Morphological and phylogenetic analyses reveal two new Penicillium species isolated from the ancient Great Wall loess in Beijing, China.

Introduction: Penicillium species exhibit a broad distribution in nature and play a crucial role in human and ecological environments. Methods: Two Penicillium species isolated from the ancient Great Wall loess in the Mentougou District of Beijing, China, were identified and described as new species, namely, Penicillium acidogenicum and P. floccosum, based on morphological characteristics and phylogenetic analyses of multiple genes including ITS, BenA, CaM, and RPB2 genes. Results: Phylogenetic analyses showed that both novel species formed a distinctive lineage and that they were most closely related to P. chrzaszczii and P. osmophilum, respectively. Discussion: Penicillium acidogenicum is characterized by biverticillate conidiophores that produce globose conidia and is distinguished from similar species by its capacity to grow on CYA at 30°C. Penicillium floccosum is typically recognized by its restricted growth and floccose colony texture. The description of these two new species provided additional knowledge and new insights into the ecology and distribution of Penicillium.

Glochidionyangchunense (Phyllanthaceae), a new species with discoid flowers from Guangdong Province, China.

Phyllanthodendron can be readily morphologically distinguished from Glochidion, but recent molecular evidence showed that Phyllanthodendron is paraphyletic due to Glochidion being nested within it. In this study, a new species of the former Phyllanthodendron is described and illustrated as Glochidionyangchunense Z.Q. Song & Gang Yao from the limestone areas of South China. This is a peculiar new species and morphologically distinguished by its discoid flowers, T-shaped disc segments, and glabrous flowering branches. A key to Glochidionyangchunense and related species in China is provided here.

Confirmation of the valid specific status of Dolichovespulakuami Kim & Yoon, 1996 (Hymenoptera, Vespidae) based on molecular and morphological evidence.

The taxonomic validity of Dolichovespulakuami, especially in relation to D.flora, has been the subject of a long-term debate. Herein, the valid specific status of the former was supported through an integrated analysis of morphological characters and DNA barcodes. The pronotal rugae and male genitalia of the two species are different, and partial mitochondrial genes (cytochrome oxidase subunit I, COI) indicate that they form significantly distinct lineages. The hitherto unknown male of D.kuami is described for the first time, and a brief discussion of the D.maculata species group is provided.

The arboreal snail genus Amphidromus Albers, 1850 (Eupulmonata, Camaenidae) of Southeast Asia: 1. Molecular systematics of some Vietnamese species and related species from Cambodia, Indonesia, and Laos.

This paper reassesses the taxonomy and systematics of 11 arboreal snail species in the genus Amphidromus from Vietnam, Cambodia, Indonesia and Laos (A.bozhii Wang, 2019, A.buelowi Fruhstorfer, 1905, A.costifer Smith, 1893, A.haematostoma Möllendorff, 1898, A.ingens Möllendorff, 1900, A.madelineae Thach, 2020, A.metabletus Möllendorff, 1900, A.pankowskianus Thach, 2020, A.placostylus Möllendorff, 1900, A.roseolabiatus Fulton, 1896, and A.thachi Huber, 2015). The taxonomic validity of each species is supported by a phylogenetic analysis of mitochondrial COI and 16S rRNA gene fragments from 17 ingroup taxa. Amphidromusbuelowi was found to comprise two populations from two distant localities, one from Mount Singgalang, West Sumatra, Indonesia and the other from southern Vietnam. The samples from southern Vietnam were previously described as A.asper Haas, 1934 and A.franzhuberi Thach, 2016, but they are now treated as junior synonyms of A.buelowi in this study. In addition, two species from Vietnam are described as new to science, viz. A.asperoides Jirapatrasilp & Lee, sp. nov. and A.ingensoides Jirapatrasilp & Lee, sp. nov., each of which is conchologically comparable to A.buelowi and A.ingens, respectively.

Four new species of Anyphaena Sundevall, 1833 from Xizang, China (Araneae, Anyphaenidae).

