A chemotaxonomic and phylogenomic re-evaluation of the genus Alicyclobacillus: A proposal for reclassification of about half of the species into the new genus, Paenalicyclobacillus gen. nov., with an emended description of the genus Alicyclobacillus, and recognition that the names Alicyclobacillus tengchongensis and Alicyclobacillus montanus are later heterotypic synonyms of Alicyclobacillus tolerans
The genus Alicyclobacillus represents a group of mostly acidophilic, meso-thermophilic bacteria, which obtained their name through the biosynthesis of uncommon, alicyclic fatty acids (FAs), i.e., ω-cyclohexyl or ω-cycloheptyl FAs. However, there are also species belonging to this genus that do not possess this trait. In addition, the difference of up to 9 % of the 16S rRNA gene sequences of 33 type strains compared with the first isolated type species, A. acidocaldarius DSM 446, exceeds the 5.5 % threshold, which is typically used for the demarcation of a genus. This suggested that the taxonomy of the genus required a re-examination. We performed a phylogenomic and chemotaxonomic survey of the genus Alicyclobacillus. Phylogenetic trees based on the 16S rRNA gene and comparison of whole proteomes reconstructed from their genomes reveal that the genus Alicyclobacillus is reflected by two distinct clades; one represented by 14 type strains with a >94.1 % 16S rRNA gene similarity to A. acidocaldarius DSM 446, and a second clade (composed of 14 type strains including A. cycloheptanicus) with a similarity of 91-94 %. This distinction fits well with their reported ability to produce alicyclic FAs, also revealed by the detection of two putative biosynthetic gene clusters (BGC) encoding their biosynthetic pathway in their genomes. The first BGC is responsible for the production of cyclohexane carboxylic acid-CoA and comprises five genes encoding proteins acting as an adjusted side branch of the shikimate pathway. The putative second BGC, responsible for production of cycloheptane carboxylic acid-CoA, comprises six genes encoding proteins acting as a side branch of the catabolic phenylacetic acid pathway. All Alicyclobacillus species of the first clade produce ω-cyclohexyl FAs and their genomes possess the corresponding BGC. In the second cluster, some species produce ω-cyclohexyl FAs, some produce ω-cycloheptyl FAs, whilst quite some members are not producing any alicyclic FAs. This corresponds to the presence or absence of the two BGCs in their genomes. We propose to reclassify all species of the second clade as members of a new genus, Paenalicyclobacillus gen. nov. and show that both Alicyclobacillus tengchongensis and Alicyclobacillus montanus are later heterotypic synonyms of Alicyclobacillus tolerans.
Chryseobacterium hilariae sp. nov., Sphingomonas larreae sp. nov., Sphingomonas astragali sp. nov., Sphingomonas radicis sp. nov., Variovorax stachyos sp. nov., Parapedobacter brassicae sp. nov., Neorhizobium descurainiae sp. nov., and Erwinia artemisiae sp. nov. isolated from dry soils revealing a diverse plant growth promoting potential
Bacteria belonging to the genera Chryseobacterium, Sphingomonas, Variovorax, Neorhizobium, Parapedobacter and Erwinia have been isolated from different soils and have also been shown to exhibit plant growth promoting (PGP) features. A polyphasic approach was employed to ascertain the taxonomic status of eight selected strains all isolated from dry soils in association with plants showing high desiccation tolerances. Based on the result of the polyphasic characterization, the following names are proposed: Chryseobacterium hilariae sp. nov., with DT-3 as the type strain (= CIP 112171 = LMG 32722 = CCM 9258); Sphingomonas astragali sp. nov., with DT-204 as the type strain (= CCM 9255 = LMG 33194 = CIP 112175); Sphingomonas radicis sp. nov., with DT-207 as the type strain (= CCM 9257 = LMG 32727 = DSM 114514); Sphingomonas larreae sp. nov., with DT-51 as the type strain (= CCM 9259 = CIP 112177 = DSM 114511 = LMG 32723); Variovorax stachyos sp. nov., with DT-64 as the type strain (= LMG 32724 = DSM 114531 = CIP 112170); Erwinia artemisiae sp. nov., with DT-104 as the type strain (CCM 9256 = LMG 32725 = DSM 114512); Parapedobacter brassicae sp. nov., with DT-150 as the type strain (LMG 32759 = DSM 115120); and Neorhizobium descurainiae sp. nov., with DT-125 as the type strain (LMG 32760 = CIP 112184).
