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

Evaluation of a Novel Streptomyces avermitilis Strain from Egyptian Soil for Biological Control of Tetranychus urticae in Greenhouse Cucumber Plantations

BACKGROUND

Infestation in greenhouse cucumber with the two-spotted spider mite (Tetranychus urticae Koch) commonly causes severe damage to crop quality and quantity and increases crop production costs.

OBJECTIVE

This study was conducted to investigate the efficacy of high-abamectinproducing isolates of S. avermitilis against T. urticae-infested cucumber and to assess their impact on biochemical stress markers in these vegetables.

METHODS

In this study, 72 non-antagonistic Streptomyces were isolated from rhizospheric soil samples collected from eight different locations in Egypt and screened for their ability to produce the secondary metabolite, abamectin.

RESULTS

The screening process identified two potent abamectin-producing isolates, EW8 and T2, which produced 42.7 and 29.6 μg/L abamectin, respectively, as confirmed by LC-MS/MS analysis. According to DNA sequence analysis of the 16S rRNA gene, these two isolates belong to the species S. avermitilis. The acaricidal activity of either culture suspensions of S. avermitilis strains WE8 and T2, or their extracts containing abamectin, against the mobile stages and egg hatchability of T. urticae was evaluated in the laboratory and the greenhouse. Data on the mortality among the examined female mites and the reduction in their number of eggs point out a potential acaricidal activity of the examined strains of S. avermitilis and their extracts containing abamectin against T. urticaes. Furthermore, the extracts containing abamectin from these two S. avermitilis strains induced oxidative stress in the infested cucumber plants by T. urticaes, as indicated by increased levels of malondialdehyde (MDA). However, the levels of MDA in T. urticae-infested cucumber plants varied depending on the strain and the specific abamectin crude extract used.

CONCLUSION

S. avermitilis strains T2 or WE8, or their crude extract could be applied in greenhouse cucumber plantations to combat red mite infestation.

Clostridium sediminicola sp. nov., a crude oil aggregation-forming anaerobic bacterium isolated from marine sediment

A crude oil aggregation-forming, strictly anaerobic, Gram-stain-positive, spore-forming, rod-shaped, motile and mesophilic bacterium, named strain SH18-2T, was isolated from marine sediment near Sado Island in the Sea of Japan. The temperature, salinity and pH ranges of this strain for the growth were 15-40 °C (optimum 35 °C), 0.5-6.0% NaCl (w/v; optimum 2.0%) and pH 6.0-8.0 (optimum 7.5), respectively. A phylogenetic analysis of the 16S rRNA gene sequence showed that this strain belongs to the genus Clostridium. It was most closely related to Clostridium grantii A-1T (97.02% homology). The draft genome size was 5616089 bp, with a G+C content of 29.7 mol%. The digital DNA-DNA hybridization values determined using the Genome-to-Genome Distance Calculator and the average nucleotide identity between this strain and C. grantii A-1T were 20.30 and 78.24%, respectively. Whole-organism hydrolysates of strain SH18-2T contained meso-diaminopimelic acid; the major fatty acid was C16:0, and the polar lipid pattern consisted of diphosphatidylglycerol, phosphatidylglycerol, glycolipid and three unidentified polar lipids. From the results of genotypic, phenotypic and chemotaxonomic analyses, SH18-2T (=NBRC 116030T=DSM 115762T) is the type strain and represents a novel species of the genus Clostridium, and the name Clostridium sediminicola sp. nov. is proposed.

Ascidiimonas meishanensis sp. nov. and Leptobacterium meishanense sp. nov., two bacteria isolated from marine sediment in the East China Sea

Two Gram-stain-negative, curved-rod-shaped, non-motile and aerobic bacteria W6T and I13T were isolated from marine sediment samples collected from Meishan Island located in the East China Sea. Catalase and oxidase activities and hydrolysis of Tween 40, 60 and 80 were positive for both strains, while nitrate reduction, indole production, methyl red reaction and H2S production were negative. Phylogenetic analyses based on 16S rRNA and genome sequences revealed that strains W6T and I13T formed distinct phylogenetic lineages within the genera Ascidiimonas and Leptobacterium, respectively. Strain W6T showed the closest relatedness to Ascidiimonas aurantiaca N5DA8-2CT with 93.9% 16S rRNA gene sequence similarity, 70.7% average nucleotide identity (ANI), 71.0% average amino acid identity (AAI) and 16.4% digital DNA-DNA hybridization (dDDH) values, while strain I13T was most closely related to Leptobacterium flavescens YM3-301T with 92.1% 16S rRNA gene sequence similarity, 70.5% ANI, 72.1% AAI and 17.2% dDDH values. The two novel strains shared 92.0% 16S rRNA gene sequence similarity to each other and were identified as two distinct species based on 70.7% ANI, 70.4% AAI and 17.1% dDDH values calculated using whole-genome sequences. The genomes of strains W6T and I13T were 4.59 Mbp with a G+C content of 34.5 mol% and 2.38 Mbp with a G+C content of 36.2 mol%, respectively. The only respiratory quinone was menaquinone-6, the major polar lipid was phosphatidylethanolamine and the major cellular fatty acids were iso-C15 : 0, iso-C15 : 1 G and iso-C17 : 0 3-OH. Based on phenotypic, chemotaxonomic and genotypic data, strains W6T and I13T are considered to represent two novel species in the genera Ascidiimonas and Leptobacterium, respectively, in the family Flavobacteriaceae, for which the names Ascidiimonas meishanensis sp. nov. and Leptobacterium meishanense sp. nov. are proposed. The type strains are W6T (=KCTC 102201T=MCCC 1K08928T) and I13T (=KCTC 102202T=MCCC 1K08929T), respectively.

Streptacidiphilus alkalitolerans sp. nov., Streptacidiphilus cavernicola sp. nov. and Streptacidiphilus jeojiensis sp. nov. isolated from a cave, and an emended description of the genus Streptacidiphilus

Six Gram-reaction-positive, strictly aerobic, mycelium-forming actinobacteria were isolated from soils collected from a natural cave in Jeju, Republic of Korea. The isolates produced well-developed, branched, substrate mycelia and white aerial mycelia that differentiated into straight or flexuous chains of smooth-surfaced spores. Cells showed growth at 15-30 °C, pH 3.5-8.0 and 0-1% (w/v) NaCl. Most of the isolates also grew at pH 10.0. The cell-wall peptidoglycan in common contained ll-diaminopimelic acid, galactose, glucose, mannose and rhamnose. The major menaquinone was MK-9(H6) and MK-9(H8). The polar lipids in common contained phosphatidylglycerol, phosphatidylinositol and an unidentified phospholipid, with the presence of diphosphatidylglycerol and phosphatidylethanolamine in some strains. The predominant fatty acids in common were anteiso-C15 : 0, iso-C16 : 0 and C16 : 0. Strains N1-1T, N1-3 and N1-12 contained genomes of 8.44-8.77 Mbp, and strains N1-5 and N1-10T consisted of genomes of 9.00-9.17 Mbp, while strain N8-3T contained the smallest genome (7.33 Mbp) among the isolates. The genomic DNA G+C contents of the isolates were 71.5-72.2%. Three representatives of the isolates encompassed 16-29 biosynthetic gene clusters predicted to encode for secondary metabolites. The core genome-based phylogenomic tree showed that they formed three distinct clusters within the genus Streptacidiphilus, with the closest relative, the type strain of Streptacidiphilus carbonis, which was also supported by 16S rRNA gene phylogeny. The orthologous average nucleotide identity (≤88.2%) and digital DNA-DNA hybridization (≤30.3%) between three representatives of the isolates and members of the genus Streptacidiphilus and among them supported that the isolates represent three new species of the genus Streptacidiphilus, for which the names Streptacidiphilus alkalitolerans [type strain, N1-1T (=KCTC 19224T=DSM 45080T)], Streptacidiphilus cavernicola [type strain, N8-3T (=KCTC 29470T=DSM 117389T)] and Streptacidiphilus jeojiensis sp. nov. [type strain, N1-10T (=KCTC 19257T=DSM 117391T=NRRL B-24556T)] are proposed.

Pseudonocardia spirodelae sp. nov., isolated from duckweed and formal proposal to reclassify Pseudonocardia antarctica as a later heterotypic synonym of Pseudonocardia alni and reclassify Pseudonocardia carboxydivorans as Pseudonocardia alni subsp. carboxydivorans

A novel Pseudonocardia strain DW16-2T, isolated from duckweed (Spirodela polyrhiza), was taxonomically studied in detail. The analysis based on its 16S rRNA gene sequence revealed that the strain was most closely related to Pseudonocardia carboxydivorans Y8T (98.8%), followed by Pseudonocardia tropica YIM 61452T (98.7%), Pseudonocardia antarctica DVS 5a1T (98.7%) and Pseudonocardia alni DSM 44104T (98.7%). The average nucleotide identity (ANI) based on blast and digital DNA-DNA hybridization (dDDH) relatedness values between strain DW16-2T and their closest type strains were below the threshold values for identifying a novel species. Morphological, physiological and chemotaxonomic features of strain DW16-2T were typical for the genus Pseudonocardia by forming extensively branched substrate mycelium and aerial mycelium that fragmented into rod-shaped spore, with a smooth surface. The whole-cell hydrolysates of strain DW16-2T contained meso-diaminopimelic acid as the diagnostic diamino acid, and the whole-cell sugars were arabinose, galactose, glucose and a trace amount of ribose. The polar lipids contained phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol and unidentified phospholipids. The menaquinone (MK) was MK-8(H4). The cellular fatty acids (>5 %) were iso-C16 : 0, iso-C16 : 1 H, summed feature 3: C16 : 1 ω7c/C16 : 1 ω6c; C16 : 1 ω6c/C16 : 1 ω7c, C17 : 1 ω8c and anteiso-C17 : 0. Characterization based on chemotaxonomic, phenotypic, genotypic and phylogenetic evidence demonstrated that strain DW16-2T represents a novel species of the genus Pseudonocardia, for which the name Pseudonocardia spirodelae sp. nov. (type strain DW16-2T = TBRC 16418T = NBRC 115857T) is proprosed. In addition, the comparison of the whole genome sequences suggested that P. alni and P. antarctica belong to the same species and P. carboxydivorans is a subspecies of P. alni. Therefore, it is proposed that P. antarctica Prabahar et al. 2004 is reclassified as a later heterotypic synonym of P. alni (Evtushenko et al. 1989) Warwick et al. 1994, and P. carboxydivorans Park et al. 2008 is proposed as a subspecies of P. alni (Evtushenko et al. 1989) Warwick et al. 1994.

