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Microbiology Resource Announcements Dec 2023Arthrobacteriophage MrAaronian contains a 54,509 bp DNA genome with 87 predicted protein-coding genes. MrAaronian has siphovirus morphology and was collected from a...
Arthrobacteriophage MrAaronian contains a 54,509 bp DNA genome with 87 predicted protein-coding genes. MrAaronian has siphovirus morphology and was collected from a flowerbed soil sample in Poughkeepsie, NY, and isolated on an B-2979 culture. MrAaronian has > 99% nucleotide identity with cluster AW arthrobacteriophages Michelle, Stayer, Sloopyjoe, and StarLord.
PubMed: 37933970
DOI: 10.1128/MRA.00778-23 -
Scientific Reports Nov 2023With the advent of long-term human habitation in space and on the moon, understanding how the built environment microbiome of space habitats differs from Earth habitats,...
Phylogenomics, phenotypic, and functional traits of five novel (Earth-derived) bacterial species isolated from the International Space Station and their prevalence in metagenomes.
With the advent of long-term human habitation in space and on the moon, understanding how the built environment microbiome of space habitats differs from Earth habitats, and how microbes survive, proliferate and spread in space conditions, is becoming more important. The microbial tracking mission series has been monitoring the microbiome of the International Space Station (ISS) for almost a decade. During this mission series, six unique strains of Gram-stain-positive bacteria, including two spore-forming and three non-spore-forming species, were isolated from the environmental surfaces of the ISS. The analysis of their 16S rRNA gene sequences revealed > 99% similarities with previously described bacterial species. To further explore their phylogenetic affiliation, whole genome sequencing was undertaken. For all strains, the gyrB gene exhibited < 93% similarity with closely related species, which proved effective in categorizing these ISS strains as novel species. Average nucleotide identity and digital DNA-DNA hybridization values, when compared to any known bacterial species, were < 94% and <50% respectively for all species described here. Traditional biochemical tests, fatty acid profiling, polar lipid, and cell wall composition analyses were performed to generate phenotypic characterization of these ISS strains. A study of the shotgun metagenomic reads from the ISS samples, from which the novel species were isolated, showed that only 0.1% of the total reads mapped to the novel species, supporting the idea that these novel species are rare in the ISS environments. In-depth annotation of the genomes unveiled a variety of genes linked to amino acid and derivative synthesis, carbohydrate metabolism, cofactors, vitamins, prosthetic groups, pigments, and protein metabolism. Further analysis of these ISS-isolated organisms revealed that, on average, they contain 46 genes associated with virulence, disease, and defense. The main predicted functions of these genes are: conferring resistance to antibiotics and toxic compounds, and enabling invasion and intracellular resistance. After conducting antiSMASH analysis, it was found that there are roughly 16 cluster types across the six strains, including β-lactone and type III polyketide synthase (T3PKS) clusters. Based on these multi-faceted taxonomic methods, it was concluded that these six ISS strains represent five novel species, which we propose to name as follows: Arthrobacter burdickii IIF3SC-B10 (= NRRL B-65660 = DSM 115933), Leifsonia virtsii F6_8S_P_1A (= NRRL B-65661 = DSM 115931), Leifsonia williamsii F6_8S_P_1B (= NRRL B-65662 = DSM 115932), Paenibacillus vandeheii F6_3S_P_1C (= NRRL B-65663 = DSM 115940), and Sporosarcina highlanderae F6_3S_P_2 (= NRRL B-65664 = DSM 115943). Identifying and characterizing the genomes and phenotypes of novel microbes found in space habitats, like those explored in this study, is integral for expanding our genomic databases of space-relevant microbes. This approach offers the only reliable method to determine species composition, track microbial dispersion, and anticipate potential threats to human health from monitoring microbes on the surfaces and equipment within space habitats. By unraveling these microbial mysteries, we take a crucial step towards ensuring the safety and success of future space missions.
Topics: Humans; Metagenome; Phylogeny; RNA, Ribosomal, 16S; Prevalence; Phenotype; Paenibacillus; Fatty Acids; DNA; DNA, Bacterial; Sequence Analysis, DNA; Bacterial Typing Techniques
PubMed: 37932283
DOI: 10.1038/s41598-023-44172-w -
PloS One 2023Sugarcane is one of the major agricultural crops with high economic importance in Thailand. Periodic waterlogging has a long-term negative effect on sugarcane...
