Metagenomics of mine tailing rhizospheric communities and its selection for plant establishment towards bioremediation

Miguel F. Romero, Diana Gallego, Arely Lechuga-Jiménez, José F. Martínez, Hugo R. Barajas, Corina Hayano-Kanashiro, Mariana Peimbert, Rocío Cruz-Ortega, Francisco E. Molina-Freaner, Luis D. Alcaraz*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

6 Scopus citations


Mining operations often generate tailing dams that contain toxic residues and are a source of contamination when left unconfined. The establishment of a plant community over the tailings has been proposed as a containment strategy known as phytostabilization. Previously, we described naturally occurring mine tailing colonizing plants such as Acacia farnesiana, Brickellia coulteri, Baccharis sarothroides, and Gnaphalium leucocephalum without finding local adaptation. We explored the rhizosphere microbes as contributors in plant establishment and described both the culturable and in situ diversity of rhizospheric bacteria using the 16S rRNA gene and metagenomic shotgun sequencing. We built a synthetic community (SC) of culturable rhizosphere bacteria from the mine tailings. The SC was then the foundation for a serial passes experiment grown in plant-derived nutrient sources, selecting for heavy metals tolerance, community cooperation, and competition. The outcome of the serial passes was named the ‘final synthetic community’ (FSC). Overall, diversity decreased from in situ uncultivable microbes from roots (399 bacteria genera) to the cultivated communities (291 genera), the SC (94 genera), and the lowest diversity was in the FSC (43 genera). Metagenomic diversity clustered into 94,245 protein families, where we found plant growth promotion-related genes such as the csgBAC and entCEBAH, coded in a metagenome-assembled genome named Kosakonia sp. Nacozari. Finally, we used the FSC to inoculate mine tailing colonizing plants in a greenhouse experiment. The plants with the FSC inocula observed higher relative plant growth rates in sterile substrates. The FSC presents promising features that might make it useful for phytostabilization tailored strategies.

Original languageEnglish
Article number126732
JournalMicrobiological Research
StatePublished - Jun 2021

Bibliographical note

Funding Information:
This work was supported by DGAPA - PAPIIT - UNAM   IN221420 , Consejo Nacional de Ciencia y Tecnología (CONACyT) Ciencia Básica 237387 to LDA, DGAPA-PAPIIT-UNAM IN209015 and UNAM-UA Consortium on Drylands Research to FMF, and DGAPA-PAPIIT-UNAM IN207418 (RN207418) to RCO. MR was supported by the Posgrado en Ciencias Biológicas , Universidad Nacional Autónoma de México ; this study as performed in partial fulfillment of the requirements for the Ph. D. degree and received a scholarship (692969) from CONACyT. We thank Dr. Julio Campo at Instituto de Ecología, Universidad Nacional Autónoma de México (IE-UNAM), for his assistance processing mine tailing material. Rodrigo García Herrera, head of the Scientific Computing Department at LANCIS-IE-UNAM, for running the HTC infrastructure used for the analyses. We thank Jazmin Blaz for field and technical work.

Publisher Copyright:
© 2021 Elsevier GmbH


  • Mesocosm
  • Metagenomics
  • Microbiome
  • Mine tailing
  • Phytostabilization
  • Rhizosphere


Dive into the research topics of 'Metagenomics of mine tailing rhizospheric communities and its selection for plant establishment towards bioremediation'. Together they form a unique fingerprint.

Cite this