Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology最新文献

Duplicated carbonic anhydrase was a member of carbonic anhydrase family. The ubiquitous carbonic anhydrase (CA) plays important roles in plants. However, the role of CA in Dunaliella parva remains to be further explored. In this study, a member of the CAs family was isolated from D. parva and named DpDCA. It was transferred into D. parva by genetic engineering techniques. The carotenoid, total carbohydrate, starch, protein, and oil contents of transgenic D. parva increased by 16.31%, 31.68%, 43.97%, 52.91%, and 12.32%, compared to control. Perhaps DpDCA affected photosynthesis through cis-element. Therefore, this study lays a foundation for studying the function of DpDCA gene in D. parva.

A single novel bacterial strain designated as H23M31^T was isolated from the faecal sample of oriental stork (Ciconia boyciana) that inhabits the Republic of Korea. It was a rod-shaped, facultative anaerobic, Gram-negative, and non-motile strain. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that it branched from Aequorivita within Flavobacteriaceae. It was most closely related to A. capsosiphonis DSM 23843 ^T, which shared the sequence similarity of 96.36%. The strain exhibited optimal growth at pH 7.0 in a marine broth medium with 1% NaCl incubated at 30 °C. Chemotaxonomic characteristics indicated that the predominant cellular fatty acids were iso-C_15:0 (24.4%), iso-C_17:0 3-OH (15.9%), and anteiso-C_15:0 (13.9%). The polar lipid of the strain contained phosphatidylcholine (PC), phosphatidylglycerol (PG), and diphosphatidylglycerol (DPG). The major isoprenoid quinone was menaquinone 6 (MK-6), which was identical with that of a closely related Aequorivita species. The genomic G + C contents of the strain was 38.25 mol%. Average nucleotide identity (ANI), average amino acid identity (AAI), and digital DNA–DNA hybridization (dDDH) values between the novel isolate and A. viscosa CGMCC 1.11023 ^T were 75.83%, 80.34% and 20.50%, respectively. Phylogenetic analyses revealed the evolutionary relationships of the strain, demonstrating that the strain clusters with other Aequorivita species. Pan-genome analyses and genome comparisons indicated that, unlike other environmentally isolated species, it possesses unique genes that enhance its ability to colonise the harsh animal gut environment. Taxonomic characterisation suggested that strain H23M31^T represents a novel Aequorivita species, and the proposed name is Aequorivita ciconiae sp. nov. The type strain of A. ciconiae is H23M31^T (= KCTC 62809 ^T = JCM 33229 ^T).

A thermophilic cellulase-producing bacterium, strain HSW-8^T, isolated from hot spring waters in South Korea, was subjected to a taxonomic analysis. Cells of strain HSW-8^T were gram-stain-negative, facultatively anaerobic, rod-shaped, with optimum growth at 45 °C, pH 7.0, in the presence of 0% (w/v) NaCl. Strain HSW-8^T showed the highest 16S rRNA gene sequence similarity to Sinimarinibacterium flocculans NH6-24^T (97.52%), followed by Fontimonas thermophila DSM 23609^T (96.97%), Solimonas flava CW-KD 4^T (95.24%), and Solimonas variicoloris DSM 15731^T (95.18%). Based on 16S rRNA phylogeny, strain HSW-8^T is phylogenetically closely related to Fontimonas thermophila DSM 23609^T and Sinimarinibacterium flocculans DSM 104150^T and could be distinguished from the type species based on their phenotypic properties. The genome length of strain HSW-8^T was 3.32 Mbp with a 67.33% G + C content. The average nucleotide identity and digital DNA–DNA hybridization values between strain HSW-8^T and its closely related type strains were 75.4–83.2 and 20.2–26.2%, respectively. Summed feature 8 (C_18:1ω7c and/or C_18:1ω6c), C_16:0, and iso-C_16:0 identified the major fatty acids (> 10%). Phosphatidylglycerol and phosphatidylethanolamine were demonstrated as the major polar lipids while the respiratory quinone is ubiquinone-8. Strain HSW-8^T exhibited multiple adaptations for survival at high temperatures, including diverse potential motility mechanisms and toxin-antitoxin systems, as evidenced by both phenotypic characteristics and genomic analysis. Based on genotypic and phenotypic features, strain HSW-8^T (= KCTC 92765^T = GDMCC 1.4313^T) represents a novel Sinimarinibacterium species, in which the name Sinimarinibacterium thermocellulolyticum sp. nov. is proposed.

