Evtushenko, Lyudmila

Shashkov A.S., Potekhina N.V., Tul'skaya E.M., Dmitrenok A.S., Senchenkova S.N., Torgov V.I., Dorofeeva L.V., Evtushenko L.I.

The cell wall of endophytic strain Rathayibacter oskolensis VKM Ac-2121

Kudryashova E.B., Ariskina E.V., Karlyshev A.V., Potekhina N.V., Shashkov A.S., Suzina N.E., Evtushenko L.I.

An aerobic, rod-shaped, non-motile, endospore-forming bacterium, strain V-9T, was found in the frozen volcanic ash, Kamchatka peninsula, Russia. Phylogenies based on 16S rRNA gene and genome sequences demonstrated that strain V-9T was affiliated with the family Paenibacillaceae and clustered outside the clade that includes the type species of this genus, Paenibacillus polymyxa, and closely related species. V-9T showed the highest 16S rRNA gene sequences similarity to Paenibacillus chartarius CCUG 55240T (96.7%). The similarity to type strains of other Paenibacillus species were below 94.7%, with 91.8% determined to Paenibacillus polymyxa IAM 13419T. The AAI and POCP values between V-9T and type species of the genera of Paenibacillaceae with available genomes, including Paenibacillus polymyxa, were below the thresholds for defining novel genera. The cell wall of new strain contained a lysine-based peptidoglycan and two teichoic acids, unsubstituted 1,3-poly(glycerol phosphate) and 1,3-poly(glycerol phosphate) substituted at the C(2) of glycerol by glucose. Acid hydrolysates of the cell wall included glucose, galactose and glycerol. Strain V-9T contained menaquinone MK-7 as the sole isoprenoid quinone, anteiso-C15:0, anteiso-C17:0, iso- C15:0 and iso-C16:0a as the dominant fatty acids, and phosphatidylglycerol, diphosphatidylglycerol, acylphosphatidylglycerol, and phosphatidylinositol as the major polar lipids. The DNA G+C content calculated from the whole genome sequence was 55 mol %. Based on the data obtained, a new genus and species, Gordonibacillus kamchatkensis gen. nov., sp. nov., is proposed with the type strain V-9T (=VKM B-2647T = DSM 26726T).

Starodumova I.P., Dorofeeva L.V., Prisyazhnaya N.V., Tarlachkov S.V., Vasilenko O.V., Avtukh A.N., Ospennikov Y.V., Subbotin S.A., Evtushenko L.I.

Two novel yellow-pigmented, rod-shaped and non-motile coryneform actinobacteria, strains VKM Ac-2596T and VKM Ac-2761, were isolated from a plant Tanacetum vulgare (Asteraceae) infested by foliar nematode Aphelenchoides sp. The strains exhibited the highest 16S rRNA gene sequence similarities to Rathayibacter agropyri CA4T (99.71%), Rathayibacter rathayi DSM 7485T (99.65%) and Rathayibacter iranicus VKM Ac-1602T (99.65%). The pairwise average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between VKM Ac-2596T and VKM Ac-2671 towards the type strains of Rathayibacter species did not exceed 85.24% and 29.40%, respectively, that are well below the thresholds for species delineation. The target strains had key chemotaxonomic properties typical of the genus Rathayibacter, namely, the DAB-based peptidoglycan, rhamnose and mannose as the predominant sugars and a rhamnomannan in the cell, the major menaquinone MK-10 and fatty acids of iso-anteiso type, with a large proportion of anteiso-15:0. The strains showed clear differences from the recognized Rathayibacter species in several phenotypic characteristics, including the difference in the composition of cell wall glycopolymers. Based on the results obtained in this study and the data published previously, we provide a description of a new species, Rathayibacter tanaceti sp. nov., with DL-642T (= VKM Ac-2596T = LMG 33114T) as the type strain.

Tul’skaya E.M., Kim D., Potekhina N.V., Shashkov A.S., Senchenkova S.N., Dorofeeva L.V., Evtushenko L.I.

Two types of cell wall glycopolymers of different structure were found in the type strains of two species of phytopathogenic bacteria, Clavibacter insidiosus VKM Ac-1402T and Clavibacter nebraskensis VKM Ac-1404T (family Microbacteriaceae, class Actinomycetes). The first type was represented by new, previously undescribed (1→6)-linked β-D-galactofuranans, which in the studied strains differed in the structure of side oligosaccharide chains (the structures are given in the text). The structure of the second glycopolymer, a pyruvate-containing galactomannan, was identical in both strains. The results obtained in this work, together with those published previously, indicate that the presence of the pyruvate-containing galactomannan and galactofuranans (with an identical core structure and different side oligosaccharide substituents) can be considered as a chemotaxonomic trait of the genus Clavibacter, and galactofuranans with di-, tri-, or tetrasaccharide substituents of different composition and structures can serve as chemotaxonomic markers of the species. The data obtained expand our understanding of the structural diversity of natural glycopolymers and structural features of the bacterial cell walls in various taxa and may be of interest for taxonomic studies and the studies aimed at elucidating the molecular mechanisms of interaction between bacteria and plant cells.

Potekhina N.V., Tul’skaya E.M., Ospennikov Y.V., Evtushenko L.I.

Information is provided on the cell wall glycopolymers of members of eight species of the genus Rathayibacter (family Microbacteriaceae, class Actinomycetes). The composition, structure, and structural components of polymers that are common to the genus and characteristic of species are noted, which can be useful as chemotaxonomic characters. The differences between Rathayibacter and other genera of the family Microbacteriaceae (Clavibacter, Curtobacterium) in the type and composition of glycopolymers are shown.

Avtukh A.N., Ariskina E.V., Baryshnikova L.M., Tul’skaya E.M., Potekhina N.V., Shashkov A.S., Suzina N.E., Prisyazhnaya N.V., Starodumova I.P., Vasilenko O.V., Dorofeeva L.V., Evtushenko L.I.

