Plant disease outbreaks are increasing and threaten food security for the vulnerable in many areas of the world. Now a global human pandemic is threatening the health of millions on our planet. A ...stable, nutritious food supply will be needed to lift people out of poverty and improve health outcomes. Plant diseases, both endemic and recently emerging, are spreading and exacerbated by climate change, transmission with global food trade networks, pathogen spillover, and evolution of new pathogen lineages. In order to tackle these grand challenges, a new set of tools that include disease surveillance and improved detection technologies including pathogen sensors and predictive modeling and data analytics are needed to prevent future outbreaks. Herein, we describe an integrated research agenda that could help mitigate future plant disease pandemics.
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Root-associated microbes are critical to plant health and performance, although understanding of the factors that structure these microbial communities and the theory to predict microbial assemblages ...are still limited. Here, we use a grafted tomato system to study the effects of rootstock genotypes and grafting in endosphere and rhizosphere microbiomes that were evaluated by sequencing 16S rRNA. We compared the microbiomes of nongrafted tomato cultivar BHN589, self-grafted BHN589, and BHN589 grafted to Maxifort or RST-04-106 hybrid rootstocks. Operational taxonomic unit (OTU)-based bacterial diversity was greater in Maxifort compared to the nongrafted control, whereas bacterial diversity in the controls (self-grafted and nongrafted) and the other rootstock (RST-04-106) was similar. Grafting itself did not affect bacterial diversity; diversity in the self-graft was similar to that of the nongraft. Bacterial diversity was higher in the rhizosphere than in the endosphere for all treatments. However, despite the lower overall diversity, there was a greater number of differentially abundant OTUs (DAOTUs) in the endosphere, with the greatest number of DAOTUs associated with Maxifort. In a permutational multivariate analysis of variance (PERMANOVA), there was evidence for an effect of rootstock genotype on bacterial communities. The endosphere-rhizosphere compartment and study site explained a high percentage of the differences among bacterial communities. Further analyses identified OTUs responsive to rootstock genotypes in both the endosphere and rhizosphere. Our findings highlight the effects of rootstocks on bacterial diversity and composition. The influence of rootstock and plant compartment on microbial communities indicates opportunities for the development of designer communities and microbiome-based breeding to improve future crop production.
Understanding factors that control microbial communities is essential for designing and supporting microbiome-based agriculture. In this study, we used a grafted tomato system to study the effect of rootstock genotypes and grafting on bacterial communities colonizing the endosphere and rhizosphere. To compare the bacterial communities in control treatments (nongrafted and self-grafted plants) with the hybrid rootstocks used by farmers, we evaluated the effect of rootstocks on overall bacterial diversity and composition. These findings indicate the potential for using plant genotype to indirectly select bacterial taxa. In addition, we identify taxa responsive to each rootstock treatment, which may represent candidate taxa useful for biocontrol and in biofertilizers.
The success of intervention projects for species management depends on both the effectiveness of management technologies and the geographical landscape of management adoption. Impact network analysis ...(INA) is a new framework for evaluating the likely level of success of regional species management before, during and after projects, for project implementers, policymakers and funders. INA evaluates the effects of management performance in a multilayer network analysis. The socioeconomic network represents manager communication about technologies and influence about technology adoption decisions in an agent‐based model. The linked biophysical network represents species dispersal, resulting in regional success or failure of species management.
The specific objectives of this paper are to (a) introduce the INA framework and ina r package; (b) illustrate the identification of key nodes for smart surveillance strategies; (c) illustrate the application of the INA framework for evaluating the likely degree of success of a project in intervention ecology, before, during and after an intervention; and (d) illustrate the use of INA for evaluating adaptation strategies under global change scenarios with pulse and press stressors, introducing ‘adaptation functions’ to evaluate the management response required for sustainability and resilience.
Examples of use of the ina package show key outcomes of analyses: identifying the limiting factors for effective regional management, pointing out when systems may be non‐responsive to the system components that are readily changed through management decisions, and identifying the additional adaptations that may be necessary for intervention success.
The broader goals for the development of impact network analysis and the ina package are to provide a common framework that integrates across intervention ecology, to enhance opportunities for lessons learned across systems and scientific disciplines, to support the development of a community of practice, and to create a general platform to operationalize analysis of sustainability, resilience and economic viability in intervention ecology applications.
Resumen
El éxito de proyectos de intervención depende de la eficacia en la adopción de tecnologías de manejo ambiental y agrícola. El análisis de impacto de redes (INA, por sus siglas en inglés) es un sistema de evaluación de la probabilidad del éxito regional sobre el manejo de especies – antes, durante, y después de un proyecto de intervención – para los encargados de implementar los proyectos, políticos, donadores e inversionistas. INA evalúa los efectos y el rendimiento del manejo utilizando un análisis de redes multicapas. La red socioeconómica represente la comunicación entre gerentes y la influencia que tienen sobre la toma de decisiones para la implementación, en un modelo basado en agentes. La red biofísica represente la dispersión de especies, resultando en el éxito o el fracaso del manejo de éstas.