Mycoplasma aquilae sp. nov., Mycoplasma paraquilae sp. nov., Mycoplasma haliaeeti sp. nov., Mycoplasma milvi sp. nov., and Mycoplasma razini sp. nov., isolated from predatory birds of the Accipitridae family
Mycoplasmas are regularly isolated from the upper respiratory tract of predatory birds; however, most of these Mycoplasma isolates remain unidentified. A cohort of such unidentified Mycoplasma strains (n = 42) recovered from birds of the Accipitridae family was subjected to a comprehensive taxonomic study. All strains grew well in modified Hayflick's medium, and colonies exhibited typical fried egg morphology. The strains neither produced acid from sugar carbon sources nor hydrolysed arginine or urea. Analyses of 16S rRNA gene, 16S23S intergenic spacer, and partial rpoB gene sequences placed the strains within the Mycoplasma (M.) synoviae cluster (Hominis group) with M. verecundum and M. seminis being their closest relatives. Phylogenetic trees inferred from 16S rRNA and rpoB gene sequences subdivided the 42 strains into five strain clusters. MALDI-ToF mass spectrometry allowed the differentiation of one strain group from the others but failed to distinguish the remaining four strain groups. Genome and proteome similarity metrics (ANIb, ANIm, TETRA, dDDH, AAI) and phylogenomic analysis provided solid evidence that the strains examined are indeed representatives of five hitherto unclassified species of genus Mycoplasma for which the names Mycoplasma aquilae sp. nov., Mycoplasma paraquilae sp. nov., Mycoplasma haliaeeti sp. nov., Mycoplasma milvi sp. nov., constituting the newly defined Mycoplasma aquilae complex, and Mycoplasma razini sp. nov. are proposed, with their designated type strains 1449 (ATCC BAA-1896 = DSM 22458), 654 (DSM 113738 = NCTC 14855), VS42A (DSM 113741 = NCTC 14856), Z331B (DSM 113740 = NCTC 14858), and 005V (DSM 113739 = NCTC 14838), respectively.
Natronorubrum marinum sp. nov., Natronorubrum amylolyticum sp. nov., Natronorubrum halobium sp. nov., and Natronorubrum salinum sp. nov., halophilic archaea from a coastal saline-alkali land and two saline lakes
Four novel halophilic archaeal strains, DTA7, DTA28, FCH18a, and WLHS9, were isolated from a coastal saline-alkali land and two saline lakes in China. The metagenomic analyses revealed that the coastal saline-alkali land from Dongtai tidal flat the highest relative abundance of archaea compared to the saline sediment samples of Feicui Salt Lake and Wulanhushao Salt Lake. These four strains showed high sequence similarities to current species within the genus Natronorubrum judged by 16S rRNA gene and rpoB' gene sequence similarities, and formed tight clusters with current Natronorubrum species based on the phylogenies of these two house-keeping genes. Phylogenomic analysis confirmed the phylogenies based on 16S rRNA gene and rpoB' genes. Comparative genomic analysis revealed that the average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH), and average amino acid identity (AAI) values among these four strains and existing species of the genus Natronorubrum were 76.8-92.7 %, 22.8-52.7 %, and 73.4-94.7 %, respectively. These overall genome-related indexes were significantly below the thresholds for species delineation. These four strains showed optimal growth at 1.7-3.1 M NaCl, 37 °C, and pH 7.0-9.5. Strain WLHS9 was found to be a neutrophilic halophile, while the others exhibited alkaliphilic halophilic characteristics. The major phospholipids detected in these four strains included phosphatidic acid (PA), phosphatidylglycerol (PG), and phosphatidylglycerol phosphate methyl ester (PGP-Me). The glycolipid of strain WLHS9 was identical to that of the current neutrophilic species of Natronorubrum. Based on phylogenetic analysis, phenotypic characteristics, polar lipid profiles, and phylogenomic data, strains DTA7, DTA28, FCH18a, and WLHS9 represent four novel species within the genus, namely, Natronorubrum marinum sp. nov., Natronorubrum amylolyticum sp. nov., Natronorubrum halobium sp. nov., and Natronorubrum salinum sp. nov., respectively.
