Lives within lives: Hidden fungal biodiversity and the importance of conservation

Divergent rainforest tree microbiomes between phases of the monsoon cycle, host plants and tissues

The Australian Monsoon Tropics (AMT) contain some of the most biodiverse forests on the continent. Little is known about the dynamics of rainforest plant microbiomes in general, and there have been no community-level studies on Australian rainforest endophytes, their seasonality, tissue and host specificity. We tested whether community composition of tropical tree endophytes (fungi and bacteria) differs: (i) at different points during a monsoon cycle, (ii) between leaf and stem tissues, (iii) between forest microclimates (gully/ridge), and between (iv) host plant species, and (v) host plant clade, using amplicon sequencing of the bacterial 16S and fungal ITS2 gene regions. Results indicated that the composition of rainforest plant microbiomes differs between wet and dry seasons, which may be explained by physiological shifts in host plants due to annual climate fluctuations from mesic to xeric. Endophyte microbiomes differed between leaves and stems. Distinct fungal communities were associated with host species and clades, with some trees enriched in a number of fungal taxa compared to host plants in other clades. Diversity of bacterial endophytes in plant stems increased in the dry season. We conclude that the microbiomes of tropical plants are responsive to monsoonal climate variation, are highly compartmentalised between plant tissues, and may be partly shaped by the relatedness of their host plants.

Plant pathogens as introduced weed biological control agents: Could antagonistic fungi be important factors determining agent success or failure?

Mycoparasitic interactions are common in nature, form part of the microbiota of plants, and are considered significant contributors to fungus-fungus antagonism. Mycoparasites kill plant pathogens, protect the plant from abiotic and biotic stressors, and reduce disease incidence and severity at the plant population level. Their exploitation as biocontrol agents in agriculture is well documented. However, mycoparasites may potentially affect classical fungal biocontrol agents of invasive weed species. Classical biological control, or biocontrol, of invasive weeds involves the intentional introduction of exotic, usually co-evolved plant pathogens and insects, for permanent establishment and long-term control of the target plant. Agent establishment, effectiveness, and safety are the critical elements for a successful weed biocontrol programme. Establishment and effectiveness of agents on the invasive plant often vary throughout the invaded range with about two-thirds of weed biocontrol agents failing to suppress their target weed. There are many documented reasons why weed biocontrol agents do not establish or are ineffective when they do, and the presence and accumulation of natural enemies in the invaded range is one of them. Endophyte-enriched, invasive weeds and those forming mutualistic associations with indigenous, native endophytes could explain the lack of consistency of some classical biological control introductions. However, another variable could be factored into the mix: mycoparasitism, where one fungus parasitises another, the natural enemies of the plant's natural enemies. In this review article, we introduce the concept of invasive weed biocontrol and the history of using plant pathogens as biocontrol agents. We discuss the success and failure of fungal agent programmes and delve into the patterns of success or failure, with a focus on the potential antagonistic role of endophytes and mycoparasites.

Fungal biodiversity and conservation mycology in light of new technology, big data, and changing attitudes

Fungi have successfully established themselves across seemingly every possible niche, substrate, and biome. They are fundamental to biogeochemical cycling, interspecies interactions, food production, and drug bioprocessing, as well as playing less heroic roles as difficult to treat human infections and devastating plant pathogens. Despite community efforts to estimate and catalog fungal diversity, we have only named and described a minute fraction of the fungal world. The identification, characterization, and conservation of fungal diversity is paramount to preserving fungal bioresources, and to understanding and predicting ecosystem cycling and the evolution and epidemiology of fungal disease. Although species and ecosystem conservation are necessarily the foundation of preserving this diversity, there is value in expanding our definition of conservation to include the protection of biological collections, ecological metadata, genetic and genomic data, and the methods and code used for our analyses. These definitions of conservation are interdependent. For example, we need metadata on host specificity and biogeography to understand rarity and set priorities for conservation. To aid in these efforts, we need to draw expertise from diverse fields to tie traditional taxonomic knowledge to data obtained from modern -omics-based approaches, and support the advancement of diverse research perspectives. We also need new tools, including an updated framework for describing and tracking species known only from DNA, and the continued integration of functional predictions to link genetic diversity to functional and ecological diversity. Here, we review the state of fungal diversity research as shaped by recent technological advancements, and how changing viewpoints in taxonomy, -omics, and systematics can be integrated to advance mycological research and preserve fungal biodiversity.

