Microbial evolution-An under-appreciated driver of soil carbon cycling.

Although substantial advances in predicting the ecological impacts of global change have been made, predictions of the evolutionary impacts have lagged behind. In soil ecosystems, microbes act as the primary energetic drivers of carbon cycling; however, microbes are also capable of evolving on timescales comparable to rates of global change. Given the importance of soil ecosystems in global carbon cycling, we assess the potential impact of microbial evolution on carbon-climate feedbacks in this system. We begin by reviewing the current state of knowledge concerning microbial evolution in response to global change and its specific effect on soil carbon dynamics. Through this integration, we synthesize a roadmap detailing how to integrate microbial evolution into ecosystem biogeochemical models. Specifically, we highlight the importance of microscale mechanistic soil carbon models, including choosing an appropriate evolutionary model (e.g., adaptive dynamics, quantitative genetics), validating model predictions with 'omics' and experimental data, scaling microbial adaptations to ecosystem level processes, and validating with ecosystem-scale measurements. The proposed steps will require significant investment of scientific resources and might require 10-20 years to be fully implemented. However, through the application of multi-scale integrated approaches, we will advance the integration of microbial evolution into predictive understanding of ecosystems, providing clarity on its role and impact within the broader context of environmental change.

Sphingomonas clade and functional distribution with simulated climate change.

Microbes are essential for the functioning of all ecosystems, and as global warming and anthropogenic pollution threaten ecosystems, it is critical to understand how microbes respond to these changes. We investigated the climate response of Sphingomonas, a widespread gram-negative bacterial genus, during an 18-month microbial community reciprocal transplant experiment across a Southern California climate gradient. We hypothesized that after 18 months, the transplanted Sphingomonas clade and functional composition would correspond with site conditions and reflect the Sphingomonas composition of native communities. We extracted Sphingomonas sequences from metagenomic data across the gradient and assessed their clade and functional composition. Representatives of at least 12 major Sphingomonas clades were found at varying relative abundances along the climate gradient, and transplanted Sphingomonas clade composition shifted after 18 months. Site had a significant effect (PERMANOVA; P < 0.001) on the distribution of both Sphingomonas functional (R2 = 0.465) and clade composition (R2 = 0.400), suggesting that Sphingomonas composition depends on climate parameters. Additionally, for both Sphingomonas clade and functional composition, ordinations revealed that the transplanted communities shifted closer to the native Sphingomonas composition of the grassland site compared with the site they were transplanted into. Overall, our results indicate that climate and substrate collectively determine Sphingomonas clade and functional composition.IMPORTANCESphingomonas is the most abundant gram-negative bacterial genus in litter-degrading microbial communities of desert, grassland, shrubland, and forest ecosystems in Southern California. We aimed to determine whether Sphingomonas responds to climate change in the same way as gram-positive bacteria and whole bacterial communities in these ecosystems. Within Sphingomonas, both clade composition and functional genes shifted in response to climate and litter chemistry, supporting the idea that bacteria respond similarly to climate at different scales of genetic variation. This understanding of how microbes respond to perturbation across scales may aid in future predictions of microbial responses to climate change.

Long-term drought promotes invasive species by reducing wildfire severity.

Anthropogenic climate change has increased the frequency of drought, wildfire, and invasions of non-native species. Although high-severity fires linked to drought can inhibit recovery of native vegetation in forested ecosystems, it remains unclear how drought impacts the recovery of other plant communities following wildfire. We leveraged an existing rainfall manipulation experiment to test the hypothesis that reduced precipitation, fuel load, and fire severity convert plant community composition from native shrubs to invasive grasses in a Southern California coastal sage scrub system. We measured community composition before and after the 2020 Silverado wildfire in plots with three rainfall treatments. Drought reduced fuel load and vegetation cover, which reduced fire severity. Native shrubs had greater prefire cover in added water plots compared to reduced water plots. Native cover was lower and invasive cover was higher in postfire reduced water plots compared to postfire added and ambient water plots. Our results demonstrate the importance of fuel load on fire severity and plant community composition on an ecosystem scale. Management should focus on reducing fire frequency and removing invasive species to maintain the resilience of coastal sage scrub communities facing drought. In these communities, controlled burns are not recommended as they promote invasive plants.

Shifts in internal stem damage along a tropical precipitation gradient and implications for forest biomass estimation.