Seven actinomycete strains assigned to seven new species of the genus Kribbella were isolated from soils of different regions in Russia. The strains exhibited 98.2–99.3% similarity of the 16S rRNA gene sequences to each other and 96.2–99.7% similarity to the type strains of the known Kribbella species. The evolutionary distances calculated on the basis of concatenated gene sequences (gyrB–rpoB–recA–relA–atpD, 4108 bp) for the studied organisms and type strains of the known species were within the range reported for Kribbella species (0.014–0.101). The dDDH and ANIb values for the strains studied and the type strains of validly described species with available genomes were below the threshold (49.8 and 92.6%, respectively) for prokaryote species delineation. Members of the putative new species possessed individual phenotypic profiles; some species were found (for the first time in Kribbella) to produce sporangium-like structures, up to 4 μm in diameter. The cell walls of the studied strains contained the teichuronic and/or teichulosonic acids specific for the species or species groups and not described previously for other prokaryotes. The unique branched α-mannan occurred in all studied strains of the genus. Based on the data obtained and the previously published data, the following new species are proposed: Kribbella orskensis sp. nov. (type strain VKM Ас-2538T), Kribbella rubisoli sp. nov. (type strain VKM Aс-2540T), Kribbella antiqua sp. nov. (type strain VKM Ас-2541T), Kribbella kalugense sp. nov. (type strain VKM Ас-2570T), Kribbella steрpae sp. nov. (type strain VKM Ас-2572T), Kribbella pratensis sp. nov. (type strain VKM Ас-2574T), and Kribbella voronezhensis sp. nov. (type strain VKM Ас-2575T) with emended description of the genus Kribbella.

Perepelov A.V., Shashkov A.S., Kim D., Potekhina N.V., Dmitrenok A.S., Senchenkova S.N., Dorofeeva L.V., Evtushenko L.I., Tul'skaya E.M.

The structures of two cell wall glycopolymers were studied in the plant pathogenic bacterium Clavibacter tesselarius VKM Ac-1406T (family Microbacteriaceae, order Micrococcales, class Actinomycetes). The predominant polymer was a novel (1 → 6)-linked β-d-galactofuranan with a highly branched repeating unit, α-L-Rhap-(1 → 3)-α-D-Galp-(1 → 2)-[α-L-Rhap-(1 → 3)]-α-D-Fucp-(1 →, at O-2 on every second galactofuranose residue. The second polymer present in small amounts was acidic with the repeating unit, →3)-α-D-Galp-(1 → 3)-α-D-[4,6-S-Pyr]-Manp-(1 → 3)-α-D-Manp-[2OAc]0.2-(1→, and was reported in all Clavibacter species investigated to date. The presented results expand our knowledges of structural diversity of phosphate-free cell wall glycopolymers and provide evidence in support of their taxonomic specificity for bacterial species and genera.

Tarlachkov S.V., Starodumova I.P., Boueva O.V., Lysak L.V., Subbotin S.A., Evtushenko L.I.

Draft genome sequences of 11 strains of putative new species of Geodermatophilaceae were generated using Illumina technology. The genome sizes ranged from 4.19 to 4.99 Mb, with G+C contents of 73.5% to 74.6%, and contained genes for microbial rhodopsins. This study will contribute to our knowledge of the ecology and diversity of members of the family Geodermatophilaceae .

Perepelov A.V., Kim D., Tul'skaya E.M., Potekhina N.V., Dmitrenok A.S., Senchenkova S.N., Dorofeeva L.V., Evtushenko L.I., Shashkov A.S.

A glycopolymer of novel structure was found in the cell wall of plant pathogen Clavibacter phaseoli VKM Ac-2641T (family Microbacteriaceae, class Actinomycetes). The glycopolymer was (1 → 6)-linked β-d-galactofuranan with side branched trisaccharide, α-D-Manp-(1 → 2)-[α-D-Manp-(1 → 3)]-α-D-Ribf-(1→ at O-2 on every second galactofuranose residue. The galactofuranan structure was established by chemical and NMR spectroscopic methods using one- and two-dimensional techniques 1H,1H COSY, TOCSY, ROESY and 1H,13C HSQC, HMBC. The results of this study provide new data on diversity of bacterial glycopolymers, may prove useful for bacterial taxonomy and contribute to the understanding of the host plant-microbiota interaction mechanisms.

Tarlachkov S.V., Efeykin B.D., Castillo P., Evtushenko L.I., Subbotin S.A.

Bacteria of the genus “Candidatus Cardinium” and related organisms composing the Cardinium clade are intracellular endosymbionts frequently occurring in several arthropod groups, freshwater mussels and plant-parasitic nematodes. Phylogenetic analyses based on two gene sequences (16S rRNA and gyrB) showed that the Cardinium clade comprised at least five groups: A, B, C, D and E. In this study, a screening of 142 samples of plant-parasitic nematodes belonging to 93 species from 12 families and two orders using PCR with specific primers and sequencing, revealed bacteria of Cardinium clade in 14 nematode samples belonging to 12 species of cyst nematodes of the family Heteroderidae. Furthermore, in this study, the genome of the Cardinium cHhum from the hop cyst nematode, Heterodera humuli, was also amplified, sequenced and analyzed. The comparisons of the average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values for the strain Cardinium cHhum with regard to related organisms with available genomes, combined with the data on 16S rRNA and gyrB gene sequence identities, showed that this strain represents a new candidate species within the genus “Candidatus Paenicardinium”. The phylogenetic position of endosymbionts of the Cardinium clade detected in nematode hosts was also compared to known representatives of this clade from other metazoans. Phylogenetic reconstructions based on analysis of 16S rRNA, gyrB, sufB, gloEL, fusA, infB genes and genomes and estimates of genetic distances both indicate that the endosymbiont of the root-lesion nematode Pratylenchus penetrans represented a separate lineage and is designated herein as a new group F. The phylogenetic analysis also confirmed that endosymbionts of ostracods represent the novel group G. Evolutionary relationships of bacterial endosymbionts of the Cardinium clade within invertebrates are presented and discussed.

Seshadri R., Roux S., Huber K.J., Wu D., Yu S., Udwary D., Call L., Nayfach S., Hahnke R.L., Pukall R., White J.R., Varghese N.J., Webb C., Palaniappan K., Reimer L.C., et. al.

The phylum Actinobacteria includes important human pathogens like Mycobacterium tuberculosis and Corynebacterium diphtheriae and renowned producers of secondary metabolites of commercial interest, yet only a small part of its diversity is represented by sequenced genomes. Here, we present 824 actinobacterial isolate genomes in the context of a phylum-wide analysis of 6,700 genomes including public isolates and metagenome-assembled genomes (MAGs). We estimate that only 30%–50% of projected actinobacterial phylogenetic diversity possesses genomic representation via isolates and MAGs. A comparison of gene functions reveals novel determinants of host-microbe interaction as well as environment-specific adaptations such as potential antimicrobial peptides. We identify plasmids and prophages across isolates and uncover extensive prophage diversity structured mainly by host taxonomy. Analysis of >80,000 biosynthetic gene clusters reveals that horizontal gene transfer and gene loss shape secondary metabolite repertoire across taxa. Our observations illustrate the essential role of and need for high-quality isolate genome sequences. • 824 new actinobacterial isolate genomes from diverse environments • Only a third of actinobacterial diversity has genome representation • New niche-specific gene determinants highlighted, such as new antimicrobial peptides • Secondary metabolite gene clusters shaped by horizontal gene transfer Seshadri et al. contribute 824 new genomes of cultivated Actinobacteria , which are important for drug discovery. They observe that the genes responsible for producing such compounds often move around between microbes, making them harder to capture without high-quality genomes. They highlight interesting adaptations such as an experimentally verified antimicrobial peptide.