Methylobacterium litchii sp. nov., Methylobacterium guangdongense sp. nov. and Methylorubrum subtropicum sp. nov., isolated from the phyllosphere of litchi

Three aerobic, pink-pigmented, Gram-negative, motile and rod-shaped bacterial strains, designated SD21T, SI9T and SB2T, were isolated from the phyllosphere of healthy litchis collected from three main producing sites of Guangdong Province, PR China. The 16S rRNA gene analysis showed that strains SD21T and SI9T belonged to the genus Methylobacterium (Mtb.) with the highest similarity to Mtb. komagatae DSM 19563T (98.7%) and Mtb. phyllosphaerae CBMB27T (99.8%), respectively, while strain SB2T belonged to the genus Methylorubrum (Mtr.) and showed the highest similarity to Mtr. suomiense DSM 14458T (98.6%). Phylogenomic analysis based on 92 core genes clearly showed that the most closely related type strains of SD21T, SI9T and SB2T were Mtb. komagatae DSM 19563T, Mtb. phyllostachyos ICMP 17619T and Mtr. salsuginis CGMCC 1.6474T, respectively. The ANI and dDDH values between the three isolates and their most closely related type strains were 85.6‒90.1% and 29.5‒40.4%, respectively, much below the threshold values for species delimitation. The isolates showed clear differences from their closely related type strains in terms of growth conditions, enzyme activities, substrates assimilation and contents of the major fatty acids. They all took summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) as the major fatty acid, ubiquinone 10 as the predominant respiratory quinone and phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine as the major polar lipids. The phenotypic, phylogenetic and chemotaxonomic analyses with genome comparison strongly support that the isolates represent three distinct novel species within the genera of Methylobacterium and Methylorubrum, for which the names Methylobacterium litchii sp. nov., Methylobacterium guangdongense sp. nov. and Methylorubrum subtropicum sp. nov. are proposed, with SD21T (=GDMCC 1.4327T=KCTC 8300T), SI9T (=GDMCC 1.4329T=KCTC 8298T) and SB2T (=GDMCC 1.4328T=KCTC 8299T) as the type strains, respectively.

Jannaschia maritima sp. nov., a novel marine bacterium isolated from the biofilm of concrete breakwater structures

Marine biofilms were newly revealed as a bank of hidden microbial diversity and functional potential. In this study, a Gram-stain-negative, aerobic, oval and non-motile bacterium, designated LMIT008T, was isolated from the biofilm of concrete breakwater structures located in the coastal area of Shantou, PR China. Strain LMIT008T was found to grow at salinities of 1-7% NaCl, at pH 5-8 and at temperatures 10-40 °C. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain LMIT008T belonged to the genus Jannaschia and was closely related to the type strains Jannaschia aquimarina KCTC23555T (96.03%) and Jannaschia marina SHC-163T (95.31%). The draft genome size of the strain LMIT008T was 3.67 Mbp, and the genomic DNA G+C content was 69.83 mol%. The average nucleotide identity value between strain LMIT008T and the closely related type strain J. aquimarina KCTC23555T was 74.82%. The predominant cellular fatty acids were identified as summed feature 8 (C18 : 1  ω7c/C18 : 1  ω6c) and C18 : 0, and the major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and phosphatidylcholine. Ubiquinone-10 (Q-10) is the sole respiratory quinone. Further, genomic analysis of strain LMIT008T showed that the strain harbours abundant genes associated with biofilm formation and environmental adaption, explaining the potential strategies for living on concrete breakwater structures. Based on the morphological, phylogenetic, chemotaxonomic and phenotypic characterization, the strain LMIT008T was considered to represent a novel species in the genus of Jannaschia, for which the name Jannaschia maritima sp. nov. was proposed, with LMIT008T (=MCCC 1K08854T=KCTC 8321T) as the type strain.

Paenibacillus zeirhizosphaerae sp. nov., isolated from surface of the maize (Zea mays) roots in a horticulture field, Hungary

A novel Gram-stain-positive, rod-shaped, endospore-forming bacterium with peritrichous flagella, designated as P96T was isolated from the surface of maize roots. Strain P96T grew optimally at 28 °C, pH 7.0. The strain contained A1γ meso-Dpm-direct in the cell-wall peptidoglycan. The dominant polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. The genome size of strain P96T was 4.8 Mb, and the G+C content was 50.01%. Phylogenomic analyses based on the whole-genome sequences classified the strain into the genus Paenibacillus. The digital DNA-DNA hybridization and average nucleotide identity relatedness analysis resulted in values below the threshold for prokaryotic species delineation, with the highest values observed for Paenibacillus enshidis KCTC 33519T (29.4 and 85.2%, respectively). Genotypic data together with phenotypic properties supported the classification of strain P96T as representative of a novel species of the genus Paenibacillus, for which the name Paenibacillus zeirhizosphaerae sp. nov. is proposed. The type strain is P96T (=LMG 32802T = NCAIM B 02678T).

Identification of Starmerella aleppica f.a., sp. nov. and large indels in the rRNA cistron that split the Starmerella genus

Yeast strains representing a novel asexual ascomycetous species were isolated from seven Malva sylvestris flowers. Sequencing of the chromosomal regions coding for the D1/D2 domains of the large subunit ribosomal RNA, the ITS1-5.8S-ITS2 segments and parts of the gene coding for the small subunit ribosomal RNA showed that the isolates were conspecific. Comparative analysis of these sequences and the corresponding sequences of the type strains of ascomycetous yeasts revealed that the strains represent a hitherto undescribed species belonging to the sensu stricto subclade of the genus Starmerella. The new species is osmotolerant and can develop invasive pseudohyphae, but does not form spores. For the new species, the name Starmerella aleppica f.a. (forma asexualis) is proposed. The holotype, preserved in a metabolically inactive state, is CBS 12960T (extype cultures: 2-1361 and CCY 90-2-1, NCAIM Y.02123). The GenBank accession numbers of barcode sequences are JX515983 (D1/D2 domain), JX515985 (ITS1-5.8S-ITS2 and partial 18S rRNA gene), PQ613837 (TEF1 partial sequence) and PQ613838 (RPB2 partial sequence). MycoBank: MB855459. The analysis of the D1/D2 and internal transcribed spacer (ITS) sequences of the type strains of species of the genus identified multiple multinucleotide indels that can be used as taxonomic markers (InDel markers). The indel patterns of the subclades are very different and homogeneous within the subclades. This result reinforces the idea raised, but also refuted, in previous studies that the Starmerella subclades may represent different genera.

Desulfovibrio falkowii sp. nov., Porphyromonas miyakawae sp. nov., Mediterraneibacter flintii sp. nov. and Owariibacterium komagatae gen. nov., sp. nov., isolated from human faeces

Small, obligately anaerobic strains 13CB8CT, 13CB11CT, 13CB18CT and 13GAM1GT were isolated from a faecal sample in a patient with Parkinson's disease with a history of duodenal resection. After conducting a comprehensive polyphasic taxonomic analysis including genomic analysis, we propose the establishment of one new genus and four new species. The novel bacteria are Desulfovibrio falkowii sp. nov. (type strain JCM 36128T = DSM 116810T), Porphyromonas miyakawae sp. nov. (type strain JCM 36129T = DSM 116947T), Mediterraneibacter flintii sp. nov. (type strain JCM 36130T = DSM 116866T) and Owariibacterium komagatae gen. nov. sp. nov. (type strain JCM 36131T = DSM 116982T), respectively.

Roseomonas cutis sp. nov., isolated from human epidermis

Five pink-pigmented bacterial strains, isolated from human skin and classified within the genus Roseomonas, were examined. Among them, four were identified as Roseomonas mucosa, while strain OT10T was deemed to be a potential novel species. Strain OT10T exhibited characteristics, such as Gram-stain-negative, oxidase positive, motile, strictly aerobic and rod shaped. The cells had multiple flagella at one end, arranged in a lophotrichous pattern. The predominant cellular fatty acids in OT10T were C18:1 ω7c/C18:1 ω6c and C18:1 2OH; ubiquinone (Q)-10 was identified as the sole quinone. Major polar lipids included phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylcholine and two aminolipids. The G+C content of the genome was determined to be 72.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequence similarities revealed that strain OT10T is closely related to Roseomonas gilardii subsp. gilardii ATCC 49956T (97.7%), Roseomonas gilardii subsp. rosea ATCC BAA-691T (97.7%) and R. mucosa ATCC BAA-692T (97.5%). For the comparative genomic analyses, whole-genome sequencing was also conducted for strain OT10T. Considering the chemotaxonomic, genotypic and phenotypic features, as well as the low average nucleotide identity and digital DNA-DNA hybridization values compared to its closest phylogenomic neighbours, OT10T is proposed to be a novel species named Roseomonas cutis sp. nov., with OT10T designated as the type strain (=KCTC 92087T =JCM 34968T).

Description of six novel species Bacillus bruguierae sp. nov., Bacillus kandeliae sp. nov., Bacillus yunxiaonensis sp. nov., Metabacillus rhizosphaerae sp. nov., Metabacillus sediminis sp. nov. and Psychrobacillus mangrovi sp. nov., isolated from mangrove ecosystem

Six Gram-stain-positive and rod-shaped strains, designated FJAT-51614T, FJAT-51639T, FJAT-52054T, FJAT-52991T, FJAT-53654T and FJAT-53711T, were isolated from a mangrove ecosystem. The condition for growth among the strains varied (pH ranging 5.0-11.0 and temperature 15-45 °C). These strains showed the highest 16S rRNA gene sequence similarity to the genera Bacillus, Metabacillus and Psychrobacillus. Menaquinone MK-7 (100%) was present in all strains except strain FJAT-51614T, which contained MK-7 (32%) and MK-8 (68%). The major fatty acids (>10%) in strains FJAT-52054T and FJAT-51614T were anteiso-C15 : 0 and iso-C14 : 0. The major fatty acid (>10%) in strain FJAT-53654T was anteiso-C15 : 0, while in strain FJAT-51639T were iso-C15 : 0 and iso-C17 : 0. The major fatty acids in strains FJAT-52991T and FJAT-53711T were iso-C15 : 0 and iso-C16 : 0. The major polar lipids in strains FJAT-51639T, FJAT-52991T and FJAT-51614T were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine, while strains FJAT-53711T, FJAT-52054T and FJAT-53654T consist of diphosphatidylglycerol and phosphatidylglycerol. The genome-relatedness values among the present study strains and the closest species were below the recognized cutoff levels for species delineation. The polyphasic analysis comparison results represent six strains as novel species for which the names Bacillus bruguierae sp. nov. (FJAT-51639T=GDMCC 1.3073T=JCM 35615T), Bacillus kandeliae sp. nov. (FJAT-52991T=GDMCC 1.3069T=JCM 35619T), Bacillus yunxiaonensis sp. nov. (FJAT-53711T=GDMCC 1.3068T=JCM 35616T), Metabacillus rhizosphaerae sp. nov. (FJAT-53654T=GDMCC 1.3075T=JCM 35614T), Metabacillus sediminis sp. nov. (FJAT-52054T=GDMCC 1.3074T=JCM 35620T) and Psychrobacillus mangrovi sp. nov. (FJAT-51614T=GDMCC 1.3072T=JCM35478T) are proposed.

