Recent ucr_plantpathmicro_rw items

Author Correction: A roadmap for equitable reuse of public microbiome data

Fri, 5 Jun 2026 00:00:00 +0000

Correction to: Nature Microbiologyhttps://doi.org/10.1038/s41564-025-02116-2, published online 26 September 2025. In the version of this article initially published, in the first paragraph of the “Survey on data reuse” section, a note on participant consent, confidentiality and institutional review was missing and has now been inserted in the HTML and PDF versions of the article.

Effects of environmental setting and diet on the gut microbial ecology of eastern hellbenders (Cryptobranchus alleganiensis alleganiensis)

Mon, 25 May 2026 00:00:00 +0000

BackgroundEastern hellbenders (Cryptobranchus alleganiensis alleganiensis) have undergone substantial population declines throughout their range, leading them to become the focus of increased conservation efforts, including care in zoo and university settings. However, effective implementation of such conservation strategies often relies on a comprehensive understanding of host health, which can be directly influenced by the gut microbiome, yet characterization of gut microbiota often remains overlooked in ex situ conservation facilities. Additionally, effects on the gut microbiome associated with releasing zoo-reared animals into the wild are poorly understood. Therefore, these circumstances make hellbenders an ideal species to examine the relationship between zoo management strategies and gut microbial dynamics.Methods16S rRNA sequencing was used to investigate dissimilarities between the gut microbiome of hellbenders in zoo and wild settings and to evaluate the impact of implementing...

STREAMS guidelines: standards for technical reporting in environmental and host-associated microbiome studies

Wed, 6 May 2026 00:00:00 +0000

The interdisciplinary nature of microbiome research, coupled with the generation of complex multi-omics data, makes knowledge sharing challenging. The Strengthening the Organization and Reporting of Microbiome Studies (STORMS) guidelines provide a checklist for the reporting of study information, experimental design and analytical methods within a scientific manuscript on human microbiome research. Here, in this Consensus Statement, we present the standards for technical reporting in environmental and host-associated microbiome studies (STREAMS) guidelines. The guidelines expand on STORMS and include 67 items to support the reporting and review of environmental (for example, terrestrial, aquatic, atmospheric and engineered), synthetic and non-human host-associated microbiome studies in a standardized and machine-actionable manner. Based on input from 248 researchers spanning 28 countries, we provide detailed guidance, including comparisons with STORMS, and case studies that demonstrate...

A roadmap for equitable reuse of public microbiome data

Mon, 27 Apr 2026 00:00:00 +0000

Science benefits from rapid open data sharing, but current guidelines for data reuse were established two decades ago, when databases were several million times smaller than they are today. These guidelines are largely unfamiliar to the scientific community, and, owing to the rapid increase in biological data generated in the past decade, they are also outdated. As a result, there is a lack of community standards suited to the current landscape and inconsistent implementation of data sharing policies across institutions. Here we discuss current sequence data sharing policies and their benefits and drawbacks, and present a roadmap to establish guidelines for equitable sequence data reuse, developed in consultation with a data consortium of 167 microbiome scientists. We propose the use of a Data Reuse Information (DRI) tag for public sequence data, which will be associated with at least one Open Researcher and Contributor ID (ORCID) account. The machine-readable DRI tag indicates...

Inferring fungal cis-regulatory networks from genome sequences via unsupervised and interpretable representation learning

Thu, 23 Apr 2026 00:00:00 +0000

Gene expression patterns are determined to a large extent by transcription factor (TF) binding to noncoding regulatory regions in the genome. However, gene expression cannot yet be systematically predicted from genome sequences, in part because nonfunctional matches to the sequence patterns (motifs) recognized by TFs occur frequently throughout the genome. Large-scale functional genomics data for many TFs has enabled characterization of regulatory networks in experimentally accessible cells such as budding yeast. Beyond yeast, fungi are important industrial organisms and pathogens, but large-scale functional data is only sporadically available. Uncharacterized regulatory networks control key pathways and gene expression programs associated with fungal phenotypes. Here, we explore a sequence-only approach to inferring regulatory networks by leveraging the 100s of genomes now available for many clades of fungi. We use gene orthology as the learning signal to infer interpretable,...

The hidden taxonomic novelty of anamorphic basidiomycetous yeasts in the phyllosphere and tidal flats in China

Thu, 23 Apr 2026 00:00:00 +0000

Basidiomycetous yeasts are taxonomically and ecologically diverse. While the phyllosphere of plants in China has been the subject of extensive research on yeast biodiversity, many unique and remote habitats remain significantly underexplored for their yeast species. The objective of this study was to investigate the hidden taxonomic novelty of basidiomycetous yeasts in these distinctive niches to comprehensively refine the current phylogenetic understanding. During intensive investigations, 164 yeast strains were identified from various samples collected from the phyllosphere and tidal flats in China. These isolates underwent detailed multi-gene phylogenetic analyses combined with phenotypic characterization for taxonomic placement. The analyses revealed a remarkable level of hidden diversity. These 164 isolates represent one new order (Sterigmoblongales), two new families (Sterigmoblongaceae and Turchettiaceae), five new genera (Nakasea, Sterigmoblongus, Buzzinia, Gracilitas,...

Effects of environmental setting and diet on the gut microbial ecology of eastern hellbenders (Cryptobranchus alleganiensis alleganiensis)

Thu, 23 Apr 2026 00:00:00 +0000

ABSTRACT Background Eastern hellbenders ( Cryptobranchus alleganiensis alleganiensis ) have undergone substantial population declines throughout their range, leading them to become the focus of increased conservation efforts, including care in zoo and university settings. However, effective implementation of such conservation strategies often relies on a comprehensive understanding of host health, which can be directly influenced by the gut microbiome, yet characterization of gut microbiota often remains overlooked in ex situ conservation facilities. Additionally, effects on the gut microbiome associated with releasing zoo-reared animals into the wild are poorly understood. Therefore, these circumstances make hellbenders an ideal species to examine the relationship between zoo management strategies and gut microbial dynamics. Methods 16S rRNA sequencing was used to investigate dissimilarities between the gut microbiome of hellbenders in zoo and wild settings and to evaluate...

Phyling: phylogenetic inference from annotated genomes

Thu, 23 Apr 2026 00:00:00 +0000

Phyling is a fast, scalable, and user-friendly tool supporting phylogenomic reconstruction of species phylogenies directly from protein-encoded genomic data. It identifies orthologous genes by searching protein sequences against a curated set of Hidden Markov Models profiles, consisting of single-copy orthologs derived from the BUSCO database. To optimize the speed of the final inference, Phyling includes a module to filter aligned orthologs based on their phylogenetic informativeness. Finally, Phyling provides a companion wrapper for automated species tree construction using either consensus or concatenation strategies. Phyling efficiently resolves large phylogenies by optimizing memory usage and data processing. Its checkpoint system enables users to incrementally add or remove samples without repeating the entire search process. For analyses involving closely related taxa, Phyling supports the use of nucleotide coding sequences, which may capture phylogenetic signals missed...

Genomic and Ecological Flexibility Shape the Global Distribution of a Black Fungus

Thu, 23 Apr 2026 00:00:00 +0000

Black fungi are among the most stress-resistant organisms known, yet the genetic and ecological foundations of their extraordinary resilience remain poorly understood. This study explores the adaptation strategies of the melanised fungus Elasticomyces elasticus by integrating genomic and ecological data. To uncover the mechanisms of adaptation, we combined whole-genome sequencing, functional annotation, environmental metadata, and large-scale soil metabarcoding analyses. Phylogenomic approaches were employed to delineate evolutionary lineages and assess ploidy levels. The results revealed that the global distribution of Elasticomyces phylotypes is primarily influenced by temperature, UV radiation, and soil organic carbon, suggesting that different phylotypes have evolved heterogeneous strategies for stress resistance. Comparative genomic analyses identified a set of 'sentinel pathways,' notably glutathione metabolism and nucleotide biosynthesis, which were enriched in strains...

Genomic and biological characterization of lytic phages infecting Pseudomonas syringae associated with almond bacterial blast.

