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OBJECTIVE: Many patients with cochlear implants (CI) and auditory brainstem implants (ABI) require magnetic resonance imaging (MRI) following implantation. This study explores the patient experience of MRI, identifying factors associated with pain, and the effect of interventions designed to enhance comfort and safety.METHODS: A prospective observational case series from a tertiary referral unit. Tight head bandaging ± local anaesthetic injection (devices with non-MRI-compatible magnets) or observation alone (implants with MRI-compatible magnets) were employed for 1.5 T MRI of consecutive adult patients with CI or ABI without magnet removal. Pain was recorded via visual analogue scale (1 = no pain, 5 = extreme pain) at three time points; (1) baseline, (2) head bandage applied (3) during scanning. Patient age, device type, body area imaged and total scan time were recorded as variables, alongside adverse events.RESULTS: Data were collected for 227 MRI scans (34 patients with ABI, 32 with CI). In patients managed with bandaging, pain score after bandaging but prior to scanning (median 2.2) did not differ from pain during scanning (2.1), but both were significantly higher than baseline (1.4, both P ≤ 0.001). Scanning areas other than the head/cervical spine was associated with higher pain scores (P = 0.036). Pain during MRI differed between different manufacturers implants (P ≤ 0.001). Adverse events occurred in 8/227 scans (3.5%), none occurring with devices containing an MRI-compatible magnet.CONCLUSION: MRI scanning with auditory implant magnets in situ is safe and well tolerated by patients.

Living amphibians (Lissamphibia) include frogs and salamanders (Batrachia) and the limbless worm-like caecilians (Gymnophiona). The estimated Palaeozoic era gymnophionan–batrachian molecular divergence suggests a major gap in the record of crown lissamphibians prior to their earliest fossil occurrences in the Triassic period. Recent studies find a monophyletic Batrachia within dissorophoid temnospondyls, but the absence of pre-Jurassic period caecilian fossils has made their relationships to batrachians and affinities to Palaeozoic tetrapods controversial. Here we report the geologically oldest stem caecilian—a crown lissamphibian from the Late Triassic epoch of Arizona, USA—extending the caecilian record by around 35 million years. These fossils illuminate the tempo and mode of early caecilian morphological and functional evolution, demonstrating a delayed acquisition of musculoskeletal features associated with fossoriality in living caecilians, including the dual jaw closure mechanism, reduced orbits and the tentacular organ. The provenance of these fossils suggests a Pangaean equatorial origin for caecilians, implying that living caecilian biogeography reflects conserved aspects of caecilian function and physiology19, in combination with vicariance patterns driven by plate tectonics. These fossils reveal a combination of features that is unique to caecilians alongside features that are shared with batrachian and dissorophoid temnospondyls, providing new and compelling evidence supporting a single origin of living amphibians within dissorophoid temnospondyls. This study was supported by the David R. Wones Geological Scholarship (to B.T.K.), the USA National Park Service (PMIS 209814 to B.T.K., W.G.P. and A.D.M.), the Virginia Tech Department of Geosciences (to B.T.K., M.R.S. and S.J.N.), the National Science Foundation (DEB1655609 to M.R.S.; EAR480383 to S.J.N., M.R.S. and B.T.K.; and DPP1947094 to C. Sidor, supporting B.M.G.), the David B. Jones Foundation (to M.R.S. and S.J.N.) and the Petrified Forest Museum Association (to B.T.K.). Published version

Patagonian collections of the corticioid genus Tomentellopsis have been treated in the past as T. echinospora, a common northern hemisphere species. New collections with DNA sequence data are distinct from the northern hemisphere taxon and must be considered a different species, endemic to the temperate subantarctic forests of Patagonia. We use molecular and morphological methodologies to study this new corticioid fungus and describe it as Tomentellopsis rosannae sp. nov.

