Lei Cai

Chinese Academy of Sciences | CAS · State Key Laboratory of Mycology Institute of Microbiology

Background The plant microbiome is an integral part of the host and increasingly recognized as playing fundamental roles in plant growth and health. Increasing evidence indicates that plant rhizosphere recruits beneficial microbes to the plant to suppress soil-borne pathogens. However, the ecological processes that govern plant microbiome assembly...

The genus Colletotrichum includes important plant pathogens, endophytes, saprobes and human pathogens. Even though the polyphasic approach has facilitated Colletotrichum species identification, knowledge of the overall species diversity and host distribution is largely incomplete. To address this, we examined 952 Colletotrichum strains isolated fro...

Abstract Rust fungi are characterized by large genomes with high repeat content and have two haploid nuclei in most life stages, which makes achieving high‐quality genome assemblies challenging. Here, we described a pipeline using HiFi reads and Hi‐C data to assemble a gigabase‐sized fungal pathogen, Puccinia polysora f.sp. zeae, to haplotype‐phase...

The role of rhizosphere microbiota in the resistance of tomato plant against soil-borne Fusarium wilt disease (FWD) remains unclear. Here, we showed that the FWD incidence was significantly negatively correlated with the diversity of both rhizosphere bacterial and fungal communities. Using the microbiological culturomic approach, we selected 205 un...

Fusarium species are important cereal pathogens that cause severe production losses to major cereal crops such as maize, rice, and wheat. However, the causal agents of Fusarium diseases on cereals have not been well documented because of the difficulty in species identification and the debates surrounding generic and species concepts. In this study...

Mulching is an important agricultural management tool for increasing watermelon productivity and land-use efficiency because it helps improve water use efficiency and reduce soil erosion. However, there is relatively little available information regarding the effects of long-term continuous monoculture farming on soil fungal communities and related...

Phytopathogens, such as phytopathogenic bacteria, fungi, and nematodes, have caused great losses of crops every year, seriously threatening human health and agricultural production. Moreover, marine-derived fungi are abundant sources of structurally unique and bioactive secondary metabolites that could be potential candidates for anti-phytopathogen...

Fungal communities are diverse and abundant in coastal waters, yet, their ecological roles and adaptations remain largely unknown. To address these gaps, ITS2 metabarcoding and metatranscriptomic analyses were used to capture the whole suite of fungal diversity and their metabolic potential in water column and sediments in the Yellow Sea during Aug...

This article is the 14th in the Fungal Diversity Notes series, wherein we report 98 taxa distributed in two phyla, seven classes, 26 orders and 50 families which are described and illustrated. Taxa in this study were collected from Australia, Brazil, Burkina Faso, Chile, China, Cyprus, Egypt, France, French Guiana, India, Indonesia, Italy, Laos, Me...

We are honored and privileged to edit this Special Issue, “Fungal Taxonomy, Phylogeny, and Ecology: A Themed Issue Dedicated to Academician Wen-Ying Zhuang” [...]

Soybean and derived products are among the most important food for both humans and animals. China is the world's largest importer of soybeans, with more than 100 million tons of annual imports, mainly from the United States of America (US), Brazil, and Argentina. However, there have been limited studies on the microbiota associated with imported so...

With the growing numbers of the urban population, an increasing number of commuters have relied on subway systems for rapid transportation in daily life. Analyzing the temporal distribution of air microbiomes in subway environments is crucial for the assessment and monitoring of air quality in the subway system, especially with regard to public hea...

Fungal taxonomy is a complex and rapidly changing subject, which makes proper naming of fungi challenging for taxonomists. A registration platform with a standardized and information-integrated database is a powerful tool for efficient research on fungal taxonomy. Fungal Names (FN, https://nmdc.cn/fungalnames/; launched in 2011) is one of the three...

