Plant disease outbreaks pose significant risks to global food security and environmental sustainability worldwide, and result in the loss of primary productivity and biodiversity that negatively impact the environmental and socio-economic conditions of affected regions. Climate change further increases outbreak risks by altering pathogen evolution and host-pathogen interactions and facilitating the emergence of new pathogenic strains. Pathogen range can shift, increasing the spread of plant diseases in new areas. In this Review, we examine how plant disease pressures are likely to change under future climate scenarios and how these changes will relate to plant productivity in natural and agricultural ecosystems. We explore current and future impacts of climate change on pathogen biogeography, disease incidence and severity, and their effects on natural ecosystems, agriculture and food production. We propose that amendment of the current conceptual framework and incorporation of eco-evolutionary theories into research could improve our mechanistic understanding and prediction of pathogen spread in future climates, to mitigate the future risk of disease outbreaks. We highlight the need for a science-policy interface that works closely with relevant intergovernmental organizations to provide effective monitoring and management of plant disease under future climate scenarios, to ensure long-term food and nutrient security and sustainability of natural ecosystems. 

/pdf/climate-change-impacts-on-plant-pathogens-food-security-and-2gkcsncm.pdf

Climate change impacts on plant pathogens, food security and paths forward

Land degradation reduces soil functioning and, consequently, the services that soil provides. Soil hydrological functions are critical to combat soil degradation and promote soil restoration. Soil microorganisms affect soil hydrology, but the role of soil microbiota in forming and sustaining soil is not well explored. Case studies indicate the potential of soil microorganisms as game-changers in restoring soil functions. We review the state of the art of microorganism use in land restoration technology, the groups of microorganisms with the greatest potential for soil restoration, knowledge of the effect of microorganisms on soil physical properties, and proposed strategies for the long-term restoration of degraded lands. We also emphasize the need to advance the emerging research field of biophysical landscape interactions to support soil-plant ecosystem restoration practices. Description Microbes repairing degraded soils Soils worldwide have become increasingly degraded by human activities, especially in drylands. Land degradation negatively affects soil hydrological functioning and thereby the ecosystem services that soil provides. Soil microbes may play an important part in the restoration of degraded soils, positively influencing moisture content and other physical features of soil. Coban et al. reviewed recent work on soil hydraulic properties, potential groups of microorganisms for hydrological soil restoration based on their resilience in dry soils, and future strategies for long-term restoration of degraded lands. —AMS A review suggests that soil microorganisms may be the key to the restoration of hydraulic function in soils degraded by human activities. BACKGROUND Soil, the living skin of Earth, provides ecosystem services critical for life: Soil acts as a filter and store of water, provides a growing medium that supplies plants and heterotrophs with water and nutrients, offers habitat for a large diversity of organisms, and is the source of most of our antibiotics. Humanity is increasingly challenged by the combination of climate change, population growth, and land degradation, including carbon loss, biodiversity decline, and erosion. In particular, land degradation reduces soil hydrological functioning and thereby several other ecosystem services. Such impacts occur through alterations of hydraulic functioning, infiltration and soil moisture storage, carbon cycling, biological activity, transport of nutrients and contaminants, and plant growth. Impacts of global environmental change and associated soil degradation need to be understood and reversed as biodiversity, food production, climate regulation, and people’s livelihoods are increasingly affected by soil ecosystem degradation. The interplay between soil biota and soil hydrological functioning plays an essential role in many biogeochemical cycles, including the water and carbon cycles. Microorganisms dominate soil life and perform an array of vital soil functions by regulating nutrient cycling, decomposing organic matter, defining soil structure, suppressing plant diseases, and supporting plant productivity. The presence of microorganisms and their activity can affect soil structure and hydraulic properties in multiple ways. Case studies indicate the potential of microorganisms as game-changers toward the restoration of soil functioning. However, the role of soil microbiota in forming and sustaining soils has historically been overlooked. ADVANCES It has been proposed that microbial communities not only are an indicator of ecosystem health and restoration level but also can be manipulated to enhance the recovery of degraded ecosystems. In the past decade, there have been an increasing number of studies suggesting the use of microorganisms as ecosystem mediators, particularly to enhance crop production and to engineer microorganisms for dryland restoration. Most current experimental approaches focus on monitoring changes in the microbial community that can be correlated with land restoration; however, microorganisms are also facilitators of ecosystem change, not just followers. We review how microorganisms can help address different types of land degradation, with a focus on physical soil loss and transformation, loss of soil chemical properties, and contamination. We discuss potentially the most valuable groups of microorganisms for soil restoration (namely, plant growth–promoting rhizobacteria, nitrogen-fixing bacteria, and mycorrhizal fungi), emphasizing drylands and advances in plant-microbe interaction studies. We review known effects of microorganisms on soil physical and, specifically, hydraulic properties at pore scale and discuss future strategies for the long-term restoration of degraded lands. We also identify the methodological challenges that have so far hampered progress in understanding soil biophysical processes. OUTLOOK Microorganisms can play the leading role in restoring degraded lands, improving soil hydraulic properties such as infiltration and water retention and reducing soil hydrophobicity, which together can facilitate ecosystem restoration. We advocate for research on mechanisms to restore degraded soils with the use of microorganisms. Given the critical role of freshwater availability to terrestrial life and the paucity of studies on hydrological restoration, we especially advocate for research on the hydrological restoration of degraded soil using microorganisms. We propose that microorganisms can improve soil hydraulic properties such as infiltration and water retention and reduce soil hydrophobicity. Along with new organic matter derived from microbes, this will promote plant growth and facilitate further ecosystem restoration. Such a restoration strategy requires collaboration across the research fields of microbiology and soil hydrology, of which there has been very little to date. Understanding the dynamics of soil microbes and connected hydrological processes would create the foundation for restoration practices that can return resilience to the soil ecosystem. Degraded land in Libya. In degraded lands, a decrease in soil nutrients and organic matter, deterioration of soil structure, increase in salinity, water deficiency, and physical instability can be observed. Credit:cinoby/istockphoto