Tarlachkov S.V., Ospennikov Y.V., Demidov A.V., Starodumova I.P., Dorofeeva L.V., Prisyazhnaya N.V., Chizhov V.N., Subbotin S.A., Evtushenko L.I.

Draft genome sequences of 9 strains of known and putative new species of Microbacteriaceae isolated from insect- and nematode-damaged plants were generated using Illumina technology. The data obtained will contribute to the development of the genome-based prokaryote taxonomy and the knowledge on the biology of the microbial group investigated.

Potekhina N.V., Shashkov A.S., Ariskina E.V., Prisyazhnaya N.V., Tul’skaya E.M., Khasaeva F.M., Evtushenko L.I.

The structure of the cell wall glycopolymer and the taxonomic position of the pyridine-degrading strain VKM Ac-1098D were established. By using chemical and NMR spectroscopic methods, the glycopopolymer was identified as 1,6-linked β-D-galactofuranan with side diaminoglucose residue (2,3-diacetamido-2,3-dideoxy-β-glucopyranose, β-GlcpNAc3NAc). This polymer structure has not been previously described in prokaryotes. Structurally similar galactofuranan which differed from the polymer of strain VKM Ac-1098D by the α-configuration of diaminoglucose (α-GlcpNAc3NAc) in the side chain was found previously in some studied Paenarthrobacter species. The results of the 16S rRNA gene sequence analysis and MALDI-TOF clustering showed that strain VKM Ac-1098D represents a new species of the genus Paenarthrobacter tentatively named “Paenarthrobacter pyridinovorans”. The data obtained in this and earlier works indicate that galactofuranan with diaminoglucose in the side chain may serve as a chemotaxonomic marker of the genus Paenarthrobacter and the α-configuration of the glycosidic bond of diaminoglucose may be a feature characteristic of the putative new species.

Potekhina N.V., Ariskina E.V., Shashkov A.S., Tul’skaya T.M., Evtushenko L.I.

The composition and structure of the cell wall glycopolymers from Arthrobacter crystallopoietes VKM Ac-1107T (family Micrococcaceae, phylum Actinobacteria), previously assigned to the “A. globiformis” group based on the high similarity of 16S rRNA gene sequences and traditional chemotaxonomic markers were studied. Teichoic acid—1,3-poly(glycerol phosphate) substituted with β-glucose residues, and diglycosyl 1-phosphate polymer with -6)-α-D-GalpNAc-(1→6)-α-D-GlcpNAc-(1-P-repeating unit were identified by chemical and NMR spectroscopy methods. The results of phylogenomic (taxogenomic) analysis, viz. determination of the average amino acid identity (AAI) and the similarity of conserved proteins (POCP), indicate that A. crystallopoietes belongs to a new genus and the composition of the cell wall glycopolymers may serve as a diagnostic characteristic of this genus, which will be described on the basis of A. crystallopoietes.

Sorokin D.Y., Elcheninov A.G., Khijniak T.V., Zaharycheva A.P., Boueva O.V., Ariskina E.V., Bunk B., Spröer C., Evtushenko L.I., Kublanov I.V., Hahnke R.L.

During a cultural diversity survey on hydrolytic bacteria in saline alkaline soils, a hydrolytic actinobacterium strain ACPA39T was enriched and isolated in pure culture from a soda solonchak soil in southwestern Siberia. It forms a substrate mycelium with rod-shaped sporangia containing 1-3 exospores. The isolate is obligately alkaliphilic, growing at pH 7.5-10.3 (optimum at 8.5-9.0) and moderately halophilic, tolerating up to 3 M total Na+ in the form of sodium carbonates. It is an obligately aerobic, organoheteroterophic, saccharolytic bacterium, utilizing various sugars and alpha/beta-glucans as growth substrates. According to the 16S rRNA gene-based phylogenetic analysis, strain ACPA39T forms a distinct branch within the family Micromonosporaceae, with the sequence identities below 94.5% with type strains of other genera. This is confirmed by phylogenomic analysis based on the 120 conserved single copy protein-based markers and genomic indexes (ANI, AAI). The cell-wall of ACPA39T contained meso-DAP, glycine, glutamic acid and alanine in a equimolar ratio, characteristic of the peptidoglycan type A1γ'. The whole-cell sugars include galactose and xylose. The major menaquinone is MK-10(H4). The identified polar lipids consist of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol. The polar lipid fatty acids were dominated by anteiso-C17:0, iso-C16:0, iso-C17:0, 10 Me-C18:0 and C18:1ω9. Based on the distinct phylogeny, the chemotaxonomy features and unique phenotypic properties, strain ACPA39T (DSM 106523T = VKM 2772T) is classified into a new genus and species in the family Micromonosporaceae for which the name Natronosporangium hydrolitycum gen. nov., sp. nov. is proposed.

Molina J., de Guzman R.C., Abzalimov R., Huang W., Guruprasad A., Pedales R., Wicaksono A., Davis D., Callado J.R., Bänziger H., Suksathan P., Eaton W., Yin P., Bürger M., Erickson M., et. al.

Coutinho T.D., Rodrigues F.A., de Assis D.A., Rebouças L.M., Ferreira T.L., Cabral V.P., Rodrigues D.S., Sá L.G., Lopes F.F., do Nascimento G.A., Mattos A.L., Cavalcanti B.C., Júnior H.V., da Silva C.R., Ricardo N.M.

Song L., Nuhamunada M., Weber T., Kovacs A.T.

