Plant Microbiome: Composition and Applications

Plant viruses and microbiomes are pivotal to plant health, growth, and their ability to withstand environmental challenges. However, the extent to which viruses engage in direct or indirect crosstalk with plant-associated microbial communities remains largely unexplored. Traditionally, plant viruses are considered as harmful agents that disrupt normal plant functions, but new research indicates they may also engage in complex interactions with the plant's microbiome. On the other hand, the plant microbiome, comprising a diverse assembly of bacteria, fungi, and other microbes, can influence the plant's responses to viral infections, potentially altering the course of the disease. Thus, we emphasize the intricate interplay between plant viruses and microbiomes, particularly how viruses might "communicate" with microbial communities to alter the host environment or bypass immune defenses. The mechanisms driving these interactions, such as virus-induced shifts in plant metabolism, signaling pathways, and immune responses that indirectly affect microbiome composition are also discussed. The beneficial effect of plant-associated microbial communities against viral infections and the strategy of microbiome-based approaches for managing viral diseases are also focused. By moving beyond the traditional view of pathogen-host interactions, this review will highlight the importance of considering the three-way relationship among plants, viruses, and microbiomes to advance our understanding of plant health and foster innovative solutions for sustainable agriculture.

Plants during their life cycle often come across multiple biotic and abiotic stress that mutilates their growth and productivity. As the world’s population is increasing gradually and the climate is changing at an alarming rate, the need for global food security has become the priority. Therefore, addressing approaches that can enhance food productivity sustainably and safeguard food availability in the future is the need of the hour. Plants possess an intrinsic defense mechanism to combat stressful environmental conditions but in severe conditions are unable to overcome persisting situations. To strengthen their defense system plants recruit associated beneficial microbiome that alleviates stresses and promotes plant growth. Plants select particular microorganisms mainly through the production of varied compounds via root exudates. The plant microbiome lives either as epiphytes in the rhizosphere and phyllosphere or as endophytes within living tissues and caters multiple beneficial effects. The plant microbiome shows resilience toward stress and promotes plant productivity through various mechanisms. These mechanisms include the production of antioxidants, antibiotics, phytohormones, exopolysaccharides, and cell wall degrading enzymes that lead to inhibition of pathogens, bioremediation of toxic metals, acquisition of nutrients, tolerance toward abiotic stress, and enhanced plant growth parameters. Engineering plant microbiome to enhance stress tolerance and plant growth may be the most sustainable approach that can ensure food security for the growing population. Thus, understanding and deciphering mechanisms employed by the plant microbiome is important to harness their potential.KeywordsRoot exudatesAntioxidantsCell wall degrading enzymesExopolysaccharidesEndophytesRhizosphere

Pesticide interference and additional effects on plant microbiomes

This chapter highlights the significance of microbiomes especially plant<br>microbiomes in the field of therapeutics. The Plant microbiome comprises epiphytes<br>and endophytes inhabiting the surface as well as inside of the tissues of the host. These<br>microbial communities occupy a well-defined habitat and perform various activities<br>developing certain interactions with the host such as commensalism, mutualism, and<br>parasitism. For the establishment and functioning of the plant microbiome, plant root<br>releases exudate according to the nutritional requirement of particular microbial<br>species. In response to the stimulus, microbes chemotactically move towards the roots,<br>colonize and move to other parts of the plant. Microbes also adopt certain mechanisms<br>not only to colonize and multiply in specific hosts but also to promote the growth of the<br>host by secreting various plant growth hormones and exopolysaccharides. The<br>numerous compounds produced by microbes make plants tolerant of biotic and abiotic<br>stresses. The microbial communities in plant microbiome have an active role in<br>maintaining the health, ecology and physiology of the host. As a major portion of the<br>world’s population is dependent on phytotherapeutic medicines according to the World<br>Health Organization, the pharmacological characteristics of major medicinal plants<br>such as Aesculus hippocastanum and Ginkgo biloba are described in detail. This<br>chapter highlights the significance of the core role of the microbiome associated with<br>plants in the synthesis of various medicinal compounds. The phytotherapeutic potential<br>of plant microbiome revealed that endophytes and epiphytes isolated from various plant<br>species showed great potential for the production of antimicrobial as well as antiinflammatory<br>substances. The medicinally rich compounds such as antibacterial<br>proteins, phenols, saponin glycosides, flavonoids, terpenoids, carbohydrates and fatty<br>acids isolated from plant-associated microbes have various applications in the<br>treatment of fetal diseases and also exhibit anti-inflammatory action. Certain public<br>concerns are raised about the side effects of medicinal plants used in phytotherapeutics.<br>A relevant case study about public concerns along with preventative measures such as<br>rigorous testing is provided in this chapter.<br>

