Search Results (61)

Nitrate reduction serves as a pivotal process in the global nitrogen cycle, playing a crucial role in natural ecosystems and industrial applications. Although the genus Alteromonas is not traditionally regarded as a nitrate reducer, several Alteromonas strains have recently been found to be capable of doing so. However, the evolutionary trajectory of this capability remains undiscovered. In this study, 32 bacterial strains were isolated and cultivated from the tidal flat sediment in Hangzhou Bay and classified into the classes Cytophagia (n = 2), Alphaproteobacteria (n = 2), Gammaproteobacteria (n = 17), Flavobacteriia (n = 5), and Bacilli (n = 6). One nitrate-reducing strain, designated as CYL-A6^T, was identified by polyphasic taxonomy and proposed as a novel Alteromonas species. Genomic analysis reveals that seven Alteromonas genomes encode the dissimilatory nitrate reduction genes narGHI. Evolutionary analysis showed that these three nitrate-reducing genes were present in the early common ancestor of the genus Alteromonas, while gene loss events occurred in the subsequent evolution. With the loss of nitrate-reducing genes in the ancestry nodes, a wide variety of genes related to energy production and conversion, as well as carbohydrate, nucleotide, coenzyme, and inorganic ion metabolism, were gained in those nodes, which enabled Alteromonas members to utilize diverse substrates for increased energy production. This study enhances the understanding of microbial diversity in marine tidal flat sediments, proposes a novel nitrate-reducing species of the genus Alteromonas, and highlights the ecological diversification and ecological niche breadth in the evolution of the microbial metabolic network. Full article

Fusarioid fungi, members of the Nectriaceae within the Hypocreales (Ascomycota), exhibit diverse ecological roles and possess complex phylogenetic relationships, including endophytic, saprophytic, and pathogenic lifestyles. Among them, the genera Fusarium and Neocosmospora are particularly significant in agriculture and medicine. However, the boundaries between their species remain taxonomically contentious. In this study, 22 representative isolates from plant, fungal, and insect hosts were subjected to a polyphasic taxonomic approach that integrated morphological characterization, multilocus phylogenetic analyses, and phylogenomic analysis based on 4,941 single-copy orthologous genes. Consequently, five new species (F. dracaenophilum, F. puerense, F. wenshanense, N. alboflava, and N. fungicola) were described, and F. qiannanense and N. solani were recorded from new host species. The resulting phylogenomic tree topology was highly congruent with the multilocus phylogeny, providing robust support for the taxonomic distinction between Fusarium and Neocosmospora. This study provides new insights into the taxonomy of fusarioid fungi and has important implications for plant disease management, biodiversity conservation, and the study of fungal evolution. Full article

A novel actinobacterial strain, designated E54^T, was isolated from a hyper-arid desert soil sample collected from the Kumtagh Desert in Dunhuang, Gansu Province, China. Phylogenetic analysis based on 16S rRNA gene sequences placed strain E54^T within the genus Lentzea, showing highest similarity to Lentzea waywayandensis DSM 44232^T (98.9%) and Lentzea flava NBRC 15743^T (98.5%). However, whole-genome comparisons revealed that the average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between E54^T and these related strains were below the thresholds for species delineation. Strain E54^T exhibited typical morphological characteristics of the genus Lentzea, forming a branched substrate. It grew optimally at 28–30 °C, pH 7.0–9.0, and tolerated up to 10% NaCl. The cell wall contained meso-diaminopimelic acid, the predominant menaquinone was MK-9(H₄), and major fatty acids included iso-C_16:0. The polar lipid profile comprised diphosphatidyl glycerol, phosphatidyl ethanolamine, phosphatidyl inositol, hydroxyphosphatidyl ethanolamine, and an unidentified lipid. The characteristic amino acid type of the cell wall was meso-DAP. Whole-cell hydrolysis experiments revealed the characteristic cell wall sugar fractions: ribose and galactose. The genome of strain E54^T is approximately 8.0 Mb with a DNA G+C content of 69.38 mol%. Genome mining revealed 39 biosynthetic gene clusters (BGCs), including non-ribosomal peptide synthetases (NRPS), polyketide synthases (PKS), terpenes, and siderophores. Comparative antiSMASH-based genome analysis across 38 Lentzea strains further demonstrated the genus’ remarkable biosynthetic diversity. NRPS and type I PKS (T1PKS) were the most prevalent BGC types, indicating a capacity to synthesize structurally complex and pharmacologically relevant metabolites. Together, these findings underscore the untapped biosynthetic potential of the genus Lentzea and support the proposal of strain E54^T as a novel species. The strain E54^T (=JCM 34936^T = GDMCC 4.216^T) should represent a novel species, for which the name Lentzea xerophila sp. nov. is proposed. Full article