Mon, 13 Apr 2026 00:00:00 +0000

Pseudomonas species are Gram-negative bacterial pathogens that affect a wide range of economically important crops, including almond. Increasing resistance of Pseudomonas syringae to conventional management strategies highlights the need for alternative disease control options. In this study, we isolated and characterized three lytic bacteriophages, including vB_PsyP_Mobley, vB_PsyP_Plaza, and vB_PsyP_Mission, targeting almond-infecting Pseudomonas strains. Host-range analysis across 36 isolates revealed partially overlapping infectivity profiles, with strongest activity against phylogroup 2 (PG2) almond-associated P. syringae pv. syringae and reduced infectivity against phylogenetically distinct isolates, including PG7 P. viridiflava and other crop-associated pathovars. Efficiency-of-plating assays quantitatively supported these host-range patterns. Plaque morphology and transmission electron microscopy demonstrated icosahedral capsids with short, non-contractile tails consistent...

New persistent plant RNA virus carries mutations to weaken viral suppression of antiviral RNA interference

Thu, 12 Mar 2026 00:00:00 +0000

Persistent plant viruses are widespread in natural ecosystems. However, little is known about why persistent infection with these viruses may cause little or no harm to their host. Here, we discovered a new polerovirus that persistently infected wild rice plants by deep sequencing and assembly of virus-derived small-interfering RNAs (siRNAs). The new virus was named Rice tiller inhibition virus 2 (RTIV2) based on the symptoms developed in cultivated rice varieties following Agrobacterium-mediated inoculation with an infectious RTIV2 clone. We showed that RTIV2 infection induced antiviral RNA interference (RNAi) in both the wild and cultivated rice plants as well as Nicotiana benthamiana. It is known that virulent virus infection in plants depends on effective suppression of antiviral RNAi by viral suppressors of RNAi (VSRs). Notably, the P0 protein of RTIV2 exhibited weak VSR activity and carries alanine substitutions of two amino acids broadly conserved among diverse poleroviruses....

Editing strigolactone hormone receptor for robust antiviral silencing in rice

Thu, 12 Mar 2026 00:00:00 +0000

The small interfering RNA (siRNA) pathway directs broad-spectrum antiviral defense through RNA silencing so that virulent infection requires efficient suppression of the defense mechanism. Here, we show that strigolactone (SL) hormone signaling promotes antiviral silencing in rice plants by transcriptional activation of RNA-dependent RNA polymerase 1 (RDR1) and RDR6. We demonstrate that protein P3 of the rice grassy stunt virus (RGSV) blocks SL signaling by directly sequestering the receptor DWARF14 from DWARF3. Structural and functional analyses of the P3-DWARF14 complex reveal that the aspartic acid at position 102 (D102) of DWARF14 is essential for the P3 interaction but not for SL perception. Notably, a single D102N substitution of DWARF14, introduced into two rice cultivars by cytosine base editing (CBE) confers resistance against RGSV by blocking viral suppression of SL signaling-dependent antiviral silencing. Our findings establish a transgene-free strategy for engineering...

Ten Pressing Questions (and Answers) About Marine Fungi and Opportunities for Collaborations in the Ocean Sciences

Tue, 10 Feb 2026 00:00:00 +0000

Nearly 200 years have passed since the first marine fungus, collected from the shores of North Africa, was described. In that time, marine mycologists have continued to observe, describe, and study fungi in every marine ecosystem examined. Nevertheless, fungi remain functionally “dark matter” of the ocean, presenting a grand opportunity to unravel their roles in ecosystem processes. This report outlines the discussion among participants of the second occasional meeting of marine mycologists at Asilomar, California, in March 2024, in which a diverse and interdisciplinary consortium of researchers enumerated the most pressing, and often basic, unanswered questions in marine fungi. We report on the questions facing the field of marine mycology, identify challenges in addressing those questions, and propose concrete and practical solutions for obtaining their answers. A common thread is the need for increasing cross talk and collaboration between mycologists and oceanographers that...

Gene duplication, horizontal gene transfer, and trait trade-offs drive evolution of postfire resource acquisition in pyrophilous fungi.

Thu, 15 Jan 2026 00:00:00 +0000

Wildfires significantly alter soil carbon (C) and nitrogen (N), reducing microbial richness and biomass, while selecting for "fire-loving" pyrophilous microbes that drive postfire nutrient cycling. However, the genomic strategies and functional trade-offs (balancing gains in one trait with costs in another) underlying the traits that enable pyrophilous microbes to survive and thrive postfire are virtually unknown. We hypothesized that pyrophilous fungi employ specialized genomic adaptations for C and N cycling, with evolutionary trade-offs between traits governing aromatic C degradation, N acquisition pathways, and rapid growth. To test these hypotheses, we performed complementary comparative genomics, transcriptomics after pyrogenic organic matter amendment, and growth rate bioassays for 18 pyrophilous fungi from five Ascomycota (Eurotiales, Pleosporales, Sordariales, Coniochaetales, and Pezizales) and three Basidiomycota (Agaricales, Holtermanniales, and Geminibasidiales) orders...

Eukaryotic MAGs recovered from deep metagenomic sequencing of the seagrass, Zostera marina, include a novel chytrid in the order Lobulomycetales

Wed, 24 Dec 2025 00:00:00 +0000

Abstract Fungi play pivotal roles in terrestrial ecosystems as decomposers, pathogens, and endophytes, yet their significance in marine environments is often understudied. Seagrasses, as globally distributed marine flowering plants, have critical ecological functions, but knowledge about their associated fungal communities remains relatively limited. Previous amplicon surveys of the fungal community associated with the seagrass, Zostera marina have revealed an abundance of potentially novel chytrids. In this study, we employed deep metagenomic sequencing to extract metagenome-assembled genomes (MAGs) from these chytrids and other microbial eukaryotes associated with Z. marina leaves. Our efforts resulted in the recovery of five eukaryotic MAGs, including a single fungal MAG in the order Loubulomycetales (65% BUSCO completeness), three MAGs representing diatoms in the family Bacillariaceae (93%, 70% and 31% BUSCO completeness) and a single MAG representing a haptophyte algae in...

Coordinated regulation of Mdr1- and Cdr1-mediated protection from antifungals by the Mrr1 transcription factor in emerging Candida spp.

Fri, 21 Nov 2025 00:00:00 +0000

Infections caused by the emerging pathogenic yeast Clavispora (Candida) lusitaniae can be difficult to manage due to multi-drug resistance. Resistance to the frontline antifungal fluconazole (FLZ) in Candida spp. is commonly acquired through gain-of-function (GOF) mutations in the gene encoding the transcription factor Mrr1. These activated Mrr1 variants enhance FLZ efflux via upregulation of the multi-drug transporter gene MDR1. Recently, it was reported that, unlike in the well-studied Candida albicans species, C. lusitaniae and Candida parapsilosis with activated Mrr1 also have high expression of CDR1, which encodes another multi-drug transporter with overlapping but distinct transported substrate profiles and Cdr1-dependent FLZ resistance. To better understand the mechanisms of Mrr1 regulation of MDR1 and CDR1, and other co-regulated genes, we performed Cleavage Under Targets and Release Using Nuclease (CUT&RUN)...

Specialized metabolites of the herptile gut fungus, Basidiobolus

Fri, 21 Nov 2025 00:00:00 +0000

Specialized metabolites of the herptile gut fungus, Basidiobolus

A haplotype-resolved chromatin landscape connects cis-regulatory variants to trait variation in Citrus

Fri, 21 Nov 2025 00:00:00 +0000

BackgroundGenetic and epigenetic perturbation of cis-regulatory sequences can shift patterns of gene expression and result in novel phenotypes. Phased genome assemblies now enable the local dissection of linkages between cis-regulatory sequences, including their epigenetic state, and allele-specific gene expression to further characterize gene regulation and resulting phenotypes in heterozygous genomes.ResultsWe assembled a locally phased genome for a mandarin hybrid named ‘Fairchild’ to explore the molecular signatures of allele-specific gene expression. With local genome phasing, genes with allele-specific expression were paired with haplotype-specific chromatin states, including levels of chromatin accessibility, histone modifications, and DNA methylation. We found that 30% of variation in allele-specific expression could be attributed to haplotype associated factors, with allelic levels of chromatin accessibility and three histone modifications in gene bodies having the most...

