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Functional Microbiome for Crop Improvement Under a Changing Environment
Abstract
In a context of a changing environment, it is crucial to maximize our knowledge on all the mechanisms involved in plant microbiome interactions at the genetic, physiological, and ecological levels. This chapter reviews some recent advances in plant microbiome investigations and describes potential applications of such associations for the mitigation of both abiotic and biotic stresses to improve crop health and productivity. Understanding the full potential of microbes in the ecosystem functioning in general and their complex beneficial interactions in improving agriculture productivity in particular requires the development and improvement of compatible tools that can be verified in biological assays, always bearing in mind their reproducibility in situ on different scales. Progress in the engineering microbiome have made it possible to show how meta‐omics (metataxonomic, metagenomics, metatranscriptomics, and metaproteomics) can be potentially powerful tools to gain deeper knowledge of the functional capabilities of the microbiome and how they can shape ecosystems.
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This book presents topics on the development, improvement and commercialization of fungi for the biological control of pests, weeds and diseases which are of economic importance. Common themes such as production, formulation and application of technologies, biosafety, risk assessment and registration requirements are all covered. The book attempts to bring together scientists, industry and government agencies involved in all aspects of fungal biological control agents for the first time.
The phyllosphere microbiome is increasingly recognised as an influential component of plant physiology, yet it remains unclear whether stable host-microbe associations generally exist in the phyllosphere. Leptospermum scoparium (mānuka) is a tea tree indigenous to New Zealand, and honey derived from mānuka is widely known to possess unique antimicrobial properties. However, the host physiological traits associated with these antimicrobial properties vary widely, and the specific cause of such variation has eluded scientists despite decades of research. Notably, the mānuka phyllosphere microbiome remains uncharacterised, and its potential role in mediating host physiology has not been considered. Working within the prevailing core microbiome conceptual framework, we hypothesise that the phyllosphere microbiome of mānuka exhibits specific host association patterns congruent with those of a microbial community under host selective pressure (null hypothesis: the mānuka phyllosphere microbiome is recruited stochastically from the surrounding environment). To examine our hypothesis, we characterised the phyllosphere and associated soil microbiomes of five distinct and geographically distant mānuka populations across the North Island of New Zealand. We identified a habitat-specific and relatively abundant core microbiome in the mānuka phyllosphere, which was persistent across all samples. In contrast, non-core phyllosphere microorganisms exhibited significant variation across individual host trees and populations that was strongly driven by environmental and spatial factors. Our results demonstrate the existence of a dominant and ubiquitous core microbiome in the phyllosphere of mānuka, supporting our hypothesis that phyllosphere microorganisms of mānuka exhibit specific host association and potentially mediate physiological traits of this nationally and culturally treasured indigenous plant. In addition, our results illustrate biogeographical patterns in mānuka phyllosphere microbiomes and offer insight into factors contributing to phyllosphere microbiome assembly.
The phyllosphere supports a tremendous diversity of microbes, which have the potential to influence plant biogeography and ecosystem function. Although biocontrol agents (BCAs) have been used extensively for controlling plant diseases, the ecological effects of BCAs on phyllosphere bacteria and the relationships between phyllosphere community and plant health are poorly understood. In this study, we explored the control efficiency of two BCA communities on bacterial wildfire disease by repeatedly spraying BCAs on tobacco leaves. The results of field tests showed that BCAs used in our study, especially BCA_B, had remarkable control effects against tobacco wildfire disease. The higher control efficiency of BCA_B might be attributed to a highly diverse and complex community in the phyllosphere. By 16S ribosomal RNA gene sequencing, we found that phyllosphere microbial community, including community diversity, taxonomic composition and microbial interactions, changed significantly by application of BCAs. According to the correlation analysis, it showed that wildfire disease infection of plants was negatively related to phyllosphere microbial diversity, indicating a highly diverse community in the phyllosphere might prevent pathogens invasion and colonization. In addition, we inferred that a more complex network in the phyllosphere might be beneficial for decreasing the chances of bacterial wildfire outbreak, and the genera of Pantoea and Sphingomonas might play important roles in wildfire disease suppression. These correlations between phyllosphere community and plant health will improve our understanding on the ecological function of phyllosphere community on plants.
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The online version of this article (10.1186/s13568-019-0765-x) contains supplementary material, which is available to authorized users.
Numerous reforestation projects have been conducted to improve soil fertility in degraded forests, often causing alterations to the soil microbial communities. However, it remains unclear whether microbial functional groups are affected and how these groups correlate with an increase in the nutrient contents during reforestation. We investigated the abundance and composition of free-living nitrogen-fixing microorganisms (diazotrophs) by quantifying and sequencing the marker gene nifH in bulk soils from five reforestation approaches, including legumes and non-legumes, in subtropical China. The relationships between diazotrophic community attributes and soil nitrogen (N) content [NO3⁻, NH4⁺, and microbial biomass N (MBN)] were examined under various approaches. Abundance of diazotrophs was highest in the native tree plantation (Schima spp. and Michelia macclurei) and Acacia mangium monoculture (AM), and lowest in the Pinus massoniana monoculture. The diazotrophic abundance correlated positively with soil organic matter and water content while there was a negative correlation to pH. The composition of diazotrophic community differed significantly among the five reforestation approaches examined and was closely correlated with variations in soil pH, NH4⁺ and water content. Diazotrophic community composition was closely related to soil NH4⁺ content, whereas abundance was not. The AM contained higher NH4⁺, NO3⁻ and MBN contents than the other reforestation approaches, which may be associated with the indicator species of diazotrophs (Actinobacteria, Proteobacteria, and Firmicutes). However, there were more indicator species of Proteobacteria in the mixed Acacia plantation (Acacia mangium and Acacia crassicarpa) than in AM, which might have contributed to the remarkedly lower N content compared to AM. Overall, the soil N content under reforestation appeared to be more related to the composition of diazotroph community than to the abundance of diazotrophs.