Members of Eubacteriaceae are involved in host health and diseases. Two Gram-stain-positive, strictly anaerobic, non-motile, non-spore-forming, and rod-shaped bacterial strains, HA2171^T and HA2172^T, were isolated from the feces of Chinese healthy donors. Based on 16S rRNA gene sequences, HA2171^T and HA2172^T belonged to the family Eubacteriaceae. Physiological and biochemical characterizations indicated that HA2171^T and HA2172^T were neutrophilic, mesophilic, and tolerant to low-concentration NaCl. The major cellular fatty acids (>10.0%) of HA2171^T were C_16:0, C_14:0, C_18:1ω7c, and C_17:0 2-OH, and those of HA2172^T were C_14:0 and C_16:0. MK-6 was the respiratory quinone in both strains. Phylogenetic and phylogenomic analyses showed that HA2171^T was closest to Anaerofustis stercorihominis ATCC BAA-858^T and that HA2172^T as closest to Pseudoramibacter alactolyticus ATCC 23263^T. Genome annotation revealed that the HA2171^T and HA2172^T were able to metabolize carbohydrates and produce acetate and butyrate. HA2172^T contains genes associated with hydrogen sulfide production, which is a potential risk for diseases. Based on the phylogenetic, phenotypic, and chemotaxonomic characteristics, we propose that HA2171^T and HA2172^T represent two novel species, and the names Anaerofustis butyriciformans sp. nov. and Pseudoramibacter faecis sp. nov. are proposed. Full article

Oculatellaceae is a family of cyanobacteria with orange spots in the apical cells and has a wide distribution in various living environments. The species of this family are widely distributed but relatively few in number. In order to enrich our knowledge of the species diversity of cyanobacteria in China, and further achieve the monophyletic development of modern cyanobacteria classification systems, we studied two algal strains, designated as SXACC0114 and SXACC0117, isolated from China and subjected to taxonomic studies using a multiphase approach. The colony of the strain SXACC0114 is bright blue-green in color and does not form a biofilm. The trichomes are yellow-green to bright blue-green. For the strain SXACC0117, no false branching is observed. It has wider filaments and more distinct sheaths, and lacks swollen cells. Based on 16S rRNA gene phylogenetic analysis, the results showed that these two algal strains clustered in Albertania and Tildeniella evolutionary branches, respectively, with high bootstrap support. In addition, the secondary structures, which are constructed based on the internal transcription spacer (ITS) of 16S-23S rRNA, exhibit differences, and the algal strain has unique D1-D1ʹ, Box-B, and V3 helix structures. These results support the establishment of two new species, described as Albertania yunnanense sp. nov. and Tildeniella yunnanense sp. nov. The discovery of these new species provides a scientific basis for the development and utilization of algae. Full article

In an investigation exploring endophytic microbiota from agricultural crops, an aerobic, non-motile, Gram-negative, coccobacillus-shaped bacterial isolate, designated as strain NGMCC 1.201697^T, was isolated from maize roots in Hunan Province, China. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain NGMCC 1.201697^T belonged to the genus Paracoccus, showing the highest sequence similarity to Paracoccus broussonetiae CPCC 101403^T (99.86%). The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) were 98.57% and 87.90% between the novel isolate and its closest phylogenetic relative. However, phenotypic characterization further differentiated the isolate from P. broussonetiae CPCC 101403^T. The isolate showed enhanced environmental tolerance adaptability (growth in 0–8% NaCl and 4–37 °C), unique enzymatic activities (esterase C4, β-glucosidase, L-proline arylamidase, and β-galactosidase), and expanded metabolic capabilities (D-mannitol, D-cellobiose, saccharose, and so on). The major polar lipids consisted of diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylcholine (PC), phosphatidylglycerol (PG), two unidentified glycolipids (GLs) and four unidentified phospholipids (PLs). The predominant respiratory quinone was ubiquinone-10, and the major fatty acid was summed feature 8 (C18:1 ω7c, 69.42%). The DNA G + C content was 64.49 mol%. Based on results of these analyses, strain NGMCC 1.201697^T represents a novel subspecies of Paracoccus broussonetiae, for which the name Paracoccus broussonetiae subsp. drimophilus subsp. nov. is proposed. The type-strain is NGMCC 1.201697^T (=CGMCC 1.61958^T =JCM 37104^T). Full article

