Disentangling strictly self-serving mutations from win-win mutations in a mutualistic microbial community

Emergence and maintenance of stable coexistence during a long-term multicellular evolution experiment

The evolution of multicellular life spurred evolutionary radiations, fundamentally changing many of Earth's ecosystems. Yet little is known about how early steps in the evolution of multicellularity affect eco-evolutionary dynamics. Through long-term experimental evolution, we observed niche partitioning and the adaptive divergence of two specialized lineages from a single multicellular ancestor. Over 715 daily transfers, snowflake yeast were subjected to selection for rapid growth, followed by selection favouring larger group size. Small and large cluster-forming lineages evolved from a monomorphic ancestor, coexisting for over ~4,300 generations, specializing on divergent aspects of a trade-off between growth rate and survival. Through modelling and experimentation, we demonstrate that coexistence is maintained by a trade-off between organismal size and competitiveness for dissolved oxygen. Taken together, this work shows how the evolution of a new level of biological individuality can rapidly drive adaptive diversification and the expansion of a nascent multicellular niche, one of the most historically impactful emergent properties of this evolutionary transition.

Condition-dependent fitness effects of large synthetic chromosome amplifications

Whole-chromosome aneuploidy and large segmental amplifications can have devastating effects in multicellular organisms, from developmental disorders and miscarriage to cancer. Aneuploidy in single-celled organisms such as yeast also results in proliferative defects and reduced viability. Yet, paradoxically, CNVs are routinely observed in laboratory evolution experiments with microbes grown in stressful conditions. The defects associated with aneuploidy are often attributed to the imbalance of many differentially expressed genes on the affected chromosomes, with many genes each contributing incremental effects. An alternate hypothesis is that a small number of individual genes are large effect 'drivers' of these fitness changes when present in an altered copy number. To test these two views, we have employed a collection of strains bearing large chromosomal amplifications that we previously assayed in nutrient-limited chemostat competitions. In this study, we focus on conditions known to be poorly tolerated by aneuploid yeast-high temperature, treatment with the Hsp90 inhibitor radicicol, and growth in extended stationary phase. To identify potential genes with a large impact on fitness, we fit a piecewise constant model to fitness data across chromosome arms, filtering breakpoints in this model by magnitude to focus on regions with a large impact on fitness in each condition. While fitness generally decreased as the length of the amplification increased, we were able to identify 91 candidate regions that disproportionately impacted fitness when amplified. Consistent with our previous work with this strain collection, nearly all candidate regions were condition specific, with only five regions impacting fitness in multiple conditions.

Emergence and maintenance of stable coexistence during a long-term multicellular evolution experiment

The evolution of multicellular life spurred evolutionary radiations, fundamentally changing many of Earth’s ecosystems. Yet little is known about how early steps in the evolution of multicellularity transform eco-evolutionary dynamics, e.g., via niche expansion processes that may facilitate coexistence. Using long-term experimental evolution in the snowflake yeast model system, we show that the evolution of multicellularity drove niche partitioning and the adaptive divergence of two distinct, specialized lineages from a single multicellular ancestor. Over 715 daily transfers, snowflake yeast were subject to selection for rapid growth in rich media, followed by selection favoring larger group size. Both small and large cluster-forming lineages evolved from a monomorphic ancestor, coexisting for over ~4,300 generations. These small and large sized snowflake yeast lineages specialized on divergent aspects of a trade-off between growth rate and survival, mirroring predictions from ecological theory. Through modeling and experimentation, we demonstrate that coexistence is maintained by a trade-off between organismal size and competitiveness for dissolved oxygen. Taken together, this work shows how the evolution of a new level of biological individuality can rapidly drive adaptive diversification and the expansion of a nascent multicellular niche, one of the most historically-impactful emergent properties of this evolutionary transition.

Data-driven causal analysis of observational biological time series

Complex systems are challenging to understand, especially when they defy manipulative experiments for practical or ethical reasons. Several fields have developed parallel approaches to infer causal relations from observational time series. Yet, these methods are easy to misunderstand and often controversial. Here, we provide an accessible and critical review of three statistical causal discovery approaches (pairwise correlation, Granger causality, and state space reconstruction), using examples inspired by ecological processes. For each approach, we ask what it tests for, what causal statement it might imply, and when it could lead us astray. We devise new ways of visualizing key concepts, describe some novel pathologies of existing methods, and point out how so-called 'model-free' causality tests are not assumption-free. We hope that our synthesis will facilitate thoughtful application of methods, promote communication across different fields, and encourage explicit statements of assumptions. A video walkthrough is available (Video 1 or https://youtu.be/AIV0ttQrjK8).