Karst caves are oligotrophic environments that appear to support a high diversity of fungi. Studies of fungi in Thailand’s caves are limited. During a 2019 exploration of the mycobiota associated with soil samples from a karst cave, namely, Phu Pha Phet in the Satun UNESCO Global Geopark in Satun Province, southern Thailand, two previously undescri...

EDITORIAL Positioning taxonomic research for the future Why do taxonomists matter? The work of taxonomists is often understated if not completely misunderstood. Without taxonomists, organisms cannot be accurately identified, neither can these organisms be given universally accepted names, and reliably positioned in the phylogenetic tree of life. Th...

Rust fungi in the order Pucciniales represent one of the largest groups of phytopathogens, which occur on mosses, ferns to advanced monocots and dicots. Seven suborders and 18 families have been reported so far, however recent phylogenetic studies have revealed para- or polyphyly of several morphologically defined suborders and families, particular...

Taxonomy plays an important role in understanding the origin, evolution, and ecological functionality of biodiversity. There are large number of unknown species yet to be described by taxonomists, which together with their ecosystem services cannot be effectively protected prior to description. Despite this, taxonomy has been increasingly underrat...

The genus Fusarium includes numerous important plant and human pathogens, as well as many industrially and commercially important species. During our investigation of fungal diversity in China, a total of 356 fusarioid isolates were obtained and identified from diverse diseased and healthy plants, or different environmental habitats, i.e., air, car...

Rust fungi are characterized by large genomes with high repeat content, and have two haploid nuclei in most life stages, which makes achieving high-quality genome assemblies challenging. Here, we describe a pipeline using HiFi reads and Hi-C data to assemble a gigabase-sized fungal pathogen, Puccinia polysora f.sp. zeae, to haplotype-phased and chr...

This paper is the fourth contribution in the Genera of Phytopathogenic Fungi (GOPHY) series. The series provides morphological descriptions and information about the pathology, distribution, hosts and disease symptoms, as well as DNA barcodes for the taxa covered. Moreover, 12 whole-genome sequences for the type or new species in the treated genera...

Rust fungi are characterized by large genomes with high repeat content, and have two haploid nuclei in most life stages, which makes achieving high-quality genome assemblies challenging. Here, we describe a pipeline using HiFi reads and Hi-C data to assemble a gigabase-sized fungal pathogen, Puccinia polysora f.sp. zeae, to haplotype-phased and chr...

High‐throughput sequencing has substantially improved our understanding of fungal diversity. However, the short read (<500 bp) length of current second‐generation sequencing approaches provides limited taxonomic and phylogenetic resolution for species discrimination. Longer sequences containing more information are highly desired to provide greater...

The global diversity of fungi has been estimated using several different approaches. There is somewhere between 2–11 million estimated species, but the number of formally described taxa is around 150,000, a tiny fraction of the total. In this paper, we examine 12 ascomycete genera as case studies to establish trends in fungal species descriptions,...

The role of fungi in both natural and managed ecosystem processes is unequivocal with mycotaxa being key drivers of soil, plant and animal health. Recent advances in DNA-based species identification and classification have enforced mycologists to update national checklists for proper exploitation of fungal traits and functions. However, in some cou...

The current list of Chinese quarantine pests includes 130 fungal species. However, recent changes in the taxonomy of fungi following the one fungus = one name initiative and the implementation of DNA phylogeny in taxonomic revisions, resulted in many changes of these species names, necessitating an update of the current list. In addition, many quar...

The website fungiofpakistan.com is a collection of all the available data about macro- as well as micro-fungi collected from Pakistan. This website comprises reported fungal species with isolation source or host record, locality and updated classification. The data on this website is based on old literature (library data, personal data of specific...

Armillaria species have a global distribution and play various roles in the natural ecosystems, e.g., pathogens, decomposers, and mycorrhizal associates. However, their taxonomic boundaries, speciation processes, and origin are poorly understood. Here, we used a phylogenetic approach with 358 samplings from Europe, East Asia, and North America to d...