Erwinia are widely known as phytopathogenic bacteria, but among them, there are also plant-friendly strains that can promote plant growth (PGPR). The Erwinia-like strain OPT-41 was isolated from Triticum aestivum seedlings as a potential PGPR. The cells (0.9–1.3 × 1.5–3.1 µm) of this microorganism are Gram-negative, rod-shaped, motile (with peritrichous flagella), and non-spore- and non-capsule-forming. The 16S rRNA gene sequence analyses showed it is located in the Erwiniaceae family and has a pairwise similarity above the species delineation threshold of 98.65% with several of its members: Erwinia tasmaniensis (99.21%), Candidatus Pantoea bathycoeliae (98.93%), Pantoea agglomerans (98.87%), Erwinia endophytica (98.83%), Erwinia persicina (98.82%), Erwinia billingiae (98.76%) and Erwinia aphidicola (98.75%). Whole genome-based taxonomy performed on the Type (Strain) Genome Server clarified the status of strain OPT-41, detecting it as a potential new species in the genus Erwinia. The microorganism under study was the most closely related to the type strain of E. phyllosphaerae, demonstrating 27.2% similarity in dDDH, 83.44% similarity in OrthoANIu, and 1.9% difference in G+C content. The major fatty acids of strain OPT-41 were 9 C_16:1, C_14:0, and C_16:0. A combination of genome-based taxonomy and traditional polyphasic taxonomy clearly indicated that strain OPT-41 belongs to a novel Erwinia species, for which the name E. plantamica sp. nov was proposed. OPT-41 (=IBPPM 712=VKM B-3873D=CCTCC AB 2024361) has been designated as the type strain. In addition, OPT-41 was found to have low degradation potential for host plant pectins and proteins and be friendly in Triticum aestivum and Hordeum vulgare crops. Full article

Background/Objectives: Ulcerative colitis (UC) and Crohn’s disease (CD) are the usual clinical forms of inflammatory bowel disease (IBD). Changes in the oral microbiota, especially the presence of emerging fungi and herpesviruses, have been shown to worsen the clinical aspects of IBD. The aim of this study was to screen for emerging pathogens in the oral yeast microbiota and the presence of herpesvirus in IBD patients. Methods: Oral swabs of seven UC or CD patients were collected. The samples were plated on Sabouraud Dextrose Agar and subcultured on CHROMagar Candida and CHROMagar Candida Plus. Polyphasic taxonomy was applied and identified using molecular tools, such as MALDI-TOF MS and ITS partial sequencing. Multiplex qPCR was used to identify the herpesvirus. Results: The mean age was 38.67 ± 14.06 years, 57.14% were female, and two had diabetes. The CD patients presented with Rhodotorula mucilaginosa, Candida orthopsilosis and Kodamaea jinghongensis, while the UC patients presented with Cutaneotrichosporon dermatis, Candida glabrata, Candida lusitanea and Candida tropicalis. Two UC individuals had at least one herpesvirus. In the first individual, a co-detection of Herpes Simplex Virus 1 (HSV-1) and C. lusitaniae was observed. The second presented with co-infections of Epstein–Barr virus (EBV), Human Herpesvirus 7 (HHV-7) and C. tropicalis. Conclusions: We identified rarely described yeasts and co-infections in IBD patients, highlighting the need to identify emerging pathogens in the oral microbiota, as they may contribute to opportunistic infections. Full article

The Taklamakan Desert is an extreme environment supporting a unique and diverse microbial community with significant potential for exploration. Strain TRM70308^T, isolated from desert soil, shares 98.43% 16S rRNA gene sequence similarity with Streptomyces alkaliterrae OF1^T. Polyphasic taxonomy confirmed TRM70308^T as a novel species, named Streptomyces xanthus. Genomic analysis revealed that only one of the strain’s 25 biosynthetic gene clusters (BGCs) formed a cluster of gene families (CGFs) within the MIBiG database, emphasizing its genomics uniqueness. LC-MS/MS and Feature-Based Molecular Networking (FBMN) identified 33 metabolites across various categories, including alkaloids, saponins, benzoic acids, and benzofurans, most of which remain uncharacterized. Further chemical investigation led to the isolation of one novel compound, aconicarpyrazine C, and four known compounds: thiolutin, dibutyl phthalate, bis(2-ethylhexyl) phthalate, and N-acetyltryptamine. Thiolutin exhibited strong activity against five local fungal pathogens that cause plant diseases, with a production yield of 270 mg/L. These results establish a foundation for pilot-scale thiolutin production and its potential development as an antifungal agent for agricultural applications. Our findings highlight deserts as a valuable source of novel actinomycetes and bioactive natural products with immense potential for future research and development. Full article