Denitraticella aggregata gen. nov., sp. nov. a denitrifying benzoate-utilizing bacterium isolated from a terrestrial mud volcano
Microorganisms play a pivotal role in denitrification and in the degradation of aromatic compounds, processes essential for nitrogen and carbon recycling in diverse ecosystems. Mud volcanoes, with their fluctuating redox conditions and hydrocarbon emissions, represent potential natural sources of such microorganisms. A novel facultatively anaerobic, facultatively lithoautotrophic bacterium (strain SMB388) was isolated from terrestrial mud volcano (Krasnodar Krai, Russia). Cells of the strain were straight motile rods. Growth was observed at temperatures up to 42 °C (optimum at 30 °C), pH 6.0-10.0 (optimum at pH 8.0) and NaCl concentrations of 0-10% (w/v) (optimum at 2.0-2.5% (w/v)). The isolate grew chemolithoautotrophically with molecular hydrogen, elemental sulfur or thiosulfate as an electron donor, nitrate or oxygen as an electron acceptor and CO/HCO as a carbon source. It also grew with organic substrates such as carboxylic acids, benzoate, glycerol, propanol, yeast extract and peptone. The isolate did not utilize mono- or disaccharides. The total size of the genome of strain SMB388 was 3.4 Mb, and the genomic DNA G + C content was 64.4 mol%. Phylogenomic analysis placed SMB388 into the family Zoogloeaceae. Based on phenotypic and phylogenetic characteristics, strain SMB388 represents a novel species of the novel genus for which we propose the name Denitraticella aggregata gen. nov., sp. nov. (the type strain is SMB388 = KCTC 25769 = VKM B-3859).
Comparative genome analysis of the Sphaerotilus-Leptothrix group supports the unification of the genera Sphaerotilus and Leptothrix into a single emended genus Sphaerotilus
The Sphaerotilus-Leptothrix group comprises two genera studied for 200 years. Attempts to unite these genera were made repeatedly, but have caused controversy due to differences in phenotypic characters identified in a small number of pure cultures. According to the latest release of Genome Taxonomy Database, Sphaerotilus and Leptothrix are combined into a single genus, Sphaerotilus. In this study, we analyzed 20 high-quality genomes forming 7 clusters on a phylogenetic tree constructed from concatenated sequences of 120 conserved genes, and investigated the distribution of metabolic genes. The Sphaerotilus-Leptothrix group formed a distinct monophyletic lineage within the family Sphaerotilaceae, where Leptothrix species were distributed among Sphaerotilus species. The average amino acid identities between the Sphaerotilus-Leptothrix genomes vary from 65 to 94.21%. All analyzed genomes contained genes of glycolysis, tricarboxylic acid cycle, and glyoxylate cycle. Genes for enzymes of dissimilatory sulfur metabolism were found, including oxidation of sulfide (sqr, fccAB), thiosulfate (soxAXBYZCD), elemental sulfur (rDSR) and sulfite (soeABC). Genes for manganese oxidation (mnxG, mofABC), previously considered unique to Leptothrix, were found in a number of other representatives of the combined genus. Also, some representatives contained genes for dissimilatory nitrate reduction and nitrogen fixation; autotrophic CO₂ fixation via the Calvin cycle; potential iron oxidation (cyc2, mtoAB). The identified metabolic pathways indicate a wide range of ecological strategies and occupied niches, determined by chemoorganoheterotrophic, chemolithoautotrophic and chemolithoheterotrophic nutritional types. Thus, the data obtained from phylogenetic analysis, large-scale genome analysis and assessment of metabolic potential support the unification of the genera Sphaerotilus and Leptothrix as a single genus Sphaerotilus.
Quyinboa mangrovi gen. nov., sp. nov., Quyinboa ferrireducens sp. nov., and Quyinboa sediminis sp. nov., three novel Fe(III)-reducing and nitrogen-fixing bacteria isolated from mangrove sediment, and the proposal of Quyinboaceae fam. nov. within the class Bacteroidia
Three marine bacteria in Bacteroidales, designated FJH62, FJH65 and FJH54, were isolated from mangrove sediments at the Zhangjiang River estuary in Fujian, China. The cells were Gram-stain-negative, facultatively anaerobic, non-motile and straight to curved rod-shaped. Comparative analysis of the 16S rRNA gene showed that strains FJH62 and FJH65 shared 88.9-89.0 % identity with Saccharicrinis carchari SS12, while strain FJH54 had the maximum similarity of 88.8 % to Carboxylicivirga taeanensis MEBiC 08093. Whole-genome relatedness indices further distinguished these isolates from other relatives, falling below the established thresholds, with strains FJH62, FJH65, and FJH54 identified as three distinct novel species. Phylogenetic analysis based on both 16S rRNA gene and whole genome sequences indicated that these three novel strains form a monophyletic branch within the order Bacteroidales. These isolates were distinguished from their closest relatives by the presence of MK-10 as the major respiratory quinone and phosphatidylethanolamine, aminolipids, and phospholipids as the predominant polar lipids. The major cellular fatty acids and DNA G + C content were identified as iso-C and anteiso-C and 38.5-39.9 %, respectively. Genomic analysis and experimental validation confirmed nitrogen-fixing and Fe(III)-reducing abilities of these three strains. Based on polyphasic characterizations, these three strains represent three novel species of a novel genus, for which the names Quyinboa mangrovi gen. nov., sp. nov. (FJH62 = KCTC 102258 = MCCC 1H01534), Quyinboa ferrireducens sp. nov. (FJH65 = KCTC 102259 = MCCC 1H01536), and Quyinboa sediminis sp. nov. (FJH54 = KCTC 102257 = MCCC 1H01535) are proposed. Furthermore, a novel family, Quyinboaceae fam. nov., is proposed within the order Bacteroidales.