OBJECTIVES: To estimate the prevalence of, and risk factors associated with electrode migration (EM) in cochlear implant (CI) recipients. DESIGN: Historical cohort study of all CIs performed between 1 January 2018 and 1 August 2021 in a single tertiary adult and paediatric CI centre in the UK. MAIN OUTCOME MEASURES: The primary aim is to determine the prevalence of electrode migration, comparing intraoperative surgeon report and examination of a routine plain radiograph performed 2 weeks after surgery. EM is defined as the detection of movement of two or more electrodes out of the cochlea from the time of surgery. Multivariate analysis was performed to investigate preoperative and intraoperative risk factors that might predispose to migration. RESULTS: Four hundred and sixty-five patients, having 516 distinct surgeries, with 628 implants were analysed. EM occurred following 11.5% of implant operations. Pre-existing cochlear abnormality was an independent associated risk factor for EM (OR: 3.40 ⟨1.20-9.62⟩ p = .021). Demographics, surgical technique, usage of a precurved electrode, CSF leak, surgeon seniority and intraoperative telemetry did not influence risk of migration. There were 5 implants (0.8%) which migrated later than 2 weeks, with a median date of imaging diagnosis (x-ray or CT scan) of 263 days ⟨IQR:198⟩, for which head injury was a common precipitating factor. There were differences in the risk of migration between different lateral wall electrodes. CONCLUSION: EM in the early postoperative period is a common occurrence and is more likely in implant recipients with obstructed or malformed cochleae.

Fungi have evolved over millions of years and their species diversity is predicted to be the second largest on the earth. Fungi have cross-kingdom interactions with many organisms that have mutually shaped their evolutionary trajectories. Zygomycete fungi hold a pivotal position in the fungal tree of life and provide important perspectives on the early evolution of fungi from aquatic to terrestrial environments. Phylogenomic analyses have found that zygomycete fungi diversified into two separate clades, the Mucoromycota which are frequently associated with plants and Zoopagomycota that are commonly animal-associated fungi. Genetic elements that contributed to the fitness and divergence of these lineages may have been shaped by the varied interactions these fungi have had with plants, animals, bacteria, and other microbes. To investigate this, we performed comparative genomic analyses of the two clades of zygomycetes in the context of Kingdom Fungi, benefiting from our generation of a new collection of zygomycete genomes, including nine produced for this study. We identified lineage-specific genomic content that may contribute to the disparate biology observed in these zygomycetes. Our findings include the discovery of undescribed diversity in CotH, a Mucormycosis pathogenicity factor, which was found in a broad set of zygomycetes. Reconciliation analysis identified multiple duplication events and an expansion of CotH copies throughout the Mucoromycotina, Mortierellomycotina, Neocallimastigomycota, and Basidiobolus lineages. A kingdom-level phylogenomic analysis also identified new evolutionary relationships within the subphyla of Mucoromycota and Zoopagomycota, including supporting the sister-clade relationship between Glomeromycotina and Mortierellomycotina and the placement of Basidiobolus as sister to other Zoopagomycota lineages.

This document is intended to introduce the general public to the chanterelle mushrooms of Florida and includes a preliminary key to Florida’s most common chanterelle species. Written by Kaori Hall, Ben Lemmond, and Matthew E. Smith, and published by the UF/IFAS Plant Pathology Department, February 2023.

Invasive plants, which cause substantial economic and ecological impacts, acquire both pathogens and beneficial microbes in their introduced ranges. Communities of fungal endophytes are known to mediate impacts of pathogens on plant fitness but few studies have examined the temporal dynamics of fungal communities on invasive plants. The annual grass Microstegium vimineum, an invader of forests and riparian areas throughout the eastern United States, experiences annual epidemics of disease caused by Bipolaris pathogens. Our objective was to characterize the dynamics of foliar fungal communities on M. vimineum over a growing season during a foliar disease epidemic. First, we asked how the fungal community in the phyllosphere changed over 2 months that corresponded with increasing disease severity. Second, we experimentally suppressed disease with fungicide in half of the plots and asked how the treatment affected fungal community diversity and composition. We found increasingly diverse foliar fungal communities and substantial changes in community composition between timepoints using high-throughput amplicon sequencing of the internal transcribed spacer 2 region. Monthly fungicide application caused shifts in fungal community composition relative to control samples. Fungicide application increased diversity at the late-season timepoint, suggesting that it suppressed dominant fungicide sensitive taxa and allowed other fungal taxa to flourish. These results raise new questions regarding the roles of putative endophytes found in the phyllosphere given the limited number of pathogens known to cause disease on M. vimineum in its invasive range.