Sugarcane is one of the major agricultural crops with high economic importance in Thailand. Periodic waterlogging has a long-term negative effect on sugarcane development, soil properties, and microbial diversity, impacting overall sugarcane production. Yet, the microbial structure in periodically waterlogged sugarcane fields across soil compartments and growth stages in Thailand has not been documented. This study investigated soil and rhizosphere microbial communities in a periodic waterlogged field in comparison with a normal field in a sugarcane plantation in Ratchaburi, Thailand, using 16S rRNA and ITS amplicon sequencing. Alpha diversity analysis revealed comparable values in periodic waterlogged and normal fields across all growth stages, while beta diversity analysis highlighted distinct microbial community profiles in both fields throughout the growth stages. In the periodic waterlogged field, the relative abundance of Chloroflexi, Actinobacteria, and Basidiomycota increased, while Acidobacteria and Ascomycota decreased. Beneficial microbes such as Arthrobacter, Azoarcus, Bacillus, Paenibacillus, Pseudomonas, and Streptomyces thrived in the normal field, potentially serving as biomarkers for favorable soil conditions. Conversely, phytopathogens and growth-inhibiting bacteria were prevalent in the periodic waterlogged field, indicating unfavorable conditions. The co-occurrence network in rhizosphere of the normal field had the highest complexity, implying increased sharing of resources among microorganisms and enhanced soil biological fertility. Altogether, this study demonstrated that the periodic waterlogged field had a long-term negative effect on the soil microbial community which is a key determining factor of sugarcane growth.
Topics: Soil; Saccharum; RNA, Ribosomal, 16S; Thailand; Bacteria; Microbiota; Edible Grain; Soil Microbiology; Rhizosphere
PubMed: 37917788
DOI: 10.1371/journal.pone.0293834 -
Microbiology Resource Announcements Nov 2023London is a predicted temperate bacteriophage with siphovirus morphology infecting NRRL strain B-2880. Sequencing of the genome revealed a length of 43,599 bp...
London is a predicted temperate bacteriophage with siphovirus morphology infecting NRRL strain B-2880. Sequencing of the genome revealed a length of 43,599 bp comprising 69 predicted open-reading frames and no tRNA genes. It is categorized as a cluster AZ1 phage along with closely related actinobacteriophages Elezi, Eraser, and Niobe.
PubMed: 37906022
DOI: 10.1128/MRA.00819-23 -
Microbiology Resource Announcements Nov 2023phage Ascela was isolated in North Georgia. Its genome is 44,192 bp with 71 open reading frames and a GC content of 67.4%. It shares 99.29% nucleotide identity with...
phage Ascela was isolated in North Georgia. Its genome is 44,192 bp with 71 open reading frames and a GC content of 67.4%. It shares 99.29% nucleotide identity with phage Iter. Actinobacteriophages that share over 50% nucleotide identity are sorted into clusters, with Ascela in cluster AZ and subcluster AZ1.
PubMed: 37905911
DOI: 10.1128/MRA.00776-23 -
Frontiers in Microbiology 2023The HSE-12 strain isolated from peanut rhizosphere soil was identified as by observation of phenotypic characteristics, physiological and biochemical tests, 16S rDNA...
The HSE-12 strain isolated from peanut rhizosphere soil was identified as by observation of phenotypic characteristics, physiological and biochemical tests, 16S rDNA and gyrB gene sequencing. experiments showed that the strain possessed biocontrol activity against a variety of pathogens including . The strain has the ability to produce hydrolytic enzymes, as well as volatile organic compounds with antagonistic and probiotic effects such as ethyleneglycol and 2,3-butanediol. In addition, HSE-12 showed potassium solubilizing (10.54 ± 0.19 mg/L), phosphorus solubilization (168.34 ± 8.06 mg/L) and nitrogen fixation (17.35 ± 2.34 mg/g) abilities, and was able to secrete siderophores [(Ar-A)/Ar × 100%: 56%] which promoted plant growth. After inoculating peanut with HSE-12, the available phosphorus content in rhizosphere soil increased by 27%, urease activity increased by 43%, catalase activity increased by 70% and sucrase activity increased by 50% ( < 0.05). The dry weight, fresh weight and the height of the first pair of lateral branches of peanuts increased by 24.7, 41.9, and 36.4%, respectively, compared with uninoculated peanuts. In addition, compared with the blank control, it increased the diversity and richness of peanut rhizosphere bacteria and changed the community structure of bacteria and fungi. The relative abundance of beneficial microorganisms such as , , , and in rhizosphere soil was increased, while the relative abundance of pathogenic microorganisms such as , , and was decreased.
PubMed: 37901825
DOI: 10.3389/fmicb.2023.1274346 -
BioRxiv : the Preprint Server For... Oct 2023The use of enzymes represents an approach to combat bacterial infections by degrading extracellular biomolecules to disperse biofilms. Commercial enzyme preparations,...
The use of enzymes represents an approach to combat bacterial infections by degrading extracellular biomolecules to disperse biofilms. Commercial enzyme preparations, including cellulase, amylase, pectinase, zymolyase, and pepsin, exhibit concentration-dependent dispersion of biofilms. Here, we report that low concentrations of these enzymes generally lack synergy when combined or added together sequentially to biofilms. Only the addition of a protease (pepsin) followed by a commercial mixture of degradative enzymes from (zymolyase 20T), demonstrated synergy and was effective at dispersing biofilms. A more purified mixture of enzymes (zymolyase 100T) showed improved dispersal of biofilms compared to zymolyase 20T but lacked synergy with pepsin. This study emphasizes the complexity of enzymatic biofilm dispersal and the need for tailored approaches based on the properties of degradative enzymes and biofilm composition.
