Response of the plant core microbiome to Fusarium oxysporum infection and identification of the pathobiome

Core hyphosphere microbiota of Fusarium oxysporum f. sp. niveum

BACKGROUND

Bacteria and fungi are dynamically interconnected, leading to beneficial or antagonistic relationships with plants. Within this interkingdom interaction, the microbial community directly associated with the pathogen make up the pathobiome. While the overall soil bacterial community associated with Fusarium wilt diseases has been widely examined, the specific bacterial populations that directly interact with the Fusarium wilt pathogens are yet to be discovered. In this study, we define the bacterial community associated with the hyphae of Fusarium oxysporum f. sp. niveum race 2 (FON2). Using the 16S rRNA gene metabarcoding, we describe the hyphosphere pathobiome of three isolates of FON2.

RESULTS

Our results show a core microbiome that is shared among the three tested hyphospheres. The core hyphosphere community was made up of 15 OTUs (Operational Taxonomic Units) that were associated with all three FON2 isolates. This core consisted of bacterial members of the families, Oxalobacteraceae, Propionibacteriaceae, Burkholderiaceae, Micrococcaceae, Bacillaceae, Comamonadaceae, Pseudomonadaceae and unclassified bacteria. The hyphosphere of FON2 was dominated by order Burkholderiales. While all three isolate hyphospheres were dominated by these taxa, the specific OTU differed. We also note that while the dominant OTU of one hyphosphere might not be the largest OTU for other hyphospheres, they were still present across all the three isolate hyphospheres. Additionally, in the correlation and co-occurrence analysis the most abundant OTU was negatively correlated with most of the other OTU populations within the hyphosphere.

CONCLUSIONS

The study indicates a core microbiota associated with FON2. These results provide insights into the microbe-microbe dynamic of the pathogen's success and its ability to recruit a core pathobiome. Our research promotes the concept of pathogens not being lone invaders but recruits from the established host microbiome to form a pathobiome.

Metagenomic insight to apprehend the fungal communities associated with leaf blight of Welsh onion in Taiwan

Plants are associated with a large diversity of microbes, and these complex plant-associated microbial communities are critical for plant health. Welsh onion (Allium fistulosum L.) is one of the key and oldest vegetable crops cultivated in Taiwan. The leaf of the Welsh onion is one of the famous spices in Taiwanese cuisine, thus, it is crucial to control foliar diseases. In recent years, Welsh onion cultivation in Taiwan has been severely threatened by the occurrence of leaf blight disease, greatly affecting their yield and quality. However, the overall picture of microbiota associated with the Welsh onion plant is still not clear as most of the recent etiological investigations were heavily based on the isolation of microorganisms from diseased plants. Therefore, studying the diversity of fungal communities associated with the leaf blight symptoms of Welsh onion may provide information regarding key taxa possibly involved in the disease. Therefore, this investigation was mainly designed to understand the major fungal communities associated with leaf blight to identify key taxa potentially involved in the disease and further evaluate any shifts in both phyllosphere and rhizosphere mycobiome assembly due to foliar pathogen infection by amplicon sequencing targeting the Internal Transcribed Spacer (ITS) 1 region of the rRNA. The alpha and beta-diversity analyses were used to compare the fungal communities and significant fungal groups were recognized based on linear discriminant analyses. Based on the results of relative abundance data and co-occurrence networks in symptomatic plants we revealed that the leaf blight of Welsh onion in Sanxing, is a disease complex mainly involving Stemphylium and Colletotrichum taxa. In addition, genera such as Aspergillus, Athelia and Colletotrichum were abundantly found associated with the symptomatic rhizosphere. Alpha-diversity in some fields indicated a significant increase in species richness in the symptomatic phyllosphere compared to the asymptomatic phyllosphere. These results will broaden our knowledge of pathogens of Welsh onion associated with leaf blight symptoms and will assist in developing effective disease management strategies to control the progress of the disease.

The core microbiota across the green lineage

The study of plant-microbe interactions and the characterization of plant-associated microbiota has been the focus of plant researchers in the last decades due to its importance for plant health in natural conditions. Here, I explore the persistent core microbiota associated with different plant species and across different environments by performing a meta-analysis of publicly available datasets. Intra-specific analyses revealed that diverse plant genotypes growing in similar habitats interact with a common set of microbial groups but that some of these core groups are species- or environment-specific. Furthermore, interspecific meta-analysis demonstrates the conservation of seven bacterial orders across diverse photosynthetic organisms, including microalgae, suggesting a conserved capacity for interaction with these core microbes throughout evolutionary history. However, the specific functions of these core members and whether these functions are conserved across hosts remain largely unexplored. I therefore discuss the importance of understanding the roles of the core microbiota and propose future research directions, including the exploration of microbial interactions across different kingdoms. By investigating the core microbiota and its functions, it will be possible to leverage this knowledge for sustainable agricultural management and conservation goals.