Response of Sugarcane Rhizosphere Bacterial Community to Drought Stress

Sugarcane is an important sugar and energy crop, and its yield is greatly affected by drought. Although a large number of studies have shown that rhizosphere microorganisms can help improve the adaptability of plants to biotic or abiotic stresses, there is a lack of studies on the adaptability of sugarcane rhizosphere microbial communities to host plants. Therefore, we conducted drought stress treatment and normal irrigation treatment on three sugarcane varieties GT21, GT31, and GT42 widely cultivated in Guangxi. Using 16S rDNA sequencing technology to analyze the changes in abundance of the sugarcane rhizosphere bacterial community under different treatments, combined with the determination of soil enzyme activity, soil nutrient content, and sugarcane physiological characteristics, we explored the sugarcane rhizosphere bacterial community response to drought stress. In addition, we used the structural equation model to verify the response path of sugarcane rhizosphere bacteria. The results show that the bacterial community structure in the rhizosphere of sugarcane is stable under normal water conditions. The change in the bacterial community structure under drought stress has a 25.2% correlation with the drought adaptability of sugarcane, but the correlation with drought stress is as high as 42.17%. The changes in abundance of rhizosphere bacteria under drought stress are mainly concentrated in the phylum Rhizobiales and Streptomycetales. This change is directly related to the physiological state of the host plant under drought stress, soil available phosphorus, soil urease and soil acid protease. We investigated the response species of rhizosphere microorganisms and their response pathways under drought stress, providing a scientific basis for rhizosphere microorganisms to assist host plants to improve drought adaptability.

Extracellular Metabolism Sets the Table for Microbial Cross-Feeding

The transfer of nutrients between cells, or cross-feeding, is a ubiquitous feature of microbial communities with emergent properties that influence our health and orchestrate global biogeochemical cycles. Cross-feeding inevitably involves the externalization of molecules. Some of these molecules directly serve as cross-fed nutrients, while others can facilitate cross-feeding. Altogether, externalized molecules that promote cross-feeding are diverse in structure, ranging from small molecules to macromolecules. The functions of these molecules are equally diverse, encompassing waste products, enzymes, toxins, signaling molecules, biofilm components, and nutrients of high value to most microbes, including the producer cell. As diverse as the externalized and transferred molecules are the cross-feeding relationships that can be derived from them. Many cross-feeding relationships can be summarized as cooperative but are also subject to exploitation. Even those relationships that appear to be cooperative exhibit some level of competition between partners. In this review, we summarize the major types of actively secreted, passively excreted, and directly transferred molecules that either form the basis of cross-feeding relationships or facilitate them. Drawing on examples from both natural and synthetic communities, we explore how the interplay between microbial physiology, environmental parameters, and the diverse functional attributes of extracellular molecules can influence cross-feeding dynamics. Though microbial cross-feeding interactions represent a burgeoning field of interest, we may have only begun to scratch the surface.

Pleiotropic mutations can rapidly evolve to directly benefit self and cooperative partner despite unfavorable conditions

Cooperation, paying a cost to benefit others, is widespread. Cooperation can be promoted by pleiotropic ‘win-win’ mutations which directly benefit self (self-serving) and partner (partner-serving). Previously, we showed that partner-serving should be defined as increased benefit supply rate per intake benefit. Here, we report that win-win mutations can rapidly evolve even under conditions unfavorable for cooperation. Specifically, in a well-mixed environment we evolved engineered yeast cooperative communities where two strains exchanged costly metabolites, lysine and hypoxanthine. Among cells that consumed lysine and released hypoxanthine, ecm21 mutations repeatedly arose. ecm21 is self-serving, improving self’s growth rate in limiting lysine. ecm21 is also partner-serving, increasing hypoxanthine release rate per lysine consumption and the steady state growth rate of partner and of community. ecm21 also arose in monocultures evolving in lysine-limited chemostats. Thus, even without any history of cooperation or pressure to maintain cooperation, pleiotropic win-win mutations may readily evolve to promote cooperation.