PubMed: 37873330
DOI: 10.1101/2023.10.05.561034 -
Journal of Environmental Health Science... Dec 2023Potential of B27Pet, B48Pet and to produce biosurfactant using four different carbon sources (naphthalene, hexadecane, diesel and petroleum crude oil) was...
Potential of B27Pet, B48Pet and to produce biosurfactant using four different carbon sources (naphthalene, hexadecane, diesel and petroleum crude oil) was investigated. Removal of petroleum crude oil from aqueous culture and degradation of diesel were also determined using single and mixed culture of strains. The biofilm existence in single and mixed culture of strains was considered using naphthalene, hexadecane and diesel in culture medium. Cell surface hydrophobicity of was higher than other isolates which also showed maximum surface tension reduction and emulsification index. As a whole, remarkable biosurfactant production occurred using petroleum crude oil as a carbon source in medium. was found to be more robust than other tested strains in removal efficiency of crude oil due to its biosurfactant production capability. Statistically significant positive correlation was observed between biofilm existence and surface tension using diesel and hexadecane as carbon source. Overall diesel biodegradation efficiency by the mix culture of three applied strains was about 75% within a short period of time (10 days) which was accompanied with high biofilm production.
PubMed: 37869592
DOI: 10.1007/s40201-023-00868-9 -
BMC Microbiology Oct 2023Astragalus mongolicus Bunge is used in traditional Chinese medicine and is thus cultivated in bulk. The cultivation of A. mongolicus requires a large amount of nitrogen...
Screening of high-efficiency nitrogen-fixing bacteria from the traditional Chinese medicine plant Astragalus mongolicus and its effect on plant growth promotion and bacterial communities in the rhizosphere.
BACKGROUND
Astragalus mongolicus Bunge is used in traditional Chinese medicine and is thus cultivated in bulk. The cultivation of A. mongolicus requires a large amount of nitrogen fertilizer, increasing the planting cost of medicinal materials and polluting the environment. Isolation and screening of plant growth-promoting rhizobacteria (PGPR) and exploring the nitrogen fixation potential of A. mongolicus rhizosphere microorganisms would effectively reduce the production cost of A. mongolicus.
RESULTS
This study used A. mongolicus roots and rhizosphere soil samples from Longxi County of Gansu Province, Jingle County, and Hunyuan County of Shanxi Province, China, to isolate and identify nitrogen-fixing bacteria. Through nitrogen fixation efficiency test, single strain inoculation test, and plant growth-promoting characteristics, three strains, Bacillus sp. J1, Arthrobacter sp. J2, and Bacillus sp. G4 were selected from 86 strains of potential nitrogen-fixing bacteria, which were the most effective in promoting the A. mongolicus growth and increasing the nitrogen, phosphorus, and potassium content in plants. The antagonistic test showed that these bacteria could grow smoothly under the co-culture conditions. The J1, J2, and G4 strains were used in a mixed inoculum and found to enhance the biomass of A. mongolicus plants and the accumulation of the main medicinal components in the field experiment. Mixed bacterial agent inoculation also increased bacterial diversity and changed the structure of the bacterial community in rhizosphere soil. Meanwhile, the relative abundance of Proteobacteria increased significantly after inoculation, suggesting that Proteobacteria play an important role in plant growth promotion.
CONCLUSIONS
These findings indicate that specific and efficient PGPRs have a significant promoting effect on the growth of A. mongolicus, while also having a positive impact on the structure of the host rhizosphere bacteria community. This study provides a basis for developing a nitrogen-fixing bacterial fertilizer and improving the ecological planting efficiency of A. mongolicus.
Topics: Nitrogen-Fixing Bacteria; Rhizosphere; Fertilizers; Medicine, Chinese Traditional; Bacteria; Bacillus; Nitrogen; Soil; Soil Microbiology; Plant Roots
PubMed: 37845638
DOI: 10.1186/s12866-023-03026-1 -
Microbiology Spectrum Dec 2023As the management of wheat fungal diseases becomes increasingly challenging, the use of bacterial agents with biocontrol potential against the two major wheat...
As the management of wheat fungal diseases becomes increasingly challenging, the use of bacterial agents with biocontrol potential against the two major wheat phytopathogens, and , may prove to be an interesting alternative to conventional pest management. Here, we have shown that dimethylpolysulfide volatiles are ubiquitously and predominantly produced by wheat-associated and actinomycetes, displaying antifungal activity against both pathogens. By limiting pathogen growth and DON virulence factor production, the use of such DMPS-producing strains as soil biocontrol inoculants could limit the supply of pathogen inocula in soil and plant residues, providing an attractive alternative to dimethyldisulfide fumigant, which has many non-targeted toxicities. Notably, this study demonstrates the importance of bacterial volatile organic compound uptake by inhibited , providing new insights for the study of volatiles-mediated toxicity mechanisms within bacteria-fungus signaling crosstalk.
Topics: Arthrobacter; Microbacterium; Triticum; Actinobacteria; Actinomyces; Soil; Plant Diseases
PubMed: 37800942
DOI: 10.1128/spectrum.05292-22