Description of the Fifth New Species of Russula subsect. Maculatinae from Pakistan Indicates Local Diversity Hotspot of Ectomycorrhizal Fungi in Southwestern Himalayas

Russula subsect. Maculatinae is morphologically and phylogenetically well-defined lineage of ectomycorrhizal fungi associated with arctic, boreal, temperate and Mediterranean habitats of Northern Hemisphere. Based on phylogenetic distance among species, it seems that this group diversified relatively recently. Russula ayubiana sp. nov., described in this study, is the fifth in the group known from relatively small area of northern Pakistan situated in southwestern Himalayas. This is the highest known number of agaric lineage members from a single area in the world. This study uses available data about phylogeny, ecology, and climate to trace phylogenetic origin and ecological preferences of Maculatinae in southwestern Himalayas. Our results suggest that the area has been recently colonised by Maculatinae members migrating from various geographical areas and adapting to local conditions. We also discuss the perspectives and obstacles in research of biogeography and ecology, and we propose improvements that would facilitate the integration of ecological and biogeographical metadata from the future taxonomic studies of fungi in the region.

Perception of fungi by farmers in the Cerrado

Fungi are important in several aspects of human life. In particular, to agriculture, pathogenic fungi are of great importance, as they are responsible for production losses of the most diverse types. Because of this, knowledge about pathogenic fungus is of extreme importance for farmers and professionals working in agricultural areas. Among farmers who use specific agroecological practices, this knowledge is even more valuable, since by not adopting conventional methods of production, they resort to non-invasive alternatives that are less or not harmful at all to the environment in consideration of production management methods. This study aimed to assess farmer perception in the Cerrado biome in the city of Goiás (GO), Brazil, in order to understand their ethnomycological perceptions to verify historical management practices, their knowledge about phytopathogenic fungi, and how these producers perceive fungi. We used the theoretical reference method "From peasant to peasant" formulated by ANPA - National Association of Small Farmers. Some aspects of farmers' ethnomycological knowledge are discussed. These ease identification the representatives of the Fungi Kingdom is associated with organisms that present easily recognizable characteristics, such as wood-ears or disease-causing fungi. In general, farmers are able to identify representatives of the Fungi Kingdom that are found in their daily lives. The perception of farmers about fungi, a group still much unknown by society, is very relevant for future actions of ethnomycology.

Caterpillar gut and host plant phylloplane mycobiomes differ: a new perspective on fungal involvement in insect guts

Compared with the highly diverse microbiota of leaves, herbivorous insects exhibit impoverished gut microbial communities. Research to date has focused on the bacterial component of these gut microbiomes, neglecting the fungal component. As caterpillar gut bacterial microbiomes are derived strongly from their diet, we hypothesized that their mycobiomes would reflect the host leaf mycobiomes. Using the ITS2 rDNA and V5-V6 16S rRNA gene regions for DNA metabarcoding of caterpillar gut and host leaf sample pairs we compared their mycobiome genus diversity and compositions and identified genera associated with caterpillar guts. Leaves and caterpillar guts harbored different mycobiomes with quite low qualitative similarity (Jaccard index = 38.03%). The fungal genera most significantly associated with the caterpillar gut included Penicillium, Mucor and unidentified Saccharomycetales, whereas leaf-associated genera included Holtermanniella, Gibberella (teleomorph of Fusarium) and Seimatosporium. Although caterpillar gut and leaf mycobiomes had similar genus richness overall, this indicator was not correlated for individual duplets. Moreover, as more samples entered the analysis, mycobiome richness increased more rapidly in caterpillar guts than in leaves. The results suggest that the mycobiota of the caterpillar gut differs from that of their feeding substrate; further, the mycobiomes appear to be richer than the well-studied bacterial microbiotas.

