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Archives of Microbiology Jun 2024Ten strains of psychrotolerant methylotrophic bacteria were isolated from the samples collected in Larsemann and Bunger Hills (Antarctica). Most of the isolates are...
Ten strains of psychrotolerant methylotrophic bacteria were isolated from the samples collected in Larsemann and Bunger Hills (Antarctica). Most of the isolates are assigned to the genus Pseudomonas, representatives of the genera Janthinobacterium, Massilia, Methylotenera and Flavobacterium were also found. Majority of isolates were able to grow on a wide range of sugars, methylamines and other substrates. Optimal growth temperatures for the isolated strains varied from 6 °C to 28 °C. The optimal concentration of NaCl was 0.5-2.0%. The optimal pH values of the medium were 6-7. It was found that three strains synthesized indole-3-acetic acid on a medium with L-tryptophan reaching 11-12 μg/ml. The values of intracellular carbohydrates in several strains exceeded 50 μg/ml. Presence of calcium-dependent and lanthanum-dependent methanol dehydrogenase have been shown for some isolates. Strains xBan7, xBan20, xBan37, xBan49, xPrg27, xPrg48, xPrg51 showed the presence of free amino acids. Bioprospection of Earth cryosphere for such microorganisms has a potential in biotechnology.
Topics: Antarctic Regions; Biotechnology; Phylogeny; Indoleacetic Acids; Methylobacteriaceae; Hydrogen-Ion Concentration; RNA, Ribosomal, 16S; Cold Temperature; Sodium Chloride; Culture Media; Tryptophan
PubMed: 38907777
DOI: 10.1007/s00203-024-04056-7 -
Antonie Van Leeuwenhoek Jun 2024Two novel Gram-stain-negative strains designated P7 and P8, were isolated from the soil of a paddy field in Goyang, Republic of Korea, and identified as new species...
Two novel Gram-stain-negative strains designated P7 and P8, were isolated from the soil of a paddy field in Goyang, Republic of Korea, and identified as new species within the genus Roseateles through a polyphasic taxonomic approach. These aerobic, rod-shaped, non-sporulating strains demonstrated optimal growth at 30 °C, pH 7, and in the absence of NaCl (0% w/v). Phylogenetic analysis based on 16S rRNA gene sequences indicated close relationships with Roseateles saccharophilus DSM654 (98.7%) and Roseateles puraquae CCUG 52769 (98.96%), respectively. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the isolates with the most closely related strains with publicly available whole genomes were 82.0-85.5% and 25.0-30.2%, respectively. The predominant fatty acids identified were C and summed feature 3 (composed of C ω6c and/or C ω7c), with minor amounts of C, C 3-OH and summed feature 8 (composed of C ω7c and/or C ω6c; 26.4%). Ubiquinone 8 was the main quinone, and the polar lipid profile included phosphatidylethanolamine, phosphatidylglycerol, two unidentified phosphoaminolipids, one unidentified phosphoglycolipid, three unidentified phospholipids, and one unidentified aminolipid. The draft genome sequences revealed genomic DNA G + C contents of 70.1% for P7 and 68.2% for P8. Comprehensive physiological, biochemical, and 16S rRNA sequence analyses confirm these isolates as novel species of the genus Roseateles, proposed to be named Roseateles caseinilyticus sp. nov for strain P7 (= KACC 22504 = TBRC 15694) and Roseateles cellulosilyticus sp. nov. for strain P8 (= KACC 22505 = TBRC 15695).
Topics: Soil Microbiology; Phylogeny; RNA, Ribosomal, 16S; Oryza; DNA, Bacterial; Fatty Acids; Base Composition; Republic of Korea; Bacterial Typing Techniques; Methylobacteriaceae; Nucleic Acid Hybridization; Phospholipids; Sequence Analysis, DNA
PubMed: 38833203
DOI: 10.1007/s10482-024-01988-4 -
Antonie Van Leeuwenhoek May 2024An aerobic, Gram-stain-negative, motile rod bacterium, designated as SYSU BS000021, was isolated from a black soil sample in Harbin, Heilongjiang province, China....
