Schauerella fraxinea gen. nov., sp. nov., a bacterial species that colonises ash trees tolerant to dieback caused by Hymenoscyphus fraxineus

The tolerance of ash trees against the pathogen Hymenoscyphus fraxineus seems to be associated with the occurrence of specific microbial taxa on leaves. A group of bacterial isolates, primarily identified on tolerant trees, was investigated with regard to their taxonomic classification and their potential to suppress the ash dieback pathogen. Examination of OGRI values revealed a separate species position. A phylogenomic analysis, based on orthologous and marker genes, indicated a separate genus position along with the species Achromobacter aestuarii. Furthermore, analysis of the ratio of average nucleotide identities and genome alignment fractions demonstrated genomic dissimilarities typically observed for inter-genera comparisons within this family. As a result of these investigations, the strains are considered to represent a separate species within a new genus, for which the name Schauerella fraxinea gen. nov., sp. nov. is proposed, with the type strain B3P038T (=LMG 33092 T = DSM 115926 T). Additionally, a reclassification of the species Achromobacter aestuarii as Schauerella aestuarii comb. nov. is proposed. In a co-cultivation assay, the strains were able to inhibit the growth of a H. fraxineus strain. Accordingly, a functional analysis of the genome of S. fraxinea B3P038T revealed genes mediating the production of antifungal substances. This potential, combined with the prevalent presence in the phyllosphere of tolerant ash trees, makes this group interesting for an inoculation experiment with the aim of controlling the pathogen in an integrative approach. For future field trials, a strain-specific qPCR system was developed to establish an efficient method for monitoring the inoculation success.

Luteimonas suaedae sp. nov., a novel bacterium isolated from rhizosphere of Suaeda aralocaspica (Bunge) Freitag & Schütze

Light yellowish-white colonies of a bacterial strain, designated LNNU 24178T, were isolated from the rhizosphere soil of halophyte Suaeda aralocaspica (Bunge) Freitag and Schütze grown at Shihezi district, Xinjiang, PR China. Cells were Gram-stain-negative, non-flagellum-forming, rod-shaped and non-motile. The results of phylogenetic analysis based on the 16S rRNA gene sequence indicated that LNNU 24178T represented a member of the genus Luteimonas and shared the highest sequence similarity with Luteimonas yindakuii CGMCC 1.13927T (97.1 %) and lower sequence similarity (< 97.0 %) to other known species. The genomic DNA G+C content of LNNU 24178T was 68.8 %. The average nucleotide identity (ANI) values between LNNU 24178T and Luteimonas yindakuii CGMCC 1.13927T, Luteimonas mephitis DSM 12574T, Luteimonas arsenica 26-35T and Luteimonas huabeiensis HB2T were 78.7, 78.6, 78.4 and 80.0 %, respectively. The digital DNA-DNA hybridisation (dDDH) values between LNNU 24178T and L. yindakuii CGMCC 1.13927T, L. mephitis DSM 12574T, L. arsenica 26-35T and L. huabeiensis HB2T were 22.0, 22.3, 22.2 and 23.5 %, respectively. The respiratory quinone detected in LNNU 24178T was ubiquinone-8 (Q-8). The major fatty acids (> 5.0 %) of LNNU 24178T were identified as iso-C15 : 0 (33.9 %), iso-C17 : 0 (8.7 %), iso-C11 : 0 (6.2 %), iso-C16 : 0 (5.7 %), C16 : 0 (5.3 %) and summed feature 9 (iso-C17 : 1ω9c/10-methyl C16 : 0) (21.1 %). The major polar lipids of LNNU 24178T were diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylethanolamine (PE), one unidentified phospholipid (PL), one unidentified glycolipid (GL) and three unidentified lipids. According to the data obtained from phenotypic, chemotaxonomic and phylogenetic analyses, strain LNNU 24178T represents a novel species of the genus Luteimonas, for which the name Luteimonas suaedae sp. nov. is proposed, with LNNU 24178T (= CGMCC 1.17331T= KCTC 62251T) as the type strain.

