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Persoonia Jun 2023The class consists of free-living protists characterised by their complex life cycle, which includes both microscopic (amoebae, flagellates and cists) and macroscopic...
The class consists of free-living protists characterised by their complex life cycle, which includes both microscopic (amoebae, flagellates and cists) and macroscopic stages (spore-bearing fruiting bodies, sclerotia, and plasmodia). Within it, the order , with more than 450 recognised species, constitutes the largest group. Although previous studies have shown the polyphyly of some of the traditionally accepted genera, its internal phylogenetic relationships have remained uncertain so far, and together with the lack of data for some key species, it prevented any taxonomic and nomenclatural revisions. We have compiled a substantially expanded dataset in terms of both taxon sampling and molecular data, including most of the genera described to date and four unlinked DNA regions, for which we provide partial sequences: nSSU, , , and mtSSU, analysed through maximum likelihood and Bayesian methods. Our results confirm that the family is paraphyletic to the rest of . Within s.lat., the recent reinstatement of the genus for most species traditionally ascribed to , except for the type (Ronikier et al. 2022), is further supported here, as well as the definite inclusion of the genus in and s.str. () in (Prikhodko et al. 2023). Additionally, the genus is redefined to include some species previously treated in ( spp. with true columella). Within the monophyletic family , most genera are recovered as polyphyletic, suggesting that they should be no longer accepted as currently defined. However, the lack of resolution of some relationships within prevents us from resuscitating or creating several new genera to mitigate polyphyly. Among the well-defined groups with clear molecular signatures, we propose two taxonomic and nomenclatural changes at generic level: 1) a new genus, , is proposed for a major clade containing and other species with heavily calcified sporophores and, often, a true calcareous columella; 2) is resurrected for the clade containing . Additionally, is suggested as the correct name for the clade containing . The taxonomy and nomenclature of some provisional genera, currently synonymous with and , are disentangled, and we provide a comprehensive and updated nomenclatural conspectus that can be used when better resolved phylogenies are obtained. In total, 22 new combinations are proposed in different genera. A provisional key to the genera of the order is also provided. : García-Martín JM, Zamora JC, Lado C. 2023. Multigene phylogeny of the order Physarales (Myxomycetes, Amoebozoa): shedding light on the dark-spored clade. Persoonia 51: 89-124. doi: 10.3767/persoonia.2023.51.02.
PubMed: 38665983
DOI: 10.3767/persoonia.2023.51.02 -
Biodiversity Data Journal 2024A significant body of valuable data about the myxomycetes of Ukraine lies in a "grey zone". This encompasses undigitised historical books and articles published in...
BACKGROUND
A significant body of valuable data about the myxomycetes of Ukraine lies in a "grey zone". This encompasses undigitised historical books and articles published in languages such as Polish, French or German, as well as proceedings from local conferences, articles featured in local scientific journals and annual reports submitted to public authorities by employees of protected areas, published in Ukrainian or Russian. Yet, due to their exclusive existence in print and often the Cyrillic alphabet, these publications remain neither findable nor accessible to a wider audience.
NEW INFORMATION
The datasets presented here aim to summarise over 150 years of myxomycetes research in Ukraine. The majority of the data has been extracted from published literature sources spanning the years 1842 to 2023, with a minor supplement from unpublished herbarium specimens. The datasets include 5036 georeferenced occurrences, 339 taxa and 91 literature sources. Seventy-one of the used literature sources, mostly published before 2010, were uploaded to Zenodo and are available in open access.
PubMed: 38645470
DOI: 10.3897/BDJ.12.e120891 -
Applications in Plant Sciences 2024Traditional moist chamber cultures (MCs) prepared in aseptic laboratory environments using sterile Petri dishes are commonly used to quantify the microbiota of...
PREMISE
Traditional moist chamber cultures (MCs) prepared in aseptic laboratory environments using sterile Petri dishes are commonly used to quantify the microbiota of rough-bark tree species and woody vines. MCs are typically expensive and may be difficult to make, so a less expensive option made from easily available supplies was developed. These cost-friendly MCs were compared with standard laboratory methods to demonstrate their efficacy.
METHODS AND RESULTS
Modified MCs were made using inexpensive, store-bought supplies; compared to a standard laboratory setting, the modified MCs are shown to be less expensive with a faster setup time and larger size that facilitates a variety of tree and woody vine species. MC use resulted in the discovery of new species of fungi and myxomycetes with associated locality records. We provide detailed instructions for creating modified MCs, as well as a list of myxomycete species and their associated bark characteristics, pH values, and water-holding capacity.
