Metagenomic survey of fungal communities in compost from dairy plant wastewater sludge and garden trimmings

Abstract

Background

Composting converts organic residues into stable organic matter and nutrients under aerobic conditions, improving soil properties and microbiome balance, while mitigating environmental impacts. Although microbiomes of various compost types have been studied, information is still fragmented and often not tailored to specific raw material combinations. In particular, little is known about the fungal communities involved in composting dairy plant wastewater sludge mixed with garden trimmings. This data paper contributes to filling that gap by providing a comprehensive taxonomic inventory.

New information

We provide a fungus-focused dataset from 18 compost samples generated from a 1:1 (w/w) mix of garden trimmings and dairy plant wastewater sludge, collected at three process stages (thermophilic start/end; mid-cooling and maturation) under two turning regimes. Shotgun metagenomes were taxonomically annotated against NCBI taxonomy (accessed 19 Feb 2025). Only Fungi were detected within Eukarya, spanning nine phyla; Ascomycota (60.8%), Mucoromycota (17.76%), Basidiomycota (8.50%) and Chytridiomycota (7.21%) comprised 94.27% of the taxonomic features. We report 417 genera (13 >1% relative abundance each); top: Aspergillus (17.93%), Rhizopus (8.61%), Chaetomium (4.83%), Aureobasidium (3.09%), Madurella (2.85%), Paramicrosporidium (2.71%), Rhizophagus (1.88%), Rasamsonia (1.81%), Hyaloraphidium (1.39%), Thermochaetoides (1.31%), Talaromyces (1.19%), Trichoderma (1.15%), Podospora (1.06%) comprised 49.81% of the taxonomic feature abundance. Overall 663 taxa were identified (578 species, 416 genera, 230 families, 106 orders, 48 classes and 9 phyla). The dataset (DwCA; 663 occurrences) is intended to serve as a reference for compost mycobiomes and will be available via GBIF (DOI 10.15468/nmpzwr).

Introduction

Composting is an aerobic process, in which microorganisms decompose organic matter into more stable compounds. The resulting product can be applied in agriculture as an organic fertiliser that improves soil physical properties, enriches the microbiome and enhances crop health while also contributing to nutrient recycling. In addition, composting reduces the environmental impact of organic residue accumulation and lowers sanitary risks through the pasteurisation effect of the thermophilic stage, which eliminates most coliform bacteria (Lin et al. 2018).

Sewage sludge, when co-composted with lignocellulosic materials, produces a stabilied, nutrient-enriched product. Nitrogen-rich wastes, such as food residues, manure and sewage sludge (C/N = 10–20), are typically combined with carbon-rich biomass (C/N > 50), which balances the C/N ratio and improves aeration while reducing leachate (Lin et al. 2018, Tarpani et al. 2020, Hoang et al. 2022). Composting also facilitates the dissipation of organic contaminants, including polycyclic aromatic hydrocarbons, pharmaceuticals, antibiotic-resistance genes and microplastics (Hoang et al. 2022).

Compared with anaerobic digestion, lime treatment, pyrolysis or incineration, composting offers several advantages, including nutrient recovery, low investment and operational costs, suitability for small- and medium-scale facilities and the potential to substitute chemical fertilisers. However, disadvantages include variable greenhouse gas emissions, high energy demand, requirement for large processing areas, limited volume reduction and no energy recovery (Hoang et al. 2022, Yu et al. 2023).

Microbial activity during composting is stage-dependent: bacteria dominate during the mesophilic and thermophilic phases, whereas fungi become more active during cooling and maturation (Tuomela et al. 2000). Labile compounds, such as sugars, starch, amino acids and lipids, are degraded early, releasing CO₂ and ammonia, whereas more recalcitrant polymers (cellulose, hemicellulose and lignin) are broken down later, contributing to humus formation. Fungi play a particularly important role due to their extracellular enzyme production, which enables the degradation of complex polymers and facilitates microbial interactions within compost piles (Awasthi et al. 2023).

General description

Purpose

This dataset provides information on the fungal community associated with the composting process. Composting is a biologically driven degradation process in which organic matter is transformed into a stable and nutrient-rich product. Fungi play an essential role in this process because of their ability to degrade complex polymers such as cellulose, hemicellulose and lignin, thereby accelerating organic matter decomposition and influencing the final quality of compost. The dataset was generated to document the diversity and taxonomic composition of fungi present in the composting material. The present Data Paper does not aim to evaluate treatment and compost stage effects (which will be addressed in a future article), but rather to provide baseline information for applied microbiology, waste management and soil fertility studies.

Project description

Title

Metagenomic Survey of Compost Fungi from Terceira (Azores Archipelago)

Personnel

The project was conceived by Paulo Monjardino.

Fieldwork: Cátia Pereira, Paulo Monjardino.

Database management: Paulo Monjardino.

Darwin Core Database management: Paulo A. V. Borges & Paulo Monjardino.

Funding

VERCOCHAR - Vermicompost, compost y biochar, herramientas para la adaptación al cambio climático, la prevención y mitigación de los efectos derivados de los riesgos naturales en el medio agrícola y forestal, MAC2/3.5b/307, FCT—Fundação para a Ciência e a Tecnologia, I.P., project UIDB/05292/2025 DOI https://doi.org/10.54499/UID/05292/2025 and from the Azorean Regional Directorate of Science, Innovation and Development, through the PROSCIENTIA Incentive System, Ref. M1.1. A/FUNC.UI&D/016/2025).

Sampling methods

Sampling description

Compost Production

Composting was performed at an open-air, industrial-scale facility operated by Teramb – Empresa Municipal de Gestão e Valorização Ambiental da Ilha Terceira, EM (38.67583° N, −27.17433° W). Wastewater sludge from a dairy processing plant was mixed with garden trimmings at a 1:1 (w/w) ratio. Garden trimmings were made of trees and shrubs branches (no more than 15 cm diameter), palm leaves, grass cuttings and garden herbaceous ornamentals. Two windrow-turning regimes were applied: (i) triweekly during the thermophilic stage and weekly during the cooling and maturation stages and (ii) once every three weeks throughout all stages.

Sample Collection and DNA Extraction

Samples were collected at the beginning and end of the thermophilic stage and at the mid-cooling and maturation. Material was obtained by digging 50–60 cm into the piles, ≈ 1 m above the ground, from three zones (external and middle) and bulked into composite samples. Each sample (200–300 g) was placed in a sterile bag and transported to the laboratory.

Samples were homogenied in PBS (pH 7.4), centrifuged, and the pellets were stored at −80 °C. Metagenomic DNA was extracted using the repeated bead-beating method (Yu and Morrison 2018) combined with a Quick-DNA Miniprep Plus Kit (Zymo Research 2017). DNA concentration and purity were measured using a NanoDrop spectrophotometer (Thermo Scientific, USA) and stored at −20 °C.

Shotgun Sequencing

Shotgun metagenomic sequencing was performed by Novogene (Cambridge, UK) on the Illumina NovaSeq 6000 platform (Illumina, San Diego, CA, USA), which provides high accuracy, scalability, and sequencing depth for complex microbiome studies (NOVOGENE 2023).

Genomic DNA (200 ng) was randomly sheared into ≈ 350 bp fragments using a Covaris ultrasonic disruptor. Libraries were prepared using Novogene NGS DNA Library Prep Set (Cat. No. PT004). Briefly, the fragmented DNA underwent end repair and A-tailing to produce blunt ends with adenine overhangs, followed by ligation of Illumina sequencing adapters containing unique barcodes. Size selection was performed to retain fragments of 350–450 bp by using AMPure XP beads (Beckman Coulter, USA). To enrich adapter-ligated fragments, PCR amplification was carried out when DNA input was low; for high-input samples, PCR-free preparation was applied to minimise bias.

Library quality was verified by fragment integrity and insert size analysis (AATI) and the effective library concentration was quantified by qPCR (> 3 nM). Qualified libraries were pooled in equimolar amounts and sequenced using the Illumina NovaSeq 6000 platform with two-channel sequencing-by-synthesis (SBS) chemistry. Paired-end sequencing (PE150) was employed to provide high-accuracy reads and improve the assembly performance, with error rates below 1%.

