Mutualistic Symbiosis Research Articles

Exploring Xenorhabdus and Photorhabdus Nematode Symbionts in Search of Novel Therapeutics

Xenorhabdus and Photorhabdus bacteria, which live in mutualistic symbiosis with entomopathogenic nematodes, are currently recognised as an important source of bioactive compounds. During their extraordinary life cycle, these bacteria are capable of fine regulation of mutualism and pathogenesis towards two different hosts, a nematode and a wide range of insect species, respectively. Consequently, survival in a specific ecological niche favours the richness of biosynthetic gene clusters and respective metabolites with a specific structure and function, providing templates for uncovering new agrochemicals and therapeutics. To date, numerous studies have been published on the genetic ability of Xenorhabdus and Photorhabdus bacteria to produce biosynthetic novelty as well as distinctive classes of their metabolites with their activity and mechanism of action. Research shows diverse techniques and approaches that can lead to the discovery of new natural products, such as extract-based analysis, genetic engineering, and genomics linked with metabolomics. Importantly, the exploration of members of the Xenorhabdus and Photorhabdus genera has led to encouraging developments in compounds that exhibit pharmaceutically important properties, including antibiotics that act against Gram- bacteria, which are extremely difficult to find. This article focuses on recent advances in the discovery of natural products derived from these nematophilic bacteria, with special attention paid to new valuable leads for therapeutics.

A simple model and rules for the evolution of microbial mutualistic symbiosis with positive fitness feedbacks

The evolution of microbe-microbe mutualistic symbiosis is considered to be promoted by repeated exchanges of fitness benefits, which can generate positive fitness feedbacks ('partner fidelity feedback') between species. However, previous evolutionary models for mutualism have not captured feedback dynamics or coupling of fitness between species. Here, a simple population model is developed to understand the evolution of mutualistic symbiosis in which two microbial species (host and symbiont) continuously grow and exchange fitness benefits to generate feedback dynamics but do not strictly control each other. The assumption that individual microbes provide constant amounts of resources, which are equally divided among interacting partner individual, enables us to reveal a simple rule for the evolution of costly mutualism with positive fitness feedbacks: the product of the benefit-to-cost ratios for each species exceeds one. When this condition holds, high cooperative investment levels are favored in both species regardless of the amount invested by each partner. The model is then extended to examine how symbiont mutation, immigration, or switching affects the spread of selfish or cooperative symbionts, which decrease and increase their investment levels, respectively. In particular, when a host associates with numerous symbionts without enforcement, neither mutation nor immigration but rather random switching would allow the spread of cooperative symbionts. Examples using symbiont switching for evolution would include large ciliates hosting numerous intracellular endosymbionts. The simple model and rules would provide a basis for understanding the evolution of microbe-microbe mutualistic symbiosis with positive fitness feedbacks and without enforcement mechanisms.

Potential for artificial symbiosis between marine microalgae and invertebrates: I. survival of marine microalgae injected into the medusa of the moon jellyfish Aurelia aurita

Some marine microalgae and cyanobacteria form mutualistic symbioses with diverse invertebrates, particularly cnidarians. Among microalgae, dinoflagellates in the family Symbiodiniaceae are the most well-known symbiotic partners of jellyfish and corals. However, the symbioses involving other dinoflagellate families, nano- and micro-flagellates, diatoms, and cyanobacteria with cnidarians are not well understood. As an initial step, it is essential to explore the survival of these microorganisms inside cnidarians. We monitored the survival of eight microalgal species (nine strains) and one cyanobacterium species every day for seven days after injecting each into the medusa of the moon jellyfish <i>Aurelia aurita</i>. The dinoflagellates <i>Effrenium voratum</i> (free-living [FL] and living-in-coral strains), <i>Cladocopium infistulum</i>, <i>Prorocentrum cordatum</i>, <i>Prorocentrum koreanum</i>, <i>Symbiodinium microadriaticum</i>, the prasinophyte <i>Tetraselmis suecica</i>, the chlorophyte <i>Dunaliella salina</i>, and the raphidophyte <i>Heterosigma akashiwo</i> survived inside the medusa, while the cyanobacterium <i>Synechococcus</i> sp. was not detected. Additionally, <i>E. voratum</i> (FL) survived within the medusa for 60 days and gradually spread to adjacent areas, indicating potential for artificially established symbiosis. The results of this study provide a basis for artificial symbiosis between microalgae and invertebrates.

