The neighbor-joining method: a new method for reconstructing phylogenetic trees

Correlation Analysis of Secondary Metabolism and Endophytic Fungal Assembles Provide Insights Into Screening Efficient Taxol-Related Fungal Elicitors

The efficacy of Taxol, a natural anticancer drug, in the treatment of various types of cancers has been certified globally. Fungal elicitors have been reported as an impressive strategy for enhancing Taxol biosynthesis. We have investigated the effect of twig age on Taxol biosynthesis and the communities of endophytic fungi. A negative correlation between Taxol content and the complexity of the endophytic fungal community in twigs was predicted. Endogenous taxoids, similar to balancing valves, might have a specific effect on controlling the microbiota assembly in Taxus twigs. Utilising the special correlation, 11 isolates of twig age-associated fungi were used to screen new fungal elicitors involved in Taxol biosynthesis. Two efficient fungal elicitors, L01 (Guignardia) and J02 (Diaporthe), were identified, increasing the Taxol contents by 5.91- and 4.83-folds, respectively. It is confirmed that effective fungal elicitors may be negatively correlated with Taxol contents in Taxus tissues. Furthermore, the J02 and L01 fungal elicitors significantly induced the jasmonic acid (JA) content, speculating the involvement of MYC2a-controlled JA signalling in fungal elicitor-activated Taxol biosynthesis. Our data revealed the effect of twig age on Taxol biosynthesis of Taxus and provided a novel approach to screen effective fungal elicitors involved in Taxol biosynthesis.

Molecular insights into Rickettsiales in blood and ticks of two-humped camels at Gansu Province, China: With an accidental detection of Colpodella sp

Emerging infectious diseases caused by various tick-borne microorganisms (TBMs) pose public and animal health concerns, including camels, with no defined global distribution. In this study, 150 blood samples and 288 ticks were collected from symptomatic two-humped camels (Camelus bactrianus) in Gaotai County, Gansu Province, China. Morphologically identified ticks were confirmed using cytochrome oxidase I (COI), and the findings revealed two species, Hyalomma asiaticum and Haemaphysalis longicornis (prevalence: 245/288 [88.19 %] and 34/288 [11.81 %], respectively). The extracted Genomic DNA from blood and ticks was processed by conventional PCR to investigate the existing TBMs based on 16S rRNA, 18S rRNA, and 17-kDa genes. Different TBMs, including Anaplasma bovis, Colpodella sp., Rickettsia rickettsii, and Candidatus Rickettsia jingxinensis, have been documented as single infections at different rates. High single infection rates (198/218; 90.83 % and 117/150; 78.00 %) of A. bovis in Hy. asiaticum and camel blood were recorded, whereas the lowest single infection rate (3/22; 13.64 %) of R. rickettsii was noted in Hae. longicornis. Co-infection with Rickettsia spp. + A. bovis (20/288; 6.94 %), Colpodella sp. + A. bovis (14/288; 4.86 %), Colpodella sp. + Rickettsia spp. (1/288; 0.35 %), and Colpodella sp. + Rickettsia spp. + A. bovis (1/288; 0.35 %) were recorded as concurrent infection. Phylogenetic analysis revealed that the representative TBMs have close similarities and clustered together with their corresponding isolates from China, South Korea, India, the USA, Mexico, Bangladesh, Malawi, Japan, Pakistan, Cyprus, Nigeria, Poland, and Brazil. These findings present a preliminary baseline regarding TBMs infection in camel blood and ticks and provide a framework for further studies on the prevalence and effective control measures for ticks and tick-associated diseases.

Eastern cottontails (Sylvilagus floridanus) as hosts for ticks infected with Borrelia burgdorferi, Anaplasma phagocytophilum, and Powassan virus in Virginia, USA

Tick-borne pathogen infections are an increasing occurrence globally, yet many aspects of pathogen maintenance and host-tick interactions remain poorly understood. Here we consider the potential role of eastern cottontails (Sylvilagus floridanus) in the enzootic cycles of tick-borne pathogens of medical importance in Virginia. Over a 3-year period, ticks and blood were collected from rabbits acquired through passive surveillance in 21 counties in Virginia. Seven hundred seventy ticks were collected from 90 of the 121 rabbits examined in this study. Tick species collected from the rabbits included Haemaphysalis leporispalustris, Haemaphysalis longicornis, Amblyomma americanum, Dermacentor variabilis, and Ixodes spp. Ticks identified as Ixodes spp. and H. leporispalustris were tested in pools for Borrelia burgdorferi, Borrelia miyamotoi, Anaplasma phagocytophilum, and Powassan virus (POWV). Borrelia burgdorferi and A. phagocytophilum were detected in several Ixodes spp. pools yielding a pooled infection rate of 4.6% and 3.7%, respectively. These bacterial pathogens along with POWV were detected in pools of H. leporispalustris yielding pooled infection rates of 0.2%, 0.2%, and 0.5%, respectively. In addition, 3 rabbits were found to have neutralizing antibodies against POWV indicating exposure to this tick-borne flavivirus. We describe the presence of infected ticks (including juvenile ticks that could bite humans as adults) utilizing rabbits as hosts, as well as evidence of POWV infection (1.75% seroprevalence) in rabbit sera. These results provide useful information about the role of rabbits as hosts to infected ticks, though cannot ascertain their role in the maintenance or the transfer of pathogens from the rabbits to naïve ticks. Future studies are warranted to explore any additional roles these and other lagomorphs may be playing in the enzootic cycle of tick-borne pathogens.

Isolation and Characterisation of Gracilimonas aurantiaca sp. nov., A Novel Bacterium Isolated from Tidal-Flat Sediment

A novel bacterium MJW-20T, was isolated from deep tidal-flat sediment in Gochang, Republic of Korea. The isolate is a bright-orange, Gram-stain-negative, aerobic, non-motile, slow-growing long-rods. The strain MJW-20T is oxidase, and catalase-positive. The growth is observed at 25-40 °C (optimum, 30 °C) and pH 5-9 (optimum, pH 7.0) in the presence of 0-9% (w/v) NaCl (optimum, 2.0% NaCl). The NCBI 16S ribosomal RNA sequences showed that the strain MJW-20T is closely affliated with Balneola vulgaris 13IX/A01/164T (94.6%), Gracilimonas halophila WDS2C40T (94.5%), Gracilimonas amylolytica LA399T (94.0%), Gracilimonas rosea CL-KR2T (93.8%) and Balneola alkaliphila CM41_14bT (93.3%) from the family Balneolaceae. The major respiratory quinone was MK-7. The major polar lipids identified were diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phospholipid (PL) and phosphatidylinositolmannosides (PIMs) for strain MJW-20T.The major cellular fatty acids of type strain MJW-20T were C15:0 iso (32.9%), C16:1 ω7c/C16:1 ω6c (11.9%), and C16:0 10-methyl/C17:1 iso ω9c (15.9%). The genome length of the type strain MJW-20T is 3.1 Mbp (DNA G + C content, 44%). It has 2,785 coding genes and 38 tRNAs. The analysis promotes that the average amino acid identity values, average nucleotide identity values, and biochemical, phylogenetic, and physiological characteristics support the genotypic and phenotypic differentiation of strain MJW-20T from other species of the genus Gracilimonas. Thereupon, the strain MJW-20T is considered to represent a novel species of the genus Gracilimonas, for which the name Gracilimonas aurantiaca sp. nov. is proposed. The type strain is MJW-20T (= KCTC 102297T = JCM 37229T).

Establishment of a Multilocus Sequence Typing Scheme for Pasteurella canis Using Isolates from Infected Humans and Diseased Companion Animals

Background

Multilocus sequence typing (MLST) is well-established for Pasteurella multocida but remains undeveloped for Pasteurella canis. We established MLST for P. canis using isolates from humans and companion animals in Japan and Korea to gain insights into its population biology.

Methods

We analyzed 39 and 22 isolates from companion animals and humans, respectively. We selected seven housekeeping genes-adk, aroA, deoD, gdhA, g6pd, mdh, and pgi-used in P. multocida MLST. Primer pairs for PCR amplification and sequencing were designed based on conserved sites in 10 whole-genome sequences. We determined fragment sequences, variable sites, allelic profiles, and sequence types (STs) of each isolate. A phylogenetic tree of concatenated sequences was constructed using the goeBURST algorithm to identify STs and clonal complexes (CCs). ompA, encoding outer membrane protein A, was genotyped for molecular characterization.

Results

The sequenced fragment lengths and allele numbers of the seven genes were 424, 451, 483, 439, 429, 419, and 440 bp and 16, 13, 15, 18, 22, 19, and 18, respectively. ST1-ST47, including CC2, CC10, CC18, CC31, and CC33, were diversely distributed among the isolates from different hosts/countries. In the seven-gene phylogenetic tree, apart from P. multocida, all isolates clustered together. goeBURST diagrams revealed diverse ST distributions among different hosts (animal/human) and countries (Japan/Korea/ others). We found clusters 1-4 in ompA genotyping, indicating that MLST discrimination is higher than ompA typing discrimination.

Conclusions

We established MLST for P. canis isolates from humans and companion animals in Japan and Korea, thereby providing a robust tool for population biology studies.

Microaceticoccus formicicus gen. nov., sp. nov., an ammonia-tolerant formate-utilizing bacterium originating from a biogas process

A strictly anaerobic bacterial strain, designated as AMB_02T, was isolated from a propionate enrichment culture obtained from a high-ammonia biogas digester. The cells were anaerobic and coccoid (0.5 µm), often appearing as diplococci or in a short chain of three to four cells. Growth was observed between 20 and 45 °C (optimum at 37-39 °C), with an initial pH of 6.5-9.0 (optimum pH 8.0-8.5), and the species tolerated up to 0.8 M NH4Cl and 0.5 M NaCl. The major cellular fatty acids were C16 : 0 (31.6%), C14 : 0 (14.6%) and C18 : 0 (13.3%). AMB_02T grew with formate, carbohydrates and aa, including asparagine, histidine, tryptone and tryptophan. Acetate was the major product formed. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain AMB_02T was most closely related to the species Citroniella saccharovorans (92.5%). The genome of strain AMB_02T was 2.5 Mb in length with a G+C content of 34.8 mol%, and 2,354 protein-coding genes were predicted. Furthermore, genes coding for the reductive glycine pathway potentially used for formate metabolism were identified. Comparative genomic analysis of AMB_02T revealed the closest similarity to C. saccharovorans [21.2% digital DNA-DNA hybridization (dDDH) and 77.4% average nt identity (ANI)] and to Parvimonas micra (24.4% dDDH and 76.9% ANI). Based on the phenotypic characteristics and phylogenetic analyses, AMB_02T is regarded as a novel genus, Microaceticoccus, within the family Peptoniphilaceae for which the species name Microaceticoccus formicicus is proposed. The type strain is AMB_02T=DSM 110248T=JCM 39108T.