Los objetivos de este manuscrito son (1) introducir el sistema INA y el programa INA en R, (2) ilustrar la identificación de los nodos claves para su monitoreo inteligente, (3) ilustrar la aplicación del sistema INA para evaluar el grado probable de éxito de un proyecto de intervención ecológica– antes, durante, y después de un proyecto, y (4) ilustrar el uso de INA para evaluar las estrategias de adopción en diferentes escenarios de cambio global con estresores intermitentes y continuos, con una serie de funciones que se adaptan para poder evaluar los niveles de manejo requeridos de sustentabilidad y resiliencia.
Los ejemplos del uso del programa INA muestran los resultados claves de los análisis: identifica los factores limitantes por el manejo regional, muestra cuando los sistemas tal vez no respondan a algunos componentes que pueden ser fácilmente cambiados por decisiones de manejo, así como también identifica qué ajustes adicionales pueden ser necesarios para el éxito de las intervenciones.
Los principales objetivos del desarrollo del análisis de impacto de redes y del programa INA, son proveen de un sistema general que integra los conceptos de intervenciones ecológicas y potencian la oportunidad de aprender de otros sistemas y disciplinas científicas, favoreciendo el desarrollo de prácticas de grupos con intereses en común, y la creación de un sistema general operacional para el análisis de sustentabilidad, resiliencia, y viabilidad económica aplicadas a la ecología de intervención.
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FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
Drought stress is an alarming constraint to plant growth, development, and productivity worldwide. However, plant-associated bacteria, fungi, and viruses can enhance stress resistance and cope with ...the negative impacts of drought through the induction of various mechanisms, which involve plant biochemical and physiological changes. These mechanisms include osmotic adjustment, antioxidant enzyme enhancement, modification in phytohormonal levels, biofilm production, increased water and nutrient uptake as well as increased gas exchange and water use efficiency. Production of microbial volatile organic compounds (mVOCs) and induction of stress-responsive genes by microbes also play a crucial role in the acquisition of drought tolerance. This review offers a unique exploration of the role of plant-associated microorganisms—plant growth promoting rhizobacteria and mycorrhizae, viruses, and their interactions—in the plant microbiome (or phytobiome) as a whole and their modes of action that mitigate plant drought stress.
Three pillars of sustainability in fisheries Asche, Frank; Garlock, Taryn M.; Anderson, James L. ...
Proceedings of the National Academy of Sciences,
10/2018, Volume:
115, Issue:
44
Journal Article
Peer reviewed
Open access
Sustainability of global fisheries is a growing concern. The United Nations has identified three pillars of sustainability: economic development, social development, and environmental protection. The ...fisheries literature suggests that there are two key trade-offs among these pillars of sustainability. First, poor ecological health of a fishery reduces economic profits for fishers, and second, economic profitability of individual fishers undermines the social objectives of fishing communities. Although recent research has shown that management can reconcile ecological and economic objectives, there are lingering concerns about achieving positive social outcomes. We examined trade-offs among the three pillars of sustainability by analyzing the Fishery Performance Indicators, a unique dataset that scores 121 distinct fishery systems worldwide on 68 metrics categorized by social, economic, or ecological outcomes. For each of the 121 fishery systems, we averaged the outcome measures to create overall scores for economic, ecological, and social performance. We analyzed the scores and found that they were positively associated in the full sample. We divided the data into subsamples that correspond to fisheries management systems with three categories of access—open access, access rights, and harvest rights—and performed a similar analysis. Our results show that economic, social, and ecological objectives are at worst independent and are mutually reinforcing in both types of managed fisheries. The implication is that rights-based management systems should not be rejected on the basis of potentially negative social outcomes; instead, social considerations should be addressed in the design of these systems.
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Climate change affects all segments of the agricultural enterprise, and there is mounting evidence that the continuing warming trend with shifting seasonality and intensity in precipitation will ...increase the vulnerability of agricultural systems. Agricultural is a complex system within the USA encompassing a large number of crops and livestock systems, and development of indicators to provide a signal of the impact of climate change on these different systems would be beneficial to the development of strategies for effective adaptation practices. A series of indicators were assembled to determine their potential for assessing agricultural response to climate change in the near term and long term and those with immediate capability of being implemented and those requiring more development. The available literature reveals indicators on livestock related to heat stress, soil erosion related to changes in precipitation, soil carbon changes in response to increasing carbon dioxide and soil management practices, economic response to climate change in agricultural production, and crop progress and productivity. Crop progress and productivity changes are readily observed data with a historical record for some crops extending back to the mid-1800s. This length of historical record coupled with the county-level observations from each state where a crop is grown and emerging pest populations provides a detailed set of observations to assess the impact of a changing climate on agriculture. Continued refinement of tools to assess climate impacts on agriculture will provide guidance on strategies to adapt to climate change.
