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Microbial Genomics Sep 2023comprises a diverse group of bacteria with various lifestyles. Although best known for their nodule-based nitrogen-fixation in symbiosis with legumes, a select group of...
comprises a diverse group of bacteria with various lifestyles. Although best known for their nodule-based nitrogen-fixation in symbiosis with legumes, a select group of bradyrhizobia are also capable of photosynthesis. This ability seems to be rare among rhizobia, and its origin and evolution in these bacteria remain a subject of substantial debate. Therefore, our aim here was to investigate the distribution and evolution of photosynthesis in using comparative genomics and representative genomes from closely related taxa in the families and . We identified photosynthesis gene clusters (PGCs) in 25 genomes belonging to three different lineages, notably the so-called Photosynthetic, and supergroups. Also, two different PGC architectures were observed. One of these, PGC1, was present in genomes from the Photosynthetic supergroup and in three genomes from a species in the supergroup. The second cluster, PGC2, was also present in some strains from the supergroup, as well as in those from the supergroup. PGC2 was largely syntenic to the cluster found in and . Bayesian ancestral state reconstruction unambiguously showed that the ancestor of lacked a PGC and that it was acquired horizontally by various lineages. Maximum-likelihood phylogenetic analyses of individual photosynthesis genes also suggested multiple acquisitions through horizontal gene transfer, followed by vertical inheritance and gene losses within the different lineages. Overall, our findings add to the existing body of knowledge on ’s evolution and provide a meaningful basis from which to explore how these PGCs and the photosynthesis itself impact the physiology and ecology of these bacteria.
Topics: Bradyrhizobium; Photosynthesis
PubMed: 37676703
DOI: 10.1099/mgen.0.001105 -
Angewandte Chemie (International Ed. in... Aug 2023Certain f-block elements-the lanthanides-have biological relevance in the context of methylotrophic bacteria. The respective strains incorporate these 4 f elements...
Certain f-block elements-the lanthanides-have biological relevance in the context of methylotrophic bacteria. The respective strains incorporate these 4 f elements into the active site of one of their key metabolic enzymes, a lanthanide-dependent methanol dehydrogenase. In this study, we investigated whether actinides, the radioactive 5 f elements, can replace the essential 4 f elements in lanthanide-dependent bacterial metabolism. Growth studies with Methylacidiphilum fumariolicum SolV and the Methylobacterium extorquens AM1 ΔmxaF mutant demonstrate that americium and curium support growth in the absence of lanthanides. Moreover, strain SolV favors these actinides over late lanthanides when presented with a mixture of equal amounts of lanthanides together with americium and curium. Our combined in vivo and in vitro results establish that methylotrophic bacteria can utilize actinides instead of lanthanides to sustain their one-carbon metabolism if they possess the correct size and a +III oxidation state.
Topics: Lanthanoid Series Elements; Americium; Curium; Methanol; Methylobacterium extorquens; Bacterial Proteins
PubMed: 37074219
DOI: 10.1002/anie.202303669 -
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 -
Environmental Microbiology Nov 2023While investigating aerobic anoxygenic phototrophs (AAP) from Lake Winnipeg's bacterial community, over 500 isolates were obtained. Relatives of 20 different species...
While investigating aerobic anoxygenic phototrophs (AAP) from Lake Winnipeg's bacterial community, over 500 isolates were obtained. Relatives of 20 different species were examined simultaneously, identifying conditions for optimal growth or pigment production to determine features that may unify this group of phototrophs. All were distributed among assorted α-Proteobacterial families including Erythrobacteraceae, Sphingomonadaceae, Sphingosinicellaceae, Acetobacteraceae, Methylobacteriaceae, and Rhodobacteraceae. Major phenotypic characteristics matched phylogenetic association, including pigmentation, morphology, metal transformations, tolerances, lipid configurations, and enzyme activities, which distinctly separated each taxonomic family. While varying pH and temperature had a limited independent impact on pigment production, bacteriochlorophyll synthesis was distinctly promoted under low nutrient conditions, whereas copiotrophy repressed its production but enhanced carotenoid yield. New AAP diversity was also reported by revealing strains related to non-phototrophic Rubellimicrobium and Sphingorhabdus, as well as spread throughout Roseomonas, Sphingomonas, and Methylobacterium/Methylorubrum, which previously only had a few known photosynthetic members. This study exemplified the overwhelming diversity of AAP in a single aquatic environment, confirming cultivation continues to be of importance in microbial ecology to discover functionality in both new and previously reported cohorts of bacteria as specific laboratory conditions were required to promote aerobic bacteriochlorophyll production.
Topics: Humans; Bacteriochlorophylls; Phylogeny; Bacteria, Aerobic; Ecosystem; Photosynthesis; Alphaproteobacteria
PubMed: 37604501
DOI: 10.1111/1462-2920.16482 -
Chemosphere Sep 2023Rare earth elements (REE) are valuable raw materials in our modern life. Extensive REE application from electronic devices to medical instruments and wind turbines, and...
