Long‐term nitrogen addition causes the evolution of less‐cooperative mutualists

Human activities have altered the global nitrogen (N) cycle, and as a result, elevated N inputs are causing profound ecological changes in diverse ecosystems. The evolutionary consequences of this global change have been largely ignored even though elevated N inputs are predicted to cause mutualism breakdown and the evolution of decreased cooperation between resource mutualists. Using a long‐term (22 years) N‐addition experiment, we find that elevated N inputs have altered the legume–rhizobium mutualism (where rhizobial bacteria trade N in exchange for photosynthates from legumes), causing the evolution of less‐mutualistic rhizobia. Plants inoculated with rhizobium strains isolated from N‐fertilized treatments produced 17–30% less biomass and had reduced chlorophyll content compared to plants inoculated with strains from unfertilized control plots. Because the legume–rhizobium mutualism is the major contributor of naturally fixed N to terrestrial ecosystems, the evolution of less‐cooperative rhizobia may have important environmental consequences.     

No selection for cheating in a natural meta‐population of rhizobia

Whether natural selection favours ‘cheating’ in mutualisms is hotly debated. Gano‐Cohen et al. (2019a) report a negative correlation between fitness and mutualist quality in rhizobia, suggesting that rhizobia evolve to cheat. However, reanalysis of their data shows that the correlation is an artefact of unequal sampling across populations.     

Cellular interactions: lessons from the nitrogen‐fixing cyanobacteria

Marine nitrogen‐fixing cyanobacteria play a central role in the open‐ocean microbial community by providing fixed nitrogen (N) to the ocean from atmospheric dinitrogen (N₂) gas. Once thought to be dominated by one genus of cyanobacteria, Trichodesmium, it is now clear that marine N₂‐fixing cyanobacteria in the open ocean are more diverse, include several previously unknown symbionts, and are geographically more widespread than expected. The next challenge is to understand the ecological implications of this genetic and phenotypic diversity for global oceanic N cycling. One intriguing aspect of the cyanobacterial N₂ fixers ecology is the range of cellular interactions they engage in, either with cells of their own species or with photosynthetic protists. From organelle‐like integration with the host cell to a free‐living existence, N₂‐fixing cyanobacteria represent the range of types of interactions that occur among microbes in the open ocean. Here, we review what is known about the cellular interactions carried out by marine N₂‐fixing cyanobacteria and where future work can help. Discoveries related to the functional roles of these specialized cells in food webs and the microbial community will improve how we interpret their distribution and abundance patterns and contributions to global N and carbon (C) cycles.     

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.     

Caught in the act: Rapid,symbiont‐driven evolution

Facultative bacterial endosymbionts can transfer horizontally among lineages of their arthropod hosts, providing the recipient with a suite of traits that can lead to rapid evolutionary response, as has been recently demonstrated. But how common is symbiont‐driven evolution? Evidence suggests that successful symbiont transfers are most likely within a species or among closely related species, although more distant transfers have occurred over evolutionary history. Symbiont‐driven evolution need not be a function of a recent horizontal transfer, however. Many endosymbionts infect only a small proportion of a host population, but could quickly increase in frequency under favorable selection regimes. Some host species appear to accumulate a diversity of facultative endosymbionts, and it is among these species that symbiont‐driven evolution should be most prevalent. It remains to be determined how frequently symbionts enable rapid evolutionary response by their hosts, but substantial ecological effects are a likely consequence whenever it does occur.     

Interspecific conflict and the evolution of ineffective rhizobia

Microbial symbionts exhibit broad genotypic variation in their fitness effects on hosts, leaving hosts vulnerable to costly partnerships. Interspecific conflict and partner‐maladaptation are frameworks to explain this variation, with different implications for mutualism stability. We investigated the mutualist service of nitrogen fixation in a metapopulation of root‐nodule forming Bradyrhizobium symbionts in Acmispon hosts. We uncovered Bradyrhizobium genotypes that provide negligible mutualist services to hosts and had superior in planta fitness during clonal infections, consistent with cheater strains that destabilise mutualisms. Interspecific conflict was also confirmed at the metapopulation level – by a significant negative association between the fitness benefits provided by Bradyrhizobium genotypes and their local genotype frequencies – indicating that selection favours cheating rhizobia. Legumes have mechanisms to defend against rhizobia that fail to fix sufficient nitrogen, but these data support predictions that rhizobia can subvert plant defenses and evolve to exploit hosts.     