Exploration on cold adaptation of Antarctic lichen via detection of positive selection genes

Lichen as mutualistic symbiosis is the dominant organism in various extreme terrestrial environment on Earth, however, the mechanisms of their adaptation to extreme habitats have not been fully elucidated. In this study, we chose the Antarctic dominant lichen species Usnea aurantiacoatra to generate a high-quality genome, carried out phylogenetic analysis using maximum likelihood and identify genes under positive selection. We performed functional enrichment analysis on the positively selected genes (PSGs) and found that most of the PSGs focused on transmembrane transporter activity and vacuole components. This suggest that the genes related to energy storage and transport in Antarctic U. aurantiacoatra were affected by environmental pressure. Inside of the 86 PSGs screened, two protein interaction networks were identified, which were RNA helicase related proteins and regulator of G-protein signaling related proteins. The regulator of the G-protein signaling gene (UaRGS1) was chosen to perform further verification by the lichen genetic manipulation system Umbilicaria muhlenbergii. Given that the absence of UmRgs1 resulted in elevated lethality to cold shock, the role for UaRgs1 in Antarctic U. aurantiacoatra resistance to cold can be inferred. The investigation of lichen adaptation to extreme environments at the molecular level will be opened up.

Mycorrhizal and non-mycorrhizal perennial ryegrass roots exhibit differential regulation of lipid and Ca2+ signaling pathways in response to low and high temperature stresses

Lipids and Ca2+ are involved as intermediate messengers in temperature-sensing signaling pathways. Arbuscular mycorrhizal (AM) symbiosis is a mutualistic symbiosis between fungi and terrestrial plants that helps host plants cope with adverse environmental conditions. Nonetheless, the regulatory mechanisms of lipid- and Ca2+-mediated signaling pathways in mycorrhizal plants under cold and heat stress have not been determined. The present work focused on investigating the lipid- and Ca2+-mediated signaling pathways in arbuscular mycorrhizal (AM) and non-mycorrhizal (NM) roots under temperature stress and determining the role of Ca2+ levels in AM symbiosis and temperature stress tolerance in perennial ryegrass (Lolium perenne L.) Compared with NM plants, AM symbiosis increased phosphatidic acid (PA) and Ca2+ signaling in the roots of perennial ryegrass, increasing the expression of genes associated with low temperature (LT) stress, including LpICE1, LpCBF3, LpCOR27, LpCOR47, LpIRI, and LpAFP, and high temperature (HT) stress, including LpHSFC1b, LpHSFC2b, LpsHSP17.8, LpHSP22, LpHSP70, and LpHSP90, under LT and HT conditions. These effects result in modulated antioxidant enzyme activities, reduced lipid peroxidation, and suppressed growth inhibition caused by LT and HT stresses. Furthermore, exogenous Ca2+ application enhanced AM symbiosis, leading to the upregulation of Ca2+ signaling pathway genes in roots and ultimately promoting the growth of perennial ryegrass under LT and HT stresses. These findings shed light on lipid and Ca2+ signal transduction in AM-associated plants under LT and HT stresses, emphasizing that Ca2+ enhances cold and heat tolerance in mycorrhizal plants.

Molecular Diversity of Ectomycorrhizal Fungi in Relation to the Diversity of Neighboring Plant Species.