ABSTRACTThe genusPaenibacillusis a prolific producer of secondary metabolites with diverse ecological and industrial applications. However, a comprehensive overview of the biosynthetic gene cluster (BGC) diversity and distribution throughout the genus has been limited. Here, we performed large-scale genome mining on 284 high-quality genomes and generated a non-redundant dataset of 126 representative genomes to explore the biosynthetic potential of this genus. A total of 3,273 BGCs were identified from the 284 genomes that clustered into 1,013 gene cluster families (GCFs), with 98.7% classified as unknown, indicating vast potential for novel secondary metabolite discovery in thePaenibacillusgenus. Comparative analysis revealed significant phylogenetic and clade-specific distribution patterns of GCFs, with certain clades enriched in unique biosynthetic pathways while others exhibited low similarity to known BGCs, suggesting evolutionary adaptation to diverse ecological niches. This study uncovers the rich and largely untapped biosynthetic potential of the genusPaenibacillus, providing a foundation for future exploration of its natural products and their applications in biotechnology and medicine.IMPORTANCEBacterial secondary metabolites have been instrumental in the development of antibiotics, antifungals, and other bioactive compounds. The genusPaenibacillusis an underexplored source of such metabolites, with significant potential for novel discoveries. By integrating genome mining and phylogenetic analysis, this study systematically characterizes the diversity, distribution, and novelty of biosynthetic gene cluster across the genus. The identification of clade-specific biosynthetic patterns and numerous unknown gene cluster families highlightsPaenibacillusas a promising target for uncovering novel compounds with ecological and therapeutic relevance. These findings not only expand our understanding of bacterial secondary metabolite biosynthesis but also offer new opportunities for the development of sustainable biotechnological applications.

Kimeklis A.K., Gladkov G.V., Orlova O.V., Lisina T.O., Afonin A.M., Aksenova T.S., Kichko A.A., Lapidus A.L., Abakumov E.V., Andronov E.E.

IntroductionSoil microbiome is a major source of physiologically active microorganisms, which can be potentially mobilized by adding various nutrients. To study this process, a long-term experiment was conducted on the decomposition of oat straw and leaf litter using soil as a microbial inoculum.MethodsCombined analyses of enzymatic activity and NGS data for 16S rRNA gene amplicon and full metagenome sequencing were applied to study taxonomic, carbohydrate-active enzyme (CAZy), and polysaccharide utilization loci (PULs) composition of microbial communities at different stages of decomposition between substrates.ResultsIn straw degradation, the microbial community demonstrated higher amylase, protease, catalase, and cellulase activities, while peroxidase, invertase, and polyphenol oxidase were more active in leaf litter. Consistent with this, the metagenome analysis showed that the microbiome of straw compost was enriched in genes for metabolic pathways of simpler compounds. At the same time, there were more genes for aromatic compound degradation pathways in leaf litter compost. We identified nine metagenome-assembled genomes (MAGs) as the most promising prokaryotic decomposers due to their abnormally high quantity of PULs for their genome sizes, which were confirmed by 16S rRNA gene amplicon sequencing to constitute the bulk of the community at all stages of substrate degradation. MAGs from Bacteroidota (Chitinophaga and Ohtaekwangia) and Actinomycetota (Streptomyces) were found in both composts, while those from Bacillota (Pristimantibacillus) were specific for leaf litter. The most frequently identified PULs were specialized on xylans and pectins, but not cellulose, suggesting that PUL databases may be underrepresented in clusters for complex substrates.DiscussionOur study explores microbial communities from natural ecosystems, such as soil and lignocellulosic waste, which are capable of decomposing lignocellulosic substrates. Using a comprehensive approach with chemical analyses of the substrates, amplicon, and full metagenome sequencing data, we have shown that such communities may be a source of identifying the highly effective decomposing species with novel PULs.

Wu D., Seshadri R., Kyrpides N.C., Ivanova N.N.

Following 30 years of sequencing, we assessed the phylogenetic diversity (PD) of >1.5 million microbial genomes in public databases, including metagenome-assembled genomes (MAGs) of uncultivated microbes. As compared to the vast diversity uncovered by metagenomic sequences, cultivated taxa account for a modest portion of the overall diversity, 9.73% in bacteria and 6.55% in archaea, while MAGs contribute 48.54% and 57.05%, respectively. Therefore, a substantial fraction of bacterial (41.73%) and archaeal PD (36.39%) still lacks any genomic representation. This unrepresented diversity manifests primarily at lower taxonomic ranks, exemplified by 134,966 species identified in 18,087 metagenomic samples. Our study exposes diversity hotspots in freshwater, marine subsurface, sediment, soil, and other environments, whereas human samples yielded minimal novelty within the context of existing datasets. These results offer a roadmap for future genome recovery efforts, delineating uncaptured taxa in underexplored environments and underscoring the necessity for renewed isolation and sequencing.

Dinglasan J.L., Otani H., Doering D.T., Udwary D., Mouncey N.J.

Microbial secondary metabolites not only have key roles in microbial processes and relationships but are also valued in various sectors of today’s economy, especially in human health and agriculture. The advent of genome sequencing has revealed a previously untapped reservoir of biosynthetic capacity for secondary metabolites indicating that there are new biochemistries, roles and applications of these molecules to be discovered. New predictive tools for biosynthetic gene clusters (BGCs) and their associated pathways have provided insights into this new diversity. Advanced molecular and synthetic biology tools and workflows including cell-based and cell-free expression facilitate the study of previously uncharacterized BGCs, accelerating the discovery of new metabolites and broadening our understanding of biosynthetic enzymology and the regulation of BGCs. These are complemented by new developments in metabolite detection and identification technologies, all of which are important for unlocking new chemistries that are encoded by BGCs. This renaissance of secondary metabolite research and development is catalysing toolbox development to power the bioeconomy. In this Review, Dinglasan and colleagues explore innovations that facilitate rapid microbial secondary metabolite discovery, focusing on recent techniques for the prediction of biosynthetic gene clusters (BGCs) from genomic data bases, isolating novel BGCs from the environment, and producing and detecting the chemical products of these sequences in the laboratory.

Mohite O.S., Jørgensen T.S., Booth T.J., Charusanti P., Phaneuf P.V., Weber T., Palsson B.O.

Background Streptomyces is a highly diverse genus known for the production of secondary or specialized metabolites with a wide range of applications in the medical and agricultural industries. Several thousand complete or nearly complete Streptomyces genome sequences are now available, affording the opportunity to deeply investigate the biosynthetic potential within these organisms and to advance natural product discovery initiatives. Results We perform pangenome analysis on 2371 Streptomyces genomes, including approximately 1200 complete assemblies. Employing a data-driven approach based on genome similarities, the Streptomyces genus was classified into 7 primary and 42 secondary Mash-clusters, forming the basis for comprehensive pangenome mining. A refined workflow for grouping biosynthetic gene clusters (BGCs) redefines their diversity across different Mash-clusters. This workflow also reassigns 2729 known BGC families to only 440 families, a reduction caused by inaccuracies in BGC boundary detections. When the genomic location of BGCs is included in the analysis, a conserved genomic structure, or synteny, among BGCs becomes apparent within species and Mash-clusters. This synteny suggests that vertical inheritance is a major factor in the diversification of BGCs. Conclusions Our analysis of a genomic dataset at a scale of thousands of genomes refines predictions of BGC diversity using Mash-clusters as a basis for pangenome analysis. The observed conservation in the order of BGCs’ genomic locations shows that the BGCs are vertically inherited. The presented workflow and the in-depth analysis pave the way for large-scale pangenome investigations and enhance our understanding of the biosynthetic potential of the Streptomyces genus.

