Using a "time machine" to test for local adaptation of aquatic microbes to temporal and spatial environmental variation

Temporal Variation in Selection Influences Microgeographic Local Adaptation

AbstractEcological heterogeneity can lead to local adaptation when populations exhibit fitness trade-offs among habitats. However, the degree to which local adaptation is affected by the spatial and temporal scale of environmental variation is poorly understood. A multiyear reciprocal transplant experiment was performed with populations of the annual plant Leptosiphon parviflorus living on adjacent serpentine and nonserpentine soil. Local adaptation over this small geographic scale was observed, but there were differences in the temporal variability of selection across habitats. On serpentine soil, the local population had a consistently large survival advantage, presumably as a result of the temporal stability in selection imposed by soil cation content. In contrast, a fecundity advantage was observed for the sandstone population on its native soil type but only in the two study years with the highest rainfall. A manipulative greenhouse experiment demonstrated that the fitness advantage of the sandstone population in its native soil type depends critically on water availability. The temporal variability in local adaptation driven by variation in precipitation suggests that continued drought conditions have the potential to erode local adaptation in these populations. These results show how different selective factors can influence spatial and temporal patterns of variation in fitness trade-offs.

Evolutionary mismatch along salinity gradients in a Neotropical water strider

The evolution of local adaptation is crucial for the in situ persistence of populations in changing environments. However, selection along broad environmental gradients could render local adaptation difficult, and might even result in maladaptation. We address this issue by quantifying fitness trade-offs (via common garden experiments) along a salinity gradient in two populations of the Neotropical water strider Telmatometra withei-a species found in both fresh (FW) and brackish (BW) water environments across Panama. We found evidence for local adaptation in the FW population in its home FW environment. However, the BW population showed only partial adaptation to the BW environment, with a high magnitude of maladaptation along naturally occurring salinity gradients. Indeed, its overall fitness was ~60% lower than that of the ancestral FW population in its home environment, highlighting the role of phenotypic plasticity, rather than local adaptation, in high salinity environments. This suggests that populations seemingly persisting in high salinity environments might in fact be maladapted, following drastic changes in salinity. Thus, variable selection imposed by salinization could result in evolutionary mismatch, where the fitness of a population is displaced from its optimal environment. Understanding the fitness consequences of persisting in fluctuating salinity environments is crucial to predict the persistence of populations facing increasing salinization. It will also help develop evolutionarily informed management strategies in the context of global change.

Locally adapted gut microbiomes mediate host stress tolerance

While evidence for the role of the microbiome in shaping host stress tolerance is becoming well-established, to what extent this depends on the interaction between the host and its local microbiome is less clear. Therefore, we investigated whether locally adapted gut microbiomes affect host stress tolerance. In the water flea Daphnia magna, we studied if the host performs better when receiving a microbiome from their source region than from another region when facing a stressful condition, more in particular exposure to the toxic cyanobacteria Microcystis aeruginosa. Therefore, a reciprocal transplant experiment was performed in which recipient, germ-free D. magna, isolated from different ponds, received a donor microbiome from sympatric or allopatric D. magna that were pre-exposed to toxic cyanobacteria or not. We tested for effects on host life history traits and gut microbiome composition. Our data indicate that Daphnia interact with particular microbial strains mediating local adaptation in host stress tolerance. Most recipient D. magna individuals performed better when inoculated with sympatric than with allopatric microbiomes. This effect was most pronounced when the donors were pre-exposed to the toxic cyanobacteria, but this effect was also pond and genotype dependent. We discuss how this host fitness benefit is associated with microbiome diversity patterns.

Competition experiments in a soil microcosm reveal the impact of genetic and biotic factors on natural yeast populations

The ability to measure microbial fitness directly in natural conditions and in interaction with other microbes is a challenge that needs to be overcome if we want to gain a better understanding of microbial fitness determinants in nature. Here we investigate the influence of the natural microbial community on the relative fitness of the North American populations SpB, SpC and SpC* of the wild yeast Saccharomyces paradoxus using DNA barcodes and a soil microcosm derived from soil associated with oak trees. We find that variation in fitness among these genetically distinct groups is influenced by the microbial community. Altering the microbial community load and diversity with an irradiation treatment significantly diminishes the magnitude of fitness differences among populations. Our findings suggest that microbial interactions could affect the evolution of yeast lineages in nature by modulating variation in fitness.

Using the resurrection approach to understand contemporary evolution in changing environments

The resurrection approach of reviving ancestors from stored propagules and comparing them with descendants under common conditions has emerged as a powerful method of detecting and characterizing contemporary evolution. As climatic and other environmental conditions continue to change at a rapid pace, this approach is becoming particularly useful for predicting and monitoring evolutionary responses. We evaluate this approach, explain the advantages and limitations, suggest best practices for implementation, review studies in which this approach has been used, and explore how it can be incorporated into conservation and management efforts. We find that although the approach has thus far been used in a limited number of cases, these studies have provided strong evidence for rapid contemporary adaptive evolution in a variety of systems, particularly in response to anthropogenic environmental change, although it is far from clear that evolution will be able to rescue many populations from extinction given current rates of global changes. We also highlight one effort, known as Project Baseline, to create a collection of stored seeds that can take advantage of the resurrection approach to examine evolutionary responses to environmental change over the coming decades. We conclude that the resurrection approach is a useful tool that could be more widely employed to examine basic questions about evolution in natural populations and to assist in the conservation and management of these populations as they face continued environmental change.

Temporal patterns of local adaptation in soil pseudomonads

Strong divergent selection leading to local adaptation is often invoked to explain the staggering diversity of bacteria in microbial ecosystems. However, examples of specialization by bacterial clones to alternative niches in nature are rare. Here, we investigate the extent of local adaptation in natural isolates of pseudomonads and their relatives to their soil environments across both space and time. Though most isolates grew well in most environments, patchily distributed low-quality environments were found to drive specialization. In contrast to experimental evolution work on microbial adaptation, temporal adaptation was stronger than spatial adaptation among the isolates and environments we sampled. Time-shift analysis of fitness across two seasons of growth revealed an unexpectedly strong effect of preadaptation. This pattern of apparent future adaptation may be caused by unknown abiotic properties of these environments, phages, bacterial competitors or general mechanisms of ecological niche release, and warrants future study.

The evolution of bacterial resistance against bacteriophages in the horse chestnut phyllosphere is general across both space and time

Insight to the spatial and temporal scales of coevolution is key to predicting the outcome of host-parasite interactions and spread of disease. For bacteria infecting long-lived hosts, selection to overcome host defences is just one factor shaping the course of evolution; populations will also be competing with other microbial species and will themselves be facing infection by bacteriophage viruses. Here, we examine the temporal and spatial patterns of bacterial adaptation against natural phage populations from within leaves of horse chestnut trees. Using a time-shift experiment with both sympatric and allopatric phages from either contemporary or earlier points in the season, we demonstrate that bacterial resistance is higher against phages from the past, regardless of spatial sympatry or how much earlier in the season phages were collected. Similarly, we show that future bacterial hosts are more resistant to both sympatric and allopatric phages than contemporary bacterial hosts. Together, our results suggest the evolution of relatively general bacterial resistance against phages in nature and are contrasting to previously observed patterns of phage adaptation to bacteria from the same tree hosts over the same time frame, indicating a potential asymmetry in coevolutionary dynamics.