Characterization of Variovorax Strain C6d Isolated from the Algae-bacteria Consortia

The rhizosphere microorganisms can form beneficial, pathogenic, or neutral relationships. These relationships can promote plant growth and productivity. Among them, a number of Variovorax isolates from the rhizosphere were isolated. Bacteria Variovorax strain C6d (AB552893) was isolated from the non axenic culture of Chlorella spp., C6. The cell was Gram-negative, motile, non-spore-forming, short and rod-shaped (0.5-1.0x1.5-2.0µm). Colonies were in white colour after 7 days on 10-fold diluted Nutrient Broth. The strain was able to tolerate NaCL to 1.0% but not to 4.0% of NaCl. It grew quite well at temperatures ranging from 10°C to 37°C, yet did not show any growth at 4°C and 42°C. The dominant isoprenoid quinone was ubiquinone 8 (Q8). The major fatty acid composition of this strain was summed feature 3, 16:0 and 18:1:w7. The DNA G+C content of strain C6d was 70.4 mol%.

Chryseobacterium paridis sp. nov., an endophytic bacterial species isolated from the root of Paris polyphylla Smith var. yunnanensis

A Gram-negative, yellow-pigmented, rod-shaped bacterial strain YIM B02567 T was isolated from the root of Paris polyphylla Smith var. yunnanensis in China. Strain YIM B02567 T grew optimally at 25–30°C and at pH 7.0 in the absence of NaCl on nutrient agar. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain YIM B02567 T belong to the genus Chryseobacterium , and closely related to Chryseobacterium piperi CTM T and Chryseobacterium soli DSM 19298 T . Whole genome sequencing indicated that the genome size was 4,774,612 bp and had a DNA G+C content of 34.5 %. Values of the ANI and the dDDH between strain YIM B02567 T and its closely related Chryseobacterium species were below 81.72 % and 24.7 %. Strain YIM B02567 T contained menaquinone-6 as the sole isoprenoid quinone, anteiso-C 15:0, iso-C 17:1 ω 9 c and iso-C 17:0 3-OH as major fatty acids and phosphatidylethanolamine as major polar lipid. Based on the polyphasic analyses, strain YIM B02567 T could be differentiated genotypically and phenotypically from recognized species of the genus Chryseobacterium . The isolate therefore represents a novel species, for which the name Chryseobacterium paridis sp. nov. is proposed. The type strain is YIM B02567 T (=CGMCC 1.18657 T =JCM 5426 T ).

Exiguobacterium Sp. HA2, isolated from the Ilam Mountains of Iran

ABSTRACTA motile, Gram-stain-positive, rod-shaped, non-sporing, tolerate up to 5% NaCl, grew at 0–25 °C, designated Exiguobacterium sp. HA2 was isolated from the soil of the Ilam Mountains of Iran during October 2016. The major isoprenoid quinone is MK-7 and in the smaller amount are MK-6 and MK-8. Polar lipids included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylserine, phosphatidylinositol, phosphatidylethanolamine. Major fatty acids (>10 %) are isoC13:0, isoC15:0 and C16:0. The bacterial cell wall peptidoglycan layer was lysine-glycine. The 16S rRNA sequence was analyzed at the phylogenetic levels. Also, A supplemental comparison was made between five other genes including csp, gyrB, hsp70, rpoB, and citC. According to the results of genotypic and phenotypic characteristics, the strain was categorized in the genus Exiguobacterium. This bacterium had the closest relation with Exiguobacterium undae, and thus was dubbed Exiguobacterium sp. HA2. The different in the Phenotypic, functional characteristics and phylogenetic indicated Exiguobacterium sp. HA2 can be regarded as representing considered a novel species within the genus Exiguobacterium.

Engineering isoprenoid quinone production in yeast

Isoprenoid quinones are bioactive molecules that include an isoprenoid chain and a quinone head. They are traditionally found to be involved in primary metabolism, where they act as electron transporters, but specialized isoprenoid quinones are also produced by all domains of life. Here, we report the engineering of a baker's yeast strain, Saccharomyces cerevisiae EPYFA3, for the production of isoprenoid quinones. Our yeast strain was developed through overexpression of the shikimate pathway in a well-established recipient strain (S. cerevisiae EPY300) where the mevalonate pathway is overexpressed. As a proof of concept, our new host strain was used to overproduce the endogenous isoprenoid quinone coenzyme Q6, resulting in a final four-fold production increase. EPYFA3 represents a valuable platform for the heterologous production of high value isoprenoid quinones. EPYFA3 will also facilitate the elucidation of isoprenoid quinone biosynthetic pathways.