An Improvised Machine Learning Model Based on Mutual Information Feature Selection Approach for Microbes Classification

The accurate classification of microbes is critical in today's context for monitoring the ecological balance of a habitat. Hence, in this research work, a novel method to automate the process of identifying microorganisms has been implemented. To extract the bodies of microorganisms accurately, a generalized segmentation mechanism which consists of a combination of convolution filter (Kirsch) and a variance-based pixel clustering algorithm (Otsu) is proposed. With exhaustive corroboration, a set of twenty-five features were identified to map the characteristics and morphology for all kinds of microbes. Multiple techniques for feature selection were tested and it was found that mutual information (MI)-based models gave the best performance. Exhaustive hyperparameter tuning of multilayer layer perceptron (MLP), k-nearest neighbors (KNN), quadratic discriminant analysis (QDA), logistic regression (LR), and support vector machine (SVM) was done. It was found that SVM radial required further improvisation to attain a maximum possible level of accuracy. Comparative analysis between SVM and improvised SVM (ISVM) through a 10-fold cross validation method ultimately showed that ISVM resulted in a 2% higher performance in terms of accuracy (98.2%), precision (98.2%), recall (98.1%), and F1 score (98.1%).

Laboulbeniomycetes: Intimate Fungal Associates of Arthropods

Arthropod-fungus interactions involving the Laboulbeniomycetes have been pondered for several hundred years. Early studies of Laboulbeniomycetes faced several uncertainties. Were they parasitic worms, red algal relatives, or fungi? If they were fungi, to which group did they belong? What was the nature of their interactions with their arthropod hosts? The historical misperceptions resulted from the extraordinary morphological features of these oddly constructed ectoparasitic fungi. More recently, molecular phylogenetic studies, in combination with a better understanding of life histories, have clearly placed these fungi among filamentous Ascomycota (subphylum Pezizomycotina). Species discovery and research on the classification of the group continue today as arthropods, and especially insects, are routinely collected and examined for the presence of Laboulbeniomycetes. Newly armed with molecular methods, mycologists are poisedto use Laboulbeniomycetes-insect associations as models for the study of a variety of basic evolutionary and ecological questions involving host-parasite relationships, modes of nutrient intake, population biology, host specificity, biological control, and invasion biology. Collaboration between mycologists and entomologists is essential to successfully advance knowledge of Laboulbeniomycetes and their intimate association with their hosts.

Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding?

True fungi (Fungi) and fungus-like organisms (e.g. Mycetozoa, Oomycota) constitute the second largest group of organisms based on global richness estimates, with around 3 million predicted species. Compared to plants and animals, fungi have simple body plans with often morphologically and ecologically obscure structures. This poses challenges for accurate and precise identifications. Here we provide a conceptual framework for the identification of fungi, encouraging the approach of integrative (polyphasic) taxonomy for species delimitation, i.e. the combination of genealogy (phylogeny), phenotype (including autecology), and reproductive biology (when feasible). This allows objective evaluation of diagnostic characters, either phenotypic or molecular or both. Verification of identifications is crucial but often neglected. Because of clade-specific evolutionary histories, there is currently no single tool for the identification of fungi, although DNA barcoding using the internal transcribed spacer (ITS) remains a first diagnosis, particularly in metabarcoding studies. Secondary DNA barcodes are increasingly implemented for groups where ITS does not provide sufficient precision. Issues of pairwise sequence similarity-based identifications and OTU clustering are discussed, and multiple sequence alignment-based phylogenetic approaches with subsequent verification are recommended as more accurate alternatives. In metabarcoding approaches, the trade-off between speed and accuracy and precision of molecular identifications must be carefully considered. Intragenomic variation of the ITS and other barcoding markers should be properly documented, as phylotype diversity is not necessarily a proxy of species richness. Important strategies to improve molecular identification of fungi are: (1) broadly document intraspecific and intragenomic variation of barcoding markers; (2) substantially expand sequence repositories, focusing on undersampled clades and missing taxa; (3) improve curation of sequence labels in primary repositories and substantially increase the number of sequences based on verified material; (4) link sequence data to digital information of voucher specimens including imagery. In parallel, technological improvements to genome sequencing offer promising alternatives to DNA barcoding in the future. Despite the prevalence of DNA-based fungal taxonomy, phenotype-based approaches remain an important strategy to catalog the global diversity of fungi and establish initial species hypotheses.

