Whole genome-scale assessment of gene fitness of Novosphingobium aromaticavorans during spaceflight.

In microgravity, bacteria undergo intriguing physiological adaptations. There have been few attempts to assess global bacterial physiological responses to microgravity, with most studies only focusing on a handful of individual systems. This study assessed the fitness of each gene in the genome of the aromatic compound-degrading Alphaproteobacterium Novosphingobium aromaticavorans during growth in spaceflight. This was accomplished using Comparative TnSeq, which involves culturing the same saturating transposon mutagenized library under two different conditions. To assess gene fitness, a novel comparative TnSeq analytical tool was developed, named TnDivA, that is particularly useful in leveraging biological replicates. In this approach, transposon diversity is represented numerically using a modified Shannon diversity index, which was then converted into effective transposon density. This transformation accounts for variability in read distribution between samples, such as cases where reads were dominated by only a few transposon inserts. Effective density values were analyzed using multiple statistical methods, including log2-fold change, least-squares regression analysis, and Welch's t-test. The results obtained across applied statistical methods show a difference in the number of significant genes identified. However, the functional categories of genes important to growth in microgravity showed similar patterns. Lipid metabolism and transport, energy production, transcription, translation, and secondary metabolite biosynthesis and transport were shown to have high fitness during spaceflight. This suggests that core metabolic processes, including lipid and secondary metabolism, play an important role adapting to stress and promoting growth in microgravity.

Microbial Communities in Saltpan Sediments Show Tolerance to Mars Analog Conditions, but Susceptibility to Chloride and Perchlorate Toxicity.

Brines at or near the surface of present-day Mars are a potential explanation for seasonally recurring dark streaks on the walls of craters, termed recurring slope lineae (RSL). Deliquescence and freezing point depression are possible drivers of brine stability, attributable to the high salinity observed in martian regolith including chlorides and perchlorates. Investigation of life, which may inhabit RSL, and the cellular mechanisms necessary for survival, must consider the tolerance of highly variable hydration, freeze-thaw cycles, and high osmolarity in addition to the anaerobic, oligotrophic, and irradiated environment. We propose the saltpan, an ephemeral, hypersaline wetland as an analogue for putative RSL hydrology. Saltpan sediment archaeal and bacterial communities showed tolerance of the Mars-analogous atmosphere, hydration, minerology, salinity, and temperature. Although active growth and a shift to well-adapted taxa were observed, susceptibility to low-concentration chloride and perchlorate addition suggested that such a composition was insufficient for beneficial water retention relative to added salt stress.

Dynamic plant-soil microbe interactions: the neglected effect of soil conditioning time.

Plant-soil feedback (PSF) may change in strength over the life of plant individuals as plants continue to modify the soil microbial community. However, the temporal variation in PSF is rarely quantified and its impacts on plant communities remain unknown. Using a chronosequence reconstructed from annual aerial photographs of a coastal dune ecosystem, we characterized > 20-yr changes in soil microbial communities associated with individuals of the four dominant perennial species, one legume and three nonlegume. We also quantified the effects of soil biota on conspecific and heterospecific seedling performance in a glasshouse experiment that preserved soil properties of these individual plants. Additionally, we used a general individual-based model to explore the potential consequences of temporally varying PSF on plant community assembly. In all plant species, microbial communities changed with plant age. However, responses of plants to the turnover in microbial composition depended on the identity of the seedling species: only the soil biota effect experienced by the nonlegume species became increasingly negative with longer soil conditioning. Model simulation suggested that temporal changes in PSF could affect the transient dynamics of plant community assembly. These results suggest that temporal variation in PSF over the life of individual plants should be considered to understand how PSF structures plant communities.

Functional diversity and coexistence of herbaceous plants in wet, species-rich savannas.