Identification of Dengue virus serotype and genotype: A comprehensive study from AIIMS Patna, Bihar

PURPOSE

Dengue virus, a major global health concern, exhibits significant genetic diversity, leading to distinct serotypes and genotypes. Dengue is the second most common disease spread by mosquitoes that infect humans, after malaria. In recent decades, there has also been a shift in the tendencies of virus transmission from urban to peri-urban and rural settings. This research study focuses on the identification and characterization of dengue virus serotypes and genotypes.

METHODS

In this study, specimens collected in one year were first subjected to serological assay (NS1 and IgM) and subsequently the NS1 positive samples were subjected to identification and characterization of the prevalent dengue virus serotypes and genotypes.

RESULTS

During the year 2021, a total of 933serum samples were tested, out of which 75 were found positive for NS1 antigen and 135 were positive for Dengue IgM antibody by ELISA. The dengue serotype specific Real-Time RT-PCR Assay detected all four serotypes in the NS1-positive samples, indicating their presence in this region. Of these, DEN-1 was detected in 4 (7.8 %), DEN-2 in 26 (50.9 %), DEN-3 in 20 (39 %), DEN-4 in 1 (1.9 %). Out of 51Real-Time RT-PCR positive samples, 33 were found positive by conventional PCR for genotyping by targeting the capsid-preMembrane (C-prM)region. The genotyping result showed that DENV-1 serotype clustering with GIII, DEN-2 serotype clustering withwide range of genotypes such as IVa, IVb, and IVc, DEN-3 clustering with GIII genotype and DEN-4 serotype showed GIII genotype.

CONCLUSIONS

This study provides the recent details about the circulating serotypes along with prevalent genotypes in this region.

Flavobacterium aerium sp. nov., a bacterium isolated from the air of the Icelandic volcanic island Surtsey

A novel bacterium, designated 19SA41, was isolated from the air of the Icelandic volcanic island Surtsey. Cells of strain 19SA41 are Gram-stain-negative, strictly aerobic, non-motile rods and form pale yellow-pigmented colonies. The strain grows at 4-30 °C (optimum, 22 °C), at pH 6-10 (optimum, pH 7.5) and with 0-4% NaCl (optimum, 0.5%). Phylogenetic analyses based on 16S rRNA gene sequences showed that 19SA41 belonged to the genus Flavobacterium and is most similar to Flavobacterium xinjiangense DSM 19743T, with a sequence similarity of 96.52%. The new strain contained iso-C15 : 0 (22%) and summed feature 3 (C16∶1ω6c/C16∶1ω7c) (20%) as the predominant fatty acids. The major respiratory quinone was menaquinone-6 (100%). The polar lipid profile consisted of phosphatidylethanolamine and several uncharacterized amino lipids, glycolipids and lipids. The genome of the new strain was 4.01 Mbp, and its G+C content was 33.2 mol%. Based on characterization and comparative results, using a polyphasic taxonomic approach, we propose that the new isolate represents a novel species of the genus Flavobacterium with the name Flavobacterium aerium sp. nov. The type strain is ISCaR-07695T (=DSM 116640T =UBOOC-M-3567T).

Virgibacillus saliphilus sp. nov. and Virgibacillus salidurans sp. nov., isolated from kimchi

This study aimed to provide a taxonomic description of two bacterial strains, NKC19-3T and NKC19-16T, isolated from commercially produced kimchi obtained from various regions within the Republic of Korea. Both strains were rod-shaped, gram-stain-positive, facultatively anaerobic, and displayed positive reactions for oxidase and catalase. Additionally, these bacteria were motile, halophilic (salt-tolerant), and proliferated under alkaline conditions. Genetically, both strains showed 98.0% similarity in their 16S rRNA gene sequences and were most closely related to Virgibacillus natechei FarDT, with 96.5 and 96.8% sequence similarity, respectively. ANI values indicated that the two novel strains were distinct from V. natechei FarDT, as they were below the species demarcation threshold. The ANI value between strains NKC19-3ᵀ and NKC19-16ᵀ was 84.64-84.75%, and the values between these strains and other related strains did not exceed 80.0%, further supporting their classification as novel species. Phylogenetic analysis revealed that strains NKC19-3T and NKC19-16T formed a distinct branch within the genus Virgibacillus, clearly distinguishing them from other species in the same genus. Regarding genomic characteristics, the GC content was 38.9% for strain NKC19-3T and 39.5% for strain NKC19-16T. The genome of strain NKC19-3T had a size of approximately 4.1 Mb and contained 3,785 protein-coding genes (CDSs). Strain NKC19-16T had a slightly smaller genome, approximately 3.9 Mb in size and harbored 3,726 CDSs. The polar lipid profiles of strains NKC19-3ᵀ and NKC19-16ᵀ included diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), glycolipids (GL), and an unidentified lipid (L). The predominant fatty acids of both strains were anteiso-C15:0 and anteiso-C17:0. Considering the comprehensive analysis encompassing phenotypic, genomic, phylogenetic, and chemotaxonomic data, strains NKC19-3T and NKC19-16T are proposed to represent two novel species within the genus Virgibacillus. The suggested names for these species are Virgibacillus saliphilus sp. nov. (type strain NKC19-3T, also referred to as KACC 22326T and DSM 112707T) and Virgibacillus salidurans sp. nov. (type strain NKC19-16T, also referred to as KACC 22327T and DSM 112708T).

Pseudoalteromonas qingdaonensis sp. nov., isolated from the intestines of Ilyoplax deschampsi

A Gram-stain-negative, aerobic, motile, catalase-positive, oxidase-positive, short rod-shaped marine bacterium, designated as YIC-827T, was isolated from Qingdao, Shandong Province, China. The results showed that cells of strain YIC-827T could grow optimally at 25-35 °C, pH 6.5-7.5 and 2-7% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequence showed that the strain YIC-827T was a member of the genus Pseudoalteromonas. The closest relative to this strain was Pseudoalteromonas ruthenica KMM 300T, with a similarity of 98.39%. The digital DNA-DNA hybridization value between the new isolate and phylogenetically related species is 19.6%. Strain YIC-827T could decompose sodium alginate, casein and esters (Tween 20, Tween 40, Tween 60 and Tween 80), but could not hydrolyse starch, cellulose and DNA. The fatty acid profile of a strain consists of a large number of C16:0, C18:1 ω7c and C16:1 ω7c/C16:1 ω6c. The G+C content of the DNA of this strain was determined to be 48.93%. Based on phenotypic characteristics, phylogenetic analysis and DNA-DNA correlation data, the strain YIC-827 T represents a novel species of the genus Pseudoalteromonas with the name Pseudoalteromonas qingdaonensis sp. nov. The type strain of P. qingdaonensis sp. is strain YIC-827T (=MCCC 1K08807T=CGMCC 1.62085T=KCTC 8212T).

Flavobacterium magnesitis sp. nov. and Flavobacterium zubiriense sp. nov., two novel Flavobacterium species isolated from alkaline magnesite residues

Three bacterial strains, designated FZUC8N2.13T, FBOR7N2.3T and FZUR7N2.5, were isolated from distinct magnesite residues in Spain. Phylogenetic and phylogenomic analysis places them within the genus Flavobacterium. Strains FBOR7N2.3T and FZUR7N2.5 share 100% of similarity in the 16S rRNA gene sequence, and both are most closely related to Flavobacterium cellulosilyticum AR-3-4T with which they share 97.5% of 16S rRNA gene similarity. Strain FZUC8N2.13T forms a distinct lineage most closely related to Flavobacterium lacustre IMCC36792T with 97.7% 16S rRNA gene similarity. The closest phylogenomic neighbours of these three strains are Flavobacterium flevense DSM 1076T, 'Flavobacterium undicola' BBQ-18T and Flavobacterium commune PK15T. The average nucleotide identity and digital DNA-DNA hybridization values between the three strains and closest members of the genus Flavobacterium are below the threshold values of 95% and 70%, respectively. Strains FZUC8N2.13T, FBOR7N2.3T and FZUR7N2.5 stain Gram-negative, are rod-shaped and form yellow colonies. Optimum growth occurs at 25 °C and pH 7. The genomic G+C contents are 33.4 mol% for strain FZUC8N2.13T and 33.2 mol% for strains FBOR7N2.3T and FZUR7N2.5. The major isoprenoid quinone is menaquinone 6. The major fatty acids are summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) (22.6-31.1%), iso-C15 : 0 (13.6-16.2 %) and anteiso-C15 : 0 (8.7-10.5%). The polar lipids consist of two aminolipids, two aminophospholipids and one glycolipid. The phylogenetic, phylogenomic, phenotypic and chemotaxonomic data indicate that FZUC8N2.13T, FBOR7N2.3T and FZUR7N2.5 are distinct from the described species of Flavobacterium and should be classified as novel species, for which we propose the names Flavobacterium zubiriense for strain FZUC8N2.13T (=UCCCB 179T=CECT 30977T) and Flavobacterium magnesitis for strains FBOR7N2.3T (=UCCCB 178T=CECT 30976T) and FZUR7N2.5 (=UCCCB 216=CECT 31036).

