Below you will find scientific publications authored by our members or those enabled by our platform services.
2020
Brereton, N J B; Gonzalez, E; Desjardins, D; Labrecque, M; Pitre, F E
Co-cropping with three phytoremediation crops influences rhizosphere microbiome community in contaminated soil Journal Article
In: Science of The Total Environment, vol. 711, pp. 135067, 2020, ISSN: 0048-9697.
Abstract | Links | BibTeX | Tags: 16S rRNA, Co-cropping, Metagenomics, Microbiome, Phytoremediation, Rhizosphere
@article{brereton_co-cropping_2020,
title = {Co-cropping with three phytoremediation crops influences rhizosphere microbiome community in contaminated soil},
author = {N J B Brereton and E Gonzalez and D Desjardins and M Labrecque and F E Pitre},
url = {https://www.sciencedirect.com/science/article/pii/S0048969719350594},
doi = {10.1016/j.scitotenv.2019.135067},
issn = {0048-9697},
year = {2020},
date = {2020-01-01},
urldate = {2021-05-26},
journal = {Science of The Total Environment},
volume = {711},
pages = {135067},
abstract = {Human industrial activities have left millions of hectares of land polluted with trace element metals and persistent organic pollutants (POPs) around the world. Although contaminated sites are environmentally damaging, high economic costs often discourage soil remediation efforts. Phytoremediation is a potential green technology solution but can be challenging due to the diversity of anthropogenic contaminants. Co-cropping could provide improved tolerance to diverse soil challenges by taking advantage of distinct crop capabilities. Co-cropping of three species with potentially complementary functions, Festuca arundinacea, Salix miyabeana and Medicago sativa, perform well on diversely contaminated soils. Here, rhizosphere microbiomes of each crop in monoculture and in all co-cropping combinations were compared using 16S rRNA gene amplification, sequencing and differential abundance analysis. The hyperaccumulating F. arundinacea rhizosphere microbiome included putative plant growth promoting bacteria (PGPB) and metal tolerance species, such as Rhizorhapis suberifaciens, Cellvibrio fibrivorans and Pseudomonas lini. The rhizosphere microbiome of the fast-growing tree S. miyabeana included diverse taxa involved in POP degradation, including the species Phenylobacterium panacis. The well-characterised nitrogen-fixing M. sativa microbiome species, Sinorhizobium meliloti, was identified alongside others involved in nutrient acquisition and putative yet-to-be-cultured Candidatus saccharibacteria (TM7-1 group). The majority of differentially abundant rhizosphere-associated bacterial species were maintained in co-cropping pairs, with pairs having higher numbers of differentially abundant taxa than monocultures in all cases. This was not the case when all three crops were co-cropped, where most host-specific bacterial species were not detected as differentially abundant, indicating the potential for reduced rhizosphere functionality. The crops cultivated in pairs here retained rhizosphere microbiome bacteria involved in these monoculture ecosystem services of plant growth promotion, POP tolerance and degradation, and improved nutrient acquisition. These findings provide a promising outlook of the potential for complementary co-cropping strategies for phytoremediation of the multifaceted anthropogenic pollution which can disastrously affect soils around the world.},
keywords = {16S rRNA, Co-cropping, Metagenomics, Microbiome, Phytoremediation, Rhizosphere},
pubstate = {published},
tppubtype = {article}
}
2018
Kou, Shumeng; Vincent, Gilles; Gonzalez, Emmanuel; Pitre, Frederic E; Labrecque, Michel; Brereton, Nicholas J B
The Response of a 16S Ribosomal RNA Gene Fragment Amplified Community to Lead, Zinc, and Copper Pollution in a Shanghai Field Trial Journal Article
In: Frontiers in Microbiology, vol. 9, 2018, ISSN: 1664-302X, (Publisher: Frontiers).
Abstract | Links | BibTeX | Tags: 16S rRNA, bioremediation, Heavy metal contamination, Metagenomics, soil bacteria
@article{kou_response_2018,
title = {The Response of a 16S Ribosomal RNA Gene Fragment Amplified Community to Lead, Zinc, and Copper Pollution in a Shanghai Field Trial},
author = {Shumeng Kou and Gilles Vincent and Emmanuel Gonzalez and Frederic E Pitre and Michel Labrecque and Nicholas J B Brereton},
url = {https://www.frontiersin.org/articles/10.3389/fmicb.2018.00366/full},
doi = {10.3389/fmicb.2018.00366},
issn = {1664-302X},
year = {2018},
date = {2018-01-01},
urldate = {2021-05-19},
journal = {Frontiers in Microbiology},
volume = {9},
abstract = {Industrial and agricultural activities have caused extensive metal contamination of land throughout China and across the globe. The pervasive nature of metal pollution can be harmful to human health and can potentially cause substantial negative impact to the biosphere. To investigate the impact of anthropogenic metal pollution found in high concentrations in industrial, agricultural and urban environments, 16S ribosomal RNA gene amplicon sequencing was used to track change in the amplified microbial community after metal contamination in a large-scale field experiment in Shanghai. 1,566 operational taxonomic units (OTUs) identified from 448,108 sequences gathered from 20 plots treated as controls or with lead, zinc, copper or all three metals. Constrained Analysis of Principal Coordinates ordination did not separate control and lead treatment but could separate control/lead, zinc, copper and three metal treatment. DESeq2 was applied to identify 93 significantly differentially abundant OTUs varing in 211 pairwise instances between the treatments. Differentially abundant OTUs representing genera or species belonging to the phyla Chloroflexi, Cyanobacteria, Firmicutes, Latescibacteria and Planctomycetes were almost universally reduced in abundance due to zinc, copper or three metal treatment; with three metal treatment abolishing the detection of some OTUs, such as Leptolyngbya, Desmonostoc muscorum and Microcoleus steenstrupii. The greatest increases due to metal treatment were observed in Bacteroidetes, Actinobacteria, Chlamydiae, Nitrospirae and Proteobacteria (α, β, ƍ and γ); the most (relative) abundant being uncharacterised species within the genera Methylobacillus, Solirubrobacter and Ohtaekwangia. Three metal treatment alone resulted in identification of 22 OTUs (genera or species) which were not detected in control soil, notably including Yonghaparkia alkaliphila, Pedobacter steynii, Pseudolabrys taiwanensis, Methylophilus methylotrophus, Nitrosospira, and Lysobacter mobilis. The capacity to track alterations of an amplified microbial community at high taxonomic resolution using modern bioinformatic approaches, as well as identifying where that resolution is lost for technical or biological reasons, provides an insight into the complexity of the microbial world resisting anthropogenic pollution. While functional assessment of uncharacterised organisms within environmental samples is technically challenging, an important step is observing those organisms able to tolerate extreme stress and to recognise the extent to which important amplifiable community members still require characterisation.},
note = {Publisher: Frontiers},
keywords = {16S rRNA, bioremediation, Heavy metal contamination, Metagenomics, soil bacteria},
pubstate = {published},
tppubtype = {article}
}