What we are reading in May, 2018
What is and what is not a mycorrhizal plant?
I am sure that most of us can quickly answer a clear definition of what is a mycorrhizal plant. However, if we try to draw clear limits to what is, and what is not a mycorrhizal plant, we will certainly find that the limits are more blurred than expected. Actually, we could find at least two schools of thought: On one hand, a classical school defines mycorrhizal plants based on the presence and absence of mycorrhizal fungi colonization in their plant roots, in line with the seminal book of Smith and Read (2008). In contrast, a second school of thought will argue that the mycorrhizal activity is what defines mycorrhizae, so only the presence of arbuscules in plant roots should define what is, and what is not a mycorrhizal plant (Brundrett 2017). Therefore, the dispute is mainly on where to put the focus on mycorrhizal symbiosis, either in the fungal colonization effects or in the lack of nutrient exchange via arbuscule. The recent paper of Cosme and coauthors reviewed and partly deepened into this question, focusing on the presence and expression of the genes that presumably control for the symbiotic nutrient exchange. Cosme et al. hold the classical perspective of non-mycorrhizal plants as the ones without fungal colonization. They suggest that the arbuscule’s view is limited to only the nutritional role of mycorrhizal symbiosis. This, per se, disregards other symbiotic roles, which at least, can equally impact plant survival, such as abiotic stress tolerance, soil amendments or resistance to pathogens.
But the story does not end here, in this grey area between mycorrhizal and non-mycorrhizal plants, there is a group of plants whose roots, after fungal colonization, can developed few or no arbuscules, depending on the environment. They proposed that these plants are in their evolutionary way to lose its mycorrhizal symbiosis. They coined the term: rudimentary arbuscular mycorrhizal (RAM) morphotype, for these species, which presumably have lost or cannot activate the genes that lead to fully form the mycorrhizal symbiotic structures. In this context, Cosme et al (2018; in press) proposed that the brassicaceae family, as it is genetically well studied and contains species of all different mycorrhizal statuses, is ideal for deepening into the genetic base in the development of mycorrhizal symbiotic structures (Figure 1). Although our current knowledge is far from clarifying the list of genes involved in mycorrhizal symbiosis and the relevance of the environment on their expression, future targeted experiments comparing brassicaceae species can shed light into the drivers of this ancient and fundamental symbiosis. While this paper does not answer the main question (what is and what is not a mycorrhizal plant), it opens up the very much needed discussion, suggesting pathways comparing whole genomes, to disentangle the apparent complexity of mycorrhizal plant-fungal coevolution.
Figure 1. Interactions between Members of the Brassicaceae Family and Arbuscular Mycorrhizal (AM) Fungi (visit the paper for details and references). On the left side, a phylogenetic tree depicts the members of the Brassicaceae family of which genome sequences have been published or are being processed according to Koenig and Weigel . The phylogenetic tree was complemented by a few additional Brassicaceae members for which information on AM host status was available in the literature. The model AM plant species used to describe the required symbiotic toolkit are listed at the bottom. The column ‘Host’ summarizes information on plant host status compiled from literature cited in this Opinion. The column ‘Toolkit’ summarizes information on the symbiotic toolkit as documented by Delaux et al. . For a detailed list of the toolkit genes that are absent in non-host plant species, see Table 1. In the center, a root transversal cross-section illustrates different host phenotypes: the (AM) host phenotype that accommodates the Paris type of colonization, the Arum type of colonization, or intermediate types of both as described by Dickson et al. ; the non-host, in which endogenous AM fungal colonization never occurs; and the rudimentary AM (RAM) host as coined in this Opinion to characterize those plant species that do not form prominent AM phenotypes but can harbor a few symbiotic fungal structures. The illustrated plant growth stages presented at the top reflect the potential variation in host ability to form AM symbiosis throughout plant development. On the right, various symbiotic functions of AM fungi are summarized, along with a phylogenetic tree of AM fungal genera according to Krüger et al. . The color-coded column associated with this tree summarizes the AM fungal genera for which at least one species was shown to interact with at least one presumed non-host plant species.
Brundrett MC. 2017. Global Diversity and Importance of Mycorrhizal and Nonmycorrhizal Plants. In: Tedersoo L, ed. Biogeography of Mycorrhizal Symbiosis. Cham: Springer International Publishing, 533–556.
