Do plants remember their microbial partners?

Rhizosphere Microbes as Essential Partners for Plant Stress Tolerance

BackgroundLegumes establish with rhizobial bacteria a nitrogen-fixing symbiosis which is of the utmost importance for both plant nutrition and a sustainable agriculture. Calcium is known to act as a key intracellular messenger in the perception of symbiotic signals by both the host plant and the microbial partner. Regulation of intracellular free Ca2+ concentration, which is a fundamental prerequisite for any Ca2+-based signalling system, is accomplished by complex mechanisms including Ca2+ binding proteins acting as Ca2+ buffers. In this work we investigated the occurrence of Ca2+ binding proteins in Mesorhizobium loti, the specific symbiotic partner of the model legume Lotus japonicus.ResultsA soluble, low molecular weight protein was found to share several biochemical features with the eukaryotic Ca2+-binding proteins calsequestrin and calreticulin, such as Stains-all blue staining on SDS-PAGE, an acidic isoelectric point and a Ca2+-dependent shift of electrophoretic mobility. The protein was purified to homogeneity by an ammonium sulfate precipitation procedure followed by anion-exchange chromatography on DEAE-Cellulose and electroendosmotic preparative electrophoresis. The Ca2+ binding ability of the M. loti protein was demonstrated by 45Ca2+-overlay assays. ESI-Q-TOF MS/MS analyses of the peptides generated after digestion with either trypsin or endoproteinase AspN identified the rhizobial protein as ferredoxin II and confirmed the presence of Ca2+ adducts.ConclusionsThe present data indicate that ferredoxin II is a major Ca2+ binding protein in M. loti that may participate in Ca2+ homeostasis and suggest an evolutionarily ancient origin for protein-based Ca2+ regulatory systems.Electronic supplementary materialThe online version of this article (doi:10.1186/s12866-015-0352-5) contains supplementary material, which is available to authorized users.

Chapter 11 - Ecology and performance of rhizosphere and endosphere microbiomes

Climate change is leading to significant biotic and abiotic stresses, which is alarming for the future of sustainable crop production and improvement. Global agriculture faces mounting challenges. Understanding epigenetic mechanisms can help improve crops. Exploring plant epigenetic mechanisms can enhance crop resilience, productivity, and stress tolerance, ensuring food security for the growing global populations. Epigenetic mechanisms often involve heritable modifications in organisms without any direct changes in the Deoxyribonucleic Acid (DNA). Epigenetics is essential for making plants adaptive to different stressed conditions. Abiotic and biotic stresses are major limiting factors for plant growth, development, and survival. Epigenetic mechanisms, such as DNA methylation, histone tail modifications, and Ribonucleic Acid (RNA)-directed pathways, regulate gene expression and allow plants to develop memory against these stresses. This memory is crucial for plants to respond effectively to uncertain stresses in the future. These epigenetic modifications are heritable to the next generations. Researchers have shown that plants use epigenetic memory to adapt to a rapidly changing environment, particularly harsh biotic and abiotic challenges, enabling plants to enhance their ability to adapt to diverse environments and withstand abrupt changes in their surroundings. A thorough understanding of these mechanisms can help us develop safer and more efficient methods of crop improvement to make crops more resilient and create a food-secure future for generations. The mechanisms of RNA-directed pathways, DNA methylation, and histone tail modifications are critical in modulating plant responses to diverse stressors, as they directly take part in the expression and suppression of targeted genes.

Sustainable agriculture aims to meet the needs of the present without compromising the ability of future generations to meet their own needs. Microorganisms, especially soil microbes, play a pivotal role in achieving this goal by enhancing soil fertility, promoting plant growth, suppressing pathogens and aiding in biogeochemical cycling. This chapter explores the types of beneficial microbes, their mechanisms of action and their application in sustainable farming practices. The integration of microbial solutions into agricultural systems holds immense potential to reduce chemical dependency, mitigate environmental degradation, and enhance long-term productivity. The growing demand for sustainable agriculture has highlighted the vital role of microorganisms in improving soil fertility, enhancing crop productivity, and reducing dependence on chemical inputs. Microorganisms such as nitrogen-fixing bacteria, phosphate-solubilizing microbes, mycorrhizal fungi, and plant growth-promoting rhizobacteria (PGPR) contribute significantly to nutrient cycling, pest management, and stress tolerance in crops. Their application through biofertilizers and biopesticides promotes eco-friendly practices that align with environmental and human health goals. This chapter explores the diversity of beneficial microbes, their mechanisms of action, applications in sustainable farming, and innovations such as microbial consortia, genome editing, and microbiome engineering. It also addresses the current challenges in field efficacy, formulation stability, and regulatory support. With the integration of biotechnology, nanotechnology, and digital tools, the future of microbial-based agriculture offers promising avenues for resilient and climate-smart farming systems. Thus, microorganisms are emerging as cornerstone agents in achieving global sustainable agriculture goals. Keywords: Microbial, Agriculture, Sustainable Development

