Bacterial community diversity in the rhizosphere of nickel hyperaccumulator species of Halmahera Island (Indonesia)

Séverine Lopez,Xavier Goux,Antony Van Der Ent,Peter D Erskine,Guillaume Echevarria,Magdalena Calusinska,Jean Louis Morel,Emile Benizri

doi:10.1016/j.apsoil.2018.09.007

Abstract

Ultramafic soils cover large areas in Indonesia, with over 8000 km2 on Halmahera Island. Nickel hyperaccumulator plants have evolved on these soils which are suspected to host highly nickel tolerant bacteria in their rhizosphere. To date, research has been limited on the characterization of the genetic diversity of such bacterial communities. The objective of this study was to investigate the genetic diversity of bacterial communities in the rhizosphere of nickel hyperaccumulator plants from Halmahera Island to improve knowledge on the factors that drive bacterial community diversity. We collected 45 rhizosphere soils from 10 woody nickel hyperaccumulator species at 16 sites to highlight the influence of plants, soil chemical parameters and site effects on bacterial diversity, richness and composition. A total of 2,508,874 bacterial 16S rRNA gene sequences were obtained and clustered into 6645 OTUs. In total, 40 phyla were identified with the most dominant phyla being Proteobacteria, Acidobacteria, Actinobacteria and Chloroflexi. Redundancy analysis between soil chemical characteristics and bacterial phyla relative abundances for the three main species (Rinorea aff. bengalensis, Ficus trachypison and Trichospermum morotaiense) showed that the main factor driving the bacterial diversity in the rhizosphere of Rinorea aff. bengalensis appears to be the plant itself (regardless of the characteristics of the soil), while the impact of soil conditions was important for the two other hyperaccumulator species. This may be explained by the fact that Rinorea aff. bengalensis (at least in Halmahera Island) is an obligate nickel hyperaccumulator.

Highlights

Indonesia is one of the most significant nickel (Ni) ore producers in the world (Mudd, 2009)
The three main hyperaccumulator species found in Halmahera Island were F. trachypison, Rinorea aff. bengalensis and T. morotaiense
Rinorea aff. bengalensis is, as far as could be established, obligate to ultramafic soils at Weda Bay, it is a facultative species to ultramafic soils throughout its range in Southeast Asia (Brooks and Wither, 1977)

Summary

Introduction

Indonesia is one of the most significant nickel (Ni) ore producers in the world (Mudd, 2009). Ultramafic soils are naturally enriched in Ni (3000–10,500 μ g−1), and in cobalt (Co), chromium (Cr) and manganese (Mn) (Proctor, 2003) These peculiar soils have a number of other unusual characteristics, such as a high magnesium (Mg) content, low cation exchange capacity (CEC) dominated by Mg, and extremely low concentrations of plant nutrients such as potassium (K), phosphorus (P) and calcium (Ca) (Read et al, 2006; Boyd and Jaffré, 2009). They can display high concentrations of bioavailable Ni, especially in tropical soils developed on serpentinised bedrocks (Echevarria, 2018). As a consequence of these unusual chemical characteristics, ultramafic soils frequently host distinctive floras (Brooks et al, 1977; Galey et al, 2017)

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