CONCLUSIONS
This new, low-cost MC technique makes the study of microbiota more inclusive and accessible for those in research laboratories, classrooms, and homes, including both amateurs and professionals. MCs are easy to prepare, versatile, and applicable for many areas of botany and the biological sciences, potentially allowing exploration into unexplored areas in urban ecosystems.
PubMed: 38638615
DOI: 10.1002/aps3.11578 -
Scientific Reports Apr 2024Modern medicine has produced large genetic datasets of high dimensions through advanced gene sequencing technology, and processing these data is of great significance...
Modern medicine has produced large genetic datasets of high dimensions through advanced gene sequencing technology, and processing these data is of great significance for clinical decision-making. Gene selection (GS) is an important data preprocessing technique that aims to select a subset of feature information to improve performance and reduce data dimensionality. This study proposes an improved wrapper GS method based on forensic-based investigation (FBI). The method introduces the search mechanism of the slime mould algorithm in the FBI to improve the original FBI; the newly proposed algorithm is named SMA_FBI; then GS is performed by converting the continuous optimizer to a binary version of the optimizer through a transfer function. In order to verify the superiority of SMA_FBI, experiments are first executed on the 30-function test set of CEC2017 and compared with 10 original algorithms and 10 state-of-the-art algorithms. The experimental results show that SMA_FBI is better than other algorithms in terms of finding the optimal solution, convergence speed, and robustness. In addition, BSMA_FBI (binary version of SMA_FBI) is compared with 8 binary algorithms on 18 high-dimensional genetic data from the UCI repository. The results indicate that BSMA_FBI is able to obtain high classification accuracy with fewer features selected in GS applications. Therefore, SMA_FBI is considered an optimization tool with great potential for dealing with global optimization problems, and its binary version, BSMA_FBI, can be used for GS tasks.
Topics: Algorithms; Clinical Decision-Making; Genetic Techniques; Physarum polycephalum; Technology
PubMed: 38615048
DOI: 10.1038/s41598-024-59064-w -
Biodiversity Data Journal 2024As a result of the ten years (2012-2022) work under the critical revision of the genera of Reticulariaceae, a set of papers was published. Collection data of hundreds of...
BACKGROUND
As a result of the ten years (2012-2022) work under the critical revision of the genera of Reticulariaceae, a set of papers was published. Collection data of hundreds of specimens, used as a material for these studies, were provided as supplements of corresponding papers, but remained unpublished in biodiversity databases.
NEW INFORMATION
Here, we represent an occurrence dataset "Barcoded Reticulariaceae of the World", published in GBIF. It includes data on 523 myxomycete collections (including 36 types) gathered from five continents and spanning 24 countries. The dataset encompasses 43 distinct species and one subspecies of myxomycetes, including rare, endemic, and recently-described taxa. Species included to the database mainly belong to the genera , , , , and (Reticulariaceae), but as well and (Cribrariaceae). Nearly all of the research material, with the exception of several old collections, underwent molecular barcoding, primarily involving the 18S rDNA gene, but also the elongation factor 1α gene and mitochondrial cytochrome oxidase subunit I gene. For those sequences that are stored in the NCBI GenBank, accession numbers are provided in the dataset. Newly-described species make up a significant part of the studied herbarium collections; many of them can be characterised as common for their region. A particularly high level of taxonomic novelty is observed in Australia, which may be explained by the endemism of the local myxomycete biota.
PubMed: 38469226
DOI: 10.3897/BDJ.12.e115630 -
Anais Da Academia Brasileira de Ciencias 2024The family Physaraceae (Physarales, Myxomycetes) is represented in Brazil by eight genera and 75 species. Based on data obtained from the GBIF, SpeciesLink, Flora and...
The family Physaraceae (Physarales, Myxomycetes) is represented in Brazil by eight genera and 75 species. Based on data obtained from the GBIF, SpeciesLink, Flora and Funga do Brasil platforms, collections from the IPA and URM Herbaria and material collected since 1960 deposited in the UFP Herbarium, the microhabitats and distribution of Badhamiopsis (1sp.) and Badhamia (10 spp.) in Brazilian biomes are commented. An identification key for the species and the first report of B. melanospora from the state of Paraíba, B. panicea from the state of Paraná and B. ovispora from Brazil are presented.
Topics: Myxomycetes; Brazil; Ecosystem
PubMed: 38451623
DOI: 10.1590/0001-3765202420220698 -
Optics Express Feb 2024Brilliant colors in nature arise from the interference of light with periodic nanostructures resulting in structural color. While such biological photonic structures...