(1) Background: Plant diversity has long been assumed to predict soil microbial diversity. The mutualistic symbiosis between forest trees and ectomycorrhizal (EM) fungi favors strong correlations of EM fungal diversity with host density in terrestrial ecosystems. Nevertheless, in contrast with host tree effects, neighboring plant effects are less well studied. (2) Methods: In the study presented herein, we examined the α-diversity, community composition, and co-occurrence patterns of EM fungi in Quercus acutissima across different forest types (pure forests, mixed forests with Pinus tabuliformis, and mixed forests with other broadleaved species) to ascertain how the EM fungi of focal trees are related to their neighboring plants and to identify the underlying mechanisms that contribute to this relationship. (3) Results: The EM fungal community exhibited an overall modest but positive correlation with neighboring plant richness, with the associations being more pronounced in mixed forests. This neighboring effect was mediated by altered abiotic (i.e., SOC, TN, LC, and LP) and biotic (i.e., bacterial community) factors in rhizosphere soil. Further analysis revealed that Tomentella_badia, Tomentella_galzinii, and Sebacina_incrustans exhibited the most significant correlations with plant and EM fungal diversity. These keystone taxa featured low relative abundance and clear habitat preferences and shared similar physiological traits that promote nutrient uptake through contact, short-distance and medium-distance smooth contact-based exploration types, thereby enhancing the potential correlations between EM fungi and the neighboring plant community. (4) Conclusions: Our findings contribute to the comprehension of the effect of neighboring plants on the EM fungal community of focal trees of different forest communities and the biodiversity sensitivity to environmental change.

The microbiota: a crucial mediator in gut homeostasis and colonization resistance.

The gut microbiota is a complex and diverse community of microorganisms that colonizes the human gastrointestinal tract and influences various aspects of human health. These microbes are closely related to enteric infections. As a foreign entity for the host, commensal microbiota is restricted and regulated by the barrier and immune system in the gut and contributes to gut homeostasis. Commensals also effectively resist the colonization of pathogens and the overgrowth of indigenous pathobionts by utilizing a variety of mechanisms, while pathogens have developed strategies to subvert colonization resistance. Dysbiosis of the microbial community can lead to enteric infections. The microbiota acts as a pivotal mediator in establishing a harmonious mutualistic symbiosis with the host and shielding the host against pathogens. This review aims to provide a comprehensive overview of the mechanisms underlying host-microbiome and microbiome-pathogen interactions, highlighting the multi-faceted roles of the gut microbiota in preventing enteric infections. We also discuss the applications of manipulating the microbiota to treat infectious diseases in the gut.

The Extracellular Metallometabolome: Metallophores, Metal Ionophores, and Other Chelating Agents as Natural Products

Natural products include inorganic as well as organic compounds. Living organisms face constant challenges in acquiring essential metal ions and getting rid of non-essential ones with toxic actions. They employ an extracellular biochemistry in these tasks and use it to engage in a chemical warfare against invaders and competitors by either increasing or decreasing the availability of metal ions for maintaining their welfare in aquatic or terrestrial ecological niches. To control mutualistic, cambialistic or parasitic symbiosis with other organisms they use a remarkably rich suite of secreted bioactive molecules with ligand donor atoms for metal binding. This overview discusses the interactions of these extracellular natural products with a multitude of metal ions in the periodic system of the elements. It focuses mainly on metallophores and metal ionophores secreted from bacteria, fungi, and plants, but metal-carrying cofactors and other chelating agents will also be mentioned in the context of related functions and with an intent to categorize. The intracellular fate of the metal ions and the controlled pathways for the biosynthesis, secretion, uptake, biodegradation or recycling of the secreted natural products that interact with metal ions will not be covered. Metallophores make extracellular metal ions available via delivery to specific transporters and unavailable to competing organisms, especially pathogens, though some invaders have developed ways to compete efficiently for metal ions. The classic concept of siderophores, carriers of iron(III) ions, is extended here to specific and broad-band metallophores for metal ions such as copper (chalkophores), zinc (zincophores), and yet others. Metal ionophores, in contrast, transport metal ions through biological membranes. There is a wide variety of chemical structures for either metallophores or metal ionophores. Together with physicochemical investigations of metal complexation und conditions mimicking the natural environment, “omics” mining and mapping the diversity of chemotypes is an on-going effort with analytic, genetic, and bioinformatic tools and comes together in defining the metallometabolome, which combines the metabolome and the metallome. Investigations are highly multidisciplinary, include an important, but academically infrequently crossed bridge between the biosciences (biochemistry) and the earth sciences (geochemistry), define significant applications in the pharmaceutical/medical sciences regarding immune modulation and the control of virulence at the host-pathogen interface, and have implications for the nutritional/toxicological and environmental/ecological sciences.