Woody biomass is a large carbon store in terrestrial ecosystems. In calculating biomass, tree stems are assumed to be solid structures. However, decomposer agents such as microbes and insects target stem heartwood, causing internal wood decay which is poorly quantified. We investigated internal stem damage across five sites in tropical Australia along a precipitation gradient. We estimated the amount of internal aboveground biomass damaged in living trees and measured four potential stem damage predictors: wood density, stem diameter, annual precipitation, and termite pressure (measured as termite damage in downed deadwood). Stem damage increased with increasing diameter, wood density, and termite pressure and decreased with increasing precipitation. High wood density stems sustained less damage in wet sites and more damage in dry sites, likely a result of shifting decomposer communities and their differing responses to changes in tree species and wood traits across sites. Incorporating stem damage reduced aboveground biomass estimates by > 30% in Australian savannas, compared to only 3% in rainforests. Accurate estimates of carbon storage across woody plant communities are critical for understanding the global carbon budget. Future biomass estimates should consider stem damage in concert with the effects of changes in decomposer communities and abiotic conditions.

Life history strategies of soil bacterial communities across global terrestrial biomes.

The life history strategies of soil microbes determine their metabolic potential and their response to environmental changes. Yet these strategies remain poorly understood. Here we use shotgun metagenomes from terrestrial biomes to characterize overarching covariations of the genomic traits that capture dominant life history strategies in bacterial communities. The emerging patterns show a triangle of life history strategies shaped by two trait dimensions, supporting previous theoretical and isolate-based studies. The first dimension ranges from streamlined genomes with simple metabolisms to larger genomes and expanded metabolic capacities. As metabolic capacities expand, bacterial communities increasingly differentiate along a second dimension that reflects a trade-off between increasing capacities for environmental responsiveness or for nutrient recycling. Random forest analyses show that soil pH, C:N ratio and precipitation patterns together drive the dominant life history strategy of soil bacterial communities and their biogeographic distribution. Our findings provide a trait-based framework to compare life history strategies of soil bacteria.

Variation in Sphingomonas traits across habitats and phylogenetic clades.

Whether microbes show habitat preferences is a fundamental question in microbial ecology. If different microbial lineages have distinct traits, those lineages may occur more frequently in habitats where their traits are advantageous. Sphingomonas is an ideal bacterial clade in which to investigate how habitat preference relates to traits because these bacteria inhabit diverse environments and hosts. Here we downloaded 440 publicly available Sphingomonas genomes, assigned them to habitats based on isolation source, and examined their phylogenetic relationships. We sought to address whether: (1) there is a relationship between Sphingomonas habitat and phylogeny, and (2) whether there is a phylogenetic correlation between key, genome-based traits and habitat preference. We hypothesized that Sphingomonas strains from similar habitats would cluster together in phylogenetic clades, and key traits that improve fitness in specific environments should correlate with habitat. Genome-based traits were categorized into the Y-A-S trait-based framework for high growth yield, resource acquisition, and stress tolerance. We selected 252 high quality genomes and constructed a phylogenetic tree with 12 well-defined clades based on an alignment of 404 core genes. Sphingomonas strains from the same habitat clustered together within the same clades, and strains within clades shared similar clusters of accessory genes. Additionally, key genome-based trait frequencies varied across habitats. We conclude that Sphingomonas gene content reflects habitat preference. This knowledge of how environment and host relate to phylogeny may also help with future functional predictions about Sphingomonas and facilitate applications in bioremediation.

Microbial drought resistance may destabilize soil carbon.

Droughts are becoming more frequent and intense with climate change. As plants and microbes respond to drought, there may be consequences for the vast stocks of organic carbon stored in soils. If microbes sustain their activity under drought, soils could lose carbon, especially if inputs from plants decline. Empirical and theoretical studies reveal multiple mechanisms of microbial drought resistance, including tolerance and avoidance. Physiological responses allow microbes to acclimate to drought within minutes to days. Along with dispersal, shifts in community composition could allow microbiomes to maintain functioning despite drought. Microbes might also adapt to drier conditions through evolutionary processes. Together, these mechanisms could result in soil carbon losses larger than currently anticipated under climate change.

Investigating the eco-evolutionary response of microbiomes to environmental change.

Microorganisms are the primary engines of biogeochemical processes and foundational to the provisioning of ecosystem services to human society. Free-living microbial communities (microbiomes) and their functioning are now known to be highly sensitive to environmental change. Given microorganisms' capacity for rapid evolution, evolutionary processes could play a role in this response. Currently, however, few models of biogeochemical processes explicitly consider how microbial evolution will affect biogeochemical responses to environmental change. Here, we propose a conceptual framework for explicitly integrating evolution into microbiome-functioning relationships. We consider how microbiomes respond simultaneously to environmental change via four interrelated processes that affect overall microbiome functioning (physiological acclimation, demography, dispersal and evolution). Recent evidence in both the laboratory and the field suggests that ecological and evolutionary dynamics occur simultaneously within microbiomes; however, the implications for biogeochemistry under environmental change will depend on the timescales over which these processes contribute to a microbiome's response. Over the long term, evolution may play an increasingly important role for microbially driven biogeochemical responses to environmental change, particularly to conditions without recent historical precedent.

Effects of experimental nitrogen deposition on soil organic carbon storage in Southern California drylands.