Microbial activity in stored rice grains could cause quality deterioration and mycotoxin accumulation that may lead to serious economic losses and food safety risks. However, limited studies have examined the spatial and temporal variation of microbial communities associated with stored rice grains. Here, we performed amplicon sequence analysis to...

Mycotoxin contamination of rice (Oryza sativa), especially that from aflatoxins (AFTs), is one of the greatest chemical hazards to humans and animals. However, few studies have investigated the relationships between fungal communities and mycotoxin contamination of rice grains. In the present study, we collected rice grain samples from 10 provinces...

Recent publications have argued that there are potentially serious consequences for researchers in recognising distinct genera in the terminal fusarioid clade of the family Nectriaceae. Thus, an alternate hypothesis, namely a very broad concept of the genus Fusarium was proposed. In doing so, however, a significant body of data that supports distin...

Rust fungi taxonomically belonging to Pucciniales (Basidiomycota) are important phytopathogens that cause many significant diseases to agricultural crops and forest trees. Hitherto, ca. 8000 and 1200 species have been reported from worldwide and China, respectively. To investigate and document the diversity of rust fungi in China, we have sampled f...

Leptosphaerulina leaf blight occurs on most turfgrasses. Hitherto, Leptosphaerulina species associated with this disease include L. americana, L. argentinensis, L. australis, and L. trifolii. However, following Koch’s postulates, L. australis was confirmed as saprobes but not pathogens, and the other three species have not been tested. The pathogen...

Epiphytic orchids exhibit varying degrees of phorophyte tree specificity. We performed a pilot study to investigate why epiphytic orchids prefer or avoid certain trees. We selected two orchid species, Panisea uniflora and Bulbophyllum odoratissimum co-occurring in a forest habitat in southern China, where they showed a specific association with Que...

Little is known about how multiple factors including land‐based inputs and ocean currents affect the spatio‐temporal distribution of the mycoplankton in coastal regions. To explore the seasonal changes of mycoplanktonic communities and potential environmental drivers, we collected water samples from the Yellow Sea, used here as a model for subtropi...

It is now a decade since The International Commission on the Taxonomy of Fungi (ICTF) produced an overview of requirements and best practices for describing a new fungal species. In the meantime the International Code of Nomenclature for algae, fungi, and plants (ICNafp) has changed from its former name (the International Code of Botanical Nomencla...

Fusarium wilt of tomato caused by the pathogen Fusarium oxysporum f. sp. lycopersici (Fol) is one of the most devastating soilborne diseases of tomato. To evaluate whether microbial community composition associated with Fol-infected tomato is different from healthy tomato, we analyzed the tomato-associated microbes in both healthy and Fol-infected...

Review on China’s nomenclature novelties of fungi in the new century (2000–2020).

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Fungi are essential components of all terrestrial ecosystems. Despite the crucial ecological role of soil fungi in grasslands, knowledge about fungal community diversity and structure in Mediterranean meadow habitats is still fragmentary. We analysed macrofungal communities in three geographically distinct Mediterranean montane calcareous grassland...

Fungi from unique environments exhibit special physiological characters and plenty of bioactive natural products. However, the recalcitrant genetics or poor transformation efficiencies prevent scientists from systematically studying molecular biological mechanisms and exploiting their metabolites. In this study, we targeted a guanophilic fungus Amp...

Two potential non-ribosomal peptide synthetases (NRPS) that assemble cyclodepsipeptides were identified in the genome of the novel bat guano-loving fungus Amphichorda guana by bioinformatics analysis and gene knockout experiments. Liquid chromatography coupled with mass spectrometry (LC-MS) guided isolation let to the discovery of a new cyclodepsip...