De novo evolution of macroscopic multicellularity

While early multicellular lineages necessarily started out as relatively simple groups of cells, little is known about how they became Darwinian entities capable of sustained multicellular evolution1-3. Here we investigate this with a multicellularity long-term evolution experiment, selecting for larger group size in the snowflake yeast (Saccharomyces cerevisiae) model system. Given the historical importance of oxygen limitation4, our ongoing experiment consists of three metabolic treatments5-anaerobic, obligately aerobic and mixotrophic yeast. After 600 rounds of selection, snowflake yeast in the anaerobic treatment group evolved to be macroscopic, becoming around 2 × 104 times larger (approximately mm scale) and about 104-fold more biophysically tough, while retaining a clonal multicellular life cycle. This occurred through biophysical adaptation-evolution of increasingly elongate cells that initially reduced the strain of cellular packing and then facilitated branch entanglements that enabled groups of cells to stay together even after many cellular bonds fracture. By contrast, snowflake yeast competing for low oxygen5 remained microscopic, evolving to be only around sixfold larger, underscoring the critical role of oxygen levels in the evolution of multicellular size. Together, this research provides unique insights into an ongoing evolutionary transition in individuality, showing how simple groups of cells overcome fundamental biophysical limitations through gradual, yet sustained, multicellular evolution.

Luteimonas deserti sp. nov., a novel strain isolated from desert soil

A Gram-stain-negative, non-motile, rod-shaped bacterial strain, named SJ-16^T, was isolated from desert soil collected in Inner Mongolia, northern PR China. Strain SJ-16^T grew at pH 6.0-11.0 (optimum, pH 8.0-9.0), 4-40 °C (optimum, 30-35 °C) and in the presence of 0-8 % (w/v) NaCl (optimum, 0-2 %). The strain was negative for catalase and positive for oxidase. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain SJ-16^T clustered with Luteimonas chenhongjianii 100111^T and Luteimonas terrae THG-MD21^T, and had 98.8, 98.6, 98.3 and <97.9 % of 16S rRNA gene sequence similarity to strains L. chenhongjianii 100111^T, L. terrae THG-MD21^T, L. aestuarii B9^T and all other type strains of the genus Luteimonas, respectively. The major cellular fatty acids were iso-C_15 : 0, iso-C_16 : 0, summed feature 3 (C_16 : 1  ω7c and/or C_16 : 1  ω6c) and summed feature 9 (C_16 : 0 10-methyl and/or iso-C_17 : 1  ω9c). Diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine were the major polar lipids, and ubiquinone-8 was the only respiratory quinone. The genomic DNA G+C content was 69.3 mol%. The digital DNA-DNA hybridization and average nucleotide identity values of strain SJ-16^T to L. chenhongjianii 100111^T, L. terrae THG-MD21^T, L. rhizosphaerae 4-12^T and L. aestuarii B9^T were 36.9, 37.5, 24.0 and 21.1 %, and 80.9, 80.6, 80.7 and 76.3 %, respectively. Based on phenotypic, physiological and phylogenetic results, strain SJ-16^T represents a novel species of the genus Luteimonas, for which the name Luteimonas deserti is proposed. The type strain is SJ-16^T (=CGMCC 1.17694^T=KCTC 82207^T).

Luteimonas wenzhouensis Sp. Nov., A Chitinolytic Bacterium Isolated from a Landfill Soil

A Gram-staining-negative, aerobic, non-motile, rod-shaped bacterium with degradation ability of chitin, designated strain YD-1 ^T, was isolated from landfill soil sample collected in Wenzhou, Zhejiang province, China. The growth of strain YD-1 ^T occurred optimally in the tryptone soy broth (TSB) with 1.0% NaCl at pH 7.0-8.0, 30 °C. Ubiquinone-8 (Q-8) was the predominant quinone. The polar lipids of strain YD-1 ^T consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, five glycolipids and four lipids. The major fatty acids were iso-C_15:0 (30.7%), iso-C_17:1ω9c (23.2%), iso-C_11:0 (18.9%), iso-C_11:0 3-OH (6.8%) and iso-C_17:0 (5.9%). Phylogenetic analysis based on the 16S rRNA gene sequences indicated that strain YD-1 ^T was affiliated to the genus Luteimonas with the highest similarity to Luteimonas marina KCTC 12327 ^T (97.3%), followed by Luteimonas aquatica DSM 22088 ^T (96.5%) and Luteimonas composti CCUG 53595 ^T (96.4%). The genomic DNA G + C content of strain YD-1 ^T was 71.8 mol%. Average nucleotide identity (ANI) and the digital DNA-DNA hybridizations (dDDH) for draft genomes between strain YD-1 ^T and Luteimonas marina KCTC 12327 ^T were 82.7% and 26.1%, respectively. On the basis of genotypic, phenotypic and chemotaxonomic data, strain YD-1 ^T is considered to represent a novel species to degrade chitin in the genus Luteimonas, for which the name Luteimonas wenzhouensis sp. nov. is proposed, with YD-1 ^T (= KCTC 72425 ^T = CCTCC AB 2019153 ^T) as the type strain.