Nuclear Multi-Microsatellite Marker Profiling Provides Clues to Molecular Genetic Diversity in Culture-Based Caspian Beluga Sturgeon (Huso huso) Brood Stocks: Ecological Mirror for Restoration

The decreasing natural genetic diversity within intense beluga sturgeon aquaculture presents a complex challenge for culture-based sturgeon stocks. The present report aims to assess the situation by utilizing advanced capillary electrophoresis (CE) and multi-microsatellite nuclear marker tools. We conducted a study involving 436 individuals of both sexes, collected from eight breeder private farms with diverse breeding histories and generational backgrounds. Through the application of eight microsatellites, we amplified a non-coding core genomic region in the species, followed by CE to provide double confirmation of observed genotype and actual allelic size SSR profiling. Utilizing molecular descriptive statistics in the POPGENE software, we calculated allele frequencies, expected and observed heterozygosity within populations, the number of observed and effective alleles (na and ne) and the Shannon's Information Index. Furthermore, we performed molecular analysis of variance (AMOVA), model-based clustering, principal coordinate analysis (PCoA) and STRUCTURE analysis to genetically characterize the populations. It was revealed that LS19 (na = 16) and Afu54 (na  = 3) exhibited the highest and lowest levels of polymorphisms, respectively, within the studied families. Moreover, the Iranian Fisheries Research Organization (IFRO) farm population was found to have the highest genetic diversity (Ave_Het = 0.67), whereas the Rajaeei Sturgeon Private Farm (RJI) displayed the lowest diversity score (Ave_Het = 0.55) among the examined populations. INS and Jahanpouri Sturgeon Private Farm (JPR) showed the highest similarity (0.91), whereas the Saeei Sturgeon Private Farm had the lowest genetic distance, with a similarity score of 0.74 among the populations studied. Furthermore, the evidence from the STRUCTURE analysis highlighted notable levels of allelic sharing and admixture among the eight studied populations, indirectly indicating the presence of genetic diversity within each population and the relatively low genetic distance between the populations. The results demonstrate a significant level of genetic variability, providing evidence that supports the low value of inbreeding in brood management.

Streptomyces lycopersici sp. nov. and Streptomyces cucumeris sp. nov., two novel actinobacteria isolated from rhizosphere soil with broad-spectrum antifungal activity

Two actinobacterial strains, designated NEAU-383T and NEAU-Y11T, exhibiting antifungal activity, were isolated from the rhizosphere soil of plants in Harbin, Heilongjiang Province, and Guangzhou, Guangdong Province, respectively. Both strains formed short, wrinkled, spiral spore chains on aerial hyphae. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strains NEAU-383T and NEAU-Y11T were most closely related to Streptomyces iranensis HM 35T, Streptomyces rapamycinicus NRRL B-5491T and Streptomyces coffeae CA1R205T. However, digital DNA-DNA hybridization values between the two strains and their close relatives (27.1% between the two strains; 27.5-59.0% for NEAU-383T; 27.0-39.8% for NEAU-Y11T) fell below the 70% species delineation threshold. The genomic G+C contents were 71.0 mol% for NEAU-383T and 70.5 mol% for NEAU-Y11T. Both strains contained glucose and ribose as whole-cell sugars. The predominant menaquinones were MK-9(H6) and MK-9(H8), with NEAU-Y11T additionally containing MK-9(H4). The major fatty acids (>10%) in both strains included iso-C15 : 0, anteiso-C15 : 0, iso-C16 : 0 and C16 : 0, whilst iso-C17 : 0 was also a major component in NEAU-383T. Both strains contained phosphatidylethanolamine and hydroxy-phosphatidylethanolamine as polar lipids. Additionally, NEAU-383T also possessed diphosphatidylglycerol, phosphatidylinositol, an unidentified ninhydride-positive lipid and five unidentified lipids, whereas NEAU-Y11T additionally contained two unidentified ninhydride-positive lipids and five unidentified lipids. Genomic analysis revealed that both strains possess abundant secondary metabolite biosynthesis gene clusters, including those for antibiotics, siderophores, polyketides and terpenoids, along with metabolic pathways associated with environmental adaptation. These findings provide insight into the potent antimicrobial activity exhibited by both strains. Based on genotypic, phenotypic and chemotaxonomic analyses, strains NEAU-383T and NEAU-Y11T represent two novel species within the genus Streptomyces, for which the names Streptomyces lycopersici (type strain NEAU-383T=JCM 36736T=MCCC 1K08878T) and Streptomyces cucumeris (type strain NEAU-Y11T=JCM 36418T=MCCC 1K08681T) are proposed.

Deciphering the genetic context of the emerging OXA-484-producing carbapenem-resistant Escherichia coli from ST167 high-risk clone in the United Arab Emirates

PURPOSE

The evolution of new carbapenemase variants is alarming. We aimed to investigate the genetic context and molecular epidemiology of the emerging OXA-484 carbapenemase in the United Arab Emirates, to decipher its resistance mechanisms and evolutionary relationships.

METHODS

Antimicrobial susceptibility testing was performed for an E. coli isolate recovered from an intrauterine contraceptive device of a patient returning to the UAE after a trip to Pakistan. Whole genome sequencing was used to characterize the genetic environment of blaOXA-484, resistance and virulence determinants. Southern blotting was used to localize OXA-484 gene. Phylogenetic analysis established the sequence type (ST) and used to investigate relationships with global strains, and differences from other OXA-48-like types.

RESULTS

The strain demonstrated selective resistance against ertapenem while maintaining susceptibility to imipenem and meropenem. OXA-484 exhibited R214G substitution affecting the enzyme's activity and distinguishing it from closely related variants like OXA-181 (214R) and OXA-232 (214 S). blaOXA-484 was located on two non-conjugative plasmids (∼ 65 and 100 kb) within a genetic environment containing multiple insertion sequences. It belonged to the high-risk clone ST167, recognized for its enhanced capacity to acquire and maintain resistance determinants. The gene was mostly prevalent in the Western part of the world with limited distribution in the Middle East.

CONCLUSION

This study presents the first comprehensive characterization of OXA-484-producing E. coli ST167 in the UAE. The presence of blaOXA-484 in high-risk clone warrants concern on its dissemination potential and underscores the importance of genomic surveillance and targeted infection control to prevent the spread of emerging resistance determinants.

Kitasatospora hibisci sp. nov., a novel actinomycete with antimicrobial potential isolated from rhizosphere soil of Hibiscus tiliaceus in Guangxi

A novel Kitasatospora strain, designated as HNM1077T, was isolated from rhizosphere soil of Hibiscus tiliaceus collected from the bank of the Beilun River in Dongxing City, Guangxi Province, China. The novel strain exhibited antimicrobial activity against a wide range of microbes, particularly Gram--negative bacteria and plant pathogenic fungi. Based on the alignment of 16S rRNA gene sequences, strain HNM1077T was closely related to Kitasatospora aburaviensis NRRL B-2218T (99.51%). Comparisons based on genome sequencing showed that strain HNM1077T was distinguished from its nearest species by average nucleotide identity of 94.36% and a digital DNA-DNA hybridization value of 54.3%. The G+C content of strain HNM1077T was 73.1 mol%. The main fatty acids of strain HNM1077T were iso-C15:0 (21.5%), anteiso-C15:0 (11.7%), iso-C16:0 (8.6%), iso-C17:0 (9.3%) and anteiso-C17:0 (8.7%). The predominant menaquinone was MK-9 (H8). The major polar lipids of strain HNM1077T consisted of phosphatidylethanolamine, phosphatidylinositol, diphosphatidylglycerol and glycosylphosphatidylinositol. Based on these polyphasic taxonomic results, strain HNM1077T represents a novel Kitasatospora species, for which the name Kitasatospora hibisci sp. nov. is proposed. The type strain is HNM1077T (=CCTCC AA 2024052T=KCTC 59330T).

Description of Labrys sedimenti sp. nov., isolated from a diclofenac-degrading enrichment culture, and genome-based reclassification of Labrys portucalensis as a later heterotypic synonym of Labrys neptuniae

A Gram-stain-negative strain, designated as Zidic-5T, was isolated from diclofenac-degrading enrichment culture and characterized using a polyphasic approach to determine its taxonomic position. The 16S rRNA gene sequence analysis revealed that strain Zidic-5T belongs to the genus Labrys, with the highest 16S rRNA gene similarity to Labrys neptuniae LMG 23578T (99.13%), followed by Labrys portucalensis F11T (99.06%), Labrys methylaminiphilus JLW10T (98.58%) and Labrys okinawensis DSM 18385T (98.32%). The draft genome sequence of strain Zidic-5T is 7.64 Mb long, and the G+C content of the genome is 63.5 mol%. The orthologous average nucleotide identity and digital DNA-DNA hybridization relatedness values between strain Zidic-5T and its closest relatives were below the threshold values for species demarcation, confirming that strain Zidic-5T is distinctly separated from its closest relatives. Additionally, comparative whole-genome analysis of type strains of L. neptuniae and L. portucalensis indicated that they belong to the same genomic species, suggesting that L. portucalensis is a later heterotypic synonym of L. neptuniae. Cells of strain Zidic-5T were strictly aerobic, coccoid-shaped and non-motile. The predominant fatty acids (>10% of the total) of strain Zidic-5T were C18 : 1 ω7c, C16 : 0 and C19 : 0 cyclo ω7c. The major ubiquinone of strain Zidic-5T was Q-10, while the major polar lipids were phosphatidylcholine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and aminophospholipid. Based on the polyphasic study, it is concluded that strain Zidic-5T represents a novel species of the genus Labrys; thus, the name of Labrys sedimenti sp. nov. is proposed. The type strain of the species is strain Zidic-5T (=LMG 33565T=NCAIM B.02686T).

Streptomyces haneummycinicus sp. nov., a new antibiotic-producing actinomycete isolated from marine sediment

An actinomycete strain that produces a new antibiotic haneummycin, designated KM77-8T, was isolated from marine sediment collected from Tokyo Bay near Haneda Airport, Japan. This strain was phylogenetically related to Streptomyces pilosus NBRC 12807T, with the highest similarity (99.65%) based on 16S rRNA gene sequences. In contrast, genome-based comparisons between strain KM77-8T and S. pilosus JCM 4403T (=NBRC 12807T) revealed that average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values were 87.29% and 33.00 %, respectively. Moreover, genome-based comparisons between strain KM77-8T and other known Streptomyces species, including close relatives (more than 98.7% similarities of 16S rRNA gene sequences), showed that their ANI and dDDH values were <90% and <70%, respectively. The DNA G+C content of strain KM77-8T was 71.34%. The whole-cell hydrolysates of strain KM77-8T contained ll-diaminopimelic acid, galactose, glucose, mannose and ribose. The major menaquinones (MKs) of this strain were MK-9(H6) and MK-9(H8), and the major fatty acids (>10%) were anteiso-C15 : 0, iso-C15 : 0, C16 : 0, iso-C16 : 0 and summed feature 3 (C16 : 1  ω7c/C16 : 1  ω6c). Several phenotypic differences were observed between strain KM77-8T and S. pilosus NBRC 12807T. Furthermore, supernatant and methanol extract of not S. pilosus NBRC 12807T but strain KM77-8T displayed antibacterial activity against Enterococcus faecium and contained haneummycin. On the basis of the polyphasic data, we propose strain KM77-8T as a novel species of the genus Streptomyces, named Streptomyces haneummycinicus sp. nov. The type strain is KM77-8T (=NBRC 115995T=DSM 115857T).