Rare earth elements (REE) are valuable raw materials in our modern life. Extensive REE application from electronic devices to medical instruments and wind turbines, and non-uniform distribution of these resources around the world, make them strategically and economically important for countries. Current REE physical and chemical mining and recycling methods could have negative environmental consequences, and biologically-mediated techniques could be applied to overcome this issue. In this study, the bioextraction of cerium oxide and neodymium oxide nanoparticles (REE-NP) by a pure culture Methylobacterium extorquens AM1 (ATCC®14718™) was investigated in batch experiments. Results show that adding up to 1000 ppm CeO or NdO nanoparticles (REE-NP) did not seem to affect the bacterial growth over 14-days contact time. Effect of methylamine hydrochloride as an essential electron donor and carbon source for microbial oxidation and growth was also observed inasmuch as there was approximately no growth when it does not exist in the medium. Although very low concentrations of cerium and neodymium in the liquid phase were measured, concentrations of 45 μg/g Ce and 154 μg/g Nd could be extracted by M. extorquens AM1. Furthermore, SEM-EDS and STEM-EDS confirmed surface and intracellular accumulation of nanoparticles. These results confirmed the ability of M. extorquens to accumulate REE nanoparticles.
Topics: Neodymium; Methylobacterium extorquens; Cerium; Metals, Rare Earth; Nanoparticles
PubMed: 37270036
DOI: 10.1016/j.chemosphere.2023.139113 -
Photochemical & Photobiological... Dec 2023Methylotrophs are a diverse group of bacteria that abundantly colonize the phyllosphere and have great potential to withstand UV irradiation because of their pigmented...
Methylotrophs are a diverse group of bacteria that abundantly colonize the phyllosphere and have great potential to withstand UV irradiation because of their pigmented nature and ability to promote plant growth through various mechanisms. The present study investigated the effects of UVB radiation on plant growth-promoting (PGP) properties of methylotrophic bacteria and the growth of Vigna radiata L. A total of 55 methylotrophic bacteria were isolated from desert plants, and 15 methylotrophs were resistant to UVB radiation for 4 h. All UVB-resistant methylotrophs possess a methyldehydrogenase gene. Identification based on 16S rRNA gene sequencing revealed that all 15 UVB-resistant methylotrophs belonged to the genera Methylorubrum (07), Methylobacterium (07), and Rhodococcus (01). Screening of methylotrophs for PGP activity in the presence and absence of UVB radiation revealed that all isolates showed ACC deaminase activity and growth on a nitrogen-free medium. Furthermore, the production of IAA-like substances ranged from 8.62 to 85.76 µg/mL, siderophore production increased from 3.47 to 65.75% compared to the control. Seed germination assay with V. radiata L. (mung bean) exposed to UVB radiation revealed that methylotrophs improved seed germination, root length, and shoot length compared to the control. The present findings revealed that the isolates SD3, SD2, KD1, KD5, UK1, and UK3 reduced the deleterious effects of UVB radiation on mung bean plants and can be used to protect seedlings from UVB radiation for sustainable agriculture.
Topics: Vigna; RNA, Ribosomal, 16S; Methylobacterium; Seedlings
PubMed: 37838625
DOI: 10.1007/s43630-023-00490-6 -
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 -
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 -
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 -
BMC Infectious Diseases Dec 2023Roseomonas mucosa (R. mucosa) is a pink-pigmented, Gram-negative short rod bacterium. It is isolated from moist environments and skin, resistant to multiple drugs,...
BACKGROUND
Roseomonas mucosa (R. mucosa) is a pink-pigmented, Gram-negative short rod bacterium. It is isolated from moist environments and skin, resistant to multiple drugs, including broad-spectrum cephalosporins, and a rare cause of infection with limited reports. R. mucosa mostly causes catheter-related bloodstream infections, with even fewer reports of skin and soft tissue infections.
CASE PRESENTATION
A 10-year-old boy received topical steroid treatment for sebum-deficient eczema. A few days before the visit, he was bitten by an insect on the front of his right lower leg and scratched it due to itching. The day before the visit, redness, swelling, and mild pain in the same area were observed. Based on his symptoms, he was diagnosed with cellulitis. He was treated with sulfamethoxazole/trimethoprim, and his symptoms improved. Pus culture revealed R. mucosa.
CONCLUSIONS
We report a rare case of cellulitis caused by R. mucosa. Infections caused by rare organisms that cause opportunistic infections, such as R. mucosa, should be considered in patients with compromised skin barrier function and regular topical steroid use. Gram stain detection of organisms other than Gram-positive cocci should be considered.
Topics: Male; Child; Humans; Cellulitis; Soft Tissue Infections; Methylobacteriaceae; Steroids
PubMed: 38082373
DOI: 10.1186/s12879-023-08875-9