The island biology of the host microbiome 

Sarkar et al., 2026

Highlights

The extraordinary biodiversity of the host-associated gut microbiome cannot be explained exclusively by host traits.

Researchers have interpreted hosts as biological islands suitable for microbial colonisation and have applied ecological theories of island biogeography and metacommunity ecology to further understand microbiome composition and variation.

To benefit from the host-as-island metaphor, the metacommunity processes characterising macroscopic and microbial diversity should be explicitly compared. On geological islands, these processes include interspecies interactions, local selection, interisland dispersal, and ecological stochasticity. In host islands, these processes are paralleled by interactions between microbes, host selection, microbial transmission, and microbial stochasticity, respectively.

A critical difference between host islands and geological islands is that host islands are mobile and undergo adaptive evolution, whereas geological islands do not.

Abstract

Microbiomes perform critical functions for their hosts, and understanding microbiome variation is important for both basic and applied science. However, host traits alone cannot explain the entirety of microbiome variation, because, alongside host traits, microbiomes are shaped by multiple ecological processes. Researchers have thus turned to theories of island biology, conceptualising animal hosts as islands and animal microbiomes as metacommunities that assemble within and disperse between host islands. To develop realistic models, this host-as-island metaphor must be examined by explicitly comparing geological and host islands. Here, we critically examine the host-as-island metaphor by evaluating how microbiome variation is shaped by the four metacommunity processes that explain biodiversity on geological islands: local interspecies interactions, local selection, dispersal, and stochasticity. Key differences between host islands and geological islands include the complexity of microbiome transmission networks arising from host mobility and sociality and the capacity of hosts to evolve to control their microbiomes. We conclude with discussions of how eco-evolutionary dynamics differ between geological islands and host islands, and the reciprocal relevance of island biology and microbiome science.

https://www.cell.com/trends/microbiology/abstract/S0966-842X(26)00040-5?

Soil microbial diversity associates with lower prevalence of human bacterial pathogens across global soils

Author links open overlay panel

Xiong et al., 2026

Soil-inhabiting pathogens threaten human health, but their biogeography and associations with soil biodiversity remain poorly understood. Here, we present global patterns of dominant human bacterial pathogens by integrating 1,602 soil metagenomes from 59 countries across continents. We show that dominant human pathogens are more prevalent (i.e., relative abundance) in wet (tropical and temperate) ecosystems and are particularly abundant in cropland soils. We find a global negative association between soil microbiome diversity and pathogen prevalence. We further reveal a significant and positive correlation between the abundance of dominant human pathogens and both disease virulence and global patterns of mortality associated with infectious diseases. Many dominant pathogens are likely to increase their proportion under global change scenarios. Our work provides a global atlas of dominant soil-inhabiting human pathogens and reveals their biogeography and ecology. These findings can guide the development of effective surveillance and risk management strategies to reduce outbreaks and pandemics.

https://www.sciencedirect.com/science/article/abs/pii/S1931312826001198

The rhizosphere microbiome as a decentralized immune system

Araujo et al., 2026

Plant immunity should be reconsidered beyond the boundaries of the plant genome. We propose that the rhizosphere microbiome may function analogously to a decentralized immune system, contributing adaptive defenselike properties and memory effects. In this forum article, we discuss how this perspective reframes immunity as an emergent property of plant–microbiome interactions, shifting the focus from a solitary host toward an integrated holobiont

https://www.cell.com/trends/microbiology/abstract/S0966-842X(26)00065-X

Biological Pesticides as Viable Alternative to Synthetic Pesticides for Sustainable Agriculture and Nutrition: A Systematic Review 

Assefa et al., 2026

The overuse of synthetic pesticides in agriculture has raised significant environmental and health concerns. Biopesticides have emerged as viable, environmentally compatible alternatives. However, recent comprehensive reviews integrating all biopesticide categories and emphasizing their contribution to synthetic-pesticide-free and health-safe products remain limited. This PRISMA-based systematic review synthesizes 98 peer-reviewed studies. It evaluates the main categories of biopesticides: microbial, biochemical, and plant-incorporated protectants (PIPs), their roles in sustainable agriculture and integrated pest management (IPM), as well as the future trajectory of biopesticides. Microbial agents (bacteria, fungi, viruses) show strong target specificity and reduced environmental persistence. Biochemical pesticides, derived from plant extracts and pheromones, disrupt the behavior or physiology of pests with minimal non-target toxicity. PIPs, developed through genetic engineering, provide crop-embedded protection and greatly reduce chemical inputs. Despite these advantages, inconsistent field performance, short shelf life, regulatory hurdles, and low farmer awareness limit commercialization. Innovations such as RNA interference (RNAi), Nano-formulations, and microbial consortia offer promising solutions. This review underscores the need for better delivery systems, harmonized regulations, and coordinated outreach to accelerate adoption. Overall, biopesticides are a scientifically robust and essential component of sustainable crop protection.

https://onlinelibrary.wiley.com/doi/10.1002/sae2.70139

 

Breeding for multi-stress resilience in crops: Myth or possibility? 

