R. Ford Denison

Host sanctions and the legume-rhizobium mutualism.

Explaining mutualistic cooperation between species remains one of the greatest problems for evolutionary biology. Why do symbionts provide costly services to a host, indirectly benefiting competitors sharing the same individual host? Host monitoring of symbiont performance and the imposition of sanctions on ‘cheats’ could stabilize mutualism. Here we show that soybeans penalize rhizobia that fail to fix N2 inside their root nodules. We prevented a normally mutualistic rhizobium strain from cooperating (fixing N2) by replacing air with an N2-free atmosphere (Ar:O2). A series of experiments at three spatial scales (whole plants, half root systems and individual nodules) demonstrated that forcing non-cooperation (analogous to cheating) decreased the reproductive success of rhizobia by about 50%. Non-invasive monitoring implicated decreased O2 supply as a possible mechanism for sanctions against cheating rhizobia. More generally, such sanctions by one or both partners may be important in stabilizing a wide range of mutualistic symbioses.

Application of Real-Time PCR To Study Effects of Ammonium on Population Size of Ammonia-Oxidizing Bacteria in Soil

ABSTRACT Ammonium oxidation by autotrophic ammonia-oxidizing bacteria (AOB) is a key process in agricultural and natural ecosystems and has a large global impact. In the past, the ecology and physiology of AOB were not well understood because these organisms are notoriously difficult to culture. Recent applications of molecular techniques have advanced our knowledge of AOB, but the necessity of using PCR-based techniques has made quantitative measurements difficult. A quantitative real-time PCR assay targeting part of the ammonia-monooxygenase gene (amoA) was developed to estimate AOB population size in soil. This assay has a detection limit of 1.3 × 105 cells/g of dry soil. The effect of the ammonium concentration on AOB population density was measured in soil microcosms by applying 0, 1.5, or 7.5 mM ammonium sulfate. AOB population size and ammonium and nitrate concentrations were monitored for 28 days after (NH4)2SO4 application. AOB populations in amended treatments increased from an initial density of approximately 4 × 106 cells/g of dry soil to peak values (day 7) of 35 × 106 and 66 × 106 cells/g of dry soil in the 1.5 and 7.5 mM treatments, respectively. The population size of total bacteria (quantified by real-time PCR with a universal bacterial probe) remained between 0.7 × 109 and 2.2 × 109 cells/g of soil, regardless of the ammonia concentration. A fertilization experiment was conducted in a tomato field plot to test whether the changes in AOB density observed in microcosms could also be detected in the field. AOB population size increased from 8.9 × 106 to 38.0 × 106 cells/g of soil by day 39. Generation times were 28 and 52 h in the 1.5 and 7.5 mM treatments, respectively, in the microcosm experiment and 373 h in the ammonium treatment in the field study. Estimated oxidation rates per cell ranged initially from 0.5 to 25.0 fmol of NH4+ h−1 cell−1 and decreased with time in both microcosms and the field. Growth yields were 5.6 × 106, 17.5 × 106, and 1.7 × 106 cells/mol of NH4+ in the 1.5 and 7.5 mM microcosm treatments and the field study, respectively. In a second field experiment, AOB population size was significantly greater in annually fertilized versus unfertilized soil, even though the last ammonium application occurred 8 months prior to measurement, suggesting a long-term effect of ammonium fertilization on AOB population size.

Legume sanctions and the evolution of symbiotic cooperation by rhizobia.

The legume‐rhizobium symbiosis is an ideal model for studying the factors that limit the evolution of microbial mutualists into parasites. Legumes are unable to consistently recognize parasitic rhizobia that, once established inside plant cells, use plant resources for their own reproduction rather than for N2 fixation. Evolution of parasitism in rhizobia, driven partly by competition among multiple rhizobial strains infecting the same plant, may be countered by postinfection legume sanctions. Both the biochemical options for rhizobial cheating and the evolutionary effect of legume sanctions depend on differences in rhizobial life history associated with nodule type. In legumes with determinate nodule growth, rhizobia typically retain the ability to reproduce after differentiating into N2‐fixing bacteroids. Sanctions against individual bacteroids (e.g., acid hydrolases) would therefore select for cooperative rhizobia. In nodules with indeterminate growth, bacteroids generally lose the ability to reproduce, so legume sanctions against bacteroids would have no effect on rhizobial evolution. Whole‐nodule sanctions (e.g., decreased nodule O2 permeability) could be effective, via kin selection of undifferentiated rhizobia that persist in indeterminate nodules and replenish soil populations after nodule senescence. Mixed nodules could reduce the effectiveness of whole‐nodule sanctions. The frequency of mixed nodules under field conditions is unknown.

Sanctions and mutualism stability: why do rhizobia fix nitrogen?