Elmanzalawi M., Fujisawa T., Mori H., Nakamura Y., Tanizawa Y.

Abstract Background Accurate taxonomic classification in genome databases is essential for reliable biological research and effective data sharing. Mislabeling or inaccuracies in genome annotations can lead to incorrect scientific conclusions and hinder the reproducibility of research findings. Despite advances in genome analysis techniques, challenges persist in ensuring precise and reliable taxonomic assignments. Existing tools for genome verification often involve extensive computational resources or lengthy processing times, which can limit their accessibility and scalability for large-scale projects. There is a need for more efficient, user-friendly solutions that can handle diverse datasets and provide accurate results with minimal computational demands. This work aimed to address these challenges by introducing a novel tool that enhances taxonomic accuracy, offers a user-friendly interface, and supports large-scale analyses. Results We introduce a novel tool for the quality control and taxonomic classification tool of prokaryotic genomes, called DFAST_QC, which is available as both a command-line tool and a web service. DFAST_QC can quickly identify species based on NCBI and GTDB taxonomies by combining genome-distance calculations using MASH with ANI calculations using Skani. We evaluated DFAST_QC's performance in species identification and found it to be highly consistent with existing taxonomic standards, successfully identifying species across diverse datasets. In several cases, DFAST_QC identified potential mislabeling of species names in public databases and highlighted discrepancies in current classifications, demonstrating its capability to uncover errors and enhance taxonomic accuracy. Additionally, the tool’s efficient design allows it to operate smoothly on local machines with minimal computational requirements, making it a practical choice for large-scale genome projects. Conclusions DFAST_QC is a reliable and efficient tool for accurate taxonomic identification and genome quality control, well-suited for large-scale genomic studies. Its compatibility with limited-resource environments, combined with its user-friendly design, ensures seamless integration into existing workflows. DFAST_QC's ability to refine species assignments in public databases highlights its value as a complementary tool for maintaining and enhancing the accuracy of taxonomic data in genomic research. The web version is available at https://dfast.ddbj.nig.ac.jp/dqc/submit/, and the source code for local use can be found at https://github.com/nigyta/dfast_qc.

Cema G., Gutwiński P., Ziembińska-Buczyńska A., Ciesielski S., Surmacz-Górska J.

The anaerobic ammonium oxidation (anammox) process, is widely applied for high nitrogen wastewater treatment, such as from reject water, landfill leachate, tannery wastewater, or coke-oven wastewater. However, the anammox process exhibits sensitivity to many substances that can be found in industrial wastewater, including heavy metals. In the present study, the long-term effect of a combination of heavy metals ions (Cr (III), Zn (II), Cd (II), Cu (II), Ni (II), and Pb (II)) on the nitrogen removal efficiency and biodiversity of the anammox bacteria in an anaerobic membrane bioreactor (AnMBR) was investigated. The findings indicated that even short-term exposure to low concentrations of these ions (Cr-0.25, Zn-1.6, Cd-0.004, Ni-0.18, Pb-0.1 and Cu-0.15 mg/L) significantly lowered the anammox bacteria’s activity, and the nitrogen removal rate decreased from 0.21 to 0.05 g N/L∙d. Moreover, the presence of these metals directly altered bacterial biodiversity.. After eliminating heavy metals from the influent, recovery of the initial nitrogen removal rate took approximately 80 days.. Concentrations of Cr-0.125, Zn-0, Cd-0.002, Ni-0.09, Pb-0.05, and Cu-0.075 mg/L were shown not to impact process performance negatively. Additionally, it was demonstrated that zinc was the least tolerated heavy metal in the reactor.

Prokofeva M.I., Elcheninov A.G., Klyukina A.A., Novikov A.A., Kachmazov G.S., Toshchakov S.V., Frolov E.N., Podosokorskaya O.A.

A novel Gram-negative, motile, rod-shaped bacterium, designated 4137-clT, was isolated from a thermal spring of North Ossetia (Russian Federation). Strain 4137-clT grew at 30–50 °C (optimum 42 °C) with 0–3.5% NaCl (optimum 0–0.3%) and within pH range 4.0–8.7 (optimum pH 6.8–7.3). It was a strictly anaerobic microorganism capable of fermentation and respiration on organic acids and proteinaceous substrates. Sulfur, sulfite, polysulfide, and arsenate were used as electron acceptors. In addition to heterotrophic growth it grew autotrophically with H2/CO2. The major fatty acids were C16:1 ω8c and C16:0. The size of the genome and genomic DNA G+C content of strain 4137-clT were 4.5 Mb and 59.2%, respectively. According to the 16S rRNA gene sequence and conserved protein sequences phylogenies, strain 4137-clT represented a distinct lineage of the family Acetonemataceae within the class Negativicutes. As inferred from the morphology, physiology, chemotaxonomical and phylogenomic analyses, strain 4137-clT ought to be recognized as a novel genus for which the name Anaeroselena agilis gen. nov., sp. nov., we propose. The type strain is 4137-clT(=KCTC 25383T = VKM B-3575T).

Tarlachkov S.V., Starodumova I.P., Boueva O.V., Chernyshov S.V., Evtushenko L.I.

Zuo S., Xiong L., Yuan Q., Chen G., Yang R., Wang L., Jiang C., Wang X., Jiang Y.

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).

Yang J., Ruan Y., Wang H., Li L., Zhao Y., Qin Y.

Nowak V.V., Hou P., Owen J.G.

