Critical transition of soil microbial diversity and composition triggered by plant rhizosphere effects

Green manure plants enhance atrazine degradation in agriculture soil through modulating rhizosphere microbial communities

The widespread use of atrazine in agriculture threatens soil health and the safety of agricultural products. In this study, the removal and mechanism of green manure plants (GMPs) hairy vetch (Vicia villosa Roth, VV) and ryegrass (Lolium perenne L., LP) to atrazine were investigated. The results showed that VV and LP show a certain tolerance to 5-25 mg/kg atrazine contamination compared to VV and LP without atrazine (VV0 and LP0), with LP exhibiting higher tolerance. Moreover, compared to CK, VV and LP significantly promoted the removal of atrazine by 13.49%∼26.41% and 13.98%∼23.42%, respectively. VV was more effective at lower concentrations (5-10 mg/kg), while LP showed better results at 25 mg/kg. Soil enzyme activities (catalase and urease), as well as bacterial abundance and diversity, were significantly increased by VV and LP treatments. LP had a stronger effect. The function analysis revealed that VV enhances the Cell growth and death pathway in the rhizosphere soil, while LP primarily boosts the Replication and repair pathway to cope with atrazine stress. This difference likely results from the distinct root structures of the two plants, which create varying rhizosphere environments. Additionally, VV and LP upregulate the Atrazine degradation pathway by enriching atrazine-degrading bacteria, thereby promoting atrazine removal. VV growth was affected under 25 mg/kg atrazine treatment, which may lead to lower Atrazine degradation pathway abundance in the rhizosphere compared to LP. This study provides a theoretical basis for selecting plant species for the remediation of atrazine-contaminated soils.

Genotypic Identification of Trees Using DNA Barcodes and Microbiome Analysis of Rhizosphere Microbial Communities

DNA barcodes can provide accurate identification of plants. We used previously reported DNA primers targeting the internal transcribed spacer (ITS1) region of the nuclear ribosomal cistron, internal transcribed spacer (ITS2), and chloroplast trnL (UAA) intron to identify four trees at Bergen Community College. Two of the four trees were identified as Acer rubrum and Fagus sylvatica. However, Quercus was only identified at the genus level, and the fourth tree did not show similar identification between barcodes. Next-generation sequencing of 16S rRNA genes showed that the predominant bacterial communities in the rhizosphere mainly consisted of the Pseudomonadota, Actinomycetota, Bacteroidota, and Acidobacteriota. A. rubrum showed the most diverse bacterial community while F. sylvatica was less diverse. The genus Rhodoplanes showed the highest relative bacterial abundance in all trees. Fungal ITS sequence analysis demonstrated that the communities predominantly consisted of the Ascomycota and Basidiomycota. Quercus showed the highest fungi diversity while F. sylvatica showed the lowest. Russula showed the highest abundance of fungi genera. Average similarity values in the rhizosphere for fungi communities at the phylum level were higher than for bacteria. However, at the genus level, bacterial communities showed higher similarities than fungi. Similarity values decreased at lower taxonomical levels for both bacteria and fungi, indicating each tree has selected for specific bacterial and fungal communities. This study confirmed the distinctiveness of the microbial communities in the rhizosphere of each tree and their importance in sustaining and supporting viability and growth but also demonstrating the limitations of DNA barcoding with the primers used in this study to identify genus and species for some of the trees. The optimization of DNA barcoding will require additional DNA sequences to enhance the resolution and identification of trees at the study site.

Cereals can trap endophytic bacteria with potential beneficial traits when grown ex-situ in harsh soils

Microbial communities associated with plants growing in harsh conditions, including salinity and water deficiency, have developed adaptive features which permit them to grow and survive under extreme environmental conditions. In the present study, an ex-situ plant trapping method has been applied to collect the culturable microbial diversity associated with the soil from harsh and remote areas. Oryza sativa cv. Baldo and Triticum durum Primadur plants were used as recruiters, while the soil surrounding the roots of Oryza glaberrima plants from remote regions of Mali (West Africa) was used as substrate for their growth. The endophytic communities recruited by the two plant species belonged to Proteobacteria and Firmicutes, and the dominant genera were Bacillus, Kosakonia, and Enterobacter. These endophytes were characterized by analyzing some of the most common plant growth promoting traits. Halotolerant, inorganic phosphate-solubilizing and N-fixing strains were found, and some of them simultaneously showing these three traits. We verified that 'Baldo' recruited mostly halotolerant and P-solubilizers endophytes, while the endophytes selected by 'Primadur' were mainly N-fixers. The applied ex-situ plant trapping method allowed to isolate endophytes with potential beneficial traits that could be applied for the improvement of rice and wheat growth under adverse environmental conditions.