Phyllosphere microbiome assists the hyperaccumulating plant in resisting heavy metal stress

A framework for utilizing leaf-associated microbes to achieve conservation and restoration goals

Plant-associated microbiomes have profound effects on ecosystem functioning and play a role in the success of plants at both small and large scales. As key components of healthy plants and ecosystems, plant microbiomes should be considered in conservation and ecosystem management strategies. Many knowledge gaps and logistical barriers exist that increase the difficulty of employing microbes in conservation; however, some success has been achieved by manipulating the root microbiome and in agricultural contexts. In contrast with the root microbiome, the role of the leaf microbiome in conservation remains largely unexplored. In this perspective, we posit that the leaf microbiome plays an essential role in plant and ecosystem health and should be considered in conservation strategies. We include a framework for approaching leaf microbiome management, including identification of sources of disturbance, identifying mechanisms to address resulting plant stress, types of microbial inoculation to achieve desired outcomes, and co-producing plans of management with interest groups and rights holders.

Plant nickel-exclusion versus hyperaccumulation: a microbial perspective

BACKGROUND

In New Caledonia, nearly 2000 plant species grow on ultramafic substrates, which contain prominent levels of heavy metals and are deficient in essential plant nutrients. To colonize these habitats, such plants, known as metallophytes, have developed various adaptive behaviors towards metals (exclusion, tolerance, or hyperaccumulation). Ultramafic substrates also host many unique microorganisms, which are adapted to metallic environments and capable of boosting plant growth while assisting plants in acquiring essential micronutrients. Hence, plant-microbiota interactions play a key role in adapting to environmental stress. Here, we hypothesised that microbial associations in the different aboveground and underground compartments of metallophytes could be associated to their metal hyperaccumulation or exclusion phenotypes. This hypothesis was tested using a systematic comparative metabarcoding approach on the different compartments of two New Caledonian metallophytes belonging to the same genus and living in sympatry on ultramafic substrates: Psychotria gabriellae, a nickel-hyperaccumulator (Ni-HA), and Psychotria semperflorens, the related non-accumulator (nA) species.

RESULTS

The study of the diversity and specificity of fungal amplicon sequence variants (ASVs) reveals a structuring of fungal communities at both the plant phenotype and compartment levels. In contrast, the structure of bacterial communities was primarily shaped by the belowground compartments. Additionally, we observed a lower diversity in the bacterial communities of the aboveground compartments of each species. For each plant species, we highlighted a distinct global microbial signature (biomarkers), as well as compartment-specific microbial associations.

CONCLUSION

To our knowledge, this study is the first to systematically compare the microbiomes associated with different compartments of New Caledonian metallophyte species growing on the same substrate and under identical environmental conditions but exhibiting different adaptive phenotypes. Our results reveal distinct microbial biomarkers between the Ni-hyperaccumulator and non-accumulator Psychotria species. Most of the highlighted biomarkers are abundant in various plants under metal stress and may contribute to improving the phytoextraction or phytostabilization processes. They are also known to tolerate heavy metals and enhance metal stress tolerance in plants. The present findings highlight that the microbial perspective is essential for better understanding the mechanisms of hyperaccumulation and exclusion at the whole-plant level. Video Abstract.

The impact of abandoned iron ore on the endophytic bacterial communities and functions in the root systems of three major crops in the local area

Introduction

Global mining activities have significant impacts on ecosystems, but most studies have focused only on the relationship between soil physicochemical properties and microbial diversity in soils. The present study provides an insight into the effects of mining activities on soil physico-chemical properties and endophytic bacterial community composition in the rhizosphere of three different crops.

Methods

Musa basjoo Siebold L., Amygdalus persica L., and Triticum aestivum L. were collected from the inter-root soils and plant roots to determine the soil physicochemical properties and endophytic bacterial communities in the root system.

Results

The results showed that mining resulted in soil acidification, altered trace element content and increased organic carbon. There was an increase in the Ascomycota and Actinobacteria phylum of crop root bacteria. Interestingly, the chao1 and shannon indices of the root endophytes of the mining crop were significantly elevated compared to the contro (p < 0.05). Among them, Musa basjoo Siebold showed the highest level of community richness in the mining environment. The mining environment resulted in functional enrichment of histidine kinases and oxidoreductases in the bacterial community. The total potassium (TK) content in the soil, as well as the Fe and Pb content, were positively correlated with the α-diversity index and Streptomyces. Zn and Ti content were significantly negatively correlated with the α-diversity index.

Discussion

This study provides data support for exploring the mechanisms of plant response to the mining environment and developing ecological restoration strategies for mining areas.