Plants and endophytes interaction: a "secret wedlock" for sustainable biosynthesis of pharmaceutically important secondary metabolites

Many plants possess immense pharmacological properties because of the presence of various therapeutic bioactive secondary metabolites that are of great importance in many pharmaceutical industries. Therefore, to strike a balance between meeting industry demands and conserving natural habitats, medicinal plants are being cultivated on a large scale. However, to enhance the yield and simultaneously manage the various pest infestations, agrochemicals are being routinely used that have a detrimental impact on the whole ecosystem, ranging from biodiversity loss to water pollution, soil degradation, nutrient imbalance and enormous health hazards to both consumers and agricultural workers. To address the challenges, biological eco-friendly alternatives are being looked upon with high hopes where endophytes pitch in as key players due to their tight association with the host plants. The intricate interplay between plants and endophytic microorganisms has emerged as a captivating subject of scientific investigation, with profound implications for the sustainable biosynthesis of pharmaceutically important secondary metabolites. This review delves into the hidden world of the "secret wedlock" between plants and endophytes, elucidating their multifaceted interactions that underpin the synthesis of bioactive compounds with medicinal significance in their plant hosts. Here, we briefly review endophytic diversity association with medicinal plants and highlight the potential role of core endomicrobiome. We also propose that successful implementation of in situ microbiome manipulation through high-end techniques can pave the way towards a more sustainable and pharmaceutically enriched future.

More Than the Sum of Its Parts: Unlocking the Power of Network Structure for Understanding Organization and Function in Microbiomes

Plant and soil microbiomes are integral to the health and productivity of plants and ecosystems, yet researchers struggle to identify microbiome characteristics important for providing beneficial outcomes. Network analysis offers a shift in analytical framework beyond "who is present" to the organization or patterns of coexistence between microbes within the microbiome. Because microbial phenotypes are often significantly impacted by coexisting populations, patterns of coexistence within microbiomes are likely to be especially important in predicting functional outcomes. Here, we provide an overview of the how and why of network analysis in microbiome research, highlighting the ways in which network analyses have provided novel insights into microbiome organization and functional capacities, the diverse network roles of different microbial populations, and the eco-evolutionary dynamics of plant and soil microbiomes.

Home-field advantage affects the local adaptive interaction between Andropogon gerardii ecotypes and root-associated bacterial communities

Due to climate change, drought frequencies and severities are predicted to increase across the United States. Plant responses and adaptation to stresses depend on plant genetic and environmental factors. Understanding the effect of those factors on plant performance is required to predict species' responses to environmental change. We used reciprocal gardens planted with distinct regional ecotypes of the perennial grass Andropogon gerardii adapted to dry, mesic, and wet environments to characterize their rhizosphere communities using 16S rRNA metabarcode sequencing. Even though the local microbial pool was the main driver of these rhizosphere communities, the significant plant ecotypic effect highlighted active microbial recruitment in the rhizosphere, driven by ecotype or plant genetic background. Our data also suggest that ecotypes planted at their homesites were more successful in recruiting rhizosphere community members that were unique to the location. The link between the plants' homesite and the specific local microbes supported the "home field advantage" hypothesis. The unique homesite microbes may represent microbial specialists that are linked to plant stress responses. Furthermore, our data support ecotypic variation in the recruitment of congeneric but distinct bacterial variants, highlighting the nuanced plant ecotype effects on rhizosphere microbiome recruitment. These results improve our understanding of the complex plant host-soil microbe interactions and should facilitate further studies focused on exploring the functional potential of recruited microbes. Our study has the potential to aid in predicting grassland ecosystem responses to climate change and impact restoration management practices to promote grassland sustainability. IMPORTANCE In this study, we used reciprocal gardens located across a steep precipitation gradient to characterize rhizosphere communities of distinct dry, mesic, and wet regional ecotypes of the perennial grass Andropogon gerardii. We used 16S rRNA amplicon sequencing and focused oligotyping analysis and showed that even though location was the main driver of the microbial communities, ecotypes could potentially recruit distinct bacterial populations. We showed that different A. gerardii ecotypes were more successful in overall community recruitment and recruitment of microbes unique to the "home" environment, when growing at their "home site." We found evidence for "home-field advantage" interactions between the host and host-root-associated bacterial communities, and the capability of ecotypes to recruit specialized microbes that were potentially linked to plant stress responses. Our study aids in a better understanding of the factors that affect plant adaptation, improve management strategies, and predict grassland function under the changing climate.

Soil and Phytomicrobiome for Plant Disease Suppression and Management under Climate Change: A Review

The phytomicrobiome plays a crucial role in soil and ecosystem health, encompassing both beneficial members providing critical ecosystem goods and services and pathogens threatening food safety and security. The potential benefits of harnessing the power of the phytomicrobiome for plant disease suppression and management are indisputable and of interest in agriculture but also in forestry and landscaping. Indeed, plant diseases can be mitigated by in situ manipulations of resident microorganisms through agronomic practices (such as minimum tillage, crop rotation, cover cropping, organic mulching, etc.) as well as by applying microbial inoculants. However, numerous challenges, such as the lack of standardized methods for microbiome analysis and the difficulty in translating research findings into practical applications are at stake. Moreover, climate change is affecting the distribution, abundance, and virulence of many plant pathogens, while also altering the phytomicrobiome functioning, further compounding disease management strategies. Here, we will first review literature demonstrating how agricultural practices have been found effective in promoting soil health and enhancing disease suppressiveness and mitigation through a shift of the phytomicrobiome. Challenges and barriers to the identification and use of the phytomicrobiome for plant disease management will then be discussed before focusing on the potential impacts of climate change on the phytomicrobiome functioning and disease outcome.

Univariate and Multivariate Statistical Analysis of Microbiome Data: An Overview

Microbiome data is high dimensional, sparse, compositional, and over-dispersed. Therefore, modeling microbiome data is very challenging and it is an active research area. Microbiome analysis has become a progressing area of research as microorganisms constitute a large part of life. Since many methods of microbiome data analysis have been presented, this review summarizes the challenges, methods used, and the advantages and disadvantages of those methods, to serve as an updated guide for those in the field. This review also compared different methods of analysis to progress the development of newer methods.