Bioinformatics Analysis

Raw reads were filtered using Trimmomatic v.0.39 to obtain high-quality clean data for downstream analysis. Reads from each sample were assembled individually to recover information from low-abundance species and the unused reads were pooled for mixed assembly using the metaSPAdes v.4.1.0 assembler. Gene prediction was carried out using MetaGeneMark v.3.25, based on the scaftigs that were assembled by single and mixed samples. The predicted genes were pooled and dereplicated to construct a non-redundant gene catalogue. Gene abundance for each sample was quantified by mapping reads back to this catalogue using a read mapper (Bowtie v.2.5.4). Taxonomic annotation was obtained for metagenomic reads against the microNR database, a curated collection of taxonomically informative gene families, using sequence alignment software called DIAMOND v.2.1.12. Taxon-specific abundance profiles were inferred from gene abundance estimates and aggregated to generate taxonomic feature tables at multiple taxonomic ranks. The taxonomic hierarchy of all fungal taxa was standardised and updated according to the NCBI Taxonomy database (accessed April 2025) using the taxize v.0.10.0 package in R v.4.5.1.

The data presented in this article originate from a composite analysis of 18 samples and represent the mean value across the entire sample set.

Geographic coverage

Description

Terceira Island, Azores Archipelago, Portugal. Solid waste processing centre managed by Teramb – Empresa Municipal de Gestão e Valorização Ambiental da Ilha Terceira, EM. In Terceira Island (Azores Archipelago).

Coordinates

38.676 and 38.676 Latitude; -27.174 and -27.174 Longitude.

Taxonomic coverage

Description

The following Phyla are covered: Ascomycota, Basidiomycota, Blastocladiomycota, Chytridiomycota, Cryptomycota, Microsporidia, Mucoromycota, Olpidiomycota, Zoopagomycota.

The following Classes are covered: Agaricomycetes, Arthoniomycetes, Basidiobolomycetes, Blastocladiomycetes, Candelariomycetes, Chytridiomycetes, Coniocybomycetes, Dacrymycetes, Dimargaritomycetes, Dipodascomycetes, Dothideomycetes, Endogonomycetes, Entomophthoromycetes, Eurotiomycetes, Exobasidiomycetes, Geoglossomycetes, Glomeromycetes, Harpellomycetes, Kickxellomycetes, Lecanoromycetes, Leotiomycetes, Lichinomycetes, Lipomycetes, Malasseziomycetes, Microbotryomycetes, Mixiomycetes, Monoblepharidomycetes, Mortierellomycetes, Mucoromycetes, Neolectomycetes, Neocallimastigomycetes, Olpidiomycetes, Orbiliomycetes, Pezizomycetes, Physodermatomycetes, Pichiomycetes, Pneumocystomycetes, Pucciniomycetes, Saccharomycetes, Schizosaccharomycetes, Sordariomycetes, Taphrinomycetes, Tremellomycetes, Umbelopsidomycetes, Ustilaginomycetes, Wallemiomycetes, Xylobotryomycetes, Zoopagomycetes.

Taxa included

Rank	Scientific Name	Common Name
kingdom	Fungi	Fungi

Temporal coverage

Data range: 2022-3-14 – 2022-11-28.

Notes

The presented data were obtained from 18 samples collected between March 14, 2022 and November 28, 2022. DNA extraction was performed between March 8 and May 19, 2023, and sequencing analysis was completed in August 2023 (exact date unknown).

Usage licence

Usage licence

Creative Commons Public Domain Waiver (CC-Zero)

Data resources

Data package title

Metagenomic Survey of Compost Fungi from Terceira (Azores Archipelago)

Resource link

https://ipt.gbif.pt/ipt/resource?r=compost_eukarya

Alternative identifiers

https://www.gbif.org/dataset/e3b9f473-b41e-427e-89fc-990c973c8e05

Number of data sets

1

Data set 1.

Data set name

Occurrence Table

Data format

Darwin Core Archive

Character set

UTF-8

Download URL

https://ipt.gbif.pt/ipt/resource?r=compost_eukarya

Data format version

1.3

Description

The dataset was published in the Global Biodiversity Information Facility platform, GBIF (Monjardino et al. 2026). The following data-table includes all the records for which a taxonomic identification of the species was possible. The dataset submitted to GBIF is structured as a sample occurrence dataset that has been published as a Darwin Core Archive (DwCA), which is a standardised format for sharing biodiversity data as a set of one or more data tables. The core data file contains 663 records (eventID; and occurrenceID). This GBIF IPT (Integrated Publishing Toolkit, Version 2.5.6) archives the data and, thus, serves as the data repository. The data and resource metadata are available for download in the Portuguese GBIF Portal IPT (Monjardino et al. 2026).

Data set 1.

Column label	Column description
id	Identifier generated by GBIF IPT.
type	The nature or genre of the resource.
licence	Reference to the licence under which the record is published.
institutionID	An identifier for the institution publishing the data.
institutionCode	The code of the institution publishing the data.
basisOfRecord	The nature of the data record (MaterialSample).
occurrenceID	Identifier of the record, coded as a global unique identifier.
recordedBy	A list (concatenated and separated) of names of people, groups or organisations who performed the sampling in the field.
organismQuantity	A number or enumeration value for the quantity of Organisms.
organismQuantityType	The type of quantification system used for the quantity of organisms.
eventID	Identifier of the events, unique for the dataset
eventDate	The date-time or interval during which an Event occurred.
year	Year the sample was collected.
eventRemarks	Comments or notes about the dwc:Event.
habitat	The surveyed habitat, in this case, a waste management site.
samplingProtocol	The sampling protocol used to capture the species.
sampleSizeValue	A numeric value for a measurement of the size (time duration, length, area or volume) of a sample in a sampling dwc:Event.
sampleSizeUnit	The unit of measurement of the size (time duration, length, area or volume) of a sample in a sampling dwc:Event.
locationID	Identifier of the location.
islandGroup	The name of the island group in which the Location occurs (Azores Archipelago).
island	The name of the island on which the Location occurs (Terceira).
country	The full, unabbreviated name of the next smaller administrative region than stateProvince (county, shire, department etc.) in which the Location occurs (Portugal).
countryCode	The standard code for the country in which the Location occurs (PT).
stateProvince	The name of the next smaller administrative region than country (state, province, canton, department, region etc.) in which the Location occurs.
municipality	The full, unabbreviated name of the next smaller administrative region than county (city, municipality etc.) in which the Location occurs.
locality	The specific description of the place.
minimumElevationInMetres	The lower limit of the range of elevation (altitude, usually above sea level), in metres.
decimalLatitude	Approximate centre point decimal latitude of the field site in GPS coordinates.
decimalLongitude	Approximate centre point decimal longitude of the field site in GPS coordinates.
geodeticDatum	Standard Global Positioning System coordinate reference for the location of the sample collection points.
coordinateUncertaintyInMetres	Uncertain value of coordinate metrics.
coordinatePrecision	Value in decimal degrees to a precision of six decimal places.
georeferenceSources	Navigation system used to record the location of sample collections.
identifiedBy	A list of names of people, groups or organisations who assigned the Taxon to the subject.
dateIdentified	The date on which the subject was determined as representing the Taxon.
identificationRemarks	Comments or notes about the dwc:Identification.
scientificName	The full scientific name, with authorship and date information if known.
kingdom	Kingdom name.
phylum	Phylum name.
class	Class name.
order	Order name.
family	Family name.
genus	Genus name.
specificEpithet	Specific epithet name.
taxonRank	Lowest taxonomic rank of the record.
scientificNameAuthorship	The authorship information for the scientificName formatted according to the conventions of the applicable nomenclaturalCode.

Additional information

The microbiome analysis revealed four major groups: Eukarya, Archaea, Bacteria and Viruses (NCBI 2025). This study focuses exclusively on the Eukarya domain.

Within Eukarya, only the Fungi kingdom was detected, representing 0.01–0.1% of all taxonomic features and ranked as the least abundant group in 16 of the 18 compost samples. No other eukaryotic organisms (e.g. invertebrates, protozoa and algae) were detected. The absence of non-fungal eukaryotes in our dataset is likely related to strong ecological filtering during the thermophilic phase of composting. Temperatures during this stage commonly exceed 55–65°C, creating prolonged heat stress conditions that eliminate or severely reduce most non-spore-forming eukaryotes (Lin et al. 2018). Many fungal taxa are capable of surviving such conditions through thermotolerance mechanisms, rapid stress-response systems or the production of resistant structures such as spores (Tuomela et al. 2000). The thermophilic phase also accelerates organic matter degradation and alters oxygen availability and moisture dynamics, further restricting the establishment of other eukaryotic groups. Temperature-driven ecological filtering is a key determinant of compost microbial succession (Awasthi et al. 2023). The eukaryotic community may already have undergone strong selective filtering, resulting in the dominance of fungi. Aditionally, the very low overall proportion of Eukarya-derived reads (0.01–0.1%) suggests that other eukaryotic groups, if present, may fall below detection thresholds in shotgun metagenomic datasets dominated by bacterial and archaeal DNA (Quince et al. 2017).