Atmospheric nitrogen (N) deposition is enriching soils with N across biomes. Soil N enrichment can increase plant productivity and affect microbial activity, thereby increasing soil organic carbon (SOC), but such responses vary across biomes. Drylands cover ~45% of Earth's land area and store ~33% of global SOC contained in the top 1 m of soil. Nitrogen fertilization could, therefore, disproportionately impact carbon (C) cycling, yet whether dryland SOC storage increases with N remains unclear. To understand how N enrichment may change SOC storage, we separated SOC into plant-derived, particulate organic C (POC), and largely microbially derived, mineral-associated organic C (MAOC) at four N deposition experimental sites in Southern California. Theory suggests that N enrichment increases the efficiency by which microbes build MAOC (C stabilization efficiency) if soil pH stays constant. But if soils acidify, a common response to N enrichment, then microbial biomass and enzymatic organic matter decay may decrease, increasing POC but not MAOC. We found that N enrichment had no effect on C fractions except for a decrease in MAOC at one site. Specifically, despite reported increases in plant biomass in three sites and decreases in microbial biomass and extracellular enzyme activities in two sites that acidified, POC did not increase. Furthermore, microbial C use and stabilization efficiency increased in a non-acidified site, but without increasing MAOC. Instead, MAOC decreased by 16% at one of the sites that acidified, likely because it lost 47% of the exchangeable calcium (Ca) relative to controls. Indeed, MAOC was strongly and positively affected by Ca, which directly and, through its positive effect on microbial biomass, explained 58% of variation in MAOC. Long-term effects of N fertilization on dryland SOC storage appear abiotic in nature, such that drylands where Ca-stabilization of SOC is prevalent and soils acidify, are most at risk for significant C loss.

Exploring Trait Trade-Offs for Fungal Decomposers in a Southern California Grassland.

Fungi are important decomposers in terrestrial ecosystems, so their responses to climate change might influence carbon (C) and nitrogen (N) dynamics. We investigated whether growth and activity of fungi under drought conditions were structured by trade-offs among traits in 15 fungal isolates from a Mediterranean Southern California grassland. We inoculated fungi onto sterilized litter that was incubated at three moisture levels (4, 27, and 50% water holding capacity, WHC). For each isolate, we characterized traits that described three potential lifestyles within the newly proposed "YAS" framework: growth yield, resource acquisition, and stress tolerance. Specifically, we measured fungal hyphal length per unit litter decomposition for growth yield; the potential activities of the extracellular enzymes cellobiohydrolase (CBH), ß -glucosidase (BG), ß -xylosidase (BX), and N-acetyl- ß - D -glucosaminidase (NAG) for resource acquisition; and ability to grow in drought vs. higher moisture levels for drought stress tolerance. Although, we had hypothesized that evolutionary and physiological trade-offs would elicit negative relationships among traits, we found no supporting evidence for this hypothesis. Across isolates, growth yield, drought stress tolerance, and extracellular enzyme activities were not significantly related to each other. Thus, it is possible that drought-induced shifts in fungal community composition may not necessarily lead to changes in fungal biomass or decomposer ability in this arid grassland.

Carbon flux and forest dynamics: Increased deadwood decomposition in tropical rainforest tree-fall canopy gaps.

Tree mortality rates are increasing within tropical rainforests as a result of global environmental change. When trees die, gaps are created in forest canopies and carbon is transferred from the living to deadwood pools. However, little is known about the effect of tree-fall canopy gaps on the activity of decomposer communities and the rate of deadwood decay in forests. This means that the accuracy of regional and global carbon budgets is uncertain, especially given ongoing changes to the structure of rainforest ecosystems. Therefore, to determine the effect of canopy openings on wood decay rates and regional carbon flux, we carried out the first assessment of deadwood mass loss within canopy gaps in old-growth rainforest. We used replicated canopy gaps paired with closed canopy sites in combination with macroinvertebrate accessible and inaccessible woodblocks to experimentally partition the relative contribution of microbes vs. termites to decomposition within contrasting understorey conditions. We show that over a 12 month period, wood mass loss increased by 63% in canopy gaps compared with closed canopy sites and that this increase was driven by termites. Using LiDAR data to quantify the proportion of canopy openings in the study region, we modelled the effect of observed changes in decomposition within gaps on regional carbon flux. Overall, we estimate that this accelerated decomposition increases regional wood decay rate by up to 18.2%, corresponding to a flux increase of 0.27 Mg C ha-1  year-1 that is not currently accounted for in regional carbon budgets. These results provide the first insights into how small-scale disturbances in rainforests can generate hotspots for decomposer activity and carbon fluxes. In doing so, we show that including canopy gap dynamics and their impacts on wood decomposition in forest ecosystems can help improve the predictive accuracy of the carbon cycle in land surface models.

