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

A rhizosphere strain, Achromobacter insolitus LCu2, was isolated from alfalfa (Medicago sativa L.) roots. It was able to degrade of 50% glyphosate as the sole phosphorus source, and was found resistant to 10 mM copper (II) chloride, and 5 mM glyphosate–copper complexes. Inoculation of alfalfa seedlings and potato microplants with strain LCu2 promoted plant growth by 30–50%. In inoculated plants, the toxicity of the glyphosate–copper complexes to alfalfa seedlings was decreased, as compared with the noninoculated controls. The genome of A. insolitus LCu2 consisted of one circular chromosome (6,428,890 bp) and encoded 5843 protein genes and 76 RNA genes. Polyphasic taxonomic analysis showed that A. insolitus LCu2 was closely related to A. insolitus DSM23807^T on the basis of the average nucleotide identity of the genomes of 22 type strains and the multilocus sequence analysis. Genome analysis revealed genes putatively responsible for (1) plant growth promotion (osmolyte, siderophore, and 1-aminocyclopropane-1-carboxylate deaminase biosynthesis and auxin metabolism); (2) degradation of organophosphonates (glyphosate oxidoreductase and multiple phn clusters responsible for the transport, regulation and C–P lyase cleavage of phosphonates); and (3) tolerance to copper and other heavy metals, effected by the CopAB–CueO system, responsible for the oxidation of copper (I) in the periplasm, and by the efflux Cus system. The putative catabolic pathways involved in the breakdown of phosphonates are predicted. A. insolitus LCu2 is promising in the production of crops and the remediation of soils contaminated with organophosphonates and heavy metals.

Bacteria of the phylum Planctomycetota have received much attention over the years due to their unique cell biology and potential for biotechnological application. Within the phylum, bacteria of the class Phycisphaerae have been found in a multitude of environmental datasets. However, only a few species have been brought into culture so far and even enrichments are scarce. Therefore, very little is known about their lifestyle, which has hindered efforts to estimate their environmental relevance. Here, we analysed all medium- and high-quality Phycisphaerae genomes represented in the genome taxonomy database to learn more about their physiology. We combined automatic and manual annotation efforts to provide a bird’s eye view of their diverse energy metabolisms. Contrasting previous reports, we did not find indications for the presence of genes for anaerobic ammonium oxidation in any Phycisphaerae genome. Instead, we found that many members of this class are adapted to a facultative anaerobic or strictly fermentative lifestyle and may be specialized in the breakdown of carbon compounds produced by other organisms. Based on these findings, we provide a practical overview of organic carbon substrates predicted to be utilized by Phycisphaerae families.

This study represents the first analysis of the bacterial community in chickens affected by swollen head syndrome, utilizing 16S rRNA gene sequencing. Samples were obtained from clinical laying chickens and were examined for the presence of Avibacterium paragallinarum (APG) and Ornithobacterium rhinotracheale (ORT) using conventional polymerase chain reaction (PCR). From the samples, five APG-positive (APG) and APG-negative (N-APG) samples were chosen, along with five specific pathogen-free chickens, for 16S rRNA gene sequencing. Results showed that APG and ORT were widely detected in the chicken samples with swollen head syndrome (SHS, 9/10), while APG was detected in all five specific pathogen-free (SPF) samples. In contrast, conventional PCR sensitivity was found to be inadequate for diagnosis, with only 35.7% (5/14) and 11.1% (1/9) sensitivity for APG and ORT, respectively, based on 16S rRNA gene sequencing data. Furthermore, 16S rRNA gene sequencing was able to quantify the bacteria in the samples, revealing that the relative abundance of APG in the APG group ranged from 2.7 to 81.3%, while the relative abundance of APG in the N-APG group ranged from 0.1 to 21.0%. Notably, a low level of APG was also detected in all 5 SPF samples. The study also identified a significant number of animal and human common bacterial pathogens, including but not limited to Gallibacterium anatis, Riemerella columbina, Enterococcus cecorum, Mycoplasma synoviae, Helicobacter hepaticus, and Staphylococcus lentus. In conclusion, 16S rRNA gene sequencing is a valuable tool for bacterial pathogen diagnosis and the discovery of novel bacterial pathogens, while conventional PCR is not reliable for diagnosis.