Sphingomonas vulcanisoli sp. nov., isolated from soil of a lava forest

A Gram-stain-negative, non-motile, yellow-pigmented and rod-shaped bacterial strain, designated SN6-13T, was isolated from soil of the Gotjawal, lava forest, located in Jeju, Republic of Korea. Cells of strain SN6-13T were oxidase- and catalase-positive. The isolate contained Q-10 as the predominant isoprenoid quinone, summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0 as the major fatty acids, sym-homospermidine as the major polyamine and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, sphingoglycolipid, ninhydrinphosphatidylglycerol and two unidentified aminophospholipids as the polar lipids. The DNA G+C content was 64.6 mol%. In phylogenetic analyses based on 16S rRNA gene sequencing, strain SN6-13T was most closely related to Sphingomonas laterariae LNB2T (95.4 % sequence similarity) and formed a separate lineage in the genus Sphingomonas. Based on phenotypic, chemotaxonomic and phylogenetic characteristics, it is concluded that strain SN6-13T represents a novel species of the genus Sphingomonas, for which the name Sphingomonas vulcanisoli sp. nov. is proposed. The type strain is SN6-13T ( = KCTC 42454T = CECT 8804T).

Solimonas terrae sp. nov., isolated from soil

A Gram-stain-negative, aerobic, motile, rod-shaped bacterium, designated strain KIS83-12T, was isolated from soil of Gaui island in the Taean region of South Korea. The strain grew at 15–33 °C (optimum, 28 °C), at pH 5.0–8.0 (optimum, pH 7.0). Growth did not occur in the presence of NaCl. The strain was catalase-negative and oxidase-positive. Phylogenetic analysis based on 16S rRNA gene sequences showed that KIS83-12T was most closely related to Solimonas soli DCY12T (96.9 %), Solimonas variicoloris MN28T (96.5 %), Solimonas flava CW-KD 4T (96.5 %) and Solimonas aquatica NAA16T (96.0 %), and formed a robust phyletic lineage with members of the genus Solimonas . The main isoprenoid quinone was Q-8. Major polar lipids included phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. Fatty acids present in large and moderate amounts (>5.0 %) were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), C16 : 0, C16 : 1ω5c, summed feature 2 (iso-C16 : 1 I and/or C14 : 0 3-OH) and C12 : 0. The DNA G+C content was 67.9 mol%. On the basis of the taxonomic data obtained in this study, KIS83-12T represents a novel species of the genus Solimonas , for which the name Solimonas terrae sp. nov. is proposed, with KIS83-12T ( = KACC 16967T = DSM 27281T) as the type strain.

Description of Actinomycetospora chibensis sp. nov., Actinomycetospora chlora sp. nov., Actinomycetospora cinnamomea sp. nov., Actinomycetospora corticicola sp. nov., Actinomycetospora lutea sp. nov., Actinomycetospora straminea sp. nov. and Actinomycetospora succinea sp. nov. and emended description of the genus Actinomycetospora

Eight actinomycete strains that form bud-like spore chains were isolated from various samples collected in Japan. Phylogenetically, the isolates formed a single clade with the type strain of Actinomycetospora chiangmaiensis according to 16S rRNA gene sequence analysis. The isolates contained meso-diaminopimelic acid, d-glutamic acid and d- and l- alanine in the cell-wall peptidoglycan, arabinose and galactose as characteristic sugars, phosphatidylcholine and phosphatidylethanolamine as diagnostic phospholipids, MK-8(H4) as the predominant isoprenoid quinone, iso-C16 : 0 as the major cellular fatty acid and DNA G+C contents of 72–74 mol%. Actinomycetospora chiangmaiensis, the type species of the genus Actinomycetospora, was also found to contain MK-8(H4) predominantly in our study, although it was earlier reported to contain MK-9(H4) as the predominant isoprenoid quinone. On the basis of the morphological, physiological, chemotaxonomic, phylogenetic and DNA–DNA hybridization data, we concluded that the isolates can be accommodated in the genus Actinomycetospora with emendation of the description of the genus and are assigned to the following seven novel species: Actinomycetospora chibensis sp. nov. (type strain TT04-21T = NBRC 103694T = KACC 14256T), Actinomycetospora chlora sp. nov. (type strain TT07I-57T = NBRC 105900T = KACC 14252T), Actinomycetospora cinnamomea sp. nov. (type strain IY07-53T = NBRC 105527T = KACC 14250T), Actinomycetospora corticicola sp. nov. (type strain 014-5T = NBRC 103689T = KACC 14253T), Actinomycetospora lutea sp. nov. (type strain TT00-04T = NBRC 103690T = KACC 14254T), Actinomycetospora straminea sp. nov. (type strain IY07-55T = NBRC 105528T = KACC 14251T) and Actinomycetospora succinea sp. nov. (type strain TT00-49T = NBRC 103691T = KACC 14255T).