Morphology of arthropods discovered in pitchers of Nepenthes at Aceh Singkil District, Indonesia

Abstract. Tarigan MRM, Faisal M, Manalu K, Khairuna, Tambunan EPS, Rahmadina, Asy’ari H, Ritonga YE. 2024. Morphology of arthropods discovered in pitchers of Nepenthes at Aceh Singkil District, Indonesia. Biodiversitas 25: 2888-2900. Nepenthes plants create unique microhabitats and are home to diverse arthropod communities. These plants, known for their complex and specialized structures, attract various species of arthropods and contribute to the region's biodiversity. The study of arthropod morphology is critical to understanding the complex interactions within these microhabitats as well as broader ecosystem dynamics. Although this plant has great ecological importance and conservation significance, detailed morphological studies of the arthropods living on it are still rare. This study aimed to identify the families of arthropods trapped in the upper and lower pitchers of Nepenthes. This study used descriptive methods to reveal the morphology of arthropods found in Nepenthes pitchers in Aceh Singkil District, Indonesia. Arthropods were obtained from the upper and lower pitchers of N. ampullaria, N. gracilis, N. mirabilis, N. rafflesiana, N. reinwardtiana, N. x hookeriana, and N. x trichocarpa. Samples were obtained through direct observations conducted between October to December 2023. The results showed the presence of arthropod families, namely Culicidae, Formicidae, Gryllidae, Calliphoridae, Coccinellidae, Curculionidae, Rhyaparochromidae, Blattellidae, Salticidae, and Araneidae. However, Culicidae and Formicidae were observed to be the most abundant and Gryllidae was observed to be the least abundant. A mutualistic symbiosis was established, in which ants used the tendrils of Nepenthes to lay eggs and collected nectar generated by the honey glands, while the egg-laying process helped in the breakdown of the pitcher. This discovery suggests that the plants provided a habitat for Culicidae and a conducive environment for Formicidae larvae. However, Araneidae, Rhyparochromidae, Salticidae, Curculionidae, and Coccinellidae are not attracted to petals and peristomes. Gryllidae and Blattellidae were present in Nepenthes pitchers as a result of their close association with the plant and UV color-trapping mechanism. The study of the morphology of arthropods found in Nepenthes pitchers has several overall implications. First, it contributes to our understanding of ecological interactions in Nepenthes plants, providing insight into predator-prey dynamics, nutrient cycling, and plant evolution. Second, it underscores the importance of Nepenthes plants as a microhabitat that supports diverse arthropod communities, and highlights the ecological role of arthropods in nutrient-poor environments. This research also informs conservation efforts, emphasizing the need to protect Nepenthes plant habitat to maintain biodiversity.

The sound of lichens: ultrasonic acoustic emissions during desiccation question cavitation events in the hyphae.

Lichens are a mutualistic symbiosis between a fungus and one or more photosynthetic partners. They are photosynthetically active during desiccation until relative water contents (RWC) as low as 30% (on dry mass). Experimental evidence suggests that during desiccation, the photobionts have a higher hydration level than the surrounding fungal pseudo-tissues. Explosive cavitation events in the hyphae might cause water movements towards the photobionts. This hypothesis was tested in two foliose lichens by measurements of ultrasonic acoustic emissions (UAE), a method commonly used in vascular plants but never in lichens, and by measurements of photosystem II efficiency, water potential and RWC. Thallus structural changes were characterised by low-temperature scanning electron microscopy. The thalli were silent between 380% and 30% RWCs, i.e. when explosive cavitation events should cause movements of liquid water. Nevertheless, the thalli emitted UAE at approximately 5% RWC. Accordingly, the medullary hyphae were partially shrunk at about 15% RWC, whereas they were completely shrunk below 5% RWC. These results do not support the hypothesis of hyphal cavitation and suggest that the UAE originate from structural changes at hyphal level. The shrinking of hyphae is proposed as an adaptation to avoid cell damage at very low RWCs.