Four new species of the genus Anyphaena Sundevall, 1833 collected from Xizang, China, are described: A.cibagou Wang & Mi, sp. nov. (♂♀), A.linzhi Wang & Mi, sp. nov. (♂♀), A.shufui Wang & Mi, sp. nov. (♀) and A.yejiei Wang & Mi, sp. nov. (♀). Diagnostic photos of the habitus and copulatory organs and a distributional map are provided.

Species divergence in valleys: the phylogeny of Phrynocephalus forsythii complex and description of a new species.

Background: Geographic isolation caused by high-altitude valleys promotes the formation of geographic segregation of species, leading to species differentiation. The subgenus Oreosaura contains viviparous species from the Tibetan Plateau and the vicinity of the Tarim Basin, which can be divided into three species complexes according to their geographical distribution: Phrynocephalus vlangalii, Phrynocephalus theobaldi, and Phrynocephalus forsythii. However, molecular data for the P. forsythii complex are limited and the diversity of this species complex has been greatly underestimated. Therefore, this study aimed to explore the species diversity of Oreosaura and species differentiation within the P. forsythii complex. Methods: We analysed the species diversity of Oreosaura by combining previous data, constructed a phylogenetic tree of the subgenus based on cytochrome c oxidase subunit I and 16S sequences, and estimated the divergence time. Results: The results suggest significant genetic differences between the Tarim Basin populations and adjacent mountain valley populations of the P. forsythii complex and that the combination of deep valley landscapes in the high mountains and ice-age events have contributed to the differentiation of the viviparous toad-headed agama lizard, which is a key factor in the phylogenetics of the P. forsythii complex. Furthermore, we identified a population collected from Wuqia County, Xinjiang, as a new species, Phrynocephalus kangsuensis sp. nov. The results will provide data for phylogenetic studies following the P. forsythii complex and help demonstrate that valleys promote the formation of Phrynocephalus species.

Ten common issues with reference sequence databases and how to mitigate them.

Metagenomic sequencing has revolutionized our understanding of microbiology. While metagenomic tools and approaches have been extensively evaluated and benchmarked, far less attention has been given to the reference sequence database used in metagenomic classification. Issues with reference sequence databases are pervasive. Database contamination is the most recognized issue in the literature; however, it remains relatively unmitigated in most analyses. Other common issues with reference sequence databases include taxonomic errors, inappropriate inclusion and exclusion criteria, and sequence content errors. This review covers ten common issues with reference sequence databases and the potential downstream consequences of these issues. Mitigation measures are discussed for each issue, including bioinformatic tools and database curation strategies. Together, these strategies present a path towards more accurate, reproducible and translatable metagenomic sequencing.

Species diversity and taxonomy of Vararia (Russulales, Basidiomycota) with descriptions of six species from Southwestern China.

Vararia is a species-rich genus in the family Peniophoraceae and has been shown to be polyphyletic. In this study, sequences of ITS and LSU rRNA markers of the studied samples were generated and phylogenetic analyses were performed with the maximum likelihood, maximum parsimony, and Bayesian inference methods. Seventeen lineages including six new species from China, i.e., V.fissurata, V.lincangensis, V.punctata, V.isabellina, V.sinensis, and V.yaoshanensis were recognized, in which V.fissurata is characterized by the brittle basidiomata with pruinose and cracking hymenophore having white to olivaceous buff hymenial surface, the clamped generative hyphae, presence of the two types gloeocystidia; V.lincangensis is characterized by the simple-septa generative hyphae, and thick-walled skeletal hyphae, and ellipsoid basidiospores; V.punctata is delimited by its thin to slightly thick-walled generative hyphae, and thick-walled skeletal hyphae, present thick-walled, clavate to cylindrical gloeocystidia; V.isabellina is characterized by having the cream to isabelline to slightly brown hymenial surface, thin to slightly thick-walled generative hyphae, and sub-fusiform to navicular basidiospores; V.sinensis is distinguishable by its white to slightly pink hymenial surface, thick-walled skeletal hyphae, and sub-fusiform to navicular basidiospores; V.yaoshanensis is characterized by cream to pinkish buff to cinnamon-buff hymenial surface, slightly thick-walled generative hyphae, the presence of two types gloeocystidia, and slightly thick-walled, ellipsoid basidiospores. Phylogram based on the ITS+nLSU rDNA gene regions included nine genera within the family Peniophoraceae as Amylostereum, Asterostroma, Baltazaria, Dichostereum, Michenera, Peniophora, Scytinostroma and Vararia, in which the six new wood-inhabiting fungi species were grouped into genus Vararia. The phylogenetic tree inferred from the combined ITS and LSU tree sequences highlighted that V.fissurata was found to be the sister to V.ellipsospora with strong supports. Additionally, V.lincangensis was clustered with V.fragilis. Furthermore, V.punctata was retrieved as a sister to V.ambigua. Moreover, V.sinensis was grouped with five taxa as V.breviphysa, V.pirispora, V.fusispora, V.abortiphysa and V.insolita. The new species V.isabellina formed a monophyletic lineage, in which it was then grouped closely with V.daweishanensis, and V.gracilispora. In addition, V.yaoshanensis was found to be the sister to V.gallica with strong supports. The present results increased the knowledge of Vararia species diversity and taxonomy of corticioid fungi in China. An identification key to 17 species of Vararia in China is provided.