Trait differences among plant species can favor species coexistence. The role that such differences play in the assembly of diverse plant communities maintained by frequent fires remains unresolved. This lack of resolution results in part from the possibility that species with similar traits may coexist because none has a significant fitness advantage and in part from the difficulty of experimental manipulation of highly diverse assemblages dominated by perennial species. We examined a 65-year chronosequence of losses of herbaceous species following fire suppression (and subsequent encroachment by Pinus elliottii) in three wet longleaf pine savannas. We used cluster analysis, similarity profile permutation tests, and k-R cluster analysis to identify statistically significant functional groups. We then used randomization tests to determine if the absence of functional groups near pines was greater (or less) than expected by chance. We also tested whether tolerant and sensitive species were less (or more) likely to co-occur by chance in areas in savannas away from pines in accordance with predictions of modern coexistence theory. Functional group richness near pines was lower than expected from random species extirpations. Wetland perennials with thick rhizomes and high leaf water content, spring-flowering wetland forbs (including Drosera tracyi), orchids, Polygala spp., and club mosses were more likely to be absent near pines than expected by chance. C3 grasses and sedges with seed banks and tall, fall-flowering C4 grasses were less likely to be absent near pines than expected by chance. Species sensitive to pine encroachment were more likely to co-occur with other such species away from pines at two of the three sites. Results suggest that herb species diversity in frequently burned wet savannas is maintained in part by a weak fitness (e.g., competitive) hierarchy among herbs, and not as a result of trait differences among co-occurring species.

Erratum: Author Correction: Evolutionary history of plant hosts and fungal symbionts predicts the strength of mycorrhizal mutualism.

[This corrects the article DOI: 10.1038/s42003-018-0120-9.].

Evolutionary history of plant hosts and fungal symbionts predicts the strength of mycorrhizal mutualism.

Most plants engage in symbioses with mycorrhizal fungi in soils and net consequences for plants vary widely from mutualism to parasitism. However, we lack a synthetic understanding of the evolutionary and ecological forces driving such variation for this or any other nutritional symbiosis. We used meta-analysis across 646 combinations of plants and fungi to show that evolutionary history explains substantially more variation in plant responses to mycorrhizal fungi than the ecological factors included in this study, such as nutrient fertilization and additional microbes. Evolutionary history also has a different influence on outcomes of ectomycorrhizal versus arbuscular mycorrhizal symbioses; the former are best explained by the multiple evolutionary origins of ectomycorrhizal lifestyle in plants, while the latter are best explained by recent diversification in plants; both are also explained by evolution of specificity between plants and fungi. These results provide the foundation for a synthetic framework to predict the outcomes of nutritional mutualisms.

Priority effects are weakened by a short, but not long, history of sympatric evolution.

Priority effects, or the effects of species arrival history on local species abundances, have been documented in a range of taxa. However, factors determining the extent to which priority effects affect community assembly remain unclear. Using laboratory populations of the bacterium Pseudomonas fluorescens, we examined whether shared evolutionary history affected the strength of priority effects. We hypothesized that sympatric evolution of populations belonging to the same guild would lead to niche differentiation, resulting in phenotypic complementarity that weakens priority effects. Consistent with this hypothesis, we found that priority effects tended to be weaker in sympatrically evolved pairs of immigrating populations than in allopatrically evolved pairs. Furthermore, priority effects were weaker under higher phenotypic complementarity. However, these patterns were observed only in populations with a relatively short history of sympatric evolution, and disappeared when populations had evolved together for a long time. Together, our results suggest that the evolutionary history of organismal traits may dictate the strength of priority effects and, consequently, the extent of historical contingency in the assembly of ecological communities.

Parallel emergence of negative epistasis across experimental lineages.

Epistatic interactions can greatly impact evolutionary phenomena, particularly the process of adaptation. Here, we leverage four parallel experimentally evolved lineages to study the emergence and trajectories of epistatic interactions in the social bacterium Myxococcus xanthus. A social gene (pilA) necessary for effective group swarming on soft agar had been deleted from the common ancestor of these lineages. During selection for competitiveness at the leading edge of growing colonies, two lineages evolved qualitatively novel mechanisms for greatly increased swarming on soft agar, whereas the other two lineages evolved relatively small increases in swarming. By reintroducing pilA into different genetic backgrounds along the four lineages, we tested whether parallel lineages showed similar patterns of epistasis. In particular, we tested whether a pattern of negative epistasis between accumulating mutations and pilA previously found in the fastest lineage would be found only in the two evolved lineages with the fastest and most striking swarming phenotypes, or rather was due to common epistatic structure across all lineages arising from the generic fixation of adaptive mutations. Our analysis reveals the emergence of negative epistasis across all four independent lineages. Further, we present results showing that the observed negative epistasis is not due exclusively to evolving populations approaching a maximum phenotypic value that inherently limits positive effects of pilA reintroduction, but rather involves direct antagonistic interactions between accumulating mutations and the reintroduced social gene.