Ants may buffer the Janzen-Connell effect in a tropical forest in Southwest China.

Mutualistic symbioses between ants and plants are widespread in nature. Ants can deter unwanted pests and provide protection for plants in return for food or housing rewards. Using a long-term demographic dataset in a tropical seasonal rain forest in Southwest China, we found that associations with ants positively influenced seedling survival and adult growth, and also, species with extrafloral nectaries experienced weaker conspecific negative density dependence compared with species without extrafloral nectaries. Furthermore, we found strong evidence suggesting that species in our forest experienced conspecific density dependence, which we interpreted as heavy pest pressure that may drive the development of anti-pest symbioses such as the plant-ant relationship. Our findings suggest that ants and conspecific neighbors play important but inverse roles on plant survival and growth and that ants can buffer tree neighborhood interactions in this tropical forest.

Root endophytic bacterial communities are shaped by the specific microbiota associated to mycorrhizal symbionts

Abstract Background and aims Arbuscular mycorrhizal fungi (AMF) are beneficial soil microorganisms establishing mutualistic symbioses with most crop plants and promoting plant growth and health. AMF beneficial activities are complemented by their associated microbiota, leading to synergistic interactions positively affecting plant performance. In this work we assessed whether AMF may act as drivers of root bacterial endophytes, facilitating root colonization of host plants by their associated bacteria. Methods Two AMF isolates were used, Funneliformis mosseae from Indiana (USA) and Septoglomus sp. from Tuscany (Italy) in an original experimental microcosm system, utilizing micropropagated plants of Prunus persica x Prunus amygdalus inoculated with either intact or mechanically crushed AMF spores, the former able and the latter unable to establish the symbiosis. Spore and root endophytic bacterial communities diversity were analysed by Illumina Miseq sequencing. Results This study revealed that AMF with their associated bacteria can shape the root endophytic bacterial communities, inducing differential recruitment depending on the composition of spore-associated microbiota. Such data were consistent between two AMF isolates, associated with diverse bacterial communities, as shown by PERMANOVA, Bray Curtis dissimilarity, hierarchical clustering and indicator species analyses. Moreover, specific bacterial taxa were found exclusively in mycorrhizal roots. Our findings suggested also a differential recruitment depending on the ability of AMF to establish mycorrhizal symbioses. Conclusion This work revealed that AMF represent drivers of the endophytic bacterial communities diversity and composition, facilitating root colonization of host plants by their associated bacteria, that become an integral part of the root microbiome as endophytes.

LITERATURE REVIEW: PERANAN ACAULOSPORA TERHADAP PENYERAPAN FOSFOR PADA AKAR TANAMAN SINGKONG

Mycorrhiza is a form of mutualistic symbiosis between plant roots (rhiza) and fungi (mykes). Plants will get various kinds of nutrients, especially phosphorus (P) from their mycorrhiza, while mycorrhiza will get carbon (C) from plants. Phosphorus is a macro nutrient that plants must have. Phosphorus has important functions in plants, namely during respiration, photosynthesis, energy transport, energy storage, cell enlargement, cell division, as well as processes within plants, stimulating plant root development and germination. Mycorrhiza is grouped into three types, namely ectendomycorrhiza, ectomycorrhiza, and endomycorrhiza. This journal review uses the SLR or Systematic Literature Review method with the aim of knowing the meaning of mycorrhiza, characteristics, enzymes that play a role, the mechanism of phosphorus absorption in mycorrhiza, mycorrhizal colonization, and mycorrhizal symbiosis in cassava plants. This article discusses mycorrhiza, one of the mycorrhizal genera, namely Acaulospora, which is included in the endomycorrhiza or Vesicular Arbuscular Mycorrhiza (VAM). The spores are characterized by a brownish yellow color and a rough surface like orange peel. The phosphatase enzyme is produced by Acaulospora hyphae. This enzyme helps increase the amount of P nutrients that are useful for plants by releasing the fixation of P nutrients from Al, Fe, and Ca in the soil, so that phosphate elements are available to plants.