Genome insights into Hydrogenophaga taeniospiralis and its R-body genetic determinants
The genome of Hydrogenophaga taeniospiralis 2K1, the type and only strain of the species, was analysed. The genes encoding elements involved in autotrophic and chemolithotrophic growth that oxidize H in addition to other metabolic traits, such as potential nitrogen fixation capability, are described. A phylogenomic analysis of the taxonomy of members of the genus reveals a high number of species not yet described in the genus, especially if the numerous metagenomes obtained from environmental samples are included. The differences from the closest related genera, Malikia and Serpentinimonas, are highlighted and the delineation of the genus Hydrogenophaga is discussed based on phylogenomic analysis. Furthermore, a survey of metagenomes available in public databases demonstrates the wide environmental and geographic distribution of Hydrogenophaga strains. H. taeniospiralis 2K1 is the first free-living bacterium described for its ability to synthesize R- bodies, which are intracytoplasmic extendable protein ribbons associated mainly with toxic effects. The genetic determinants of R-body synthesis are analysed and compared with those found in other Hydrogenophaga genomes and strains from other genera.
Metagenome-assembled genomes reveal Pseudogracilibacillus amylolyticus sp. nov., a functional uncultured microorganism in high-temperature Daqu
Daqu, a traditional fermentation starter for Chinese liquor production, harbors a complex microbial community that plays a pivotal role in shaping the flavor and quality of the final product of Baijiu. This study characterized three metagenome-assembled genomes (MAGs) from high-temperature Daqu of Jiang-flavor Baijiu, revealing a novel taxon within the genus Pseudogracilibacillus. Phylogenomic analysis demonstrated that three MAGs (A3-12A_bin_9, M2-6-2A_bin_27 and M2-7-9A_bin_18) formed a distinct monophyletic clade, supported by the threshold value of ANI recommended for bacterial species, while showing significant divergence from other related type species within the genus Pseudogracilibacillus. Functional annotation revealed the metabolic versatility of this taxon, including starch and aromatic compound degradation (potentially contributing to flavor formation), biosynthetic capacity and adaptive traits such as oxidative phosphorylation flexibility and ABC transporter diversity, underscoring its ecological role in Daqu fermentation. Based on genomic and phylogenetic characteristics, these MAGs should be classified as representing a new taxon of this genus, for which the name Pseudogracilibacillus amylolyticus sp. nov. is proposed following the rules of the published Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode). This discovery expands the diversity of the family Bacillaceae in Baijiu fermentation and provides insights into the functional potential of uncultured microbes in traditional food ecosystems.
Characterization and description of plant-growth-promoting methanotrophic bacteria belonging to the genus of Methylocaldum
Arid soil microbiomes present untapped resources of microbial diversity. Here, we describe twelve isolates, all belonging to the Methylocaldum genus. Based on metagenomic studies, the isolates represent the major clades of methanotrophic bacteria inhabiting the arid biomes of Southern California, comprising up to 0.03 % of the total soil microbiota. Phenotyping of isolates indicates that they are obligate methanotrophic bacteria, some capable of methanol utilization. All strains can fix nitrogen, use nitrate and ammonia as a N-source, and have key genetic signatures of autotrophy, methylotrophy, and NO assimilation. Based on the 16S rRNA phylogeny and whole -genome analyses, all strains are assigned to the species M. gracile. Three isolates from the rhizosphere of native Californian plants (Strains 0917, YM2 and S3V3) and GT1B-W are set apart from the other M. gracile strains, despite sharing <98 % of average nucleotide identity. Microbes isolated from plant rhizosphere display 150 unique genetic features and a series of tandem gene duplications predicted to contribute to their interactions with plants, including the 20-gene polyketide biosynthesis cluster and the TRAP C4-dicarboxylate transport system. Consistent with the genetic properties that may indicate an enhancement of plant-cooperation functions, the rhizosphere isolates support the survival of plants, Boechera depauperata and Arabidopsis thaliana, under drought conditions. Based on genetic and phenotypic characteristics, we propose to designate strains 0917, YM2, S3V3, and GT1B-W as a new subspecies of Methylocaldum gracile - Methylocaldum gracile subspecies dēsertum, L.n. dēsertum - a desert, to represent the native habitat of the species. The amended description of the M.gracile species is provided.