Four new species of Dothideomycetes (Ascomycota) from Pará Rubber (Heveabrasiliensis) in Yunnan Province, China.

The tropical areas in southern and south-western Yunnan are rich in fungal diversity. Additionally, the diversity of seed flora in Yunnan Province is higher than in other regions in China and the abundant endemic species of woody plants provide favourable substrates for fungi. Rubber plantations in Yunnan Province are distributed over a large area, especially in Xishuangbanna. During a survey of rubber-associated fungi in Yunnan Province, China, dead rubber branches with fungal fruiting bodies were collected. Morphological characteristics and multigene phylogenetic analyses (ITS, LSU, SSU, rpb2 and tef1-α) revealed four distinct new species, described herein as Melomastiapuerensis, Nigrogranalincangensis, Pseudochaetosphaeronemalincangensis and Pseudochaetosphaeronemaxishuangbannaensis. Detailed descriptions, illustrations and phylogenetic trees are provided to show the taxonomic placements of these new species.

Identification of long-preserved specimens reveals the historical geographic range of the Patagonian lamprey Geotria macrostoma (Burmeister, 1868) in southern South America.

The lamprey genus Geotria Gray, 1851 currently includes only two species: G. australis and G. macrostoma. However, taxonomic relationships within the genus have traditionally been ambiguous and difficult to establish due to the extreme changes in morphology, dentition, and coloration that lampreys undergo during their life cycles, particularly during upstream migration and sexual maturation. Consequently, several lamprey specimens held in museum collections have remained unidentified, especially those from Argentina. In this study, a series of morphometric characters were subjected to discriminant function analysis (DFA) to identify the lamprey species collected during 1867-2004 from the de la Plata River and Patagonia. These specimens are housed at the Museo Argentino de Ciencias Naturales "Bernardino Rivadavia" in Buenos Aires, the Museo de Historia Natural de Montevideo, and the Naturhistoriska riksmuseet in Stockholm. Based on the proportions of the length of the oral disc, prebranchial, and pre-caudal body regions, and the depth of the trunk, DFA provided conclusive evidence that the specimens corresponded to the recently revalidated G. macrostoma (Burmeister, 1868), which was originally incorrectly named as Petromyzon macrostomus Burmeister, 1868, Exomegas macrostomus (Berg, 1899), Geotria chilensis (Berg, 1895), and Geotria macrostoma f. gallegensis Smitt, 1901, as well as other nontype museum individuals of uncertain taxonomic status. The identifications of these long-preserved museum specimens provided key information on the historical geographic range of Argentinian lampreys and suggest that the disappearance of the species reported from northern localities (the Pampean Region) can be attributed to the degradation of their critical habitats, primarily caused by anthropogenic impact and climate change.

Isoptericola luteus sp. nov., a novel yellow bacterium isolated from soil.