ABSTRACT Marine sponges are a prolific source of biologically active small molecules, many of which originate from sponge-associated bacteria. Identifying the producing bacteria is a key step in developing sustainable routes for the production of these metabolites. To facilitate the required computational analyses, we developed MetaSing, a reproducible singularity-based pipeline for assembly, identification of high-quality metagenome-assembled genomes (MAGs), and analysis of biosynthetic gene clusters (BGCs) from metagenomic short-read data. We applied this pipeline to metagenomic sequencing data from 16 marine sponges collected from New Zealand, Tonga, and the Mediterranean Sea. This analysis yielded 643 MAGs representing 510 species. Of the 2,670 BGCs identified across all samples, 70.8% were linked to a MAG. Comparison of BGCs to those identified from previously sequenced bacteria revealed high biosynthetic novelty in variety of underexplored phyla, including Poribacteria, Acidobacteriota, and Dadabacteria. Alongside the observation that each sample contains unique biosynthetic potential, this holds great promise for natural product discovery and for furthering the understanding of different sponge holobionts. IMPORTANCE Discovery of new chemical compounds such as natural products is a crucial endeavor to combat the increasing resistance to antibiotics and other drugs. This manuscript demonstrates that microbial communities associated with marine sponges investigated in this work encode the potential to produce novel chemistry. Lesser studied bacterial taxa that are often difficult to cultivate are particularly rich in potential.

Zhao J., Liu X., Hou L., Xu G., Guan F., Zhang W., Luo H., Wu N., Yao B., Zhang C., Delaplace P., Tian J.

The potential of seed endophytic microbes to enhance plant growth and resilience is well recognized, yet their role in alleviating cold stress in rice remains underexplored due to the complexity of these microbial communities. In this study, we investigated the diversity of seed endophytic microbes in two rice varieties, the cold-sensitive CB9 and the cold-tolerant JG117. Our results revealed significant differences in the abundance of Microbacteriaceae, with JG117 exhibiting a higher abundance under both cold stress and room temperature conditions compared to CB9. Further analysis led to the identification of a specific cold-tolerant microbe, Microbacterium testaceum M15, in JG117 seeds. M15-inoculated CB9 plants showed enhanced growth and cold tolerance, with a germination rate increase from 40 % to 56.67 % at 14℃ and a survival rate under cold stress (4℃) doubling from 22.67 % to 66.67 %. Additionally, M15 significantly boosted chlorophyll content by over 30 %, increased total protein by 16.31 %, reduced malondialdehyde (MDA) levels by 37.76 %, and increased catalase activity by 26.15 %. Overall, our study highlights the potential of beneficial endophytic microbes like M. testaceum M15 in improving cold tolerance in rice, which could have implications for sustainable agricultural practices and increased crop productivity in cold-prone regions.

Potekhina N.V., Tul’skaya E.M., Ospennikov Y.V., Evtushenko L.I.

Information is provided on the cell wall glycopolymers of members of eight species of the genus Rathayibacter (family Microbacteriaceae, class Actinomycetes). The composition, structure, and structural components of polymers that are common to the genus and characteristic of species are noted, which can be useful as chemotaxonomic characters. The differences between Rathayibacter and other genera of the family Microbacteriaceae (Clavibacter, Curtobacterium) in the type and composition of glycopolymers are shown.

Perepelov A.V., Shashkov A.S., Kim D., Potekhina N.V., Dmitrenok A.S., Senchenkova S.N., Dorofeeva L.V., Evtushenko L.I., Tul'skaya E.M.

The structures of two cell wall glycopolymers were studied in the plant pathogenic bacterium Clavibacter tesselarius VKM Ac-1406T (family Microbacteriaceae, order Micrococcales, class Actinomycetes). The predominant polymer was a novel (1 → 6)-linked β-d-galactofuranan with a highly branched repeating unit, α-L-Rhap-(1 → 3)-α-D-Galp-(1 → 2)-[α-L-Rhap-(1 → 3)]-α-D-Fucp-(1 →, at O-2 on every second galactofuranose residue. The second polymer present in small amounts was acidic with the repeating unit, →3)-α-D-Galp-(1 → 3)-α-D-[4,6-S-Pyr]-Manp-(1 → 3)-α-D-Manp-[2OAc]0.2-(1→, and was reported in all Clavibacter species investigated to date. The presented results expand our knowledges of structural diversity of phosphate-free cell wall glycopolymers and provide evidence in support of their taxonomic specificity for bacterial species and genera.

Stoll D.A., Grimmler C., Hetzer B., Kulling S.E., Huch M.

The novel, aerobic, Gram-stain-positive, rod-shaped bacterial strain, ZW T2_19T, was isolated from an onion sample (Allium cepa var. Rijnsburger). Analyses of the 16S rRNA gene sequence revealed that ZW T2_19T represented a member of the genus Rathayibacter but may represent a novel species of this genus. Analyses of the whole draft genome sequences, i.e. digital DNA–DNA hybridisation (dDDH) and average nucleotide identity (ANI) of ZW T2_19T and all type strains of species of the genus Rathayibacter confirmed that ZW T2_19T represents a novel species of the genus Rathayibacter . The genome size of ZW T2_19T is 4.01 Mbp and the DNA G+C content is 71.8 mol%. Glucose, mannose, rhamnose and ribose were detected as whole-cell sugars of ZW T2_19T. The major respiratory quinone of ZW T2_19T is menaquinone MK-10, at 78.9 %. The detected peptidoglycan type in ZW T2_19T is a variant of type B2γ with {Gly} [l-diaminobutyric acid (l-DAB)/l-homoserine (l-Hse)] d-Glu-l-DAB. Polar lipids in ZW T2_19T consisted of one diphosphatidylglycerol, one phosphatidylglycerol, seven glycolipids, one phospholipid and one lipid. The fatty acid profile of ZW T2_19T predominantly consisted of anteiso-C15 : 0 (53 %), iso-C16 : 0 (21 %) and anteiso-C17 : 0 (18 %). In addition, API 20NE, API 50CH, API Coryne, API ZYM, antibiotic susceptibility, haemolysis and growth at different temperatures and with different supplements was investigated. On the basis of the results obtained using this polyphasic approach, including molecular, phenotypic and biochemical analyses, we propose the novel species Rathayibacter rubneri with the type and only strain ZW T2_19T (= DSM 114294T = LMG 32700T).

Perepelov A.V., Kim D., Tul'skaya E.M., Potekhina N.V., Dmitrenok A.S., Senchenkova S.N., Dorofeeva L.V., Evtushenko L.I., Shashkov A.S.

A glycopolymer of novel structure was found in the cell wall of plant pathogen Clavibacter phaseoli VKM Ac-2641T (family Microbacteriaceae, class Actinomycetes). The glycopolymer was (1 → 6)-linked β-d-galactofuranan with side branched trisaccharide, α-D-Manp-(1 → 2)-[α-D-Manp-(1 → 3)]-α-D-Ribf-(1→ at O-2 on every second galactofuranose residue. The galactofuranan structure was established by chemical and NMR spectroscopic methods using one- and two-dimensional techniques 1H,1H COSY, TOCSY, ROESY and 1H,13C HSQC, HMBC. The results of this study provide new data on diversity of bacterial glycopolymers, may prove useful for bacterial taxonomy and contribute to the understanding of the host plant-microbiota interaction mechanisms.