Twenty-seven Colletotrichum isolates associated with asymptomatic tissues of bamboo (Bambusoideae, Gramineae) were isolated from Anhui, Beijing, and Guangxi in China. Based on multilocus (internal transcribed spacer [ITS], glyceraldehyde-3-phosphate dehydrogenase [GAPDH], chitin synthase [CHS], actin [ACT], beta-tubulin [TUB2]) phylogenetic analyse...

Karst caves are widely distributed subsurface systems, and the microbiomes therein are proposed to be the driving force for cave evolution and biogeochemical cycling. In past years, culture-independent studies on the microbiomes of cave systems have been conducted, yet intensive microbial cultivation is still needed to validate the sequence-derived...

Gymnosporangium species ( Pucciniaceae , Pucciniales , Basidiomycota ) are the causal agents of cedar-apple rust diseases, which can lead to significant economic losses to apple cultivars. Currently, the genus contains 17 described species that alternate between spermogonial/aecial stages on Malus species and telial stages on Juniperus or Chamaecyp...

Uzbekistan, located in Central Asia, harbors a high diversity of woody plants. Diversity of wood-inhabiting fungi in the country, however, remained poorly known. This study summarizes the wood-inhabiting basidiomycte fungi (poroid and corticoid fungi plus similar taxa such as Merismodes, Phellodon, and Sarcodon) (Agaricomycetes, Basidiomycota) that...

Seven new genera, 26 new species, 10 new combinations, two epitypes, one new name, and 20 interesting new host and / or geographical records are introduced in this study. New genera are: Italiofungus (based on Italiofungus phillyreae ) on leaves of Phillyrea latifolia (Italy); Neolamproconium (based on Neolamproconium silvestre ) on branch of Tilia...

Background: Plant microbiome is an integral part of the host influencing its growth and health. The increasing evidence indicates that plant rhizosphere may recruit beneficial microbes to suppress soil-borne pathogen, but the ecological mechanisms that govern plant microbiome assembly and functions under disease in both below and aboveground compar...

Rock-inhabiting fungi (RIF) are nonlichenized fungi that naturally colonize rock surfaces and subsurfaces. The extremely slow growth rate and lack of distinguishing morphological characteristics of RIF resulted in a poor understanding on their biodiversity. In this study, we surveyed RIF colonizing historical stone monuments and natural rock format...

Despite numerous studies on marine prokaryotes, the vertical distribution patterns of bacterial community, either on the taxonomic composition or the functional structure, remains relatively unexplored. Using HiSeq-derived 16S rRNA data, the depth-related distribution patterns of taxonomic diversity and functional structure predicted from diversity...

Five new chromone methide polymers, (±)-amplisins A-D (1-4) and amplisin E (5), were isolated from a new fungicolous fungus Amplistroma fungicola. Compounds 1-5 were determined to have unusual chemical skeletons by two or three chromoe methide groups linking with different polyketides. A non-enzymatic 1,4-Michael addition of chromone methide was ve...

This article is the ninth in the series of Fungal Diversity Notes, where 107 taxa distributed in three phyla, nine classes, 31 orders and 57 families are described and illustrated. Taxa described in the present study include 12 new genera, 74 new species, three new combinations, two reference specimens, a re-circumscription of the epitype, and 15 r...

Karst caves are characterized by darkness, low temperature, high humidity, and oligotrophic organisms due to its relatively closed and strongly zonal environments. Up to now, 1626 species in 644 genera of fungi have been reported from caves and mines worldwide. In this study, we investigated the culturable mycobiota in karst caves in southwest Chin...

Seeds play key roles in the acquisition of plant pioneer microbiota, including the transmission of microbes from parent plants to offspring. However, the issues about seed microbial communities are mostly unknown, especially for their potential origins and the factors influencing the structure and composition. In this study, samples of rice seed an...

Global species diversity of fungi has been estimated to be 2.2 million to 3.8 million species. Currently, only about 120,000 species were described, less than 8% of the total species number. A number of most recent studies based on high-throughput sequencing technologies have shown that the diversity of fungi in the natural environment may even lar...