Previous studies have similarly reported a relatively low abundance of fungi during composting (Martins et al. 2013, Wang et al. 2022, Aguilar-Paredes et al. 2023), suggesting that, while fungi contribute to the composting process, bacteria consistently dominate the microbial community. Although fungi represent a relatively small fraction of total metagenomic reads, their ecological importance in composting is disproportionate to their numerical abundance. Fungi are key degraders of recalcitrant polymers, such as cellulose, hemicellulose and lignin during both the thermophilic and subsequent cooling and maturation stages (Mello et al. 2017, Varma et al. 2017).

The present dataset provides an extensive inventory of fungal taxa identified in compost. While many have previously been reported in composting systems, others were not found in Web of Science, Scopus, Google Scholar or GBIF searches. This may reflect database limitations, as taxa not explicitly cited in titles, abstracts or indexed keywords are easily overlooked. Records from Google Scholar and GBIF can complement this gap, but require validation due to lower precision.

Another important consideration is the evolving state of fungal taxonomy. Over the past decade, major revisions have occurred following the abandonment of dual nomenclature and the adoption of molecular methods, which have clarified earlier misclassifications (Kidd et al. 2023). Consequently, even recent articles (as late as 2024) may report taxa using outdated classification. Taxonomic databases, including the NCBI database (NCBI 2025), are frequently updated. Between our first survey in 2023 and the present, 40–50 taxa have undergone reclassification, mainly at the species, genus and family levels and, in some cases, at the order and class levels.

The dominance of Ascomycota (Table 1) is consistent with other composting studies (Lin et al. 2018, Awasthi et al. 2023). However, the relatively high abundance of Mucoromycota, Basidiomycota and Chytridiomycota, which ranked second, third and fourth in taxonomic feature abundance, respectively, has not been reported elsewhere. Factors, such as raw material composition, mixture ratio, aeration, C/N balance, moisture, pH, shredding of garden trimmings and local environmental conditions, strongly affect the compost microbiome and may explain these differences. In metabolic terms, these fungal phyla play distinct roles during composting. Ascomycota and Mucoromycota contribute to the rapid degradation of simple carbohydrates and hemicellulose, Basidiomycota are particularly important lignin degraders through oxidative enzymes such as laccases and peroxidases and Chytridiomycota participate in the hydrolysis of cellulose and other recalcitrant polymers (Tuomela et al. 2000, Awasthi et al. 2023). Nevertheless, all phyla identified in this study have been reported previously in compost (Tuomela et al. 2000, Cai et al. 2018, Lin et al. 2018, He et al. 2022, Awasthi et al. 2023, Liu et al. 2024, Mahongnao et al. 2024, Ahmad et al. 2024).

Table 1.

List of phyla detected during the composting process, with corresponding classified reads aggregated at phylum level and relative abundances (RA) within the Eukarya domain, confirmed in the NCBI Taxonomy Browser.

Phylum	Classified reads	RA
Ascomycota	135741	60.80%
Basidiomycota	18971	8.50%
Blastocladiomycota	1068	0.48%
Chytridiomycota	16096	7.21%
Cryptomycota	6508	2.92%
Microsporidia	2318	1.04%
Mucoromycota	39638	17.76%
Olpidiomycota	98	0.04%
Zoopagomycota	2802	1.26%
Total	223241

At the genus level, the most abundant taxa (relative abundance of classified reads > 1%) were Aspergillus, Rhizopus, Chaetomium, Aureobasidium, Madurella, Paramicrosporidium, Rhizophagus, Rasamsonia, Hyaloraphidium, Thermochaetoides, Talaromyces, Trichoderma and Podospora (Table 2). These genera can be broadly grouped according to their metabolic or ecological roles during composting: (i) decomposers and nutrient cyclers (Aspergillus, Rhizopus, Podospora, Thermochaetoides); (ii) biocontrol and cellulolytic fungi (Trichoderma, Chaetomium, Talaromyces, Rasamsonia); (iii) yeasts and opportunistic fungi (Aureobasidium, Madurella); (iv) microsporidia and chytrids associated with aquatic or anaerobic niches (Paramicrosporidium, Hyaloraphidium) and (v) mycorrhizal fungi (Rhizophagus). Most of these genera have been previously reported in compost or during composting (Tuomela et al. 2000, Sebők et al. 2015, Anastasi et al. 2017, Cai et al. 2018, Lu et al. 2024, Mahongnao et al. 2024, Ahmad et al. 2024). Paramicrosporidium and Hyaloraphidium have been reported in non-aerated compost tea (Mengesha et al. 2017) and Paramicrosporidium was also detected in the gut of Hermetia illucens larvae grown in urban compost (Vallejo-Arróliga and Rojas-Jimenez 2024), suggesting that both genera may be associated with the composting environment.

Table 2.

List of classes, orders, families and genera detected during the composting process, with corresponding classified reads counts and relative abundances (RA) within the Eukarya domain, confirmed in the NCBI Taxonomy Browser.