Two novel Gram-stain-negative, aerobic, and non-motile strains, designated FZY0004^T and YYF002^T, were isolated from an agar-degrading co-culture, which was obtained from seawater of the intertidal zone of Yancheng City, the Yellow Sea of China. Strain FZY0004^T optimally grew at 28 °C, pH 7.0, and 2–6% NaCl, while strain YYF002^T optimally grew at 28 °C, pH 7.5, and 2–4% NaCl. Strain FZY0004^T possessed Q-9 as the major respiratory quinone, and its major fatty acids (> 10%) were summed feature 8 (C_18:1 ω7c), C_16:0, and summed feature 3 (C_16:1 ω7c/C_16:1 ω6c). The polar lipids identified in strain FZY0004^T were phosphatidylethanolamine (PE), phosphatidylglycerol (PG), and several unidentified phospholipids (PL) and lipids (L). On the other hand, strain YYF002^T had MK-6 as the predominant respiratory quinone and its major fatty acids consisted of iso-C_15:0, iso-C_15:1 G, and iso-C_15:0 3-OH. The polar lipids identified in strain YYF002^T were aminolipid (AL), PE, and several unidentified lipids. Strain FZY0004^T shared 99.5% 16S rRNA gene sequence similarity and 90.1% average nucleotide identity (ANI) with T. povalilytica Zumi 95^T, and strain YYF002^T shared 99.2% 16S rRNA gene sequence similarity and 88.2% ANI with W. poriferorum JCM 12885^T. The genomic DNA G + C contents of strains FZY0004^T and YYF002^T were 54.5% and 33.5%, respectively. The phylogenetic, phenotypic, and physiological characteristics permitted the distinction of the two strains from their neighbors, and we thus propose the names Thalassospira aquimaris sp. nov. (type strain FZY0004^T = JCM 35895^T = MCCC 1K08380^T) and Winogradskyella marincola sp. nov. (type strain YYF002^T = JCM 35950^T = MCCC 1K08382^T).

An isolate of a Gram-positive, strictly aerobic, motile, rod-shaped, endospore forming bacterium was originally isolated from soil when screening and bioprospecting for plant beneficial microorganisms. Phylogenetic analysis of the 16S rRNA gene sequences indicated that this strain was closely related to Lysinibacillus fusiformis NRRL NRS-350^T (99.7%) and Lysinibacillus sphaericus NRRL B-23268^T (99.2%). In phenotypic characterization, the novel strain was found to grow between 10 and 45 °C and tolerate up to 8% (w/v) NaCl. Furthermore, the strain grew in media with pH 5 to 10 (optimal growth at pH 7.0). The predominant cellular fatty acids were observed to be iso-C_15: 0 (52.3%), anteiso-C_15: 0 (14.8%), C_16:1ω7C alcohol (11.2%), and C_16: 0 (9.5%). The cell-wall peptidoglycan contained lysine-aspartic acid, the same as congeners. A draft genome was assembled and the DNA G+C content was determined to be 37.1% (mol content). A phylogenomic analysis on the core genome of the new strain and 5 closest type strains of Lysinibacillus revealed this strain formed a distinct monophyletic clade with the nearest neighbor being Lysinibacillus fusiformis. DNA–DNA relatedness studies using in silico DNA–DNA hybridizations (DDH) showed this species was below the species threshold of 70%. Based upon the consensus of phylogenetic and phenotypic analyses, we conclude that this strain represents a novel species within the genus Lysinibacillus, for which the name Lysinibacillus pinottii sp. nov. is proposed, with type strain PB211^T (= NRRL B-65672^T, = CCUG 77181^T).

A novel Gram-negative, white-pigmented, and auxin-producing strain, 20NA77.5^T, was isolated from fresh water during cyanobacterial bloom period. Pairwise comparison of the 16S rRNA gene sequences showed that strain 20NA77.5^T belonged to the genus Undibacterium and exhibited the highest sequence similarity to the type strains of Undibacterium danionis (98.00%), Undibacterium baiyunense (97.93%), Undibacterium macrobrachii (97.92%), and Undibacterium fentianense (97.71%). The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between strain 20NA77.5^T and its related type strains were below 79.93 and 23.80%, respectively. The predominant fatty acids (> 10% of the total fatty acids) were C_16:0 and summed feature 3 (C_16:1ω7c and/or C_16:1ω6c). The genomic DNA G + C content of strain 20NA77.5^T was found to be 48.61%. Based on the phylogenetic distinctness, chemotaxonomic features, and phenotypic features, strain 20NA77.5^T is considered to represent a novel species of the genus Undibacterium, for which the name Undibacterium cyanobacteriorum sp. nov is proposed. The type strain is 20NA77.5^T (= KCTC 8005^T = LMG 33136^T).