Tarasov K., Yakhnenko A., Zarubin M., Gangapshev A., Potekhina N.V., Avtukh A.N., Kravchenko E.

In this study, we present the characterization of the BNO1T bacterial strain isolated from the deep subsurface saline spring at the Baksan Neutrino Observatory INR RAS (Kabardino-Balkaria, Russia). The complete genome sequence of the strain BNO1T is 5,347,902 bp, with a GC content 41 and 49%. The cell wall peptidoglycan contains meso-diaminopimelic acid. The major isoprenoid quinone is MK-7 and the polar lipids are diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine. The major fatty acids are anteiso-C15:0 (23.34%), iso-C15:0 (20.10%), C16:0 (11.96%), iso-C16:0 (10.88%), and anteiso-C17:0 (10.79%). The 16S rRNA gene sequence clearly demarcated the strain as belonging to Cytobacillus genera. Based on the phylogenetic analysis, ANI (average nucleotide identity) and dDDH (digital DNA-DNA hybridization) assessments we propose to assign the strain BNO1T and other related strains to new species and to name it Cytobacillus pseudoceanisediminis sp. nov. (The values of ANI and dDDH between BNO1T and Cytobacillus oceanisediminis CGMCC 1.10115 T are 80.65% and 24.7%, respectively; values of ANI and dDDH between BNO1T and Cytobacillus firmus NCTC 10335 T are 89% and 38%, respectively). Genomic analysis of strain BNO1T revealed pathways for C1 compounds oxidation and two pathways for C1 compounds assimilation: serine and ribulose monophosphate pathways. In addition, strain BNO1T contains a plasmid (342,541 bp) coding multiple genes involved in heavy metal ion balance. Moreover, heavy metal toxicity testing confirmed the high potential of the strain BNO1T as a source of metal resistance genes and enzymes. The type strain is BNO1T (= BIM B-1921 T = VKM B-3664 T).

Olson R.D., Assaf R., Brettin T., Conrad N., Cucinell C., Davis J., Dempsey D., Dickerman A., Dietrich E., Kenyon R., Kuscuoglu M., Lefkowitz E., Lu J., Machi D., Macken C., et. al.

Abstract The National Institute of Allergy and Infectious Diseases (NIAID) established the Bioinformatics Resource Center (BRC) program to assist researchers with analyzing the growing body of genome sequence and other omics-related data. In this report, we describe the merger of the PAThosystems Resource Integration Center (PATRIC), the Influenza Research Database (IRD) and the Virus Pathogen Database and Analysis Resource (ViPR) BRCs to form the Bacterial and Viral Bioinformatics Resource Center (BV-BRC) https://www.bv-brc.org/. The combined BV-BRC leverages the functionality of the bacterial and viral resources to provide a unified data model, enhanced web-based visualization and analysis tools, bioinformatics services, and a powerful suite of command line tools that benefit the bacterial and viral research communities.

Guérin H., Kulakauskas S., Chapot-Chartier M.

Rhamnose-rich cell wall polysaccharides (Rha-CWPSs) have emerged as crucial cell wall components of numerous Gram-positive, ovoid-shaped bacteria-including streptococci, enterococci, and lactococci-of which many are of clinical or biotechnological importance. Rha-CWPS are composed of a conserved polyrhamnose backbone with side-chain substituents of variable size and structure. Because these substituents contain phosphate groups, Rha-CWPS can also be classified as polyanionic glycopolymers, similar to wall teichoic acids, of which they appear to be functional homologs. Recent advances have highlighted the critical role of these side-chain substituents in bacterial cell growth and division, as well as in specific interactions between bacteria and infecting bacteriophages or eukaryotic hosts. Here, we review the current state of knowledge on the structure and biosynthesis of Rha-CWPS in several ovoid-shaped bacterial species. We emphasize the role played by multicomponent transmembrane glycosylation systems in the addition of side-chain substituents of various sizes as extracytoplasmic modifications of the polyrhamnose backbone. We provide an overview of the contribution of Rha-CWPS to cell wall architecture and biogenesis and discuss current hypotheses regarding their importance in the cell division process. Finally, we sum up the critical roles that Rha-CWPS can play as bacteriophage receptors or in escaping host defenses, roles that are mediated mainly through their side-chain substituents. From an applied perspective, increased knowledge of Rha-CWPS can lead to advancements in strategies for preventing phage infection of lactococci and streptococci in food fermentation and for combating pathogenic streptococci and enterococci.

Arizala D., Dobhal S., Alvarez A.M., Arif M.

The Gram-positive genus Clavibacter is currently divided into seven species ( Clavibacter michiganensis , Clavibacter nebraskensis , Clavibacter capsici , Clavibacter sepedonicus , Clavibacter tessellarius , Clavibacter insidiosus and Clavibacter zhangzhiyongii ) and three subspecies ( C. michiganensis subsp. californiensis , C. michiganensis subsp. chilensis and C. michiganensis subsp. phaseoli ). Recent studies have indicated that the taxonomic rank of the subspecies must be re-evaluated. In this research, we assessed the taxonomic position of the three C. michiganensis subspecies and clarified the taxonomic nomenclature of other 75 Clavibacter strains. The complete genomes of the type strains of the three Clavibacter subspecies, the type strain of C. tessellarius and C. nebraskensis A6096 were sequenced using PacBio RSII technology. Application of whole-genome-based computational approaches such as average nucleotide identity (ANI), digital DNA–DNA hybridization, multi-locus sequence analysis of seven housekeeping genes (acnA, atpD, bipA, icdA, mtlD, recA and rpoB), a phylogenomic tree reconstructed from 1 028 core genes, and ANI-based phylogeny provided sufficient justification for raising C. michiganensis subsp. californiensis to the species level. These results led us to propose the establishment of Clavibacter californiensis sp. nov. as a species with its type strain C55T (=CFBP 8216T=ATCC BAA-2691T). Moreover, the orthologous and in silico dot plot analyses, along with the above described bioinformatic strategies, revealed a high degree of similarity between C. michiganensis subsp. chilensis and C. michiganensis subsp. phaseoli . Based on these analyses, we propose that both subspecies be combined into a single taxon and elevated to the species level as Clavibacter phaseoli sp. nov., with LPPA 982T (= CECT 8144T= LMG 27667T) as the type strain.

Sangal V., Goodfellow M., Jones A.L., Sutcliffe I.C.

