Genomic evidence of symbiotic adaptations in fungus-associated bacteria

Fungi harbor diverse bacteria that engage in various relationships. While these relationships potentially influence fungal functioning, their underlying genetic mechanisms remain unexplored. Here, we aimed to elucidate the key genomic features of fungus-associated bacteria (FaB) by comparing 163 FaB genomes to 1,048 bacterial genomes from other hosts and habitats. Our analyses revealed several distinctive genomic features of FaB. We found that FaB are enriched in carbohydrate transport/metabolism- and motility-related genes, suggesting an adaptation for utilizing complex fungal carbon sources. They are also enriched in genes targeting fungal biomass, likely reflecting their role in recycling and rebuilding fungal structures. Additionally, FaB associated with plant-mutualistic fungi possess a wider array of carbon-acquisition enzymes specific to fungal and plant substrates compared to those residing with saprotrophic fungi. These unique genomic features highlight FaB' potential as key players in fungal nutrient acquisition and decomposition, ultimately influencing plant-fungal symbiosis and ecosystem functioning.

Microfluidics and Metabolomics Reveal Symbiotic Bacterial-Fungal Interactions Between Mortierella elongata and Burkholderia Include Metabolite Exchange

We identified two poplar (Populus sp.)-associated microbes, the fungus, Mortierella elongata strain AG77, and the bacterium, Burkholderia strain BT03, that mutually promote each other’s growth. Using culture assays in concert with a novel microfluidic device to generate time-lapse videos, we found growth specific media differing in pH and pre-conditioned by microbial growth led to increased fungal and bacterial growth rates. Coupling microfluidics and comparative metabolomics data results indicated that observed microbial growth stimulation involves metabolic exchange during two ordered events. The first is an emission of fungal metabolites, including organic acids used or modified by bacteria. A second signal of unknown nature is produced by bacteria which increases fungal growth rates. We find this symbiosis is initiated in part by metabolic exchange involving fungal organic acids.

Ultra-low input transcriptomics reveal the spore functional content and phylogenetic affiliations of poorly studied arbuscular mycorrhizal fungi

Arbuscular mycorrhizal fungi (AMF) are a group of soil microorganisms that establish symbioses with the vast majority of land plants. To date, generation of AMF coding information has been limited to model genera that grow well axenically; Rhizoglomus and Gigaspora. Meanwhile, data on the functional gene repertoire of most AMF families is non-existent. Here, we provide primary large-scale transcriptome data from eight poorly studied AMF species (Acaulospora morrowiae, Diversispora versiforme, Scutellospora calospora, Racocetra castanea, Paraglomus brasilianum, Ambispora leptoticha, Claroideoglomus claroideum and Funneliformis mosseae) using ultra-low input ribonucleic acid (RNA)-seq approaches. Our analyses reveals that quiescent spores of many AMF species harbour a diverse functional diversity and solidify known evolutionary relationships within the group. Our findings demonstrate that RNA-seq data obtained from low-input RNA are reliable in comparison to conventional RNA-seq experiments. Thus, our methodology can potentially be used to deepen our understanding of fungal microbial function and phylogeny using minute amounts of RNA material.

Biology of Fungi and Their Bacterial Endosymbionts

Heritable symbioses, in which endosymbiotic bacteria (EB) are transmitted vertically between host generations, are an important source of evolutionary novelties. A primary example of such symbioses is the eukaryotic cell with its EB-derived organelles. Recent discoveries suggest that endosymbiosis-related innovations can be also found in associations formed by early divergent fungi in the phylum Mucoromycota with heritable EB from two classes, Betaproteobacteria and Mollicutes. These symbioses exemplify novel types of host-symbiont interactions. Studies of these partnerships fuel theoretical models describing mechanisms that stabilize heritable symbioses, control the rate of molecular evolution, and enable the establishment of mutualisms. Lastly, by altering host phenotypes and metabolism, these associations represent an important instrument for probing the basic biology of the Mucoromycota hosts, which remain one of the least explored filamentous fungi.

