The UNITE database for molecular identification and taxonomic communication of fungi and other eukaryotes: sequences, taxa and classifications reconsidered

Nucleic Acids Research, Год журнала: 2023, Номер 52(D1), С. D791 - D797

Опубликована: Ноя. 11, 2023

Abstract UNITE (https://unite.ut.ee) is a web-based database and sequence management environment for molecular identification of eukaryotes. It targets the nuclear ribosomal internal transcribed spacer (ITS) region offers nearly 10 million such sequences reference. These are clustered into ∼2.4M species hypotheses (SHs), each assigned unique digital object identifier (DOI) to promote unambiguous referencing across studies. users have contributed over 600 000 third-party annotations, which shared with range databases other community resources. Recent improvements facilitate detection cross-kingdom biological associations integration undescribed groups organisms everyday pursuits. Serving as twin eukaryotic biodiversity communities worldwide, latest release improved avenues discovery, precise taxonomic communication knowledge platforms.

Язык: Английский

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Current trends, limitations and future research in the fungi?

Fungal Diversity, Год журнала: 2024, Номер 125(1), С. 1 - 71

Опубликована: Март 20, 2024

Abstract The field of mycology has grown from an underappreciated subset botany, to a valuable, modern scientific discipline. As this study grown, there have been significant contributions science, technology, and industry, highlighting the value fungi in era. This paper looks at current research, along with existing limitations, suggests future areas where scientists can focus their efforts, mycology. We show how become important emerging diseases medical discuss trends potential drug novel compound discovery. explore phylogenomics, its potential, outcomes address question phylogenomics be applied fungal ecology. In addition, functional genomics studies are discussed importance unravelling intricate mechanisms underlying behaviour, interactions, adaptations, paving way for comprehensive understanding biology. look research building materials, they used as carbon sinks, biocircular economies. numbers always great interest often written about estimates varied greatly. Thus, we needs order obtain more reliable estimates. aspects machine learning (AI) it mycological research. Plant pathogens affecting food production systems on global scale, such, needed area, particularly disease detection. latest data High Throughput Sequencing if still gaining new knowledge same rate before. A review nanotechnology is provided addressed. Arbuscular Mycorrhizal Fungi addressed acknowledged. Fungal databases becoming important, therefore provide major databases. Edible medicinal huge medicines, especially Asia prospects discussed. Lifestyle changes (e.g., endophytes, pathogens, and/or saprobes) also extremely trend special issue Diversity.

Язык: Английский

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Fungal biodeterioration and preservation of cultural heritage, artwork, and historical artifacts: extremophily and adaptation

Microbiology and Molecular Biology Reviews, Год журнала: 2024, Номер 88(1)

Опубликована: Янв. 5, 2024

SUMMARYFungi are ubiquitous and important biosphere inhabitants, their abilities to decompose, degrade, otherwise transform a massive range of organic inorganic substances, including plant matter, rocks, minerals, underpin major significance as biodeteriogens in the built environment cultural heritage. Fungi often most obvious agents heritage biodeterioration with effects ranging from discoloration, staining, biofouling destruction building components, historical artifacts, artwork. Sporulation, morphological adaptations, explorative penetrative lifestyle filamentous fungi enable efficient dispersal colonization solid substrates, while many species able withstand environmental stress factors such desiccation, ultra-violet radiation, salinity, potentially toxic substances. Many can grow under nutrient-limited conditions, produce resistant cell forms that survive through long periods adverse conditions. The fungal chemoorganotrophic metabolism therefore adaptation success frequently encountered extremophilic conditions associated indoor outdoor Apart free-living fungi, lichens growth form pioneer colonizers materials, especially stone- mineral-based components. This article surveys roles heritage, reference mechanisms involved relation substances encountered, well methods by which be assessed combated, how certain processes may utilized bioprotection.