Why do rhizobia expend resources on fixing N2 for the benefit of their host plant, when they could use those resources for their own reproduction? We present a series of theoretical models which counter the hypotheses that N2 fixation is favoured because it (i) increases the exudation of useful resources to related rhizobia in the nearby soil, or (ii) increases plant growth and therefore the resources available for rhizobia growth. Instead, we suggest that appreciable levels of N2 fixation are only favoured when plants preferentially supply more resources to (or are less likely to senesce) nodules that are fixing more N2 (termed plant sanctions). The implications for different agricultural practices and mutualism stability in general are discussed.

Experimental evolution of multicellularity

Multicellularity was one of the most significant innovations in the history of life, but its initial evolution remains poorly understood. Using experimental evolution, we show that key steps in this transition could have occurred quickly. We subjected the unicellular yeast Saccharomyces cerevisiae to an environment in which we expected multicellularity to be adaptive. We observed the rapid evolution of clustering genotypes that display a novel multicellular life history characterized by reproduction via multicellular propagules, a juvenile phase, and determinate growth. The multicellular clusters are uniclonal, minimizing within-cluster genetic conflicts of interest. Simple among-cell division of labor rapidly evolved. Early multicellular strains were composed of physiologically similar cells, but these subsequently evolved higher rates of programmed cell death (apoptosis), an adaptation that increases propagule production. These results show that key aspects of multicellular complexity, a subject of central importance to biology, can readily evolve from unicellular eukaryotes.

Lifestyle alternatives for rhizobia: mutualism, parasitism, and forgoing symbiosis

Strains of rhizobia within a single species can have three different genetically determined strategies. Mutualistic rhizobia provide their legume hosts with nitrogen. Parasitic rhizobia infect legumes, but fix little or no nitrogen. Nonsymbiotic strains are unable to infect legumes at all. Why have rhizobium strains with one of these three strategies not displaced the others? A symbiotic (mutualistic or parasitic) rhizobium that succeeds in founding a nodule may produce many millions of descendants. The chances of success can be so low, however, that nonsymbiotic rhizobia can have greater reproductive success. Legume sanctions against nodules that fix little or no nitrogen favor more mutualistic strains, but parasitic strains that use plant resources only for their own reproduction may do well when they share nodules with mutualistic strains.

Human selection and the relaxation of legume defences against ineffective rhizobia

Enforcement mechanisms are thought to be important in maintaining mutualistic cooperation between species. A clear example of an enforcement mechanism is how legumes impose sanctions on rhizobial symbionts that fail to provide sufficient fixed N2. However, with domestication and breeding in high-soil-N environments, humans may have altered these natural legume defences and reduced the agricultural benefits of the symbiosis. Using six genotypes of soya beans, representing 60 years of breeding, we show that, as a group, older cultivars were better able to maintain fitness than newer cultivars (seed production) when infected with a mixture of effective and ineffective rhizobial strains. Additionally, we found small differences among cultivars in the ratio of effective : ineffective rhizobia released from their nodules, an indicator of future rhizobial strain fitness. When infected by symbionts varying in quality, legume defences against poor-quality partners have apparently worsened under decades of artificial selection.

Darwinian Agriculture: When Can Humans Find Solutions Beyond The Reach of Natural Selection?

Progress in genetic improvement of crop yield potential has slowed since 1985. Simultaneously, more sustainable management of agricultural ecosystems is needed. A better understanding of natural selection can help solve both problems. We illustrate this point with two specific examples. First, the genetic legacy of crop plants has been refined by millions of years of natural selection, often driven by competition among plants. We therefore suggest that most simple, tradeoff‐free options to increase competitiveness (e.g., increased gene expression, or minor modifications of existing plant genes) have already been tested by natural selection. Further genetic improvement of crop yield potential over the next decade will mainly involve tradeoffs, either between fitness in past versus present environments, or between individual competitiveness and the collective performance of plant communities. Eventually, we may develop the ability to predict the consequences of genetic alterations so radical that they have not yet been tested by natural selection. Second, natural selection acts mainly at the level of genes, individuals, and family groups, rather than ecosystems as a whole. Consequently, there is no reason to expect the structure of natural ecosystems (diversity, spatial, or temporal patterns) to be a reliable blueprint for agricultural ecosystems. Natural ecosystems are nonetheless an important source of information that could be used to improve agriculture.