An aerobic, Gram-stain-negative, motile rod bacterium, designated as SYSU BS000021, was isolated from a black soil sample in Harbin, Heilongjiang province, China. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate belongs to the genus Methylobacterium, and showed the highest sequence similarity to Methylobacterium segetis KCTC 62267 (98.51%) and Methylobacterium oxalidis DSM 24028 (97.79%). Growth occurred at 20-37℃ (optimum, 28 °C), pH 6.0-8.0 (optimum, pH 7.0) and in the presence of 0% (w/v) NaCl. Polar lipids comprised of phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, one unidentified aminolipid and one unidentified polar lipid. The major cellular fatty acids (> 5%) were C and C ω7c and/or C ω6c. The predominant respiratory quinone was Q-10. The genomic G + C content was 68.36% based on the whole genome analysis. The average nucleotide identity (≤ 83.5%) and digital DNA-DNA hybridization (≤ 27.3%) values between strain SYSU BS000021 and other members of the genus Methylobacterium were all lower than the threshold values recommended for distinguishing novel prokaryotic species. Based on the results of phenotypic, chemotaxonomic and phylogenetic analyses, strain SYSU BS000021 represents a novel species of the genus Methylobacterium, for which the name Methylobacterium nigriterrae sp. nov. is proposed. The type strain of the proposed novel species is SYSU BS000021 (= GDMCC 1.3814 = KCTC 8051).
Topics: Soil Microbiology; Phylogeny; RNA, Ribosomal, 16S; DNA, Bacterial; Base Composition; Fatty Acids; Methylobacterium; Bacterial Typing Techniques; China; Nucleic Acid Hybridization; Sequence Analysis, DNA; Phospholipids
PubMed: 38806744
DOI: 10.1007/s10482-024-01981-x -
International Journal of Systematic and... May 2024Two strictly aerobic and rod-shaped bacteria, labelled as DB1703 and DB2414S, were obtained from an automobile air conditioning system. Strain DB1703 was...
Two strictly aerobic and rod-shaped bacteria, labelled as DB1703 and DB2414S, were obtained from an automobile air conditioning system. Strain DB1703 was Gram-stain-negative, while strain DB2414S was Gram-stain-positive. Both strains were catalase-positive and oxidase-negative. Strains DB1703 and DB2414S were able to grow at 18-42 °C. Strain DB1703 grew within a NaCl range of 0-3 % and a pH range of 6.0-8.0; while strain DB2414S grew at 0-1 % and pH 6.5-8.5. The phylogenetic and 16S rRNA gene sequence analysis indicated that strains DB1703 and DB2414S belonged to the genera and , respectively. Strain DB1703 showed the closest phylogenetic similarity to YIM 100770 (94.8 %), whereas strain DB2414S was most closely related to ATCC BAA-1496 (97.7 %). The genome sizes of strains DB1703 and DB2414S were 4 652 148 and 4 282 418 bp, respectively, with DNA G+C contents of 68.8 and 70.5 mol%, respectively. Chemotaxonomic data showed Q-10 as the sole ubiquinone in DB1703 and ML-8 (H4) in DB2414S. The predominant cellular fatty acid in DB1703 was summed feature 8 (C 7 and/or C 6), whereas iso-C, C 8, and iso-C were dominant in DB2414S. Overall, the polyphasic taxonomic comparisons showed that strains DB1703 and DB2414S were distinct from their closest taxa and represent novel species within the genera and , respectively. Accordingly, we propose the names sp. nov., with the type strain DB1703 (=KCTC 72724=NBRC 114759), and sp. nov., with the type strain DB2414S (=KCTC 49355=NBRC 114620).
Topics: Phylogeny; Base Composition; Fatty Acids; RNA, Ribosomal, 16S; DNA, Bacterial; Bacterial Typing Techniques; Sequence Analysis, DNA; Air Conditioning; Ubiquinone; Automobiles; Republic of Korea
PubMed: 38743058
DOI: 10.1099/ijsem.0.006383 -
Animals : An Open Access Journal From... Apr 2024The gut microbiome significantly influences the health and productivity of silkworms (), the cornerstone of sericulture. With the increasing use of cost-effective...
The gut microbiome significantly influences the health and productivity of silkworms (), the cornerstone of sericulture. With the increasing use of cost-effective artificial diets in sericulture, it is crucial to understand how these diets impact the silkworm gut microbiomes. Here we employed 16S rRNA sequencing to delineate the impact of three distinct dietary regimens on the silkworm gut microbiomes: exclusive mulberry leaf diet (SY), exclusive artificial feed diet (SL), and a sequential transition from artificial feed to mulberry leaves (ZS). Our results unveiled stark differences in microbial diversity across the groups, with the ZS group displaying an intermediary complexity. LefSe and random forest analyses identified Methylobacteriaceae, , and as significantly enriched in the ZS group, suggesting their potential to facilitate silkworms' adaptation to dietary transitions. Functional profiling revealed differential pathway regulation, indicating a metabolic reconfiguration in response to dietary modulations. Notably, the enrichment of and in both the SL and ZS groups highlights their potential as probiotics in artificial diets. Our findings provide insights into the diet adaptation mechanisms of silkworm gut microbiota, paving the way for harnessing the intestinal bacteria to enhance silkworm health and silk production through targeted microbial interventions in sericulture practices.