Peijinzhouia sedimentorum gen. Nov., sp. nov., isolated from polymetallic nodule fields of the Eastern Pacific, and proposal of the family Peijinzhouiaceae fam. Nov
Deep-sea polymetallic nodules represent an important but unexploited resource of a wide range of critical metals, which indicates huge economic and scientific value. During an investigation in the bacterial diversity in the polymetallic nodule fields of the Eastern Pacific, strain EPR-FJ-38 was isolated and characterized. Another strain SYC-11 was obtained from seawater sample of South China Sea. Strains EPR-FJ-38 and SYC-11 showed the highest similarity to Fulvivirga imtechensis SW1-E11 (89.6 %, family Fulvivirgaceae), followed by Marinoscillum luteum SJP7 (89.3 %, family Reichenbachiellaceae), Fulvivirga imtechensis AK7 (89.3 %), Fulvivirga sediminis 2943 (89.0 %) and Marivirga tractuosa DSM 4126 (89.0 %, family Marivirgaceae). Results of phylogenomic analysis showed that the strains EPR-FJ-38 and SYC-11 form an independent branch separated from the family Cyclobacteriaceae. The AAI value between EPR-FJ-38 and the reference strains was 46.0-53.3 %. Phenotypic, physiological, chemotaxonomic, genotypic properties and phylogenetic relationship indicate that strains EPR-FJ-38 and SYC-11 possibly represents a novel family belonging to the Cytophagales order, for which the named Peijinzhouiaceae fam. Nov. is proposed. The genus and species of the Peijinzhouiaceae is Peijinzhouia sedimentorum sp. nov. (type strain EPR-FJ-38, MCCC M28192 = KCTC 92505). In addition, two strains showed resistance and removal ability to Mn and possessed biomineralization function, whereas microbes create an alkaline environment by carbonic anhydrase to form rhodochrosite. This study proposed a novel family belonging to the Cytophagales order and presents potential candidates for bioremediation in deep-sea environments.
Natronocytophaga cellulosiphila, gen. nov., sp. nov., and Marinimicrobium hydrolyticum sp. nov., aerobic haloalkaliphilic bacteria of a cellulose-mineralizing consortium from soda lakes
Aerobic enrichments with three forms of insoluble cellulose at moderate salinity from soda lakes in southwestern Siberia selected a binary consortium consisting of a primary cellulolotrophic bacteroidetes and its gammaproteobacterial hemicellulolytic partner. The bacteroidetes strain ABcell3 was separated in pure culture from colonies formed in soft agar with amorphous cellulose, while the gammaproteobacterial satellite, strain ABcell2, was selectively purified using glucomannan instead of cellulose. ABcell3 was identified as a new-genus lineage in the family Cytophagaceae, and ABcell2 formed a new species within the genus Marinimicrobium (family Cellvibrionaceae). ABcell3 is characterized by a complex cell morphogenesis with young cells as long flexible rods with gliding motility turning into cyst-like refractive circles. It is a highly-specialized cellulotroph, growing best with various forms of native celluloses and less actively on xyloglucan and cellobiose. ABcell2 is a motile vibrio forming yellow pigment. It has a broad-range hydrolytic potential, growing with various glucans (but not cellulose) and sugars. Its function as a saccharolytic scavenger was confirmed by a successful reconstitution of the binary consortium on cellulose. Both bacteria are aerobic, moderately salt-tolerant alkaliphiles, growing optimally at 0.4-0.8 M total Na as carbonates and pH 9.0-9.5. Functional genome analysis of strain ABcell3 identified fourteen gene copies for potential cellulases from the GH families 5_1/5_2, 9 and 8. The genome of ABcell2 also contains four GH9 cellulase genes but none of the others. Instead, multiple copies of different GH5 subfamilies were present with a potential hemicellulose substrate specificity. Based on phenotypic characteristics and results of phylogenomic analysis, strain ABcell3 is proposed as a new genus and species Natronocytophaga cellulosiphila (DSM 115919 = UQM 41578), and strain ABcell2 - as Marinimicrobium hydrolyticum sp. nov. (DSM 115774 = JCM 35976).