The thylakoid- and pyrenoid-localized phosphate transporter PHT4-9 is essential for photosynthesis in Chlamydomonas

Phosphate (Pi) is essential for photosynthesis in the chloroplast of algae and plants. Pi homeostasis in the chloroplast is maintained by transporters from several families, whose identities in algae are largely unknown as compared with land plants. Here, we assess the role of the putative PHOSPHATE TRANSPORTER 4-9 from Chlamydomonas reinhardtii (CrPHT4-9) in maintaining chloroplast Pi homeostasis and modulating photosynthesis. Based on phylogenetic analyses and heterologous expression in a yeast (Saccharomyces cerevisiae) strain lacking Pi transporters, we demonstrate that CrPHT4-9 is a Pi transporter closely related to the chloroplast members of the PHT4 family in Arabidopsis (Arabidopsis thaliana). CrPHT4-9 is localized within the chloroplast, more specifically in the thylakoid membrane network and the tubules traversing the CO2-fixing pyrenoid. Two mutants lacking CrPHT4-9 (Crpht4-9) exhibit defective photoautotrophic growth, altered cell morphology and chloroplast ultrastructure under CO2-limiting conditions. In the Crpht4-9 mutants, we further show an increased proton motive force across the thylakoid membrane, enhanced energy- and state-transition-dependent non-photochemical quenching of chlorophyll a fluorescence, and diminished photosynthetic electron transport and ATP synthase activity. The Crpht4-9 mutants exhibit reduced affinity to inorganic carbon, indicating an impaired carbon-concentrating mechanism. These phenotypes are largely recovered by genetic complementation as well as by ample CO2 supply and, interestingly, by Pi deprivation. Therefore, we conclude that the thylakoid- and pyrenoid-localized CrPHT4-9 maintains Pi homeostasis within the chloroplast and is essential for photosynthesis and growth.

Integrating phylogenies with chronology to assemble the tree of life

Reconstructing the global Tree of Life necessitates computational approaches to integrate numerous molecular phylogenies with limited species overlap into a comprehensive supertree. Our survey of published literature shows that individual phylogenies are frequently restricted to specific taxonomic groups due to investigators' expertise and molecular evolutionary considerations, resulting in any given species present in a minuscule fraction of phylogenies. We present a novel approach, called the chronological supertree algorithm (Chrono-STA), that can build a supertree of species from such data by using node ages in published molecular phylogenies scaled to time. Chrono-STA builds a supertree by integrating chronological data from molecular timetrees. It fundamentally differs from existing approaches that generate consensus phylogenies from gene trees with missing taxa, as Chrono-STA does not impute nodal distances, use a guide tree as a backbone, or reduce phylogenies to quartets. Analyses of simulated and empirical datasets show that Chrono-STA can combine taxonomically restricted timetrees with extremely limited species overlap. For such data, approaches that impute missing distances or assemble phylogenetic quartets did not perform well. We conclude that integrating phylogenies via temporal dimension enhances the accuracy of reconstructed supertrees that are also scaled to time.

A phylogenetic analysis of the CDKL protein family unravels its evolutionary history and supports the Drosophila model of CDKL5 deficiency disorder

The human CDK-like (CDKL) family of serine‒threonine kinases has five members (CDKL1-5), with a conserved N-terminal kinase domain and variable C-termini. Among these, CDKL5 is of particular interest because of its involvement in CDKL5 deficiency disorder (CDD), a rare epileptic encephalopathy with several comorbidities for which there are no specific treatments. Current CDD vertebrate models are seizure resistant, which could be explained by the genetic background, including leaky expression of other CDKLs. Thus, phylogenetic analysis of the protein family would be valuable for understanding current models and developing new ones. Our phylogenetic studies revealed that ancestral CDKLs were present in all major eukaryotic clades and had ciliary/flagellar functions, which may have diversified throughout evolution. The original CDKL, which was likely similar to human CDKL5, gave rise to the remaining family members through successive duplications. In addition, particular clades have undergone further gene duplication and loss, a pattern that suggests some functional redundancy among them. A separate study focusing on the C-terminal tail of CDKL5 suggested that this domain is only functionally relevant in jawed vertebrates. We have developed a model of CDD in Drosophila based on downregulation of the single Cdkl gene by RNAi, which results in phenotypes similar to those of CDD patients, that are rescued by re-expression of fly Cdkl and human CDKL5. CDKL proteins contain a conserved kinase domain, originally involved in ciliary maintenance; therefore, invertebrate model organisms can be used to investigate CDKL functions that involve the aforementioned domain.

Terrimonas alba sp. nov., an Ochratoxin A-Degrading Strain Isolated from Lakeside Soil

A Gram-negative, aerobic, rod-shaped, and non-motile bacterium, designated strain R1T, was isolated from lakeside soil in Nanchang, Jiangxi Province, China. Growth was observed at 15-37 °C (optimum 30 °C), pH 6-8 (optimum pH 7) and salinity of 0-1.0% (w/v; optimum 0.5%). Strain R1T completely degraded 5 mg/L of ochratoxin A within 48 h of incubation. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain R1T belongs to the genus Terrimonas, and showed 99% sequences similarity with Terrimonas pollutisoli H1YJ31T. The draft genome of strain R1T was approximately 6.2 Mb with a 41.5% G + C content. The average nucleotide identity and digital DNA-DNA hybridization values between strain R1T and T. pollutisoli H1YJ31T were 90.4% and 41.2%, respectively. The predominant fatty acids of strain R1T were iso-C15:0, summed feature 3 (C16:1 ω6c and/or C16:1 ω7c), iso-C17:0 3-OH and iso-C15:1 G. The major isoprenoid quinone was menaquinone 7 (MK-7). The major polar lipids of strain R1T were phosphatidylethanolamine, phosphatidylglycerol, a phospholipid, two unidentified glycolipids, two unidentified aminophospholipids, and five unidentified polar lipids. Based on phenotypic, genotypic and phylogenetic evidence, strain R1T represents a novel species in the genus Terrimonas, for which the name Terrimonas alba sp. nov. is proposed. The type strain is R1T (= GDMCC 1.4673 T = JCM 37058 T = KCTC 102293 T = KACC 23743 T).

Molecular characterization and evolutionary analysis of human adenovirus type 55, related to febrile respiratory illness in the South Korean military

Adenoviruses are non-enveloped, double-stranded deoxyribonucleic acid (DNA) viruses that belong to the family Adenoviridae. Human adenovirus (HAdV)-55 is associated with severe respiratory illnesses that often lead to respiratory failure and death. HAdV-55 caused a febrile respiratory illness (FRI) outbreak at a military base in the Republic of Korea. The Army Forces Capital Hospital provided DNA samples from 79 patients with FRI; among them, we obtained seven whole-genome sequences of HAdV-55 using next-generation sequencing. Phylogenetic analysis of the complete genome and penton base, hexon, and fiber gene sequences demonstrated type-specific genetic clustering among the seven HAdV-55 strains. We also demonstrated protein modeling, molecular phylogeny, and evolution based on whole-genome sequences of seven HAdV-55 isolates characterized using next-generation sequencing and bioinformatics. Additionally, HAdV-55 strains from different countries have contributed to multiple lineages and genetic evolution. Our findings provide important insights into the evolution, molecular phylogeny, protein modeling, and genome sequencing of HAdV-55 isolates. Further studies are needed to better understand the genetic variants of emerging or re-emerging HAdVs.

Frateuria hangzhouensis sp. nov. Isolated from Soil of Moso Bamboo Forest in Hangzhou, China

A novel bacterium, designated STR12T, was isolated from the soil of a moso bamboo (Phyllostachys edulis) forest in Hangzhou, China. The strain was a Gram-stain-negative, rod-shaped, motile bacterium; the colonies of which were yellow, round, flat, sticky, and non-moist with a smooth margin after cultivation for 3 days at 28 °C. The strain grew at temperatures between 15 and 37 °C (optimum, 28 °C), pH values from 4.0 to 8.0 (optimum, pH 7.0), and salinities ranging from 0 to 5% (w/v) NaCl (optimum, 1%). Phylogenetic analyses based on the 16S rRNA gene sequence revealed that the strain was grouped within a cluster of the genus Frateuria, showing the highest similarity with Frateuria flava MAH-13T (97.7%). The genome of strain STR12T was 3.74 Mb in length with a G+C content of 67.9%. Genome comparisons of strain STR12T with other species within the genus Frateuria revealed that the range of average nucleotide identity, DNA-DNA hybridization, and average amino acid identity values were 73.9-85.9%, 20.8-30.7%, and 62.7-86.7%, respectively, all of those were below the respective prokaryotic species delineation thresholds. The predominant quinone in strain STR12T was ubiquinone-8 and the major fatty acids were iso-C15:0, iso-C16:0, iso-C17:0, and Summed Feature 9. Polar lipids included diphosphatidylglycerol, phosphatidylethanolamine, two unidentified aminophospholipids, and one unidentified phosphoglycolipid. On basis of the finding of phylogenetic, physiological, and chemotaxonomic analyses, we proposed the name Frateuria hangzhouensis sp. nov. for the novel species in the genus Frateuria, of which the type strain was strain STR12T (= ACCC 61897T = GDMCC 1.2964T = JCM 35226T).

Robust phylogenetic profile clustering for Saccharomyces cerevisiae proteins

Background

Genes are continually formed and lost as a genome evolves. However, new genes may tend to appear during specific evolutionary epochs rather than others, or disappear together in a more recent organismal clade. Methods to identify gene origination might simply use the last common ancestor to contain an ortholog as the putative gene origination point, or use a heuristic threshold that allows for a certain amount of missing orthologs in the cohort of species examined. Here, to avoid such issues, an alternative approach based on the clustering of phylogenetic profiles is applied, and the results are examined for any evidence of epochal trends in gene origination, and associated trends in specific sequence traits or functional associations.

Methods

A phylogenetic profile is simply an array indicating the presence or absence of a gene in a list of species. These profiles were compared and clustered to discern patterns in gene occurrences across >800 fungal species, centering the analysis on the budding yeast Saccharomyces cerevisiae.

Results

Clear epochs of gene origination were observed linked to the last common ancestors of Saccharomycetaceae and Saccharomycetes, and also to Fungi and earlier ancestors. These trends are independent of the proteome and genome-assembly quality of the underlying data. Clusters of phylogenetic profiles demonstrated some significant functional associations, such as to cellular spore formation and chromosome segregation in genes originating in Saccharomycetaceae. The phylogenetic profile clustering analysis enabled detection of parameter-independent trends in intrinsic disorder, prion-like composition and gene uniqueness as a function of epochal gene age. For example: new proteins with prion-like domains have arisen at a similar rate for most of fungal evolution centred on S. cerevisiae; the most proteins with mild intrinsic disorder have appeared during the early Saccharomycetaceae epoch rather than more recently, and very recently formed genes are the least likely to be single-copy (i.e., 'unique' yeast proteins).

Conclusions

For individual proteins, the profile cluster data generated here are useful for investigating experimental hypotheses, since they provide evidence for functional linkages that have yet to be discerned.