Polymicrobial Multi-functional Approach for Enhancement of Crop Productivity

There is an increasing global need for enhancing the food production to meet the needs of the fast-growing human population. Traditional approach to increasing agricultural productivity through high inputs of chemical nitrogen and phosphate fertilizers and pesticides is not sustainable because of high costs and concerns about global warming, environmental pollution, and safety concerns. Therefore, the use of naturally occurring soil microbes for increasing productivity of food crops is an attractive eco-friendly, cost-effective, and sustainable alternative to the use of chemical fertilizers and pesticides. There is a vast body of published literature on microbial symbiotic and nonsymbiotic nitrogen fixation, multiple beneficial mechanisms used by plant growth-promoting rhizobacteria (PGPR), the nature and significance of mycorrhiza-plant symbiosis, and the growing technology on production of efficacious microbial inoculants. These areas are briefly reviewed here. The construction of an inoculant with a consortium of microbes with multiple beneficial functions such as N(2) fixation, biocontrol, phosphate solubilization, and other plant growth-promoting properties is a positive new development in this area in that a single inoculant can be used effectively for increasing the productivity of a broad spectrum of crops including legumes, cereals, vegetables, and grasses. Such a polymicrobial inoculant containing several microorganisms for each major function involved in promoting the plant growth and productivity gives it greater stability and wider applications for a range of major crops. Intensifying research in this area leading to further advances in our understanding of biochemical/molecular mechanisms involved in plant-microbe-soil interactions coupled with rapid advances in the genomics-proteomics of beneficial microbes should lead to the design and development of inoculants with greater efficacy for increasing the productivity of a wide range of crops.

Evolution of small prokaryotic genomes

As revealed by genome sequencing, the biology of prokaryotes with reduced genomes is strikingly diverse. These include free-living prokaryotes with ∼800 genes as well as endosymbiotic bacteria with as few as ∼140 genes. Comparative genomics is revealing the evolutionary mechanisms that led to these small genomes. In the case of free-living prokaryotes, natural selection directly favored genome reduction, while in the case of endosymbiotic prokaryotes neutral processes played a more prominent role. However, new experimental data suggest that selective processes may be at operation as well for endosymbiotic prokaryotes at least during the first stages of genome reduction. Endosymbiotic prokaryotes have evolved diverse strategies for living with reduced gene sets inside a host-defined medium. These include utilization of host-encoded functions (some of them coded by genes acquired by gene transfer from the endosymbiont and/or other bacteria); metabolic complementation between co-symbionts; and forming consortiums with other bacteria within the host. Recent genome sequencing projects of intracellular mutualistic bacteria showed that previously believed universal evolutionary trends like reduced G+C content and conservation of genome synteny are not always present in highly reduced genomes. Finally, the simplified molecular machinery of some of these organisms with small genomes may be used to aid in the design of artificial minimal cells. Here we review recent genomic discoveries of the biology of prokaryotes endowed with small gene sets and discuss the evolutionary mechanisms that have been proposed to explain their peculiar nature.

The genome of the obligate endobacterium of an AM fungus reveals an interphylum network of nutritional interactions

As obligate symbionts of most land plants, arbuscular mycorrhizal fungi (AMF) have a crucial role in ecosystems, but to date, in the absence of genomic data, their adaptive biology remains elusive. In addition, endobacteria are found in their cytoplasm, the role of which is unknown. In order to investigate the function of the Gram-negative Candidatus Glomeribacter gigasporarum, an endobacterium of the AMF Gigaspora margarita, we sequenced its genome, leading to an ∼1.72-Mb assembly. Phylogenetic analyses placed Ca. G. gigasporarum in the Burkholderiaceae whereas metabolic network analyses clustered it with insect endobacteria. This positioning of Ca. G. gigasporarum among different bacterial classes reveals that it has undergone convergent evolution to adapt itself to intracellular lifestyle. The genome annotation of this mycorrhizal-fungal endobacterium has revealed an unexpected genetic mosaic where typical determinants of symbiotic, pathogenic and free-living bacteria are integrated in a reduced genome. Ca. G. gigasporarum is an aerobic microbe that depends on its host for carbon, phosphorus and nitrogen supply; it also expresses type II and type III secretion systems and synthesizes vitamin B12, antibiotics- and toxin-resistance molecules, which may contribute to the fungal host's ecological fitness. Ca. G. gigasporarum has an extreme dependence on its host for nutrients and energy, whereas the fungal host is itself an obligate biotroph that relies on a photosynthetic plant. Our work represents the first step towards unraveling a complex network of interphylum interactions, which is expected to have a previously unrecognized ecological impact.

New paradigms for the evolution of beneficial infections

A longstanding paradigm predicts that microbial parasites and mutualists exhibit disparate evolutionary patterns. Parasites are predicted to promote arms races with hosts, rapid evolution and sexual recombination. By contrast, mutualists have been linked with beneficial coadaptation, evolutionary stasis and asexuality. In this review we discuss the recent surge of molecular data on microbes that are being used to test and reshape these ideas. New analyses reveal that beneficial microbes often share mechanisms of infection and defense with parasites, and can also exhibit rapid evolution and extensive genetic exchange. To explain these patterns, new paradigms must take into account the varied population biology of beneficial microbes, their potential conflicts with hosts, and the mosaic nature of genome evolution that requires locus-based tests to analyze the genetics of host adaptation.