Khazaei et al., 2026

Social Impact Statement

Climate change threatens millions of farmers worldwide by exposing crops to multiple concurrent or sequential environmental stresses such as drought, heat, waterlogging, and diseases. Although crops have long been selected under naturally occurring multi-stress conditions, breeding pipelines largely focus on optimal or single-stress environments, leaving complex stress combinations under-addressed. Developing crop cultivars that withstand multiple stress scenarios is essential for ensuring food security, food safety, and strengthening farmer resilience. Breeding for multi-stress resilience seems feasible but requires international collaboration among applied crop scientists, pure biologists, and policymakers to develop climate-resilient crops that sustain people and ecosystems.

Summary

Climate change is increasing the frequency and intensity of combined abiotic and biotic stressors that may occur simultaneously or sequentially, dramatically reducing crop growth and yield stability. Plant breeding activities primarily target crop improvement for a single stressor, limiting crop resilience under complex environmental conditions. This opinion paper highlights the complexity of crop breeding for multi-stress growing conditions and discusses major challenges and opportunities to enable plant breeders to develop more climate-resilient crops. It also outlines the importance of integrating conventional breeding approaches with multi-omics and novel breeding technologies to develop multi-stress resilient crop cultivars. Identifying and validating key regulatory genes involved in multi-stress resilience and evaluating their performance across diverse genetic backgrounds, environments, and stress combination scenarios are needed. Although achieving complete multi-stress resilience remains an immense challenge, advances in integrative approaches and cross-disciplinary collaboration are steadily improving the potential to enhance crop resilience to multiple environmental stresses.

Graphical Abstract

Climate change threatens millions of farmers worldwide by exposing crops to multiple concurrent or sequential environmental stresses such as drought, heat, waterlogging, and diseases. Although crops have long been selected under naturally occurring multi-stress conditions, breeding pipelines largely focus on optimal or single-stress environments, leaving complex stress combinations under-addressed. Developing crop cultivars that withstand multiple stress scenarios is essential for ensuring food security, food safety, and strengthening farmer resilience. Breeding for multi-stress resilience seems feasible but requires international collaboration among applied crop scientists, pure biologists, and policymakers to develop climate-resilient crops that sustain people and ecosystems.

https://nph.onlinelibrary.wiley.com/doi/10.1002/ppp3.70185?af=R

Root Microbiota: Orchestrating Architecture-Smart Crops

Chen et al., 2026

Crops depend on microbial partners for their growth, development, and overall resilience. A pivotal understanding has emerged showing the direct involvement of the root microbiota in regulating the tiller number of rice, a crucial architecture that influences yield. Novel frontiers in microbiological applications for agriculture highlight the profound role of the root microbiota in shaping crop architecture to boost productivity. We propose that improvements in crop production are moving from a genetic perspective on “architecture” to embracing “holobiont architecture.” As such, microbial orchestration provides a dynamic fine-tune function for breeding “architecture-smart crops” characterised by phenotypic plasticity under environmental uncertainty.

https://enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/1751-7915.70307

From bacterial predators to partners: phages in agriculture

Salehimoghaddam et al., 2026

Bacteriophages, viruses that infect bacteria, are critical players for shaping the taxonomic and functional composition of plant-associated microbiomes. Yet, their roles in plant health remain overlooked, along with their implications for sustainable agriculture. While phages are recognized as bacterial predators, they can also promote bacterial survival and competitiveness. Here, we highlight the roles phage play in shaping soil microbiomes and promising phage-based applications for sustainable agriculture. Ongoing research highlights the diverse roles of phages in regulating bacterial populations, enhancing nutrient cycling, improving stress tolerance, and suppressing soil-borne pathogens – microbial traits that directly link to plant health. Additionally, emerging applications such as bioremediation, phage-based biosensors, and microbiome engineering underscore phages' potential to revolutionize sustainable farming and optimize agricultural productivity.

https://nph.onlinelibrary.wiley.com/doi/10.1111/nph.70959

Harnessing Plant–Microorganism Interactions to Mitigate Biotic and Abiotic Stresses for Sustainable Crops

