Molecular Diversity of Legume Root-Nodule Bacteria in Kakadu National Park, Northern Territory, Australia

BACKGROUND: Symbiotic relationships between leguminous plants (family Fabaceae) and nodule-forming bacteria in Australia native ecosystems remain poorly characterized despite their importance. Most studies have focused on temperate parts of the country, where the use of molecular approaches have already revealed the presence of Bradyrhizobium, Ensifer (formerly Sinorhizobium), Mesorhizobium and Rhizobium genera of legume root-nodule bacteria. We here provide the first molecular characterization of nodulating bacteria from tropical Australia. METHODOLOGY/PRINCIPAL FINDINGS: 45 nodule-forming bacterial strains, isolated from eight native legume hosts at eight locations in Kakadu National Park, Northern Territory, Australia, were examined for their genetic diversity and phylogenetic position. Using SSU rDNA PCR-RFLPs and phylogenetic analyses, our survey identified nine genospecies, two of which, Bradyrhizobium genospp. B and P, had been previously identified in south-eastern Australia and one, Mesorhizobium genospecies AA, in southern France. Three of the five newly characterized Bradyrhizobium genospecies were more closely related to B. japonicum USDA110, whereas the other two belonged to the B. elkanii group. All five were each more closely related to strains sampled in various tropical areas outside Australia than to strains known to occur in Australia. We also characterized an entirely novel nodule-forming lineage, phylogenetically distant from any previously described rhizobial and non-rhizobial legume-nodulating lineage within the Rhizobiales. CONCLUSIONS/SIGNIFICANCE: Overall, the present results support the hypothesis of tropical areas being centres of biodiversity and diversification for legume root-nodule bacteria and confirm the widespread occurrence of Bradyrhizobium genosp. B in continental Australia

Disease influences host population growth rates in a natural wild plant-pathogen association over a 30-year period

1. The epidemiological and demographic dynamics of plant-pathogen interactions in natural environments are strongly affected by spatial and temporal influences. Here we assess the interaction between Filipendula ulmaria and its rust pathogen Triphragmium ulmariae by analysing a 30-year long dataset that has followed pathogen and plant population dynamics in a metapopulation of similar to 230 host patches growing on islands of the Skeppsvik archipelago in northern Sweden.2. Over this period, the host metapopulation initially expanded in both number and size of individual patches before plateauing. In contrast, the pathogen metapopulation showed greater change. Disease incidence showed a convex pattern rising for the first decade before showing a marked decline in the last decade. At the same time, the prevalence of disease in infected populations showed a constant 30-year long decline.3. At the individual host population level, each population was annually classified into one of four inter-year states: healthy, recolonization, extinction and diseased. Host populations that were healthy from 1 year to the next were significantly smaller than all other host population categories, while host populations in which disease was constantly present were significantly larger.4. Host populations in which the pathogen underwent either an extinction or a recolonization event were of similar size and represented a measure of the host threshold size for long-term pathogen survival.5. Host population growth rates declined as disease levels increased. The growth rate of host populations in which disease was continuously present was 75% lower than in populations that were free disease.6. The sensitivity of the association to climate change as demonstrated through a decline in disease incidence and prevalence and an increase in drought damage to plant populations as temperatures rise has only become apparent through analysis of an extensive long-term dataset.7. Synthesis. To date wild plant-pathogen studies have focused on the epidemiology of the pathogen and its effect on individual plant fitness. Here we have established a link to the impact of the pathogen on the long-term dynamics of host populations. This has the potential to trigger a cascade of changes in the species composition and diversity of communities

Triple bottom-line consideration of sustainable plant disease management: From economic, sociological and ecological perspectives

Plant disease management plays an important role in achieving the sustainable development goals of the United Nations (UN) such as food security, human health, socio-economic improvement, resource conservation and ecological resilience. However, technologies available are often limited due to different interests between producers and society and lacks of proper understanding of economic thresholds and the complex interactions among ecology, productivity and profitability. A comprehensive synergy and conflict evaluation of economic, sociological and ecological effects with technologies, productions and evolutionary principles as main components should be used to guide sustainable disease management that aims to mitigate crop and economic losses in the short term while maintaining functional farm ecosystem in the long term. Consequently, there should be an increased emphasis on technology development, public education and information exchange among governments, researchers, producers and consumers to broaden the options for disease management in the future

Genetic analysis reveals long-standing population differentiation and high diversity in the rust pathogen Melampsora lini