Selection for cheating across disparate environments in the legume‐rhizobium mutualism

The primary dilemma in evolutionarily stable mutualisms is that natural selection for cheating could overwhelm selection for cooperation. Cheating need not entail parasitism; selection favours cheating as a quantitative trait whenever less‐cooperative partners are more fit than more‐cooperative partners. Mutualisms might be stabilised by mechanisms that direct benefits to more‐cooperative individuals, which counter selection for cheating; however, empirical evidence that natural selection favours cheating in mutualisms is sparse. We measured selection on cheating in single‐partner pairings of wild legume and rhizobium lineages, which prevented legume choice. Across contrasting environments, selection consistently favoured cheating by rhizobia, but did not favour legumes that provided less benefit to rhizobium partners. This is the first simultaneous measurement of selection on cheating across both host and symbiont lineages from a natural population. We empirically confirm selection for cheating as a source of antagonistic coevolutionary pressure in mutualism and a biological dilemma for models of cooperation.     

The impact of transmission mode on the evolution of benefits provided by microbial symbionts

While past work has often examined the effects of transmission mode on virulence evolution in parasites, few studies have explored the impact of horizontal transmission on the evolution of benefits conferred by a symbiont to its host. Here, we identify three mechanisms that create a positive covariance between horizontal transmission and symbiont‐provided benefits: pleiotropy within the symbiont genome, partner choice by the host, and consumption of host waste by‐products by symbionts. We modify a susceptible‐infected model to incorporate the details of each mechanism and examine the evolution of symbiont benefits given variation in either the immigration rate of susceptible hosts or the rate of successful vertical transmission. We find conditions for each case under which greater opportunity for horizontal transmission (higher migration rate) favors the evolution of mutualism. Further, we find the surprising result that vertical transmission can inhibit the evolution of benefits provided by symbionts to hosts when horizontal transmission and symbiont‐provided benefits are positively correlated. These predictions may apply to a number of natural systems, and the results may explain why many mutualisms that rely on partner choice often lack a mechanism for vertical transmission.     

Effects of low temperatures on nitrogenase activity in sainfoin (Onobrychis viciifolia) nodulated by arctic rhizobia

The temperate forage legume sainfoin (Onobrychis viciifolia) is readly nodulated by rhizobia isolated from arctic legumes (Astragalus and Oxytropis species). We have investigated the effects of low temperatures on nitrogenase activity in sainfoin nodulated by arctic and temperate (homologous) rhizobia. At low temperatures, nitrogenase activity of arctic rhizobia measured either with detached nodules or with whole plants, was higher than that of temperate rhizobia. At 5°C and 10°C, nitrogenase activity values of arctic rhizobia represented 12% and 33% of those measured at 20°C, while lower values of 3.7% and 22.4% were observed with temperate rhizobia. This cold adaptation was also reflected on bacterial growth where, at 5°C and 10°C, arctic rhizobia showed a shorter doubling time and synthesized more protein than temperate rhizobia.     

Nitrogen‐fixing tree abundance in higher‐latitude North America is not constrained by diversity

The rarity of nitrogen (N)‐fixing trees in frequently N‐limited higher‐latitude (here, > 35°) forests is a central biogeochemical paradox. One hypothesis for their rarity is that evolutionary constraints limit N‐fixing tree diversity, preventing N‐fixing species from filling available niches in higher‐latitude forests. Here, we test this hypothesis using data from the USA and Mexico. N‐fixing trees comprise only a slightly smaller fraction of taxa at higher vs. lower latitudes (8% vs. 11% of genera), despite 11‐fold lower abundance (1.2% vs. 12.7% of basal area). Furthermore, N‐fixing trees are abundant but belong to few species on tropical islands, suggesting that low absolute diversity does not limit their abundance. Rhizobial taxa dominate N‐fixing tree richness at lower latitudes, whereas actinorhizal species do at higher latitudes. Our results suggest that low diversity does not explain N‐fixing trees' rarity in higher‐latitude forests. Therefore, N limitation in higher‐latitude forests likely results from ecological constraints on N fixation.     