Paludibacillus litoralis gen. nov., sp. nov.: a novel species of a novel genus in the family Paracoccaceae, isolated from the sediment of a tidal flat located in Zhoushan, China

A Gram-stain-negative, aerobic and rod-shaped bacterium, designated as HZG-20T, was isolated from a tidal flat in Zhoushan, Zhejiang Province, China. The 16S rRNA sequence similarities between strain HZG-20T and Pikeienuella piscinae RR4-56T, Coraliihabitans acroporae NNCM2T, Parvibaculum indicum P31T and Zhengella mangrovi X9-2-2T were 98.9, 91.7, 91.0 and 91.0%, respectively. Colonies of strain HZG-20T were 1.4 mm in diameter, milky white, round, smooth and convex after cultivating on marine agar at 30 °C for 48 h. Cells were catalase and oxidase-negative. Growth occurred at 15-37 ℃ (optimum, 28 ℃), pH 5.0-9.0 (optimum, pH 6.0-8.0) and with 0-8% (w/v) NaCl (optimum, 1-3%). It contained Menaquinone-8 (H2) as the sole respiratory quinone, and C16:0 (11.8-13.6%), C18:1  ω9c (6.8-13.3%) and C15:0 anteiso (10.9-27.7%) as the major cellular fatty acids. The main polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, one unidentified phospholipid, one unidentified aminolipid, one unidentified phosphoglycolipid, two unidentified glycolipids (GL1-GL2) and three unidentified lipids (L1-L3). The genome of strain HZG-20T was 3 835 886 bp in length, comprised 3746 protein-coding genes, with DNA G+C content of 67.1 mol%. The phylogenetic and phylogenomic trees indicated that strain HZG-20T formed an independent and stable clade with P. piscinae RR4-56T. However, the average nucleotide identity, digit DNA-DNA hybridization and average amino acid identity values between strain HZG-20T and P. piscinae RR4-56T, C. acroporae NNCM2T, P. indicum P31T and Z. mangrovi X9-2-2T were 81.6, 71.1, 68.7 and 69.5%; 23.0, 18.5, 17.9 and 17.5%; and 78.2, 56.8, 56.5 and 61.9%, respectively, together with distinct chemotaxonomic features, indicating strain HZG-20T should not be assigned to known genera. As a result, a novel species of a novel genus within the family Paracoccaceae, designated as Paludibacillus litoralis gen. nov., sp. nov., was proposed. The type strain is HZG-20T (MCCC 1K08468T=KCTC 82692T).

Comprehensive genomic and phenotypic characterization of thermophilic bacterium Sinimarinibacterium thermocellulolyticum sp. nov. HSW-8T, a cellulase-producing bacterium isolated from hot spring water in South Korea

A thermophilic cellulase-producing bacterium, strain HSW-8T, isolated from hot spring waters in South Korea, was subjected to a taxonomic analysis. Cells of strain HSW-8T were gram-stain-negative, facultatively anaerobic, rod-shaped, with optimum growth at 45 °C, pH 7.0, in the presence of 0% (w/v) NaCl. Strain HSW-8T showed the highest 16S rRNA gene sequence similarity to Sinimarinibacterium flocculans NH6-24T (97.52%), followed by Fontimonas thermophila DSM 23609T (96.97%), Solimonas flava CW-KD 4T (95.24%), and Solimonas variicoloris DSM 15731T (95.18%). Based on 16S rRNA phylogeny, strain HSW-8T is phylogenetically closely related to Fontimonas thermophila DSM 23609T and Sinimarinibacterium flocculans DSM 104150T and could be distinguished from the type species based on their phenotypic properties. The genome length of strain HSW-8T was 3.32 Mbp with a 67.33% G + C content. The average nucleotide identity and digital DNA-DNA hybridization values between strain HSW-8T and its closely related type strains were 75.4-83.2 and 20.2-26.2%, respectively. Summed feature 8 (C18:1ω7c and/or C18:1ω6c), C16:0, and iso-C16:0 identified the major fatty acids (> 10%). Phosphatidylglycerol and phosphatidylethanolamine were demonstrated as the major polar lipids while the respiratory quinone is ubiquinone-8. Strain HSW-8T exhibited multiple adaptations for survival at high temperatures, including diverse potential motility mechanisms and toxin-antitoxin systems, as evidenced by both phenotypic characteristics and genomic analysis. Based on genotypic and phenotypic features, strain HSW-8T (= KCTC 92765T = GDMCC 1.4313T) represents a novel Sinimarinibacterium species, in which the name Sinimarinibacterium thermocellulolyticum sp. nov. is proposed.

Genetic diversity and population structure of cowpea mutant collection using SSR and ISSR molecular markers

Cowpea is a seed legume, important for food and nutritional security in Africa's arid and semi-arid zones. Despite its importance, cowpea is experiencing a loss of genetic diversity due to climate change. Therefore, this study aimed to evaluate the genetic variability of 33 cowpea mutant collections using 20 SSR and 13 ISSR markers. This analysis shows an average number of alleles of 5.15 for SSR and 6.7 for ISSR. The highest average genetic distance based on Nei's index among subgroups was 0.740 and the value of polymorphism information content varied from 0.02 to 0.23 for SSR and from 0.05 to 0.36 for ISSR. Our results revealed high genetic diversity based on the GD (0.126), Fst (0.513), and Shannon information index (0.246). The population structure analysis showed 3 and 4 clusters for ISSR and SSR markers, respectively. Genetic variation, as assessed by analysis of molecular variance, mostly indicates higher genetic diversity within the population than among populations. The hierarchical clustering of combined SSR and ISSR markers grouped the accessions into four groups, supporting the STRUCTURE analysis results. Additionally, the combination of SSR and ISSR provided better information on the level of genetic diversity, and population structure, and was more effective in determining the relationship between cowpea collection. This study enhances our understanding of the genetic organization of our mutant collection which can be used in breeding programs in the era of climate change.

Leifsonia stereocauli sp. nov., Isolated from Stereocaulon tomentosum Fr. Lichen

A Gram-stain-positive, aerobic, yellow-pigmented, catalase-positive, oxidase-positive, non-motile with no flagella and irregularly rod-shaped, denominated strain YIM 134122T, was isolated from a Stereocaulon tomentosum Fr. lichen gathered on Baima Snow Mountain in Diqing Tibetan Autonomous Prefecture, Yunnan Province, China. The novel strain grew at pH 6.0-8.0 (optimum, pH 7.0-7.2), 4-35 ℃ (optimum,25-35 ℃), and with the existence of 0-10% (w/v) NaCl (optimum, 0-2%). Phylogenetic analysis on the basis of 16S rRNA gene sequences indicated that strain YIM 134122T belonged to the genus Leifsonia and presented high levels of 16S rRNA gene sequence similarity with Leifsonia kafniensis JCM 17021T (97.92%) and Leifsonia psychrotolerans CGMCC 1.12166T (97.79%). Based on the draft genome sequence, the G + C content of strain YIM 134122T was found to be 68.41%, and the average nucleotide identity and digital DNA-DNA hybridizations values between strain YIM 134122T and Leifsonia kafniensis JCM 17021T and Leifsonia psychrotolerans CGMCC 1.12166T were 73.78% and 73.75%, and 19.6% and 19.9%, respectively, which were extremely lower than the generally proposed threshold value for species delineation. The predominant polar lipids in strain YIM 134122T consisted of phosphatidylglycerol, diphosphatidylglycerol, three unknown glycolipids, two unknown phospholipids, and one unknown lipid, whereas MK-10, MK-11 and MK-12 were the main menaquinones. The major fatty acids (> 4%) of the strain contained iso-C15:0, anteiso-C15:0, iso-C16:0 and anteiso-C17:0. On the basis of phylogenetic, chemotaxonomic, phenotypic and genotypic evidences, it is concluded that strain YIM 134122T represents a novel species of the genus Leifsonia, for with the name Leifsonia stereocauli sp. nov. is proposed. The type strain is YIM 134122T (= CGMCC 1.62033T = MCCC 1K08590T = KCTC 59219T).

Arvimicrobium flavum gen. nov., sp. nov., A Novel Genus in the Family Phyllobacteriaceae Isolated From Forest Soil

During the study of microbial diversity of forest soil in the Republic of Korea, a yellow pigment-producing, Gram-stain-negative, rod-shaped, motile bacterium was isolated and designated as strain 1W2T. This strain grew at temperature of 10-37 °C, at pH of 5.0-9.0, and at NaCl concentration of 0-3.0% (w/v). The 16S rRNA gene sequencing and genome sequencing revealed that strain 1W2T is a member of the family Phyllobacteriaceae but exhibits low similarity with known genera, suggesting that this strain is a new genus within the family. This strain showed the closest similarity to the genera Mesorhizobium (96.6-96.9%), Aminobacter (96.4 -96.6%), Aquamicrobium (96.5-96.7%), and Pseudaminobacter (96.6-96.7%). The nearest relative of 1W2T was Mesorhizobium shangrilense CCBAU 65327 T with the 16S rRNA gene sequence similarity of 96.9%. The genome size was 5,545,526 bp with DNA G + C content of 64.7%. The values of overall genomic relatedness indices between strain 1W2T and the reference members were 20.4-21.3% for digital DNA-DNA hybridization, 74.0-76.6% for average nucleotide identity, and 68.1-61.2% for amino acids identity. Chemotaxonomic profiling revealed that Q-10 was the sole ubiquinone; summed feature 8 (C18:1ω7c and/or C18:1ω6c), iso-C13:0, and C19:0 cyclo ω8c were the predominant fatty acids; and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylcholine, and phosphatidylethanolamine were the major polar lipids. Based on these data, strain 1W2T represents a novel species of a new genus in the family Phyllobacteriaceae. Accordingly, we proposed the name Arvimicrobium flavum gen. nov., sp. nov., with the type strain 1W2T (= KCTC 92441 T = NBRC 116019 T).

Taxonomic and genomic characterization of a siderophore-producing bacterium, Rhodoligotrophos ferricapiens sp. nov isolated from lettuce cultivation soil

A Gram-stain-negative, aerobic, non-spore-forming, non-motile, coccus-shaped, and red-pigmented bacterial strain designated as CJ14T was isolated from lettuce cultivation soil in Yong-In, South Korea. Strain CJ14T grew optimally on Luria-Bertani agar at 37 ℃ and pH 7.0 in the absence of NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain CJ14T belonged to the genus Rhodoligotrophos in the family Rhodoligotrophaceae and was closely related to Rhodoligotrophos defluvii lm1T (98.4% similarity). The genome size of strain CJ14T was 4.8 Mbp consisting of a single contig, and the DNA G + C content of strain CJ14T was 61.8%. The genomic comparison of strain CJ14T to R. defluvii lm1T showed an average nucleotide identity value of 77.9%, and the digital DNA-DNA hybridization value was 22.4%. Genomic analyses revealed that strain CJ14T possessed a gene cluster for ochrobactin biosynthesis, highly homologous to the siderophore gene cluster from Nitratireductor thuwali Nit1536T. Strain CJ14T contained ubiquinone (Q-10) as the predominant respiratory quinone. The major cellular fatty acids of strain CJ14T were C16:0, C19:0 cyclo ω8c and summed feature 8. The polar lipid profile was composed of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol, one unidentified aminolipid, one unidentified glycolipid and five unidentified lipids. Based on polyphasic taxonomy study, strain CJ14T could be classified as a novel species of the genus Rhodoligotrophos, for which the name Rhodoligotrophos ferricapiens sp. nov. is proposed. The type strain is CJ14T (= KACC 23063T = JCM 36057T).