Santana dos Santos et al., 2026

Climate change has intensified the occurrence of biotic and abiotic stresses, representing a major threat to agricultural productivity. This climate variability, coupled with the excessive use of agrochemicals, not only compromises environmental sustainability but also exacerbates food insecurity, directly affecting food availability and quality. In this context, biotechnological strategies have proven essential for mitigating the effects of stress on plants, promoting practices focused on agricultural sustainability. Notable among these strategies is the use of plant growth-promoting microorganisms, which are emerging as promising alternatives capable of improving plant tolerance to stress conditions and simultaneously reducing dependence on agrochemicals. These microorganisms can act as nitrogen fixers and solubilizers of nutrients, such as phosphorus and potassium. Additionally, they can influence plant immune responses by inducing systemic resistance and promoting the synthesis of phytohormones, such as auxins, cytokinins, and abscisic acid, which support plant development during the stress response. The interaction between plants and microorganisms represents a sustainable agricultural management strategy capable of enhancing crop tolerance to environmental adversities. In this review, we discuss the microorganisms known to establish beneficial interactions with plants, leading to improved performance under biotic and abiotic stress. Overall, this work highlights the potential of plant–microbe partnerships as a cornerstone for advancing sustainable agriculture in the face of global challenges.

https://www.mdpi.com/2223-7747/15/4/647

Dual-scale drivers of soil biodiversity in agroecosystems: Field management outweighs landscape effects, but both matter

Gao et al., 2026

1. Soil communities in agricultural fields are shaped by both farm management and surrounding landscape structure. However, their relative contribution and potential interactions remain unclear. Understanding these relationships is essential for conserving soil biodiversity, which underpins key ecosystem functions and services.
2. To address this knowledge gap, we conducted a field soil sampling campaign across 87 farms in the Netherlands to assess how field-scale management and landscape structure in combination determine multiple soil communities, including bacteria, fungi, protists and invertebrates, in agroecosystems.
3. Landscape structure significantly influenced the diversity and composition of soil organisms in addition to the strong influence of field-scale management. In particular, the compositional landscape heterogeneity played a stronger role than configurational heterogeneity in shaping soil community composition. Importantly, the influence of landscape structure on soil diversity was independent of land use intensity at the field scale, with the exception of soil invertebrates.
4. Synthesis and applications. These findings highlight the need for conservation strategies that integrate both field-scale and landscape-scale planning. The promotion of diverse land use types might offer a practical pathway to maximize the effectiveness of soil biodiversity conservation within an intensively managed agricultural matrix.

https://besjournals.onlinelibrary.wiley.com/doi/10.1111/1365-2664.70295

 

Holobiont:

a biological system consisting of an organism (e.g., an animal, a plant) and the community of microorganisms that live in close association with it.

https://www.sciencedirect.com/science/article/abs/pii/S1471492226000073

Increasing applied pesticide toxicity trends counteract the global reduction target to safeguard biodiversity

Wolfram et al., 2026

The 15th united Nations biodiversity Conference (COP15) obligates all countries to reduce pesticide risks by 50% by 2030. In this study, we derived the trends of total applied toxicity (TaT) globally between 2013 and 2019, weighting applied masses by ecotoxicity, of 625 pesticides for eight species groups to assess pathways toward this reduction goal. We found that the TaT of most species groups has increased; that only20 ± 14 pesticides per group define >90% of the TaT nationally; that fruits, vegetables, maize, soybean, rice, and other cereals contribute 76 to 83% of the global TaT; and that China, brazil, the united States, and India contribute 53 to 68% of the global TaT. Our target achievement categorization shows that substantial actions, combining shifts to less-toxic pesticides, increased adoption of organic agriculture, and also provision of national pesticide use data, will be required globally to approach the united Nations’ target.

https://www.science.org/doi/epdf/10.1126/science.aea8602

Los árboles son santuarios. Quien sabe hablar con ellos, quien sabe escucharlos, puede aprender la verdad. No predican doctrinas ni preceptos; predican, sin dejarse perturbar por lo particular, la antigua ley de la vida.

Hesse, H. (1920). Árboles.