Detection of Puccinia graminis f. sp. tritici Race RRTTF in Ecuador in 2016

Tue, 14 Oct 2025 00:00:00 +0000

Wheat stem rust is a devastating disease that has incited severe epidemics, resulting in extreme yield losses over the past century. Stem rust infection in plots of wheat line UC11075, known to carry the Sr38 resistance gene, was unusual and severe in February 2016 in a nursery at the Instituto Nacional de Investigaciones Agropecuarias Austro station near Cuenca, Ecuador. Stems with heavy infection by Puccinia graminis f. sp. tritici (Pgt) were sent for genotyping in labs at Ottawa, ON, and St. Paul, MN, and for phenotyping at Morden, MB. None of the samples received directly from the field had viable spores, but genotyping was done in Ottawa and St. Paul using DNA extracted from spores or infected plant materials killed in ethanol. DNA was extracted using the OmniPrep kit (G-Biosciences, St. Louis, MO). Results from the Ottawa genotyping lab using 11 of 20 simple sequence repeat markers (Stoxen 2012) indicated that all February 2016 samples from the Austro station were genotypically...

Macrocyclic Edythea quitensis rust on Berberis hallii in Ecuador

Tue, 14 Oct 2025 00:00:00 +0000

The full macrocyclic autoecious life cycle of five spore stages was confirmed for Edythea quitensis on Berberis hallii in the highlands of Ecuador. The spermogonial and aecial stages had not previously been recorded. Spore descriptions and DNA sequence analysis are included.

Soil drivers of fungal, bacterial and plant diversity in contaminated Southern Californian sites: Implications for dryland bioremediation

Wed, 24 Sep 2025 00:00:00 +0000

This exploratory study surveyed seven contaminated brownfields and Superfund sites in Southern California to identify locally adapted species tolerant of mixed organic and metal contamination under arid and semi-arid conditions. Five novel native plants, including Brickellia californica, Baccharis salicifolia, Baccharis sarothroides, Eriogonum fasciculatum, and Heterotheca grandiflora were identified as hyperaccumulators of copper (Cu), alongside a non-native species from the Asteraceae family, Helminthotheca echioides. Additional metal-accumulating plants (including native plants) for lead (Pb), chromium (Cr), arsenic (As), and nickel (Ni) were identified, and warrant further evaluation for their phytoremediation potential. Dominant microbial communities included fungal taxa from the Ascomycota and bacterial taxa from the Proteobacteria, with bioremediation candidates detected across sites. Redundancy and principal component analyses revealed that site variability, water-extractable...

Xylariales: First results of mycological exploration in the Sangay and Llanganates National Parks, Ecuador

Thu, 11 Sep 2025 00:00:00 +0000

Fungal samples were collected in the Sangay (SP) and Llanganates (LP) National Parks in Ecuador. Sequences of the internal transcribed spacer regions (ITS1-5.8S-ITS2) of the ribosomal DNA of the samples were analyzed.Taxonomic identification of fungi of the order Xylariales was done through phylogenetic analysis using a Maximun Likelihood method. All analyzed collections presented here belong to the genus Xylaria, of these eight belong to PL and two to SP. Four samples were not identified at the species level, suggesting it could be a new species. This data contributes with base information on the biodiversity of the Parks, necessary to design and implement measures for the conservation of fungi in Ecuador.

New Findings on the Biology and Ecology of the Ecuadorian Amazon Fungus Polyporus leprieurii var. yasuniensis

Thu, 11 Sep 2025 00:00:00 +0000

Polyporus leprieurii var. yasuniensis is a prolific wood-decay fungus inhabiting the forest floor of one of the most biodiverse places on earth, the Yasuní National Park in Ecuador. Basidiocarps and aerial rhizomorphs are commonly found growing on woody debris distributed along the floor of this forest ecosystem. Because of the extraordinary abundance of this fungus in the tropical rainforest, we carried out investigations to better understand the biological and ecological aspects contributing to its prolific distribution. Data on growth inhibition in paired competition studies with sixteen fungal isolates exemplifies defense mechanisms used to defend its territory, including pseudosclerotial plates and the development of a melanized rhizomorphic mat. Results of biomass loss on eleven types of tropical wood in microcosm experiments demonstrated the broad decay capacity of the fungus. In and ex situ observations provided information on how long rhizomorphs can prevail...

Ecuadorian Coptoborus beetles harbor Fusarium and Graphium fungi previously associated with Euwallacea ambrosia beetles

Thu, 11 Sep 2025 00:00:00 +0000

Ambrosia beetles from the scolytine tribe Xyleborini (Curculionidae) are important to the decomposition of woody plant material on every continent except Antarctica. These insects farm fungi on the walls of tunnels they build inside recently dead trees and rely on the fungi for nutrition during all stages of their lives. Such ambrosia fungi rely on the beetles to provide appropriate substrates and environmental conditions for growth. A small minority of xyleborine ambrosia beetle-fungal partnerships cause significant damage to healthy trees. The xyleborine beetle Coptoborus ochromactonus vectors a Fusarium (Hypocreales) fungus that is lethal to balsa (Ochroma pyramidale (Malvaceae)) trees in Ecuador. Although this pathogenic fungus and its associated beetle are not known to be established in the United States, several other non-native ambrosia beetle species are vectors of destructive plant diseases in this country. This fact and the acceleration of trade...

Wildfire‐Induced Losses of Soil Particulate and Mineral‐Associated Organic Carbon Persist for Over 4 Years in a Chaparral Ecosystem

Thu, 11 Sep 2025 00:00:00 +0000

Wildfires can lower soil carbon (C) stocks directly through combustion, but also indirectly during post-fire recovery if microbial C demands outpace photosynthetic C inputs. However, how much C is respired by soil microorganisms post-fire may depend on wildfire effects on particulate organic carbon (POC; mostly plant material accessible to microbes) and/or mineral-associated organic carbon (MAOC; considered C protected by minerals from decomposers), meaning assessment of wildfire impacts on these pools is necessary to predict microbial decomposition rates and, thus, the fate of soil C. Here, we measured POC, MAOC, pyrogenic organic matter C, plant cover, extracellular enzyme activity (EEA), and microbial community abundance and composition 17 days, and 1, 3, and 4 years after the Holy Fire burned 94 km² of fire-adapted chaparral. The wildfire immediately decreased POC by 50% (from 51 ± 21 to 26 ± 6 g C kg^-1) and MAOC by 33% (from 9.3 ± 0.9 to 6.3 ± 0.9 g C kg^-1),...

Taxonomy of the major rhizomorphic species of the “Melanopus group” within Polyporaceae in Yasuní National Park, Ecuador

Thu, 11 Sep 2025 00:00:00 +0000

Yasuní National Park in Ecuador is one of the most biodiverse places on earth. The fungi in this tropical rainforest are also diverse but have received little research attention. This research paper focuses on an important group of fungi in the family Polyporaceae and examines the genera Polyporus, Atroporus, and Neodictyopus that form aerial melanized cord-like structures called rhizomorphs. Phylogenetic analyses, macro and micromorphological descriptions of basidiomata and rhizomorphs, as well as cultural characterization were completed to better understand these ecologically important fungi. Here we describe four new species: Atroporus yasuniensis, Atroporus tagaeri, Neodictyopus sylvaticus, and Polyporus taromenane, and a new variety Polyporus leprieurii var. yasuniensis. The information presented in this study adds important new knowledge about the unusual rhizomorph producing fungi found in Yasuní National Park, Ecuador and other tropical rainforests.