Detection and taxonomic identification of emerging pathogenic yeasts in surface waters from Lagoon Systems in Rio de Janeiro, Brazil

This study aimed to detect and identify emerging pathogenic yeasts in surface waters from two Lagoon Systems in Rio de Janeiro, Brazil, by polyphasic taxonomy. The monitoring of potentially pathogenic fungi in aquatic environments, especially in regions impacted by human actions, is highlighted in this study as one of the axes of the One Health approach. Water samples were collected, and after isolation, fungi were identified by polyphasic taxonomy, including MALDI-TOF-MS, which is also used for bacteria identification. Our results describe the physicochemical parameters of the surface water of these lagoons and reveal a significant diversity of yeast species, some of which are known to exhibit pathogenic potential and resistance to common antifungal treatments, as well as bacteria with resistance profiles to several currently used antibiotics. We conclude that Jacarepaguá Lagoon is the most impacted compared to Piratininga Lagoon; however, we highlight the urgent need for targeted interventions to mitigate pollution in both Lagoons, reinforcing the value of long-term surveillance in both ecosystems. We believe that monitoring emerging species is as critical as analyzing traditional water quality parameters. Early detection of resistant or invasive pathogens in aquatic ecosystems can prevent disease outbreaks, protect biodiversity, and mitigate public health risks, preventing loss of life, and optimizing public healthcare system expenditures.

Glutamicibacter sp. ZY1 antagonizes pathogenic Vibrio parahaemolyticus via iron competition

Probiotics are prior agents for treating bacterial infection with advantages of inhibiting pathogenic bacteria and improving immune responses of hosts, thus increasing the survival rate of cultured animals. In this study, one Vibrio parahaemolyticus YDE17 pathogenic to shrimp and its antagonist Glutamicibacter sp. ZY1 were screened, and ZY1 showed stable inhibitory effects on diverse Vibrio spp., especially V. parahaemolyticus. ZY1 secreted inhibitory substances into supernatant, and the activity of inhibitory substances did not change after being treated under different temperatures, proteinase K, and pH (6-10), which indicated that the inhibitory substances might be small molecules, which led us to trace the siderophore production. The siderophore production of YDE17 co-incubated with the cell-free supernatant of ZY1 was greater than that of YDE17 alone, which indicated that the cell-free supernatant of ZY1 created iron-limiting conditions for YDE17. This finding was confirmed by iron supplementation assays, in which the inhibitory activity of the cell-free supernatant of ZY1 on YDE17 as well as the siderophore production of YDE17 decreased in the presence of FeCl3. The effect of iron on inhibition was further confirmed by in vivo infection. The relative percent survival of ZY1 to shrimp challenged by YDE17 was 83.3%, but the survival rates of shrimp challenged with YDE17/ZY1/FeCl3 were similar to that of YDE17, both of which were significantly lower than the 70% survival rate of shrimps simultaneously challenged by ZY1/YDE17. Our study offers a new probiotic resource to control vibriosis, which works through iron competition with the opportunistic pathogens of Vibrio spp.IMPORTANCEBacteria belonging to Vibrio spp., especially Vibrio parahaemolyticus, are important opportunistic pathogens infecting a wide range of hosts including fish, shrimp, shellfish, and crab. Antibiotics are effective but show the disadvantages of antibiotic generation, microecology destruction, and biological toxicology; thus, new treatments of Vibrio infection are urgently recommended. In our present study, Glutamicibacter sp. ZY1, belonging to the phylum Actinomycetes, was selected and showed high inhibitory activity to inhibit V. parahaemolyticus pathogenic to shrimp. Glutamicibacter sp. ZY1 antagonized V. parahaemolyticus YDE17 through producing siderophore to compete for iron, based on the results of both in vitro and in vivo experiments under different iron levels. This study offers a new strategy to control Vibrio infection in aquaculture.

Bioprospecting Bacteria From Psychrophilic Anaerobic Digestate for Potential Plant Growth-Promoting Attributes

The psychrophilic anaerobic digestion (PAD) system is a diverse and underexplored microbial ecosystem that typically harbors cold-adapted microorganisms with possible agronomic potential. The plant growth-promoting bacteria in the residue of PAD have the potential to enhance crop production, particularly during cold winter months. In this context, the characteristics of cultivable, cold-tolerant bacteria isolated from digestate obtained during PAD were investigated. Of the 20 isolates, 12 (60%) were able to solubilize phosphate from insoluble compounds at 15°C. Furthermore, nine (45%) and six (30%) isolates exhibited nitrogen fixation activity and produced indole acetic acid (IAA), respectively, while only two (10%) isolates were capable of producing siderophores. Hydrolytic enzyme production varied with cellulase production observed as a common trait since all isolates produced varying levels of cellulase ranging from 3.3 ± 0.5 to 15.3 ± 4 mm activity diameter. Isolates Comamonas sp._A3-1, Acinetobacter iwoffi_B5-1, and Pseudomonas sp._B5-5 displayed maximum cellulolytic activity with activity diameters of 13 ± 2, 13 ± 1.2, and 15.3 ± 4 mm, respectively. However, only two (10%) of the bacterial isolates produced protease with Pseudomonas sp._B5-5 demonstrating maximum proteolytic activity as depicted by an activity diameter of 11.3 ± 2.5 mm. Nucleotide sequence analysis of seven isolates, possessing multiple plant-beneficial traits, revealed their affiliation to three genera: Acinetobacter (57%), Comamonas (28.7%), and Pseudomonas (14%). Biolog Phenotype MicroArray plates revealed varied catabolic capability among bacterial strains, with isolate B5-5 demonstrating the highest metabolic diversity. The findings of this study revealed that cold-tolerant isolates from low-temperature AD possess promising plant growth-promoting characteristics, which indicates the potential of psychrophilic digestate for application in agriculture.

Paracoccus yibinensis sp. nov., a novel bacterium with astaxanthin producing isolated from the environment of Chinese distilled Baijiu

An aerobic, Gram-stain-negative bacterium, designated as strain WLY502T, was isolated from the environment of Baobaoqu starter production. The strain was with a short rod shape cells 0.5-0.7 μm wide and 1.1-2.0 μm long, arranged singly or in pairs. The isolate was able to grow at temperatures of 20-37 °C (optimum growth at 25 °C), at pH 5.0-10.0 (optimum growth at pH 7.0) and in the presence of 0-5% (w/v) NaCl (optimum growth with 0% NaCl). Ribose, xylose, arabinose, mannose, glucose and galactose were the major cell-wall sugar. The meso-diaminopimelic acid (meso-DAP) was the diagnostic amino acid. The main polar lipids of strain WLY502T included diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylethanolamine (PE), unidentified aminolipids (UAL 1-2), unidentified aminophospholipid (UAPL), unidentified aminophospholipid (UAPL), unidentified phospholipid (UPL), unidentified lipids (UL 1-5), glycolipid (GL). Ubiquinone Q-10 was predominant menaquinone and C18:1 ω7c (80.5%) was the major fatty acid. Comparisons of 16S rRNA gene sequence indicated that strain WLY502T was most closely related to Paracoccus acridae SCU-M53T (98.48%), Paracoccus haematequi M1-83T (98.40%). The average nucleotide identity (ANI) values strain WLY502T and the two type strains mentioned above were 91.19% and 70.96%. The average amino identity (AAI) value between them were 93.42% and 87.19%. Additionally, the digital DNA-DNA hybridization (dDDH) value between them is 42.9% and 30.1%. The genomic DNA G + C content was 64.99%. Strain WLY502T could produce astaxanthin and contains several genes (such as MalK, UgpE, UgpA, PRK07067, PBP2 TMBP ike, YcjU, YjiC, crtI-fam, crtY, ERG9, and IspA) involved in astaxanthin. Therefore, strain WLY502T may have development and utilisation value in flavouring agents. Based on the evidence presented, strain WLY502T (CICC 25237T = JCM 36429T) is proposed as the type strain of a novel species, designated as Paracoccus yibinensis sp. nov.

Trujillonella humicola sp. nov., a siderophore-synthesizing bacterium isolated from black soil in Northeast China

A Gram-stain-positive, motile, and oval-shaped bacterium, designated as SYSU BS000539T, was isolated from black soil in Heilongjiang Province, China. 16S rRNA gene sequencing revealed that the isolate shared the highest similarity to Trujillonella endophytica DSM 45413T (98.32%), and phylogenetic analysis confirmed that it belonged to the genus Trujillonella. The strain could grow at temperatures from 15 to 37 °C (with an optimum at 28 °C), in salt concentrations of 0-5% (w/v) (with an optimum at 0%), and at pH levels from 6.0 to 10.0 (with an optimum at 8.0). The dominant cellular fatty acids (> 5%) were iso-C16:0, iso-C15:0, and iso-C16:1, while the principal respiratory quinones was menaquinone MK-9 (H4) with menaquinone MK-8 as minor components. Polar lipids were composed of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol methylphosphonolipid, an unidentified aminolipid and two unidentified polar lipids. The G + C content of the genome was 74.97%. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain SYSU BS000539T and T. endophytica DSM 45413T were 84.10% and 27.60%, respectively, falling below species delineation thresholds. Combining phylogenetic, genotypic, chemotaxonomic, physiological and biochemical analyses, it is evident that SYSU BS000539T represented a novel species within the genus Trujillonella, for which the name Trujillonella humicola sp. nov. is proposed. The type strain of the proposed novel species is SYSU BS000539T (= MCCC 1K09330T = KCTC 59402T).

Gracilibacillus pellucidus sp. nov., a moderately halophilic bacterium isolated from saline soil in Xinjiang province, China

A motile, Gram-positive, moderately halophilic, catalase-positive and oxidase-negative, obligate aerobic, slender rod-shaped bacterium, strain S3-1-1T was isolated from the plant rhizosphere soil in saline soil of Xinjiang Uygur Autonomous Region. Strain S3-1-1T grew in the presence of 1-21% NaCl and at pH 7.0-9.0, with optimum growth at 3% NaCl and pH 7.5. It grew at 16-45 °C, with optimum growth at 40 °C.Phylogenetic analysis based on 16S rRNA gene sequences showed that strain S3-1-1T should be placed within the genus Gracilibacillus and formed a separate branch. It exhibited highest similarities to Gracilibacillus ureilyticus MF38T (sequence similarity 97.7%), Gracilibacillus massiliensis Awa-1T (sequence similarity 97.5%), Gracilibacillus xinjiangensis J2T (sequence similarity 97.4%) and Gracilibacillus salitolerans SCU50T (sequence similarity 97.4%). Genomic comparisons revealed that strain S3-1-1T shares closest phylogenetic relationships with Gracilibacillus saliphilus YIM 91119T (ANI 77.4%, AAI 78.4%), Gracilibacillus thailandensis TP2-8T (ANI 77.2%, AAI 78.3%), and Gracilibacillus salitolerans SCU50T (ANI 77.3%, AAI 78.1%). However, the digital DNA-DNA hybridization (19.3-22.1%), average nucleotide identity (71.1-77.4%), and average amino acid identity (66.9-78.6%) values all fell below the recommended thresholds for species delineation, supporting its novel taxonomic status. The major cellular fatty acids were anteiso-C15:0, C16:0, iso-C15:0, and anteiso-C17:0. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and aminophospholipids. On the basis of their phenotypic, physiological, biochemical and phylogenetic characteristics, S3-1-1T represented a novel species of the genus Gracilibacillus, for which the name Gracilibacillus pellucidus sp. nov. is proposed, with S3-1-1T (= JCM 36422T = GDMCC 1.4017T) as the type strain.