Description of Massilia orientalis sp. nov., Isolated from Rhizosphere Soil of Ageratina adenophora

A novel bacteria strain, designated YIM B02787T, was isolated from rhizosphere soil of Ageratina adenophora, in Yunnan, southwest China. The strain was aerobic, Gram-stain-negative, rod-shaped and motile with one polar flagellum. Growth occurred at 4-45 °C (optimum, 20-30 °C) and pH 6.0-10.0 (optimum, 7.0-8.0), and in presence of 0-1% (w/v) NaCl. Phylogenetic analyses based on both 16S rRNA gene and genome sequences data revealed that strain YIM B02787T belongs to the genus Massilia, being closely related to Massilia phosphatilytica KCTC 52513T (98.93% similarity), M. putida KCTC 42761T (98.86%), and M. kyonggiensis JCM 19189T (98.78%). The DNA G+C content was 65.9%. The digital DNA-DNA hybridization and average nucleotide identity values between the isolate strain and aforementioned closely neighbors were low, at 35.8-48.9 and 88.5-92.5%, respectively. Strain YIM B02787T contained Q-8 as the ubiquinone and major fatty acids were summed feature 3 (C16:1ω7c and/or C16:1ω6c, 45.5%) and C16:0 (27.5%). The polar lipid profile consisted of phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, two unidentified phospholipids, two unidentified aminophospholipids, and one unidentified polar lipid. On the basis of its phylogenetic, phenotypic and chemotaxonomic characteristics, strain YIM B02787Trepresents a novel species of the genus Massilia, for which the name Massilia orientalis sp. nov. is proposed. The type strain is YIM B02787T (= NBRC 116628T = CGMCC 1.61539T).

Revisiting the emerging pathosystem of rice sheath blight: deciphering the Rhizoctonia solani virulence, host range, and rice genotype-based resistance

Sheath blight, caused by Rhizoctonia solani AG1 IA, is a challenging disease of rice worldwide. In the current study, nine R. solani isolates, within the anastomosis group AG-1 IA, were isolated, characterized based on their macroscopic and microscopic features, as well as their ability to produce cell wall degrading enzymes (CWDEs), and further molecularly identified via ITS sequencing. Although all isolates were pathogenic and produced typical sheath blight symptoms the susceptible rice cultivar, Sakha 101, R. solani AG1 IA -isolate SHBP9 was the most aggressive isolate. The virulence of isolate SHBP9 was correlated with its overproduction of CWDEs, where it had the highest pectinase, amylase, and cellulase activity in vitro. R. solani AG1 IA -isolate SHBP9 was able to infect 12 common rice-associated weeds from the family Poaceae, as well as over 25 economic crops from different families, except chickpea (Cicer arietinum) from Fabaceae, Rocket (Eruca sativa) from Brassicaceae, and the four crops from Solanaceae. Additionally, rice genotype-based resistance was evaluated using 11 rice genotypes for their response to R. solani isolates, morphological traits, yield components, and using 12 SSR markers linked to sheath blight resistance. Briefly, the tested 11 rice genotypes were divided into three groups; Cluster "I" included only two resistant genotypes (Egyptian Yasmine and Giza 182), Cluster "II" included four moderately resistant genotypes (Egyptian hybrid 1, Giza 178, 181, and 183), whereas Cluster "III" included five susceptible (Sakha 104, 101, 108, Super 300 and Giza 177). Correspondingly, only surface-mycelium growth was microscopically noticed on the resistant cultivar Egyptian Yasmine, as well as the moderately resistant Egyptian hybrid 1, however, on the susceptible Sakha 104, the observed mycelium was branched, shrunk, and formed sclerotia. Accordingly, Indica and Indica/Japonica rice genotypes showed more resistance to R. solani than Japonica genotypes. These findings provide insights into its pathogenicity mechanisms and identify potential targets for disease control which ultimately contributes to the development of sustainable eco-friendly disease management strategies. Moreover, our findings might pave the way for developing resistant rice varieties by using more reliable resistance sources of non-host plants, as well as, rice genotype-based resistance as a genetic resource.

Tailored Enzymes for Difructose Anhydrides: From Biosynthesis to Degradation

Difructose anhydrides (DFAs), distinctive cyclic disaccharides mainly naturally produced by heating (caramelization), serve as potential candidates of functional sugars that modern humans consume on a daily basis due to their remarkable physiological effects. This review explores the complex domain of specialized enzymes implicated in the metabolism of DFAs, covering the entire process from biosynthesis to degradation. We provide a detailed examination of the enzymes responsible for DFA formation and degradation, specifically those classified within the GH91, GH32, and GH172 glycoside hydrolase families. Furthermore, the evolutionary relationships among the related enzymes were systematically analyzed. Subsequently, the underlying enzymatic mechanisms that drive DFAs' metabolism were elucidated, and key insights into the intricate interplay between enzyme structure and function were unveiled. Additionally, innovative strategies for enzyme engineering were discussed, aimed at improving thermostability, enhancing catalytic activity, and altering catalytic function. Finally, the applications of the related enzymes were comprehensively summarized with a focus on their product yields, conversion rates, and methods for product purification. Here, the review presents a comprehensive investigation into enzymatic degradation and biosynthesis pathways of DFAs.

Characterization and bioefficacy of grapevine bacterial endophytes against Colletotrichum gloeosporioides causing anthracnose disease

Introduction

Grapevine (Vitis vinifera L.), one of the economically important fruit crops cultivated worldwide, harbours diverse endophytic bacteria (EBs) responsible for managing various fungal diseases. Anthracnose (Colletotrichum gloeosporioides) (Penz.) is one of the major constraints in quality grape production and therefore its management is a major concern among the grape growers.

Materials and methods

Among the 50 EBs isolated from healthy leaf segments from the eight grapevine genotypes, biologically potential 20 EBs were purified and identified based on morphological, and biological characteristics and sequence analysis of 16S rRNA region. The antagonistic activities of EBs against Colletotrichum gloeosporioides were studied in vitro conditions.

Results

The colony morphologies of EBs are white and yellow-coloured colonies, circular to irregular in shape, and entire, and flat margins. Among the 20 purified EBs, 19 isolates were found to be Gram-positive except one i.e., MS2 isolate. The 12 isolates reduced nitrate and 14 isolates produced urease enzyme. The in vitro assay revealed that two isolates, SB4 and RF1, inhibited 56.1% and 55.6% mycelial growth of C. gloeosporioides, respectively. Further, the identity of EBs was confirmed through PCR amplification of the 16S rRNA region resulting in ~1400 bp size amplicons. The sequence analysis of representative 15 isolates revealed that 5 EB isolates viz., SB5, CS2, RG1, RF1, C1 were identified as Bacillus subtilis with >99% sequence identity, two EBs viz., SB3, and CS1 were identified as B. subtilis subsp. subtilis, two EBs viz., SB1, and CS4 were identified as B. licheniformis. The SB2 isolate was identified as Bacillus sp., whereas SB4 as Brevibacillus borstelensis, TH1 as B. velezensis, TH2 as B. tequilensis, CS3 as B. pumilus and MS1 as Micrococcus luteus were identified.

Conclusion

The phylogenetic analysis of 16S rRNA sequence revealed eight distinct clades and showed the close clustering of identified species with the reference species retrieved from NCBI GenBank. The current investigation provides the scope for further field evaluations of these endophytic microbes for managing anthracnose disease.

CCDC113 stabilizes sperm axoneme and head-tail coupling apparatus to ensure male fertility

The structural integrity of the sperm is crucial for male fertility, defects in sperm head-tail linkage and flagellar axoneme are associated with acephalic spermatozoa syndrome (ASS) and the multiple morphological abnormalities of the sperm flagella (MMAF). Notably, impaired head-tail coupling apparatus (HTCA) often accompanies defects in the flagellum structure, however, the molecular mechanisms underlying this phenomenon remain elusive. Here, we identified an evolutionarily conserved coiled-coil domain-containing (CCDC) protein, CCDC113, and found the disruption of CCDC113 produced spermatozoa with disorganized sperm flagella and HTCA, which caused male infertility. Further analysis revealed that CCDC113 could bind to CFAP57 and CFAP91, and function as an adaptor protein for the connection of radial spokes, nexin-dynein regulatory complex (N-DRC), and doublet microtubules (DMTs) in the sperm axoneme. Moreover, CCDC113 was identified as a structural component of HTCA, collaborating with SUN5 and CENTLEIN to connect sperm head to tail during spermiogenesis. Together, our studies reveal that CCDC113 serve as a critical hub for sperm axoneme and HTCA stabilization in mice, providing insights into the potential pathogenesis of infertility associated with human CCDC113 mutations.

Acarbose impairs gut Bacteroides growth by targeting intracellular glucosidases

Acarbose is a type 2 diabetes medicine that prevents dietary starch breakdown into glucose by inhibiting host amylase and glucosidase enzymes. Numerous gut species in the Bacteroides genus enzymatically break down starch and change in relative abundance within the gut microbiome in acarbose-treated individuals. To mechanistically explain this observation, we used two model starch-degrading Bacteroides, Bacteroides ovatus (Bo), and Bacteroides thetaiotaomicron (Bt). Bt growth on starch polysaccharides is severely impaired by acarbose, whereas Bo growth is much less affected by the drug. The Bacteroides use a starch utilization system (Sus) to grow on starch. We hypothesized that Bo and Bt Sus enzymes are differentially inhibited by acarbose. Instead, we discovered that although acarbose primarily targets the Sus periplasmic GH97 enzymes in both organisms, the drug affects starch processing at multiple other points. Acarbose competes for transport through the TonB-dependent SusC proteins and binds to the Sus transcriptional regulators. Furthermore, Bo expresses a non-Sus GH97 (BoGH97D) when grown in starch with acarbose. The Bt homolog, BtGH97H, is not expressed in the same conditions, nor can overexpression of BoGH97D complement the Bt growth inhibition in the presence of acarbose. This work informs us about unexpected complexities of Sus function and regulation in Bacteroides, including variation between related species. Furthermore, this indicates that the gut microbiome may be a source of variable response to acarbose treatment for diabetes.

IMPORTANCE

Acarbose is a type 2 diabetes medication that works primarily by stopping starch breakdown into glucose in the small intestine. This is accomplished by the inhibition of host enzymes, leading to better blood sugar control via reduced ability to derive glucose from dietary starches. The drug and undigested starch travel to the large intestine where acarbose interferes with the ability of some bacteria to grow on starch. However, little is known about how gut bacteria interact with acarbose, including microbes that can use starch as a carbon source. Here, we show that two gut species, Bacteroides ovatus (Bo) and Bacteroides thetaiotaomicron (Bt), respond differently to acarbose: Bt growth is inhibited by acarbose, while Bo growth is less affected. We reveal a complex set of mechanisms involving differences in starch import and sensing behind the different Bo and Bt responses. This indicates the gut microbiome may be a source of variable response to acarbose treatment for diabetes via complex mechanisms in common gut microbes.