Evolutionary history shapes patterns of mutualistic benefit in Acacia-rhizobial interactions.

The ecological and evolutionary factors that drive the emergence and maintenance of variation in mutualistic benefit (i.e., the benefits provided by one partner to another) in mutualistic symbioses are not well understood. In this study, we evaluated the role that host and symbiont phylogeny might play in determining patterns of mutualistic benefit for interactions among nine species of Acacia and 31 strains of nitrogen-fixing rhizobial bacteria. Using phylogenetic comparative methods we compared patterns of variation in mutualistic benefit (host response to inoculation) to rhizobial phylogenies constructed from housekeeping and symbiosis genes; and a multigene host phylogeny. We found widespread genotype-by-genotype variation in patterns of plant growth. A relatively large component of this variation (21-28%) was strongly influenced by the interacting evolutionary histories of both partners, such that phylogenetically similar host species had similar growth responses when inoculated with phylogenetically similar rhizobia. We also found a relatively large nonphylogenetic effect for the average mutualistic benefit provided by rhizobia to plants, such that phylogenetic relatedness did not predict the overall benefit provided by rhizobia across all hosts. We conclude that phylogenetic relatedness should frequently predict patterns of mutualistic benefit in acacia-rhizobial mutualistic interactions; but that some mutualistic traits also evolve independently of the phylogenies.

MycoDB, a global database of plant response to mycorrhizal fungi.

Plants form belowground associations with mycorrhizal fungi in one of the most common symbioses on Earth. However, few large-scale generalizations exist for the structure and function of mycorrhizal symbioses, as the nature of this relationship varies from mutualistic to parasitic and is largely context-dependent. We announce the public release of MycoDB, a database of 4,010 studies (from 438 unique publications) to aid in multi-factor meta-analyses elucidating the ecological and evolutionary context in which mycorrhizal fungi alter plant productivity. Over 10 years with nearly 80 collaborators, we compiled data on the response of plant biomass to mycorrhizal fungal inoculation, including meta-analysis metrics and 24 additional explanatory variables that describe the biotic and abiotic context of each study. We also include phylogenetic trees for all plants and fungi in the database. To our knowledge, MycoDB is the largest ecological meta-analysis database. We aim to share these data to highlight significant gaps in mycorrhizal research and encourage synthesis to explore the ecological and evolutionary generalities that govern mycorrhizal functioning in ecosystems.

Rapid and widespread de novo evolution of kin discrimination.

Diverse forms of kin discrimination, broadly defined as alteration of social behavior as a function of genetic relatedness among interactants, are common among social organisms from microbes to humans. However, the evolutionary origins and causes of kin-discriminatory behavior remain largely obscure. One form of kin discrimination observed in microbes is the failure of genetically distinct colonies to merge freely upon encounter. Here, we first use natural isolates of the highly social bacterium Myxococcus xanthus to show that colony-merger incompatibilities can be strong barriers to social interaction, particularly by reducing chimerism in multicellular fruiting bodies that develop near colony-territory borders. We then use experimental laboratory populations to test hypotheses regarding the evolutionary origins of kin discrimination. We show that the generic process of adaptation, irrespective of selective environment, is sufficient to repeatedly generate kin-discriminatory behaviors between evolved populations and their common ancestor. Further, we find that kin discrimination pervasively evolves indirectly between allopatric replicate populations that adapt to the same ecological habitat and that this occurs generically in many distinct habitats. Patterns of interpopulation discrimination imply that kin discrimination phenotypes evolved via many diverse genetic mechanisms and mutation-accumulation patterns support this inference. Strong incompatibility phenotypes emerged abruptly in some populations but strengthened gradually in others. The indirect evolution of kin discrimination in an asexual microbe is analogous to the indirect evolution of reproductive incompatibility in sexual eukaryotes and linguistic incompatibility among human cultures, the commonality being indirect, noncoordinated divergence of complex systems evolving in isolation.

A shift from magnitude to sign epistasis during adaptive evolution of a bacterial social trait.