A Gram-staining-positive, aerobic bacterium, designated strain JJ-181 ^T, was isolated from the root surface of soybean. Based on the 16S rRNA gene sequence similarities, strain JJ-181 ^T was grouped into the genus Cohnella, most closely related to Cohnella hashimotonis F6_2S_P_1^T (98.85%) and C. ginsengisoli GR21-5 ^T (98.3%). The pairwise average nucleotide identity and digital DNA-DNA hybridisation values of the JJ-181 ^T genome assembly against publicly available Cohnella type strain genomes were below 84% and 28%, respectively. The fatty acid profile from whole cell hydrolysates, the cell wall diaminoacid, the quinone system, the polar lipid profile, and the polyamine pattern supported the allocation of strain JJ-181 ^T to the genus Cohnella. In addition, the results of physiological and biochemical tests also allowed phenotypic differentiation of strain JJ-181 ^T from its closely-related Cohnella species. Functional analysis revealed that strain JJ-181 ^T has different gene clusters related to swarming motility, chemotaxis ability, and endospore and biofilm formations. The gene content also suggests the ability of strain JJ-181 ^T to synthesise biotin and riboflavin, as well as indole-3-acetic acid, an important phytohormone for plant growth. Based on polyphasic analyses, strain JJ-181 ^T can be classified as a new species of the genus Cohnella, for which we propose the name Cohnella rhizoplanae sp. nov., with strain JJ-181 ^T (= LMG 31678 ^T = CIP 112018 ^T = CCM 9031 ^T = DSM 110650 ^T) as the type strain.

Larvae from the petroleum oil fly, Helaeomyia petrolei, live in the asphaltene and polyaromatic hydrocarbon rich asphalt seeps of Rancho La Brea, Los Angeles, California. These larvae pass high amounts of viscous asphalt through their digestive system, and their gut microbiota is exposed to these extreme conditions. Environmental stress response mechanisms can co-select for antibiotic resistance, and in the current study we used 16S rRNA and genomic sequencing along with the Comprehensive Antibiotic Resistance Database (CARD) tools to characterize antibiotic resistance profiles from six bacteria previously isolated from the oil fly larval intestinal tract, linking phenotypic and genotypic resistance profiles. The isolates contain a core set of antibiotic resistance determinants along with determinants that are rarely found in these species. Comparing these oil fly isolates to the phenotypic prevalence data generated by the CARD Resistance Gene Identifier revealed sixteen instances where the oil fly bacteria appeared to carry a resistance not seen in related taxa in the database, suggesting a novel suite of resistance families in the oil fly isolates compared to other members of the same taxa. Results highlight the functional duality of genes that simultaneously code for antibiotic resistance and survival under extreme conditions, and expand our understanding of the ecological and evolutionary role of antibiotic resistance genes in environmental habitats.

A Gram-stain-negative, aerobic, non-spore-forming, non-motile, coccus-shaped, and red-pigmented bacterial strain designated as CJ14^T was isolated from lettuce cultivation soil in Yong-In, South Korea. Strain CJ14^T grew optimally on Luria–Bertani agar at 37 ℃ and pH 7.0 in the absence of NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain CJ14^T belonged to the genus Rhodoligotrophos in the family Rhodoligotrophaceae and was closely related to Rhodoligotrophos defluvii lm1^T (98.4% similarity). The genome size of strain CJ14^T was 4.8 Mbp consisting of a single contig, and the DNA G + C content of strain CJ14^T was 61.8%. The genomic comparison of strain CJ14^T to R. defluvii lm1^T showed an average nucleotide identity value of 77.9%, and the digital DNA–DNA hybridization value was 22.4%. Genomic analyses revealed that strain CJ14^T possessed a gene cluster for ochrobactin biosynthesis, highly homologous to the siderophore gene cluster from Nitratireductor thuwali Nit1536^T. Strain CJ14^T contained ubiquinone (Q-10) as the predominant respiratory quinone. The major cellular fatty acids of strain CJ14^T were C_16:0, C_19:0 cyclo ω8c and summed feature 8. The polar lipid profile was composed of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol, one unidentified aminolipid, one unidentified glycolipid and five unidentified lipids. Based on polyphasic taxonomy study, strain CJ14^T could be classified as a novel species of the genus Rhodoligotrophos, for which the name Rhodoligotrophos ferricapiens sp. nov. is proposed. The type strain is CJ14^T (= KACC 23063^T = JCM 36057^T).