Luteimonas chenhongjianii, a novel species isolated from rectal contents of Tibetan Plateau pika (Ochotona curzoniae)

Two Gram-stain-negative, strictly aerobic, bright-yellow-pigmented and rod-shaped bacteria (strains 100069 and 100111^T) with a single polar flagellum were isolated from the rectal contents of plateau pika (Ochotona curzoniae). Based on the results of nearly full-length 16S rRNA gene sequence and phylogenetic analyses, strains 100069 and 100111^T belong to the genus Luteimonas, and are closest to Luteimonas rhizosphaerae 4-12^T (98.02 % similarity), Luteimonas aestuarii B9^T (97.8 %) and Luteimonas terrae THG-MD21^T (97.74 %). The DNA G+C contents of these two isolates were 68.30 mol% and 68.29 mol%, respectively. The highest average nucleotide identity (ANI) value between strain 100111^T and its closely related species was 83.34 %, well below the threshold of 95-96 %. The major cellular fatty acids were iso-C_11 : 0, iso-C_15 : 0 and iso-C_17 : 1  ω9. Polar lipid content was dominated by diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified phospholipid and an unidentified lipid. Ubiquinone-8 (Q-8) was the predominant respiratory quinone. These two isolates grew optimally at 35-37 °C, pH 7.0-8.0 and with 1.0 % (w/v) NaCl. The results of ANI analysis and other characteristics obtained from our polyphasic study showed that strains 100069 and 100111^T represent a novel species in genus Luteimonas, for which the name Luteimonas chenhongjianii sp. nov. (type strain 100111^T=DSM 104077^T=CGMCC 1.16429^T) is proposed.

Luteimonas granuli sp. nov., Isolated from Granules of the Wastewater Treatment Plant

A Gram-reaction negative, aerobic, non-motile, light yellow colored, and rod-shaped bacterium (designated Gr-4^T) isolated from granules of a wastewater treatment plant, was characterized by a polyphasic approach to clarify its taxonomic position. Strain Gr-4^T was observed to grew optimally at 30 ºC and at pH 7.0 on R2A medium. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain Gr-4^T belongs to the genus Luteimonas of the family Xanthomonadaceae and was most closely related to Luteimonas padinae CDR SL 15^T (99.1%), Luteimonas terricola DSM 22344^T (98.5%) and Luteimonas arsenica 26-35^T (97.6). The genome comprises 2,917,404 bp with a G+C content of 70.5 mol%. The ANI value between strain Gr-4^T and Luteimonas padinae CDR SL 15^T was 87.3%. The DNA-DNA relatedness value between strain Gr-4^T and Luteimonas padinae CDR SL 15^T, Luteimonas terricola DSM 22344^T was 36.4 ± 1.3% and 14.2 ± 1.7%, respectively. The predominant quinone was Q-8. The major fatty acids were iso-C_15:0, iso-C_16:0 and summed feature 9 (comprising iso-C_17:1ω9c and/or C_16:0 10-methyl) supported the affiliation of strain Gr-4^T to the genus Luteimonas. Moreover, the physiological, biochemical results, and low level of ANI and DNA-DNA relatedness value allowed the phenotypic and genotypic differentiation of strains Gr-4^T from other Luteimonas species with validly published names. The novel isolate therefore represents a novel species, for which the name Luteimonas granuli sp. nov. is proposed, with the type strain Gr-4^T (=KACC 16614^T = JCM 18203^T).

Luteimonas gilva sp. nov., isolated from farmland soil

A Gram-stain-negative, rod-shaped bacterium, strain H23^T, was isolated from farmland soil sampled in Enshi City, Hubei Province, PR China. The isolate grew optimally at 28-32 °C, pH 8.0 and with 0.5 % (w/v) NaCl. Based on the results of 16S rRNA gene sequence and phylogenetic analyses, strain H23^T belonged to the genus Luteimonas with the highest degree of 16S rRNA gene sequence similarity to Luteimonas cucumeris Y4^T (97.41 %). The DNA G+C content was 65.88 mol%. The average nucleotide identity and the Genome-to-Genome Distance Calculator results also showed low relatedness (below 95 and 70 %, respectively) between strain H23^T and type strains in the genus Luteimonas. Ubiquinone-8 was the predominant quinone. The major fatty acids were iso-C_15 : 0, iso-C_16 : 0, iso-C_17 : 0 and iso-C_17 : 1 ω9c. Polar lipids were dominated by diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and unidentified phospholipids. Low digital DNA-DNA hybridization values, as well as physiological and biochemical differences, such as no casein hydrolysis, being catalase-negative, and tesing positive for cystine arylamidase, α-chymotrypsin and N-acetyl-β-glucosaminidase, could distinguish strain H23^T from its closely related species. Strain H23^T is considered to represent a novel species in the genus Luteimonas, for which the name Luteimonas gilva sp. nov. is proposed, with strain H23^T (=CCTCC AB 2019255^T=KCTC 72593^T) as the type strain.

