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Both plants and their associated microbiomes can respond strongly to anthropogenic environmental changes. These responses can be both ecological (e.g. a global change affecting plant demography or microbial community composition) and evolutionary (e.g. a global change altering natural selection on plant or microbial populations). As a result, global changes can catalyse eco-evolutionary feedbacks. Here, we take a plant-focused perspective to discuss how microbes mediate plant ecological responses to global change and how these ecological effects can influence plant evolutionary response to global change.Weargue that the strong and functionally important relationships between plants and their associated microbes are particularly likely to result in eco-evolutionary feedbacks when perturbed by global changes and discuss how improved understanding of plant–microbe eco-evolutionary dynamics could inform conservation or even agriculture.

Pre-sowing seed treatment with systemic fungicides is a firmly entrenched practice for most agricultural crops worldwide. The treatment is intended to protect the crop against seed- and soil-borne diseases. In recent years, there is increasing evidence that fungicidal applications to manage diseases might inadvertently also affect non-target organisms, such as endophytes. Endophytes are ubiquitously present in plants and contribute to plant growth and development besides offering resistance to biotic and abiotic stresses. In seeds, endophytes may play a role in seed development, seed germination, seedling establishment and crop performance. In this paper, we review the recent literature on non-target effects of fungicidal applications on endophytic fungal community and discuss the possible consequences of indiscriminate seed treatment with systemic fungicide on seed endophytes. It is now well recognized that endophytes are ubiquitously present in all parts of the plant, including the seeds. They may be transmitted vertically from seed to seed as in many grasses and/or acquired horizontally from the soil and the environment. Though the origins and evolution of these organisms in plants are a matter of conjecture, numerous studies have shown that they symbiotically aid in plant growth and development, in nutrient acquisition as well in protecting the plants from abiotic and biotic stresses. Against this background, it is reasonable to assume that the use of systemic fungicides in seed treatment may not only affect the seed endophytes but also their attendant benefits to seedling growth and establishment. While there is evidence to indicate that fungicidal applications to manage plant diseases also affect foliar endophytes, there are only few studies that have documented the effect of seed treatment on seed-borne endophytes. Some of the convincing examples of the latter come from studies on the effect of fungicide application on rye grass seed endophyte AR37. More recently, experiments have shown that removal of seed endophytes by treatment with systemic fungicides leads to significant loss of seedling vigour and that such losses could be partially restored by enriching the seedlings with the lost endophytes. Put together, these studies reinforce the importance of seed endophytes to seedling growth and establishment and draw attention on how to trade the balance between the benefits of seed treatments and the direct and indirect costs incurred due to loss of endophytes. Among several approaches, use of reduced-risk fungicides and identifying fungicide-resistant endophytes are suggested to sustain the endophyte contribution to early seedling growth.

Over evolutionary time, Wolbachia has been repeatedly transferred between host species contributing to the widespread distribution of the symbiont in arthropods. For novel infections to be maintained, Wolbachia must infect the female germ line after being acquired by horizontal transfer. Although mechanistic examples of horizontal transfer exist, there is a poor understanding of factors that lead to successful vertical maintenance of the acquired infection. Using Anopheles mosquitoes (which are naturally uninfected by Wolbachia) we demonstrate that the native mosquito microbiota is a major barrier to vertical transmission of a horizontally acquired Wolbachia infection. After injection into adult Anopheles gambiae, some strains of Wolbachia invade the germ line, but are poorly transmitted to the next generation. In Anopheles stephensi, Wolbachia infection elicited massive blood meal-induced mortality, preventing development of progeny. Manipulation of the mosquito microbiota by antibiotic treatment resulted in perfect maternal transmission at significantly elevated titers of the wAlbB Wolbachia strain in A. gambiae, and alleviated blood meal-induced mortality in A. stephensi enabling production of Wolbachia-infected offspring. Microbiome analysis using high-throughput sequencing identified that the bacterium Asaia was significantly reduced by antibiotic treatment in both mosquito species. Supplementation of an antibiotic-resistant mutant of Asaia to antibiotic-treated mosquitoes completely inhibited Wolbachia transmission and partly contributed to blood meal-induced mortality. These data suggest that the components of the native mosquito microbiota can impede Wolbachia transmission in Anopheles. Incompatibility between the microbiota and Wolbachia may in part explain why some hosts are uninfected by this endosymbiont in nature.