Understanding factors influencing microbial interactions, and designing methods to identify key taxa that are candidates for synthetic communities, or SynComs, are complex challenges for achieving ...microbiome-based agriculture. Here, we study how grafting and the choice of rootstock influences root-associated fungal communities in a grafted tomato system. We studied three tomato rootstocks (BHN589, RST-04-106, and Maxifort) grafted to a BHN589 scion and profiled the fungal communities in the endosphere and rhizosphere by sequencing the internal transcribed spacer (ITS2). The data provided evidence for a rootstock effect (explaining ~2% of the total captured variation,
< 0.01) on the fungal community. Moreover, the most productive rootstock, Maxifort, supported greater fungal species richness than the other rootstocks or controls. We then constructed a phenotype-operational taxonomic unit (OTU) network analysis (PhONA) using an integrated machine learning and network analysis approach based on fungal OTUs and associated tomato yield as the phenotype. PhONA provides a graphical framework to select a testable and manageable number of OTUs to support microbiome-enhanced agriculture. We identified differentially abundant OTUs specific to each rootstock in both endosphere and rhizosphere compartments. Subsequent analyses using PhONA identified OTUs that were directly associated with tomato fruit yield and others that were indirectly linked to yield through their links to these OTUs. Fungal OTUs that are directly or indirectly linked with tomato yield may represent candidates for synthetic communities to be explored in agricultural systems.
The realized benefits of microbiome analyses for plant health and disease management are often limited by the lack of methods to select manageable and testable synthetic microbiomes. We evaluated the composition and diversity of root-associated fungal communities from grafted tomatoes. We then constructed a phenotype-OTU network analysis (PhONA) using these linear and network models. By incorporating yield data in the network, PhONA identified OTUs that were directly predictive of tomato yield and others that were indirectly linked to yield through their links to these OTUs. Follow-up functional studies of taxa associated with effective rootstocks, identified using approaches such as PhONA, could support the design of synthetic fungal communities for microbiome-based crop production and disease management. The PhONA framework is flexible for incorporation of other phenotypic data, and the underlying models can readily be generalized to accommodate other microbiome or 'omics data.
Pyrosequencing was used to study the effect of rotation and tillage on total bacterial communities. We designed primers to the bacterial 16s rDNA and amplified DNA from soil samples from a long-term ...tillage/rotation trial in Kansas for two seasons. The 2 × 2 factorial trial had two rotation treatments (wheat–wheat and wheat–soybean) and two tillage treatments (conventional and no-till). A total of 20,180 16s rDNA sequences were generated and 2337 operational taxonomic units (OTUs) were assembled using a 97% similarity cut-off. The phylum Proteobacteria represented 38% of 299 identified taxa. The second most abundant phylum was Acidobacteria, making up 20% of the sequences, the majority of which were Acidobacteria Group 1. The phyla Actinobacteria and Gemmatimonadetes comprised 12% and 3.5% of the sequences. Other groups detected included TM7, Nitrospira, Verrucomicrobia, and Bacteroidetes. Some clusters of Acidobacteria Group 1 were more frequent in continuous wheat versus wheat–soybean rotation, some Acidobacteria Group 2 were more frequent in no-till, and some Acidobacteria Group 4 were more frequent in wheat–soybean rotation. These results were validated by quantitative real-time PCR. Pyrosequencing provided taxonomic information about the overall bacterial community, and detected community shifts resulting from different cropping practices.
► Pyrosequencing can detect shifts in bacterial taxa due to tillage and crop rotation. ► The Phylum Acidobacteria was a predominant component of the soil in a long-term wheat study site in Kansas. ► Groups of Acidobacteria were affected by tillage and crop rotation in a long-term wheat study site in Kansas.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK, ZRSKP
Weather affects the severity of many plant diseases, and climate change is likely to alter the patterns of crop disease severity. Evaluating possible future patterns can help focus crop breeding and ...disease management research. We examined the global effect of climate change on potato late blight, the disease that caused the Irish potato famine and still is a common potato disease around the world. We used a metamodel and considered three global climate models for the A2 greenhouse gas emission scenario for three 20‐year time‐slices: 2000–2019, 2040–2059 and 2080–2099. In addition to global analyses, five regions were evaluated where potato is an important crop: the Andean Highlands, Indo‐Gangetic Plain and Himalayan Highlands, Southeast Asian Highlands, Ethiopian Highlands, and Lake Kivu Highlands in Sub‐Saharan Africa. We found that the average global risk of potato late blight increases initially, when compared with historic climate data, and then declines as planting dates shift to cooler seasons. Risk in the agro‐ecosystems analyzed, varied from a large increase in risk in the Lake Kivu Highlands in Rwanda to decreases in the Southeast Asian Highlands of Indonesia.
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