To review the outcomes of cochlear implants (CI) in patients with neurofibromatosis type 2 (NF2) in a large cohort, and identify factors associated with poor hearing benefit.Fifteen-year retrospective national observational case series.United Kingdom regional NF2 multidisciplinary teams.Consecutive patients with NF2 receiving a CI.CI for hearing rehabilitation.1) Audiometric performance at 9 to 12 months after implantation using City University of New York (CUNY) sentence recognition score, and Bamford- Kowal-Bench (BKB) word recognition score in quiet (BKBq), and in noise (BKBn). 2) CI use at most recent review.Sixty four consecutive patients, median age 43 years, were included. Nine to 12 months mean audiometric scores were: CUNY 60.9%, BKBq 45.8%, BKBn 41.6%. There was no difference in audiometric outcomes between VS treatment modalities. At most recent review (median 3.6 years from implantation), 84.9% with device in situ/available data were full or part-time users. Between 9 and 12 months and most recent review there was an interval reduction in mean audiometric scores: CUNY -12.9%, BKBq -3.3%, BKBn -4.9%. Larger tumor size and shorter duration of profound hearing loss were the only variables associated with poorer audiometric scores. Tumor growth at the time of surgery was the only variable associated with CI non-use. Individual patient response was highly variable.CI can provide significant and sustained auditory benefits to patients with NF2 independent of tumor treatment modality, with the majority of those implanted becoming at least part-time users. Larger datasets are required to reliably assess the role of independent variables.

Mushroom-forming fungi are important sources of food and medicine in many regions of the world, and their development and health are known to depend on various microbes. Recent studies have examined the structure of mushroom-inhabiting bacterial (MIB) communities and their association with local environmental variables, but global-scale diversity and determinants of these communities remain poorly understood. Here we examined the MIB global diversity and community composition in relation to climate, soil and host factors. We found a core global mushroom microbiome, accounting for 30% of sequence reads, while comprising a few bacterial genera such as Halomonas, Serratia, Bacillus, Cutibacterium, Bradyrhizobium and Burkholderia. Our analysis further revealed an important role of host phylogeny in shaping the communities of MIB, whereas the effects of climate and soil factors remained negligible. The results suggest that the communities of MIB and free-living bacteria are structured by contrasting community assembly processes and that fungal-bacterial interactions are an important determinant of MIB community structure.

In this study we review recent collections and historical records of epigeous members of the Pezizales formerly placed in the large, heterogenous genus Peziza from temperate southern South America. Recent analyses using molecular phylogenetic methods allow placement of these species in several previously described genera in recognition of the heterogeneity of Peziza. We include species in nine genera, describe one new species (Peziza gamundiae sp. nov.), and propose one new combination (Phylloscypha nothofageti comb. nov.). We also demonstrate that Pustularia microspora is a synonym of the previously described taxon Peziza pseudosylvestris. Our purpose is to draw attention to these taxa in order to promote their collection and study in a modern framework.

We describe a novel sequestrate genus and species, Asperosporus subterraneus gen. et sp. nov., found associated with nursery production of ferns in south Florida. This truffle species has a unique combination of morphological characters among described Agaricaceae in that it lacks a stipe or columella, has large, ornamented spores, the fresh sporocarps rapidly stain pink-red when cut or bruised, and they have a rancid smell. Although this fungus does not appear to be a direct plant pathogen, the hyphae of A. subterraneus produce a thick hydrophobic mycelial mat that binds the organic matter and therefore prevents water and fertilizer from being absorbed by plants, consequently causing wilting and chlorosis. Using morphological characteristics and phylogenetic reconstruction based on the internal transcribed spacer (ITS), partial large subunit nuclear ribosomal DNA (LSU), second largest subunit of RNA polymerase II (rpb2) and translation elongation factor 1-alpha (tef1) regions, we describe this taxon as a new genus and species in Agaricaceae.

Fungi in the Nidulariaceae, otherwise known as ‘bird's nest fungi’, are among the least studied groups of Agaricomycetes (Basidiomycota). Bird's nest fungi are globally distributed and typically grow on woody debris or animal dung as saprotrophs. This group of fungi is morphologically diverse with ca. 200 described species. Phylogenetic relationships of bird's nest fungi were investigated with four commonly used loci (ITS, LSU, tef, and rpb2). The family was resolved as a monophyletic group with Squamanitaceae as a potential sister taxon. Cyathus and Crucibulum each formed its own independent and well-supported clade. Nidula and Nidularia formed a clade together, but each genus is polyphyletic. Two Mycocalia species included in our analyses were on their own separate branches, indicating that this genus is also polyphyletic. Misidentifications were detected in most genera, suggesting that species concepts need to be revisited and refined throughout Nidulariaceae. Several bird's nest fungi species have global geographical distributions whereas others may have more limited ranges. Basic morphological characters of bird's nest fungi have likely been lost or gained multiple times. The phylogenetic placement of Crucibulum is unclear and the sister lineage of bird's nest fungi is not conclusive. Further studies with data from rare species and additional informative genes are needed to fully resolve the topology of Nidulariaceae and identify its sister group with more certainty.