Although the importance of epistasis in evolution has long been recognized, remarkably little is known about the processes by which epistatic interactions evolve in real time in specific biological systems. Here, we have characterized how the epistatic fitness relationship between a social gene and an adapting genome changes radically over a short evolutionary time frame in the social bacterium Myxococcus xanthus. We show that a highly beneficial effect of this social gene in the ancestral genome is gradually reduced--and ultimately reversed into a deleterious effect--over the course of an experimental adaptive trajectory in which a primitive form of novel cooperation evolved. This reduction and reversal of a positive social allelic effect is driven solely by changes in the genetic context in which the gene is expressed as new mutations are sequentially fixed during adaptive evolution, and explicitly demonstrates a significant evolutionary change in the genetic architecture of an ecologically important social trait.

Joint evolution of kin recognition and cooperation in spatially structured rhizobium populations.

In the face of costs, cooperative interactions maintained over evolutionary time present a central question in biology. What forces maintain this cooperation? Two potential ways to explain this problem are spatially structured environments (kin selection) and kin-recognition (directed benefits). In a two-locus population genetic model, we investigated the relative roles of spatial structure and kin recognition in the maintenance of cooperation among rhizobia within the rhizobia-legume mutualism. In the case where the cooperative and kin recognition loci are independently inherited, spatial structure alone maintains cooperation, while kin recognition decreases the equilibrium frequency of cooperators. In the case of co-inheritance, spatial structure remains a stronger force, but kin recognition can transiently increase the frequency of cooperators. Our results suggest that spatial structure can be a dominant force in maintaining cooperation in rhizobium populations, providing a mechanism for maintaining the mutualistic nodulation trait. Further, our model generates unique and testable predictions that could be evaluated empirically within the legume-rhizobium mutualism.

Evolution of transmission mode in obligate symbionts.

BACKGROUND: A host obtains symbionts by horizontal transmission when infected from the environment or contagiously from other hosts in the same generation. In contrast, vertical transmission occurs when a host obtains its symbionts directly from its parents. Either vertical or horizontal transmission can sustain an association between a host and its symbiont. QUESTIONS: What evolutionary forces are necessary to evolve from an ancestral state of horizontal transmission to a derived state of vertical transmission? MATHEMATICAL METHODS: We explore a general model of fitness interaction, including both additive and epistatic effects, between host and symbiont genes. Recursion equations allow us to analyse the short-term behaviour of the model and to study long-term deterministic effects with numerical iterations. KEY ASSUMPTIONS: Obligate interaction between a symbiont and a single host species with genetically determined horizontal and vertical transmission. No free-living symbionts or uninfected hosts and each host is infected by only a single symbiont genetic lineage (no multiple infections). No population structure. CONCLUSIONS: Epistasis for fitness between host and symbiont genes, like that in a matching alleles model, is a necessary condition for the evolution of vertical from horizontal transmission. Stochastic individual-based simulations show that (1) mutation facilitates the switch to vertical transmission and (2) vertical transmission is a stable evolutionary endpoint for a matching alleles model.

A generalization of Hamilton's rule for the evolution of microbial cooperation.

Hamilton's rule states that cooperation will evolve if the fitness cost to actors is less than the benefit to recipients multiplied by their genetic relatedness. This rule makes many simplifying assumptions, however, and does not accurately describe social evolution in organisms such as microbes where selection is both strong and nonadditive. We derived a generalization of Hamilton's rule and measured its parameters in Myxococcus xanthus bacteria. Nonadditivity made cooperative sporulation remarkably resistant to exploitation by cheater strains. Selection was driven by higher-order moments of population structure, not relatedness. These results provide an empirically testable cooperation principle applicable to both microbes and multicellular organisms and show how nonlinear interactions among cells insulate bacteria against cheaters.

Multilevel and kin selection in a connected world.

Wild et al. argue that the evolution of reduced virulence can be understood from the perspective of inclusive fitness, obviating the need to evoke group selection as a contributing causal factor. Although they acknowledge the mathematical equivalence of the inclusive fitness and multilevel selection approaches, they conclude that reduced virulence can be viewed entirely as an individual-level adaptation by the parasite. Here we show that their model is a well-known special case of the more general theory of multilevel selection, and that the cause of reduced virulence resides in the opposition of two processes: within-group and among-group selection. This distinction is important in light of the current controversy among evolutionary biologists in which some continue to affirm that natural selection centres only and always at the level of the individual organism or gene, despite mathematical demonstrations that evolutionary dynamics must be described by selection at various levels in the hierarchy of biological organization.