DNA barcoding of fungal specimens using PacBio long-read high-throughput sequencing

Third-generation PacBio sequencing to explore gut bacteria and gender in colorectal cancer

BACKGROUND

Gut bacteria have an important influence on colorectal cancer (CRC). The differences of gut bacteria between genders have been the hot spots.

OBJECTIVE

To analyze the relationship between gut bacteria and gender differences in patients with CRC.

METHODS

A total of 212 patients with CRC and 212 healthy volunteers were recruited. The subjects' fecal samples were obtained, and the fecal microorganisms were analyzed by the third-generation sequencing PacBio. The composition of gut bacteria was analyzed. Linear discriminant analysis Effect Size (LEfSe) was used to analyze the differences in gut bacteria. Pearson coefficient was used to calculate the correlation between differential bacteria. CRC risk prediction models were used to rank the importance of effective differential bacteria.

RESULTS

Escherichia flexneri and Phocaeicola vulgatus were the most frequent bacteria in both male and female CRC patients. Bacteroides, Verrucomicrobia and Akkermansiaceae were highly enriched in male CRC group, while Bacteroidetes, Phocaeicola and Tissierellales were highly enriched in female CRC group. Peptostreptococcus anaerobius and Phocaeicola vulgatus were important CRC related bacteria in males and females, respectively. Peptostreptococcus anaerobius was the most important characteristic bacterium of males (AUC = 0.951), and the sensitivity and specificity of the discovery set were 78.74 % and 93.98 %, respectively. Blautia stercoris was the most important characteristic bacterium of females (AUC = 0.966), and the sensitivity and specificity of the discovery set were 90.63 % and 90.63 %, respectively.

CONCLUSION

Gut bacteria varied in different genders. Therefore, gender should be considered when gut bacteria are applied in the diagnose and prevention of CRC.

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

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

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

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

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

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 and offers nearly 10 million such sequences for reference. These are clustered into ∼2.4M species hypotheses (SHs), each assigned a unique digital object identifier (DOI) to promote unambiguous referencing across studies. UNITE users have contributed over 600 000 third-party sequence annotations, which are shared with a range of databases and other community resources. Recent improvements facilitate the detection of cross-kingdom biological associations and the integration of undescribed groups of organisms into everyday biological pursuits. Serving as a digital twin for eukaryotic biodiversity and communities worldwide, the latest release of UNITE offers improved avenues for biodiversity discovery, precise taxonomic communication and integration of biological knowledge across platforms.

Cryptic Species in Ecotoxicology

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

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

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

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

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

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

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

Applying a modified metabarcoding approach for the sequencing of macrofungal specimens from fungarium collections

PREMISE

Fungaria are an underutilized resource for understanding fungal biodiversity. The effort and cost of producing DNA barcode sequence data for large numbers of fungal specimens can be prohibitive. This study applies a modified metabarcoding approach that provides a labor-efficient and cost-effective solution for sequencing the fungal DNA barcodes of hundreds of specimens at once.

METHODS

We applied a two-step PCR approach using nested, barcoded primers to sequence the fungal nrITS2 region of 766 macrofungal specimens using the Illumina platform. The specimens represent a broad taxonomic sampling of the Dikarya. Of these, 382 Lactarius specimens were analyzed to identify molecular operational taxonomic units (MOTUs) using a phylogenetic approach. The raw sequences were trimmed, filtered, assessed, and analyzed using the DADA2 amplicon de-noising toolkit and Biopython. The sequences were compared to the NCBI and UNITE databases and Sanger nrITS sequences from the same specimens.

RESULTS

The taxonomic identities derived from the nrITS2 sequence data were >90% accurate across all specimens sampled. A phylogenetic analysis of the Lactarius sequences identified 20 MOTUs.

DISCUSSION

The results demonstrate the capacity of these methods to produce nrITS2 sequences from large numbers of fungarium specimens. This provides an opportunity to more effectively use fungarium collections to advance fungal diversity identification and documentation.

Soil mycobiome in sustainable agriculture

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

Next-Generation Sequencing of Ancient and Recent Fungarium Specimens

Fungaria are an unmatched resource for providing genetic data from authoritative, taxonomically-correct fungal species, especially type specimens. These specimens serve to anchor species hypotheses by enabling the correct taxonomic placement of taxa in systematic studies. The DNA from ancient specimens older than 30 years is commonly fragmented, and sometimes highly contaminated by exogenous, non-target fungal DNA, making conventional PCR amplification and Sanger sequencing difficult or impossible. Here, we present the results of DNA extraction, PCR amplification of the ITS2 region, and Illumina MiSeq Nano sequencing of nine recent and 11 ancient specimens, including seven type specimens. The taxa sampled included a range of large and fleshy, to small and tough, or small, melanized specimens of Discina, Gyromitra, Propolis, Stictis, and Xerotrema, with a culture of Lasiosphaeria serving as a positive control. DNA was highly fragmented and in very low quantity for most samples, resulting in inconclusive or incorrect results for all but five samples. Taxonomically-correct sequences were generated from the holotype specimens of G. arctica, G. korshinskii, and G. leucoxantha, from the neotype of G. ussuriensis, and from the positive control. Taxonomic assignments were confirmed through morphology, top BLASTn hits, and maximum likelihood phylogenetic analyses. Though this study was not cost-effective due to the small number of samples submitted and few generating correct sequences, it did produce short DNA barcode fragments for four type specimens that are essential for their correct taxonomic placement in our ongoing systematic studies.