Soil microbiota as game-changers in restoration of degraded lands

Global biodiversity loss and mass extinction of species are two of the most critical environmental issues the world is currently facing, resulting in the disruption of various ecosystems central to environmental functions and human health. Microbiome-targeted interventions, such as probiotics and microbiome transplants, are emerging as potential options to reverse deterioration of biodiversity and increase the resilience of wildlife and ecosystems. However, the implementation of these interventions is urgently needed. We summarize the current concepts, bottlenecks and ethical aspects encompassing the careful and responsible management of ecosystem resources using the microbiome (termed microbiome stewardship) to rehabilitate organisms and ecosystem functions. We propose a real-world application framework to guide environmental and wildlife probiotic applications. This framework details steps that must be taken in the upscaling process while weighing risks against the high toll of inaction. In doing so, we draw parallels with other aspects of contemporary science moving swiftly in the face of urgent global challenges. Careful and responsible microbiome management is a critical strategy to counter biodiversity loss, but practical and regulatory hurdles must be addressed to maximize its utility. 

/pdf/harnessing-the-microbiome-to-prevent-global-biodiversity-1wcixb82.pdf

Harnessing the microbiome to prevent global biodiversity loss

Plants can recruit beneficial microbes to enhance their ability to defend against pathogens. However, in contrast to the intensively studied roles of the rhizosphere microbiome in suppressing plant pathogens, the collective community-level change and effect of the phyllosphere microbiome in response to pathogen invasion remains largely elusive.Here, we integrated 16S metabarcoding, shotgun metagenomics and culture-dependent methods to systematically investigate the changes in phyllosphere microbiome between infected and uninfected citrus leaves by Diaporthe citri, a fungal pathogen causing melanose disease worldwide. Multiple microbiome features suggested a shift in phyllosphere microbiome upon D. citri infection, highlighted by the marked reduction of community evenness, the emergence of large numbers of new microbes, and the intense microbial network. We also identified the microbiome features from functional perspectives in infected leaves, such as enriched microbial functions for iron competition and potential antifungal traits, and enriched microbes with beneficial genomic characteristics. Glasshouse experiments demonstrated that several bacteria associated with the microbiome shift could positively affect plant performance under D. citri challenge, with reductions in disease index ranging from 65.7 to 88.4%. Among them, Pantoea asv90 and Methylobacterium asv41 identified as "recruited new microbes" in the infected leaves, exhibited antagonistic activities to D. citri both in vitro and in vivo, including inhibition of spore germination and/or mycelium growth. Sphingomonas spp. presented beneficial genomic characteristics and were found to be the main contributor for the functional enrichment of iron complex outer membrane receptor protein in the infected leaves. Moreover, Sphingomonas asv20 showed a stronger suppression ability against D. citri in iron-deficient conditions than iron-sufficient conditions, suggesting a role of iron competition during their antagonistic action.Overall, our study revealed how phyllosphere microbiomes differed between infected and uninfected citrus leaves by melanose pathogen, and identified potential mechanisms for how the observed microbiome shift might have helped plants cope with pathogen pressure. Our findings provide novel insights into understanding the roles of phyllosphere microbiome responses during pathogen challenge. Video abstract. 