Impact of altitudinal variations on plant growth dynamics, nutritional composition, and free living rhizospheric N2 fixing bacterial community of Eruca sativa

High-altitude environments present unique abiotic stresses, yet their impact on the growth, nutritional quality, and rhizospheric interactions of E. sativa remains underexplored. Here, we investigate the altitudinal variations in growth dynamics, nutritional composition, and rhizospheric free-living N2-fixing bacteria (NFBs) of E. sativa (Arugula) grown at higher (3,524 m, Leh-Ladakh) and lower (321 m, Chandigarh) altitudes. Results revealed significant physiological adaptations to high-altitude conditions, with increased concentrations of magnesium (748.84 ± 4.06 mg/100 g), iron (189.83 ± 2.16 mg/100 g), and manganese (8.48 ± 0.27 mg/100 g), while potassium (3,400.83 ± 3.82 mg/100 g), sodium (175.83 ± 1.44 mg/100 g), and copper (1.69 ± 0.01 mg/100 g) were higher at lower-altitude. Zinc content remained unchanged. Notably, dietary nitrate was higher (155.67 ± 22.12 mg/100 g) at high-altitudes. Rhizospheric NFBs were isolated and functionally characterized for N2-fixation efficacy along with various plant growth-promoting (PGP) attributes; viz., production of ammonia, siderophores, HCN, IAA and phosphate solubilization. Field inoculation with selected strains significantly enhanced nitrogen content and plant growth. Soil chemical analysis further revealed significant differences between the altitudes. A total of twenty-seven NFBs belonging to Actinobacteria (77%), Proteobacteria (11%), Firmicutes(8%), and Bacteroidetes(4%) were isolated, with Streptomyces being the predominant genus, exhibiting distinct species at different altitudes. Remarkably, high-altitude strains showed significantly higher N2-fixing efficiencies (88.15 ± 17.41 µgN mL-1) than lower-altitude (65.7 ± 14.36 µgN mL-1) along with superior PGP traits. Overall, these findings suggest that E. sativa, enriched in key nutrients at high-altitudes, could be a valuable functional food crop, addressing the dietary needs of high-altitude populations. Furthermore, the rhizospheric NFBs identified in this study may be potentially beneficial for the development of novel bio-fertilizers, promoting eco-friendly agricultural practices through improved N2-fixation. Further field trials are recommended to validate their potential for sustainable crop production.

The DNA binding of plant-specific GROWTH-REGULATING FACTOR transcription factors is stabilized by GRF-INTERACTING FACTOR coactivators

The plant-specific GROWTH-REGULATING FACTOR (GRF) transcription factor family proteins play crucial role in regulating diverse aspects of plant life. The transcriptional activity of GRFs is known to be enhanced through direct interaction with the GRF-INTERACTING FACTOR (GIF) coactivators. However, it remains unclear how the binding to GIF affects the biochemical ability of GRFs. Herein, we present evidence that GIFs also stabilize the DNA binding of GRFs. A combination of biochemical experiments and AlphaFold-predicted structural models suggests that the GIF-binding domain in GRFs may partially restrict their own DNA binding through direct interaction with the DNA-binding domain in the absence of GIFs. These findings deepen our understanding of the GRF:GIF module in plant regulation and provide a basis for strategies to manipulate this module for agricultural and biotechnological applications.

Characterization and Enzymatic Potential of Bacteria and Fungi From Mwakirunge Dumpsite, Kenya

Accumulation of solid waste is a major global challenge. The conventional waste disposal methods are often ineffective in mitigating solid waste pollution, highlighting the need for other sustainable alternatives. This study is aimed at isolating and identifying potential waste-degrading microorganisms from Mwakirunge dumpsite in Mombasa, Kenya. A total of 16 soil samples were collected using a randomized block design. The samples were inoculated in enriched basal media containing mixed municipal solid waste and incubated at 37°C for 21 days. Microbial identification was conducted using standard morphological, biochemical, and molecular approaches. DNA was extracted using organic isolation methods, and PCR amplification of the 16S rRNA gene for bacteria and the ITS gene for fungi was performed. Phylogenetic analysis grouped bacterial isolates into phylum Bacillota (Firmicutes), Pseudomonadota (Proteobacteria), and Actinomycetota (Actinobacteria) that included members of the genera bacilli, Pseudomonas, brevibacilli, Microbacterium, Ochrobactrum, Paenibacillus, Staphylococcus, Isoptericola, and Streptomyces. Fungal isolates belonged to the genus Aspergillus within the phylum Ascomycota. Three bacterial isolates B4S2 b (MZ571886), B3S1 (MZ571907), and B3S4 B (MZ571915) and one fungal isolate B2S2 a1 (MZ569413) had low sequence similarities with their closely known taxonomic relatives. The ability of the isolates to produce lipase, esterase, cellulase, amylase, and gelatinase enzymes was tested using the agar diffusion method. The results showed a significant level of enzyme production (p < 0.05). Bacillus cereus (MZ571899) exhibited the highest esterase activity; Streptomyces thermocarboxydus (MZ571882) exhibited the highest lipase activity, Bacillus subtilis (MZ571887) exhibited the highest amylase activity, and Bacillus licheniformis (MZ571888) exhibited the highest cellulase activity, while Pseudomonas stutzeri (MZ571900) exhibited the highest gelatinase activity. We recommend further studies to characterize the isolates with low sequence percentage similarities to establish their true identities. In addition, further enzymatic studies are required to quantify, characterize, and purify these enzymes for industrial applications.

Proposal of Paenibacillus kandeliae sp. nov, Isolataed from Leaf of Kandelia candel

A novel bacterial strain, designated JQZ6Y-1T, was isolated from the leaf of Kandelia candel at Maowei sea Mangrove Nature Reserve, Guangxi Zhuang Autonomous Region, China. The 16S rRNA gene sequence phylogenetic and phylogenomic analysis revealed that strain JQZ6Y-1T formed a stable clade with Paenibacillus wenxiniae DSM 100576T and Paenibacillus hunanensis CGMCC 1.8907T within the genus Paenibacillus. The 16S rRNA gene sequence similarities of strain JQZ6Y-1T with the related species P. wenxiniae DSM 100576T and P. hunanensis CGMCC 1.8907T were 98.3% and 98.2%, respectively. The average nucleotide identity values of strain JQZ6Y-1T with the related species P. wenxiniae DSM 100576T and P. hunanensis CGMCC 1.8907T were 77.5% and 80.4%, respectively. The digital DNA-DNA hybridization values of strain JQZ6Y-1T with the related species P. wenxiniae DSM 100576T and P. hunanensis CGMCC 1.8907T were 22.9% and 23.0%, respectively. These values clearly indicated that strain JQZ6Y-1T represented a novel species. The diagnostic diamino acid in the cell-wall peptidoglycan of strain JQZ6Y-1T was meso-diaminopimelic acid, and MK-7 was the predominant menaquinone. The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two unidentified aminophospholipids, two unidentified phospholipids, and one unidentified lipid. The major fatty acids were anteiso-C15:0 and C16:0. Cells of strain JQZ6Y-1T were Gram positive and rod shaped. Optimum growth occurred at pH 7.0, 30 ℃, and with 1-2% (w/v) NaCl. Based on phylogenomic and phylogenetic analyses coupled with phenotypic and chemotaxonomic characterizations, strain JQZ6Y-1T could be classified as a novel species of the genus Paenibacillus, for which the name Paenibacillus kandeliae sp. nov. is proposed. The type strain is JQZ6Y-1T (=CGMCC 1.18974T = JCM 34547T).

Identification of EcpK, a bacterial tyrosine pseudokinase important for exopolysaccharide biosynthesis in Myxococcus xanthus

Bacteria synthesize chemically diverse capsular and secreted polysaccharides that function in many physiological processes and are widely used in industrial applications. In the ubiquitous Wzx/Wzy-dependent biosynthetic pathways for these polysaccharides, the polysaccharide co-polymerase (PCP) facilitates the polymerization of repeat units in the periplasm, and in Gram-negative bacteria, also polysaccharide translocation across the outer membrane. These PCPs belong to the PCP-2 family, are integral inner membrane proteins with extended periplasmic domains, and functionally depend on alternating between different oligomeric states. The oligomeric state is determined by a cognate cytoplasmic bacterial tyrosine kinase (BYK), which is either part of the PCP or a stand-alone protein. Interestingly, BYK-like proteins, which lack key catalytic residues and/or the phosphorylated Tyr residues, have been described. In Myxococcus xanthus, the exopolysaccharide (EPS) is synthesized and exported via the Wzx/Wzy-dependent EPS pathway in which EpsV serves as the PCP. Here, we confirm that EpsV lacks the BYK domain. Using phylogenomics, experiments, and computational structural biology, we identify EcpK as important for EPS biosynthesis and show that it structurally resembles canonical BYKs but lacks residues important for catalysis and Tyr phosphorylation. Using proteomic analyses, two-hybrid assays, and structural modeling, we demonstrate that EcpK directly interacts with EpsV. Based on these findings, we suggest that EcpK is a BY pseudokinase and functions as a scaffold, which by direct protein-protein interactions, rather than by Tyr phosphorylation, facilitates EpsV function. EcpK and EpsV homologs are present in other bacteria, suggesting broad conservation of this mechanism and establishing a phosphorylation-independent PCP-2 subfamily.IMPORTANCEBacteria produce a variety of polysaccharides with important biological functions. In Wzx/Wzy-dependent pathways for the biosynthesis of secreted and capsular polysaccharides in Gram-negative bacteria, the polysaccharide co-polymerase (PCP) is a key protein that facilitates repeat unit polymerization and polysaccharide translocation across the outer membrane. PCP function depends on assembly/disassembly cycles that are determined by the phosphorylation/dephosphorylation cycles of an associated bacterial tyrosine kinase (BYK). Here, we identify the BY pseudokinase EcpK as essential for exopolysaccharide biosynthesis in Myxococcus xanthus. Based on experiments and computational structural biology, we suggest that EcpK is a scaffold protein, guiding the assembly/disassembly cycles of the partner PCP via binding/unbinding cycles independently of Tyr phosphorylation/dephosphorylation cycles. We suggest that this novel mechanism is broadly conserved.

Prospecting the biotechnological potential of culturable halophilic bacteria isolated from Provadia salt deposit (Bulgaria) near the oldest salt production and urban complex in Europe

Halophilic bacteria are recognized as a promising source of novel enzymes and biopolymers with various applications in biotechnology and the industry. In comparison with their mesophilic analogues, halophilic metabolites are stable under extreme conditions typically encountered in the industrial processes. In this study, the biotechnological potential of twenty strains of halophilic bacteria isolated from the Provadia salt deposit, Bulgaria was investigated for the first time. The strains were identified based on the sequencing of the 16S rRNA gene and were assigned to 13 different species falling in the Bacillota and Pseudomonadota phyla. The majority (90%) of them showed single or combined hydrolytic enzyme activity. Half of the strains (55%) were able to produce between three and eight extracellular hydrolytic enzymes-arabinase, cellulase, gelatinase, glucanase, L-glutaminase, pectinase, and xylanase. Ten strains were able to synthesise exopolysaccharides (EPS) in concentration between 32 and 227 μg/ml. The optimal EPS production kinetics (1.6 ± 0.15 g/l) by Virgibacillus halodenitrificans PSZ-34 was systematically investigated for the first time. Three strains also exhibited antimicrobial activity. The present study involved culture-dependant isolation of halophilic bacteria from the Provadia salt deposit and shed more light on their capability to synthesise hydrolytic enzymes and EPS with potential industrial exploitation.