Язык: Английский

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The influence of tree genus, phylogeny, and richness on the specificity, rarity, and diversity of ectomycorrhizal fungi

Environmental Microbiology Reports, Год журнала: 2024, Номер 16(2)

Опубликована: Апрель 1, 2024

Abstract Partner specificity is a well‐documented phenomenon in biotic interactions, yet the factors that determine plant‐fungal associations remain largely unknown. By utilizing composite soil samples, we identified predictors drive partner both plants and fungi, with particular focus on ectomycorrhizal associations. Fungal guilds exhibited significant differences overall preference avoidance, richness, to specific tree genera. The highest level of was observed root endophytic associations, while lowest found arbuscular mycorrhizal majority fungal species showed for one their trees, primarily at plant genus level. Specialist fungi were dominant belowground communities terms richness relative abundance. Moreover, all genera (and occasionally species) demonstrated certain groups. not related rarity or environmental conditions, except pH. Depending genus, became more prevalent relatively abundant increasing stand age, dominance, pH conditions optimal genus. increased evenness multi‐host enhanced fungi. However, it partner‐generalist contributed high diversity mixed forests.

Язык: Английский

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How, not if, is the question mycologists should be asking about DNA-based typification

MycoKeys, Год журнала: 2023, Номер 96, С. 143 - 157

Опубликована: Апрель 10, 2023

Fungal metabarcoding of substrates such as soil, wood, and water is uncovering an unprecedented number fungal species that do not seem to produce tangible morphological structures defy our best attempts at cultivation, thus falling outside the scope International Code Nomenclature for algae, fungi, plants. The present study uses new, ninth release hypotheses UNITE database show discovery through environmental sequencing vastly outpaces traditional, Sanger sequencing-based efforts in a strongly increasing trend over last five years. Our findings challenge stance some mycological community - current situation satisfactory no change needed "the code" suggest we should be discussing whether allow DNA-based descriptions (typifications) by extension higher ranks but what precise requirements typifications be. We submit tentative list criteria further discussion. authors hope revitalized deepened discussion on typification, because us it seems harmful counter-productive intentionally deny overwhelming majority extant fungi formal standing under

Язык: Английский

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Single-worm long-read sequencing reveals genome diversity in free-living nematodes

Nucleic Acids Research, Год журнала: 2023, Номер 51(15), С. 8035 - 8047

Опубликована: Авг. 1, 2023

Obtaining sufficient genetic material from a limited biological source is currently the primary operational bottleneck in studies investigating biodiversity and genome evolution. In this study, we employed multiple displacement amplification (MDA) Smartseq2 to amplify nanograms of genomic DNA mRNA, respectively, individual Caenorhabditis elegans. Although reduced coverage was observed repetitive regions, produced assemblies covering 98% reference using long-read sequences generated with Oxford Nanopore Technologies (ONT). Annotation sequenced transcriptome coupled available assembly revealed that gene predictions were more accurate, complete contained far fewer false positives than de novo approaches. We sampled genomes transcriptomes 13 nematodes early-branching species Chromadoria, Dorylaimia Enoplia. The basal Chromadoria Enoplia had larger sizes, ranging 136.6 738.8 Mb, compared those other clades. Nine mitogenomes fully assembled, displayed lack synteny species. Phylogenomic analyses based on new annotations strong support for as sister rest Nematoda. Our result demonstrates robustness MDA combination ONT, paving way study diversity phylum Nematoda beyond.

Язык: Английский

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Planktonic Marine Fungi: A Review

Journal of Geophysical Research Biogeosciences, Год журнала: 2024, Номер 129(3)

Опубликована: Март 1, 2024

Abstract Fungi in marine ecosystems play crucial roles as saprotrophs, parasites, and pathogens. The definition of fungi has evolved over the past century. Currently, “marine fungi” are defined any recovered repeatedly from habitats that able to grow and/or sporulate environments, form symbiotic relationships with other organisms, adapt evolve at genetic level, or active metabolically environments. While there a number recent reviews synthesizing our knowledge derived century research on fungi, this review article focuses state planktonic coastal open ocean, suspension attached particles, substrates association hosts pelagic zone their remineralization organic matter major biogeochemical cycles. This differs previous ones by focusing impacts methodological considerations for investigating diversity ecological functions. Importantly, we point out gaps potential biases might have contributed these gaps. Finally, highlight recommendations will facilitate future studies fungi. first provides brief overview followed discussion wide range methods can be used study