class	order	family	genus	Classified reads	RA
Dothideomycetes	Pleosporales		Aaosphaeria	48	0.02%
Mucoromycetes	Mucorales	Cunninghamellaceae	Absidia	269	0.12%
Exobasidiomycetes	Exobasidiales	Cryptobasidiaceae	Acaromyces	17	0.01%
Glomeromycetes	Diversisporales	Acaulosporaceae	Acaulospora	96	0.04%
Dothideomycetes	Mycosphaerellales	Teratosphaeriaceae	Acidomyces	23	0.01%
Mortierellomycetes	Mortierellales	Mortierellaceae	Actinomortierella	91	0.04%
Agaricomycetes	Agaricales	Agaricaceae	Agaricus	34	0.02%
Agaricomycetes	Agaricales	Strophariaceae	Agrocybe	48	0.02%
Dothideomycetes	Pleosporales	Pleosporaceae	Alternaria	60	0.03%
Arthoniomycetes	Arthoniales	Lecanographaceae	Alyxoria	29	0.01%
Glomeromycetes	Archaeosporales	Ambisporaceae	Ambispora	1196	0.54%
Dothideomycetes	Pleosporales	Amniculicolaceae	Amniculicola	59	0.03%
		Amphiacanthidae	Amphiamblys	17	0.01%
Leotiomycetes	Helotiales		Amylocarpus	38	0.02%
Neocallimastigomycetes	Neocallimastigales	Neocallimastigaceae	Anaeromyces	104	0.05%
Sordariomycetes	Xylariales	Hypoxylaceae	Annulohypoxylon	1963	0.88%
Dothideomycetes	Botryosphaeriales	Aplosporellaceae	Aplosporella	62	0.03%
Mucoromycetes	Mucorales	Mucoraceae	Apophysomyces	1266	0.57%
Orbiliomycetes	Orbiliales	Orbiliaceae	Arthrobotrys	389	0.17%
Eurotiomycetes	Onygenales	Arthrodermataceae	Arthroderma	18	0.01%
Agaricomycetes	Agaricales	Lyophyllaceae	Arthromyces	18	0.01%
Eurotiomycetes	Onygenales	Ascosphaeraceae	Ascosphaera	31	0.01%
Eurotiomycetes	Eurotiales	Aspergillaceae	Aspergillus	40031	17.93%
Agaricomycetes	Agaricales	Lyophyllaceae	Asterophora	26	0.01%
Agaricomycetes	Boletales	Astraeaceae	Astraeus	787	0.35%
Agaricomycetes	Atheliales	Atheliaceae	Athelia	62	0.03%
Dothideomycetes	Dothideales	Saccotheciaceae	Aureobasidium	6896	3.09%
Lecanoromycetes	Lecanorales	Ramalinaceae	Bacidia	19	0.01%
Mucoromycetes	Mucorales	Backusellaceae	Backusella	30	0.01%
Basidiobolomycetes	Basidiobolales	Basidiobolaceae	Basidiobolus	220	0.10%
Chytridiomycetes	Rhizophydiales		Batrachochytrium	2052	0.92%
Sordariomycetes	Hypocreales	Cordycipitaceae	Beauveria	627	0.28%
Mucoromycetes	Mucorales	Mucoraceae	Benjaminiella	20	0.01%
Endogonomycetes	Endogonales		Bifiguratus	328	0.15%
Blastocladiomycetes	Blastocladiales	Blastocladiaceae	Blastocladiella	490	0.22%
Eurotiomycetes	Onygenales	Ajellomycetaceae	Blastomyces	276	0.12%
Chytridiomycetes			Blyttiomyces	132	0.06%
Agaricomycetes	Boletales	Boletaceae	Boletus	39	0.02%
Agaricomycetes	Russulales	Bondarzewiaceae	Bondarzewia	171	0.08%
Chytridiomycetes	Rhizophydiales	Terramycetaceae	Boothiomyces	53	0.02%
Chytridiomycetes	Rhizophlyctidales	Borealophlyctidaceae	Borealophlyctis	131	0.06%
Leotiomycetes	Helotiales	Sclerotiniaceae	Botryotinia	22	0.01%
Leotiomycetes	Helotiales	Sclerotiniaceae	Botrytis	230	0.10%
Pichiomycetes	Pichiales	Pichiaceae	Brettanomyces	25	0.01%
Leotiomycetes	Helotiales	Ploettnerulaceae	Cadophora	51	0.02%
Dacrymycetes	Dacrymycetales	Dacrymycetaceae	Calocera	415	0.19%
Sordariomycetes	Hypocreales	Nectriaceae	Calonectria	203	0.09%
Candelariomycetes	Candelariales	Candelariaceae	Candelaria	194	0.09%
Pichiomycetes	Serinales	Debaryomycetaceae	Candida	794	0.36%
Agaricomycetes	Cantharellales	Hydnaceae	Cantharellus	42	0.02%
Entomophthoromycetes	Entomophthorales	Ancylistaceae	Capillidium	110	0.05%
Blastocladiomycetes	Blastocladiales	Catenariaceae	Catenaria	89	0.04%
Sordariomycetes	Microascales	Microascaceae	Cephalotrichum	876	0.39%
Agaricomycetes	Cantharellales	Ceratobasidiaceae	Ceratobasidium	997	0.45%
Sordariomycetes	Microascales	Ceratocystidaceae	Ceratocystis	127	0.06%
Glomeromycetes	Diversisporales	Gigasporaceae	Cetraspora	863	0.39%
Sordariomycetes	Sordariales	Chaetomiaceae	Chaetomium	10780	4.83%
Mucoromycetes	Mucorales	Choanephoraceae	Choanephora	71	0.03%
Agaricomycetes	Boletales	Gomphidiaceae	Chroogomphus	50	0.02%
Sordariomycetes	Diaporthales	Cryphonectriaceae	Chrysoporthe	1935	0.87%
Chytridiomycetes	Chytridiales	Chytridiaceae	Chytridium	21	0.01%
Chytridiomycetes	Chytridiales	Chytriomycetaceae	Chytriomyces	1061	0.48%
Mucoromycetes	Mucorales	Lichtheimiaceae	Circinella	409	0.18%
Xylobotryomycetes	Xylobotryales	Cirrosporiaceae	Cirrosporium	48	0.02%
Sordariomycetes	Hypocreales	Hypocreaceae	Cladobotryum	184	0.08%
Chytridiomycetes	Cladochytriales	Cladochytriaceae	Cladochytrium	408	0.18%
Eurotiomycetes	Chaetothyriales	Herpotrichiellaceae	Cladophialophora	103	0.05%
Sordariomycetes	Hypocreales	Clavicipitaceae	Claviceps	43	0.02%
Pichiomycetes	Serinales	Metschnikowiaceae	Clavispora	18	0.01%
Dothideomycetes	Pleosporales	Lindgomycetaceae	Clohesyomyces	48	0.02%
Chytridiomycetes	Lobulomycetales	Lobulomycetaceae	Clydaea	20	0.01%
Eurotiomycetes	Onygenales	Onygenaceae	Coccidioides	200	0.09%
Blastocladiomycetes	Blastocladiales	Coelomomycetaceae	Coelomomyces	137	0.06%
Kickxellomycetes	Kickxellales	Kickxellaceae	Coemansia	322	0.14%
Leotiomycetes	Helotiales	Dermateaceae	Coleophoma	109	0.05%
Sordariomycetes	Sordariales	Chaetomiaceae	Collariella	114	0.05%
Sordariomycetes	Glomerellales	Glomerellaceae	Colletotrichum	1965	0.88%
Entomophthoromycetes	Entomophthorales	Ancylistaceae	Conidiobolus	107	0.05%
Sordariomycetes	Coniochaetales	Coniochaetaceae	Coniochaeta	169	0.08%
Dothideomycetes	Pleosporales	Coniothyriaceae	Coniothyrium	623	0.28%
Agaricomycetes	Agaricales	Psathyrellaceae	Coprinellus	56	0.03%
Dothideomycetes	Pleosporales	Corynesporascaceae	Corynespora	88	0.04%
Agaricomycetes	Agaricales	Crepidotaceae	Crepidotus	18	0.01%
Sordariomycetes	Diaporthales	Cryphonectriaceae	Cryphonectria	196	0.09%
Tremellomycetes	Tremellales	Cryptococcaceae	Cryptococcus	112	0.05%
			Cucumispora	341	0.15%
Leotiomycetes	Helotiales	Tricladiaceae	Cudoniella	6	0.00%
Mucoromycetes	Mucorales	Cunninghamellaceae	Cunninghamella	24	0.01%
Agaricomycetes	Agaricales	Nidulariaceae	Cyathus	64	0.03%
Dacrymycetes	Dacrymycetales	Dacrymycetaceae	Dacryopinax	58	0.03%
Orbiliomycetes	Orbiliales	Orbiliaceae	Dactylella	518	0.23%
Sordariomycetes	Hypocreales	Nectriaceae	Dactylonectria	23	0.01%
Sordariomycetes	Xylariales	Hypoxylaceae	Daldinia	630	0.28%
Pichiomycetes	Serinales	Debaryomycetaceae	Debaryomyces	303	0.14%
Agaricomycetes	Agaricales		Dendrothele	49	0.02%
Glomeromycetes	Diversisporales	Gigasporaceae	Dentiscutata	85	0.04%
Sordariomycetes	Diaporthales	Diaporthaceae	Diaporthe	78	0.03%
Agaricomycetes	Polyporales	Polyporaceae	Dichomitus	77	0.03%
Mucoromycetes	Mucorales	Lichtheimiaceae	Dichotomocladium	146	0.07%
			Dictyocoela	69	0.03%
Dimargaritomycetes	Dimargaritales	Dimargaritaceae	Dimargaris	169	0.08%
Chytridiomycetes	Chytridiales	Chytridiaceae	Dinochytrium	76	0.03%
Leotiomycetes	Helotiales	Drepanopezizaceae	Diplocarpon	37	0.02%
Lecanoromycetes	Ostropales	Graphidaceae	Diploschistes	128	0.06%
Kickxellomycetes	Kickxellales	Kickxellaceae	Dipsacomyces	120	0.05%
Mortierellomycetes	Mortierellales	Mortierellaceae	Dissophora	62	0.03%
Glomeromycetes	Diversisporales	Diversisporaceae	Diversispora	1695	0.76%
Orbiliomycetes	Orbiliales	Orbiliaceae	Drechslerella	108	0.05%
Sordariomycetes	Xylariales	Xylariaceae	Durotheca	28	0.01%
Eurotiomycetes	Eurotiales	Elaphomycetaceae	Elaphomyces	304	0.14%
Eurotiomycetes	Onygenales	Ajellomycetaceae	Emergomyces	17	0.01%
Sordariomycetes	Hypocreales	Bionectriaceae	Emericellopsis	144	0.06%
Endogonomycetes	Endogonales	Endogonaceae	Endogone	418	0.19%
			Enteropsectra	55	0.02%
		Enterocytozoonidae	Enterospora	84	0.04%
Entomophthoromycetes	Entomophthorales	Entomophthoraceae	Entomophthora	30	0.01%
Mortierellomycetes	Mortierellales	Mortierellaceae	Entomortierella	67	0.03%
Chytridiomycetes	Chytridiales	Chytriomycetaceae	Entophlyctis	23	0.01%
Glomeromycetes	Entrophosporales	Entrophosporaceae	Entrophospora	322	0.14%
Dothideomycetes	Eremomycetales	Eremomycetaceae	Eremomyces	152	0.07%
Saccharomycetes	Saccharomycetales	Saccharomycetaceae	Eremothecium	13	0.01%
Leotiomycetes	Erysiphales	Erysiphaceae	Erysiphe	509	0.23%
Agaricomycetes	Auriculariales	Exidiaceae	Exidia	47	0.02%
Exobasidiomycetes	Exobasidiales	Exobasidiaceae	Exobasidium	15	0.01%
Eurotiomycetes	Chaetothyriales	Herpotrichiellaceae	Exophiala	61	0.03%
Dothideomycetes	Pleosporales	Pleosporaceae	Exserohilum	873	0.39%
Tremellomycetes	Filobasidiales	Filobasidiaceae	Filobasidium	256	0.11%
Chytridiomycetes	Spizellomycetales	Powellomycetaceae	Fimicolochytrium	42	0.02%
Agaricomycetes	Agaricales	Tricholomataceae	Flagelloscypha	18	0.01%
Agaricomycetes	Hymenochaetales	Hymenochaetaceae	Fomitiporia	314	0.14%
Agaricomycetes	Polyporales	Fomitopsidaceae	Fomitopsis	62	0.03%
Eurotiomycetes	Chaetothyriales	Herpotrichiellaceae	Fonsecaea	65	0.03%
Dothideomycetes	Mycosphaerellales	Teratosphaeriaceae	Friedmanniomyces	595	0.27%
Glomeromycetes	Glomerales	Glomeraceae	Funneliformis	1048	0.47%
Sordariomycetes	Hypocreales	Nectriaceae	Fusarium	599	0.27%
Chytridiomycetes	Spizellomycetales	Spizellomycetaceae	Gaertneriomyces	90	0.04%
Mortierellomycetes	Mortierellales	Mortierellaceae	Gamsiella	63	0.03%