/pdf/the-phyllosphere-microbiome-shifts-toward-combating-melanose-6jy18o4t.pdf

The phyllosphere microbiome shifts toward combating melanose pathogen

Developing an effective and safe technology to control severe bacterial diseases in agriculture has attracted significant attention. Here, ZnO nanosphere and ZIF-8 are employed as core and shell, respectively, and then a pH-responsive core-shell nanocarrier (ZnO-Z) was prepared by in situ crystal growth strategy. The bactericide berberine (Ber) was further loaded to form Ber-loaded ZnO-Z (Ber@ZnO-Z) for control of tomato bacterial wilt disease. Results demonstrated that Ber@ZnO-Z could release Ber rapidly in an acidic environment, which corresponded to the pH of the soil where the tomato bacterial wilt disease often outbreak. In vitro experiments showed that the antibacterial activity of Ber@ZnO-Z was about 4.5 times and 1.8 times higher than that of Ber and ZnO-Z, respectively. It was because Ber@ZnO-Z could induce ROS generation, resulting in DNA damage, cytoplasm leakage, and membrane permeability changes so the released Ber without penetrability more easily penetrated the bacteria to achieve an efficient synergistic bactericidal effect with ZnO-Z carriers after combining with DNA. Pot experiments also showed that Ber@ZnO-Z significantly reduced disease severity with a wilt index of 45.8% on day 14 after inoculation, compared to 94.4% for the commercial berberine aqueous solution. More importantly, ZnO-Z carriers did not accumulate in aboveground parts of plants and did not affect plant growth in a short period. This work provides guidance for the effective control of soil-borne bacterial diseases and the development of sustainable agriculture.

pH-Responsive On-Demand Alkaloids Release from Core-Shell ZnO@ZIF-8 Nanosphere for Synergistic Control of Bacterial Wilt Disease.

Cereal crop production is severely affected by seed-borne bacterial diseases across the world. Locally occurring disease resistance in various crops remains elusive. Here, we have observed that rice plants of the same cultivar can be differentiated into disease-resistant and susceptible phenotypes under the same pathogen pressure. Following the identification of a seed-endophytic bacterium as the resistance-conferring agent, integration of high-throughput data, gene mutagenesis and molecular interaction assays facilitated the discovery of the underlying mode of action. Sphingomonas melonis that is accumulated and transmitted across generations in disease-resistant rice seeds confers resistance to disease-susceptible phenotypes by producing anthranilic acid. Without affecting cell growth, anthranilic acid interferes with the sigma factor RpoS of the seed-borne pathogen Burkholderia plantarii, probably leading to impairment of upstream cascades that are required for virulence factor biosynthesis. The overall findings highlight the hidden role of seed endophytes in the phytopathology paradigm of 'disease triangles', which encompass the plant, pathogens and environmental conditions. These insights are potentially exploitable for modern crop cultivation threatened by globally widespread bacterial diseases.

Bacterial seed endophyte shapes disease resistance in rice

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Bacterial seed endophyte shapes disease resistance in rice