Experimental studies of the evolution of reproductive isolation (RI) in real time are a powerful way in which to reveal fundamental, early processes that initiate divergence. In a classic speciation experiment, populations of Drosophila pseudoobscura were subjected to divergent dietary selection and evolved significant positive assortative mating by diet. More recently, a direct role for the gut microbiome in determining this type of RI in Drosophila melanogaster has been proposed. Manipulation of the diet, and hence the gut microbiome, was reported to result in immediate assortative mating by diet, which could be eliminated by reducing gut microbes using antibiotics and recreated by adding back Lactobacillus plantarum. We suggest that the evolutionary significance of this result is unclear. For example, in D. melanogaster, the microbiome is reported as flexible and largely environmentally determined. Therefore, microbiome-mediated RI would be transient and would break down under dietary variation. In the absence of evolutionary coassociation or recurrent exposure between host and microbiome, there are no advantages for the gut bacteria or host in effecting RI. To explore these puzzling effects and their mechanisms further, we repeated the tests for RI associated with diet-specific gut microbiomes in D. melanogaster. Despite observing replicable differences in the gut microbiomes of flies maintained on different diets, we found no evidence for diet-associated RI, for any role of gut bacteria, or for L. plantarum specifically. The results suggest that there is no general role for gut bacteria in driving the evolution of RI in this species and resolve an evolutionary riddle.

Background Small RNAs, such as microRNAs (miRNAs), are candidates for mediating communication between the host and its microbiota, regulating bacterial gene expression and influencing microbiome functions and dynamics. Here, we introduce HolomiRA (Holobiome miRNA Affinity Predictor), a computational pipeline developed to predict target sites for host miRNAs in microbiome genomes. HolomiRA operates within a Snakemake workflow, processes microbial genomic sequences in FASTA format using freely available bioinformatics software and incorporates built-in data processing methods. The pipeline begins by annotating protein-coding sequences from microbial genomes using Prokka. It then identifies candidate regions, evaluates them for potential host miRNA binding sites and the accessibility of these target sites using RNAHybrid and RNAup software. The predicted results that meet the quality filter parameters are further summarized and used to perform a functional analysis of the affected genes using SUPER-FOCUS software. Results In this paper, we demonstrate the use of the HolomiRA pipeline by applying it to publicly available metagenome-assembled genomes obtained from human feces, as well as from bovine feces and ruminal content. This approach enables the prediction of bacterial genes and biological pathways within microbiomes that could be influenced by host miRNAs. It also allows for the identification of shared or unique miRNAs, target genes, and taxonomies across phenotypes, environments, or host species. Conclusions HolomiRA is a practical and user-friendly pipeline designed as a hypothesis-generating tool to support the prediction of host miRNA binding sites in prokaryotic genomes, providing insights into host-microbiota communication mediated by miRNA regulation. HolomiRA is publicly available on GitHub: https://github.com/JBruscadin/HolomiRA .

Pine wilt disease (PWD) is a devastating disease caused by the pinewood nematode ( Bursaphelenchus xylophilus ). Its substantial ecological disruption harms global forestry and poses serious economic challenges. Although previous research has demonstrated that Bacillus subtilis JCK-1398 has the potential to induce systemic resistance in pine trees, the ecological mechanisms underlying its biocontrol efficacy remain underexplored. This study investigated how JCK-1398 treatment influences rhizosphere- and nematode-associated microbial communities to mitigate PWD. Metabarcoding analyses revealed that JCK-1398 treatment increased the abundance of beneficial microbial taxa (e.g., Nocardioides and Mesorhizobium ) in the rhizosphere microbiome. Concurrently, nematode-associated microbial communities became dominated by Pantoea , a genus with known nematicidal properties. Isolation and characterization of Pantoea dispersa BC11 confirmed that it significantly limits nematode viability. These findings highlight the multifaceted defense that JCK-1398 offers, not only inducing systemic resistance, but also orchestrating beneficial microbiome dynamics. This study emphasizes the potential of manipulating a microbial holobiont for eco-friendly and sustainable disease management. The ability of JCK-1398 to recruit and enhance microbial allies offers a novel framework for developing biocontrol agents, with implications for managing PWD and other plant-pathogen systems.

Plants are functional macrobes living in a close association with diverse communities of microbes and viruses as complex systems that continuously interact with the surrounding environment. The microbiota within the plant holobiont serves various essential and beneficial roles, such as in plant growth at different stages, starting from seed germination. Meanwhile, pathogenic microbes—differentiated from the rest of the plant microbiome based on their ability to damage the plant tissues through transient blooming under specific conditions—are also a part of the plant microbiome. Recent advances in multi-omics have furthered our understanding of the structure and functions of plant-associated microbes, and a pathobiome paradigm has emerged as a set of organisms (i.e., complex eukaryotic, microbial, and viral communities) within the plant’s biotic environment which interact with the host to deteriorate its health status. Recent studies have demonstrated that the one pathogen–one disease hypothesis is insufficient to describe the disease process in many cases, particularly when complex organismic communities are involved. The present review discusses the plant holobiont and covers the steady transition of plant pathology from the one pathogen–one disease hypothesis to the pathobiome paradigm. Moreover, previous reports on model plant diseases, in which more than one pathogen or co-operative interaction amongst pathogenic microbes is implicated, are reviewed and discussed.