Isolation of diverse Undibacterium-related strains from alpine lakes and re-examining the taxonomic status of this genus
The genus Undibacterium is an important member of Oxalobacteraceae and most species of this genus were isolated from freshwater environments. The recent study based on the genomic analyses revised the taxonomic status of 23 Undibacterium species and proposed that these species should be assigned into four genera (Undibacterium, Neoundibacterium, Affinundibacterium and Paraundibacterium), respectively. During the investigation of microbial resources inhabited in alpine lakes from the southwestern China in 2023, 25 strains show the highest 16S rRNA gene sequence similarities with Undibacterium species were isolated. Utilizing the genomes of these 25 strains and 26 Undibacterium species, the phylogenies among these strains are reconstructed based on the core and pan-genome, respectively. The phylogenomic trees show that the 26 Undibacterium species should be divided into six clades and each clade should represent an independent genus. As the clades 2, 3, 4 and 5 proposed in this study have been revised in other study, the genera Cognatundibacterium and Pseudundibacterium are proposed in this study to accommodate the clades 1 and 6, respectively. The detailed genomic annotations reveal that all the 25 isolated Undibacterium-related strains harbor complete amino acids metabolisms and genes encoding DNA replication and repair, homologous recombination proteins, two-component and phosphate transport systems in response to the oligotrophic, high UV radiation and phosphorus-limited environments of alpine lakes. This study clarifies the role of Undibacterium-related strains in alpine lakes and demonstrates that isolating more strains is of great benefit to the bacterial taxonomy.
Genomic insights into Izemobacterium crustae gen. nov., sp. nov., reveal metabolic adaptations for persistence in the oceanic crust
Subsurface environments are often conceptualized as static ecosystems governed by slow processes and persistent energy scarcity, reinforcing the notion that microbial life is largely inactive or maintained in a state of metabolic dormancy. Yet mounting evidence suggests that the subseafloor crustal biosphere is more dynamic, shaped by hydrothermal circulation, fluid-rock interactions, and steep, fluctuating redox gradients. These processes create transient phases of increased energy supply that can sustain ecologically significant microbial activity. To better understand the metabolic strategies enabling survival under these conditions, we investigated the genomic and physiological potential of a spore-forming bacterium, strain JdFR-1ᵀ, enriched from crustal fluids of the Juan de Fuca Ridge. Its genome encodes traits associated with survival and metabolic maintenance under extreme resource limitation, including pathways for sporulation and germination, fermentative and hydrolytic metabolism, and scavenging of organic substrates. These features suggest a capacity to alternate between dormancy and metabolic activity in response to environmental fluctuations. Strain JdFR-1ᵀ represents a new lineage within the Izemoplasmataceae family, for which we propose the name Izemobacterium crustae gen. nov., sp. nov., in accordance with the SeqCode rules. Together, these findings provide genomic evidence for potential adaptive strategies that enable persistence and energy-efficient metabolism in the deep oceanic crustal biosphere.
Genomic characterization of Gillisia xinjiangensis sp. nov.: insights into nitrogen metabolism, stress adaptation, and application potential
High-altitude saline lakes host distinctive microbial communities characterized by specialized adaptations to extreme environmental conditions. However, the underlying mechanisms enabling bacterial survival and physiological function in these habitats remain largely unexplored. In this study, a novel Gram-stain-negative, non-motile, rod-shaped bacterium, designated strain Q332, was isolated from sediment samples collected from Achikkul Lake, a high-altitude saline lake in Xinjiang, northwestern China. The strain was facultatively aerobic, and grew optimally at 28 °C, pH 7.0, and 3.0 % (w/v) NaCl. Catalase and oxidase activities were positive. Major fatty acids identified in strain Q332 included anteiso-C, anteiso-C, iso-C and C. The primary respiratory quinone detected was menaquinone-6 (MK-6). Polar lipid analyses identified phosphatidylethanolamine (PE), one unidentified acyloxyacyl phosphatidylglycerol (APGL), three unidentified lipids (L), three glycolipids (GL), one phospholipid (PL), and four amidolipids (AL). The genomic DNA G + C content is 38.9 %. Genomic characterization revealed a versatile metabolic repertoire, including unique C1-unit metabolic pathways and comprehensive nitrogen cycling capabilities, notably denitrification and assimilatory nitrate reduction. Furthermore, strain Q332 displayed robust mechanisms for stress adaptation, encompassing tolerance to cold and osmotic stress, defenses against oxidative stress, and resistance to heavy metals. Based on phenotypic, chemotaxonomic, phylogenetic, and genomic features, strain Q332 is considered to represent a novel species of the genus Gillisia, for which the name Gillisia xinjiangensis sp. nov. is proposed. The type strain is Q332 (=KCTC 102200 = MCCC 1K09490).