 Rhizophagy Cycle Explained by Dr. James White

A bacterial nutrition strategy for plant disease control

Wang et al., 2025

Xanthomonas spp. cause serious diseases in more than 400 plant species. The conserved AvrBs2 family effectors are among the most important virulence factors in xanthomonads, but how AvrBs2 promotes infection remains elusive. We found that AvrBs2 is a glycerophosphodiesterase-derived synthetase that catalyzes uridine 5′-diphosphate-α-d-galactose into a sugar phosphodiester, bis-(1,6)-cyclic dimeric α-d-galactose-phosphate, which is referred to as xanthosan. Xanthosan is synthesized by AvrBs2 in host cells and released into apoplastic spaces. Xanthomonas bacteria uptake xanthosan through the XanT transporter and hydrolyze it through the XanP phosphodiesterase for nutrition. AvrBs2, XanT, and XanP form a xanthosan “generation-uptake-utilization” system to provide a dedicated nutritional strategy to feed xanthomonads. Furthermore, elucidation of the AvrBs2-XanT-XanP virulence mechanism inspired us to develop an “anti-nutrition” strategy that should be applicable to control a wide variety of Xanthomonas diseases.

https://www.science.org/doi/10.1126/science.ady8325

Keystone Pseudomonas species in the wheat phyllosphere microbiome mitigate Fusarium head blight by altering host pH

Xu et al., 2025

Phyllosphere microbiota play crucial roles in supporting host performance. However, the dynamic changes of phyllosphere-associated microbiome during pathogen infections and their impacts on plant health remain unknown. Here, we found phyllosphere microbes can mitigate wheat Fusarium head blight (FHB), a severe disease caused by Fusarium graminearum (F. graminearum) pathogen that promotes infection by inducing host alkalinization. Using wheat head microbial community profiling and metatranscriptomics, we found Pseudomonas spp. significantly enriched on infected wheat heads. Through isolating 595 bacterial strains from infected wheat heads—including 196 Pseudomonas isolates—we identified certain enriched Pseudomonas isolates capable of producing organic acids that counteract pathogen-induced pH upshift. In vitro experiments confirm the selective promotion of specific host-acidifying Pseudomonas in wheat heads. Field trials confirmed that host-acidifying Pseudomonas strains effectively controlled FHB. These findings highlight the pivotal role of plant-beneficial microbes in host pH regulation and offer innovative avenues for sustainable plant disease control.

https://www.cell.com/cell-host-microbe/fulltext/S1931-3128%2825%2900450-0

Plant-plant nitrogen transfer is prevalent in a semi-arid shrubland and affects the foliar N content of recipient plants

González-Díaz & Montesinos-Navarro

In dry ecosystems, plants cope with limited nutrients such as nitrogen (N), which is vital for growth. While nitrogen sharing between plants is known in agriculture, it is less understood in natural, semi-arid environments.

We studied nitrogen transfer between plants in a semi-arid shrubland in Spain and how this affects the nutrition of the neighbours. Using a stable isotope of nitrogen (¹⁵N), we labelled donor plants and tracked its movement to nearby plants over more than a year.

Nitrogen transfer was widespread: over 70% of neighbouring plants received nitrogen, most within a week of labelling. N transfer started in less than a week, and reached the maximum values approximately 60 days after labelling, getting back to pre-labelling values after 120 days. Repeated pulses increased both the transfer magnitude and the leaf nitrogen content of receiver plants. These results show that nitrogen exchange among plants is common in semi-arid shrublands and may help species coexist and thrive in nutrient-poor environments.

https://besjournals.onlinelibrary.wiley.com/doi/10.1111/1365-2435.70241

Rhizobium tropici Metabolites Induce Defence-Related Genes and Promote Sclerotinia Sclerotiorum Stem Rot Control in Chickpeas

de Sousa et al., 2025

Brazil has seen a steady increase in domestic chickpea production, and the crop is expected to gain growing importance across the country. However, solutions for effective pest and disease management remain limited. Many soil-borne phytopathogens that affect other crops can also infect chickpeas, increasing disease incidence due to higher initial inoculum levels. This study aimed to evaluate the effects of concentrated metabolites produced by Rhizobium tropici (CM-RT) on resistance induction and control of Sclerotinia sclerotiorum in chickpeas. Different CM-RT application methods were tested and disease incidence was assessed. Additionally, the relative expression of several defence-related genes was analyzed in CM-RT treated plants. Our results show that root application of CM-RT significantly reduced disease incidence and was statistically equivalent to the commercial elicitor based on acibenzolar-S-methyl. Gene expression analysis revealed the upregulation of key defence genes involved in jasmonic acid, ethylene, and oxidative stress pathways, suggesting a priming effect. These findings suggest that CM-RT can serve as an effective and eco-friendly alternative for disease control by resistance induction in chickpeas.

https://onlinelibrary.wiley.com/doi/10.1002/sae2.70103