Comprehensive Genomic Analysis of Klebsiella pneumoniae and Its Temperate N-15-like Phage: From Isolation to Functional Annotation

Antibiotic resistance to Klebsiella pneumoniae poses a major public health threat, particularly in intensive care unit (ICU) settings. The emergence of extensively drug-resistant (XDR) strains complicates treatment options, requiring a deeper understanding of their genetic makeup and potential therapeutic targets. This research delineated an extensively drug-resistant (XDR) Klebsiella pneumoniae strain obtained from an ICU patient and telomeric temperate phage derived from hospital effluent. The bacteria showed strong resistance to multiple antibiotics, including penicillin (≥16 μg/mL), ceftriaxone (≥32 μg/mL), and meropenem (≥8 μg/mL), which was caused by SHV-11 beta-lactamase, NDM-1 carbapenemase, and porin mutations (OmpK37, MdtQ). The strain was categorized as K46 and O2a types and carried virulence genes involved in iron acquisition, adhesion, and immune evasion, as well as plasmids (IncHI1B_1_pNDM-MAR, IncFIB) and eleven prophage regions, reflecting its genetic adaptability and resistance dissemination. The 172,025 bp linear genome and 46.3% GC content of the N-15-like phage showed strong genomic similarities to phages of the Sugarlandvirus genus, especially those that infect K. pneumoniae. There were structural proteins (11.8%), DNA replication and repair enzymes (9.3%), and a toxin-antitoxin system (0.4%) encoded by the phage genome. A protelomerase and ParA/B partitioning proteins indicate that the phage is replicating and maintaining itself in a manner similar to the N15 phage, which is renowned for maintaining a linear plasmid prophage throughout lysogeny. Understanding the dynamics of antibiotic resistance and pathogen development requires knowledge of phages like this one, which are known for their temperate nature and their function in altering bacterial virulence and resistance profiles. The regulatory and structural proteins of the phage also provide a model for research into the biology of temperate phages and their effects on microbial communities. The importance of temperate phages in bacterial genomes and their function in the larger framework of microbial ecology and evolution is emphasized in this research.

Overexpression, Purification, and Biochemical Characterization of the vanC2 d-Ala-d-Ser Ligase from Enterococcus casseliflavus SSK and Its Inhibition by an Oxadiazole Derivative

The bacterial cell wall and enzymes involved in peptidoglycan biosynthesis are prime targets for the discovery of novel antibacterial agents. Among these enzymes, d-alanine-d-alanine ligases (Ddl) are particularly significant due to their utilization of specific substrates (d-amino acids) essential for bacterial viability. Isozymes of Ddl that utilize alternative substrates such as d-lactate or d-serine are found in vancomycin-resistant Gram-positive bacteria, initially identified in Enterococcus species, and now represent a growing concern in clinical settings. In this study, we isolated and identified vancomycin-resistant Enterococcus casseliflavus (E. casseliflavus) strain SSK and used it for amplification, cloning, and purification of the vanC2 type of d-alanine-d-serine ligase (EcfDdls). Investigations of substrate specificity and enzyme kinetics provided insights into the enzyme's mechanistic action. Evaluation of the inhibitory potential of the previously virtually screened oxadiazole derivative 1-[(5-methyl-1,2-oxazol-3-yl)methyl]-4-{[3-(propan-2-yl)-1,2,4-oxadiazol-5-yl]methyl}piperazine (CID 45805715) was carried out using an inorganic phosphate detection assay, which demonstrated complete enzymatic inhibition of purified EcfDdls. When tested, CID 45805715 significantly inhibited activity of Ddl, with an IC50 of 76.7 μM, compared to 313 μM for the reference compound DCS. Moreover, this compound also exhibited antimicrobial activity against vancomycin-resistant E. casseliflavus strain SSK. Thus, these findings provide valuable insights into the activity and inhibition of vanC2 EcfDdls, offering a promising avenue for addressing vancomycin resistance in enterococci, particularly in nosocomial infections affecting immunocompromised patients.

A novel carotenoid-producing bacterium, Paenibacillus roseopurpureus sp. nov., isolated from Korean marine mud

A novel bacterial strain, designated MBLB1832T, was isolated from marine mud in Uljin, Republic of Korea. The strain was Gram-stain-positive, endospore-forming, and exhibited rod-shaped morphology. It grew at temperatures ranging from 10 to 45 °C (optimum 30 °C), at pH 6.0-9.0 (optimum 7.0), and in the presence of 0-2% NaCl (optimum 0%). Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain MBLB1832T is closely related to Paenibacillus allorhizoplanae JJ-42T, with 98.3% similarity. The predominant fatty acids were anteiso-C15:0 and iso-C16:0, and menaquinone-7 was identified as major isoprenoid quinone. Strain MBLB1832T contained meso-diaminopimelic acid within the cell wall peptidoglycan. Polar lipid profiling indicated the presence of diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine as the major lipids. The genome of strain MBLB1832T is 5.8 Mb in size with a G + C content of 46.9%. Average nucleotide identity, average amino acid identity, and DNA-DNA hybridization values confirmed that this strain is distinct from previously described species. Genome analysis revealed the presence of a complete C30 carotenoid biosynthetic pathway, including genes encoding farnesyl diphosphate synthase, diapophytoene synthase, several diapophytoene desaturases, and distinct carotenoid glycosyltransferases and acyltransferases. Notably, the carotenoid pigments produced by the strain imparted a pink color, consistent with the coloration of its cell pellets. Based on these polyphasic taxonomic data, strain MBLB1832T is proposed as a novel species of the genus Paenibacillus, for which the name Paenibacillus roseopurpureus sp. nov. is suggested (type strain MBLB1832T = KCTC 43262T = JCM 34221T).

Roseateles cavernae sp. nov., a Bacterium Isolated from Freshwater of the Old Huanglong Cave in Yunnan Province, South-West China

A novel bacteria, designated as YIM B04394T, was isolated from a freshwater sample collected from the Old Huanglong Cave in Kunming, Yunnan province, South-west China. The cells of this strain were Gram negative and rod shaped. The strain was found to be aerobic, oxidase positive, and weakly catalase positive, grew at 10-40℃ (optimum, 28 °C), pH 6.0-8.0 (optimum, pH 7.0), and low NaCl concentrations (up to 5.0%). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain YIM B04394T clustered with Roseateles species. The DNA-DNA and ANI relatedness values of strain YIM B04394T with the related species R. toxinivorans DSM 16998 T and R. saccharophilus DSM 25082 T were 21.50-22.9%% and 76.47-76.93%, respectively. The predominant fatty acids included C16:1ω6c and/or C16:1 ω7c and C16:0. Ubiquinone- 8 was detected as the respiratory quinone, and the major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, and an unknown phospholipid. The DNA G + C content was 67.89%. Based on phylogenomic and phylogenetic analyses, combined with phenotypic and chemotaxonomic characterizations, this strain represents a novel Roseateles species for which the name Roseateles cavernae sp. nov. is proposed. The type strain is YIM B04394T (= NBRC 115775 T = KCTC 92438 T = CCTCC AB2021502T).

Functional Characterization of a Highly Efficient Endoglucanase from Bacillus licheniformis BJ2022 and Its Application in the Preparation of Low-Molecular-Weight Konjac Glucomannan

Endoglucanases may not only act on β-1,4-linkages in β-glucan but also target d-glucose in glucomannan, which can expand their utility in the preparation of prebiotics. In this study, a highly efficient endoglucanase (BlGH5) from Bacillus licheniformis BJ2022 was expressed and characterized. BlGH5 exhibited the highest activity at pH 7.0 and 60 °C. It maintained over 80% activity at pH 4.0-7.0 and 30-60 °C. BlGH5 specifically cleaved β-1,4-glycosidic bonds linked to d-glucose. Site-directed mutagenesis results suggested that Arg91, Asn167, Glu168, Trp206, His228, Tyr230, Ser263, and Trp290 are key residues for its binding and catalytic activity. Moreover, BlGH5 displayed high activity against konjac glucomannan (KGM), indicating that BlGH5 could be used to prepare low-molecular-weight konjac glucomannan (KGM-L). Based on the physicochemical properties of KGM and KGM-L, KGM-L was characterized by reduced molecular weight and viscosity. Fecal fermentation experiments demonstrated that KGM and KGM-L could promote the production of short-chain fatty acids (SCFAs). Still, KGM-L was more conducive to the growth of the gut probiotics. In conclusion, we identified an endoglucanase for the degradation of KGM. Results indicated that KGM-L would have superior prebiotic effects. Thus, our study provides a basis for the future development and application of KGM-L as a prebiotic.

Insights into the physiological and metabolic features of Thalassobacterium, a novel genus of Verrucomicrobiota with the potential to drive the carbon cycle

Verrucomicrobiota are widely distributed across various habitats but are difficult to culture. Some previous multiomics analyses reported that Verrucomicrobiota have outstanding metabolic capacity for organic matter degradation and are able to degrade and synthesize polysaccharides, two activities that could contribute significantly to the Earth's carbon cycle. Here, we isolated from marine sediment two novel strains, Thalassobacterium maritimum SDUM461003T and Thalassobacterium sedimentorum SDUM461004T, that represent a new genus of the difficult-to-culture phylum Verrucomicrobiota. Genome analysis, functional annotation, and experimental verification revealed that these two strains degrade polysaccharides and antibiotics, including some complex sulfated polysaccharides (SPs), primarily fucoidan and chondroitin sulfate. Moreover, electron microscopy images revealed that these bacteria can synthesize and store large amounts of glycogen. These polysaccharide degradation and synthesis capacities also exist but differ under nitrogen-deficient conditions, indicating that Verrucomicrobiota may have the potential to maintain their normal metabolism by nitrogen fixation under aerobic conditions. Given that polysaccharides and their degradation products are particularly crucial carbon sources for marine microorganisms, Verrucomicrobiota are thought to be important contributors to biogeochemical cycling in the ocean.

IMPORTANCE

Verrucomicrobiota are widely distributed and able to utilize a variety of difficult-to-biodegrade polysaccharides, which have a significant impact on the marine carbon cycle. However, there are not enough pure culture strains of Verrucomicrobiota, as hard-to-cultivate bacteria, for us to study. Here, our study reports a new genus in the phylum Verrucomicrobiota and investigates their ability to degrade and synthesize a variety of polysaccharides as well as the mechanism of utilizing difficult-to-degrade polysaccharides. We also explored their special performance on carbon utilization in marine nitrogen-deficient environments. This contributes to deepening our understanding of the involvement of marine microorganisms in the marine carbon cycle.