PubMed: 38731265
DOI: 10.3390/ani14091261 -
Journal of Hazardous Materials Jun 2024Microcystis typically forms colonies under natural conditions, which contributes to occurrence and prevalence of algal blooms. The colonies consist of Microcystis and...
Dissolved organic matter, calcium ion and extracellular polymeric substances on living associated bacteria of Microcystis colony are crucial for unicellular Microcystis to efficiently form colonies.
Microcystis typically forms colonies under natural conditions, which contributes to occurrence and prevalence of algal blooms. The colonies consist of Microcystis and associated bacteria (AB), embedded in extracellular polymeric substances (EPS). Previous studies indicate that AB can induce Microcystis to form colonies, however the efficiency is generally low and results in a uniform morphotype. In this study, by using filtrated natural water, several AB strains induced unicellular M. aeruginosa to form colonies resembling several Microcystis morphotypes. The mechanisms were investigated with Methylobacterium sp. Z5. Ca was necessary for Z5 to induce Microcystis to form colonies, while dissolved organic matters (DOM) facilitated AB to agglomerate Microcystis to form large colonies. EPS of living Z5, mainly the aromatic protein components, played a key role in colony induction. Z5 initially aggregated Microcystis via the bridging effects of Ca and DOM, followed by the induction of EPS synthesis and secretion in Microcystis. In this process, the colony forming mode shifted from cell adhesion to a combination of cell adhesion and cell division. Intriguingly, Z5 drove the genomic rearrangement of Microcystis by upregulating some transposase genes. This study unveiled a novel mechanism about Microcystis colony formation and identified a new driver of Microcystis genomic evolution.
Topics: Microcystis; Calcium; Extracellular Polymeric Substance Matrix; Methylobacterium
PubMed: 38677120
DOI: 10.1016/j.jhazmat.2024.134352 -
PloS One 2024Assessing the microbes present on tree fruit carpospheres as the fruit enters postharvest processing could have useful applications, as these microbes could have a major...
Assessing the microbes present on tree fruit carpospheres as the fruit enters postharvest processing could have useful applications, as these microbes could have a major influence on spoilage, food safety, verification of packing process controls, or other aspects of processing. The goal of this study was to establish a baseline profile of bacterial communities associated with apple (pome fruit), peach (stone fruit), and Navel orange (citrus fruit) at harvest. We found that commercial peaches had the greatest bacterial richness followed by oranges then apples. Time of harvest significantly changed bacterial diversity in oranges and peaches, but not apples. Shifts in diversity varied by fruit type, where 70% of the variability in beta diversity on the apple carposphere was driven by the gain and loss of species (i.e., nestedness). The peach and orange carposphere bacterial community shifts were driven by nearly an even split between turnover (species replacement) and nestedness. We identified a small core microbiome for apples across and between growing seasons that included only Methylobacteriaceae and Sphingomonadaceae among the samples, while peaches had a larger core microbiome composed of five bacterial families: Bacillaceae, Geodermtophilaceae, Nocardioidaceae, Micrococcaeceae, and Trueperaceae. There was a relatively diverse core microbiome for oranges that shared all the families present on apples and peaches, except for Trueperaceae, but also included an additional nine bacterial families not shared including Oxalobacteraceae, Cytophagaceae, and Comamonadaceae. Overall, our findings illustrate the important temporal dynamics of bacterial communities found on major commercial tree fruit, but also the core bacterial families that constantly remain with both implications being important entering postharvest packing and processing.
Topics: Humans; Prunus persica; Seasons; Bacteria; Citrus sinensis; Fruit
PubMed: 38625898
DOI: 10.1371/journal.pone.0297453 -
Chemosphere Mar 2024The increasing concern for environmental remediation has led to a search for effective methods to remove eutrophic nutrients. In this study, Methylobacterium gregans...