Diverse Xylaria in the Ecuadorian Amazon and their mode of wood degradation

Thu, 11 Sep 2025 00:00:00 +0000

BackgroundXylaria is a diverse and ecologically important genus in the Ascomycota. This paper describes the xylariaceous fungi present in an Ecuadorian Amazon Rainforest and investigates the decay potential of selected Xylaria species. Fungi were collected at Yasuní National Park, Ecuador during two collection trips to a single hectare plot divided into a 10-m by 10-m grid, providing 121 collection points. All Xylaria fruiting bodies found within a 1.2-m radius of each grid point were collected. Dried fruiting bodies were used for culturing and the internal transcribed spacer region was sequenced to identify Xylaria samples to species level. Agar microcosms were used to assess the decay potential of three selected species, two unknown species referred to as Xylaria 1 and Xylaria 2 and Xylaria curta, on four different types of wood from trees growing in Ecuador including balsa (Ochroma pyramidale), melina (Gmelina arborea), saman (Samanea saman), and moral (Chlorophora tinctoria). ANOVA...

Dynamic remodeling of centrioles and the microtubule cytoskeleton in the lifecycle of chytrid fungi.

Thu, 11 Sep 2025 00:00:00 +0000

Cell movement and division are complex behaviors driven by a dynamic internal cytoskeleton. The molecular components and principles of cytoskeletal assembly are well studied, but less is known about cytoskeletal remodeling events, including how centrioles transition from ciliary base to centrosome. Here, we address this using the chytrid Rhizoclosmatium globosum, a zoosporic fungus that has centrioles and cilia, lost in most fungal lineages. Chytrids undergo reorganization of their microtubule cytoskeleton as they grow from zoospore to multinucleated coenocyte. We use evolutionary comparison, RNA-sequencing, and expansion microscopy to understand this reorganization and further develop this organism as a model for evolutionary cell biology. We find that when motile zoospores transition to sessile sporangia, cilia are retracted into the cytoplasm and degraded, while centrioles detach from the ciliary axoneme yet persist. During the mitotic cycles, short centrioles are associated...

Endemic and panglobal genetic groups, and divergence of host-associated forms in worldwide collections of the wheat leaf rust fungus Puccinia triticina as determined by genotyping by sequencing

Thu, 11 Sep 2025 00:00:00 +0000

The wheat leaf rust fungus, Puccinia triticina, is found in the major wheat growing regions of the world and is a leading cause of yield loss in wheat. Populations of P. triticina are highly variable for virulence to resistance genes in wheat and adapt quickly to resistance genes in wheat cultivars. The objectives of this study were to determine the genetic relatedness of worldwide collections of P. triticina using restriction site associated genotyping by sequencing. A total of 558 isolates of P. triticina from wheat producing regions in North America, South America, Europe, the Middle East, Ethiopia, Russia, Pakistan, Central Asia, China, New Zealand, and South Africa were characterized at 6745 single nucleotide loci. Isolates were also tested for virulence to 20 near-isogenic lines that differ for leaf rust resistance genes. Populations that were geographically proximal were also more closely related for genotypes. In addition, groups of isolates within regions that varied...

Effect of Oceanic Islands on an Insect Symbiont Genome in Transition to a Host-Restricted Lifestyle

Fri, 29 Aug 2025 00:00:00 +0000

Islands offer unique opportunities to study adaptive radiations and their impacts on host genome evolution. In Hawaiian Pariaconus psyllids, all species harbor the ancient nutritional symbiont Carsonella, while only free-living and open-gall species on younger islands host a second stable cosymbiont, Makana. In contrast, a third cosymbiont, Malihini, appears to be in an early stage of host restriction and genome degradation, making it a valuable model for understanding symbiont evolution during island radiations. Here, we examine Malihini genome evolution across multiple Pariaconus lineages using 16S rRNA sequencing, metagenomics, phylogenetic reconstruction, and microscopy. We find that Malihini is codiversifying with its hosts on the oldest island Kaua'i (kamua group; open- and closed-gall makers) and on the younger islands only in free-living species (bicoloratus group). Comparison of five Malihini genomes-including three newly assembled in this study-shows ongoing genome reduction...

Kingdom-wide CRISPR guide design with ALLEGRO

Thu, 28 Aug 2025 00:00:00 +0000

Designing CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) single guide RNA (sgRNA) libraries targeting entire kingdoms of life will significantly advance genetic research in diverse and underexplored taxa. Current sgRNA design tools are often species-specific and fail to scale to large, phylogenetically diverse datasets, limiting their applicability to comparative genomics, evolutionary studies, and biotechnology. Here, we introduce ALLEGRO, a combinatorial optimization algorithm designed to compose minimal, yet highly effective sgRNA libraries targeting thousands of species at the same time. Leveraging integer linear programming, ALLEGRO identified compact sgRNA sets simultaneously targeting multiple genes of interest for over 2000 species across the fungal kingdom. We experimentally validated sgRNAs designed by ALLEGRO in Kluyveromyces marxianus, Komagataella phaffii, Yarrowia lipolytica, and Saccharomyces cerevisiae, confirming successful genome...

Genome annotation of Aspergillus melleus strain CBS 546.65

Thu, 28 Aug 2025 00:00:00 +0000

The fungus Aspergillus melleus is an important biosynthesis host for varied commercial applications. Gene annotation of a previously published genome produced 12,841 protein-coding genes and identified 102 biosynthetic gene clusters.

Absolute abundance unveils Basidiobolus as a cross-domain bridge indirectly bolstering gut microbiome homeostasis

Thu, 28 Aug 2025 00:00:00 +0000

The host microbiome is integral to metabolism, immune function, and pathogen resistance. Yet, reliance on relative abundance in microbiome studies introduces compositional biases that obscure ecological interpretation, while the absence of robust tools for absolute abundance quantification has limited biological discovery. Here, we apply absolute abundance profiling to uncover host-specific microbial patterns across herpetofauna orders that are masked in relative abundance data. Relative- and absolute abundance-derived bacterial and fungal microbiomes exhibit divergent profiles shaped by compositional bias and multifactorial effects. Absolute abundance identified key genera, Lactococcus, Parabacteroides, and Cetobacterium in salamanders, and Basidiobolus and Mortierella in lizards, turtles, snakes, and tortoises, that consistently emerged as core taxa, revealing host-associated patterns previously obscured by compositional constraints. In closely related Desmognathus species,...

Activation of the Trichodimerol Pathway through Deletion of mcrA in Marine Penicillium rubens YAP001

Thu, 28 Aug 2025 00:00:00 +0000

Fungal secondary metabolites (SMs) are complex organic compounds comprising a variety of biological activities that are essential in medicine. These natural products can be found in various environments, with studies demonstrating the importance of studying marine-sourced fungi due to the increased potency of the compounds they produce. In this study, we sourced a Penicillium rubens YAP001 strain isolated from Exaiptasia diaphana and explored an avenue for the upregulation of its SMs by combining the one-strain-many-compounds (OSMAC) strategy with genetic manipulation of negative global regulator of secondary metabolism, mcrA. Here, we generated a mcrAΔ strain of marine P. rubens (YAP001), which led to the detection of sorbicillinoids, which is significant due to the prior discovery that these compounds illicit cytotoxic effects that have the potential as an anticancer agent. Specifically, we found that sorbicillin was not only upregulated but...

Phyling: phylogenetic inference from annotated genomes

Thu, 14 Aug 2025 00:00:00 +0000

Phyling is a fast, scalable, and user-friendly tool supporting phylogenomic reconstruction of species phylogenies directly from protein-encoded genomic data. It identifies orthologous genes by searching a sample's protein sequences against a Hidden Markov Models marker set, containing single-copy orthologs, retrieved from the BUSCO database. In the final step, users can choose between consensus and concatenation strategies to construct the species tree from the aligned orthologs. Phyling efficiently resolves large phylogenies by optimizing memory usage and data processing. Its checkpoint system enables users to incrementally add or remove samples without repeating the entire search process. For analyses involving closely related taxa, Phyling supports the use of nucleotide coding sequences, which may capture phylogenetic signals missed by protein sequences. The benchmark results show that Phyling substantially runs faster than OrthoFinder, a Reciprocal Best Hit based method, while...