A practical guide on environmental genomics for prokaryotic systematics
Environmental shotgun sequencing can provide great insight into microbial community profiles, functional capabilities, and the recovery of metagenome-assembled genomes (MAGs) which represent individual microbiome members. Similarly, assembly of single-cell amplified genomes (SAGs) is possible through advances in microfluidics and sequencing techniques. These fields have experienced tremendous growth in the amount of data produced, the ongoing development of analytical tools, and ultimately, the number of genomes recovered lacking valid names. As most microbes are uncultivable and therefore incompatible with traditional naming requirements, sequence databases are filled with genomes of varying quality and without standardized nomenclature, hindering communication and data usability. Overcoming these limitations, the recently introduced Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode) includes genome quality criteria and nomenclature standards to validly name uncultivated prokaryotes based on DNA sequence. Metagenomics and systematics can be overwhelming fields for new users, so here we provide a guide to help clarify topics and point out special considerations. These topics include metagenomic pipelines, genome quality assessment criteria, followed by taxonomy and trait prediction tools. Next, we cover source metadata, methods for abundance and occupancy measurement, and lastly, nomenclature and name registration. Community efforts to generate high-quality prokaryotic genomes with thorough descriptions and valid names are crucial for the future usability and communication of environmental genomic data.
BISMiS Live: a digital platform for global communication among microbial systematists
BISMiS Live, launched on March 20, 2021, emerged as a timely response to the disruption caused by the CoViD-19 pandemic, offering a global virtual platform for discourse in microbial systematics. Spearheaded by the Bergey's International Society for Microbial Systematics (BISMiS), this monthly webinar series hosted renowned experts and engaged thousands of participants across 84 countries. The initiative emphasized inclusivity, scientific depth, and digital accessibility, with sessions archived on YouTube (@BISMiS_) for broader impact. Behind each event lies a dedicated team managing speaker coordination, technical execution, and global outreach. BISMiS Live has grown into an educational resource, integrated into university curricula and inspiring the next generation of microbial taxonomists. With suggestions for future innovation, such as student lightning talks, thematic series, and podcast formats, the platform is poised to evolve further. BISMiS Live stands as a digital bridge connecting systematists worldwide, sustaining knowledge exchange and community through innovation and collaboration.
Carnimonas bestiolae sp. nov. and Cernens ardua gen. nov., sp. nov.: new halotolerant bacteria from the invasive solitary bee Megachile sculpturalis
Fifteen isolates from gut samples of the invasive solitary bee Megachile sculpturalis remained unidentified after matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis. Phylogenomic and overall genome relatedness indices analyses of five representative isolates demonstrated that 14 isolates represented a novel Carnimonas species for which we propose the name Carnimonas bestiolae sp. nov., with LMG 33810 as the type strain. A single isolate represented a distinct lineage within the Halomonadaceae family with the genera Carnimonas and Halotalea as nearest neighbor taxa and is classified as Cernens ardua gen. nov., sp. nov., with LMG 33818 as the type strain. Comparative genomic analysis and physiological characterization revealed functional differences between C. bestiolae, Ce. ardua and established Carnimonas and Halotalea species in central metabolism, fatty acid metabolism, and osmoregulatory pathways, the latter being consistent with adaptation to a saline environment. A reanalysis of previously published insect microbiome studies in which Carnimonas was reported, revealed 16S rRNA amplicon sequence variants with >99 % identity to C. bestiolae LMG 33810 16S rRNA in gut samples of Megachile sculpturalis, Anthidium florentinum, and the psyllid Leptynoptera sulfurea. In contrast, 16S rRNA amplicon sequence variants corresponding to Ce. ardua were rarely detected and only at low relative abundances, suggesting a transient association with the insect gut.