The increasing concern for environmental remediation has led to a search for effective methods to remove eutrophic nutrients. In this study, Methylobacterium gregans DC-1 was utilized to improve nitrogen removal in a sequencing batch biofilm reactor (SBBR) via aerobic denitrification. This bacterium has the extraordinary characteristics of strong auto-aggregation and a high ability to remove nitrogen efficiently, making it an ideal candidate for enhanced treatment of nitrogen-rich wastewater. This strain was used for the bioassessment of a test reactor (SBBRbio), which showed a shorter biofilm formation time compared to a control reactor (SBBRcon) without this strain inoculation. Moreover, the enhanced biofilm was enriched in TB-EPS and had a wider variety of protein secondary structures than SBBRcon. During the stabilization phase of SBBRbio, the EPS molecules showed the highest proportion of intermolecular hydrogen bonding. It is possible that bioaugmentation with this strain positively affects the structural stability of biofilm. At influent ammonia loadings of 100 and 150 mg. L, the average reduction of ammonia and nitrate-nitrogen was higher in the experimental system compared to the control system. Additionally, nitrite-N accumulation was lower and NO production decreased compared to the control. Analysis of the microbial community structure demonstrated successful colonization in the bioreactor by a highly nitrogen-tolerant strain that efficiently removed inorganic nitrogen. These results illustrate the great potential of this type of denitrifying bacteria in the application of bioaugmentation systems.
Topics: Denitrification; Ammonia; Nitrogen; Biofilms; Methylobacterium; Bioreactors; Water Purification; Nitrification
PubMed: 38387667
DOI: 10.1016/j.chemosphere.2024.141467 -
Scientific Reports Feb 2024Formate dehydrogenase (FDH) is critical for the conversion between formate and carbon dioxide. Despite its importance, the structural complexity of FDH and difficulties...
Formate dehydrogenase (FDH) is critical for the conversion between formate and carbon dioxide. Despite its importance, the structural complexity of FDH and difficulties in the production of the enzyme have made elucidating its unique physicochemical properties challenging. Here, we purified recombinant Methylobacterium extorquens AM1 FDH (MeFDH1) and used cryo-electron microscopy to determine its structure. We resolved a heterodimeric MeFDH1 structure at a resolution of 2.8 Å, showing a noncanonical active site and a well-embedded Fe-S redox chain relay. In particular, the tungsten bis-molybdopterin guanine dinucleotide active site showed an open configuration with a flexible C-terminal cap domain, suggesting structural and dynamic heterogeneity in the enzyme.
Topics: Cryoelectron Microscopy; Formate Dehydrogenases; Methylobacterium extorquens; Bacterial Proteins
PubMed: 38360844
DOI: 10.1038/s41598-024-54205-7 -
Antonie Van Leeuwenhoek Dec 2023Strain CN29, isolated from the stem of 5- to 6-year-old Populus tomentosa in Shandong, China, was characterized using a polyphasic taxonomic approach. Cells of CN29 were...
Strain CN29, isolated from the stem of 5- to 6-year-old Populus tomentosa in Shandong, China, was characterized using a polyphasic taxonomic approach. Cells of CN29 were Gram-stain negative, aerobic, nonspore-forming, and nonmotile coccoid. Growth occurred at 20-37 °C, pH 4.0-9.0 (optimum, pH 6.0), and with 0-1% NaCl (optimum, 1%). Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain CN29 was closely related to members of the genus Roseomonas and closest to Roseomonas pecuniae N75 (96.6%). This classification was further supported by phylogenetic analysis using additional core genes. The average nucleotide identity and digital DNA‒DNA hybridization values between strain CN29 and Roseomonas populi CN29 were 82.7% and 27.8%, respectively. The genome size of strain CN29 was 5.87 Mb, with a G + C content of 70.9%. The major cellular fatty acids included summed feature 8 (C ω7c/C ω6c), C cyclo ω8c and C. The major respiratory quinone was Q-10. The polar lipids were phosphatidylcholine, aminolipid, phosphatidylglycerol, and diphosphatidylglycerol. Strain CN29 can utilize acetate as a carbon source for growth and metabolism. Additionally, it contains acid phosphatase (2-naphthyl phosphate), which catalyzes the hydrolysis of phosphoric monoesters. The CN29 strain contains several genes, including maeB, gdhB, and cysJ, involved in carbon, nitrogen, and sulfur cycling. These findings suggest that the strain may actively participate in ecosystem cycling, leading to soil improvement and promoting the growth of poplar trees. Based on the phylogenetic, phenotypic, and genotypic characteristics, strain CN29 is concluded to represent a novel species of the genus Roseomonas, for which the name Roseomonas populi sp. nov. is proposed. The type strain is CN29 (= JCM 35579 = GDMCC 1.3267).
Topics: Acetates; Phylogeny; Populus; RNA, Ribosomal, 16S; Methylobacteriaceae; Plant Stems; China; Nucleic Acid Hybridization; DNA, Bacterial; Bacterial Typing Techniques
PubMed: 38147266
DOI: 10.1007/s10482-023-01911-3