Targeted dual-receptor phage cocktail against Cronobacter sakazakii: insights into phage-host interactions and resistance mechanisms

Introduction

Cronobacter sakazakii is a notorious foodborne pathogen, frequently contaminating powdered infant formula and causing life-threatening diseases in infants. The escalating emergence of antibiotics-resistant mutants has led to increased interest in using bacteriophage as an alternative antimicrobial agent.

Methods

Two phages, CR8 and S13, were isolated from feces and soil samples and their morphology, physiology, and genomics were characterized. Phage receptor was determined using deletion mutants lacking flgK, rfaC, fhuA, btuB, lamb, or ompC genes, followed by complementation. Phage-resistant mutants were analyzed for phenotypic changes and fitness trade-offs using motility assays and Caco-2 cell invasion models.

Results

CR8 and S13 were identified as members of Caudoviricetes. Phage CR8 and phage S13 utilize flagella and LPS, respectively, to adhere to host cells. Bacterial challenge assay demonstrated delayed emergence of the resistant mutant as well as stronger lytic activity of a phage cocktail consisting of CR8 and S13 than the single phage treatment. Phenotypic analysis of the phage cocktail resistant strain, designated as CSR strain, revealed that the resistance resulted from the impaired receptor proteins for phage, such as defects in motility and alteration in LPS structure. CSR strain exhibited significant attenuation in invading human intestinal epithelial Caco-2 cells compared to WT cells.

Conclusion

This study demonstrates that the development of the phage cocktail targeting distinct host receptors can serve as a promising antimicrobial strategy to effectively control C. sakazakii.

Analysis of the effects of Bacillus velezensis HJ-16 inoculation on tobacco leaves based on multi-omics methods

In this study, a strain isolated from the surface of flue-cured tobacco leaves, identified as Bacillus velezensis HJ-16, was applied in the solid-state fermentation of tobacco leaves. This strain, known for producing thermally stable enzymes, including amylase, cellulase, and protease, significantly improved the sensory qualities of tobacco, enhancing aromatic intensity, density, and softness, while reducing irritation. Whole-genome sequencing and functional annotation revealed that B. velezensis HJ-16 possesses a single circular chromosome containing genes associated with enzyme production and metabolic activities, particularly in carbohydrate metabolism and amino acid metabolism. Untargeted metabolomics analysis identified significant changes in non-volatile metabolites induced by fermentation. These metabolites were enriched in pathways related to flavonoid biosynthesis, alkaloid biosynthesis, aromatic amino acid metabolism, lipid metabolism, and carbon metabolism. Metagenomic analysis showed that Bacillus became the dominant genus on the tobacco leaf surface following inoculation with B. velezensis HJ-16, altering the microbial community composition, reducing diversity and evenness, and enhancing microbial metabolic activity. These findings underscore the potential of B. velezensis HJ-16 as a biotechnological tool to improve tobacco leaf quality.

Description of Wickerhamia europaea sp. nov. and revisitation of the ascospore number of W. fluorescens

During the course of two independent studies, six conspecific yeast strains were recovered from flowers, soil, bird faeces and wood of different geographical origins. The six strains share identical DNA sequences in two barcoding regions, the D1/D2 domain of the LSU rRNA gene and the internal transcribed spacer (ITS) region (ITS1-5.8S rRNA gene-ITS2). According to sequence comparisons and phylogenetic analysis, they represent an undescribed Wickerhamia species. The novel species is not only genetically distinct from W. fluorescens, the single species of the genus but can also be distinguished from it by some phenotypic characters. We propose Wickerhamia europaea sp. nov. (holotype: NCAIM Y.01938; isotype: CBS 18675; MycoBank no.: 856571) to accommodate the above noted strains. Under certain fermentation conditions, we detected the production of phenyllactic acid, a potential broad-spectrum antimicrobial compound against food-borne pathogens, by the type strain of the novel species, although in smaller concentrations than in the case of W. fluorescens. Comparing our observations on the formation and properties of the ascospores of Wickerhamia europaea sp. nov. and the ambiguous data on the number of ascospores per ascus of W. fluorescens, we suggest a possible explanation to reconcile the different data regarding the number of ascospores per ascus formed by W. fluorescens.

Severe fever with thrombocytopenia syndrome virus was found in Northern Jiangxi Province, China

INTRODUCTION

Severe fever with thrombocytopenia syndrome (SFTS) is an emerging infectious disease discovered in China in 2009. SFTS monitoring has been carried out since 2010 in mainland China. In recent years, human infection with SFTS virus (SFTSV) has frequently been detected in Jiujiang of Jiangxi Province, Central China.

METHODS

Sera of SFTS surveillance cases and samples collected from humans, animals and ticks surrounding the cases were used to detect SFTSV RNA by real-time RT-PCR. SFTSV-positive samples were further subjected to sequencing and analysis of the S, M, and L segments of SFTSV.

RESULTS

Four patients were positive for SFTSV infection. However, the subjects like humans, animals and ticks around the cases were all detected as negative for the virus infection. Phylogenetic analysis of the partial segments revealed that SFTSVs in three patients from Jiujiang were clustered with genotype C4 and C5 on the L and M segment-established phylogenetic tree; however, phylogenetic analysis of the S segment showed that the strains were grouped into genotype J1. These results suggested that the S, M, and L segments of these strains underwent segmental reassortment, which was later supported by recombination signal detection. The reassortment event was detected by at least four methods with a significance level of p value <0.05. In addition, the RDP recombination consensus score (RDPRCS) was greater than 0.40. To avoid poor tree topology support with the partial S, M, and L segments, we further performed analysis of the complete genome of SFTSV. The full-length L, M, and S segment sequences of the strains were consistently clustered into two genotypes, namely the genotype C5 and the genotype C4. The strains belonging to genotype C5 were detected for recombination signal with moderate confidence by all the six methods, with a significance level of p value <0.05 and an RDPRCS of 0.41. The recombination event might have occurred between the minor parent (2011YPQ11, C3/C3/C3) and major parent (SPL053A, J1/ J1/ J1). However, there was no genetic recombination detected in the strains belonging to genotype C4. The event was detected by only two methods with a significance level of p value <0.05.

CONCLUSION

Two genotypes of SFTSVs were identified in Jiujiang City, Jiangxi Province of Central China, and they were genotype C5 and genotype C4. The genotype C5 underwent genetic recombination in this region, with the minor parent of the strain 2011YPQ11 and the major parent of the strain SPL053A.

The new genus Purpurata (Lepidoptera, Crambidae, Spilomelinae), with descriptions of two new species from China

The male genitalia characters of four species, Botysiopasalis Walker, 1859, Pleuroptyaobfuscalis Yamanaka, 1998, Botysplagiatalis Walker, 1859 and Pataniashompen Singh et Ahmad, 2022, placed in the genus Patania Moore, 1888 before the present study, do not conform to the diagnosis of Patania. A new genus, Purpurata gen. nov., is established for these four species, and two new species, Purpuratadirecta sp. nov. and Purpuratalurida sp. nov. are described based on their external morphology and genitalia characters. Purpuratadirecta sp. nov. is designated as the type species of the new genus. Five species of the new genus were clearly separated from Patania species in the Maximum likelihood phylogenetic tree constructed based on COI sequence data. Compared to Patania, the new genus Purpurata exhibits distinctive characters in male genitalia: the uncus is short, broad, and arc-shaped posteriorly; the gnathos is present and setose, or reduced; and the fibula is very small and setose. In addition, Pataniaclava (Xu & Du), syn. nov. is synonymized with Purpurataiopasalis comb. nov. An identification key to species of the new genus is presented based on morphological characters of habitus and genitalia. Images of the habitus and genitalia are provided.

Thermostable bacterial L-asparaginase for polyacrylamide inhibition and in silico mutational analysis

The L-asparaginase (ASPN) enzyme has received recognition in various applications including acrylamide degradation in the food industry. The synthesis and application of thermostable ASPN enzymes is required for its use in the food sector, where thermostable enzymes can withstand high temperatures. To achieve this goal, the bacterium Bacillus subtilis was isolated from the hot springs of Tapovan for screening the production of thermostable ASPN enzyme. Thus, ASPN with a maximal specific enzymatic activity of 0.896 U/mg and a molecular weight of 66 kDa was produced from the isolated bacteria. The kinetic study of the enzyme yielded a Km value of 1.579 mM and a Vmax of 5.009 µM/min with thermostability up to 100 min at 75 °C. This may have had a positive indication for employing the enzyme to stop polyacrylamide from being produced. The current study has also been extended to investigate the interaction of native and mutated ASPN enzymes with acrylamide. This concluded that the M10 (with 10 mutations) has the highest protein and thermal stability compared to the wild-type ASPN protein sequence. Therefore, in comparison to a normal ASPN and all other mutant ASPNs, M10 is the most favorable mutation. This research has also demonstrated the usage of ASPN in food industrial applications.

Segatella asaccharophila sp. nov., an anaerobic pectinophile isolated from a two-phase methane fermentation system

An obligately anaerobic, Gram-stain-negative, non-spore-forming and non-motile rod (strain LPYR103-PreT) was isolated from a two-phase methane fermentation system. Using 16S rRNA gene sequence-based phylogenetic analysis, strain LPYR103-PreT was classified in the genus Segatella. The 16S rRNA gene sequence similarity, average nucleotide identity and digital DNA-DNA hybridization between strain LPYR103-PreT and its phylogenetically nearest species - Segatella cerevisiae JCM 30867T - were 94.4, 77.9 and 23.4%, respectively. The genome size of strain LPYR103-PreT was 3 326 733 bp, and its genomic DNA G+C content was 44.05%. The most abundant cellular fatty acid was anteiso-C15 : 0. The growth of strain LPYR103-PreT was stimulated by the addition of pectin, d-galacturonate and d-glucuronate; in contrast, the strain exhibited poor growth in the presence of common sugars, such as glucose. Therefore, strain LPYR103-PreT was classified as a pectinophile - a bacterium that shows a preference for pectin and a few related compounds as substrates. Glucose is degraded by type strains of 12 species belonging to the genus Segatella; thus, strain LPYR103-PreT is the first described pectinophile belonging to this genus. Strain LPYR103-PreT produced succinate and acetate as its major metabolic end products. Based on the differences in the phylogenetic, genomic, physiological and chemotaxonomic characteristics of strain LPYR103-PreT and related species, the name Segatella asaccharophila sp. nov. is proposed to accommodate strain LPYR103-PreT (= NRIC 0997T = JCM 37351T=DSM 118531T = KCTC 25923T).