Symbiotic Electromagnetic Shadow for Regional Invisibility and Camouflage.

Low detectability and camouflage skills in the electromagnetic wave and light frequency range provide survival advantages for natural creatures and are essential for understanding the operational principles of the biosphere. Taking inspiration from natural mutualistic symbiosis, this paper proposes a symbiotic electromagnetic shadow camouflage mechanism based on a superdispersive surface, aiming to investigate its impact on the observability of specific objects. The design and experimental results indicate that the symbiotic shadow dihedral can significantly reduce overall scattering quantity, which reaches at least 10 dB shrink in the 12-18 GHz frequency range compared to the contrast object. Unlike known camouflage methods, the electromagnetic shadow technology shrinks the overall scattering without any coating and shield metal target while probably offering extensive functional design freedom for the concealed object, creature, or equipment. This also provides a hint to explore symbiosis-related camouflage phenomena in nature.

Genome reduction and horizontal gene transfer in the evolution of Endomicrobia-rise and fall of an intracellular symbiosis with termite gut flagellates.

Bacterial endosymbionts of eukaryotic hosts typically experience massive genome reduction, but the underlying evolutionary processes are often obscured by the lack of free-living relatives. Endomicrobia, a family-level lineage of host-associated bacteria in the phylum Elusimicrobiota that comprises both free-living representatives and endosymbionts of termite gut flagellates, are an excellent model to study evolution of intracellular symbionts. We reconstructed 67 metagenome-assembled genomes (MAGs) of Endomicrobiaceae among more than 1,700 MAGs from the gut microbiota of a wide range of termites. Phylogenomic analysis confirmed a sister position of representatives from termites and ruminants, and allowed to propose eight new genera in the radiation of Endomicrobiaceae. Comparative genome analysis documented progressive genome erosion in the new genus Endomicrobiellum, which comprises all flagellate endosymbionts characterized to date. Massive gene losses were accompanied by the acquisition of new functions by horizontal gene transfer, which led to a shift from a glucose-based energy metabolism to one based on sugar phosphates. The breakdown of glycolysis and many anabolic pathways for amino acids and cofactors in several subgroups was compensated by the independent acquisition of new uptake systems, including an ATP/ADP antiporter, from other gut microbiota. The putative donors are mostly flagellate endosymbionts from other bacterial phyla, including several, hitherto unknown lineages of uncultured Alphaproteobacteria, documenting the importance of horizontal gene transfer in the convergent evolution of these intracellular symbioses. The loss of almost all biosynthetic capacities in some lineages of Endomicrobiellum suggests that their originally mutualistic relationship with flagellates is on its decline.IMPORTANCEUnicellular eukaryotes are frequently colonized by bacterial and archaeal symbionts. A prominent example are the cellulolytic gut flagellates of termites, which harbor diverse but host-specific bacterial symbionts that occur exclusively in termite guts. One of these lineages, the so-called Endomicrobia, comprises both free-living and endosymbiotic representatives, which offers the unique opportunity to study the evolutionary processes underpinning the transition from a free-living to an intracellular lifestyle. Our results revealed a progressive gene loss in energy metabolism and biosynthetic pathways, compensated by the acquisition of new functions via horizontal gene transfer from other gut bacteria, and suggest the eventual breakdown of an initially mutualistic symbiosis. Evidence for convergent evolution of unrelated endosymbionts reflects adaptations to the intracellular environment of termite gut flagellates.