Agaricomycetes	Polyporales	Polyporaceae	Ganoderma	37	0.02%
Sordariomycetes	Sordariales	Sordariaceae	Gelasinospora	68	0.03%
Geoglossomycetes	Geoglossales	Geoglossaceae	Geoglossum	469	0.21%
Glomeromycetes	Archaeosporales	Geosiphonaceae	Geosiphon	80	0.04%
Dipodascomycetes	Dipodascales	Dipodascaceae	Geotrichum	373	0.17%
Chytridiomycetes	Spizellomycetales	Powellomycetaceae	Geranomyces	126	0.06%
Glomeromycetes	Diversisporales	Gigasporaceae	Gigaspora	1068	0.48%
Chytridiomycetes	Rhizophydiales	Globomycetaceae	Globomyces	276	0.12%
Glomeromycetes	Glomerales	Glomeraceae	Glomus	40	0.02%
Geoglossomycetes	Geoglossales	Geoglossaceae	Glutinoglossum	359	0.16%
Sordariomycetes	Diaporthales	Gnomoniaceae	Gnomoniopsis	19	0.01%
Leotiomycetes	Erysiphales	Erysiphaceae	Golovinomyces	297	0.13%
Lecanoromycetes	Ostropales	Graphidaceae	Gomphillus	297	0.13%
Monoblepharidomycetes	Monoblepharidales	Gonapodyaceae	Gonapodya	597	0.27%
Dothideomycetes	Acrospermales	Acrospermaceae	Gonatophragmium	87	0.04%
Mucoromycetes	Mucorales	Cunninghamellaceae	Gongronella	197	0.09%
Chytridiomycetes	Rhizophydiales	Gorgonomycetaceae	Gorgonomyces	1147	0.51%
Mortierellomycetes	Mortierellales	Mortierellaceae	Gryganskiella	40	0.02%
Lecanoromycetes	Teloschistales	Teloschistaceae	Gyalolechia	20	0.01%
Mucoromycetes	Mucorales	Cunninghamellaceae	Halteromyces	24	0.01%
Saccharomycetes	Saccharomycodales	Saccharomycodaceae	Hanseniaspora	44	0.02%
Mortierellomycetes	Mortierellales	Mortierellaceae	Haplosporangium	59	0.03%
Sordariomycetes	Hypocreales	Bionectriaceae	Hapsidospora	16	0.01%
Agaricomycetes	Agaricales	Hymenogastraceae	Hebeloma	330	0.15%
Eurotiomycetes	Onygenales	Ajellomycetaceae	Helicocarpus	111	0.05%
Agaricomycetes	Russulales	Hericiaceae	Hericium	218	0.10%
Agaricomycetes	Polyporales	Meruliaceae	Hermanssonia	76	0.03%
Agaricomycetes	Russulales	Bondarzewiaceae	Heterobasidion	35	0.02%
Sordariomycetes	Hypocreales	Ophiocordycipitaceae	Hirsutella	50	0.02%
Eurotiomycetes	Onygenales	Ajellomycetaceae	Histoplasma	1379	0.62%
Dothideomycetes	Mycosphaerellales	Teratosphaeriaceae	Hortaea	213	0.10%
Monoblepharidomycetes	Monoblepharidales		Hyaloraphidium	3105	1.39%
Leotiomycetes	Helotiales	Hyaloscyphaceae	Hyaloscypha	33	0.01%
Agaricomycetes	Boletales	Hygrophoropsidaceae	Hygrophoropsis	30	0.01%
Sordariomycetes	Xylariales	Hypoxylaceae	Hypomontagnella	12	0.01%
Sordariomycetes	Hypocreales	Hypocreaceae	Hypomyces	61	0.03%
Sordariomycetes	Xylariales	Hypoxylaceae	Hypoxylon	196	0.09%
Agaricomycetes	Agaricales	Lyophyllaceae	Hypsizygus	114	0.05%
Sordariomycetes	Hypocreales	Nectriaceae	Ilyonectria	270	0.12%
Agaricomycetes	Hymenochaetales	Hymenochaetaceae	Inonotus	39	0.02%
Chytridiomycetes	Chytridiales	Chytridiaceae	Irineochytrium	257	0.12%
Agaricomycetes	Polyporales	Irpicaceae	Irpex	89	0.04%
Agaricomycetes	Jaapiales	Jaapiaceae	Jaapia	65	0.03%
Endogonomycetes	Endogonales	Endogonaceae	Jimgerdemannia	61	0.03%
Sordariomycetes	Diaporthales	Juglanconidaceae	Juglanconis	1238	0.55%
Sordariomycetes	Microascales	Microascaceae	Kernia	297	0.13%
Tremellomycetes	Tremellales	Cryptococcaceae	Kwoniella	267	0.12%
Agaricomycetes	Agaricales	Hydnangiaceae	Laccaria	54	0.02%
Saccharomycetes	Saccharomycetales	Saccharomycetaceae	Lachancea	496	0.22%
Agaricomycetes	Polyporales	Laetiporaceae	Laetiporus	47	0.02%
Lecanoromycetes	Umbilicariales	Umbilicariaceae	Lasallia	24	0.01%
Agaricomycetes	Agaricales	Omphalotaceae	Lentinula	57	0.03%
Agaricomycetes	Polyporales	Polyporaceae	Lentinus	77	0.03%
Dothideomycetes	Pleosporales	Lentitheciaceae	Lentithecium	82	0.04%
Dothideomycetes	Mytilinidiales	Argynnaceae	Lepidopterella	70	0.03%
Leotiomycetes	Helotiales	Leptodontidiaceae	Leptodontidium	1666	0.75%
Sordariomycetes	Ophiostomatales	Ophiostomataceae	Leptographium	52	0.02%
Agaricomycetes	Boletales		Leucogyrophana	188	0.08%
Mucoromycetes	Mucorales	Lichtheimiaceae	Lichtheimia	561	0.25%
Kickxellomycetes	Kickxellales	Kickxellaceae	Linderina	42	0.02%
Mortierellomycetes	Mortierellales	Mortierellaceae	Linnemannia	1196	0.54%
Lipomycetes	Lipomycetales	Lipomycetaceae	Lipomyces	9	0.00%
Mortierellomycetes	Mortierellales	Mortierellaceae	Lobosporangium	21	0.01%
Chytridiomycetes	Lobulomycetales	Lobulomycetaceae	Lobulomyces	19	0.01%
Sordariomycetes	Microascales	Microascaceae	Lomentospora	38	0.02%
Dothideomycetes	Pleosporales	Lophiotremataceae	Lophiotrema	28	0.01%
Agaricomycetes	Agaricales	Lyophyllaceae	Lyophyllum	60	0.03%
Dothideomycetes	Botryosphaeriales	Botryosphaeriaceae	Macrophomina	1885	0.84%
Sordariomycetes	Sordariales		Madurella	6366	2.85%
Dipodascomycetes	Dipodascales	Dipodascaceae	Magnusiomyces	92	0.04%
Malasseziomycetes	Malasseziales	Malasseziaceae	Malassezia	236	0.11%
Entomophthoromycetes	Entomophthorales	Entomophthoraceae	Massospora	25	0.01%
Exobasidiomycetes	Exobasidiales	Brachybasidiaceae	Meira	434	0.19%
Sordariomycetes	Hypocreales	Clavicipitaceae	Metarhizium	340	0.15%
Pichiomycetes	Serinales	Metschnikowiaceae	Metschnikowia	40	0.02%
Entomophthoromycetes	Entomophthorales	Ancylistaceae	Microconidiobolus	198	0.09%
Sordariomycetes	Xylariales	Microdochiaceae	Microdochium	31	0.01%
			Mitosporidium	933	0.42%
Mixiomycetes	Mixiales	Mixiaceae	Mixia	11	0.00%
Sordariomycetes	Hypocreales	Clavicipitaceae	Moelleriella	104	0.05%
Leotiomycetes	Helotiales	Mollisiaceae	Mollisia	19	0.01%
Eurotiomycetes	Eurotiales	Aspergillaceae	Monascus	147	0.07%
Leotiomycetes	Helotiales	Sclerotiniaceae	Monilinia	771	0.35%
Agaricomycetes	Agaricales	Marasmiaceae	Moniliophthora	71	0.03%
Monoblepharidomycetes	Monoblepharidales	Monoblepharidaceae	Monoblepharella	512	0.23%
Sordariomycetes	Xylariales		Monosporascus	144	0.06%
Pezizomycetes	Pezizales	Morchellaceae	Morchella	1020	0.46%
Mortierellomycetes	Mortierellales	Mortierellaceae	Mortierella	855	0.38%
Mucoromycetes	Mucorales	Mucoraceae	Mucor	1315	0.59%
Agaricomycetes	Agaricales	Mycenaceae	Mycena	797	0.36%
Sordariomycetes	Sordariales	Chaetomiaceae	Mycothermus	12	0.01%
Mucoromycetes	Mucorales	Mycotyphaceae	Mycotypha	63	0.03%
Tremellomycetes	Filobasidiales	Filobasidiaceae	Naganishia	22	0.01%
Saccharomycetes	Saccharomycetales	Saccharomycetaceae	Nakaseomyces	59	0.03%
Eurotiomycetes	Onygenales	Arthrodermataceae	Nannizzia	30	0.01%
Sordariomycetes	Xylariales	Xylariaceae	Nemania	71	0.03%
			Nematocida	225	0.10%
Sordariomycetes	Xylariales	Apiosporaceae	Neoarthrinium	100	0.04%
Neocallimastigomycetes	Neocallimastigales	Neocallimastigaceae	Neocallimastix	50	0.02%
Entomophthoromycetes	Entomophthorales	Ancylistaceae	Neoconidiobolus	14	0.01%
Dothideomycetes	Mycosphaerellales	Teratosphaeriaceae	Neohortaea	48	0.02%
Neolectomycetes	Neolectales	Neolectaceae	Neolecta	41	0.02%
Sordariomycetes	Xylariales	Sporocadaceae	Neopestalotiopsis	106	0.05%
Sordariomycetes	Sordariales	Sordariaceae	Neurospora	619	0.28%
		Nosematidae	Nosema	382	0.17%
Chytridiomycetes	Cladochytriales	Nowakowskiellaceae	Nowakowskiella	175	0.08%
Chytridiomycetes	Chytridiales	Chytriomycetaceae	Obelidium	20	0.01%
Pichiomycetes	Pichiales	Pichiaceae	Ogataea	13	0.01%
Olpidiomycetes	Olpidiales	Olpidiaceae	Olpidium	98	0.04%
Sordariomycetes	Hypocreales	Ophiocordycipitaceae	Ophiocordyceps	858	0.38%
Sordariomycetes	Diaporthales	Gnomoniaceae	Ophiognomonia	456	0.20%
Sordariomycetes	Ophiostomatales	Ophiostomataceae	Ophiostoma	799	0.36%
Orbiliomycetes	Orbiliales	Orbiliaceae	Orbilia	1955	0.88%
Eurotiomycetes	Eurotiales	Thermoascaceae	Paecilomyces	1119	0.50%
Agaricomycetes	Agaricales	Galeropsidaceae	Panaeolus	197	0.09%
			Pancytospora	92	0.04%
Agaricomycetes	Polyporales	Panaceae	Panus	17	0.01%
Eurotiomycetes	Onygenales	Ajellomycetaceae	Paracoccidioides	392	0.18%
Glomeromycetes	Paraglomerales	Paraglomeraceae	Paraglomus	360	0.16%
Sordariomycetes	Hypocreales	Ophiocordycipitaceae	Paraisaria	40	0.02%
			Paramicrosporidium	6046	2.71%
Sordariomycetes	Hypocreales	Stachybotryaceae	Paramyrothecium	16	0.01%
Physodermatomycetes	Physodermatales	Physodermataceae	Paraphysoderma	353	0.16%
Mucoromycetes	Mucorales	Mucoraceae	Parasitella	602	0.27%
Agaricomycetes	Boletales	Paxillaceae	Paxillus	56	0.02%
Lecanoromycetes	Peltigerales	Peltigeraceae	Peltigera	188	0.08%
Lichinomycetes	Lichinales	Phylliscaceae	Peltula	78	0.04%
Eurotiomycetes	Eurotiales	Aspergillaceae	Penicilliopsis	539	0.24%
Eurotiomycetes	Eurotiales	Aspergillaceae	Penicillium	1845	0.83%
Agaricomycetes	Russulales	Peniophoraceae	Peniophora	312	0.14%
Sordariomycetes	Xylariales	Sporocadaceae	Pestalotiopsis	191	0.09%
Tremellomycetes	Cystofilobasidiales	Mrakiaceae	Phaffia	16	0.01%
Agaricomycetes	Polyporales	Phanerochaetaceae	Phanerochaete	207	0.09%
Mucoromycetes	Mucorales	Lichtheimiaceae	Phascolomyces	14	0.01%
Eurotiomycetes	Chaetothyriales	Herpotrichiellaceae	Phialophora	19	0.01%
Chytridiomycetes	Chytridiales	Chytridiaceae	Phlyctochytrium	822	0.37%
Agaricomycetes	Agaricales	Strophariaceae	Pholiota	53	0.02%
Mucoromycetes	Mucorales	Phycomycetaceae	Phycomyces	96	0.04%
Lichinomycetes	Lichinales	Phylliscaceae	Phylliscum	38	0.02%
