Identifying the Specific Root Microbiome of the Hyperaccumulator Noccaea brachypetala Growing in Non-metalliferous Soils

Trade-offs and adaptation to metalliferous soils: The role of soil microbiome in metal tolerance and uptake in Arabidopsis halleri ecotypes from a reciprocal transplant experiment

Soil contamination with trace metal elements is a worldwide issue, prompting research on plant species capable of hyperaccumulating metals to reduce soil toxicity. Previous research suggests that both plant species and their populations can affect soil microbial communities, yet little is known about how different populations of hyperaccumulator species influence these microbial communities to enhance metal-uptake and tolerance. This study evaluated the effect of soil origin, soil microbiome, and plant population on phytoextraction efficiencies of Cd and Zn among four A. halleri populations: two each from metalliferous and non-metalliferous sites. In a controlled transplant experiment, clonal replicates of A. halleri were grown in native and three non-native soils for six months. Biogeochemical analyses of plants and soils were conducted, alongside sequencing of root-associated soil bacterial/archaeal and fungal DNA. Soil treatments primarily differed in pH, total Cd, Pb, and Zn, as well as acid and alkaline phosphatase enzyme activities. A combined effect of soil origin and population was noted for arylsulfatase and β-glucosidase activities, as well as ammonium and nitrate concentrations. Both non-metallicolous and metallicolous populations accumulated high levels of Cd and Zn in metalliferous soils with the non-metallicolous population NM_PL14 outperforming the metallicolous populations in Zn hyperaccumulation. Interestingly, non-metallicolous populations grown in metalliferous soils exhibited no trade-offs in plant performance despite higher Cd and Zn accumulation. Soil origin had a stronger effect on the bacterial/archaeal and fungal community composition than plant ecotype. Partial least square regression models explained 66 % and 79 % of the variability in A. halleri Cd and Zn hyperaccumulation. There was a positive association between Zn-uptake and specific microbial taxa (e.g., Cornebacteriales, Microbacteriaceae, Propionibacteriales, Rhizobiaceae, Basidiomycota, Oidiodendron, Phallaceae) and functional activity (e.g., arylsulfatase, S oxidation) in metalliferous soils. Taken together, our findings suggest that non-metallicolous A. halleri populations may be better suited for Zn phytoextraction applications.

Rhizobiome diversity of field-collected hyperaccumulating Noccaea sp

Hyperaccumulating plants are able to (hyper)accumulate high concentrations of metal(loid)s in their above-ground tissues without any signs of toxicity. Studies on the root-associated microbiome have been previously conducted in relation to hyperaccumulators, yet much remains unknown about the interactions between hyperaccumulating hosts and their microbiomes, as well as the dynamics within these microbial communities. Here, we assess the impact of the plant host on shaping microbial communities of three naturally occurring populations of Noccaea species in Slovenia: Noccaea praecox and co-occurring N. caerulescens from the non-metalliferous site and N. praecox from the metalliferous site. We investigated the effect of metal enrichment on microbial communities and explored the interactions within microbial groups and their environment. The abundance of bacterial phyla was more homogeneous than fungal classes across all three Noccaea populations and across the three root-associated compartments (roots, rhizosphere, and bulk soil). While most fungal and bacterial Operational Taxonomic Units (OTUs) were found at both sites, the metalliferous site comprised more unique OTUs in the root and rhizosphere compartments than the non-metalliferous site. In contrast to fungi, bacteria exhibited differentially significant abundance between the metalliferous and non-metalliferous sites as well as statistically significant correlations with most of the soil parameters. Results revealed N. caerulescens had the highest number of negative correlations between the bacterial phyla, whereas the population from the metalliferous site had the fewest. This decrease was accompanied by a big perturbation in the bacterial community at the metalliferous site, indicating increased selection between the bacterial taxa and the formation of potentially less stable rhizobiomes. These findings provide fundamentals for future research on the dynamics between hyperaccumulators and their associated microbiome.

Metaphors as design tools for microbial consortia: An analysis of recent peer-reviewed literature

Single engineered microbial species cannot always conduct complex transformations, while complex, incompletely defined microbial consortia have heretofore been suited to a limited range of tasks. As biodesigners bridge this gap with intentionally designed microbial communities, they will, intentionally or otherwise, build communities that embody particular ideas about what microbial communities can and should be. Here, we suggest that metaphors-ideas about what microbial communities are like-are therefore important tools for designing synthetic consortia-based bioreactors. We identify a range of metaphors currently employed in peer-reviewed microbiome research articles, characterizing each through its potential structural implications and distinctive imagery. We present this metaphor catalogue in the interest of, first, making metaphors visible as design choices, second, enabling deliberate experimentation with them towards expanding the potential design space of the field, and third, encouraging reflection on the goals and values they embed.

Assessing heavy metal contamination in Amomum villosum Lour. fruits from plantations in Southern China: Soil-fungi-plant interactions

Amomum villosum Lour. fruit is a common healthy food widely cultivated in southern China. Heavy metal contamination of farmland soils has becomes a serious environmental concern in China. Heavy metals in soil can be introduced into the food chain and pose health risks to humans. However, microbial communities may play beneficial roles in plants grown in metal-polluted soils. This study aimed to assess the potential health risks of heavy metals in soils and A. villosum fruits from different production areas and to explore the soil-microbe-plant regulation pattern for heavy metals in A. villosum fruits. Soil and A. villosum fruit samples were collected from nine planting fields in four provinces of southern China. The results showed that soils from seven areas were polluted with heavy metals to different degrees. Cr and Mn were the most serious contaminating elements. However, the accumulation of heavy metals in A. villosum fruit was negligible with no expected human health risks. Partial least squares path analysis of structural equation modeling showed that the accumulation of heavy metals in A. villosum fruits was influenced by multiple factors. More importantly, the PLS-SEM revealed that the heavy metal content in A. villosum fruits was indirectly affected by soil heavy metals through the regulation of the microbial community. Furthermore, some fungal phyla (e.g., Ascomycota and Chytridiomycota) and genera (e.g., Mucor) were related to the heavy metal content in the soil and in A. villosum fruits. The results of this study verified that soil fungal community play an important role in the accumulation of heavy metals in A. villosum fruits. Using fungi provides a potential biological strategy for reducing the health risk posed by heavy metals in food.