Strain C29^T, a Gram-staining-negative, straight rod occurring singly, in pairs or short chains, was isolated from floating filamentous biomass of the Uruguay River. The strain was catalase and oxidase positive, chemoorganotrophic, strictly aerobic, non-motile, and grew at pH 6.0–9.0, 15–45 °C, and 0–0.5% (w/v) NaCl. Polyhydroxybutyrate was accumulated in nutrient-limited conditions. Phylogenetic analysis based on the 16S rRNA gene revealed that strain C29^T had the highest sequence similarity with Leptothrix discophora SS-1^T (97.82%), Ideonella livida TBM-1^T (97.82%), Vitreoscilla filiformis L1401-2^T (97.52%), Sphaerotilus sulfidivorans D-501^T (97.50%) and Sphaerotilus natans DSM 6575^T (97.46%). Other type strains with validly published names had similarities below 97.46%. Further phylogenomic analysis showed that strain C29^T was affiliated to the family Sphaerotilaceae. Average nucleotide identity (ANI) and in silico DNA–DNA hybridization (dDDH) values with its phylogenetic relatives were lower than 91 and 41%, respectively, revealing that strain C29^T represented a new species. The DNA G + C content of strain C29^T was 70.9%. The annotation of the genome of the novel strain shows it possessed genes for the degradation of aromatic compounds. It also contained genes that encode sigma factors involved in response regulation of stress resistance, which is an important function for adaptation and survival in natural niches. Based on the results of the phylogenetic and phenotypic analyses, we propose that strain C29^T represents a novel species, for which the name Sphaerotilus uruguayifluvii sp. nov. is proposed. The type strain is C29^T (= CCM 9043^T = DSM 113250^T).

A Gram–staining–negative, facultative aerobic, motile strain, designated strain ZSDE20^T, was isolated from the surface seawater of Qingdao offshore. Phylogenetic analysis of the 16S rRNA gene of strain ZSDE20^T, affiliated it to the genus Photobacterium. It was closely related to Photobacterium lutimaris DF-42 ^T (98.92% 16S rRNA gene sequence similarity). Growth occurred at 4-28ºC (optimum 28ºC), pH 1.0–7.0 (optimum 7.0) and in the presence of 1–7% (w/v) NaCl (optimum 3%). The dominant fatty acids were summed feature 3 (C16:1 ω7c or/and C16:1 ω6c, 34.23%), summed feature 8 (C18:1 ω7c and C18:1 ω6c, 10.36%) and C16:0 (20.05%). The polar lipids of strain ZSDE20^T comprised phosphatidylethanolamine, phosphatidylcholine, lyso-phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol dimannoside, phosphatidylinositol mannosides and two unknown lipids. The major respiratory quinone was ubiquinone-8 (Q-8). The DNA G + C content of strain ZSDE20^T was 45.6 mol%. Average nucleotide identity (ANI) values between ZSDE20^T and its reference species were lower than the threshold for species delineation (95–96%); in silico DNA-DNA hybridization further showed that strain ZSDE20^T had less than 70% similarity to its relatives. Based on the polyphasic evidences, strain ZSDE20^T is proposed as representing a novel species of the genus Photobacterium, for which the name Photobacterium pectinilyticum sp. nov. is proposed. The type strain is ZSDE20^T (= MCCC 1K06283^T = KCTC 82885 ^T).

An aerobic, Gram-stain-negative bacterium, designated as SYSU D00382^T, was sourced from soil of Gurbantunggut Desert, PR China. The strain was short-rod-shaped, oxidase-positive and catalase-negative, with yellow-colored, convex, round, and smooth colonies on TSA plate. Growth and proliferation occurred at 4–37 °C (optimal: 28–30 °C), pH 5.0–8.0 (optimal: pH 6.0–7.0) and NaCl concentration of 0–2.5% (optimal: 0–0.5%). The 16S rRNA gene based phylogenetic assessment showed that SYSU D00382^T belonged to the genus Pedobacter, and was most closely related to Pedobacter ginsengisoli Gsoil 104^T with similarity of 97.7%. The genomic DNA G+C content of SYSU D00382^T was 46.4%. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between SYSU D00382^T and P. ginsengisoli Gsoil 104^T were 75.7% and 17.5%, respectively. The main polar lipid was phosphatidylethanolamine. The major fatty acids (> 5%) were iso-C_15:0, iso-C_17:0 3-OH, summed features 3 and 9. The sole respiratory quinone identified was MK-7. The phylogeny based on 16S rRNA gene and whole-genome sequences revealed that SYSU D00382^T formed a robust lineage with P. ginsengisoli Gsoil 104^T. Based on phenotypic, phylogenetic and genotypic data, a novel specie named Pedobacter deserti sp. nov. is proposed. The type strain is SYSU D00382^T (= CGMCC 1.18627^T = MCCC 1K04972^T = KCTC 82279^T).