxa.…”

“…Besides the description of taxa within an ecosystem, metabarcoding techniques have also been recently used for predicting the functionality of community members (Langille et al, 2013;Tedersoo et al, 2015;Bouchez et al, 2016;Louca et al, 2016). To date, investigation of the fungal and bacterial communities associated with water in greenhouses is very limited, mostly dedicated to nutrient recirculating solutions and culture substrates (Meot-Duros et al, 2011) and has rarely been achieved through NGS approaches, with the exception of the study of López-Leal et al (2018). These authors sequenced a water drain metagenome from one sample collected from an experimental greenhouse using a shotgun sequencing strategy.…”

The Hydroponic Rockwool Root Microbiome: Under Control or Underutilised?

“…These include culture-based methods [62][63][64], including community-level physiological profiling (CLPP) [11,41]; molecular methods such as phospholipid fatty acid (PLFA) profiling [65,66]; and DNA-based technologies such as community fingerprinting via denaturing gradient gel electrophoresis (DGGE) [41,63]; and single-strand conformational polymorphism [11,15,67]. Currently, the predominant methods for characterising microbial ecology are DNA-based and include taxonomic barcoding, such as 16S rRNA amplification [61,63], and metagenomic analysis of environmental DNA [21,68].…”