Giant transposons promote strain heterogeneity in a major fungal pathogen

Thu, 14 Aug 2025 00:00:00 +0000

Fungal infections are difficult to prevent and treat in large part due to strain heterogeneity, which confounds diagnostic predictability. Yet, the genetic mechanisms driving strain-to-strain variation remain poorly understood. Here, we determined the extent to which Starships-giant transposons capable of mobilizing numerous fungal genes-generate genetic and phenotypic variability in the opportunistic human pathogen Aspergillus fumigatus. We analyzed 519 diverse strains, including 11 newly sequenced with long-read technology and multiple isolates of the same reference strain, to reveal 20 distinct Starships that are generating genomic heterogeneity over timescales relevant for experimental reproducibility. Starship-mobilized genes encode diverse functions, including known biofilm-related virulence factors and biosynthetic gene clusters, and many are differentially expressed during infection and antifungal exposure in a strain-specific manner. These...

Celebrating the fifth edition of the International Symposium on Fungal Stress – ISFUS, a decade after its 2014 debut

Thu, 14 Aug 2025 00:00:00 +0000

The Fifth International Symposium on Fungal Stress (ISFUS) brought together in Brazil many of the leaders in the field of fungal stress responses, from fourteen countries, for four days of outstanding science ranging from basic research to studies with agricultural, medical, industrial, and environmental significance. In addition to the excellent oral and poster presentations, the Symposium organisers ensured that all participants had ample opportunity to engage, socialise, and network to exchange ideas and share research. The conference was enhanced by the world-class venue near Iguazu Falls, probably the greatest natural phenomenon in South America.

Revealing cyanosphere microbial diversity of terrestrial cyanobacteria

Thu, 14 Aug 2025 00:00:00 +0000

The cyanosphere contains heterotrophic microorganisms living within the exopolysaccharide sheath of cyanobacteria and serves as an interface between the cyanobacteria and their surrounding ecosystem. The symbiosis between the cyanobacterial host and its cyanosphere microbes spans the mutualistic-antagonistic spectrum. Understanding these relationships will predict the success of terrestrial cyanobacteria and the ecosystem services they provide including primary production in often oligotrophic environments. However, our understanding of the microbial diversity within the cyanosphere is limited. In this study, we used metagenomic sequencing to construct 528 metagenome-assembled genomes (MAGs) from the cyanosphere microbes associated with 50 unialgal terrestrial Cyanobacteria cultures, spanning 12 orders. We found that the composition of cyanosphere microbial communities was unique between Cyanobacteria hosts and was largely influenced by environmental (habitat, precipitation, and...

Draft genome of Conoideocrella luteorostrata ARSEF 14590 (Clavicipitaceae), an entomopathogenic fungus with a wealth of biosynthetic and biocontrol potential

Thu, 14 Aug 2025 00:00:00 +0000

The fungus Conoideocrella luteorostrata is a recently discovered pathogen of invasive elongate hemlock scale insects (EHS; Fiorinia externa) in Christmas tree farms in the eastern U.S. Here, we report a scaffold-level genome and assembly along with an initial survey of biosynthetic gene clusters for strain ARSEF 14590 from EHS.

Draft genome sequence of an uncultured archaeon from Antarctic endolithic communities

Thu, 14 Aug 2025 00:00:00 +0000

A draft genome sequence was assembled and annotated for an uncultured archaeon reconstructed from shotgun metagenomes obtained from Antarctic endoliths. The assembled genome is 1.99 megabases and encodes 2,405 predicted protein-coding genes. This genome sequence provides insights into the microbial diversity and functional potential of extremophiles inhabiting Antarctic rock environments.

Do You Know that there are Fungi in the Ocean?

Thu, 14 Aug 2025 00:00:00 +0000

Did you know that fungi, like mushrooms and molds, are super important for our planet? Fungi can form critical relationships with other organisms. For example, many plants rely on fungi to help them grow and thrive. However, fungi are not always friendly and sometimes they can hurt plants by causing disease. Did you also know that there are fungi in the ocean? While you might not be able to see these fungi when you go to the beach (because they can only be seen with a microscope), they are found everywhere in the ocean. Marine fungi are pretty cool, but we do not know a lot about them yet or what roles they play in the ocean. Scientists are starting to learn more about how marine fungi help the ocean and keep our planet healthy. This article will explore the amazing world of marine fungi!

A comparative study: impact of chemical and biological fungicides on soil bacterial communities

Mon, 9 Jun 2025 00:00:00 +0000

Soil microbial communities play key roles in agroecosystems, particularly in processes like organic matter decomposition and nutrient cycling. However, human activities can negatively impact their community structure and, consequently, soil function. SoilGard and Ridomil are effective methods for controlling carrot cavity spots caused by Pythium spp., but their effects on bacterial taxonomic and metabolic function shifts are not well understood. This study aims to investigate the comparative impact of the chemical fungicide Ridomil and the biological fungicide SoilGard on the bacterial communities in soils cultivated with carrots. Our results showed that both SoilGard and Ridomil significantly impacted soil bacterial diversity, but their effects were distinct and time-dependent. Ridomil had an immediate negative effect on soil bacterial diversity two weeks after treatment, whereas SoilGard was initially less disruptive but showed delayed negative consequences 12 weeks after treatment,...

Comparative Genomics Reveals Intra and Inter Species Variation in the Pathogenic Fungus Batrachochytrium dendrobatidis

Thu, 5 Jun 2025 00:00:00 +0000

The Global Panzootic Lineage (GPL) of Batrachochytrium dendrobatidis (Bd) has been described as a main driver of amphibian extinctions. Pathogen studies have benefited from three Bd-GPL strain genomes, but identifying the genetic and molecular features that distinguish the B. dendrobatidis lineages requires additional high-quality genomes from diverse lineages. We sequenced and assembled genomes with Oxford Nanopore Technologies to produce assemblies of three Bd-BRAZIL isolates and one nonpathogen outgroup species Polyrhizophydium stewartii. The Bd-BRAZIL assembly sizes ranged between 22.0 and 26.1 Mb with 8,495 to 8,620 predicted protein-coding genes. We sought to categorize the pangenome of the species by identifying homologous genes across the sampled genomes as either being core and present in all strains, or accessory and shared among strains in a lineage, an analysis that has not yet been conducted on B. dendrobatidis and its lineages. We identified a core genome consisting...

Section-level genome sequencing and comparative genomics of Aspergillus sections Cavernicolus and Usti

Thu, 22 May 2025 00:00:00 +0000

The genus Aspergillus is diverse, including species of industrial importance, human pathogens, plant pests, and model organisms. Aspergillus includes species from sections Usti and Cavernicolus, which until recently were joined in section Usti, but have now been proposed to be non-monophyletic and were split by section Nidulantes, Aenei and Raperi. To learn more about these sections, we have sequenced the genomes of 13 Aspergillus species from section Cavernicolus (A. cavernicola, A. californicus, and A. egyptiacus), section Usti (A. carlsbadensis, A. germanicus, A. granulosus, A. heterothallicus, A. insuetus, A. keveii, A. lucknowensis, A. pseudodeflectus and A. pseudoustus), and section Nidulantes (A. quadrilineatus, previously A. tetrazonus). We compared these genomes with 16 additional species from Aspergillus to explore their genetic diversity, based on their genome content, repeat-induced point mutations (RIPs), transposable elements, carbohydrate-active enzyme (CAZyme)...

Section-level genome sequencing and comparative genomics of Aspergillus sections Cavernicolus and Usti.

Thu, 8 May 2025 00:00:00 +0000

The genus Aspergillus is diverse, including species of industrial importance, human pathogens, plant pests, and model organisms. Aspergillus includes species from sections Usti and Cavernicolus, which until recently were joined in section Usti, but have now been proposed to be non-monophyletic and were split by section Nidulantes, Aenei and Raperi. To learn more about these sections, we have sequenced the genomes of 13 Aspergillus species from section Cavernicolus (A. cavernicola, A. californicus, and A. egyptiacus), section Usti (A. carlsbadensis, A. germanicus, A. granulosus, A. heterothallicus, A. insuetus, A. keveii, A. lucknowensis, A. pseudodeflectus and A. pseudoustus), and section Nidulantes (A. quadrilineatus, previously A. tetrazonus). We compared these genomes with 16 additional species from Aspergillus to explore their genetic diversity, based...