Diketopiperazines from Batnamyces globulariicola, gen. & sp. nov. (Chaetomiaceae), a fungus associated with roots of the medicinal plant Globularia alypum in Algeria

Eight diketopiperazines including five previously unreported derivatives were isolated from an endophytic fungus cultured from the medicinal plant Globularia alypum collected in Algeria. The strain was characterised by means of morphological studies and molecular phylogenetic methods and was found to represent a species of a new genus in the Chaetomiaceae, for which we propose the name Batnamyces globulariicola. The taxonomic position of the new genus, which appears phylogenetically related to Stolonocarpus and Madurella, was evaluated by a multi-locus genealogy and by morphological studies in comparison to DNA sequence data reported in the recent monographs of the family. The culture remained sterile on several culture media despite repeated attempts to induce sporulation, and only some chlamydospores were formed. After fermentation in submerged culture and extraction of the cultures with organic solvents, the major secondary metabolites of B. globulariicola were isolated and their chemical structures were elucidated by extensive spectral analysis including nuclear magnetic resonance (NMR) spectroscopy, high-resolution electrospray ionisation mass spectrometry (HRESIMS), and electronic circular dichroism (ECD) measurements. The isolated compounds were tested for their biological activities against various bacteria, fungi, and two mammalian cell lines, but only three of them exhibited weak cytotoxicity against KB3.1 cells, but no antimicrobial effects were observed.

Diversity, Bacterial Symbionts, and Antimicrobial Potential of Termite-Associated Fungi

The phylogenetic diversity of fungi isolated from the Odontotermes formosanus was investigated by dilution-plate method, combined with morphological characteristics and 5.8S rDNA sequencing. Thirty-nine fungi were isolated and purified from O. formosanus, which were belonging to two phyla and four classes (Sordariomycetes, Dothideomycetes, Eurotiomycetes, Agaricomycetes). Furthermore, nine bacterial 16S rRNA sequences were obtained from total fungal genomic DNA. All bacterial symbionts were segmented into four genera: Bacillus, Methylobacterium, Paenibacillus, and Trabulsiella. The antimicrobial activities of all endophytic fungi extracts were tested by using the filter paper method against Escherichia coli (ATCC 8739), Bacillus subtilis (ATCC 6633), Staphylococcus aureus (ATCC 6538), and Canidia albicans (ATCC 10231). The results exhibited that 25 extracts (64%) exhibited antibacterial activity against at least one of the tested bacterial strains. Furthermore, the secondary metabolites 1 [5-hydroxyramulosin (1a):biatriosporin M (1b) = 2:1] from the Pleosporales sp. BYCDW4 exhibited potent antimicrobial activities against E. coli, C. albicans, B. subtilis, and S. aureus with the inhibition zone diameter (IZD) of 13.67, 14.33, 12.17, and 11.33 mm, respectively, which were comparable with those of the positive control. 1-(2,5-Dihydroxyphenyl)-3-hydroxybutan-1-one (2) from the Microdiplodia sp. BYCDW8 showed medium inhibitory activities against B. subtilis and S. aureus, with the IZD range of 8.32–9.13 mm. In conclusion, the study showed the diversity of insect symbionts could be expected to develop the resource of new species and antibiotics.

Fungal evolution: major ecological adaptations and evolutionary transitions

Fungi are a highly diverse group of heterotrophic eukaryotes characterized by the absence of phagotrophy and the presence of a chitinous cell wall. While unicellular fungi are far from rare, part of the evolutionary success of the group resides in their ability to grow indefinitely as a cylindrical multinucleated cell (hypha). Armed with these morphological traits and with an extremely high metabolical diversity, fungi have conquered numerous ecological niches and have shaped a whole world of interactions with other living organisms. Herein we survey the main evolutionary and ecological processes that have guided fungal diversity. We will first review the ecology and evolution of the zoosporic lineages and the process of terrestrialization, as one of the major evolutionary transitions in this kingdom. Several plausible scenarios have been proposed for fungal terrestralization and we here propose a new scenario, which considers icy environments as a transitory niche between water and emerged land. We then focus on exploring the main ecological relationships of Fungi with other organisms (other fungi, protozoans, animals and plants), as well as the origin of adaptations to certain specialized ecological niches within the group (lichens, black fungi and yeasts). Throughout this review we use an evolutionary and comparative-genomics perspective to understand fungal ecological diversity. Finally, we highlight the importance of genome-enabled inferences to envision plausible narratives and scenarios for important transitions.