Plants have many different microorganisms which have been proved to play pivotal role in plant health and to some extent in human health. They have proven effects in plant growth as well. Before 1980s, there was no substantial information available on plant microbiota. But now, a considerable amount of information can be found easily on the said topic. There is unprecedented potential in plant microbiota and has numerous functions in plant growth, production, and health. Owing to this, there is a dire need to conduct more research and bring microbial innovations into practice. In this regard considerable and sagacious thinking approach is needed in selection of needed microorganisms. Suitable plant breeding and farming practices lead to improved plant microbiome interaction and resultantly great benefits can be achieved by plant microbiota. This mini review presents, first, an introduction to plant microbiota, factors affecting plant microbiome, diversity of plant microbiota; and, secondly, focuses on the functions of rhizospheric plant microbiome, its effects on plant and human health, agricultural benefits and environmental advantages. The main databases used to structure this review were PubMed and Google Scholar.  

The plant microbiome is considered as an extended part of plant genome and performs number of key functions for plants such as stress tolerance, housekeeping activities, and nutrient availability. The plant microbiome can be further classified into soil dwelling microbes (rhizosphere soil microbiome), interior tissue inhabiting endophytes in compartments such as root, leaf, stem, flowers, and exterior surface-dwelling epiphytes. The plant microbiome assembly is driven by numerous factors such as soil edaphic properties and nutrients, plant compartments, plant genotype and climatic and geographic conditions. However, the ecological and evolutionary processes (e.g., host selection, host evolutionary relationship vs impacts of soil microbial diversity, climatic and soil factors) that underpin plant microbiome assembly remain unclear due to limited number of multi factorial studies addressing different drivers of plant microbiome assembly. Especially, there are limited studies which have focused on drivers of endophyte assemblies across multiple species. In my thesis, I have attempted to decipher impacts and mechanisms of various drivers of plant microbiome assembly across multiple plant species which includes trees, native and exotic Australian flora. I have performed multifactorial experiment which involves microbial profiling-based studies in different conditions such as managed plantation, a glasshouse experiment, and a large-scale field experiment across three different experiments. In summary, my thesis provides consistent and important insights into the different factors that govern microbiome assembly in plants. The key drivers of leaf and root microbiome assembly belong to host associated factors such as host identity, host phylogenetic relatedness, and interaction between host species whereas soil microbiome mainly respond to varying soil properties and microbial recruitment pool or initial soil microbial diversity. This thesis significantly advances the ecological and evolutionary processes of plant microbiome assemblies and opens up new areas of future fundamental (e.g., biochemical and molecular mechanisms of microbiome selection by host) and applied (compartment specific microbial tools (inoculants or SynComs) research in plant-microbiome discipline.