An aerobic, non-motile, Gram-stain-positive bacterium, designated strain NEAU-Y5T, was isolated from a soil sample collected from Northeast Agricultural University, Heilongjiang province. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NEAU-Y5T belonged to the genus and showed high 16S rRNA sequence similarity to Isoptericola variabilis (98.9 %), Isoptericola nanjingensis (98.9 %), Isoptericola cucumis (98.5 %), Isoptericola hypogeus (98.5 %), Isoptericola dokdonensis (98.5 %), Isoptericola jiangsuensis (98.3 %), and Isoptericola halalbus (98.1 %), followed by other members of the genus Isoptericola (<98 %), and phylogenetically clustered with I. dokdonensis and I. jiangsuensis. Strain NEAU-Y5T was found to grow at 4-40 °C (optimum, 28 °C), pH 6.0-12.0 (optimum, pH 7.0), and tolerated 0-6 % NaCl (w/v). The cell-wall peptidoglycan type was l-Lys-d-Asp. The whole-cell hydrolysates contained glucose, galactose, and ribose. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, hydroxyphosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside, and glucosamine unknown phospholipid. Major fatty acids were anteiso-C15 : 0 and anteiso-C17 : 0. The predominant menaquinone was MK-9(H4). The DNA G+C content was 73.4 mol%. The digital DNA-DNA hybridization and average nucleotide identity values between strain NEAU-Y5T and the type strains of the genus Isoptericola ranged from 18.6 to 23.5 % and from 77.3 to 81.6 %, respectively. Based on morphological, physiological, chemotaxonomic, and phylogenetic data, as well as digital DNA-DNA hybridization and average nucleotide identity values, the novel strain NEAU-Y5T could be differentiated from its closest relatives. Therefore, the strain represents a novel species of the genus Isoptericola, for which the name Isoptericola luteus sp. nov. is proposed. The type strain is NEAU-Y5T (=CCTCC AA 2019087T=DSM 110637T).

Proposal of Helicobacter higonensis sp. nov. isolated from a human clinical specimen, and emended description of Helicobacter valdiviensis Collado, 2014.

We have previously isolated a gram-negative microaerophilic strain, PAGU2000T from a patient presenting with a fever in Kumamoto Prefecture, Japan. The present study aimed to comprehensively analyze the taxonomy of the isolated strain using a polyphasic approach. The 16S rRNA gene sequence analysis indicated that the strain was a member of enterohepatic Helicobacter. The strain PAGU2000T shared a 97.5% 16S rRNA gene nucleotide identity with Helicobacter valdiviensis, and this taxonomic position was confirmed by phylogenetic analysis of the GyrA amino acid sequences. The proposed strain PAGU2000T has a 1.482 Mbp chromosome with a DNA G + C content of 31.3 mol% and encodes 1520 predicted coding sequences. The average nucleotide identity between the strain PAGU2000T and type strain of H. valdiviensis was 70.3%, which was lower than the recommended threshold of 95% for species delineation. The strain PAGU2000T was a motile, non-spore-forming, and spiral-shaped bacterium, exhibiting catalase and oxidase activities but not urease and nitrate reduction. This study demonstrates that the isolate represents a novel species within enterohepatic Helicobacter, for which the name Helicobacter higonensis is proposed (type strain: PAGU2000T = GTC 16811T = LMG 33095T). In this study, we describe the phenotypic and morphological features of this strain and propose an emended description of some biochemical traits of H. valdiviensis.

Marinobacter qingdaonensis sp. nov., a moderately halotolerant bacterium isolated from intertidal sediment.

