Trees, fungi and bacteria: tripartite metatranscriptomics of a root microbiome responding to soil contamination.

Autor: Gonzalez E; Canadian Center for Computational Genomics, McGill University and Genome Quebec Innovation Center, Montréal, H3A 1A4, Canada.; Department of Human Genetics, McGill University, Montreal, H3A 1B1, Canada., Pitre FE; Institut de recherche en biologie végétale, University of Montreal, Montreal, QC, H1X 2B2, Canada.; Montreal Botanical Garden, Montreal, QC, H1X 2B2, Canada., Pagé AP; Aquatic and Crop Resource Development (ACRD), National Research Council Canada, Montréal, QC, H4P 2R2, Canada., Marleau J; Institut de recherche en biologie végétale, University of Montreal, Montreal, QC, H1X 2B2, Canada., Guidi Nissim W; Department of Agri-food and Environmental Science, University of Florence, Viale delle Idee, Sesto Fiorentino, FI, Italy., St-Arnaud M; Institut de recherche en biologie végétale, University of Montreal, Montreal, QC, H1X 2B2, Canada.; Montreal Botanical Garden, Montreal, QC, H1X 2B2, Canada., Labrecque M; Institut de recherche en biologie végétale, University of Montreal, Montreal, QC, H1X 2B2, Canada.; Montreal Botanical Garden, Montreal, QC, H1X 2B2, Canada., Joly S; Institut de recherche en biologie végétale, University of Montreal, Montreal, QC, H1X 2B2, Canada.; Montreal Botanical Garden, Montreal, QC, H1X 2B2, Canada., Yergeau E; Institut National de la Recherche Scientifique, Centre INRS-Institut Armand-Frappier, Laval, QC, Canada., Brereton NJB; Institut de recherche en biologie végétale, University of Montreal, Montreal, QC, H1X 2B2, Canada. Nicholas.brereton@umontreal.ca.
Jazyk: angličtina
Zdroj: Microbiome [Microbiome] 2018 Mar 21; Vol. 6 (1), pp. 53. Date of Electronic Publication: 2018 Mar 21.
DOI: 10.1186/s40168-018-0432-5
Abstrakt: Background: One method for rejuvenating land polluted with anthropogenic contaminants is through phytoremediation, the reclamation of land through the cultivation of specific crops. The capacity for phytoremediation crops, such as Salix spp., to tolerate and even flourish in contaminated soils relies on a highly complex and predominantly cryptic interacting community of microbial life.
Methods: Here, Illumina HiSeq 2500 sequencing and de novo transcriptome assembly were used to observe gene expression in washed Salix purpurea cv. 'Fish Creek' roots from trees pot grown in petroleum hydrocarbon-contaminated or non-contaminated soil. All 189,849 assembled contigs were annotated without a priori assumption as to sequence origin and differential expression was assessed.
Results: The 839 contigs differentially expressed (DE) and annotated from S. purpurea revealed substantial increases in transcripts encoding abiotic stress response equipment, such as glutathione S-transferases, in roots of contaminated trees as well as the hallmarks of fungal interaction, such as SWEET2 (Sugars Will Eventually Be Exported Transporter). A total of 8252 DE transcripts were fungal in origin, with contamination conditions resulting in a community shift from Ascomycota to Basidiomycota genera. In response to contamination, 1745 Basidiomycota transcripts increased in abundance (the majority uniquely expressed in contaminated soil) including major monosaccharide transporter MST1, primary cell wall and lamella CAZy enzymes, and an ectomycorrhiza-upregulated exo-β-1,3-glucanase (GH5). Additionally, 639 DE polycistronic transcripts from an uncharacterised Enterobacteriaceae species were uniformly in higher abundance in contamination conditions and comprised a wide spectrum of genes cryptic under laboratory conditions but considered putatively involved in eukaryotic interaction, biofilm formation and dioxygenase hydrocarbon degradation.
Conclusions: Fungal gene expression, representing the majority of contigs assembled, suggests out-competition of white rot Ascomycota genera (dominated by Pyronema), a sometimes ectomycorrhizal (ECM) Ascomycota (Tuber) and ECM Basidiomycota (Hebeloma) by a poorly characterised putative ECM Basidiomycota due to contamination. Root and fungal expression involved transcripts encoding carbohydrate/amino acid (C/N) dialogue whereas bacterial gene expression included the apparatus necessary for biofilm interaction and direct reduction of contamination stress, a potential bacterial currency for a role in tripartite mutualism. Unmistakable within the metatranscriptome is the degree to which the landscape of rhizospheric biology, particularly the important but predominantly uncharacterised fungal genetics, is yet to be discovered.
Databáze: MEDLINE
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