Lecanoromycetes	Caliciales	Physciaceae	Physcia	30	0.01%
Agaricomycetes	Polyporales	Meripilaceae	Physisporinus	243	0.11%
Pichiomycetes	Pichiales	Pichiaceae	Pichia	111	0.05%
Mucoromycetes	Mucorales	Mucoraceae	Pilaira	29	0.01%
Mucoromycetes	Mucorales	Pilobolaceae	Pilobolus	61	0.03%
Zoopagomycetes	Zoopagales	Piptocephalidaceae	Piptocephalis	65	0.03%
Neocallimastigomycetes	Neocallimastigales	Neocallimastigaceae	Piromyces	619	0.28%
Sordariomycetes	Glomerellales	Plectosphaerellaceae	Plectosphaerella	1257	0.56%
Dothideomycetes	Pleosporales	Leptosphaeriaceae	Plenodomus	25	0.01%
Agaricomycetes	Agaricales	Pleurotaceae	Pleurotus	18	0.01%
Pneumocystomycetes	Pneumocystales	Pneumocystaceae	Pneumocystis	72	0.03%
Sordariomycetes	Hypocreales	Clavicipitaceae	Pochonia	106	0.05%
Mortierellomycetes	Mortierellales	Mortierellaceae	Podila	73	0.03%
Chytridiomycetes	Chytridiales	Chytriomycetaceae	Podochytrium	12	0.01%
Leotiomycetes	Erysiphales	Erysiphaceae	Podosphaera	161	0.07%
Sordariomycetes	Sordariales	Podosporaceae	Podospora	2356	1.06%
Chytridiomycetes	Polychytriales		Polychytrium	248	0.11%
Dothideomycetes	Pleosporales	Tetraplosphaeriaceae	Polyplosphaeria	47	0.02%
Chytridiomycetes	Rhizophydiales		Polyrhizophydium	73	0.03%
Eurotiomycetes	Onygenales		Polytolypa	74	0.03%
Chytridiomycetes	Spizellomycetales	Powellomycetaceae	Powellomyces	264	0.12%
Dothideomycetes	Mycosphaerellales	Mycosphaerellaceae	Pseudocercospora	14	0.01%
Leotiomycetes	Thelebolales	Thelebolaceae	Pseudogymnoascus	819	0.37%
			Pseudoloma	48	0.02%
Ustilaginomycetes	Ustilaginales	Ustilaginaceae	Pseudozyma	24	0.01%
Agaricomycetes	Agaricales	Strophariaceae	Psilocybe	561	0.25%
Pucciniomycetes	Pucciniales	Pucciniaceae	Puccinia	483	0.22%
Pezizomycetes	Pezizales	Pyronemataceae	Pyronema	306	0.14%
Chytridiomycetes		Quaeritorhizaceae	Quaeritorhiza	1731	0.78%
Glomeromycetes	Diversisporales	Gigasporaceae	Racocetra	299	0.13%
Mucoromycetes	Mucorales	Radiomycetaceae	Radiomyces	61	0.03%
Agaricomycetes	Gomphales	Gomphaceae	Ramaria	103	0.05%
	Ramicandelaberales	Ramicandelaberaceae	Ramicandelaber	34	0.02%
Dothideomycetes	Mycosphaerellales	Mycosphaerellaceae	Ramularia	62	0.03%
Eurotiomycetes	Eurotiales	Trichocomaceae	Rasamsonia	4036	1.81%
Chytridiomycetes	Chytridiales	Chytriomycetaceae	Rhizoclosmatium	962	0.43%
Agaricomycetes	Cantharellales	Ceratobasidiaceae	Rhizoctonia	758	0.34%
Dothideomycetes	Aulographales	Rhizodiscinaceae	Rhizodiscina	15	0.01%
Glomeromycetes	Glomerales	Glomeraceae	Rhizophagus	4204	1.88%
Chytridiomycetes	Rhizophlyctidales	Rhizophlyctidaceae	Rhizophlyctis	462	0.21%
Agaricomycetes	Boletales	Rhizopogonaceae	Rhizopogon	47	0.02%
Mucoromycetes	Mucorales	Rhizopodaceae	Rhizopus	19211	8.61%
Agaricomycetes	Agaricales	Omphalotaceae	Rhodocollybia	33	0.01%
Agaricomycetes	Polyporales	Fomitopsidaceae	Rhodofomes	117	0.05%
Agaricomycetes	Polyporales	Adustoporiaceae	Rhodonia	493	0.22%
Microbotryomycetes	Sporidiobolales	Sporidiobolaceae	Rhodotorula	107	0.05%
Sordariomycetes	Xylariales	Xylariaceae	Rosellinia	154	0.07%
			Rozella	462	0.21%
Agaricomycetes	Russulales	Russulaceae	Russula	942	0.42%
Leotiomycetes	Helotiales	Rutstroemiaceae	Rutstroemia	38	0.02%
Saccharomycetes	Saccharomycetales	Saccharomycetaceae	Saccharomyces	542	0.24%
Saccharomycetes	Saccharomycodales	Saccharomycodaceae	Saccharomycodes	31	0.01%
			Saitoella	284	0.13%
Tremellomycetes	Tremellales	Trimorphomycetaceae	Saitozyma	792	0.35%
Agaricomycetes	Hymenochaetales	Hymenochaetaceae	Sanghuangporus	202	0.09%
Agaricomycetes	Agaricales	Schizophyllaceae	Schizophyllum	100	0.04%
Agaricomycetes	Hymenochaetales	Schizoporaceae	Schizopora	42	0.02%
Schizosaccharomycetes	Schizosaccharomycetales	Schizosaccharomycetaceae	Schizosaccharomyces	22	0.01%
Agaricomycetes	Boletales	Sclerodermataceae	Scleroderma	28	0.01%
Coniocybomycetes	Coniocybales	Coniocybaceae	Sclerophora	198	0.09%
Leotiomycetes	Helotiales	Sclerotiniaceae	Sclerotinia	281	0.13%
Sordariomycetes	Microascales	Microascaceae	Scopulariopsis	1907	0.85%
Glomeromycetes	Diversisporales	Gigasporaceae	Scutellospora	21	0.01%
Leotiomycetes			Scytalidium	740	0.33%
Agaricomycetes	Sebacinales	Serendipitaceae	Serendipita	345	0.15%
Agaricomycetes	Boletales	Serpulaceae	Serpula	23	0.01%
Harpellomycetes	Harpellales	Legeriomycetaceae	Smittium	423	0.19%
Sordariomycetes	Sordariales	Sordariaceae	Sordaria	752	0.34%
Agaricomycetes	Geastrales	Sphaerobolaceae	Sphaerobolus	88	0.04%
Pezizomycetes	Pezizales	Pyronemataceae	Sphaerosporella	13	0.01%
Kickxellomycetes	Kickxellales	Kickxellaceae	Spiromyces	77	0.03%
Chytridiomycetes	Spizellomycetales	Spizellomycetaceae	Spizellomyces	123	0.06%
Dothideomycetes	Pleosporales	Massarinaceae	Stagonospora	24	0.01%
Sordariomycetes	Sordariales	Chaetomiaceae	Staphylotrichum	350	0.16%
Agaricomycetes	Agaricales	Strophariaceae	Stropharia	181	0.08%
Agaricomycetes	Boletales	Suillaceae	Suillus	313	0.14%
Mucoromycetes	Mucorales	Syncephalastraceae	Syncephalastrum	51	0.02%
Zoopagomycetes	Zoopagales	Piptocephalidaceae	Syncephalis	781	0.35%
Chytridiomycetes	Synchytriales	Synchytriaceae	Synchytrium	187	0.08%
Eurotiomycetes	Eurotiales	Trichocomaceae	Talaromyces	2651	1.19%
Taphrinomycetes	Taphrinales	Taphrinaceae	Taphrina	30	0.01%
Dothideomycetes	Mycosphaerellales	Teratosphaeriaceae	Teratosphaeria	2041	0.91%
Pezizomycetes	Pezizales	Pezizaceae	Terfezia	47	0.02%
Agaricomycetes	Agaricales	Lyophyllaceae	Termitomyces	1006	0.45%
Chytridiomycetes	Rhizophydiales	Terramycetaceae	Terramyces	37	0.02%
Agaricomycetes	Agaricales	Marasmiaceae	Tetrapyrgos	183	0.08%
Mucoromycetes	Mucorales	Mucoraceae	Thamnidium	125	0.06%
Lecanoromycetes	Thelocarpales	Thelocarpaceae	Thelocarpon	22	0.01%
Sordariomycetes	Sordariales	Chaetomiaceae	Thermochaetoides	2930	1.31%
Eurotiomycetes	Eurotiales	Trichocomaceae	Thermomyces	172	0.08%
Sordariomycetes	Sordariales	Chaetomiaceae	Thermothelomyces	1758	0.79%
Sordariomycetes	Sordariales	Chaetomiaceae	Thermothielavioides	1116	0.50%
Sordariomycetes	Chaetosphaeriales	Chaetosphaeriaceae	Thozetella	28	0.01%
Sordariomycetes		Thyridiaceae	Thyridium	317	0.14%
Exobasidiomycetes	Tilletiales	Tilletiaceae	Tilletia	100	0.04%
Exobasidiomycetes	Entylomatales		Tilletiopsis	14	0.01%
Sordariomycetes	Hypocreales	Ophiocordycipitaceae	Tolypocladium	23	0.01%
Saccharomycetes	Saccharomycetales	Saccharomycetaceae	Torulaspora	69	0.03%
Dothideomycetes	Venturiales	Cylindrosympodiaceae	Tothia	477	0.21%
Agaricomycetes	Polyporales	Polyporaceae	Trametes	723	0.32%
Agaricomycetes	Polyporales	Irpicaceae	Trametopsis	16	0.01%
Tremellomycetes	Tremellales	Tremellaceae	Tremella	70	0.03%
Dothideomycetes	Phaeotrichales	Phaeotrichaceae	Trichodelitschia	28	0.01%
Sordariomycetes	Hypocreales	Hypocreaceae	Trichoderma	2559	1.15%
Geoglossomycetes	Geoglossales	Geoglossaceae	Trichoglossum	49	0.02%
Agaricomycetes	Agaricales	Lyophyllaceae	Tricholomella	37	0.02%
Eurotiomycetes	Onygenales	Arthrodermataceae	Trichophyton	149	0.07%
Tremellomycetes	Trichosporonales	Trichosporonaceae	Trichosporon	33	0.01%
Leotiomycetes	Helotiales	Helotiaceae	Tricladium	24	0.01%
Pezizomycetes	Pezizales	Tuberaceae	Tuber	764	0.34%
		Tubulinosematidae	Tubulinosema	15	0.01%
Agaricomycetes	Cantharellales	Tulasnellaceae	Tulasnella	303	0.14%
Agaricomycetes	Agaricales	Psathyrellaceae	Tulosesus	73	0.03%
Agaricomycetes	Boletales	Boletaceae	Tylopilus	446	0.20%
Umbelopsidomycetes	Umbelopsidales	Umbelopsidaceae	Umbelopsis	234	0.10%
Eurotiomycetes	Onygenales	Onygenaceae	Uncinocarpus	15	0.01%
Ustilaginomycetes	Ustilaginales	Ustilaginaceae	Ustilago	434	0.19%
Sordariomycetes	Xylariales	Xylariaceae	Ustulina	74	0.03%
		Nosematidae	Vairimorpha	27	0.01%
Tremellomycetes	Trichosporonales	Trichosporonaceae	Vanrija	53	0.02%
Agaricomycetes	Russulales	Lachnocladiaceae	Vararia	11	0.00%
Leotiomycetes	Helotiales	Discinellaceae	Varicosporium	31	0.01%
Dothideomycetes	Venturiales	Venturiaceae	Venturia	59	0.03%
Leotiomycetes	Helotiales	Pleuroascaceae	Venustampulla	126	0.06%
Dothideomycetes	Venturiales	Sympoventuriaceae	Verruconis	20	0.01%
Sordariomycetes	Glomerellales	Plectosphaerellaceae	Verticillium	231	0.10%
		Nosematidae	Vittaforma	30	0.01%
Agaricomycetes	Agaricales	Pluteaceae	Volvariella	17	0.01%
Wallemiomycetes	Wallemiales	Wallemiaceae	Wallemia	1304	0.58%
Lichinomycetes	Lichinales	Porocyphaceae	Watsoniomyces	33	0.01%
Dipodascomycetes	Dipodascales	Trichomonascaceae	Wickerhamiella	83	0.04%
Saccharomycetes	Phaffomycetales	Wickerhamomycetaceae	Wickerhamomyces	181	0.08%
Agaricomycetes	Polyporales	Phaeolaceae	Wolfiporia	44	0.02%
Sordariomycetes	Xylariales	Xylariaceae	Xylaria	591	0.26%
Sordariomycetes	Xylariales	Xylariaceae	Xylariaceae	31	0.01%
Leotiomycetes			Xylogone	108	0.05%
Pichiomycetes	Serinales	Debaryomycetaceae	Yamadazyma	22	0.01%
Harpellomycetes	Harpellales	Legeriomycetaceae	Zancudomyces	65	0.03%
Dothideomycetes		Zopfiaceae	Zopfia	117	0.05%
Mucoromycetes	Mucorales	Lichtheimiaceae	Zychaea	48	0.02%
Eurotiomycetes	Chaetothyriales			69	0.03%
Chytridiomycetes	Chytridiales			62	0.03%