A Gram-stain-negative, aerobic, rod-shaped and halotolerant bacterium, designated as strain ASW11-75T, was isolated from intertidal sediments in Qingdao, PR China, and identified using a polyphasic taxonomic approach. Growth of strain ASW11-75T occurred at 10-45 °C (optimum, 37 °C), pH 6.5-9.0 (optimum, pH 8.0) and 0.5-18.0 % NaCl concentrations (optimum, 2.5 %). Phylogenetic analyses based on 16S rRNA gene sequences and 1179 single-copy orthologous clusters indicated that strain ASW11-75T is affiliated with the genus Marinobacter. Strain ASW11-75T showed highest 16S rRNA gene sequence similarity to 'Marinobacter arenosus' CAU 1620T (98.5 %). The digital DNA-DNA hybridization and average nucleotide identity values between strain ASW11-75T and its closely related strains (Marinobacter salarius R9SW1T, Marinobacter similis A3d10T, 'Marinobacter arenosus' CAU 1620T, Marinobacter sediminum R65T, Marinobacter salinus Hb8T, Marinobacter alexandrii LZ-8T and Marinobacter nauticus ATCC 49840T) were 19.8-24.5 % and 76.6-80.7 %, respectively. The predominant cellular fatty acids were C16 : 0, C18 : 1 ω9c and C16 : 0 N alcohol. The polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, one unidentified aminophospholipid and two unidentified lipids. The major isoprenoid quinone was ubiquinone-9. The genomic DNA G+C content was 62.2 mol%. Based on genomic and gene function analysis, strain ASW11-75T had lower protein isoelectric points with higher ratios of acidic residues to basic residues and possessed genes related to ion transport and organic osmoprotectant uptake, implying its potential tolerance to salt. The results of polyphasic characterization indicated strain ASW11-75T represents a novel Marinobacter species, for which the name Marinobacter qingdaonensis sp. nov. with the type strain ASW11-75T is proposed. The type strain is ASW11-75T (=KCTC 82497T=MCCC 1K05587T).

Description of Corynebacterium hiratae sp. nov. isolated from a human tissue bone a novel member of Corynebacterium Genus.

BACKGROUND: Corynebacterium spp. are widely disseminated in the environment, and they are part of the skin and mucosal microbiota of animals and humans. Reports of human infections by Corynebacterium spp. have increased considerably in recent years and the appearance of multidrug resistant isolates around the world has drawn attention. OBJECTIVES: To describe a new species of Corynebacterium from human tissue bone is described after being misidentified using available methods. METHODS: For taxonomic analyses, phylogenetic analysis of 16S rRNA and rpoB genes, in silico DNA-DNA hybridization, average nucleotide and amino acid identity, multilocus sequence analysis, and phylogenetic analysis based on the complete genome were used. FINDINGS: Genomic taxonomic analyzes revealed values of in silico DNA-DNA hybridization, average nucleotide and amino acids identity below the values necessary for species characterization between the analyzed isolates and the closest phylogenetic relative Corynebacterium aurimucosum DSM 44532T. MAIN CONCLUSIONS: Genomic taxonomic analyzes indicate that the isolates analyzed comprise a new species of the Corynebacterium genus, which we propose to name Corynebacterium hiratae sp. nov. with isolate 332T (= CBAS 826T = CCBH 35,014T) as the type strain.

Rostrupomyces, a new genus to accommodate Xerocomussisongkhramensis, and a new Hemileccinum species (Xerocomoideae, Boletaceae) from Thailand.

A new genus, Rostrupomyces is established to accommodate Xerocomussisongkhramensis based on multiple protein-coding genes (atp6, cox3, tef1, and rpb2) analyses of a wide taxon sampling of Boletaceae. In our phylogeny, the new genus was sister to Rubinosporus in subfamily Xerocomoideae, phylogenetically distant from Xerocomus, which was highly supported as sister to Phylloporus in the same subfamily Xerocomoideae. Rostrupomyces is different from other genera in Boletaceae by the following combination of characters: rugulose to subrugulose pileus surface, white pores when young becoming pale yellow in age, subscabrous stipe surface scattered with granulose squamules, white basal mycelium, unchanging color in any parts, yellowish brown spore print, and broadly ellipsoid to ellipsoid, smooth basidiospores. In addition, Hemileccinuminferius, also from subfamily Xerocomoideae, is newly described. Detailed descriptions and illustrations of the new genus and new species are presented.

Revised taxon definition in European Cortinarius subgenus Dermocybe based on phylogeny, chemotaxonomy, and morphology.