Single-cell transcriptome atlases of soybean root and mature nodule reveal new regulatory programs that control the nodulation process

The soybean root system is complex. In addition to being composed of various cell types, the soybean root system includes the primary root, the lateral roots, and the nodule, an organ in which mutualistic symbiosis with N-fixing rhizobia occurs. A mature soybean root nodule is characterized by a central infection zone where atmospheric nitrogen is fixed and assimilated by the symbiont, resulting from the close cooperation between the plant cell and the bacteria. To date, the transcriptome of individual cells isolated from developing soybean nodules has been established, but the transcriptomic signatures of cells from the mature soybean nodule have not yet been characterized. Using single-nucleus RNA-seq and Molecular Cartography technologies, we precisely characterized the transcriptomic signature of soybean root and mature nodule cell types and revealed the co-existence of different sub-populations of B. diazoefficiens–infected cells in the mature soybean nodule, including those actively involved in nitrogen fixation and those engaged in senescence. Mining of the single-cell-resolution nodule transcriptome atlas and the associated gene co-expression network confirmed the role of known nodulation-related genes and identified new genes that control the nodulation process. For instance, we functionally characterized the role of GmFWL3, a plasma membrane microdomain-associated protein that controls rhizobial infection. Our study reveals the unique cellular complexity of the mature soybean nodule and helps redefine the concept of cell types when considering the infection zone of the soybean nodule.

Evolutionary history of arbuscular mycorrhizal fungi and genomic signatures of obligate symbiosis

BackgroundThe colonization of land and the diversification of terrestrial plants is intimately linked to the evolutionary history of their symbiotic fungal partners. Extant representatives of these fungal lineages include mutualistic plant symbionts, the arbuscular mycorrhizal (AM) fungi in Glomeromycota and fine root endophytes in Endogonales (Mucoromycota), as well as fungi with saprotrophic, pathogenic and endophytic lifestyles. These fungal groups separate into three monophyletic lineages but their evolutionary relationships remain enigmatic confounding ancestral reconstructions. Their taxonomic ranks are currently fluid.ResultsIn this study, we recognize these three monophyletic linages as phyla, and use a balanced taxon sampling and broad taxonomic representation for phylogenomic analysis that rejects a hard polytomy and resolves Glomeromycota as sister to a clade composed of Mucoromycota and Mortierellomycota. Low copy numbers of genes associated with plant cell wall degradation could not be assigned to the transition to a plant symbiotic lifestyle but appears to be an ancestral phylogenetic signal. Both plant symbiotic lineages, Glomeromycota and Endogonales, lack numerous thiamine metabolism genes but the lack of fatty acid synthesis genes is specific to AM fungi. Many genes previously thought to be missing specifically in Glomeromycota are either missing in all analyzed phyla, or in some cases, are actually present in some of the analyzed AM fungal lineages, e.g. the high affinity phosphorus transporter Pho89.ConclusionBased on a broad taxon sampling of fungal genomes we present a well-supported phylogeny for AM fungi and their sister lineages. We show that among these lineages, two independent evolutionary transitions to mutualistic plant symbiosis happened in a genomic background profoundly different from that known from the emergence of ectomycorrhizal fungi in Dikarya. These results call for further reevaluation of genomic signatures associated with plant symbiosis.

Phylogenomics reveals the evolutionary origins of lichenization in chlorophyte algae

Mutualistic symbioses have contributed to major transitions in the evolution of life. Here, we investigate the evolutionary history and the molecular innovations at the origin of lichens, which are a symbiosis established between fungi and green algae or cyanobacteria. We de novo sequence the genomes or transcriptomes of 12 lichen algal symbiont (LAS) and closely related non-symbiotic algae (NSA) to improve the genomic coverage of Chlorophyte algae. We then perform ancestral state reconstruction and comparative phylogenomics. We identify at least three independent gains of the ability to engage in the lichen symbiosis, one in Trebouxiophyceae and two in Ulvophyceae, confirming the convergent evolution of the lichen symbioses. A carbohydrate-active enzyme from the glycoside hydrolase 8 (GH8) family was identified as a top candidate for the molecular-mechanism underlying lichen symbiosis in Trebouxiophyceae. This GH8 was acquired in lichenizing Trebouxiophyceae by horizontal gene transfer, concomitantly with the ability to associate with lichens fungal symbionts (LFS) and is able to degrade polysaccharides found in the cell wall of LFS. These findings indicate that a combination of gene family expansion and horizontal gene transfer provided the basis for lichenization to evolve in chlorophyte algae.