In mycorrhizal research, we usually envision fungi as the microbial symbionts of plants. This review by Deveau et al. (2018; in press) of bacterial-fungal (BF) interactions gives a totally different vision where fungi are this time the “hosts” and bacteria the “microbes”. Bacteria can affect the biology of its fungal host in many ways, therefore also influencing the ability of the fungus to interact with its own host plant. These multilevel inter-kingdom interactions are, indeed, highly complex and still poorly known.
Let’s start with some definitions! The microbiome is the microbial community in a particular environment (the gut, the rhizosphere). Fungal microbiomes can be specific to particular tissues: the mycelium, fruiting bodies, spores, etc. Benefits to their fungal hosts include mycelial growth, secondary metabolite production, or even reproduction. The holobiont refers to the microbial community associated with a host. But when it comes to microbial interactions, it is often difficult to determine who is, in fact, the “host”? So the authors redefined the holobiont as a “unit of biological organization composed of several distinct genomes, that influence the genomic evolution of each other”.
Bacteria inside fungi. In the Ascomycota and Basidiomycota, endobacteria appear to be ephemeral in nature and may be involved with local adaptation to specific habitats. In contrast, in the Mucoromycota, some endobacteria have developed tight relationships with their host and endured significant genome reductions. These mutualistic interactions between endobacteria and Mucoromycota fungi have many outcomes. In the parasitic fungi Rhizopus, endobacteria control the asexual sporulation of the fungi thus enhancing its pathogenicity. In the Glomeromycotina, Glomeribacter symbionts are vertically transmitted. They also promote metabolic assistance in the production of vitamin B12, not only for the fungus but also for its plant mycorrhizal partner. Interestingly, a similar bacterial-assisted production of vitamin B12 has also been detected in the ascomycete lichen Lobaria pulmonaria, illustrating the wide range of fungi with which these endobacteria associate.
But endobacteria are not always “the good guys”. Several parasitic endosymbionts of Glomeromycotina have been detected. In Mortierellomycotina, Mycoavidus bacteria decreased fungal growth and may consume the metabolic products of their host, despite being closely related to Glomeribacter (described above as mutualistic).
Bacterial-fungal networks. Next-generation sequencing enable to study microbial communities across habitats, but few studies have considered fungi and bacteria together. Non-random associations between fungi and bacteria and an over-representation of positive associations compared to negative ones have been demonstrated in plants, leaf litter, soils, and other microbiomes. In these BF networks, some fungal species acted as hub or keystone species that drive the microbial community assembly of the entire microbiome. Keystone species are taxa that have a disproportionately large impact on the community relative to their abundance, thus on which the functioning of the community relies (Dodds & Whiles, 2010). For example, the yeast Dioszegia was the fungal hub of the phyllosphere microbiome of Arabidopsis thaliana and its bacterial components. Yet another reason to emphasize the importance of fungi in ecosystems!
These BF interactions also drive important ecosystem functions. For example the co-occurrence of lignocellulose decomposers Clitocybe and Mycena with N-fixing bacteria was correlated with N deposition in the soil during leaf-decay. These bacteria may contribute to the N nutrition of the fungi while the later make C available for bacteria. Maintaining the ecological balance within the microbiome, and with their host, is fundamental for the health of both animal and plant hosts. Indeed, BF interactions can impact the virulence of both partners in human diseases or plant pathogens. Therefore, these complex interactions need to be taken into account when designing strategies to improve the growth and health of crops.
How do bacteria and fungi communicate? Many studies demonstrated that both fungi and bacteria react specifically to the presence of their partner through the perception of small signaling molecules. Quorum sensing (QS) is a widespread phenomenon in bacteria, where gene expression is regulated in response to fluctuations in cell/population density (Miller & Bassler, 2001). When the population of bacteria reaches a minimal threshold, the bacteria will release signal metabolites that alter the gene expression of the entire population, for example to regulate virulence, antibiotic production or sporulation. QS has recently been detected in fungi as well, for mechanisms including morphogenesis, germination or pathogenicity. It seems that bacteria can react to QS molecules of their fungal partners and vice-versa. Such inter-kingdom signaling is likely a common mechanism of communication in mixed fungal-bacterial communities such as biofilms or bacterial endofungal symbioses.