Improved sequencing technologies have profoundly altered global views of fungal diversity and evolution. High-throughput sequencing methods are critical for studying fungi due to the cryptic, symbiotic nature of many species, particularly those that are difficult to culture. However, the low coverage genome sequencing (LCGS) approach to phylogenomic inference has not been widely applied to fungi. Here we analyzed 171 Kickxellomycotina fungi using LCGS methods to obtain hundreds of marker genes for robust phylogenomic reconstruction. Additionally, we mined our LCGS data for a set of nine rDNA and protein coding genes to enable analyses across species for which no LCGS data were obtained. The main goals of this study were to: 1) evaluate the quality and utility of LCGS data for both phylogenetic reconstruction and functional annotation, 2) test relationships among clades of Kickxellomycotina, and 3) perform comparative functional analyses between clades to gain insight into putative trophic modes. In opposition to previous studies, our nine-gene analyses support two clades of arthropod gut dwelling species and suggest a possible single evolutionary event leading to this symbiotic lifestyle. Furthermore, we resolve the mycoparasitic Dimargaritales as the earliest diverging clade in the subphylum and find four major clades of Coemansia species. Finally, functional analyses illustrate clear variation in predicted carbohydrate active enzymes and secondary metabolites (SM) based on ecology, that is biotroph versus saprotroph. Saprotrophic Kickxellales broadly lack many known pectinase families compared with saprotrophic Mucoromycota and are depauperate for SM but have similar numbers of predicted chitinases as mycoparasitic.

The tropics were long considered to have few ectomycorrhizal fungi, presumably due to a paucity of ectomycorrhizal host plants relative to higher-latitude ecosystems. However, an increase in research in tropical regions over the past 30 years has greatly expanded knowledge about the occurrence of tropical ectomycorrhizal fungi. To assess their broad biogeographic and diversity patterns, we conducted a comprehensive review and quantitative data analysis of 49 studies with 80 individual data sets along with additional data from GlobalFungi to elucidate tropical diversity patterns and biogeography of ectomycorrhizal fungi across the four main tropical regions: the Afrotropics, the Neotropics, Southeast Asia, and Oceania. Generalized linear models were used to explore biotic and abiotic influences on the relative abundance of the 10 most frequently occurring lineages. We also reviewed the available literature and synthesized current knowledge about responses of fungi to anthropogenic disturbances, and their conservation status and threats. We found that /russula-lactarius and /tomentella-thelephora were the most abundant lineages in the Afrotropics, the Neotropics, and Southeast Asia, whereas /cortinarius was the most abundant lineage in Oceania, and that /russula-lactarius, /inocybe, and /tomentella-thelephora were the most species-rich lineages across all of the tropical regions. Based on these analyses, we highlight knowledge gaps for each tropical region. Increased sampling of tropical regions, collaborative efforts, and use of molecular methodologies are needed for a more comprehensive view of the ecology and diversity of tropical ectomycorrhizal fungi.

The occurrence and distribution of morels in Nothofagaceae forests of South America is addressed based on our field studies in Southern Chile and Argentina. Both ascomata and mitosporic colonies were collected and ascomata were procured from commercial harvesters. A four-gene (ITS, RPB1, RPB2, TEF1-α) and ITS phylogeny assigned these Morchella ascomatal and mitosporic collections to four Elata clade lineages, M. tridentina, M. eximia, M. andinensis and M. aysenina, which were each well supported by ML and Bayesian analyses. The placement of our collections of the two lineages unique to South America, M. andinensis (previously cited as Mel-37) and M. aysenina expand their known distribution in South America. Most of the mitosporic colonies collected in our study belong to the M. eximia “fire adapted lineage.” This is the first report of M. eximia, under this name, in Chile. Since the mitosporic colonies can be found frequently, these collections help to expand the geographical range of currently described species.

Bog hemp ( Boehmeria cylindrica) is a perennial herbaceous plant widely distributed across the Americas. In September of 2016, a rust disease was observed on leaves of bog hemp in Florida, U.S.A. The specimen was sent to the Arthur Fungarium at Purdue University for further identification and long-term deposit. Based on morphological characteristics and sequence analysis, the rust species was identified as Pucciniastrum boehmeriae. To our knowledge, this is the first report of P. boehmeriae in North America from any host.