Rubrolithibacter danxiaensis gen. nov., sp. nov. isolated from red sandy conglomerate in the Danxia Mountain

A Gram-stain-negative, rod-shaped and non-motile bacterium, designated as strain SYSU DXS3258T, was isolated from red sandy conglomerate sample collected from the Danxia Mountain in Guangdong Province, PR China. The bacterium was found to grow optimally at 28 °C, pH 7.0, and with 0-1% (w/v) NaCl. Phylogenetic analyses based on the 16S rRNA gene sequences placed strain SYSU DXS3258T within the family Sphingobacteriaceae. Strain SYSU DXS3258T showed the highest 16S rRNA gene sequence similarity to Pararcticibacter tournemirensis TF5-37.2-LB10T (95.5%), Paradesertivirga mongoliensis 1-32 T (95.3%) and Desertivirga xinjiangensis 12157 T (95.2%). Digital DNA-DNA hybridization, orthologous average nucleotide identity and average amino acid identity values between strain SYSU DXS3258T and the closest related members within the Sphingobacteriaceae were ≤ 13%, 70.3% and 69.9%, respectively. The genomic DNA G + C content was 38.8%. The major fatty acid was iso-C15:0, C18:0 and C15:0 2-OH. The predominant polar lipids were phosphatidylethanolamine, three glycolipids, one phospholipid and one unidentified polar lipid. The major respiratory quinone was Q-7. Based on phenotypic, phylogenetic, chemotaxonomic and genomic results, we propose that strain SYSU DXS3258T represents a novel species of a novel genus within the family Sphingobacteriaceae, for which the name Rubrolithibacter danxiaensis gen. nov., sp. nov. was proposed. The type strain is SYSU DXS3258T (= MCCC 1K09420T = KCTC 102322 T).

Sedimentitalea sediminis sp. nov., a novel bacterium isolated from marine sediment

Strain HM32M-2 T, an aerobic, catalase-positive, oxidase-positive, and Gram-stain-negative bacterium, was isolated from a sandy sediment sample collected from Qinzhou Gulf in Guangxi Zhuang Autonomous Region, China. Strain HM32M-2 T grew at 15-37 °C (optimum, 30 °C), at pH 5.5-9.5 (optimum, pH 8.5), and with 1.0-12.0% (w/v) NaCl (optimum, 3.0%). Strain HM32M-2 T exhibited the highest 16S rRNA gene sequence similarity with Sedimentitalea nanhaiensis NH52FT (98.4%). Phylogenetic analyses based on 16S rRNA gene sequences and whole-genome sequences showed that strain HM32M-2 T formed a distinct lineage with Sedimentitalea nanhaiensis NH52FT. The draft genome of strain HM32M-2 T was 3.40 Mbp in size and its DNA G + C content was 63.6%. Comparative genome analysis revealed that average nucleotide identity and digital DNA-DNA hybridization among strain HM32M-2 T and other Sedimentitalea species were below cut-off levels of 95-96% and 70%, respectively. Chemotaxonomic analyses indicated that strain HM32M-2 T contained Q-10 as the respiratory quinone, C18:1ω7c as the major cellular fatty acid, and diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, one unidentified aminolipid, and one unidentified lipid as the major polar lipids. Strain HM32M-2 T had a typical chemical composition of fatty acids, polar lipids, and quinones for Sedimentitalea species, but could be distinguished from known species of the genus Sedimentitalea. On the basis of the polyphasic evidence, strain HM32M-2 T should be classified as a novel species of the genus Sedimentitalea, for which the name Sedimentitalea sediminis sp. nov. is proposed. The type strain is HM32M-2 T (= MCCC 1K08873T = KCTC 8272 T).

Excavation of resources of Streptomyces species in frozen soils of the Qinghai-Tibet Plateau based on RpfA protein of Streptomyces coelicolor

This study is aimed at the actual demand for exploring new species resources of Streptomyces, and aims to solve the technical bottleneck of Streptomyces isolation and culture. A new method was established based on the resuscitation function of the RpfA protein from Streptomyces coelicolor CGMCC 4.1658T to isolate unculturable or difficult-to-culture Streptomyces species, and it was applied to explore Streptomyces species resources in special habitats in the frozen soils of the Qinghai-Tibet Plateau. The RpfA protein of S. coelicolor was heterologously expressed and validated for its in vitro activity. The purified RpfA protein was then used to isolate Streptomyces from soil samples in the frozen soils of the Qinghai-Tibet Plateau, followed by an investigation into the impact of the RpfA protein on the cultivability of Streptomyces species. The results showed that the RpfA protein had a significant promoting effect on the germination of spores of both S. coelicolor itself and other species of the Streptomyces genus, and when a suitable concentration of RpfA protein was added to the culture medium, it could significantly improve the culturability of members of phylum Actinomycetota, especially Streptomyces species. In addition, many new species of the genus Streptomyces and other genera of phylum Actinomycetota were discovered. This study provides a new approach for further exploring Streptomyces species resources in special environments such as the Qinghai-Tibet Plateau and developing new biologically active substances produced by Streptomyces.

Unraveling the functional dynamics of Caenorhabditis elegans stress-responsive omega class GST-44

Glutathione transferases from the omega class are notable for their roles in redox regulation and cellular stress response. In this study, we conducted a comprehensive functional characterization of GST-44, an omega-class glutathione S-transferase (GSTO), in Caenorhabditis elegans, focusing on its role in cellular defense mechanisms against stress. Biochemical analysis revealed GSTO-specific enzymatic activities of recombinant GST-44, including dehydroascorbate reductase, thioltransferase, and arsenate reductase activities. Using transgenic GFP reporter strains, we identified predominant expression of GST-44 in the intestine and excretory H-cell, with significant upregulation observed under diverse stress conditions. Induction of GST-44 was particularly pronounced in the intestine in response to pathogen-, oxidative-, and endoplasmic reticulum stress. Notably, under arsenic stress, the expression of gst-44 was significantly upregulated in the excretory system of the worm, underscoring its critical role in mediating arsenic detoxification. Moreover, we demonstrated the induction of GST-44 using dimethyl fumarate, a highly specific mammalian Nrf-2 activator. The upregulation of GST-44 during arsenic stress was dependent not only on the oxidative stress response transcription factor SKN-1/Nrf2 but also on PHA-4. The deletion mutant strain gst-44(tm6133) exhibited reduced stress resistance and a shortened lifespan, with a highly diminished survival rate under arsenic stress compared to other CRISPR-generated C. elegans GSTO deletion mutants. Our findings highlight the essential role of GST-44 in mediating arsenic detoxification, as well as in stress adaptation and defense mechanisms in C. elegans.

Three Novel Bacterial Species, Roseateles flavus sp. nov., Roseateles paludis sp. nov., and Roseateles hydrophilus sp. nov., Isolated from Various Water-Related Environments

A polyphasic study was conducted to determine the taxonomic positions of three bacterial strains, designated as strains 2.12 T, DJS-2-20 T, and UHG3T, isolated from the water of an agricultural water pipe, wetland, and artificial lake, respectively. These strains were Gram-stain-negative, rod-shaped, and oxidase positive. The fatty acid profiles of all three strains revealed that the major fatty acids (> 10%) were C16:0 and summed features 3 (comprising C16:1ω6c and/or C16:1ω7c), with strain UHG3T additionally featuring C16:0 3-OH as its main fatty acid. Phosphatidylethanolamine was the major polar lipid. Ubiquinone 8 (Q-8) was the only respiratory quinone detected. The genomic G + C contents were 68.5% for strain 2.12 T, 68% for strain DJS-2-20 T, and 69% for strain UHG3T. Strains 2.12 T, DJS-2-20 T, and UHG3T had the closest 16S rRNA gene sequence similarity with R. subflavus APW6T (98.5%), R. puraquae CCUG 52769 T (98.2%), and R. puraquae CCUG 52769 T (99.4%), respectively. The pairwise amino acid identity, average nucleotide identity, and digital DNA-DNA hybridization values for strains 2.12 T, DJS-2-20 T, and UHG3T with its closely related type strain of the species were below the species delineation thresholds. The genotypic and phenotypic characteristics observed in this study indicated that strains 2.12 T (= KACC 23730 T = TBRC 19013 T), DJS-2-20 T (= KACC 23731 T = TBRC 19014 T), and UHG3T (= KACC 22636 T = TBRC 16347 T) represent three novel Roseateles species, for which we propose the names Roseateles flavus sp. nov., Roseateles paludis sp. nov., and Roseateles hydrophilus sp. nov., respectively.

Genome mining reveals the biosynthetic potential of a novel Lysinibacillus zambalensis sp. nov., isolated from a hyperalkaline spring

A novel bacterium, designated as strain M3T, was isolated from a hyperalkaline spring in the Philippines and identified as a new species within the genus Lysinibacillus through 16 S rRNA gene sequence and genomic analyses. Although strain M3T shared a high 16 S rRNA gene sequence similarity (> 98.7%) with many Lysinibacillus species, the digital DNA-DNA hybridization and orthologous average nucleotide identity values between strain M3T and its closet relative, Lysinibacillus xylanilyticus DSM 23,493T, were 41.2% and 90.6%, respectively-both below the established threshold for prokaryotic species delineation. Genome mining of the 5.3 Mbp-draft genome of strain M3T revealed eight biosynthetic gene clusters, which shared little sequence similarity with characterized clusters, suggesting the potential for encoding novel specialized metabolites. The cells of strain M3T were Gram-stain-positive, aerobic, rod-shaped, non-motile, and capable of endospore formation. Optimum growth was observed at 30 °C, pH 8.0, and 0.5% (w/v) NaCl. The major respiratory quinone was menaquinone-7, and the predominant polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, and two unknown phospholipids. Its fatty acid profile showed an elevated level of iso-C15:0, and the peptidoglycan type was determined to be A4α (L-Lys-D-Asp). This study contributes to the growing database and understanding of the genus and aims to help drive future research on the bioactive potential of the genus. Lysinibacillus zambalensis sp. nov. is proposed with strain M3T as the type strain (= TISTR 10640T = BIOTECH 10973T).

The protein kinases KIPK and KIPK-LIKE1 suppress overbending during negative hypocotyl gravitropic growth in Arabidopsis

Plants use environmental cues to orient organ and plant growth, such as the direction of gravity or the direction, quantity, and quality of light. During the germination of Arabidopsis thaliana seeds in soil, negative gravitropism responses direct hypocotyl elongation such that the seedling can reach the light for photosynthesis and autotrophic growth. Similarly, hypocotyl elongation in the soil also requires mechanisms to efficiently grow around obstacles such as soil particles. Here, we identify KIPK (KINESIN-LIKE CALMODULIN-BINDING PROTEIN-INTERACTING PROTEIN KINASE) and the paralogous KIPKL1 (KIPK-LIKE1) as genetically redundant regulators of gravitropic hypocotyl bending. Moreover, we demonstrate that the homologous KIPKL2 (KIPK-LIKE2), which shows strong sequence similarity, must be functionally distinct. KIPK and KIPKL1 are polarly localized plasma membrane-associated proteins that can activate PIN-FORMED auxin transporters. KIPK and KIPKL1 are required to efficiently align hypocotyl growth with the gravity vector when seedling hypocotyls are grown on media plates or in soil, where contact with soil particles and obstacle avoidance impede direct negative gravitropic growth. Therefore, the polar KIPK and KIPKL1 kinases have different biological functions from the related AGC1 family kinases D6PK (D6 PROTEIN KINASE) or PAX (PROTEIN KINASE ASSOCIATED WITH BRX).