Global climate change will increase the abundance of symbiotic nitrogen‐fixing trees in much of North America

Symbiotic nitrogen (N)‐fixing trees can drive N and carbon cycling and thus are critical components of future climate projections. Despite detailed understanding of how climate influences N‐fixation enzyme activity and physiology, comparatively little is known about how climate influences N‐fixing tree abundance. Here, we used forest inventory data from the USA and Mexico (>125,000 plots) along with climate data to address two questions: (1) How does the abundance distribution of N‐fixing trees (rhizobial, actinorhizal, and both types together) vary with mean annual temperature (MAT) and precipitation (MAP)? (2) How will changing climate shift the abundance distribution of N‐fixing trees? We found that rhizobial N‐fixing trees were nearly absent below 15°C MAT, but above 15°C MAT, they increased in abundance as temperature rose. We found no evidence for a hump‐shaped response to temperature throughout the range of our data. Rhizobial trees were more abundant in dry than in wet ecosystems. By contrast, actinorhizal trees peaked in abundance at 5–10°C MAT and were least abundant in areas with intermediate precipitation. Next, we used a climate‐envelope approach to project how N‐fixing tree relative abundance might change in the future. The climate‐envelope projection showed that rhizobial N‐fixing trees will likely become more abundant in many areas by 2080, particularly in the southern USA and western Mexico, due primarily to rising temperatures. Projections for actinorhizal N‐fixing trees were more nuanced due to their nonmonotonic dependence on temperature and precipitation. Overall, the dominant trend is that warming will increase N‐fixing tree abundance in much of the USA and Mexico, with large increases up to 40° North latitude. The quantitative link we provide between climate and N‐fixing tree abundance can help improve the representation of symbiotic N fixation in Earth System Models.     

Poly-3-hydroxybutyrate (PHB) supports survival and reproduction in starving rhizobia

The carbon that rhizobia in root nodules receive from their host powers both N₂ fixation, which mainly benefits the host, and rhizobium reproduction. Rhizobia also store energy in the lipid poly-3-hydroxybutyrate (PHB), which may enhance rhizobium survival when they are carbon limited, either in nodules or in the soil between hosts. There can be a conflict of interest between rhizobia and legumes over the rate of PHB accumulation, due to a metabolic tradeoff between N₂ fixation and PHB accumulation. To quantify the benefits of PHB to carbon-limited rhizobia, populations of genetically uniform rhizobia with high vs. low PHB (confirmed by flow cytometry) were generated by fractionating Sinorhizobium meliloti via density gradient centrifugation, and also by harvesting cells at early vs. late stationary phase. These rhizobia were starved for 165 days. PHB use during starvation was highly predictive of both initial reproduction and long-term population maintenance. Cultured S. meliloti accumulated enough PHB to triple their initial population size when starved, and to persist for c . 150 days before the population fell below its initial value. During the first 21 days of nodule growth, undifferentiated S. meliloti within alfalfa nodules accumulated enough PHB to support significant increases in reproduction and survival during starvation.     

Small traits with big consequences: how seed traits of nitrogen‐fixing plants might influence ecosystem nutrient cycling