Enhanced growth and metabolite production from a novel strain of Porphyridium sp

Microalgae are capable of generating numerous metabolites that possess notable biological activities and hold substantial promise for various industrial applications. Nevertheless, the taxonomic diversity of these photosynthetic microorganisms has not received thorough investigation. Using the 18S rRNA encoding gene, a recently discovered strain originating from the Tunisian coast (the governorate of Mahdia) was identified as a member of the Porphyridium genus. The growth response as well as the metabolite accumulation of Porphyridium sp. to different culture media (Pm, F/2, and Hemerick) was investigated over a period of 52 days. The highest biomass production was recorded with Pm medium (2 × 107 cell/mL). The apparent growth rates (µ) and the doubling time (Dt) were about 0.081 day-1 and 12.34 days, respectively. The highest chlorophyll a (0.678 ± 0.005 pg/cell), total carotenoids (0.18 ± 0.003 pg/cell), phycoerythrin (3.88 ± 0.003 pg/cell), and proteins (14.58 ± 0.35 pg/cell) contents were observed with F/2 medium. Cultivating Porphyridium sp. in both F/2 and Hemerick media yielded similar levels of starch accumulation. The Hemerick medium has proven to be the most suitable for the production of lipids (2.23% DW) and exopolysaccharides (5.41 ± 0.56 pg/cell).

Testacosides A-D, glycoglycerolipids produced by Microbacterium testaceum isolated from Tedania brasiliensis

Marine bacteria living in association with marine sponges have proven to be a reliable source of biologically active secondary metabolites. However, no studies have yet reported natural products from Microbacterium testaceum spp. We herein report the isolation of a M. testaceum strain from the sponge Tedania brasiliensis. Molecular networking analysis of bioactive pre-fractionated extracts from culture media of M. testaceum enabled the discovery of testacosides A-D. Analysis of spectroscopic data and chemical derivatizations allowed the identification of testacosides A-D as glycoglycerolipids bearing a 1-[α-glucopyranosyl-(1 → 3)-(α-mannopyranosyl)]-glycerol moiety connected to 12-methyltetradecanoic acid for testacoside A (1), 14-methylpentadecanoic acid for testacoside B (2), and 14-methylhexadecanoic acid for testacosides C (3) and D (4). The absolute configuration of the monosaccharide residues was determined by 1H-NMR analysis of the respective diastereomeric thiazolidine derivatives. This is the first report of natural products isolated from cultures of M. testaceum. KEY POINTS: • The first report of metabolites produced by Microbacterium testaceum. • 1-[α-Glucopyranosyl-(1 → 3)-(α-mannopyranosyl)]-glycerol lipids isolated and identified. • Microbacterium testaceum strain isolated from the sponge Tedania brasiliensis.

PI3KR1 and AKT1 in largemouth bass (Micropterus salmoides): molecular cloning, characterization, and its involvement in the alleviation of hepatic glycogen deposition caused by insulin inclusion in vitro

In this study, the full-length cDNA sequences of the phosphatidylinositol-3-kinase p85 alpha (PI3KR1) and serine/threonine kinase 1 (AKT1) genes in largemouth bass (Micropterus salmoides) were obtained using the rapid amplification of cDNA ends (RACE) method. Sequence analysis revealed that the cloned sequences of PI3KR1 and AKT1 are 4170 bp and 3672 bp in length, with open reading frames (ORFs) of 1389 bp and 1422 bp encoding 462 and 473 amino acids, respectively. Sequence alignment and evolutionary tree analysis indicated their close relationship to other teleosts, especially those with similar feeding habits. Tissue distribution demonstrated widespread distribution of both genes in various tissues, with the highest abundance in the liver. Further results found that the upregulation of the expression of p-PI3KR1, p-AKT1, p-FoxO1, and GLUT2 proteins by insulin, while suppressing the expression of the total FoxO1 protein, effectively triggers a significant activation of the PI3KR1-AKT1 insulin signaling pathway. Meanwhile, the mRNA levels of the key glycolytic genes, including glucokinase (gk), pyruvate kinase (pk), and phosphofructokinase liver type (pfkl), have been enhanced evidently. In contrast, the expression of gluconeogenic genes such as phosphoenolpyruvate carboxykinase (pepck), glucose-6-phosphatase catalytic subunit (g6pc), and fructose-1,6-bisphosphatase-1 (fbp1) has been notably down-regulated. In addition, insulin treatment promoted the phosphorylation of glycogen phosphorylase (PYGL) and the dephosphorylation of glycogen synthase (GS), and the glycogen content in the insulin-treated group was remarkably reduced compared to the control group. Overall, our study indicates that the activation of PI3KR1-AKT1 insulin signaling pathway represses the hepatic glycogen deposition via the regulation of glycolysis and gluconeogenesis, which provides some new insights into nutritional strategy to effectively regulate the glucose metabolism in carnivorous fish.

Detection of Arsenophonus in Glycaspis brimblecombei (Hemiptera: Aphalaridae) populations in Brazil

Eucalyptus is the most intensively managed tree genus in the world. Different factors, including damage by insect pests, affect its growth and productivity. Among these pests is Glycaspis brimblecombei Moore (Hemiptera: Aphalaridae), an exotic insect of Australian origin. The evolutionary success of this insect depends on symbiotic associations with microorganisms. The influence of these microorganisms on insect pests and their natural enemies is important for integrated management tactics. Within this context, this work aimed to detect Arsenophonus in populations of G. brimblecombei in Brazil. Eucalyptus branches infested with G. brimblecombei nymphs were collected in commercial eucalyptus plantations in six Brazilian states. Specimens of this pest were sampled soon after emergence and frozen for molecular analysis. The genomic DNA of G. brimblecombei adults from each population was extracted and used to detect the endosymbiont Arsenophonus by polymerase chain reaction (PCR) employing specific primers that target its 23 S rRNA gene. This endosymbiont was identified in all of the studied G. brimblecombei populations. This is the first report on the association between Arsenophonus and G. brimblecombei in Brazil.

Identification of a novel monocyclic carotenoid and prediction of its biosynthetic genes in Algoriphagus sp. oki45

Bacteria belonging to the genus Algoriphagus have been isolated from various sources, such as Antarctic sea ice, seawater, and sediment, and some strains are known to produce orange to red pigments. However, the pigment composition and biosynthetic genes have not been fully elucidated. A new red-pigmented Algoriphagus sp. strain, oki45, was isolated from the surface of seaweed collected from Senaga-Jima Island, Okinawa, Japan. Genome comparison revealed oki45's average nucleotide identity of less than 95% to its closely related species, Algoriphagus confluentis NBRC 111222 T and Algoriphagus taiwanensis JCM 19755 T. Comprehensive chemical analyses of oki45's pigments, including 1H and 13C nuclear magnetic resonance and circular dichroism spectroscopy, revealed that the pigments were mixtures of monocyclic carotenoids, (3S)-flexixanthin ((3S)-3,1'-dihydroxy-3',4'-didehydro-1',2'-dihydro-β,ψ-caroten-4-one) and (2R,3S)-2-hydroxyflexixanthin ((2R,3S)-2,3,1'-trihydroxy-3',4'-didehydro-1',2'-dihydro-β,ψ-caroten-4-one); in particular, the latter compound was new and not previously reported. Both monocyclic carotenoids were also found in A. confluentis NBRC 111222 T and A. taiwanensis JCM 19755 T. Further genome comparisons of carotenoid biosynthetic genes revealed the presence of eight genes (crtE, crtB, crtI, cruF, crtD, crtYcd, crtW, and crtZ) for flexixanthin biosynthesis. In addition, a crtG homolog gene encoding 2,2'-β-hydroxylase was found in the genome of the strains oki45, A. confluentis NBRC 111222 T, and A. taiwanensis JCM 19755 T, suggesting that the gene is involved in 2-hydroxyflexixanthin synthesis via 2-hydroxylation of flexixanthin. These findings expand our knowledge of monocyclic carotenoid biosynthesis in Algoriphagus bacteria. KEY POINTS: • Algoriphagus sp. strain oki45 was isolated from seaweed collected in Okinawa, Japan. • A novel monocyclic carotenoid 2-hydroxyflexixanthin was identified from strain oki45. • Nine genes for 2-hydroxyflexixanthin biosynthesis were found in strain oki45 genome.

Hepatitis E Virus RNA Detection in Liver and Muscle Tissues Sampled from Home Slaughtered Domestic Pigs in Central Italy

Hepatitis E virus is a worldwide emerging foodborne pathogen; raw or undercooked meats and liver pork products can cause infection through the orofecal route. In Central-Southern Italy, small traditional farming method, associated with the possibility of environmental sharing with wild species, can facilitate HEV diffusion and persistence. The aim of this study was to determine HEV genotype and subtype in Marche region from home slaughtered domestic pigs involved in small and traditional food chains. A total of 236 liver and muscle tissues and 6 pooled salami samples were screened. Laboratory workflow started with homogenization, followed by RNA extraction. Nested reverse transcription PCR and qRT-PCR were used to amplify specific parts of overlapping open reading frames belonging to the HEV genome. A total of 42/236 (17.79%) liver and 8/236 (3.39%) diaphragm specimens were positive; none of the pooled salami specimens showed positive HEV signal. The discovered HEV3c presented high nucleotide similarities with ones amplified from wild boar populations hunted in the same province. Extensive farming methods and environmental sharing with wild animal species support cross-infection infections, as observed in the present study. Although salami resulted negative for HEV RNA detection, the effects of food technologies on viral loads remain unclear. Therefore, further scientific investigations coupled with efficacious standardized laboratory procedures will be the next challenge.

Expression and characterization of monofunctional alcohol dehydrogenase enzymes in Clostridium thermocellum

Clostridium thermocellum is a thermophilic anaerobic bacterium that could be used for cellulosic biofuel production due to its strong native ability to consume cellulose, however its ethanol production ability needs to be improved to enable commercial application. In our previous strain engineering work, we observed a spontaneous mutation in the native adhE gene that reduced ethanol production. Here we attempted to complement this mutation by heterologous expression of 18 different alcohol dehydrogenase (adh) genes. We were able to express all of them successfully in C. thermocellum. Surprisingly, however, none of them increased ethanol production, and several actually decreased it. Our findings contribute to understanding the correlation between C. thermocellum ethanol production and Adh enzyme cofactor preferences. The identification of a set of adh genes that can be successfully expressed in this organism provides a foundation for future investigations into how the properties of Adh enzymes affect ethanol production.