Amongst the 13 most abundant genera, Rhizophagus (an arbuscular mycorrhizal fungus - AMF) is the only one without published reports linking it directly to composting. However, its presence in soil is well documented and studies have shown that compost addition stimulates hyphal growth and sporulation, benefiting multiple crops (Yang et al. 2018, Boutasknit et al. 2020, Tahiri et al. 2022). Rhizophagus, an obligate arbuscular mycorrhizal fungus (AMF), requires a living plant host for active growth (Smith and Read 2008). These fungi produce resistant spores capable of persisting in soil and plant residues and may be introduced into compost through yard trimmings or soil particles (Aguilar-Paredes et al. 2023). Shotgun metagenomic sequencing detects environmental DNA (eDNA) irrespective of metabolic state. Nevertheless, the observed relative abundance of 1.88% (within Fungi) suggests that additional factors may be involved beyond the mechanisms currently identified. The potential survival of AMF propagules during composting may have implications for the agricultural use of the final product.

Amongst the detected taxa (Monjardino et al. 2025), some correspond to host-specific or host-obligate parasites, including human-associated Pneumocystis jirovecii (Cissé et al. 2020), insect-associated Entomophthora muscae and Massospora cicadina (Elya and De Fine Licht 2021), amphibian-associated Batrachochytrium salamandrivorans (Martel et al. 2013) and amoeba-associated Paramicrosporidium saccamoebae (Quandt et al. 2017). Shotgun metagenomics identifies DNA fragments based on sequence similarity and does not discriminate amongst active organisms, dormant propagules or residual environmental DNA. Their detection may, therefore, reflect resistant spores, residual host material introduced through garden trimmings, undetected microscopic hosts or taxonomic assignments to closely-related environmental lineages. However, for relatively abundant taxa, such as Batrachochytrium salamandrivorans (RA = 0.59%) and Paramicrosporidium saccamoebae (RA = 2.71%) and, given that their known host species were not identified, additional factors may account for their presence in the composting material. These findings highlight the complexity of compost-associated microbial diversity and warrant further ecological investigation.