Live cultures, including Nannochloropsis oculata and Brachionus plicatilis, are essential in aquaculture due to its economic and nutritional value for commercial fish species. Pathogens and probiotics can be introduced to aquaculture systems by live feed, with variations in abundance influenced by environmental physicochemical parameters. To investigate this, amplicon sequencing of the V3-V4 region of the 16S rRNA was conducted using Illumina MiSeq to elucidate bacterial abundances and their variations in response to changes in physicochemical parameters in live feed cultures. Results revealed that pathogens like, Tenacibaculum, predominantly found in rotifer cultures, was inhibited under dissolved oxygen levels of 6.87–8.19 mg/L and pH levels of 8.63–9.23. Winogradskyella, mainly present on day 1 of the microalgae culture, thrived under these same conditions. Potential probiotics were also analyzed. Phaeodactylibacter, primarily found on day 1 of microalgae cultures, was favored by dissolved oxygen levels of 7.11–7.68 mg/L and pH levels of 8.63–9.23 but was inhibited by nitrite levels of 0.46–0.5 mg/L. Overall, dissolved oxygen was the key parameter modulating microbial diversity. This study shows that optimizing environmental parameters can enhance culture health by promoting probiotics and reducing harmful bacteria.

Four salt-tolerant and aromatics degrading strains used in this study were isolated from polluted technogenic soil on the territory of the Verkhnekamsk potash deposit (Russia). The strains were aerobic, Gram-stain-positive, non-motile, non-endospore-forming irregular rods, exhibiting a marked rod-coccus growth cycle. They contained lysine-based peptidoglycan, teichulosonic acid and poly(glycosyl phosphate) polymers in the cell walls. The major menaquinone was MK-9(H₂), the predominant fatty acids were saturated, anteiso- and iso-branched, and the major compounds of polar lipid profiles included phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol and two glycolipids (monogalactosyldiacylglycerol and dimannosylglyceride). The strains showed the highest 16S rRNA gene sequence similarity to Arthrobacter crystallopoietes (99.6–99.9%), followed by A. mangrovi (98.3–98.5%) and A. globiformis, the type species of the genus Arthrobacter (97.6–97.8%). The values of overall genome related indices (ANI, dDDH, AAI and POCP) indicated that the target strains and A. crystallopoietes represented three species within a new genus. These species clearly differed from each other and from A. mangrovi and A. globiformis in the phenotypic traits, including the peptidoglycan type and the structures and compositions of cell wall glycopolymers. Based on the findings of this study and the previously published data, we provide the description of the new genus Crystallibacter gen. nov. with the type species Crystallibacter crystallifaciens comb. nov. (type strain, VKM Ac-1107 ^T) and two newly revealed species, Crystallibacter permensis sp. nov. (type strain, B905^T = VKM Ac-2550^T = LMG 33113^T) and Crystallibacter degradans sp. nov. (type strain, SF27^T = VKM Ac-2063^T = LMG 33112^T).

Two Gram-stain-negative, aerobic, motile and short-rod-shaped bacterial strains, designated CSK15Z-1 ^T and MSK8Z-1, were isolated from branch of Kandelia candel and Rhizophora stylosa, respectively, collected from Shankou Mangrove Nature Reserve in Guangxi, China, and had the ability to produce carotenoid. The 16S rRNA gene sequence similarity, average nucleotide identity (ANI) values, amino acid identity (AAI) values, and the digital DNA-DNA hybridization (dDDH) values between the two strains indicated that they should be affiliated with the same species. The AAI values between the two strains and other related species in the family Aurantimonadaceae ranged between 61.0 and 66.6%. Phylogenetic analyses based on 16S rRNA gene sequences indicated that the two strains belong to the family Aurantimonadaceae and were most closely related to Aurantimonas endophytica EGI 6500337 ^T and Aureimonas glaciistagni PAMC 27157 ^T. Phylogenomic analysis based on genome sequences showed that the two strains formed a single and stable branch within the family Aurantimonadaceae. The major respiratory quinone was Q-10. The predominant fatty acids were C_18:1ω7c, C_19:0 cycle ω8c and C_16:0. The polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, an unidentified aminolipid and an unidentified lipid. In accordance with the AAI values, phylogenomic and phylogenetic analysis, phenotypic and chemotaxonomic characteristics, and genomic characterization, strains CSK15Z-1 ^T and MSK8Z-1 should be considered as a novel genus and species in the family Aurantimonadaceae, for which the name Mangrovibrevibacter kandeliae gen. nov. sp. nov. is proposed. The type strain is CSK15Z-1 ^T (= MCCC 1K07183^T = JCM 34923 ^T).