Symbiosis between beetles and fungi arose multiple times during the evolution of both organisms. Some of the most biologically diverse and economically important are mutualisms in which the beetles cultivate and feed on fungi. Among these are bark beetles and Harringtonia, a fungal genus that produces Raffaelea-like asexual morph and hosts the causal agent of laurel wilt, H. lauricola (formerly Raffaelea lauricola). In this study, we propose four new species of Harringtonia associated with beetles from Belize and Florida (USA). We hope to contribute towards a more robust and inclusive phylogenetic framework for future studies on these beetle-fungi relationships and their potential impact in crops and forests worldwide.

Objectives: Nurses are increasingly providing routine and emergency ENT care; yet there are often limited training opportunities. The aim of this study was to validate an intensive 1-day ENT emergency simulation course for nurses. Methods: The course included short lectures, practical skills stations and mannequin simulation scenarios. Sixteen nurse participants were video-recorded managing simulated scenarios before and after the course. Two assessors scored individual participant performance on a 15-point competency grid (maximum score 30), blinded to the timing of the recording. Participants also rated their confidence and skill before and immediately following the course across 11 items using a 5-point Likert score (maximum score 55). Results: Blinded assessor ratings for performance were significantly improved after the course compared to baseline (overall score 12 vs 7, respectively; P = .015). There was strong assessor inter-rater reliability ( R = 0.965). Self-rated skills and confidence also increased following the course (46.7 vs 24.4 at baseline; P Conclusion: Simulation-based training is an effective and desirable method of teaching ENT emergency management to nurses, with greatest impact on participant confidence. Future courses need to refine the content and increase the validation sample size using a nurse-specific scoring system.

Sequestrate fungi have enclosed hypogeous, subhypogeous, or epigeous basidiomes and have lost the ability to actively discharge their spores. They can be distinguished as gasteroid (basidiome fully enclosed with a loculated hymenophore) or secotioid (basidiome with some agaricoid or pileate-stipitate features, but the lamellae are misshapen and unexposed or mostly unexposed at maturity). There are only four reports of sequestrate taxa within the ectomycorrhizal family Inocybaceae, three from Australia and one from western North America. Recent field work in Nothofagaceae forests in the Chilean coastal range revealed novel sequestrate forms of Inocybe. We examined specimens using a combination of morphological and molecular data from nuc rDNA internal transcribed spacer region ITS1-5.8S-ITS2 (ITS) and portions of nuc 28S rDNA (28S) and the gene encoding the second largest subunit of RNA polymerase II (rpb2). Here, we describe four new sequestrate Inocybe species, I. ranunculiformis, I. anfractuosa, I. illariae, and I. nahuelbutensis. Results of our phylogenetic analysis resolved the four new species as distinct species-level clades with strong support, suggesting that these fungi have convergently evolved sequestrate forms independently. The species described here were all placed along with members of the "smooth-spored temperate austral clade," which includes almost exclusively Australasian and South American species of Inocybe.

There were errors in the name of author Laszlo G. Nagy and in affiliation no. 31 in the original publication. The original article has been corrected.

INTRODUCTION Nasal packing is the mainstay of epistaxis management; however, packs cause patient discomfort and can lead to hospital admission. Absorbable haemostats provide clotting factors or act as a substrate to stimulate clotting and represent a potential treatment alternative. A systematic review was performed to evaluate the efficacy of topical haemostats in the management of epistaxis. METHODS A systematic literature search of 7 databases was performed. Only eligible randomised controlled trials (RCTs) and observational studies were included. The primary outcome was short-term haemostatic success (

Objectives To assess the safety of paediatric tonsillectomy procedures conducted in NHS hospitals in England between 2008 and 2019. Design Retrospective observational cohort study using Hospital Episode Statistics (HES) data. Setting Acute NHS trusts in England conducting paediatric tonsillectomy procedures. Participants Children (≤16 years old) undergoing bilateral tonsillectomy. Main outcome measures Number of tonsillectomies performed per year by procedural method. In‐hospital complications including return to theatre for arrest of haemorrhage. Readmission within 28 days, including those for pain, haemorrhage and surgical arrest of haemorrhage. Long‐term outcomes: all‐cause mortality, revision tonsillectomy. Results A total of 318 453 paediatric tonsillectomies were performed from 2008 to 2019:278,772 dissection (87.5%) and 39 681 coblation (12.5%). The proportion of tonsillectomy performed using coblation increased from 7% in 2008/9 to 27% in 2018/9. Five patients died in hospital (including 4 due to respiratory complications). In‐hospital complications occurred in 4202 children (1.3%), with the most frequent being haemorrhage. Within 28 days of tonsillectomy, 28 170 patients (8.8%) were readmitted and 7 deaths occurred. Readmission rates for haemorrhage and pain have increased since 2008. The proportion of children undergoing revision tonsillectomy procedures within 5 years following coblation tonsillectomy (1.4%) was approximately double that of dissection (0.6%). Conclusions Clinical practice of paediatric tonsillectomy has changed in England over the past 11 years. The overall mortality rate associated with the procedure is 0.0037%. Differences in outcomes have been identified for different procedural methods. However, routine administrative data are limited in differentiating procedural detail (eg we are unable to differentiate intra or extra‐capsular techniques from current clinical coding of tonsillectomy procedures). Therefore, prospective national data collection or more granular clinical coding is essential to capture relative outcomes of the different tonsillectomy methods and techniques being used in the NHS.