A review on the encapsulation of “eco-friendly” compounds in natural polymer-based nanoparticles as next generation nano-agrochemicals for sustainable agriculture and crop management

Plants continuously adapt to their environments by responding to various intrinsic and extrinsic signals. They face numerous biotic and abiotic stresses such as extreme temperatures, drought, or pathogens, requiring complex regulatory mechanisms to control gene activity and adapt their proteome for survival. Epigenetic regulation plays a crucial role in these adaptations, potentially leading to both heritable and non-heritable changes across generations. This process enables plants to adjust their gene expression profiles and acclimate effectively. It is also vital for plant development and productivity, affecting growth, yield, and seed quality, and enabling plants to "remember" environmental stimuli and adapt accordingly. Key epigenetic mechanisms that play significant roles include DNA methylation, histone modification, and ubiquitin ligase complex activity. These processes, which have been extensively studied in the last two decades, have led to a better understanding of the underlying mechanisms and expanded the potential for improving agriculturally and economically important plant traits. DNA methylation is a fundamental process that regulates gene expression by altering chromatin structure. The addition of methyl groups to cytosines by DNA methylases leads to gene suppression, whereas DNA demethylases reverse this effect. Histone modifications, on the other hand, collectively referred to as the "histone code", influence chromatin structure and gene activity by promoting either gene transcription or gene silencing. These modifications are either recognized, added, or removed by a variety of enzymes that act practically as an environmental memory, having a significant impact on plant development and the responses of plants to environmental stimuli. Finally, ubiquitin ligase complexes, which tag specific histones or regulatory proteins with ubiquitin, are also crucial in plant epigenetic regulation. These complexes are involved in protein degradation and play important roles in regulating various cellular activities. The intricate interplay between DNA methylation, histone modifications, and ubiquitin ligases adds complexity to our understanding of epigenetic regulation. These mechanisms collectively control gene expression, generating a complex and branching network of interdependent regulatory pathways. A deeper understanding of this complex network that helps plants adapt to environmental changes and stressful conditions will provide valuable insights into the regulatory mechanisms involved. This knowledge could pave the way for new biotechnological approaches and plant breeding strategies aimed at enhancing crop resilience, productivity, and sustainable agriculture.

Rice planthoppers, including Nilaparvata lugens (Stål), Laodelphax striatellus (Fallén), and Sogatella furcifera (Horváth), pose substantial threats to global rice production through direct feeding damage and transmission of viral diseases. Although chemical control remains the primary management approach, insecticide concentrations below lethal levels (also referred to as ‘sublethal doses’) produce significant biological effects that extend well beyond immediate mortality. This review synthesises current knowledge on how sublethal insecticide exposure fundamentally alters rice planthopper biology through multiple pathways, including nerve system disruption, hormonal imbalance, cellular stress, and heritable genetic changes. Sublethal exposure modifies rice planthopper behaviour by disrupting feeding activity and movement coordination, while simultaneously activating detoxification enzyme systems (cytochrome P450s, glutathione‐ S ‐transferases, and carboxylesterases) that promote insecticide resistance. Reproductive impacts are substantial, with egg production commonly reduced by more than 60%, alongside delayed egg‐laying and damaged ovarian tissues. Interestingly, low doses occasionally stimulate increased reproduction, causing temporary population increases. Developmental effects include prolonged immature stages, enhanced production of winged forms capable of long‐distance migration, and impacts that persist across multiple generations through epigenetic mechanisms. The ecological consequences including pest resurgence, secondary pest outbreak, and impact on non‐target organisms are equally important. Insecticides affect natural enemies (predators and parasitoids) more severely than pests and as a result, surviving rice planthopper populations can rebound rapidly when predation pressure decreases. Broad‐spectrum insecticide applications also enable formerly minor pests to become major problems. Furthermore, beneficial organisms such as pollinators, parasitic wasps, and aquatic predators suffer collateral damage, compromising essential ecosystem functions and creating feedback loops that progressively reduce pesticide effectiveness. Following this review, sustainable rice planthopper management requires integrated strategies combining resistant rice varieties, biological control organisms, precision application technologies, and innovative approaches such as RNA interference‐based biopesticides. Future research should prioritise quantifying impacts on beneficial insects, understanding molecular mechanisms of transgenerational effects, and developing practical decision‐support tools for farmers.