The assemblage of microbes that inhabit the plant as symbionts comprises the plant microbiome. The activities of plant roots have a great effect on the density and composition of bacteria and fungi growing around them, known as the rhizosphere effect. Plant–microbe and microbe–microbe interactions in the rhizosphere have large impacts on plant health. Rhizobia are symbiotic bacteria that fix nitrogen in association with legumes, relying on a complex signaling process that results in the production of root nodules. Mycorrhizae are plant–fungal symbioses that extend the capacity of roots to absorb nutrients and water; the four major groups are ectomycorrhizae, arbuscular mycorrhizae, ericoid mycorrhizae, and orchid mycorrhizae. Common mycorrhizal networks connect plants and result in the transfer of signals, carbon, and nutrients among individuals and even among species. Endophytic fungi and bacteria colonize all parts of plants including the phylloplane; endophytes may be commensals, parasites, or mutualists, with a variety of impacts on the hosts. Endophytes may be horizontally transmitted or vertically transmitted, colonizing seeds and then growing in the next generation of plants. Microbes in the plant microbiome interact with each other through parasitism, predation, competition, antibiosis, and sometimes syntrophy. Such microbe–microbe interactions shape access to the plant by plant pathogens.

Single pathogen‐targeted disease management measure has shown drawbacks in field efficacy under the scenario of global change. An in‐depth understanding of plant pathogenesis will provide a promising solution but faces the challenges of the emerging paradigm involving the plant microbiome. While the beneficial impact of the plant microbiome is well characterized, their potential role in facilitating pathological processes has so far remained largely overlooked. To address these unsolved controversies and emerging challenges, we hereby highlight the pathobiome, the disease‐assisting portion hidden in the plant microbiome, in the plant pathogenesis paradigm. We review the detrimental actions mediated by the pathobiome at multiple scales and further discuss how natural and human triggers result in the prevalence of the plant pathobiome, which would probably provide a clue to the mitigation of plant disease epidemics. Collectively, the article would advance the current insight into plant pathogenesis and also pave a new way to cope with the upward trends of plant disease by designing the pathobiome‐targeted measure.

Microeukaryotes in animal and plant microbiomes: Ecologies of disease?

Summary It is increasingly evident that the plant microbiome is a strong determinant of plant health. While the ability to manipulate the microbiome in plants and ecosystems recovering from disturbance may be useful, our understanding of the plant microbiome in regenerating plant communities is currently limited.Using 16S ribosomal RNA (rRNA) gene and internal transcribed spacer (ITS) region amplicon sequencing, we characterized the leaf, stem, fine root, rhizome, and rhizosphere microbiome of < 1‐yr‐old aspen saplings and the associated bulk soil after a recent high‐intensity prescribed fire across a burn severity gradient.Consistent with previous studies, we found that soil microbiomes are responsive to fire. We extend these findings by showing that certain plant tissue microbiomes also change in response to fire. Differences in soil microbiome compositions could be attributed to soil chemical characteristics, but, generally, plant tissue microbiomes were not related to plant tissue elemental concentrations. Using source tracking modeling, we also show that fire influences the relative dominance of microbial inoculum and the vertical inheritance of the sapling microbiome from the parent tree.Overall, our results demonstrate how fire impacts plant microbiome assembly, diversity, and composition and highlights potential for further research towards increasing plant fitness and ecosystem recovery after fire events.

Plant mutualistic association with various beneficial microbes is referred to as the plant enhancer microbiome. These microbes are found either in episphere or endosphere of the plant tissues. Several pieces of evidence have highlighted that plant microbiomes and soil play a pivotal role in making soil nutrient balance which is readily available to plants and provide strength under various stresses. Recently different technologies relevant to plant microbiome and diversity such as sequencing technologies, metagenomics, and bioinformatics have been utilized. Knowledge about factors that shape the composition of plant microbes is still less explored. Here, current insights into the issues driving the above/below plant microbial diversities are explored. Primarily, we address the distribution of microbial communities above and below ground across plant habitats that has benefitted plants. Microbial communities are efficient regulators of biogeochemical cycle which is a better approach to mitigate changing climatic patterns aids in proper utilization of greenhouse gases for their metabolic mechanisms. The present review is thereby significant for assessing microbiome mitigation toward climate change and multiple avenues of plant- microbe interaction under commuting climatic scenario. Finally, we summarize factors that promote the structure and composition of the plant microbiome.