Applying evolutionary biology to address global challenges

BACKGROUND Differences among species in their ability to adapt to environmental change threaten biodiversity, human health, food security, and natural resource availability. Pathogens, pests, and cancers often quickly evolve resistance to control measures, whereas crops, livestock, wild species, and human beings often do not adapt fast enough to cope with climate change, habitat loss, toxicants, and lifestyle change. To address these challenges, practices based on evolutionary biology can promote sustainable outcomes via strategic manipulation of genetic, developmental, and environmental factors. Successful strategies effectively slow unwanted evolution and reduce fitness in costly species or improve performance of valued organisms by reducing phenotype-environment mismatch or increasing group productivity. Tactics of applied evolutionary biology range broadly, from common policies that promote public health or preserve habitat for threatened species—but are easily overlooked as having an evolutionary rationale, to the engineering of new genomes. Tactics and tools of applied evolutionary biology. (Top) Evolutionary tactics to address the major societal challenges treated in the present study are shown as a wheel. Challenges in the food, health, and environment sectors are caused by rapid contemporary evolution or, in more slowly reproducing or threatened species, phenotype-environment mismatch. Gene flow and selection agents make challenges in one sector dependent on actions in others. Current progress in implementing tactics of applied evolutionary biology to address challenges varies widely. (Bottom) Many of these tactics use a common toolbox of strategies to prevent unwanted evolution or to reduce fitness in harmful organisms, as well as to reduce mismatch between organisms and human-altered environments or to increase group performance in desired organisms. Each of these strategies uses a combination of manipulations of the organismal genotype, phenotypic plasticity (development), or environmental conditions. ADVANCES The scope and development of current tactics vary widely. In particular, genetic engineering attracts much attention (and controversy) but now is used mainly for traits under simple genetic control. Human gene therapy, which mainly involves more complex controls, has yet to be applied successfully at large scales. In contrast, other methods to alter complex traits are improving. These include artificial selection for drought- and flood-tolerant crops through bioinformatics and application of “life course” approaches in medicine to reduce human metabolic disorders. Successful control of unwanted evolution depends on governance initiatives that address challenges arising from both natural and social factors. Principal among these challenges are (i) global transfer of genes and selection agents; (ii) interlinked evolution across traditional sectors of society (environment, food, and health); and (iii) conflicts between individual and group incentives that threaten regulation of antibiotic use and crop refuges. Evolutionarily informed practices are a newer prospect in some fields and require more systematic research, as well as ethical consideration—for example, in attempts to protect wild species through assisted migration, in the choice of source populations for restoration, or in genetic engineering. OUTLOOK A more unified platform will better convey the value of evolutionary methods to the public, scientists, and decision-makers. For researchers and practitioners, applications may be expanded to other disciplines, such as in the transfer of refuge strategies that slow resistance evolution in agriculture to slow unwanted evolution elsewhere (for example, cancer resistance or harvest-induced evolution). For policy-makers, adoption of practices that minimize unwanted evolution and reduce phenotype-environment mismatch in valued species is likely essential to achieve the forthcoming Sustainable Development Goals and the 2020 Aichi Biodiversity Targets. Exploiting evolution for humanitys sake Using artificial selection, humans have tapped into evolutionary processes for thousands of years. The results of this process we see all around us, from the dogs we share our homes with to the food we put on our table. Carroll et al. review the ways that a more intentional harnessing of evolution may be able to help us meet some of Earths most pressing challenges, including disease, climate change, and food security. Science, this issue 10.1126/science.1245993 Two categories of evolutionary challenges result from escalating human impacts on the planet. The first arises from cancers, pathogens, and pests that evolve too quickly and the second, from the inability of many valued species to adapt quickly enough. Applied evolutionary biology provides a suite of strategies to address these global challenges that threaten human health, food security, and biodiversity. This Review highlights both progress and gaps in genetic, developmental, and environmental manipulations across the life sciences that either target the rate and direction of evolution or reduce the mismatch between organisms and human-altered environments. Increased development and application of these underused tools will be vital in meeting current and future targets for sustainable development.

Life Histories of Symbiotic Rhizobia and Mycorrhizal Fungi

Research on life history strategies of microbial symbionts is key to understanding the evolution of cooperation with hosts, but also their survival between hosts. Rhizobia are soil bacteria known for fixing nitrogen inside legume root nodules. Arbuscular mycorrhizal (AM) fungi are ubiquitous root symbionts that provide plants with nutrients and other benefits. Both kinds of symbionts employ strategies to reproduce during symbiosis using host resources; to repopulate the soil; to survive in the soil between hosts; and to find and infect new hosts. Here we focus on the fitness of the microbial symbionts and how interactions at each of these stages has shaped microbial life-history strategies. During symbiosis, microbial fitness could be increased by diverting more resources to individual reproduction, but that may trigger fitness-reducing host sanctions. To survive in the soil, symbionts employ sophisticated strategies, such as persister formation for rhizobia and reversal of spore germination by mycorrhizae. Interactions among symbionts, from rhizobial quorum sensing to fusion of genetically distinct fungal hyphae, increase adaptive plasticity. The evolutionary implications of these interactions and of microbial strategies to repopulate and survive in the soil are largely unexplored.