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Most organisms are built from a single genome. In striking contrast, arbuscular mycorrhizal fungi appear to maintain genomic variation within an individual fungal network. Arbuscular mycorrhizal fungi dwell in the soil, form mutualistic networks with plants, and bear multiple, potentially genetically diverse nuclei within a network. We explore, from a theoretical perspective, why such genetic diversity might be maintained within individuals. We consider selection acting within and between individual fungal networks. We show that genetic diversity could provide a benefit at the level of the individual, by improving growth in variable environments, and that this can stabilize genetic diversity even in the presence of nuclear conflict. Arbuscular mycorrhizal fungi complicate our understanding of organismality, but our findings offer a way of understanding such biological anomalies.

Strigolactones are phytohormones that influence arbuscular mycorrhizal fungal (AMF) spore germination, pre-symbiotic hyphal branching, and metabolic rates. Historically, strigolactone effects have been tested on single AMF strains. An open question is whether intraspecific variation in strigolactone effects and intraspecific interactions can influence AMF competition. Using the Rhizophagus irregularis strains A5 and C2, we tested for intraspecific variation in the response of germination and pre-symbiotic growth (i.e., hyphal length and branching) to the strigolactones GR24 and 5-deoxystrigol. We also tested if interactions between these strains modified their germination rates and pre-symbiotic growth. Spore germination rates were consistently high (> 90%) for C2 spores, regardless of treatment and the presence of the other strain. For A5 spores, germination was increased by strigolactone presence from approximately 30 to 70% but reduced when grown in mixed culture. When growing together, branching increased for both strains compared to monocultures. In mixed cultures, strigolactones increased the branching for both strains but led to an increase in hyphal length only for the strain A5. These strain-specific responses suggest that strigolactones may have the potential to shift competitive dynamics among AMF species with direct implications for the establishment of the AMF community. [ABSTRACT FROM AUTHOR]

Societal Impact Statement: Cities are stressful environments for plants, plagued by heat, pollution, and biodiversity loss. As a result, plant communities tend to suffer in green roofs, parks, and living walls. Finding solutions to help plants grow in stressful environments is a goal of the sustainable city. One solution is to better incorporate plant–microbe symbiosis in green architecture. Symbiotic fungi and bacteria can provide nutrients, water, and help plants to cope with urban stress. The reconceptualization of green infrastructure from a microbial‐focused perspective has the potential to improve plant health, growth, and diversity in cities. Summary: Plant communities in cities help maintain the health and stability of urban ecosystems and inhabitants. Ensuring that greenspace is healthy and productive is a key goal of green infrastructure and landscape architecture (GILA). However, cities are stressful environments for plants. In natural ecosystems, plants live in symbiosis with fungi, bacteria, and other microbes that can help alleviate stress. Microbial communities may also help with stress associated with urban environments. Incorporating mutualistic symbioses into GILA is a sustainable way to enhance urban greenspace. Here, we address key stressors for GILA in cities, including dependency on fertilizers, pathogens, drought, fewer pollinators, pollution, and reduced plant biodiversity. For each of these stressors, we discuss how symbiotic fungi and bacteria can help mitigate these issues, including case‐use scenarios. We conclude with new approaches to deliberately incorporate mutualisms in cities and open dialogues with stakeholders. [ABSTRACT FROM AUTHOR]

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Species utilizing the same resources often fail to coexist for extended periods of time. Such competitive exclusion mechanisms potentially underly microbiome dynamics, causing breakdowns of communities composed of species with similar genetic backgrounds of resource utilization. Although genes responsible for competitive exclusion among a small number of species have been investigated in pioneering studies, it remains a major challenge to integrate genomics and ecology for understanding stable coexistence in speciesrich communities. Here, we examine whether community-scale analyses of functional gene redundancy can provide a useful platform for interpreting and predicting collapse of bacterial communities. Through 110-day time-series of experimental microbiome dynamics, we analyzed the metagenome-assembled genomes of co-occurring bacterial species. We then inferred ecological niche space based on the multivariate analysis of the genome compositions. The analysis allowed us to evaluate potential shifts in the level of niche overlap between species through time. We hypothesized that community-scale pressure of competitive exclusion could be evaluated by quantifying overlap of genetically determined resource-use profiles (metabolic pathway profiles) among coexisting species. We found that the degree of community compositional changes observed in the experimental microbiome was correlated with the magnitude of gene-repertoire overlaps among bacterial species, although the causation between the two variables deserves future extensive research. The metagenome-based analysis of genetic potential for competitive exclusion will help us forecast major events in microbiome dynamics such as sudden community collapse (i.e., dysbiosis). [ABSTRACT FROM AUTHOR]