Opinion 106 of the Judicial Commission has clarified the nomenclature of the taxon variously named Rhodococcus equi , ‘Prescottella equi’ and Rhodococcus hoagii . As a consequence, we present here the genus name Prescottella and that of its nomenclatural type species, Prescottella equi comb. nov., for valid publication and propose the reclassification of four rhodococcal species as novel combinations in the genus, namely Prescottella agglutinans Guo et al. 2015 comb. nov., Prescottella defluvii Kämpfer et al. 2014 comb. nov., Prescottella soli Li et al. 2015 comb. nov. and Prescottella subtropica Lee et al. 2019 comb. nov. In addition, we note that a clinical isolate, strain 86–07 (=W8901), likely represents an additional species within the genus Prescottella . Nearly a century after the original description of the type strain of the type species as Corynebacterium equi , we provide a stable home for Prescottella equi and its relatives.

Yushin V.V., Gliznutsa L.A., Ryss A.

Summary Ultrastructural observations of the wood-inhabiting fungal- and plant-feeding nematode, Bursaphelenchus mucronatus, revealed intracellular bacteria in the male and female gonads. In males, bacteria were present inside the testis epithelial cells, spermatocytes, spermatids and immature spermatozoa. Spermatheca of females contained amoeboid pseudopod-bearing mature spermatozoa with bacteria closely associated with the sperm nucleus. Tissues of the females studied were free from bacteria. The gram-negative bacteria in their localisation, size, ultrastructure, and especially characteristic internal bundle of parallel filaments, were identified preliminary as related to the genus Cardinium (Bacteroidetes), which includes obligate endosymbionts of diverse arthropods and is known to be associated with several species of plant-parasitic nematodes.

Guo F., Castillo P., Li C., Qing X., Li H.

Abstract A new bisexual species of Rotylenchus is described and illustrated based on morphological, morphometric and molecular characterizations. Rotylenchus zhongshanensis sp. nov. is characterized by having a conoid lip region complying with the basic pattern for Hoplolaimidae, but with pharyngeal glands slightly overlapping intestine dorsally and cuticle thickened abnormally in female tail terminus. Females have robust stylet (30.1–33.8 μm). The pharyngeal gland has short dorsal (11.2–16.8 μm) overlap on the intestine. The vulva is located at 48.0–56.5% of body length, and phasmids are pore-like, 4–6 annuli posterior to the anus. For males, phasmids are pore-like, 11–17 annuli posterior to cloaca. The spicules are ventrally arcuate (21.0–28.5 μm) with gubernaculum in 5–8 μm length. The rRNA and mitochondrial COI genes were successfully sequenced from the assembled whole-genome sequences of the new species, and were used for reconstructing the phylogenetic relationships of the new species. A new strain of cyto-endosymbiont Cardinium was also discovered from the genome sequences of R. zhongshanensis sp. nov. The 16S rRNA phylogeny analyses revealed that this new bacterial strain is closed to that from cyst and root-lesion nematodes.

Subbotin S.A., Roubtsova T.V., Bostock R.M., Tanha Maafi Z., Chizhov V.N.

Summary The Humuli group of the genus Heterodera contains species that parasitise dicotyledons and are characterised by a lemon-shaped cyst having a bifenestrate vulval cone (ambifenestrate for H. fici), long vulval slit and weak underbridge. Presently, the Humuli group includes seven species: H. amaranthusiae, H. fici, H. humuli, H. litoralis, H. ripae, H. turcomanica and H. vallicola. In this study we provided comprehensive phylogenetic analyses of COI and ITS rRNA gene sequences of species from the Humuli group using Bayesian inference, maximum likelihood, and maximum and statistical parsimony. All seven valid species from the Humuli group, one putatively new species belonging to this group and the willow cyst nematode, H. salixophila, sharing a common ancestor with the Humuli group, were analysed. Some 84 COI and 5 ITS rRNA new gene sequences from 37 nematode populations collected from 12 countries were obtained in this study. Our results confirmed that the COI gene is a powerful DNA barcoding marker for identification of populations and species from the Humuli group. Based on the results of phylogeographical analysis and age estimation of clades with a molecular clock approach, it was hypothesised that some species of the Humuli group primarily originated and diversified in Western and Middle Asian regions during the Pleistocene and Holocene periods and then dispersed from this region across the world. Two secondary diversification centres of the Humuli group were likely located in East and Southeast Asia, Russian Far East, and Oceania.

Gavriilidou A., Kautsar S.A., Zaburannyi N., Krug D., Müller R., Medema M.H., Ziemert N.

Bacterial specialized metabolites are a proven source of antibiotics and cancer therapies, but whether we have sampled all the secondary metabolite chemical diversity of cultivated bacteria is not known. We analysed ~170,000 bacterial genomes and ~47,000 metagenome assembled genomes (MAGs) using a modified BiG-SLiCE and the new clust-o-matic algorithm. We estimate that only 3% of the natural products potentially encoded in bacterial genomes have been experimentally characterized. We show that the variation in secondary metabolite biosynthetic diversity drops significantly at the genus level, identifying it as an appropriate taxonomic rank for comparison. Equal comparison of genera based on relative evolutionary distance revealed that Streptomyces bacteria encode the largest biosynthetic diversity by far, with Amycolatopsis, Kutzneria and Micromonospora also encoding substantial diversity. Finally, we find that several less-well-studied taxa, such as Weeksellaceae (Bacteroidota), Myxococcaceae (Myxococcota), Pleurocapsa and Nostocaceae (Cyanobacteria), have potential to produce highly diverse sets of secondary metabolites that warrant further investigation. A comprehensive survey of secondary metabolites encoded in bacteria identifies large differences in biosynthetic diversity among genera and pinpoints those that can be targeted for novel chemistries provisionally suitable as antimicrobials.

Rodriguez-R L.M., Konstantinidis K.T.

Genomic and metagenomic analyses are increasingly becoming commonplace in several areas of biological research, but recurrent specialized analyses are frequently reported as in-house scripts rarely available after publication. We describe the enveomics collection, a growing set of actively maintained scripts for several recurrent and specialized tasks in microbial genomics and metagenomics, and present a graphical user interface and several case studies. Our resource includes previously described as well as new algorithms such as Transformed-space Resampling In Biased Sets (TRIBS), a novel method to evaluate phylogenetic underor over-dispersion in reference sets with strong phylogenetic bias. The enveomics collection is freely available under the terms of the Artistic License 2.0 at https://github.com/lmrodriguezr/enveomics and for online analysis at http://enve-omics.ce.gatech.edu .