Altererythrobacter guangdongensis sp. nov. and Tsuneonella sediminis sp. nov., two novel carotenoid-producing species isolated from tidal flat sediment
Four aerobic, Gram-stain-negative, rod-shaped, and non-motile bacterial strains, designated SYSU HZ0097ᵀ, SYSU HZ0136, SYSU LHT278ᵀ, and SYSU LHT272, were isolated from tidal flat sediment collected in Zhuhai, China. Phylogenetic analysis based on 16S rRNA gene sequences assigned all four strains to the family Erythrobacteraceae. Strains SYSU HZ0097ᵀ and SYSU HZ0136 showed the highest 16S rRNA gene sequence similarity (98.6 %) to Altererythrobacter epoxidivorans CGMCC 1.7731ᵀ, while SYSU LHT278ᵀ and SYSU LHT272 were most closely related (98.5 %) to Tsuneonella litorea KCTC 82812ᵀ. Whole-genome comparisons, including average nucleotide identity (ANI < 85.0 %) and digital DNA-DNA hybridization (dDDH <30.0 %), supported their assignment to two distinct species. All isolates contained ubiquinone-10 (Q-10) as the predominant respiratory quinone, and the major fatty acids (>10 %) were Cω7c and Cω6c. The polar lipid profiles included phosphatidylglycerol, phosphatidylethanolamine, and an unidentified glycolipid. The colonies exhibited yellow pigmentation, and genes associated with carotenoid biosynthesis (crtB, crtI) were identified in their genomes. Based on phylogenetic, genomic, phenotypic, and chemotaxonomic characteristics, strains SYSU HZ0097ᵀ and SYSU HZ0136 represent a new species of the genus Altererythrobacter, for which the name Altererythrobacter guangdongensis sp. nov. is proposed (type strain SYSU HZ0097ᵀ = MCCC 1K09423ᵀ = KCTC 8714ᵀ). Strains SYSU LHT278ᵀ and SYSU LHT272 represent a new species of the genus Tsuneonella, for which the name Tsuneonella sediminis sp. nov. is proposed (type strain SYSU LHT278ᵀ = MCCC 1K09543ᵀ = KCTC 8862ᵀ).
Taxonomic and metabolic diversity of microbial communities in a thermal water stream in Uzbekistan and proposal of two new classes of uncultivated bacteria, Desulfocorpusculia class. nov. and Tepidihabitantia class. nov., named following the rules of SeqCode
Thermal ecosystems in Uzbekistan remain poorly characterized, particularly through culture-independent approaches. In this study, we performed 16S rRNA gene metabarcoding and metagenomic sequencing of microbial communities from a hot stream formed by the discharge of thermal artesian groundwater in the Navoiy region. The taxonomic composition of microbial communities varied with temperature and sample type, with the phylum Chloroflexota abundant in most samples. Members of Aquificota, Deinococcota, and Thermotogota dominated in sediments with temperatures around 60 °C, while Desulfobacterota and Cyanobacteriota were more abundant at lower temperatures. Metagenomic sequencing of the microbial community in sediment under orange-brown mat (54 °C) revealed a dominance of the phyla Chloroflexota, Armatimonadota, Aquificota, Ignavibacteriota, Desulfobacterota and Bacteroidota. Metagenomic data indicated that fermentation, aerobic degradation of organic matter, hydrogen oxidation, and sulfur cycling are the main metabolic processes. Two high-quality metagenome-assembled genomes (MAGs) were described as novel taxa named following the rules of SeqCode. Genome analysis suggests that both organisms are heterotrophic anaerobes capable of sulfate reduction or fermentation. We provide the description of Desulfocorpusculum asiaticum gen. nov., sp. nov. affiliated with the novel family Desulfocorpusculaceae fam. nov., order Desulfocorpusculales ord. nov. and class Desulfocorpusculia class. nov.; and the description of the new species and genus Tepidihabitans asiaticus gen. nov., sp. nov. affiliated with the novel family Tepidihabitantaceae fam. nov., order Tepidihabitantales ord. nov. and class Tepidihabitantia class. nov.
Erratum to "Polyphasic taxonomic description of Streptomyces tritrimontium sp. nov., actinomycetes isolated from moonmilk in Szczelina Chochołowska cave of Tatra Mountains in Poland and emended descriptions of Streptomyces manipurensis Nimaichand et al. 2021 and Streptomyces nojiriensis Ishida et al. 1967" [Syst. Appl. Microbiol. 48 (2025) 126627]