A cost and community perspective on the barriers to microbiome data reuse

Thu, 8 May 2025 00:00:00 +0000

Microbiome research is becoming a mature field with a wealth of data amassed from diverse ecosystems, yet the ability to fully leverage multi-omics data for reuse remains challenging. To provide a view into researchers' behavior and attitudes towards data reuse, we surveyed over 700 microbiome researchers to evaluate data sharing and reuse challenges. We found that many researchers are impeded by difficulties with metadata records, challenges with processing and bioinformatics, and problems with data repository submissions. We also explored the cost constraints of data reuse at each step of the data reuse process to better understand "pain points" and to provide a more quantitative perspective from sixteen active researchers. The bioinformatics and data processing step was estimated to be the most time consuming, which aligns with some of the most frequently reported challenges from the community survey. From these two approaches, we present evidence-based recommendations for...

Familiar fungal friends and foes Molds, Mushrooms, and Medicines: Our Lifelong Relationship with Fungi Nicholas P. Money (Princeton University Press, Princeton, NJ; 2024) ISBN: 978-0-691236-308

Thu, 8 May 2025 00:00:00 +0000

Familiar fungal friends and foes Molds, Mushrooms, and Medicines: Our Lifelong Relationship with Fungi Nicholas P. Money (Princeton University Press, Princeton, NJ; 2024) ISBN: 978-0-691236-308

Enhancing soil health and nutrient availability for Carrizo citrange (X Citroncirus sp.) through bokashi and biochar amendments: An exploration into indoor sustainable soil ecosystem management

Mon, 14 Apr 2025 00:00:00 +0000

This study investigated the efficacy of organic soil amendments: bokashi (Bok), biochar (BC), and their combination (Bok_BC) in promoting soil health, nutrient availability, and growth of Carrizo citrange (X Citroncirus sp. Rutaceae, Parentage Citrus sinensis × Poncirus trifoliata) under indoor greenhouse settings. Results indicate significant alterations in soil parameters like total carbon (C), total nitrogen (N), and C:N ratio due to Bok, BC, and Bok_BC treatments. BC treatments boosted total C, while Bok increased total N, compared to controls. A note-worthy 25 % average decrease in C:N ratio was observed with Bok and Bok_BC, nearing the optimal 24:1 C:N for microbial growth. This highlights the potential of waste by-products in balancing nutrient release to benefit soil health and plant development. Analysis of nitrite (NO2-), nitrate (NO3-), and ammonium (NH4-N) levels revealed a dynamic relationship between soil treatments and time. Bok and Bok_BC amendments...

Nitrogen Availability and Changes in Precipitation Alter Microbially Mediated NO and N2O Emissions From a Pinyon–Juniper Dryland

Thu, 10 Apr 2025 00:00:00 +0000

Climate change is altering precipitation regimes that control nitrogen (N) cycling in terrestrial ecosystems. In ecosystems exposed to frequent drought, N can accumulate in soils as they dry, stimulating the emission of both nitric oxide (NO; an air pollutant at high concentrations) and nitrous oxide (N₂O; a powerful greenhouse gas) when the dry soils wet up. Because changes in both N availability and soil moisture can alter the capacity of nitrifying organisms such as ammonia-oxidizing bacteria (AOB) and archaea (AOA) to process N and emit N gases, predicting whether shifts in precipitation may alter NO and N₂O emissions requires understanding how both AOA and AOB may respond. Thus, we ask: How does altering summer and winter precipitation affect nitrifier-derived N trace gas emissions in a dryland ecosystem? To answer this question, we manipulated summer and winter precipitation and measured AOA- and AOB-derived N trace gas emissions, AOA and AOB abundance,...

Nitrogen Availability and Changes in Precipitation Alter Microbially Mediated NO and N2O Emissions From a Pinyon–Juniper Dryland

Mon, 7 Apr 2025 00:00:00 +0000

Using Genomes and Evolutionary Analyses to Screen for Host-Specificity and Positive Selection in the Plant Pathogen Xylella fastidiosa

Fri, 4 Apr 2025 00:00:00 +0000

Xylella fastidiosa infects several economically important crops in the Americas, and it also recently emerged in Europe. Here, using a set of Xylella genomes reflective of the genus-wide diversity, we performed a pan-genome analysis based on both core and accessory genes for two purposes: (i) to test associations between genetic divergence and plant host species and (ii) to identify positively selected genes that are potentially involved in arms-race dynamics. For the former, tests yielded significant evidence for the specialization of X. fastidiosa to plant host species. This observation contributes to a growing literature suggesting that the phylogenetic history of X. fastidiosa lineages affects the host range. For the latter, our analyses uncovered evidence of positive selection across codons for 5.3% (67 of 1,257) of the core genes and 5.4% (201 of 3,691) of the accessory genes. These genes are candidates to encode interacting factors with plant and insect hosts. Most...

Diversity of sulfur cycling halophiles within the Salton Sea, California’s largest lake

Thu, 3 Apr 2025 00:00:00 +0000

BackgroundMicroorganisms are the biotic foundation for nutrient cycling across ecosystems, and their assembly is often based on the nutrient availability of their environment. Though previous research has explored the seasonal lake turnover and geochemical cycling within the Salton Sea, California’s largest lake, the microbial community of this declining ecosystem has been largely overlooked. We collected seawater from a single location within the Salton Sea at 0 m, 3 m, 4 m, 5 m, 7 m, 9 m, 10 m, and 10.5 m depths in August 2021, December 2021, and April 2022.ResultsWe observed that the water column microbiome significantly varied by season (R2 = 0.59, P = 0.003). Temperature (R2 = 0.27, P = 0.004), dissolved organic matter (R2 = 0.13, P = 0.004), and dissolved oxygen (R2 = 0.089, P = 0.004) were significant drivers of seasonal changes in microbial composition. In addition, several halophilic mixotrophs and other extremotolerant bacteria...

Whole genome sequence of five strains of Spiroplasma citri isolated from different host plants and its leafhopper vector

Fri, 7 Mar 2025 00:00:00 +0000

ObjectivesSpiroplasma citri is a bacterium with a wide host range and is the causal agent of citrus stubborn and brittle root diseases of citrus and horseradish, respectively. S. citri is transmitted in a circulative, persistent manner by the beet leafhopper, Neoaliturus (Circulifer) tenellus (Baker), in North America. Five strains of S. citri were cultured from citrus, horseradish, and N. tenellus from different habitats and times. DNA from cultures were sequenced and genome assembled to expand the database to improve detection assays and better understand its genetics and evolution.Data descriptionThe whole genome sequence of five strains of S. citri are described herein. The S. citri chromosome was circularized for all five strains and ranged from 1,576,550 to 1,742,208 bp with a G + C content of 25.4–25.6%. Characterization of extrachromosomal DNAs resulted in identification of one or two plasmids, with a G + C content of 23.3 to 27.6%, from plant hosts; and eight or...

Wildfire impact on soil microbiome life history traits and roles in ecosystem carbon cycling

Fri, 7 Mar 2025 00:00:00 +0000

Wildfires, which are increasing in frequency and severity with climate change, reduce soil microbial biomass and alter microbial community composition and function. The soil microbiome plays a vital role in carbon (C) and nitrogen (N) cycling, but its complexity makes it challenging to predict post-wildfire soil microbial dynamics and resulting impacts on ecosystem biogeochemistry. The application of biogeochemically relevant conceptual trait-based frameworks to the soil microbiome can distill this complexity, enabling enhanced predictability of soil microbiome recovery following wildfire and subsequent impacts to biogeochemical cycles. Conceptual frameworks that have direct links to soil C and N cycling have been developed for the soil microbiome; the Y-A-S framework overviews soil microbiome life history strategies that have tradeoffs with one another and others have proposed frameworks specific to wildfire. Here, we aimed to delineate post-wildfire changes of bacterial traits...