Symbiotic nitrogen (N)‐fixing plants have important effects on the biogeochemical processes of the sites they inhabit, but their ability to reach these sites is determined by the dispersal of their seeds. Differences in seed size and dispersal vectors of N‐fixing and non‐fixing plants could influence the spatial and temporal distributions of N fixers, and thus could have important impacts on biogeochemical cycling. Using seed mass, dispersal vector, and biome data retrieved from online public databases, we ask if there are systematic differences in seed mass and dispersal vectors between N‐fixing and non‐fixing plants. We demonstrate that rhizobial N fixers tend to have larger seeds that are more likely to be biotically dispersed than seeds of non‐fixers, whereas actinorhizal N‐fixing trees tend to have small, abiotically dispersed seeds. We then synthesize existing evidence from the literature to draw links between these dispersal traits and the spatio–temporal patterns of N fixers, as well as their biogeochemical effects on terrestrial ecosystems. Using this literature, we argue that the spatio–temporal distributions of N fixers are influenced by their seed dispersal characteristics, and that these distribution patterns have important effects on the total amount of N fixed at a site and the timing of N inputs during processes such as succession.     

Expression of the Arabidopsis thaliana immune receptor EFR in Medicago truncatula reduces infection by a root pathogenic bacterium,but not nitrogen‐fixing rhizobial symbiosis

Interfamily transfer of plant pattern recognition receptors (PRRs) represents a promising biotechnological approach to engineer broad‐spectrum, and potentially durable, disease resistance in crops. It is however unclear whether new recognition specificities to given pathogen‐associated molecular patterns (PAMPs) affect the interaction of the recipient plant with beneficial microbes. To test this in a direct reductionist approach, we transferred the Brassicaceae‐specific PRR ELONGATION FACTOR‐THERMO UNSTABLE RECEPTOR (EFR), conferring recognition of the bacterial EF‐Tu protein, from Arabidopsis thaliana to the legume Medicago truncatula. Constitutive EFR expression led to EFR accumulation and activation of immune responses upon treatment with the EF‐Tu‐derived elf18 peptide in leaves and roots. The interaction of M. truncatula with the bacterial symbiont Sinorhizobium meliloti is characterized by the formation of root nodules that fix atmospheric nitrogen. Although nodule numbers were slightly reduced at an early stage of the infection in EFR‐Medicago when compared to control lines, nodulation was similar in all lines at later stages. Furthermore, nodule colonization by rhizobia, and nitrogen fixation were not compromised by EFR expression. Importantly, the M. truncatula lines expressing EFR were substantially more resistant to the root bacterial pathogen Ralstonia solanacearum. Our data suggest that the transfer of EFR to M. truncatula does not impede root nodule symbiosis, but has a positive impact on disease resistance against a bacterial pathogen. In addition, our results indicate that Rhizobium can either avoid PAMP recognition during the infection process, or is able to actively suppress immune signaling.     

Why mutualist partners vary in quality: mutation–selection balance and incentives to cheat in the fig tree–fig wasp mutualism

Mutualisms between species are ecologically ubiquitous but evolutionarily puzzling. Host discrimination mechanisms that reduce the fitness of uncooperative symbionts can stabilise mutualism against collapse, but also present a paradox – if discrimination is effective, why do uncooperative symbionts persist? Here, we test whether mutations or fitness benefits of cheating best explain the prevalence of uncooperative wasps in the fig tree–fig wasp mutualism. By combining theory with field‐collected data we demonstrate that the proportions of pollen‐free wasps of strongly discriminating hosts are reached with reasonable mutation rates. In contrast, in weakly discriminating hosts, the required mutation rates, assuming a single locus, are untenably high, but the required cheater advantages fall within expected ranges. We propose that when discrimination is weak, uncooperative symbionts proliferate until they reach the equilibrium proportion that balances costs and benefits of cheating. Our results suggest that mechanisms that resolve the paradox of uncooperative symbionts differ among host species.     