Microbiomes influence plant establishment, development, nutrient acquisition, pathogen defense, and health. Plant microbiomes are shaped by interactions between the microbes and a selection process of host plants that distinguishes between pathogens, commensals, symbionts and transient bacteria. In this work, we explore the microbiomes through massive sequencing of the 16S rRNA genes of microbiomes two Marchantia species of liverworts. We compared microbiomes from M. polymorpha and M. paleacea plants collected in the wild relative to their soils substrates and from plants grown in vitro that were established from gemmae obtained from the same populations of wild plants. Our experimental setup allowed identification of microbes found in both native and in vitro Marchantia species. The main OTUs (97% identity) in Marchantia microbiomes were assigned to the following genera: Methylobacterium, Rhizobium, Paenibacillus, Lysobacter, Pirellula, Steroidobacter, and Bryobacter. The assigned genera correspond to bacteria capable of plant-growth promotion, complex exudate degradation, nitrogen fixation, methylotrophs, and disease-suppressive bacteria, all hosted in the relatively simple anatomy of the plant. Based on their long evolutionary history Marchantia is a promising model to study not only long-term relationships between plants and their microbes but also the transgenerational contribution of microbiomes to plant development and their response to environmental changes.
We face major agricultural challenges that remain a threat for global food security. Soil microbes harbor enormous potentials to provide sustainable and economically favorable solutions that could introduce novel approaches to improve agricultural practices and, hence, crop productivity. In this review we give an overview regarding the current state-of-the-art of microbiome research by discussing new technologies and approaches. We also provide insights into fundamental microbiome research that aim to provide a deeper understanding of the dynamics within microbial communities, as well as their interactions with different plant hosts and the environment. We aim to connect all these approaches with potential applications and reflect how we can use microbial communities in modern agricultural systems to realize a more customized and sustainable use of valuable resources (e.g., soil).
Soil microbes that colonize plant roots and are responsive to differences in plant genotype remain to be ascertained for agronomically important crops. From a very large-scale longitudinal field study of 27 maize inbred lines planted in three fields, with partial replication 5 y later, we identify root-associated microbiota exhibiting reproducible associations with plant genotype. Analysis of 4,866 samples identified 143 operational taxonomic units (OTUs) whose variation in relative abundances across the samples was significantly regulated by plant genotype, and included five of seven core OTUs present in all samples. Plant genetic effects were significant amid the large effects of plant age on the rhizosphere microbiome, regardless of the specific community of each field, and despite microbiome responses to climate events. Seasonal patterns showed that the plant root microbiome is locally seeded, changes with plant growth, and responds to weather events. However, against this background of variation, specific taxa responded to differences in host genotype. If shown to have beneficial functions, microbes may be considered candidate traits for selective breeding.
Agriculture sector is often hit badly by various abiotic environmental stresses resulting in huge economic losses. It is an important technical challenge for agriculture science community to facilitate adaptation of crop plants to abiotic stresses such as high temperatures, draught, salinity, pathogens, nutrient limitation, and other climatic disasters. The abiotic stresses encountered by crop plants are routinely managed by widespread use of fertilizers and pesticides which enhance the growth and survival of plants under stress conditions as they provide protection against nutrient limitation as well as attack by potential microbial pathogens. The pretreatment of seeds with fertilizers and pesticides has also been shown to enhance stress tolerance in various laboratory studies. As alternative strategy for the future, several research studies have been carried out to develop stress-resistant transgenic crop varieties. However, use of transgenic crops has not been widely accepted due to various ethical and scientific reasons. This situation has led to an unprecedented opportunity for progress in plant stress management for crops by understanding, engineering, and exploiting the plant-microbe interaction within rhizospheric regions. Recent development with culture-independent studies on microbial communities has clearly indicated that composition, diversity, and dynamics of the rhizospheric soil microflora play a vital role in plant growth promotion under stressed environment. The rhizospheric microbial community contributes to the plant stress response not only via improving the availability of nutrition and resources, but also by mitigating the abiotic stresses encountered by the concerned plant. Thus, rhizospheric microbial diversity can be the most critical component for abiotic stress tolerance in crop plants and could be exploited as an exemplary means for abiotic stress management necessary for sustainable agriculture. This chapter provides an insight into the literature available pertaining to role of rhizospheric diversity in abiotic stress management in crop plants, comparison of cultivable and non-cultivable rhizospheric microbial diversity, merits and demerits of available stress management strategies and future prospective for use of rhizospheric microbial diversity as abiotic stress management system.