Transcriptome Analysis of Citrus Dwarfing Viroid Induced Dwarfing Phenotype of Sweet Orange on Trifoliate Orange Rootstock

Fri, 7 Mar 2025 00:00:00 +0000

Dwarfed citrus trees for high-density plantings or mechanized production systems will be key for future sustainable citrus production. Citrus trees consist of two different species of scion and rootstock. Therefore, any observed phenotype results from gene expression in both species. Dwarfed sweet orange trees on trifoliate rootstock have been produced using citrus dwarfing viroid (CDVd). We performed RNA-seq transcriptome analysis of CDVd-infected stems and roots and compared them to non-infected controls. The identified differentially expressed genes validated with RT-qPCR corresponded to various physiological and developmental processes that could be associated with the dwarfing phenotype. For example, the transcription factors MYB13 and MADS-box, which regulate meristem functions and activate stress responses, were upregulated in the stems. Conversely, a calcium-dependent lipid-binding protein that regulates membrane transporters was downregulated in the roots. Most transcriptome...

Phoronids and their tubes harbor distinct microbiomes compared to surrounding sediment

Mon, 10 Feb 2025 00:00:00 +0000

Abstract Phoronids are a phylum of animals with only ∼12 described species, all of which are marine filter feeders that build external tubes for shelter and produce chemical deterrents against predators. Many tube-building invertebrates host distinct microbial communities and even have obligate symbionts for survival in sulfur-rich marine sediments. However, the microbiome of phoronids has yet to be comprehensively described. To address this, we surveyed the composition of the microbiome of the phoronid, Phoronopsis harmeri , using 16S rRNA gene amplicon and metagenomic sequencing. We found that the phoronid microbiome was dominated by members of the orders Campylobacterales, Desulfobulbales, and Desulfobacterales. We also found that the microbiomes of tubes and phoronids were less diverse than that of surrounding sediment, and that the microbiomes of phoronids, tubes and surrounding sediment were all distinctly structured. Based on analysis of metagenomic data, and even though...

Maternal probiotic supplementation protects against PBDE-induced developmental, behavior and metabolic reprogramming in a sexually dimorphic manner: Role of gut microbiome

Mon, 10 Feb 2025 00:00:00 +0000

Polybrominated diphenyl ethers (PBDEs) are endocrine-disrupting persistent organic pollutants (POPs) used as flame retardants in a wide range of commercial applications. We have previously reported neurobehavioral and metabolic reprogramming produced by developmental PBDEs. PBDEs perturb the microbiome, an influencer of life-long health, while probiotic supplementation with Limosilactobacillus reuteri (LR) can avert neurobehavioral and endocrine disruption. We, therefore, tested the hypothesis that perinatal maternal LR supplementation would protect gut microbiome richness and diversity, developmental milestones, adult neurobehavior and metabolic homeostasis in PBDE-exposed offspring. C57BL/6N dams were orally exposed to a commercial penta-mixture of PBDEs, DE-71, at 0.1 mg/kg/day, or corn oil vehicle (VEH/CON) during gestation and lactation. Mice offspring received DE-71 or VEH/CON with or without co-administration of LR (ATCC-PTA-6475) indirectly via their mother from gestational...

Genomic streamlining of seagrass-associated Colletotrichum sp. may be related to its adaptation to a marine monocot host

Mon, 10 Feb 2025 00:00:00 +0000

Abstract Colletotrichum spp. have a complicated history of association with land plants. Perhaps most well-known as plant pathogens for the devastating effect they can have on agricultural crops, some Colletotrichum spp. have been reported as beneficial plant endophytes. However, there have been only a handful of reports of Colletotrichum spp. isolated from aquatic plant hosts and their ecological role in the marine ecosystem is underexplored. To address this, we present the draft genome and annotation of Colletotrichum sp. CLE4, previously isolated from rhizome tissue from the seagrass Zostera marina . This genome (48.03 Mbp in length) is highly complete (BUSCO ascomycota: 98.8%) and encodes 12,015 genes, of which 5.7% are carbohydrate-active enzymes (CAZymes) and 12.6% are predicted secreted proteins. Phylogenetic placement puts Colletotrichum sp. CLE4 within the C. acutatum complex, closely related to C. godetiae . We found a 8.69% smaller genome size, 21.90% smaller gene...

Rhinocladiella similis: A Model Eukaryotic Organism for Astrobiological Studies on Microbial Interactions with Martian Soil Analogs

Thu, 6 Feb 2025 00:00:00 +0000

The exploration of our solar system for microbial extraterrestrial life is the primary goal of several space agencies. Mars has attracted substantial attention owing to its Earth-like geological history and potential niches for microbial life. This study evaluated the suitability of the polyextremophilic fungal strain Rhinocladiella similis LaBioMMi 1217 as a model eukaryote for astrobiology. Comprehensive genomic analysis, including taxonomic and functional characterization, revealed several R. similis genes conferring resistance to Martian-like stressors, such as osmotic pressure and ultraviolet radiation. When cultured in a synthetic Martian regolith (MGS-1), R. similis exhibited altered morphology and produced unique metabolites, including oxylipins, indolic acid derivatives, and siderophores, which might be potential biosignatures. Notably, oxylipins were detected using laser desorption ionization mass spectrometry, a technique slated for its use in the...

Draft genome sequences for Neonectria magnoliae and Neonectria punicea, canker pathogens of Liriodendron tulipifera and Acer saccharum in West Virginia

Tue, 28 Jan 2025 00:00:00 +0000

The fungal genus Neonectria contains many phytopathogenic species currently impacting forests and fruit trees worldwide. Despite their importance, a majority of Neonectria spp. lack sufficient genomic resources to resolve suspected cryptic species. Here, we report draft genomes and assemblies for Neonectria magnoliae NRRL 64651 and Neonectria punicea NRRL 64653.

Characterisation of the genetic diversity of citrus viroid VII using amplicon sequencing

Mon, 20 Jan 2025 00:00:00 +0000

Viroids occur in plants as swarms of sequence variants clustered around a dominant variant, leading to adoption of the term ‘quasispecies’ to describe the viroid population in an individual host. The composition of the quasispecies can potentially change according to the age of the infection, the position of the leaf or branch in the canopy, and the host species. The primary aim of this study was to investigate the quasispecies concept for citrus viroid VII (CVd-VII), a recently discovered member of the family Pospiviroidae. Three experiments were conducted to determine factors affecting viroid variability (i) within different tissues of a lemon plant, (ii) among different plants of the same species (citron), and (iii) among different species and hybrids of citrus. Using two primer sets to produce amplicons for high-throughput sequencing, viroid population profiles were generated for each sample. The number of variants that were identified with both primer sets ranged from 2 to...

RNAseq and targeted metabolomics implicate RIC8 in regulation of energy homeostasis, amino acid compartmentation, and asexual development in Neurospora crassa

Fri, 20 Dec 2024 00:00:00 +0000

Heterotrimeric G protein signaling pathways control growth and development in eukaryotes. In the multicellular fungus Neurospora crassa, the guanine nucleotide exchange factor RIC8 regulates heterotrimeric Gα subunits. In this study, we used RNAseq and liquid chromatography-mass spectrometry (LC-MS) to profile the transcriptomes and metabolomes of N. crassa wild type, the Gα subunit mutants Δgna-1 and Δgna-3, and Δric8 strains. These strains exhibit defects in growth and asexual development (conidiation), with wild-type and Δgna-1 mutants producing hyphae in submerged cultures, while Δgna-3 and Δric8 mutants develop conidiophores, particularly in the Δric8 mutant. RNAseq analysis showed that the Δgna-1 mutant possesses 159 mis-regulated genes, while Δgna-3 and Δric8 strains have more than 1,000 each. Many of the mis-regulated genes are involved in energy homeostasis, conidiation, or metabolism....