As our comprehension of cyanobacterial classification in diverse ecosystems broadens, it becomes essential to explore the biodiversity of lesser-known areas for a thorough understanding of both global and local diversity. This research, which is part of a larger investigation into soil biocrust algae diversity in the Sanyang Wetland located in Zhejiang Province, China, introduces a novel taxon of non-heterocystous filamentous cyanobacteria employing a polyphasic approach for cyanobacterial classification, integrating morphological, molecular, ecological, and biogeographical considerations. The findings from morphological analysis, 16S rRNA gene sequencing, and the identification of the 16S-23S ITS rRNA region have led to the discovery of a new genus, Paludothrix, which is categorized within the family Coleofasciculaceae. The proposed generic name and specific epithet of these new taxa adhere completely to the guidelines established by the International Code of Nomenclature for algae, fungi, and plants. The modern taxonomic system of cyanobacteria is constantly being updated and improved. The description of new taxa using the polyphasic approach can enrich the relevant knowledge in the field of cyanobacteria classification. The results of this study will increase our understanding of terrestrial cyanobacteria within wetland environments. Full article

Background: The identification of novel bacterial species from the intestines of yaks residing on the Qinghai–Tibet Plateau is pivotal in advancing our understanding of host–microbiome interactions and represents a promising avenue for microbial drug discovery. Methods: In this study, we conducted a polyphasic taxonomic analysis and bioactive assays on a Bacillus strain, designated Bos-x6-28, isolated from yak feces. Results: The findings revealed that strain Bos-x6-28 shares a high 16S rRNA gene sequence similarity (98.91%) with B. xiamenensis HYC-10^T and B. zhangzhouensis DW5-4^T, suggesting close phylogenetic affinity. Physiological and biochemical characterizations demonstrated that Bos-x6-28 could utilize nine carbon sources, including D-galactose, inositol, and fructose, alongside nine nitrogen sources, such as threonine, alanine, and proline. Analysis of biochemical markers indicated that Bos-x6-28’s cell wall hydrolysates contained mannose, glucose, and meso-2,6-diaminopimelic acid, while menaquinone-7 (MK-7), phosphatidylethanolamine (PE), phosphatidylcholine (PC), and phosphatidylglycerol (DPG) were found in the cell membrane. The primary cellular fatty acids included C16:0 (28.00%), cyclo-C17:0 (19.97%), C14:0 (8.75%), cyclo-C19:0 (8.52%), iso-C15:0 (5.49%), anteiso-C15:0 (4.61%), and C12:0 (3.15%). Whole-genome sequencing identified a genome size of 3.33 Mbp with 3353 coding genes. Digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANI) analyses confirmed Bos-x6-28 as a novel species, hereby named B. maqinnsis Bos-x6-28 (MCCC 1K09379). Further genomic analysis unveiled biosynthetic gene clusters encoding bioactive natural compounds, including β-lactones, sactipeptides, fengycin, and lichenysin analogs. Additionally, in vitro assays demonstrated that this strain exhibits antibacterial and cytotoxic activities. Conclusions: These findings collectively indicate the novel Bacillus species B. maqinnsis Bos-x6-28 as a promising source for novel antibiotic and antitumor agents. Full article

In our large-scale search for antimicrobial-producing bacteria, we isolated an actinomycete strain from rhizospheric soil of Bambusa vulgaris. The strain designated BP-8 showed noticeable antibacterial activity. BP-8 was subjected to a whole-genome analysis via a polyphasic taxonomy approach, and its antibacterial metabolite was identified by HRLS-MS. The results of the physiological and morphological analyses indicated that BP-8 is an aerobic, neutrophilic, mesophilic organism that is tolerant to 8% NaCl and can use a wide range of carbohydrates. It forms curly sporophores with a warty surface. The results of the phylogenetic and average nucleotide identity analyses and in silico DNA–DNA hybridization calculation indicated that BP-8 represents the type strain of a novel Streptomyces species. A comparative in silico analysis of the genome sequences of BP-8 and its closest related strains revealed the presence of genes encoding chemotaxonomic markers characteristic of Streptomyces. The antibacterial compound was identified as amicetin. Genomic mining also revealed more than 10 biosynthetic gene clusters that have not been described previously and may lead to the discovery of new valuable compounds. On the basis of these results, strain BP-8^T (=VKM Ac-3066^T = CCTCC AA 2024094^T) is proposed as the type strain of the novel species Streptomyces sirii sp. nov. Full article