Other mechanisms of ‘long-distance’ signaling involve volatile organic compounds (VOC), such as terpenes, that easily diffuse through water- and gas-filled tissues. These VOC can originate from bacteria, fungi, or synergistically from both partners. Examples include VOCs produced by bacteria that stimulate the growth of the fungal pathogen Aspergillus, or terpenes produced by the pathogenic fungus Fusarium that induce the motility of bacteria. Interestingly, VOC production is highly influenced by nutrient availability, thus microorganism senses may shift with variations in environmental conditions via VOCs.
Lastly, fungi may also recognize bacteria using receptors that are similar to plant and animal immune receptors. These receptors seem to have the ability to rapidly adapt to new ligants through recombination of tandem repeat sequences. Whether these receptors trigger immunity-like responses, or are used in the signaling of generic BF interactions still needs further investigation.
Bacteria driving on the fungal highway. Given that mycelia vastly extend in soils, they constitute ideal transport route for bacteria. Fungal mycelium easily adapt to environmental disturbances or the heterogeneous distribution of nutrients. For example, fungi can translocate resources between ‘feeder’ hyphae growing in optimal environments, to exploration hyphae in more unfavorable areas. By re-allocating their biomass, they can colonize new habitats or access heterogeneously distributed nutrients. These ‘fungal highways’ can also serve as dispersal vectors for bacteria, giving them access to new habitats and nutrients. Mycelia-facilitated bacterial dispersal likewise promotes new niche colonization, food degradation, or the co-invasion of tissues during pathogenesis.
The nutrient warfare. Competition or cooperation for nutrient acquisition has led to the development of a large chemical arsenal in both fungi and bacteria. In response, a multitude of defensive mechanisms have also been developed by microorganisms to protect themselves, including cooperative behaviors between toxic fungi and bacteria to overcome the defense mechanisms of their target plant host.
In soils, bacteria also play an important role in fungal biomass decomposition, where fungal hyphae constitute an important source of nutrients. Some Collimonas bacteria even kill and consume living fungi (mycophagy). On the other hand, fungi may also use bacteria as food source. For example, species of Morchella developed a sophisticated mechanism of ‘bacterial farming’ in which the fungus first feeds the bacteria then harvests this self-created C source. Of course, both bacteria and fungi also participate in the degradation of plant biomass. All these mechanisms have consequences for ecosystem functioning and biogeochemical cycles, such as carbon flow in the rhizosphere.
Niche modulation. By modifying their environment in ways that positively or negatively affect their partners, bacteria and fungi can indirectly modulate their interactions. Many fungi sense and actively modulate the pH in their surroundings, thus stimulating overall bacterial growth and metabolism at neural pH, or inhibiting them at lower pH. Oxygen modulation is another mechanism in which the fungus Candida enhances its respiration rate to create an anaerobic niche that favor anaerobic bacteria in the detriment of aerobic bacteria in the oral cavity.
What is next? Several questions emerge from this review: Who is there? Who is actively doing what? What are the factors that modify the output of the interaction?’ Current challenges of microbial ecology include identifying keystone members and functions of microbiomes, their responses to perturbations, as well as taking into account the spatial and temporal scales of BF interactions. There is still an important gap between studies performed in the laboratory and the ‘in vivo’ reality at the ecosystem scale. Fungal and bacterial have the advantages of being fast growing and easy to manipulate and to track genetically. Thus they are the prefect candidates to be used as model systems to analyze complex interactions. If you find ‘contaminating’ bacterial DNA in your data, keep in mind of the possibility of endobacterial associates before discarding it!
Deveau, A., Bonito, G., Uehling, J., Paoletti, M., Becker, M., Bindschedler, S., … & Mieszkin, S. (2018). Bacterial-Fungal Interactions: ecology, mechanisms and challenges. FEMS microbiology reviews.
Dodds WK, Whiles MR. 2010. Complex community interactions. In: Freshwater Ecology. London: Academic Press, 587–609.
Miller, M. B., & Bassler, B. L. (2001). Quorum sensing in bacteria. Annual Reviews in Microbiology, 55(1), 165-199.