Ancient Heavy Metal Contamination in Soils as a Driver of Tolerant Anthyllis vulneraria Rhizobial Communities

Appl Environ Microbiol. 2016 Dec 30;83(2):e01735-16. doi: 10.1128/AEM.01735-16. Print 2017 Jan 15.


Anthyllis vulneraria is a legume associated with nitrogen-fixing rhizobia that together offer an adapted biological material for mine-soil phytostabilization by limiting metal pollution. To find rhizobia associated with Anthyllis at a given site, we evaluated the genetic and phenotypic properties of a collection of 137 rhizobia recovered from soils presenting contrasting metal levels. Zn-Pb mine soils largely contained metal-tolerant rhizobia belonging to Mesorhizobium metallidurans or to another sister metal-tolerant species. All of the metal-tolerant isolates harbored the cadA marker gene (encoding a metal-efflux PIB-type ATPase transporter). In contrast, metal-sensitive strains were taxonomically distinct from metal-tolerant populations and consisted of new Mesorhizobium genospecies. Based on the symbiotic nodA marker, the populations comprise two symbiovar assemblages (potentially related to Anthyllis or Lotus host preferences) according to soil geographic locations but independently of metal content. Multivariate analysis showed that soil Pb and Cd concentrations differentially impacted the rhizobial communities and that a rhizobial community found in one geographically distant site was highly divergent from the others. In conclusion, heavy metal levels in soils drive the taxonomic composition of Anthyllis-associated rhizobial populations according to their metal-tolerance phenotype but not their symbiotic nodA diversity. In addition to heavy metals, local soil physicochemical and topoclimatic conditions also impact the rhizobial beta diversity. Mesorhizobium communities were locally adapted and site specific, and their use is recommended for the success of phytostabilization strategies based on Mesorhizobium-legume vegetation.

Importance: Phytostabilization of toxic mine spoils limits heavy metal dispersion and environmental pollution by establishing a sustainable plant cover. This eco-friendly method is facilitated by the use of selected and adapted cover crop legumes living in symbiosis with rhizobia that can stimulate plant growth naturally through biological nitrogen fixation. We studied microsymbiont partners of a metal-tolerant legume, Anthyllis vulneraria, which is tolerant to very highly metal-polluted soils in mining and nonmining sites. Site-specific rhizobial communities were linked to taxonomic composition and metal tolerance capacity. The rhizobial species Mesorhizobium metallidurans was dominant in all Zn-Pb mines but one. It was not detected in unpolluted sites where other distinct Mesorhizobium species occur. Given the different soil conditions at the respective mining sites, including their heavy-metal contamination, revegetation strategies based on rhizobia adapting to local conditions are more likely to succeed over the long term compared to strategies based on introducing less-well-adapted strains.

Keywords: Aminobacter; Mesorhizobium; PIB-type ATPase; metal tolerance; multilocus sequence analysis; nodulation gene; phytostabilization; symbiotic nitrogen fixation.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Acyltransferases / genetics
  • Bacterial Proteins / genetics
  • Biodegradation, Environmental
  • DNA, Bacterial / genetics
  • Fabaceae / microbiology*
  • France
  • Germany
  • Mesorhizobium / classification
  • Mesorhizobium / drug effects
  • Mesorhizobium / genetics
  • Mesorhizobium / physiology*
  • Metals, Heavy / toxicity*
  • Mining*
  • Phylogeny
  • RNA, Ribosomal, 16S / genetics
  • Rec A Recombinases / genetics
  • Seasons
  • Sequence Analysis, DNA
  • Soil Microbiology*
  • Soil Pollutants / toxicity*
  • Symbiosis / drug effects*


  • Bacterial Proteins
  • DNA, Bacterial
  • Metals, Heavy
  • RNA, Ribosomal, 16S
  • Soil Pollutants
  • Acyltransferases
  • NodA protein, Rhizobiales
  • Rec A Recombinases