Microbial diversity formed by ages of evolution in soils plays an important role in sustainability of crop production by enriching soil and alleviating biotic and abiotic stresses. This diversity is as an essential part of the agro-ecosystems, which is being pushed to edges by pumping agrochemicals and constant soil disturbances. Consequently, efficiency of cropping system has been decreasing, aggravated further by the increased incidence of abiotic stresses due to changes in climatic patterns. Thus, the sustainability of agriculture is at stake. Understanding the microbiota inhabiting phyllosphere, endosphere, spermosphere, rhizosphere, and non-rhizosphere, and its utilization could be a sustainable crop production strategy. This review explores the available information on diversity of beneficial microbes in agricultural ecosystem and synthesizes their commercial uses in agriculture. Microbiota in agro-ecosystem works by nutrient acquisition, enhancing nutrient availability, water uptake, and amelioration of abiotic and abiotic stresses. External application of such beneficial microbiota or microbial consortia helps in boosting plant growth and provides resistance to drought, salinity, heavy metal, high-temperature and radiation stress in various crop plants. These have been instrumental in enhancing tolerance to diseases, insect pest and nematodes in various cropping system. However, studies on the microbiome in revolutionary production systems like conservation agriculture and protected cultivation, which use lesser agrochemicals, are limited and if exploited can provide valuable input in sustainable agriculture production.

In this era of dwindling natural resources and climate change, the target of increasing crop production for feeding 10 billion people by the year 2050 has mounted huge pressure on the scientific community. The cultivation of hybrid varieties has contributed immensely towards food security and made it possible to meet the requirements of the rapidly increasing human population. A typical plant breeding approach involves hybridization i.e. crossing two genetically different individuals, to create genetic variation. At the genetic level, the genomes of two individuals combine to form a hybrid, but what happens to the associated microbiota is largely unknown. Endophytes are one such class of plant-associated microbiota that have been reported to inhabit the internal tissues of plants, without causing any disease symptoms. With the advent of the holobiome concept, the importance of microbiome in plant health and productivity is being increasingly realized. In this perspective, understanding the nature of plant-endophyte association in hybrids and transmission/colonization of endophytes upon hybridization (i.e. from parents to progenies) is a pre-requisite for laying the foundation of plant holobiont breeding . This emerging discipline aims to integrate the best of both worlds (hybrid plant genome and microbiome) for realizing the untapped potential of the plant microbiota (and hence, the holobiont) to adverse environmental conditions. This review attempts to summarize our current understanding of the hybrid plant-associated microbiome with respect to its parental lines and wild progenitors. Further, the review highlights some research gaps in the field and beckons the attention of scientific community towards understanding and applying this knowledge for further boosting the crop productivity, the need of the hour.

The aquaculture industry faces many challenges regarding the intensification of shrimp rearing systems. One of these challenges is the release of excessive amounts of nitrogen and phosphorus into coastal areas, causing disruption in nutrient cycling and microbial equilibrium, which are important for coastal productivity. Biosecurity within the shrimp rearing systems can also be compromised by disruption to the nutrient fluxes, and as consequence the microbiome of the system. In certain conditions, these changes could lead to the blooming of potentially pathogenic bacteria. These changes in the external microbiome of the system and the constant fluctuations of nutrients can affect the intestinal microbiome of shrimp, which is involved in the growth and development of the host, affecting nutrient absorption, regulating metabolic processes, synthesising vitamins, modulating the immune response and preventing growth of pathogenic bacteria. It has been suggested that specific changes in the intestinal microbiome of Litopenaeus vannamei may be an avenue through which to overcome some of the problems that this industry faces, in terms of health, growth and waste. Recent research, however, has focussed mainly on changes in the intestinal microbiome. Researchers have overlooked the relevance of other aspects of the system, such as the microbiome from the benthic biofilms; zooplankton, plankton and bacterioplankton; and other sources of microorganisms that can directly affect the microbial status of the intestinal and epiphytic communities, especially in rearing systems that are based on intensification and microbial maturation processes, such as a biofloc system. It is therefore necessary to place holobiome studies into context, including the ‘holobiome of the aquaculture system’ (microbiomes that make up the culture system and their interactions) and not only the intestinal microbiome. Thus, we describe factors that affect the shrimp microbiome, the methodology of study, from sampling to bioinformatic workflows, and introduce the concept of the ‘holobiome of the aquaculture system’ and how this enables us to promote the intensification, biosafety and eco-efficiency of shrimp farming. The holobiome perspective implies a greater investment of resources and time for research, but it will accelerate the development of technology that will benefit the development and sustainability of the aquaculture industry.