Язык: Английский

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Soil mycobiome in sustainable agriculture

Frontiers in Microbiology, Год журнала: 2022, Номер 13

Опубликована: Ноя. 28, 2022

The soil microbiome contributes to several ecosystem processes. It plays a key role in sustainable agriculture, horticulture and forestry. In contrast the vast number of studies focusing on bacteria, amount research concerning fungal communities is limited. This despite fact that fungi play crucial cycling matter energy Earth. Fungi constitute significant part pathobiome plants. Moreover, many them are indispensable plant health. group includes mycorrhizal fungi, superparasites pathogens, generalists; they stabilize mycobiome biogeochemical cycles. Several species also contribute bioremediation through their uptake high amounts contaminants from environment. mycelia stretch below ground like blood vessels human body, transferring water nutrients various Recent advances high-throughput sequencing combined with bioinformatic tools have facilitated detailed mycobiome. review discusses beneficial effects mycobiomes interactions other microbes hosts both healthy unhealthy ecosystems. may be argued studying such fashion an essential step promoting regenerative agriculture.

Язык: Английский

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Cryptic Species in Ecotoxicology

Environmental Toxicology and Chemistry, Год журнала: 2023, Номер 42(9), С. 1889 - 1914

Опубликована: Июнь 14, 2023

The advent of genetic methods has led to the discovery an increasing number species that previously could not be distinguished from each other on basis morphological characteristics. Even though there been exponential growth publications cryptic species, such are rarely considered in ecotoxicology. Thus, particular question ecological differentiation and sensitivity closely related is addressed. Tackling this question, however, key importance for evolutionary ecology, conservation biology, and, particular, regulatory At same time, use with (known or unknown) diversity might a reason lack reproducibility ecotoxicological experiments implies false extrapolation findings. Our critical review includes database literature search through which we investigated how many most frequently used assessments show evidence diversity. We found high proportion reports indicating overlooked diversity, especially invertebrates. In terrestrial aquatic realms, at least 67% 54% commonly respectively, were identified as complexes. issue less prominent vertebrates, complexes 27% 6.7% vertebrates. further exemplified why different histories may significantly determine species' ecology pollutants. This turn have major impact results tests consequently, outcome environmental risk assessments. Finally, provide brief guideline deal practically studies general its implementation assessment procedures particular. Environ Toxicol Chem 2023;42:1889-1914. © 2023 Authors. Environmental Toxicology Chemistry published by Wiley Periodicals LLC behalf SETAC.

Язык: Английский

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Does One Size Fit All? Variations in the DNA Barcode Gaps of Macrofungal Genera

Journal of Fungi, Год журнала: 2023, Номер 9(8), С. 788 - 788

Опубликована: Июль 26, 2023

The nuclear ribosomal internal transcribed spacer (nrITS) region has been widely used in fungal diversity studies. Environmental metabarcoding increased the importance of DNA barcode documenting and distribution. gap is seen as difference between intra- inter-specific pairwise distances a barcode. current understanding macrofungi limited, inhibiting development best practices applying nrITS toward research on diversity. This study examined using 5146 sequences representing 717 species from eleven genera, eight orders two phyla datasets assembled by taxonomic experts. Intra- were measured sequence phylogenetic data. results demonstrate that gaps are influenced differences variance distances. In terms behavior, greater ITS1 than ITS2, both relative to combined region. Due variance, ITS2 ITS1. Additionally, approach "splitting" taxa into numerous units produces when compared "lumping". show variability taxa, demonstrating need understand accuracy barcoding quantifying richness. For studies, data supports application multiple molecular markers corroborate systematic delineation species.

Язык: Английский

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