Ambrosia beetles in the subtribe Hyorrhynchini are one example of an entire ambrosia beetle lineage whose fungi have never been studied. Here, we identify one dominant fungus associated with a widespread Asian hyorrhynchine beetle Sueus niisimai. This fungus was consistently isolated from beetle galleries from multiple collections. Phylogenetic analyses of combined ITS rDNA and β-tubulin sequences identified the primary fungal symbiont as Diatrypella japonica Higuchi, Nikaido & Hattori (Diatrypaceae, Xylariales, Sordariomycetes), which was recently described as a pathogen of sycamore (Platanus spp.) in Japan. To assess the invasion potential of this beetle-fungus interaction into the U.S., we have investigated the pathogenicity of two D. japonica strains on four species of healthy landscape trees native to the southeastern United States. Only Shumard oak (Quercus shumardii) responded with lesions significantly greater than the control inoculations, but there was no observable dieback or tree mortality. Although disease symptoms were not as prominent as in previous studies of the same fungus in Japan, routine reisolation from the inoculation point suggests that this species is capable of colonizing healthy sapwood of several tree species. Our study shows that the geographical area of its distribution is broader in Asia and potentially includes many hosts of its polyphagous vector. We conclude that the Sueus-Diatrypella symbiosis has high invasion potential but low damage potential, at least on young trees during the growing season.

Summary We describe environmental microbial eukaryotes (EMEs) sample collection, single-cell isolation, lysis, and genome amplification, followed by the rDNA amplification and OTU screening for recovery of high-quality species-specific genomes for de novo assembly. These protocols are part of our pipeline that also includes bioinformatic methods. The pipeline and its application on a wide range of phyla of different sample complexity are described in our complementary paper. In addition, this protocol describes optimized lysis, genome amplification, and OTU screening steps of the pipeline. For complete details on the use and execution of this protocol, please refer to Ciobanu et al. (2021)., Graphical Abstract, Highlights • We describe EME sample-collection, single-cell isolation, lysis, genome amplification • These protocols are suitable for mining single-cell EME genomes • These protocols are directed towards recovery of high-quality genomes • The genomes are suitable for species-specific de novo genome assembly, We describe environmental microbial eukaryotes (EMEs) sample collection, single-cell isolation, lysis, and genome amplification, followed by the rDNA amplification and OTU screening for recovery of high-quality species-specific genomes for de novo assembly. These protocols are part of our pipeline that also includes bioinformatic methods. The pipeline and its application on a wide range of phyla of different sample complexity are described in our complementary paper. In addition, this protocol describes optimized lysis, genome amplification, and OTU screening steps of the pipeline.

Fungi survive in diverse ecological niches by secreting proteins and other molecules into the environment to acquire food and interact with various biotic and abiotic stressors. Fungal secretome content is, therefore, believed to be tightly linked to fungal ecologies. We sampled 132 genomes from the early-diverging terrestrial fungal lineage zygomycetes (Mucoromycota and Zoopagomycota) and characterized their secretome composition. Our analyses revealed that phylogeny played an important role in shaping the secretome composition of zygomycete fungi with trophic mode contributing a smaller amount. Reconstruction of the evolution of secreted digestive enzymes revealed lineage-specific expansions, indicating that Mucoromycota and Zoopagomycota followed different trajectories early in their evolutionary history. We identified the presence of multiple pathogenicity-related proteins in the lineages known as saprotrophs, suggesting that either the ecologies of these fungi are incompletely known, and/or that these pathogenicity-related proteins have important functions associated with saprotrophic ecologies, both of which invite further investigation.