Streptomyces citrinus sp. nov., with yellow diffusible pigment

An actinomycete, designated strain Q6T, was isolated from tea plant rhizosphere soil sample in Hefei, China. Strain Q6T produced straight chains of smooth-surfaced spores and grew well on International Streptomyces Project 1-7 media. Phenotypic and genotypic analyses indicated that strain Q6T represented a member of the genus Streptomyces. The 16S rRNA gene sequence data of strain Q6T indicated that strain Q6T had the highest sequence similarity to Streptomyces xanthii CRXT-Y-14T (98.9%), Streptomyces davaonensis JCM 4913T (98.9%) and Streptomyces atriruber NRRL B-24165T (98.9%), followed by Streptomyces adustus WH-9T (98.8%), Streptomyces avermitilis MA-4680T (98.6%) and Streptomyces kunmingensis NBRC 14463T (98.6%). The phylogenomic tree, using the genome blast distance phylogeny method, showed that strain Q6T represents a new branch among the Streptomyces and has the closest genetic relationship with S. kunmingensis 80-3024T. The diagnostic diamino acid was ll-diaminopimelic acid. The major menaquinones were MK-9 (H6), MK-9 (H8) and MK-8 (H6). The dominant fatty acids were C16 : 0 (18.6%), iso-C16 : 0 (18.3%), anteiso-C15 : 0 (15.4%) and summed feature 3 (C16 : 1  ω7c and/or C16 : 1  ω6c; 13.8%). The main polar lipids were diphosphatidylglycerol, phosphatidylinositol, phosphatidylethanolamine (PE) and phosphatidylinositol mannoside. The DNA G+C content of strain Q6T was 71.3 mol%. Average nucleotide identity and digital DNA-DNA hybridization values between the genome sequence of strain Q6T and its closely related type strains were 77.0-87.5% and 22.4-29.7%, respectively. On the basis of these data, strain Q6T represents a novel species within the genus Streptomyces, for which the name Streptomyces citrinus sp. nov. is proposed. The type strain is strain Q6T (=CGMCC 4.7886T=NBRC 116061T).

Flavobacterium anseongense sp. nov. and Flavobacterium wongokense sp. nov., isolated from freshwater and freshwater soil in South Korea

Two novel, non-motile, Gram-stain-negative, rod-shaped bacterial strains, designated AS60T and WG47T, were isolated from freshwater in South Korea. To clarify their taxonomic positions, both strains were characterized based on genomic information, including 16S rRNA gene and draft genome sequences. Phylogenetic analyses revealed that both isolates belong to the genus Flavobacterium. Based on 16S rRNA gene sequencing, AS60T clustered with Flavobacterium silvisoli KACC 21178T (96.09%), Flavobacterium cheonhonense KACC 14967T (96.07%) and Flavobacterium sangjuense KACC 17473T (95.96%). Strain WG47T showed the highest similarity to Flavobacterium dankookense KACC 23179T (97.14%), F. cheonhonense KACC 14967T (97.07%) and Flavobacterium chungnamense KACC 14971T (96.71%). The draft genomes of AS60T and WG47T were 3.07 and 3.30 Mb, with G+C contents of 35.6 and 38.9 mol%, respectively. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values were calculated. For AS60T, ANI values compared to F. silvisoli KACC 21178T, F. cheonhonense KACC 14967T and WG47T were 76.67, 79.38 and 76.01%, respectively, with dDDH values of 20, 19.6 and 22.1%. For WG47T, ANI values compared to F. dankookense KACC 23179T and F. cheonhonense KACC 14967T were 75.12 and 74.75%, with dDDH values of 19.9 and 19.2%. Both strains exhibited MK-6 as the predominant respiratory quinone, and their fatty acid profiles included iso-C15:1, iso-C15:0 3OH, iso-C15:1 G, iso-C16:0, iso-C16:0 3OH and iso-C17:0 3OH. Phosphatidylethanolamine was the major polar lipid. Strain WG47T was found to produce flexirubin-type pigments, while AS60T did not. These results, combined with phenotypic and biochemical data, suggest that strains AS60T and WG47T represent two novel species of Flavobacterium, for which the names Flavobacterium anseongense sp. nov. (AS60T=KACC 22413T=LMG 32491T) and Flavobacterium wongokense sp. nov. (WG47T=KACC 22407T=LMG 32500T) are proposed.

Proposal of Paraglaciecola agarilytica (Yong et al. 2007) Shivaji and Reddy 2014 as a later heterotypic synonym of Paraglaciecola chathamensis (Matsuyama et al. 2006) Shivaji and Reddy 2014 and an emended description of Paraglaciecola chathamensis

In this paper, the comparative genome analysis was used to re-evaluate the taxonomic relationship between Paraglaciecola chathamensis and Paraglaciecola agarilytica. The 16S rRNA gene sequence analysis indicated that P. chathamensis S18K6T shared the highest sequence identity with P. agarilytica NO2T (99.9%), Paraglaciecola mesophila KMM 241T (99.2%) and Paraglaciecola polaris LMG 21857T (98.5%). Phylogenetic analysis based on 16S rRNA gene sequences and whole-genome sequences showed that P. chathamensis S18K6T was most closely related to P. agarilytica NO2T. However, the average nucleotide identity and digital DNA-DNA hybridization values among them were greater than the threshold of 95-96% and 70 % for the delineation of prokaryotic genomic species, confirming that they represented the same species. Besides, phenotypic characteristics and chemotaxonomic properties between P. agarilytica KCTC 12755T and P. chathamensis JCM 13645T were almost identical, further verifying this result. Consequently, we propose that P. agarilytica (Yong et al. 2007) Shivaji and Reddy 2014 is a later heterotypic synonym of P. chathamensis (Matsuyama et al. 2006) Shivaji and Reddy 2014.

Phylogenomics as baseline for taxonomy description: Amphibiibacter pelophylacis gen. nov., sp. nov., a novel taxon of the family Sphaerotilaceae, class Betaproteobacteria, isolated from the skin microbiota of Pelophylax perezi from different populations

Bacterial strain SL12-8T was characterized and isolated from the skin microbiota of Pelophylax perezi, the Perez's frog. Strain SL12-8T stained Gram-negative and formed rod-shaped cells that grew optimally at 25 °C and pH 7.0-7.5. The G+C content of the DNA was 66.2 mol%. Ubiquinone 8 was the respiratory quinone identified in the studied strain and the most closely related taxon. The major fatty acids were summed in feature 3 and summed in feature 8 and C16:0, representing 84% of the total fatty acids. Phylogenetic analyses based on the 16S rRNA gene sequence placed strain SL12-8T within the order Burkholderiales in a distinct lineage. The 16S rRNA gene sequence similarities of strain SL12-8T to that of Rubrivivax albus, Scleromatobacter humisilvae, Piscinibacter aquaticus, Azohydromonas caseinilytica and Aquincola agrisoli were 94.41, 94.08, 93.72, 93.72 and 93.64%, respectively. The draft genome sequence of strain SL12-8T comprises 3,115,197 bases with a 313-fold mapped genome coverage. The assembled genome consists of 53 large contigs with more than 500 bp, and the genome encodes 2,814 putative coding sequences. The analysis of the available genomes from the closest genera showed 124 core genes that reveal a novel genus-level clade including the strain SL12-8T. Analysis of the SL12-8T genome revealed the presence of the beta-lactone and terpene biosynthetic gene clusters. The phylogenomic, phylogenetic, phenotypic and chemotaxonomic data showed that strain SL12-8T (=UCCCB 131T=CECT 30762T) represents the type of a novel species and genus, for which we propose the name Amphibiibacter pelophylacis gen. nov., sp. nov.

Pantoea phytostimulans sp. nov., a novel strain with plant growth-promoting properties

A phosphate-solubilizing bacterial strain, designated C3T, was isolated from the rhizosphere of sorghum. The taxonomic classification of this novel isolate was investigated by using a polyphasic approach. Cells of this strain were Gram-stain-negative, facultatively anaerobic and motile short rods with a polar flagellum. Phylogenetic analyses based on the 16S rRNA gene indicated that strain C3T showed high similarity (98.66%) to certain Pantoea species, indicating that the isolate belongs to this genus. The genome of strain C3T was 5.05 Mb in size with a G+C content of 51.1 mol%. Whole-genome analysis revealed that the novel strain shared 21.60-27.10% digital DNA-DNA hybridization values and 78.35-83.87% average nucleotide identity with closely related Pantoea species; both values below the accepted thresholds for defining a novel species. The predominant cellular fatty acids of strain C3T were C16:0, summed feature 3 (C16:1 ω6c and/or C16 :1 ω7c), summed feature 8 (C18: 1 ω7c and/or C18:1 ω6c), summed feature 2 (C12: 0 aldehyde and/or C14:0 3OH and/or C16:1 iso I and/or an unidentified fatty acid of 10.9525 chain length) and C17:0 cyclo. Apart from the ability to solubilize phosphates, stain C3T exhibited other in vitro plant growth-promoting activities such as K, Ca and Si solubilization, and the production of indole-3-acetic acid (IAA) and siderophores. Several genes related to phosphate solubilization, siderophore biogenesis and IAA, cytokinin and gamma-aminobutyric acid production were identified in the C3T genome. Summarizing, based on phylogenetic, genomic, phenotypic and chemotaxonomic criteria, the isolate represents a novel species of the genus Pantoea, for which the name Pantoea phytostimulans sp. nov. is proposed. The type strain is C3T (=CECT 31163T=NCIMB 15596T).

Phyloformer: Fast, Accurate, and Versatile Phylogenetic Reconstruction with Deep Neural Networks

Phylogenetic inference aims at reconstructing the tree describing the evolution of a set of sequences descending from a common ancestor. The high computational cost of state-of-the-art maximum likelihood and Bayesian inference methods limits their usability under realistic evolutionary models. Harnessing recent advances in likelihood-free inference and geometric deep learning, we introduce Phyloformer, a fast and accurate method for evolutionary distance estimation and phylogenetic reconstruction. Sampling many trees and sequences under an evolutionary model, we train the network to learn a function that enables predicting a tree from a multiple sequence alignment. On simulated data, we compare Phyloformer to FastME-a distance method-and two maximum likelihood methods: FastTree and IQTree. Under a commonly used model of protein sequence evolution and exploiting graphics processing unit (GPU) acceleration, Phyloformer outpaces all other approaches and exceeds their accuracy in the Kuhner-Felsenstein metric that accounts for both the topology and branch lengths. In terms of topological accuracy alone, Phyloformer outperforms FastME, but falls behind maximum likelihood approaches, especially as the number of sequences increases. When a model of sequence evolution that includes dependencies between sites is used, Phyloformer outperforms all other methods across all metrics on alignments with fewer than 80 sequences. On 3,801 empirical gene alignments from five different datasets, Phyloformer matches the topological accuracy of the two maximum likelihood implementations. Our results pave the way for the adoption of sophisticated realistic models for phylogenetic inference.