Luteimonas yindakuii sp. nov. isolated from the leaves of Dandelion (Taraxacum officinale) on the Qinghai-Tibetan Plateau

Two strains (S-1072^T and 1626) of Gram-stain-negative, oxidase- and catalase-positive, aerobic, rod-shaped, motile bacteria with a single polar flagellum, were isolated from the leaves of Dandelion (Taraxacum officinale) on the Qinghai-Tibet Plateau of China. The cells grew optimally at 28 °C, pH 7.0 and with 0.5 % (w/v) NaCl on brain-heart infusion agar. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strains S-1072^T and 1626 belong to the genus Luteimonas, sharing the highest similarity with Luteimonas arsenica CCTCC AB 2014326^T (97.0 %), Luteimonas terricola CGMCC 1.8985^T (96.9 %) and Luteimonas aestuarii KCTC 22048^T (96.6 %). The phylogenomic tree indicated that strains S-1072^T and 1626 were most closely related to Luteimonas abyssi CGMCC 1.12611^T. The biochemical characteristics revealed that strains S-1072^T and 1626 could neither produce trypsin nor produce acid from d-glucose, N-acetylglucosamine and maltose, distinguishing them from four closest relatives. The DNA G+C contents of strains S-1072^T and 1626 were 69.2 and 69.3 mol% respectively. The digital DNA-DNA hybridization values of our isolates with their four closely related species were below the 70 % threshold. The predominant menaquinone was Q-8 (98.7 %) and the major polar lipids included diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The major fatty acids (>10 %) were iso-C_15 : 0, iso-C_16 : 0 and summed feature 9 (10-methyl C_16 : 0 and/or iso-C_17 : 1 ω9c). Based on the data obtained, strains S-1072^T and 1626 should be classified as a novel species of the genus Luteimonas, for which the name Luteimonas yindakuii sp. nov. is proposed. The type strain is S-1072^T (=CGMCC 1.13927^T=JCM 33487^T).

Luteimonas lumbrici sp. nov., a novel bacterium isolated from wormcast

A Gram-stain-negative, yellow-green bacterium, designated 1.1416^T, was isolated from wormcast of Eisenia foetida. The strain was non-motile, rod-shaped, and grew optimally on NA medium at 30 °C, pH 7.0 and with 0 % (w/v) NaCl. On the basis of the 16S rRNA gene sequence and phylogenetic analysis, 1.1416^T showed the highest degree of 16S rRNA gene sequence similarity to Luteimonas arsenica 26-35^T (96.2 %), followed by Luteimonas lutimaris G3^T (96.1 %). The respiratory quinone of 1.1416^T was ubiquinone-8 (Q-8), and its major cellular fatty acids were iso-C_15 : 0 (39.8 %), summed feature 9 (iso-C_17 : 1  ω9c or C_16 : 0 10-methyl) (18.6 %). The major polar lipids of 1.1416^T were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and six unidentified phospholipids. The genomic DNA G+C content of 1.1416^T was 71.0 mol%. According to the results of the phenotypic and chemotaxonomic phylogenetic analyses, strain 1.1416^T represents a novel species of the genus Luteimonas, for which the name Luteimonas lumbrici sp. nov. is proposed, with strain 1.1416^T (=KCTC 62979^T=CCTCC AB 2018348^T) as the type strain.