Regulator of G Protein Signaling Proteins Control Growth, Development and Cellulase Production in Neurospora crassa

Fri, 6 Dec 2024 00:00:00 +0000

Heterotrimeric (αβγ) G protein signaling pathways are critical environmental sensing systems found in eukaryotic cells. Exchange of GDP for GTP on the Gα subunit leads to its activation. In contrast, GTP hydrolysis on the Gα is accelerated by Regulator of G protein Signaling (RGS) proteins, resulting in a return to the GDP-bound, inactive state. Here, we analyzed growth, development and extracellular cellulase production in strains with knockout mutations in the seven identified RGS genes (rgs-1 to rgs-7) in the filamentous fungus, Neurospora crassa. We compared phenotypes to those of strains with either knockout mutations or expressing predicted constitutively activated, GTPase-deficient alleles for each of the three Gα subunit genes (gna-1^Q204L, gna-2^Q205L or gna-3^Q208L). Our data revealed that six RGS mutants have taller aerial hyphae than wild type and all seven mutants exhibit reduced asexual sporulation,...

Multiple calcium signaling genes play a role in the circadian period of Neurospora crassa

Fri, 6 Dec 2024 00:00:00 +0000

The Ca2+ signaling genes cpe-1, plc-1, ncs-1, splA2, camk-1, camk-2, camk-3, camk-4, cmd, and cnb-1 are necessary for a normal circadian period length in Neurospora crassa. In addition, the Q10 values ranged between 0.8 and 1.2 for the single mutants lacking cpe-1, splA2, camk-1, camk-2, camk-3, camk-4, and cnb-1, suggesting that the circadian clock exhibits standard temperature compensation. However, the Q10 value for the ∆plc-1 mutant was 1.41 at 25 and 30 °C, 1.53 and 1.40 for the ∆ncs-1 mutant at 20 and 25 °C, and at 20 and 30 °C, respectively, suggesting a partial loss of temperature compensation in these two mutants. Moreover, expression of frq, a regulator of the circadian period, and the blue light receptor wc-1, were increased >2-fold in the Δplc-1, ∆plc-1; ∆cpe-1, and the ∆plc-1; ∆splA2 mutants at 20 °C. The frq mRNA level was increased >2-fold in the Δncs-1 mutant compared to the ras-1bd strain at 20 °C. Therefore, multiple Ca2+ signaling genes regulate the circadian...

Nanocarrier mediated delivery of insecticides into tarsi enhances stink bug mortality

Tue, 19 Nov 2024 00:00:00 +0000

Current delivery practices for insecticide active ingredients are inefficient with only a fraction reaching their intended target. Herein, we developed carbon dot based nanocarriers with molecular baskets (γ-cyclodextrin) that enhance the delivery of active ingredients into insects (southern green stink bugs, Nezara viridula L.) via their tarsal pores. Nezara viridula feeds on leguminous plants worldwide and is a primary pest of soybeans. After two days of exposure, most of the nanocarriers and their active ingredient cargo (>85%) remained on the soybean leaf surface, rendering them available to the insects. The nanocarriers enter stink bugs through their tarsi, enhancing the delivery of a fluorescent chemical cargo by 2.6 times. The insecticide active ingredient nanoformulation (10 ppm) was 25% more effective in controlling the stink bugs than the active ingredient alone. Styletectomy experiments indicated that the improved active ingredient efficacy was due to the nanoformulation...

Three New Records of Ascomycetes Isolates from Field Soils in Korea

Mon, 11 Nov 2024 00:00:00 +0000

Three new records of Ascomycota species (Chaetomium acropullum, Phialemonium globosum, Phialemonium atrogriseum) from field soils in Korea are presented in this study. These newly discovered fungal isolates were isolated from field soils from various places across Gyeongnam, Korea in 2016. All the isolates were identified and described based on morphological characteristics, and rDNA internal transcribed spacer and β-tubulin gene sequence data. Morphological features of these fungal species were studied on different agar media: potato dextrose agar, oatmeal agar, malt extract agar, Czapek yeast extract agar, and yeast extract sucrose agar. Full description and illustrations of their morphological characters are provided. These fungal species have not officially been previously reported in Korea.

Discovery of Two Chrysosporium Species with Keratinolytic Activity from Field Soil in Korea

Mon, 11 Nov 2024 00:00:00 +0000

In an ongoing survey of Korean indigenous fungi, two fungal strains (KNU16-74 and KNU16-99) belonging to the genus Chrysosporium were isolated from field soil in Gyeongnam, Korea. Morphological characterization and phylogenetic analysis using sequence of the internal transcribed spacer regions were carried out to confirm its precise identification. These strains were identified as Chrysosporium indicum (KNU16-74) and Chrysosporium fluviale (KNU16-99). To examine the keratin degradation efficiency of these two fungal species, human hair strands were incubated with fungus culture. Results revealed that these two fungal species have the ability to degrade keratin substrate. This is the first report of these two species in Korea.

Deciphering key factors in pathogen-suppressive microbiome assembly in the rhizosphere

Fri, 8 Nov 2024 00:00:00 +0000

In a plant-microbe symbiosis, the host plant plays a key role in promoting the association of beneficial microbes and maintaining microbiome homeostasis through microbe-associated molecular patterns (MAMPs). The associated microbes provide an additional layer of protection for plant immunity and help in nutrient acquisition. Despite identical MAMPs in pathogens and commensals, the plant distinguishes between them and promotes the enrichment of beneficial ones while defending against the pathogens. The rhizosphere is a narrow zone of soil surrounding living plant roots. Hence, various biotic and abiotic factors are involved in shaping the rhizosphere microbiome responsible for pathogen suppression. Efforts have been devoted to modifying the composition and structure of the rhizosphere microbiome. Nevertheless, systemic manipulation of the rhizosphere microbiome has been challenging, and predicting the resultant microbiome structure after an introduced change is difficult. This...

Rapid Loss of Nutritional Symbionts in an Endemic Hawaiian Herbivore Radiation Is Associated with Plant Galling Habit

Fri, 8 Nov 2024 00:00:00 +0000

Insect herbivores frequently cospeciate with symbionts that enable them to survive on nutritionally unbalanced diets. While ancient symbiont gain and loss events have been pivotal for insect diversification and feeding niche specialization, evidence of recent events is scarce. We examine the recent loss of nutritional symbionts (in as little as 1 MY) in sap-feeding Pariaconus, an endemic Hawaiian insect genus that has undergone adaptive radiation, evolving various galling and free-living ecologies on a single host-plant species, Metrosideros polymorpha within the last ∼5 MY. Using 16S rRNA sequencing, we investigated the bacterial microbiomes of 19 Pariaconus species and identified distinct symbiont profiles associated with specific host-plant ecologies. Phylogenetic analyses and metagenomic reconstructions revealed significant differences in microbial diversity and functions among psyllids with different host-plant ecologies. Within a few millions of years, Pariaconus species...

Determinants of raffinose family oligosaccharide use in Bacteroides species

Sat, 2 Nov 2024 00:00:00 +0000

Bacteroides species are successful colonizers of the human colon and can utilize a wide variety of complex polysaccharides and oligosaccharides that are indigestible by the host. To do this, they use enzymes encoded in polysaccharide utilization loci (PULs). While recent work has uncovered the PULs required for the use of some polysaccharides, how Bacteroides utilize smaller oligosaccharides is less well studied. Raffinose family oligosaccharides (RFOs) are abundant in plants, especially legumes, and consist of variable units of galactose linked by α-1,6 bonds to a sucrose (glucose α-1-β-2 fructose) moiety. Previous work showed that an α-galactosidase, BT1871, is required for RFO utilization in Bacteroides thetaiotaomicron. Here, we identify two different types of mutations that increase BT1871 mRNA levels and improve B. thetaiotaomicron growth on RFOs. First, a novel spontaneous duplication of BT1872 and BT1871 places these genes...

Whole-Genome Sequence of Pseudomonas frederiksbergensis Strain A6, Isolated from the Rhizosphere of Pepper (Capsicum annuum L.)