Brilliant colors in nature arise from the interference of light with periodic nanostructures resulting in structural color. While such biological photonic structures have long attracted interest in insects and plants, they are little known in other groups of organisms. Unexpected in the kingdom of Amoebozoa, which assembles unicellular organisms, structural colors were observed in myxomycetes, an evolutionary group of amoebae forming macroscopic, fungal-like structures. Previous work related the sparkling appearance of Diachea leucopodia to thin film interference. Using optical and ultrastructural characterization, we here investigated the occurrence of structural color across 22 species representing two major evolutionary clades of myxomycetes including 14 genera. All investigated species showed thin film interference at the peridium, producing colors with hues distributed throughout the visible range that were altered by pigmentary absorption. A white reflective layer of densely packed calcium-rich shells is observed in a compound peridium in Metatrichia vesparium, whose formation and function are still unknown. These results raise interesting questions on the biological relevance of thin film structural colors in myxomycetes, suggesting they may be a by-product of their reproductive cycle.
Topics: Myxomycetes; Amoebozoa; Calcium; Nanostructures; Photons
PubMed: 38439270
DOI: 10.1364/OE.511875 -
Protist Apr 2024The nivicolous species of the genus Diderma are challenging to identify, and there are several competing views on their delimitation. We analyzed 102 accessions of...
The nivicolous species of the genus Diderma are challenging to identify, and there are several competing views on their delimitation. We analyzed 102 accessions of nivicolous Diderma spp. that were sequenced for two or three unlinked genes to determine which of the current taxonomic treatments is better supported by molecular species delimitation methods. The results of a haplotype web analysis, Bayesian species delimitation under a multispecies coalescent model, and phylogenetic analyses on concatenated alignments support a splitting approach that distinguishes six taxa: Diderma alpinum, D. europaeum, D. kamchaticum, D. meyerae, D. microcarpum and D. niveum. The first two approaches also support the separation of Diderma alpinum into two species with allopatric distribution. An extended dataset of 800 specimens (mainly from Europe) that were barcoded with 18S rDNA revealed only barcode variants similar to those in the species characterized by the first data set, and showed an uneven distribution of these species in the Northern Hemisphere: Diderma microcarpum and D. alpinum were the only species found in all seven intensively sampled mountain regions. Partial 18S rDNA sequences serving as DNA barcodes provided clear signatures that allowed for unambiguous identification of the nivicolous Diderma spp., including two putative species in D. alpinum.
Topics: Myxomycetes; DNA Barcoding, Taxonomic; Bayes Theorem; Phylogeny; DNA, Ribosomal
PubMed: 38368650
DOI: 10.1016/j.protis.2024.126023 -
PeerJ 2024A new myxomycete species, , was described based on morphological evidence and phylogenetic analyses. The species was discovered in the arid region at the confluence of...
A new myxomycete species, , was described based on morphological evidence and phylogenetic analyses. The species was discovered in the arid region at the confluence of the Badain Jaran desert and Tengger desert on the leaves of and was cultivated in a moist chamber culture. Morphologically, the species is distinguished by the greenish-yellow calcium carbonate crystals on the surface and the spores covered with small warts, some of which are connected into a short line. A phylogenetic analysis of strongly supports its classification as a separate clade. The spore to spore agar culture of . requires 23 days, and this study provides a detailed description of its life cycle.
Topics: Myxomycetes; Phylogeny; Microscopy, Electron, Scanning; Desert Climate; Spores, Protozoan; Physarida
PubMed: 38213774
DOI: 10.7717/peerj.16725 -
Mycology 2023Species in the class Myxomycetes (or Myxogastrea) are essential components of biodiversity and play important ecological roles in terrestrial ecosystems, especially in... (Review)
Review
Species in the class Myxomycetes (or Myxogastrea) are essential components of biodiversity and play important ecological roles in terrestrial ecosystems, especially in forests. Studies on the taxonomy and diversity of these organisms started late in China. However, significant progress in China has been made in modern taxonomic studies on myxomycetes based on long-term species surveying and specimen collecting. The existing achievements have shown that comprehensive and continuous studies on the taxonomy and diversity of myxomycetes in China have the potential to enhance global biodiversity and improve the geographic distribution pattern of myxomycetes. Therefore, building on the current research foundation and expanding myxomycete research in a wider and more in-depth approach is imperative.
PubMed: 38187883
DOI: 10.1080/21501203.2023.2255031