Although composting typically requires no inoculation, several studies demonstrated positive effects of fungal amendments, despite fungi often being amongst the least abundant microbial groups (He et al. 2022). Different taxa have been inoculated for: (i) detoxification of inhibitory compounds, for example, supplementation with Paecilomyces sp. FA13 enhances the degradation of furan derivatives during food waste pretreatment (Nakasaki et al. 2015); (ii) lignocellulose degradation and humification, with Phanerochaete chrysosporium and Trichoderma longibrachiatum increasing cellulose, hemicellulose and lignin breakdown, while elevating humus and humic acid content, all of which were also detected in our samples (Table 2); and (iii) synergistic effects with other microbes, such as inoculation with thermotolerant actinomycetes, which accelerates humification and increases humic substance content by 50–100% (Zhao et al. 2017).

Most of the fungi listed in Table 2 are relevant to composting. Based on previous studies and their relative abundances (> 0.5% of classified reads), three main functional groups emerge with the greatest potential for agricultural applications: (i) biocontrol fungi (Trichoderma, Chaetomium, Aureobasidium, Penicillium, Paecilomyces); (ii) mycorrhizal fungi (Rhizophagus, Diversispora, Ambispora) and (iii) nutrient cyclers and decomposers (Aspergillus, Rhizopus, Mucor, Podospora, Thermothelomyces, Linnemannia). The remaining genera detected were either pathogenic or of limited agricultural value.

In summary, this study provides a shotgun metagenomic inventory of fungal taxa detected across composting stages, documenting their relative read abundance and reinforcing the ecological and agricultural relevance of fungal communities within compost systems.

Funding Statement

The research was funded by VERCOCHAR - Vermicompost, compost y biochar, herramientas para la adaptación al cambio climático, la prevención y mitigación de los efectos derivados de los riesgos naturales en el medio agrícola y forestal, MAC2/3.5b/307

Author contributions

P.M.: Conceptualisation, Funding acquisition, project administration, Investigation, Methodology, Data curation, writing —original draft; A.R.A.: Investigation, Methodology, Writing — review and editing; D.M.: Conceptualisation, Methodology, Writing — review and editing; G.P.: Data curation, Writing — review and editing; P.A.V.B.: Methodology, Writing — review and editing; J.F.: Data curation, Writing — review and editing; D.T.: Conceptualisation, Methodology; Investigation, Data curation, Validation, Writing — review and editing. All authors have read and agreed to the published version of the manuscript.