Prairie restoration promotes the abundance and diversity of mutualistic arbuscular mycorrhizal fungi.

Predicting how biological communities assemble in restored ecosystems can assist in conservation efforts, but most research has focused on plants, with relatively little attention paid to soil microbial organisms that plants interact with. Arbuscular mycorrhizal (AM) fungi are an ecologically significant functional group of soil microbes that form mutualistic symbioses with plants and could therefore respond positively to plant community restoration. To evaluate the effects of plant community restoration on AM fungi, we compared AM fungal abundance, species richness, and community composition of five annually cultivated, conventionally managed agricultural fields with paired adjacent retired agricultural fields that had undergone prairie restoration 5-9 years prior to sampling. We hypothesized that restoration stimulates AM fungal abundance and species richness, particularly for disturbance-sensitive taxa, and that gains of new taxa would not displace AM fungal species present prior to restoration due to legacy effects. AM fungal abundance was quantified by measuring soil spore density and root colonization. AM fungal species richness and community composition were determined in soils and plant roots using DNA high-throughput sequencing. Soil spore density was 2.3 times higher in restored prairies compared to agricultural fields, but AM fungal root colonization did not differ between land use types. AM fungal species richness was 2.7 and 1.4 times higher in restored prairies versus agricultural fields for soil and roots, respectively. The abundance of Glomeraceae, a disturbance-tolerant family, decreased by 25% from agricultural to restored prairie soils but did not differ in plant roots. The abundance of Claroideoglomeraceae and Diversisporaceae, both disturbance-sensitive families, was 4.6 and 3.2 times higher in restored prairie versus agricultural soils, respectively. Species turnover was higher than expected relative to a null model, indicating that AM fungal species were gained by replacement. Our findings demonstrate that restoration can promote a relatively rapid increase in the abundance and diversity of soil microbial communities that had been degraded by decades of intensive land use, and community compositional change can be predicted by the disturbance tolerance of soil microbial taxonomic and functional groups.

Evaluation of the initial growth of Shorea platyclados wildlings through the application of mycorrhizal biofertilizer under different levels of shading

The obstacles to the propagation of Shorea platyclados involve the uncertain flowering and fruiting seasons, the recalcitrant nature of the seeds, and the dependence on shade for growth. Furthermore, a mutualistic symbiosis, called mycorrhizae, usually exists between the roots and fungi, similar to other species of Dipterocarpaceae. This consequently hinders the regeneration process, which in turn may threaten the sustainability of this species in the wild. Ex-situ conservation using wildings is one of the measures that can be taken to overcome this issue. This study aimed to assess the initial growth of S. platyclados seedlings by administering different amountsof mycorrhizal biofertilizers under varying shade conditions at four and eight weeks of age in the nursery. A randomised complete block design was employed with the dose of biofertilizer as the treatment (0, 2.5, 5, 7 and 9 g/polybag) and shade as the group (0, 50, 60 and 70%). Observations were taken in the nursery at four and eight weeks of age. The observation parameters included the survival percentage, height growth, diameter growth, and vigour of the seedlings. There were significant differences in percentage of survival. Still, significant differences in height growth were observed with different doses of biofertilizer and shading at both four and eight weeks of age. Significant differences in diameter growth were observed with different doses of biofertilizer at both four and eight weeks of age, but not with different shades. No significant differences were observed for seedling vigour with different doses of biofertilizer and shade at both four and eight weeks of age. The optimal amount of biofertilizer was 5 g/polybag, resulting in maximum growth. This was achieved in a shade of 60%.