Chapter 8 - Biodiversity and bioresources: impact of biodiversity loss on agricultural sustainability

Optimistic contributions of plant growth-promoting bacteria for sustainable agriculture and climate stress alleviation

Sustainable agriculture has emerged as a critical paradigm for addressing the dual challenges of food security and environmental sustainability in the 21st Century. This study provides an empirical assessment of the adoption, drivers, barriers, and impacts of sustainable agricultural practices among Indian farmers. Using a mixed-methods research approach, the study evaluates key sustainable practices, examines their socio-economic and environmental benefits, and offers policy recommendations to enhance their adoption. Descriptive statistics, linear regression, t-tests, One-way ANOVA, and Chi-square tests have been applied to analyse primary data sourced from 400 farmers and 20 key stakeholders. The findings underscore the significance of context-specific interventions, capacity building, and stakeholder collaboration for advancing sustainable agriculture in India. The study recommends an urgent need for integrated policy frameworks and community-driven initiatives to scale up sustainable agricultural practices for a resilient and secure food system

Nanofertilizers towards sustainable agriculture and environment

Listing of oral and poster presentations from SIP 10. Opening address L.M. Schoonhoven. Session 1: Central neural bases of host plant recognition. Oral Presentations. Session 2: Chemosensory bases of host plant recognition. Oral presentations. Poster Presentations. Session 3: Integrative studies of insect behaviour. Oral Presentations. Poster Presentations. Session 4: Insect behaviour in tritrophic systems. Oral Presentations. Poster Presentations. Session 5: Plant Defences. Oral Presentations. Poster Presentations. Session 6: Insect life histories and plant growth responses. Oral presentations. Poster Presentations. Session 7: Choosing host plants: mechanisms and evolution. Poster Presentations. Session 8: Microbial partners in insect-plant associations. Poster Presentations. Session 9: Genetic bases of host-plant associations. Oral Presentations. Poster Presentations. Session 10: The phylogeny of insect-plant associations. Oral presentations. Poster Presentation. Closing Address R.F. Chapman.

Plants live in constant contact with microorganisms, many of which have profound effects on the growth and development of plant hosts. The plant hormone auxin regulates cell enlargement, cell division, and organogenesis, and is therefore a likely target for microorganisms that manipulate plants. In context of this chapter, the term microorganisms will be used to include bacteria, fungi, nematodes, and protozoans. Many microorganisms can synthesize auxin themselves. Others produce specific signals that indirectly alter the plant auxin balance, for example, through effects on auxin transport, metabolism, or signaling. This chapter highlights plant–microorganism interactions, in which auxin is targeted by symbionts and pathogens to manipulate the development of their plant host. Auxin signaling is also necessary for the regulation of plant defense responses against pathogens, and downregulation of auxin signaling has emerged as a strategy of plants to inhibit pathogen infection. Thus, the regulation of auxin signaling is a balancing act between influences of both the plant and the microbial partner. One future challenge will be to identify the microbial signal molecules that regulate the plant auxin balance, and to find out how the plant integrates the perception of several of these signals at the same time.

The aim of this study is to analyse the evolutionary trajectories of these agroforestry systems in order to identify the main drivers of change that influence their resilient and sustainable management in the Sudanian zone of Togo. Specifically, the aim is to: analyse the main changes that have occurred since 1960; characterise the evolutionary trajectories; and determine the drivers of change that could help to understand the evolution of these systems. The data were collected using a retrospective and prospective diagnostic survey of a sample of farmers, including resource persons, following the Historical-Sociological Investigation Method by means of semi-structured interviews. A Principal Component Analysis coupled with an Ascending Hierarchical Classification was used to study the main stages in the development of these systems. Despite having adopted various measures to promote their adaptability, profound changes have marked the evolution of these systems, testing their limits in the face of these challenges. In this context of adaptability, the results reveal two major transition models: a ‘model of transition from indigenous agricultural systems to extensive and sustainable systems’, dominant in ecological zone I with 47.44% of the systems surveyed, and an ‘agro-ecological transition model towards sustainable, innovative and resilient systems’, dominant in ecological zone II with 52.56% of the said systems. In this duality of agroforestry system management models, it is essential to analyse the evolutionary trajectories and drivers of change in order to draw up appropriate agricultural and environmental policies, with a view to the possible transplantation of these trajectories for sustainable and resilient agriculture both within and between ecological zones.