Phenotypic plasticity of fungal traits in response to moisture and temperature.

Phenotypic plasticity of traits is commonly measured in plants to improve understanding of organismal and ecosystem responses to climate change but is far less studied for microbes. Specifically, decomposer fungi are thought to display high levels of phenotypic plasticity and their functions have important implications for ecosystem dynamics. Assessing the phenotypic plasticity of fungal traits may therefore be important for predicting fungal community response to climate change. Here, we assess the phenotypic plasticity of 15 fungal isolates (12 species) from a Southern California grassland. Fungi were incubated on litter at five moisture levels (ranging from 4-50% water holding capacity) and at five temperatures (ranging from 4-36 °C). After incubation, fungal biomass and activities of four extracellular enzymes (cellobiohydrolase (CBH), ß-glucosidase (BG), ß-xylosidase (BX), and N-acetyl-ß-D-glucosaminidase (NAG)) were measured. We used response surface methodology to determine how fungal phenotypic plasticity differs across the moisture-temperature gradient. We hypothesized that fungal biomass and extracellular enzyme activities would vary with moisture and temperature and that the shape of the response surface would vary between fungal isolates. We further hypothesized that more closely related fungi would show more similar response surfaces across the moisture-temperature gradient. In support of our hypotheses, we found that plasticity differed between fungi along the temperature gradient for fungal biomass and for all the extracellular enzyme activities. Plasticity also differed between fungi along the moisture gradient for BG activity. These differences appear to be caused by variation mainly at the moisture and temperature extremes. We also found that more closely related fungi had more similar extracellular enzymes activities at the highest temperature. Altogether, this evidence suggests that with global warming, fungal biodiversity may become increasingly important as functional traits tend to diverge along phylogenetic lines at higher temperatures.

Drought and plant litter chemistry alter microbial gene expression and metabolite production.

Drought represents a significant stress to microorganisms and is known to reduce microbial activity and organic matter decomposition in Mediterranean ecosystems. However, we lack a detailed understanding of the drought stress response of microbial decomposers. Here we present metatranscriptomic and metabolomic data on the physiological response of in situ microbial communities on plant litter to long-term drought in Californian grass and shrub ecosystems. We hypothesised that drought causes greater microbial allocation to stress tolerance relative to growth pathways. In grass litter, communities from the decade-long ambient and reduced precipitation treatments had distinct taxonomic and functional profiles. The most discernable physiological signatures of drought were production or uptake of compatible solutes to maintain cellular osmotic balance, and synthesis of capsular and extracellular polymeric substances as a mechanism to retain water. The results show a clear functional response to drought in grass litter communities with greater allocation to survival relative to growth that could affect decomposition under drought. In contrast, communities on chemically more diverse and complex shrub litter had smaller physiological differences in response to long-term drought but higher investment in resource acquisition traits across precipitation treatments, suggesting that the functional response to drought is constrained by substrate quality. Our findings suggest, for the first time in a field setting, a trade off between microbial drought stress tolerance, resource acquisition and growth traits in plant litter microbial communities.

Embracing a new paradigm for temperature sensitivity of soil microbes.

The temperature sensitivity of soil processes is of major interest, especially in light of climate change. Originally formulated to explain the temperature dependence of chemical reactions, the Arrhenius equation, and related Q10 temperature coefficient, has a long history of application to soil biological processes. However, empirical data indicate that Q10 and Arrhenius model are often poor metrics of temperature sensitivity in soils. In this opinion piece, we aim to (a) review alternative approaches for characterizing temperature sensitivity, focusing on macromolecular rate theory (MMRT); (b) provide strategies and tools for implementing a new temperature sensitivity framework; (c) develop thermal adaptation hypotheses for the MMRT framework; and (d) explore new questions and opportunities stemming from this paradigm shift. Microbial ecologists should consider developing and adopting MMRT as the basis for predicting biological rates as a function of temperature. Improved understanding of temperature sensitivity in soils is particularly pertinent as microbial response to temperature has a large impact on global climate feedbacks.

Phylogenetic conservation of bacterial responses to soil nitrogen addition across continents.

Soil microbial communities are intricately linked to ecosystem functioning such as nutrient cycling; therefore, a predictive understanding of how these communities respond to environmental changes is of great interest. Here, we test whether phylogenetic information can predict the response of bacterial taxa to nitrogen (N) addition. We analyze the composition of soil bacterial communities in 13 field experiments across 5 continents and find that the N response of bacteria is phylogenetically conserved at each location. Remarkably, the phylogenetic pattern of N responses is similar when merging data across locations. Thus, we can identify bacterial clades - the size of which are highly variable across the bacterial tree - that respond consistently to N addition across locations. Our findings suggest that a phylogenetic approach may be useful in predicting shifts in microbial community composition in the face of other environmental changes.