The phyllosphere microbiome shifts toward combating melanose pathogen.

BACKGROUND: Plants can recruit beneficial microbes to enhance their ability to defend against pathogens. However, in contrast to the intensively studied roles of the rhizosphere microbiome in suppressing plant pathogens, the collective community-level change and effect of the phyllosphere microbiome in response to pathogen invasion remains largely elusive. RESULTS: Here, we integrated 16S metabarcoding, shotgun metagenomics and culture-dependent methods to systematically investigate the changes in phyllosphere microbiome between infected and uninfected citrus leaves by Diaporthe citri, a fungal pathogen causing melanose disease worldwide. Multiple microbiome features suggested a shift in phyllosphere microbiome upon D. citri infection, highlighted by the marked reduction of community evenness, the emergence of large numbers of new microbes, and the intense microbial network. We also identified the microbiome features from functional perspectives in infected leaves, such as enriched microbial functions for iron competition and potential antifungal traits, and enriched microbes with beneficial genomic characteristics. Glasshouse experiments demonstrated that several bacteria associated with the microbiome shift could positively affect plant performance under D. citri challenge, with reductions in disease index ranging from 65.7 to 88.4%. Among them, Pantoea asv90 and Methylobacterium asv41 identified as "recruited new microbes" in the infected leaves, exhibited antagonistic activities to D. citri both in vitro and in vivo, including inhibition of spore germination and/or mycelium growth. Sphingomonas spp. presented beneficial genomic characteristics and were found to be the main contributor for the functional enrichment of iron complex outer membrane receptor protein in the infected leaves. Moreover, Sphingomonas asv20 showed a stronger suppression ability against D. citri in iron-deficient conditions than iron-sufficient conditions, suggesting a role of iron competition during their antagonistic action. CONCLUSIONS: Overall, our study revealed how phyllosphere microbiomes differed between infected and uninfected citrus leaves by melanose pathogen, and identified potential mechanisms for how the observed microbiome shift might have helped plants cope with pathogen pressure. Our findings provide novel insights into understanding the roles of phyllosphere microbiome responses during pathogen challenge. Video abstract.

Microbial communities and soil chemical features associated with commercial production of the medicinal mushroom Ganoderma lingzhi in soil.

Crop production, including mushroom farming, may cause significant changes to the underlying substrates which in turn, can influence crop quality and quantity during subsequent years. Here in this study, we analyzed the production of the medicinal mushroom Ganoderma lingzhi and the associated soil microbial communities and soil chemical features over 24 months from April 2015 to April 2017. This Basidiomycete mushroom, known as Lingzhi in China, is commonly found on dead trees and wood logs in temperate and subtropical forests. Its economic and medicinal importance have propelled the development of a diversity of cultivation methods. The dominant method uses wood logs as the main substrate, which after colonization by Lingzhi mycelia, are buried in the soil to induce fruiting. The soil microbial communities over the 24 months were analyzed using the Illumina HiSeq platform targeting a portion of the bacterial 16S rRNA gene and the fungal internal transcribed spacer 1 (ITS1). Overall, a significant reduction of Lingzhi yield was observed over our experimentation period. Interestingly, temporal changes in soil microbial compositions were detected during the 24 months, with the fungal community showing more changes than that of bacteria in terms of both species richness and the relative abundance of several dominant species after each fruiting. The soil chemical features also showed significant changes, with decreasing soil nitrogen and phosphorus concentrations and increasing soil pH and iron content after each fruiting. We discuss the implications of our results in sustainable Lingzhi production in soil.

Metabarcoding reveals differences in fungal communities between unflooded versus tidal flat soil in coastal saline ecosystem.

In the saline-affected ecosystem, fungi have huge potential to promote growth, induce disease resistance and enhance tolerance against salt-stress of host plants. Since areas of plowland are gradually decreasing, the reclamation of coastal saline lands could play a crucial role in maintaining agricultural productivity and crop security globally. Therefore, it is of great significance to explore the fungal diversity in the coastal saline ecosystem. Here, we collected saline soil samples from unflooded areas and tidal flat areas, the two typical distinct landforms in coastal saline ecosystems, and used ITS metabarcoding to depict the diversity of fungal communities. We found that fungal species evenness had a remarkably higher variation from the tidal flat compared to unflooded soil samples. Furthermore, we also confirmed that the fungal niches differentiation reports in the coastal saline ecosystem. Our ITS based DNA sequencing revealed that both unflooded and tidal flat soil were mainly composed of amplicon sequence variants (ASVs) belonging to Ascomycota (93.43% and 86.91% respectively). Based on our findings, understanding the associations and distinctions of fungal microbiome between unflooded soil and tidal flat could provide the basis for the development of reclamation in coastal saline lands.