Cortinarius (Fr.) Fr. is one of the most species-rich genera in the Agaricales (Basidiomycota). Cortinarius subgen. Dermocybe (Fr.) Trog includes brightly coloured Cortinarii with anthraquinone pigments. The chemotaxonomic approach has always been as important as classical methods for species definition of Dermocybe and helped to improve overall species concepts. However, some species concepts within this group remain unclear. We therefore address this topic based on a combined phylogenetic, morphological, and pigment-chemical approach. For this, sequence data, HPLC-MS pigment profiles and spore sizes were included were included to obtain a better resolution of taxa. The study was based on 173 recent collections and 12 type specimens. A total of 117 rDNA ITS sequences were produced from the collections in this study, 102 sequences were retrieved from databases. We could detect and clearly delimit 19 Dermocybe species occurring in central European habitats, from which 16 are discussed in detail. Additionally, we grouped the detected anthraquinone pigments into four groups. This detailed analysis of dermocyboid Cortinarius species occurring in a restricted number of habitat types confirmed our hypothesis that species diversity is much higher than currently assumed. This high diversity is blurred by too wide and incorrect species concepts of several classical species like C. croceus and C. cinnamomeus. Molecular and chemotaxonomical studies carried out together with careful phenotypical analyses resulted in a good differentiation of species. A key is presented for these taxa to allow a better identification of Cortinarius subgenus Dermocybe spp. occurring in Central Europe mainly in the alpine range. Supplementary Information: The online version contains supplementary material available at 10.1007/s11557-024-01959-z.

Three new species of the leafhopper genus Arboridia Zachvatkin (Hemiptera, Cicadellidae, Typhlocybinae), with a key and checklist to known species of China.

Three new species of the leafhopper genus ArboridiaZachvatkin 1946, Arboridia (Arboridia) furcata Han, sp. nov., Arboridia (Arboridia) rubrovittata Han, sp. nov., and Arboridia (Arboridia) robustipenis Han, sp. nov., are described and illustrated from fruit trees in Southwest China. A key and checklist to known species from China are provided.

A new species of freshwater snail of Fenouilia (Gastropoda, Pomatiopsidae) from northern Guangxi, China, based on morphological and DNA evidence.

A new species of pomatiopsid freshwater snail, Fenouiliaundata Chen & He, sp. nov., is described from Guangxi, China, based on morphological and molecular evidence. The new species can be distinguished from its congeners by the following combination of characters: shell with low, prosocline, rounded axial ribs and fine spiral striae, broader than high; aperture broader than shell height; radula with lateral teeth have only two or three faint, wavy ridges on inner side. A molecular analysis of partial mitochondrial COI and 16S DNA sequences supports the systematic position of the new taxon.

Two new species of the Cnemaspisgalaxia complex (Squamata, Gekkonidae) from the eastern slopes of the southern Western Ghats.

Two new species allied to Cnemaspisgalaxia are described from the eastern slopes of the south Western Ghats, Tamil Nadu, India. Both new species are members of the ornata subclade within the beddomei clade. The two new species can be easily distinguished from all other members of the beddomei clade and each other by a combination of nonoverlapping morphological characters such as small body size, distinct colouration of both sexes, the number of dorsal tubercles around the body, the number or arrangement of paravertebral tubercles, the number of midventral scales across the belly and longitudinal ventral scales from mental to cloaca, besides uncorrected pairwise ND2 and 16S sequence divergence of ≥ 7.4% and ≥ 2.7%. The two new species are distributed from low elevation, deciduous forests of Srivilliputhur, and add to the five previously known endemic vertebrates from Srivilliputhur-Megamalai Tiger Reserve.

A new loach species of the genus Oreonectes (Teleostei, Cypriniformes, Nemacheilidae) from Guangxi, China.

A new loach species, Oreonectesandongensissp. nov. is described from the Guangxi Zhuang Autonomous Region, China. The new species can be differentiated from other members of the genus by combinations of characters: a developed posterior chamber of the swim bladder, 13-14 branched caudal-fin rays, 8-16 lateral-line pores, body width 12-15% of standard length (SL), interorbital width 42-47% of head length (HL), and caudal peduncle length 11-16% of SL. Bayesian inference phylogenetic analysis based on mitochondrial Cyt b provided strong support for validity of O.andongensissp. nov. (uncorrected p-distance 6.0-7.5%).