Enhanced nutrient uptake is sufficient to drive emergent cross-feeding between bacteria in a synthetic community

Interactive microbial communities are ubiquitous, influencing biogeochemical cycles and host health. One widespread interaction is nutrient exchange, or cross-feeding, wherein metabolites are transferred between microbes. Some cross-fed metabolites, such as vitamins, amino acids, and ammonium (NH₄⁺), are communally valuable and impose a cost on the producer. The mechanisms that enforce cross-feeding of communally valuable metabolites are not fully understood. Previously we engineered a cross-feeding coculture between N₂-fixing Rhodopseudomonas palustris and fermentative Escherichia coli. Engineered R. palustris excretes essential nitrogen as NH₄⁺ to E. coli, while E. coli excretes essential carbon as fermentation products to R. palustris. Here, we sought to determine whether a reciprocal cross-feeding relationship would evolve spontaneously in cocultures with wild-type R. palustris, which is not known to excrete NH₄⁺. Indeed, we observed the emergence of NH₄⁺ cross-feeding, but driven by adaptation of E. coli alone. A missense mutation in E. coli NtrC, a regulator of nitrogen scavenging, resulted in constitutive activation of an NH₄⁺ transporter. This activity likely allowed E. coli to subsist on the small amount of leaked NH₄⁺ and better reciprocate through elevated excretion of fermentation products from a larger E. coli population. Our results indicate that enhanced nutrient uptake by recipients, rather than increased excretion by producers, is an underappreciated yet possibly prevalent mechanism by which cross-feeding can emerge.

Metabolic excretion associated with nutrient-growth dysregulation promotes the rapid evolution of an overt metabolic defect

In eukaryotes, conserved mechanisms ensure that cell growth is coordinated with nutrient availability. Overactive growth during nutrient limitation ("nutrient-growth dysregulation") can lead to rapid cell death. Here, we demonstrate that cells can adapt to nutrient-growth dysregulation by evolving major metabolic defects. Specifically, when yeast lysine-auxotrophic mutant lys- encountered lysine limitation, an evolutionarily novel stress, cells suffered nutrient-growth dysregulation. A subpopulation repeatedly evolved to lose the ability to synthesize organosulfurs (lys-orgS-). Organosulfurs, mainly reduced glutathione (GSH) and GSH conjugates, were released by lys- cells during lysine limitation when growth was dysregulated, but not during glucose limitation when growth was regulated. Limiting organosulfurs conferred a frequency-dependent fitness advantage to lys-orgS- by eliciting a proper slow growth program, including autophagy. Thus, nutrient-growth dysregulation is associated with rapid organosulfur release, which enables the selection of organosulfur auxotrophy to better tune cell growth to the metabolic environment. We speculate that evolutionarily novel stresses can trigger atypical release of certain metabolites, setting the stage for the evolution of new ecological interactions.

The microbial exometabolome: ecological resource and architect of microbial communities

All microorganisms release many metabolites, collectively known as the exometabolome. The resultant multi-way cross-feeding of metabolites among microorganisms distributes resources, thereby increasing total biomass of the microbial community, and promotes the recruitment and persistence of phylogenetically and functionally diverse taxa in microbial communities. Metabolite transfer can also select for evolutionary diversification, yielding multiple closely related but functionally distinct strains. Depending on starting conditions, the evolved strains may be auxotrophs requiring metabolic outputs from producer cells or, alternatively, display loss of complementary reactions in metabolic pathways, with increased metabolic efficiency. Metabolite cross-feeding is widespread in many microbial communities associated with animals and plants, including the animal gut microbiome, and these metabolic interactions can yield products valuable to the host. However, metabolite exchange between pairs of intracellular microbial taxa that share the same host cell or organ can be very limited compared to pairs of free-living microorganisms, perhaps as a consequence of host controls over the metabolic function of intracellular microorganisms. Priorities for future research include the development of tools for improved quantification of metabolite exchange in complex communities and greater integration of the roles of metabolic cross-feeding and other ecological processes, including priority effects and antagonistic interactions, in shaping microbial communities. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.

Simulations reveal challenges to artificial community selection and possible strategies for success

Multispecies microbial communities often display "community functions" arising from interactions of member species. Interactions are often difficult to decipher, making it challenging to design communities with desired functions. Alternatively, similar to artificial selection for individuals in agriculture and industry, one could repeatedly choose communities with the highest community functions to reproduce by randomly partitioning each into multiple "Newborn" communities for the next cycle. However, previous efforts in selecting complex communities have generated mixed outcomes that are difficult to interpret. To understand how to effectively enact community selection, we simulated community selection to improve a community function that requires 2 species and imposes a fitness cost on one or both species. Our simulations predict that improvement could be easily stalled unless various aspects of selection are carefully considered. These aspects include promoting species coexistence, suppressing noncontributors, choosing additional communities besides the highest functioning ones to reproduce, and reducing stochastic fluctuations in the biomass of each member species in Newborn communities. These considerations can be addressed experimentally. When executed effectively, community selection is predicted to improve costly community function, and may even force species to evolve slow growth to achieve species coexistence. Our conclusions hold under various alternative model assumptions and are therefore applicable to a variety of communities.