Sulfidogenic bacteria cause numerous issues in the oil industry since they produce sulfide, corroding steel equipment, reducing oil quality, and worsening the environmental conditions in oil fields. The purpose of this work was to isolate and taxonomically identify the sulfidogenic bacteria responsible for the corrosion of steel equipment at the Karazhanbas oil field (Kazakhstan). In this study, we characterized five sulfidogenic strains of the genera Pseudodesulfovibrio, Oleidesulfovibrio, and Acetobacterium isolated from the formation water of the Karazhanbas oil field (Kazakhstan). Sulfate-reducing strain 9FUS^T revealed 98.9% similarity of the 16S rRNA gene sequence with the closely related strain ‘Pseudodesulfovibrio methanolicus’ 5S69^T and was studied in detail to enhance the taxonomic resolution. Strain 9FUS^T grew optimally at 23–28 °C, pH 6.5, and 0–2% (w/v) NaCl. The strain used lactate, pyruvate, methanol, ethanol, fructose, ribose, and H₂/CO₂ (in the presence of acetate) as carbon and energy sources for sulfate reduction. Iso-C_17:1 ω11, C_15:0, iso-C_15:0, and C_16:0 were the predominant fatty acids. The genome is 4.20 Mbp with a G + C content of 64.0%. The average nucleotide identity and digital DNA–DNA hybridization values with Pseudodesulfovibrio spp. genomes were 72.5–91.6% (<95%) and 18.5–45.0% (<70%), respectively, and supported our conclusion that 9FUS^T (=VKM B-3654^T = KCTC 25498^T) belonged to a novel Pseudodesulfovibrio species, for which the name Pseudodesulfovibrio karagichevae sp. nov. is proposed. Pangenome analysis of sixteen Pseudodesulfovibrio species and functional annotation analysis of identified genes revealed complete modules of enzymes of the main metabolic pathways, characteristic of bacteria of this genus, and unique genes highlighting the adaptations of strain 9FUS^T in carbohydrate metabolism, nutrient uptake, and environmental stress response. Isolation of these strains expands our understanding of the diversity of sulfidogens in oil reservoirs and can be used to test the effectiveness of biocides used in an oil field. Full article

Fungal infections significantly threaten public health, and many strains are resistant to antifungal drugs. Marine Actinobacteria have been identified as the generators of powerful bioactive compounds with antifungal activity and can be used to address this issue. In this context, strains of Actinomycetes were isolated from the marine area of Rachgoun Island, located in western Algeria. The isolates were phenotypically and genetically characterized. The most potent antifungal isolate was selected, and its crude extract was purified and characterized by the GC/MS method. The results revealed that the STR2 strain showed the strongest activity against at least one target fungal species tested on a panel of fungal pathogens, including Candida albicans, Aspergillus fumigatus, Aspergillus niger, and Fusarium oxysporum. The molecular assignment of the STR2 strain based on the 16S rRNA gene positioned this isolate as a Streptomyces bacillaris species. The presence of safranal (2,3-dihydro-2,2,6-trimethylbenzaldehyde) in the crude chloroform extract of Streptomyces bacillaris STR2 strain was discovered for the first time in bacteria using chromatographic analysis of its TLC fractions. Moreover, certain molecules of biotechnological interest, such as phenols, 1,3-dioxolane, and phthalate derivatives, were also identified. This study highlights the potential of marine actinomycetes to produce structurally unique natural compounds with antifungal activity. Full article

Two novel bacterial species were isolated from the rhizosphere of Solanum lycopersicum (tomato plant), both exhibiting plant growth-promoting properties. Two isolated strains, Rhodanobacter lycopersici sp. nov. Si-c^T and Rhodanobacter geophilus sp. nov. S2-g^T, were classified through a polyphasic approach, confirming their novel status within the Rhodanobacter genus. The strains demonstrated a remarkable tolerance to extreme pH conditions, with R. lycopersici Si-c^T surviving in pH 3.0–13.0 and R. geophilus S2-g^T tolerating pH 2.0–13.0. Additionally, both strains exhibited multiple plant growth-promoting traits, including indole-3-acetic acid and ammonia production, phosphate solubilization, and siderophore formation. These characteristics suggest that the two strains may play an important role in promoting plant growth, especially in soils with variable pH levels. However, since the direct impact on plant growth was not experimentally tested, the potential of these bacteria for agricultural applications remains to be confirmed through further research. This study expands our understanding of the diversity within the Rhodanobacter genus and provides insights into the potential use of these novel species in sustainable agriculture. Full article