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

Overview of attention for article published in Microbiome, March 2018
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About this Attention Score

  • In the top 5% of all research outputs scored by Altmetric
  • Among the highest-scoring outputs from this source (#47 of 1,193)
  • High Attention Score compared to outputs of the same age (98th percentile)

Mentioned by

11 news outlets
1 blog
102 tweeters
3 Facebook pages


61 Dimensions

Readers on

181 Mendeley
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Trees, fungi and bacteria: tripartite metatranscriptomics of a root microbiome responding to soil contamination
Published in
Microbiome, March 2018
DOI 10.1186/s40168-018-0432-5
Pubmed ID

E. Gonzalez, F. E. Pitre, A. P. Pagé, J. Marleau, W. Guidi Nissim, M. St-Arnaud, M. Labrecque, S. Joly, E. Yergeau, N. J. B. Brereton


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. 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. 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. 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.

Twitter Demographics

The data shown below were collected from the profiles of 102 tweeters who shared this research output. Click here to find out more about how the information was compiled.

Mendeley readers

The data shown below were compiled from readership statistics for 181 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 181 100%

Demographic breakdown

Readers by professional status Count As %
Student > Master 36 20%
Researcher 35 19%
Student > Ph. D. Student 27 15%
Student > Bachelor 14 8%
Student > Doctoral Student 13 7%
Other 25 14%
Unknown 31 17%
Readers by discipline Count As %
Agricultural and Biological Sciences 72 40%
Biochemistry, Genetics and Molecular Biology 23 13%
Environmental Science 23 13%
Immunology and Microbiology 5 3%
Medicine and Dentistry 3 2%
Other 12 7%
Unknown 43 24%

Attention Score in Context

This research output has an Altmetric Attention Score of 156. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 03 April 2020.
All research outputs
of 19,800,203 outputs
Outputs from Microbiome
of 1,193 outputs
Outputs of similar age
of 295,034 outputs
Outputs of similar age from Microbiome
of 1 outputs
Altmetric has tracked 19,800,203 research outputs across all sources so far. Compared to these this one has done particularly well and is in the 99th percentile: it's in the top 5% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 1,193 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 40.8. This one has done particularly well, scoring higher than 96% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 295,034 tracked outputs that were published within six weeks on either side of this one in any source. This one has done particularly well, scoring higher than 98% of its contemporaries.
We're also able to compare this research output to 1 others from the same source and published within six weeks on either side of this one. This one has scored higher than all of them