The plant microbiome, which can be found in every accessible tissue of healthy plants, is made up of a diverse collection of microorganisms that are classified according to their taxonomy. Plants with plant-associated microbiomes have improved growth, nutrient uptake, stress tolerance, and disease resistance, among other characteristics. Microbes associated with plants show several genetic, biochemical, physical, and metabolic links, all of which have implications for plant health. Beyond identifying information gaps and potential initiatives, we are investigating how a plant’s microbiome can be influenced by these interactions, which can then alter the plant’s ability to absorb nutrients and stay healthy.KeywordsPlant microbiomesMicrobiotaAbioticAgriculture

There are multiple distinct habitats for microbiota inhabiting the plant microbiome (phyllosphere, endosphere, litter, rhizosphere) and habitats that act as additional sources (and sinks) of microbes and nutrients for the plant microbiome (atmosphere, pedosphere, bedrock, and fauna). These habitats harbor distinctive microbial communities that differ in structure, composition, function, and spatiotemporal dynamics. Each habitat also differs in the mechanisms that provide “gateways” of exchange of microbes (and microbial products) between two communities, or in their access to “highways” that connect multiple communities. Of the environmental processes driving microbial community exchanges, precipitation events seem to represent the only one highway that can connect all the abovementioned habitats—the “hydrologic highway”. When precipitation contacts plants, it is partitioned into interception (water stored on, and evaporated from, plant surfaces), throughfall (water that drips from canopy surfaces and through gaps), and stemflow (water that is drained down the stem). This chapter describes the ways that precipitation partitioning in vegetated ecosystems (into interception, throughfall, and stemflow) may connect microbial communities from the top (atmospheric boundary layer) to the bottom (bedrock face) of the critical zone via these hydrologic highways.

The plant microbiome may be bottlenecked at the level of endophytes of individual seeds. Strong defense of developing seeds is predicted by optimal defense theory, and we have experimentally demonstrated exclusionary interactions among endophytic microbes infecting individual seeds of Centaurea stoebe. Having found a single, PDA-culturable microbe per seed or none in an exploratory study with Centaurea stoebe, we completed a more extensive survey of an additional 98 plant species representing 39 families. We again found that individual, surface-sterilized seeds of all species hosted only one PDA-culturable bacterial or fungal endophyte per seed, or none. PDA-unculturables were not determined but we expect them to also be bottlenecked in individual seeds, as they too should be governed by exclusionary interactions. If the bottleneck were confirmed with high-throughput sequencing of individual seeds then it would make sense to further investigate the Primary Symbiont Hypothesis (PSH). This includes the prediction that primary symbionts (i.e., the winners of the exclusionary battles among seed endophytes) have strong effects on seedlings depending on symbiont identity.

Microbial co-occurrence network analysis is being widely used for data exploration in plant microbiome research. Still, challenges lie in how well these microbial networks represent natural microbial communities and how well we can interpret and extract eco-evolutionary insights from the networks. Although many technical solutions have been proposed, in this perspective, we touch on the grave problem of kingdom-level bias in network representation and interpretation. We underscore the eco-evolutionary significance of using cross-kingdom (bacterial-fungal) co-occurrence networks to increase the network’s representability of natural communities. To do so, we demonstrate how ecosystem-level interpretation of plant microbiome evolution changes with and without multi-kingdom analysis. Then, to overcome oversimplified interpretation of the networks stemming from the stereotypical dichotomy between bacteria and fungi, we recommend three avenues for ecological interpretation: (1) understanding dynamics and mechanisms of co-occurrence networks through generalized Lotka-Volterra and consumer-resource models, (2) finding alternative ecological explanations for individual negative and positive fungal-bacterial edges, and (3) connecting cross-kingdom networks to abiotic and biotic (host) environments.