A priority for research on infectious disease is to understand how epidemiological and evolutionary processes interact to influence pathogen population dynamics and disease outcomes. However, little is understood about how population adaptation changes across time, how sexual vs. asexual reproduction contribute to the spread of pathogens in wild populations and how diversity measured with neutral and selectively important markers correlates across years. Here, we report results from a long-term study of epidemiological and genetic dynamics within several natural populations of theLinum marginale-Melampsora liniplant-pathogen interaction. Using pathogen isolates collected from three populations of wild flax (L.marginale) spanning 16 annual epidemics, we probe links between pathogen population dynamics, phenotypic variation for infectivity and genomic polymorphism. Pathogen genotyping was performed using 1567 genome-wide SNP loci and sequence data from two infectivity loci (AvrP123,AvrP4). Pathogen isolates were phenotyped for infectivity using a differential set. Patterns of epidemic development were assessed by conducting surveys of infection prevalence in one population (Kiandra) annually. Bayesian clustering analyses revealed host population and ecotype as key predictors of pathogen genetic structure. Despite strong fluctuations in pathogen population size and severe annual bottlenecks, analysis of molecular variance revealed that pathogen population differentiation was relatively stable over time. Annually, varying levels of clonal spread (0-44.8%) contributed to epidemics. However, within populations, temporal genetic composition was dynamic with rapid turnover of pathogen genotypes, despite the dominance of only four infectivity phenotypes across the entire study period. Furthermore, in the presence of strong fluctuations in population size and migration, spatial selection may maintain pathogen populations that, despite being phenotypically stable, are genetically highly dynamic. Author summary Melampsora liniis a rust fungus that infects native flax,Linum marginalein south-eastern Australia where its epidemiology and evolution have been intensively studied since 1987. Over that time, substantial diversity in the pathotypic structure ofM.linihas been demonstrated but an understanding of how genetic diversity in pathogen populations is maintained through space and time is lacking. Here we integrated phenotypic, genotypic and epidemiological datasets spanning 16 annual epidemics across three host populations to examine long-term pathogen genetic dynamics. The results show that host ecotype is the dominant selective force in the face of strong bottlenecks and annual patterns of genetic turnover. Results from previous studies indicate that in this geographic region,M.linilacks the capacity to reproduce sexually-we thus expected to find limited genetic diversity and evidence for strong clonality influencing genetic dynamics within growing seasons. However, the breadth of genomic coverage provided by the SNP markers revealed high levels of genotypic variation withinM.linipopulations. This discovery contrasts with observed phenotypic dynamics as the epidemics of this pathogen were largely dominated by four pathotypes across the study period. Based on a detailed assessment and comparison of pathotypic and genotypic patterns, our study increases the understanding of how genetic diversity is generated and maintained through space and time within wild pathogen populations. The implications for the management of resistance to pathogens in agricultural or conservation contexts are significant: the appearance of clonality may be hiding high levels of pathogen diversity and recombination. Understanding how this diversity is generated could provide new and unique ways to mitigate or suppress the emergence of infectious strains, allowing to efficiently combat harmful diseases.Peer reviewe

Increasing forest loss worldwide from invasive pests requires new trade regulations

Loss of forests due to non-native invasive pests (including insects, nematodes, and pathogens) is a global phenomenon with profound population, community, ecosystem, and economic impacts. We review the magnitude of pest-associated forest loss worldwide and discuss the major ecological and evolutionary causes and consequences of these invasions. After compiling and analyzing a dataset of pest invasions from 21 countries, we show that the number of forest pest invasions recorded for a given country has a significant positive relationship with trade (as indicated by gross domestic product) and is not associated with the amount of forested land within that country. We recommend revisions to existing international protocols for preventing pest entry and proliferation, including prohibiting shipments of non-essential plants and plant products unless quarantined. Because invasions often originate from taxa that are scientifically described only after their introduction, current phytosanitary regulations – which target specific, already named organisms – are ineffective

Optimizing Plant Disease Management in Agricultural Ecosystems Through Rational In-Crop Diversification

Biodiversity plays multifaceted roles in societal development and ecological sustainability. In agricultural ecosystems, using biodiversity to mitigate plant diseases has received renewed attention in recent years but our knowledge of the best ways of using biodiversity to control plant diseases is still incomplete. In term of in-crop diversification, it is not clear how genetic diversity per se in host populations interacts with identifiable resistance and other functional traits of component genotypes to mitigate disease epidemics and what is the best way of structuring mixture populations. In this study, we created a series of host populations by mixing different numbers of potato varieties showing different late blight resistance levels in different proportions. The amount of naturally occurring late blight disease in the mixture populations was recorded weekly during the potato growing seasons. The percentage of disease reduction (PDR) in the mixture populations was calculated by comparing their observed late blight levels relative to that expected when they were planted in pure stands. We found that PDR in the mixtures increased as the number of varieties and the difference in host resistance (DHR) between the component varieties increased. However, the level of host resistance in the potato varieties had little impact on PDR. In mixtures involving two varieties, the optimum proportion of component varieties for the best PDR depended on their DHR, with an increasing skewness to one of the component varieties as the DHR between the component varieties increased. These results indicate that mixing crop varieties can significantly reduce disease epidemics in the field. To achieve the best disease mitigation, growers should include as many varieties as possible in mixtures or, if only two component mixtures are possible, increase DHR among the component varieties

Evolution in agriculture: the application of evolutionary approaches to the management of biotic interactions in agro-ecosystems

Anthropogenic impacts increasingly drive ecological and evolutionary processes at many spatio-temporal scales, demanding greater capacity to predict and manage their consequences. This is particularly true for agro-ecosystems, which not only comprise a significant proportion of land use, but which also involve conflicting imperatives to expand or intensify production while simultaneously reducing environmental impacts. These imperatives reinforce the likelihood of further major changes in agriculture over the next 30–40 years. Key transformations include genetic technologies as well as changes in land use. The use of evolutionary principles is not new in agriculture (e.g. crop breeding, domestication of animals, management of selection for pest resistance), but given land-use trends and other transformative processes in production landscapes, ecological and evolutionary research in agro-ecosystems must consider such issues in a broader systems context. Here, we focus on biotic interactions involving pests and pathogens as exemplars of situations where integration of agronomic, ecological and evolutionary perspectives has practical value. Although their presence in agro-ecosystems may be new, many traits involved in these associations evolved in natural settings. We advocate the use of predictive frameworks based on evolutionary models as pre-emptive management tools and identify some specific research opportunities to facilitate this. We conclude with a brief discussion of multidisciplinary approaches in applied evolutionary problems

Population Processes at Multiple Spatial Scales Maintain Diversity and Adaptation in the Linum marginale - Melampsora lini Association

Peer reviewe