Evolutionary emergence and maintenance of horizontally transmitted mutualism that do not rely on the supply of standing variation in symbiont quality

Mutualism based on reciprocal exchange of costly services must avoid exploitation by ‘free‐rides’. Accordingly, hosts discriminate against free‐riding symbionts in many mutualistic relationships. However, as the selective advantage of discriminators comes from the presence of variability in symbiont quality that they eliminate, discrimination and thus mutualism have been considered to be maintained with exogenous supply of free‐riders. In this study, we tried to resolve the ‘paradoxical’ co‐evolution of discrimination by hosts and cooperation by symbionts, by comparing two different types of discrimination: ‘one‐shot’ discrimination, where a host does not reacquire new symbionts after evicting free‐riders, and ‘resampling’ discrimination, where a host does from the environment. Our study shows that this apparently minor difference in discrimination types leads to qualitatively different evolutionary outcomes. First, although it has been usually considered that the benefit of discriminators is derived from the variability of symbiont quality, the benefit of a certain type of discriminators (e.g. one‐shot discrimination) is proportional to the frequency of free‐riders, which is in stark contrast to the case of resampling discrimination. As a result, one‐shot discriminators can invade the free‐rider/nondiscriminator population, even if standing variation for symbiont quality is absent. Second, our one‐shot discriminators can also be maintained without exogenous supply of free‐riders and hence is free from the paradox of discrimination. Therefore, our result indicates that the paradox is not a common feature of evolution of discrimination but is a problem of specific types of discrimination.     

Is the distribution of nitrogen‐fixing cyanobacteria in the oceans related to temperature?

Approximately 50% of the global natural fixation of nitrogen occurs in the oceans supporting a considerable part of the new primary production. Virtually all nitrogen fixation in the ocean occurs in the tropics and subtropics where the surface water temperature is 25°C or higher. It is attributed almost exclusively to cyanobacteria. This is remarkable firstly because diazotrophic cyanobacteria are found in other environments irrespective of temperature and secondly because primary production in temperate and cold oceans is generally limited by nitrogen. Cyanobacteria are oxygenic phototrophic organisms that evolved a variety of strategies protecting nitrogenase from oxygen inactivation. Free-living diazotrophic cyanobacteria in the ocean are of the non-heterocystous type, namely the filamentous Trichodesmium and the unicellular groups A–C. I will argue that warm water is a prerequisite for these diazotrophic organisms because of the low-oxygen solubility and high rates of respiration allowing the organism to maintain anoxic conditions in the nitrogen-fixing cell. Heterocystous cyanobacteria are abundant in freshwater and brackish environments in all climatic zones. The heterocyst cell envelope is a tuneable gas diffusion barrier that optimizes the influx of both oxygen and nitrogen, while maintaining anoxic conditions inside the cell. It is not known why heterocystous cyanobacteria are absent from the temperate and cold oceans and seas.     

Loss‐of‐function of ASPARTIC PEPTIDASE NODULE‐INDUCED 1 (APN1) in Lotus japonicus restricts efficient nitrogen‐fixing symbiosis with specific Mesorhizobium loti strains

The nitrogen‐fixing symbiosis of legumes and Rhizobium bacteria is established by complex interactions between the two symbiotic partners. Legume Fix^– mutants form apparently normal nodules with endosymbiotic rhizobia but fail to induce rhizobial nitrogen fixation. These mutants are useful for identifying the legume genes involved in the interactions essential for symbiotic nitrogen fixation. We describe here a Fix^– mutant of Lotus japonicus, apn1, which showed a very specific symbiotic phenotype. It formed ineffective nodules when inoculated with the Mesorhizobium loti strain TONO. In these nodules, infected cells disintegrated and successively became necrotic, indicating premature senescence typical of Fix^– mutants. However, it formed effective nodules when inoculated with the M. loti strain MAFF303099. Among nine different M. loti strains tested, four formed ineffective nodules and five formed effective nodules on apn1 roots. The identified causal gene, ASPARTIC PEPTIDASE NODULE‐INDUCED 1 (LjAPN1), encodes a nepenthesin‐type aspartic peptidase. The well characterized Arabidopsis aspartic peptidase CDR1 could complement the strain‐specific Fix^– phenotype of apn1. LjAPN1 is a typical late nodulin; its gene expression was exclusively induced during nodule development. LjAPN1 was most abundantly expressed in the infected cells in the nodules. Our findings indicate that LjAPN1 is required for the development and persistence of functional (nitrogen‐fixing) symbiosis in a rhizobial strain‐dependent manner, and thus determines compatibility between M. loti and L. japonicus at the level of nitrogen fixation.