Genome-based reclassification of Sphingobacterium soli Fu et al. 2017 as a later heterotypic synonym of Sphingobacterium cellulitidis Huys et al. 2017 and proposal of Sphingobacterium siyangense subsp. siyangense subsp. nov. and Sphingobacterium siyangense subsp. cladoniae subsp. nov

Sphingobacterium, as the type genus of the family Sphingobacteriaceae, comprises a diverse array of species found in various environments. In this study, we aim to reassess and elucidate the taxonomic relationships of Sphingobacterium species. Based on 16S rRNA gene sequences, the phylogeny of 70 validly published Sphingobacterium species was reconstructed. Of which, 50 species with available genomes were further subjected to overall genome relatedness indices (OGRI) analysis, resulting in the identification of distinct pairs of closely related species. One such pair, consisting of the type strains of Sphingobacterium soli and Sphingobacterium cellulitidis, exhibited an average nucleotide identity (ANI) of 97.7%, a digital DNA-DNA hybridization (dDDH) of 80.1% and an average amino acid identity (AAI) of 98.3%, alongside a 16S rRNA gene sequence similarity of 99.8%. Based on the phylogenetic, OGRI and phenotypical evidence, we propose S. soli as a later heterotypic synonym of S. cellulitidis. Additionally, another pair of type strains, Sphingobacterium siyangense and Sphingobacterium cladoniae, possessed ANI, dDDH, AAI and 16S rRNA gene sequence similarity values of 96.3, 70.1, 96.0 and 99.0%, respectively. These values, together with differences in phenotypic traits, support the proposal of two subspecies within this taxonomic lineage. Thus, we propose the establishment of two new subspecies, S. siyangense subsp. siyangense subsp. nov. and S. siyangense subsp. cladoniae subsp. nov.

Exploration of a multifunctional biocontrol agent Streptomyces sp. JCK-8055 for the management of apple fire blight

Apple fire blight, caused by the bacterium Erwinia amylovora, is a devastating disease of apple and pear trees. Biological control methods have attracted much attention from researchers to manage plant diseases as they are eco-friendly and viable alternatives to synthetic pesticides. Herein, we isolated Streptomyces sp. JCK-8055 from the root of pepper and investigated its mechanisms of action against E. amylovora. Streptomyces sp. JCK-8055 produced aureothricin and thiolutin, which antagonistically affect E. amylovora. JCK-8055 and its two active metabolites have a broad-spectrum in vitro activity against various phytopathogenic bacteria and fungi. They also effectively suppressed tomato bacterial wilt and apple fire blight in in vivo experiments. Interestingly, JCK-8055 colonizes roots as a tomato seed coating and induces apple leaf shedding at the abscission zone, ultimately halting the growth of pathogenic bacteria. Additionally, JCK-8055 can produce the plant growth regulation hormone indole-3-acetic acid (IAA) and hydrolytic enzymes, including protease, gelatinase, and cellulase. JCK-8055 treatment also triggered the expression of salicylate (SA) and jasmonate (JA) signaling pathway marker genes, such as PR1, PR2, and PR3. Overall, our findings demonstrate that Streptomyces sp. JCK-8055 can control a wide range of plant diseases, particularly apple fire blight, through a combination of mechanisms such as antibiosis and induced resistance, highlighting its excellent potential as a biocontrol agent. KEY POINTS: • JCK-8055 produces the systemic antimicrobial metabolites, aureothricin, and thiolutin. • JCK-8055 treatment upregulates PR gene expression in apple plants against E. amylovora. • JCK-8055 controls plant diseases with antibiotics and induced resistance.

Molecular identification and management of mycotoxigenic fungi in stored corn Grains

Mycotoxin-producing molds which considered as common maize grains contaminants are the genera Fusarium, Aspergillus and Penicillium. There are natural and safe ways to protect grains from mold contamination as the use of essential oils and chemical treatments. A total number of 25 samples were used to study the natural frequency in five governorates in Egypt, Molecular identification indicated that the most frequent fungi were Fusarium verticillioides, Aspergillus niger, Talaromyces verruculosus, Aspergillus flavus and Aspergillus terreus. The in vitro studies have been done to determine mycelial growth and spore germination inhibition of the two A. flavus; isolated and reference isolates. Thyme and acetic acid were tested in direct contact assay to study their effects on mycelial growth. Treatments showed significant impact on mycelial growth and spore germination inhibition of both A. flavus isolates. In the postharvest application treatments: as vapour and carrier contact assay, Thyme and Acetic acid were tested to determine their influence on growth and aflatoxin production in A. flavus isolates by liquid chromatography–electrospray ionization–tandem mass spectrometry (LC–ESI–MS/MS). Results indicated that both treatments were effective in inhibition of aflatoxin production in both vapour and carrier assays as they succeeded in reducing AFB1 while they inhibited completely the production of AFB2. The extent of the inhibition of aflatoxin production was dependent on the concentration and storage duration of treatments applied.

Visualizing metagenomic and metatranscriptomic data: A comprehensive review

The fields of Metagenomics and Metatranscriptomics involve the examination of complete nucleotide sequences, gene identification, and analysis of potential biological functions within diverse organisms or environmental samples. Despite the vast opportunities for discovery in metagenomics, the sheer volume and complexity of sequence data often present challenges in processing analysis and visualization. This article highlights the critical role of advanced visualization tools in enabling effective exploration, querying, and analysis of these complex datasets. Emphasizing the importance of accessibility, the article categorizes various visualizers based on their intended applications and highlights their utility in empowering bioinformaticians and non-bioinformaticians to interpret and derive insights from meta-omics data effectively.

Dictyobacter halimunensis sp. nov., a new member of the phylum Chloroflexota, from forest soil in a geothermal area

Three Gram-stain-positive aerobic bacteria, characterized by branched mycelia with putative sporangia, were isolated from forest soil inside a decayed bamboo stem from a geothermal area in West Java, Indonesia. The strain S3.2.2.5T grew at 15-37 °C (optimum 30 °C), at pH 5.0-7.0 (optimum 7.0) and in the presence of 0-1% NaCl (optimum 0%). Strain S3.2.2.5T was able to hydrolyse cellulose, xylan, starch and skim milk. The cell-wall sugars were composed of xylose and mannose, and the peptidoglycan hydrolysates contained d-glutamic acid, glycine, d-alanine, l-alanine, β-alanine and l-ornithine. The major fatty acids (>10%) were anteiso-C17:0, iso-C17:0, C16:1 2-OH and iso-C16:1. The major polar lipids were phosphatidylinositol, phosphatidylglycerol, diphosphatidylglycerol, unidentified glycolipids and unidentified phospholipids. The major menaquinone was MK-9 (H2). The results of the analysis of the phylogenetic tree based on the 16S rRNA gene indicated that these three isolates belong to the genus Dictyobacter and they were most closely related to the type strain of species Dictyobacter aurantiacus S-27T (97.41-98.00%). The strain S3.2.2.5T exhibited a genome size of 9.41 Mbp, which was significantly larger than the known Dictyobacter species. The G+C content was 54.3 mol%. The average nucleotide identity (90.77%) and the digital DNA-DNA hybridization values (42.6%) between strain S3.2.2.5T and D. aurantiacus S-27T were below the threshold value for species delineation. Based on the phenotypic, chemotaxonomic and molecular characteristics of strain S3.2.2.5T, a novel species of the genus Dictyobacter, for which the name Dictyobacter halimunensis sp. nov., is proposed. The type strain is S3.2.2.5T (= UICC B-128T = CGMCC 1.61913T = KCTC 43728T).

First reports of several viruses and a viroid including a novel vitivirus in Japan, found through virome analysis of bulk grape genetic resources

Virome analysis was performed on 174 grape genetic resources from the National Agriculture and Food Research Organization, Japan. A total of 20 bulk samples was prepared by grouping the vines into batches of 6-10 plants. Each of the bulk samples was analyzed using high-throughput sequencing, which detected 27 viruses and 5 viroids, including six viruses and one viroid reported in Japan for the first time (grapevine viruses F, L, and T, grapevine Kizil Sapak virus, grapevine Syrah virus 1, grapevine satellite virus, and grapevine yellow speckle viroid 2). In addition, a novel vitivirus was detected with a maximum nucleotide sequence identity of only 58% to its closest relative, grapevine virus A (GVA). The genome of this novel virus was 7,461 nucleotides in length and encoded five open reading frames showing the typical genomic structure of vitiviruses. Phylogenetic trees of vitiviruses placed it in a distinct position nearest to GVA or grapevine virus F (GVF) in genomes and amino acids of deduced replication-associated protein (RAP) and coat protein (CP). The amino acid sequence identities of RAP and CP with GVA, GVF, and other vitiviruses were a maximum of 53% and 73%, respectively, which were significantly below the species demarcation threshold of 80% in the genus. The low identity and phylogenetic analyses indicate the discovery of a novel vitivirus species provisionally named grapevine virus P.

Actinomadura monticuli sp. nov., isolated from Darangshi Oreum (a volcanic cone), and the reclassification of Actinomadura glauciflava Lu et al. 2003 as a later heterotypic synonym of Actinomadura luteofluorescens (Shinobu 1962) Preobrazhenskaya et al. 1975 (Approved Lists 1980)

Two mycelium-forming actinobacterial strains, designated as DLS-47 and DLS-62T, were isolated from volcanic ash collected from the surface of a rock on the peak of Darangshi Oreum (a volcanic cone) in Jeju, Republic of Korea, and their taxonomic positions were investigated by a polyphasic approach. Both of the isolates showed growth at 20-42 °C, pH 6.0-9.0 and 0-1% (w/v) NaCl. Furthermore, DLS-47 was found to grow at 45 °C, while strain DLS-62T grew at pH 10.0 and 3% (w/v) NaCl. The 16S rRNA gene-based phylogeny showed that both of the isolates belonged to the genus Actinomadura; strain DLS-47 was most closely related to Actinomadura chokoriensis DSM 45346T (100% sequence identity), while strain DLS-62T formed a tight cluster with Actinomadura bangladeshensis DSM 45347T (99.5% sequence similarity). Morphological and chemotaxonomic characteristics supported the affiliation of the two isolates to the genus Actinomadura. Phylogenomic analysis based on 92 core gene sequences showed that both of the isolates were most closely related to A. chokoriensis DSM 45346T. Strain DLS-47 shared 100% of orthologous average nucleotide identity and digital DNA-DNA hybridization values with A. chokoriensis DSM 45346T, while strain DLS-62T showed orthologous average nucleotide identity ≤89.8% and digital DNA-DNA hybridization values ≤39.4% with strain DLS-47 and members of the genus Actinomadura. The results of phenotypic assays and comparison of overall genomic relatedness indices support the conclusion that strain DLS-47 (= KACC 23347=DSM 116423) is a strain of A. chokoriensis, while strain DLS-62T (= KACC 23345T = DSM 116424T) represents a new species of the genus Actinomadura, for which the name Actinomadura monticuli sp. nov. is proposed. Also, Actinomadura glauciflava Lu et al. 2003 is reclassified as a later heterotypic synonym of Actinomadura luteofluorescens (Shinobu 1962) Preobrazhenskaya et al. 1975 (Approved Lists 1980) based on analysis of overall genomic relatedness indices and phenotypic similarity.