Ahniella affigens gen. nov., sp. nov., a gammaproteobacterium isolated from sandy soil near a stream

A bacterial strain, designated D13^T, was isolated from sandy soil near a stream in Sinan-gun, Republic of Korea. Cells were Gram-stain-negative, aerobic, non-motile and flexible rod-shaped. Growth occurred at 15-35 °C (optimum 30 °C) and pH 6.5-8.0 (pH 7.0). NaCl was not obligatory for growth but could be tolerated at up to 0.5 % (w/v) NaCl. The DNA G+C content of the genomic DNA of strain D13^T was 57.7 mol% and a phylogenetic analysis of the 16S rRNA gene sequence revealed that strain D13^T formed a distinct evolutionary lineage within the family Rhodanobacteraceae of the order Lysobacterales. Strain D13^T showed highest 16S rRNA sequence similarity to Lysobacter hankyongensis KTCe-2^T (92.7 %), followed by Luteimonas cucumeris Y4^T (92.7 %), Dyella japonica XD53^T (92.6 %) and Aquimonas voraii GPTSA 20^T (92.5 %). The major cellular fatty acids (>10 % of the total) were iso-C16 : 0, iso-C15 : 0 and summed feature 9 (iso-C17 : 1ω9с and/or C16 : 0 10-methyl). The respiratory quinone was ubiquinone-8 and the major polar lipids of the isolate consisted of phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and phosphatidylmonomethylethanolamine. Based on polyphasic analysis, strain D13^T could be differentiated from other genera in the family Rhodanobacteraceae, which suggests that strain D13^T represents a novel species of a new genus in the family Rhodanobacteraceae, for which the name Ahniella affigens gen. nov., sp. nov. is proposed. The type strain is D13^T (=KACC 19270^T=JCM 31634^T).

Polybacterial community analysis in human conjunctiva through 16S rRNA gene libraries

The conjunctival sac of healthy human harbours a variety of microorganisms. When the eye is compromised, an occasional inadvertent spread happens to the adjacent tissue, resulting in bacterial ocular infections. Microbiological investigation of the conjunctival swab is one of the broadly used modality to study the aetiological agent of conjunctiva. However, most of the time such methods yield unsatisfactory results. Hence, the present study intends to identify the bacterial community in human conjunctiva of pre-operative subjects through 16S rRNA gene libraries. Out of 45 samples collected from preoperative patients undergoing cataract surgery, 36 libraries were constructed with bacterial nested-PCR-positive samples. The representative clones with unique restriction pattern were generated through Amplified Ribosomal DNA Restriction Analysis (ARDRA) which were sequenced for phylogenetic affiliation. A total of 211 representative clones were obtained which were distributed in phyla Actinobacteria, Firmicutes, α-Proteobacteria, β-Proteobacteria, γ-Proteobacteria, Bacteroidetes, and Deinococcus-Thermus. Findings revealed the presence of polybacterial community, especially in some cases even though no bacterium or a single bacterium alone was identified through cultivable method. Remarkably, we identified 17 species which have never been reported in any ocular infections. The sequencing data reported 6 unidentified bacteria suggesting the possibility of novel organisms in the sample. Since, polybacterial community has been identified consisting of both gram positive and gram negative bacteria, a broad spectrum antibiotic therapy is advisable to the patients who are undergoing cataract surgery. Consolidated effort would significantly improve a clear understanding of the nature of microbial community in the human conjunctiva which will promote administration of appropriate antibiotic regimen and also help in the development of oligonucleotide probes to screen the predominant pathogens for early predisposition.

Niabella hibiscisoli sp. nov., isolated from soil of a Rose of Sharon garden

A Gram-stain-negative, strictly aerobic, non-motile, rod-shaped and yellow-pigmented bacterium, designated strain THG-DN5.5T, was isolated from soil of a Rose of Sharon garden in Daejeon, South Korea. According to 16S rRNA gene sequence comparisons, strain THG-DN5.5T was found to be most closely related to Niabella yanshanensis CCBAU 05354T (97.7 % sequence similarity), Niabella ginsengisoli GR10-1T (97.0 %), 'Niabella terrae' ICM 1-15 (96.0 %), Niabella soli DSM 19437T (95.7 %) and Niabella aquatica RP-2T (95.6 %). The DNA-DNA relatedness between strain THG-DN5.5T and its phylogenetically closest neighbours was below 50.0 %. The DNA G+C content was 43.1 mol%. The major polar lipid of strain THG-DN5.5T was found to be phosphatidylethanolamine. The major fatty acids were identified as C16 : 0, iso-C15 : 0, iso-C15 : 1 G, and iso-C17 : 0 3-OH. MK-7 was the only menaquinone present. These data supported the affiliation of strain THG-DN5.5T to the genus Niabella. Strain THG-DN5.5T was distinguished from related species of the genus Niabellaby physiological and biochemical tests. In conclusion, strain THG-DN5.5T represents a novel species of the genus Niabella, for which the name Niabella hibiscisolisp. nov. is proposed. The type strain is THG-DN5.5T (=KACC 18857T=CCTCC AB 2016086T).