Canadian journal of microbiology最新文献

The surface morphology of mature biofilms is heterogeneous and can be divided into concentric rings wrinkles (I), labyrinthine networks wrinkles (II), radial ridges wrinkles (III), and branches wrinkles (IV), according to surface wrinkle structure and distribution characteristics. Due to the wrinkle structures, channels are formed between the biofilm and substrate and transport nutrients, water, metabolic products, etc. We find that expansion rate variations of biofilms growing on substrates with high and low agar concentrations (1.5, 2.0, 2.5 wt.%) are not in the same phase. In the first 3 days' growth, the interaction stress between biofilm and each agar substrate increases, which makes the biofilm expansion rate decreases before wrinkle pattern IV (branches) comes up. After 3 days, in the later growth stage after wrinkle pattern IV appears, the biofilm has larger expansion rate growing on 2.0 wt.% agar concentration, which has the larger wrinkle distance in wrinkle pattern IV reducing energy consumption. Our study shows that the stiff substrate does not always inhibit the biofilm expansion, although it does in the earlier stage; after that, mature biofilms acquire larger expansion rate by adjusting the growth mode through the wrinkle evolution even in nutrient extremely depletion.

The aim of this study was to determine the plant growth-promoting effect of Bacillus subtilis PE7 on growth of melon plants. B. subtilis PE7 isolated from kimchi was identified based on colonial and microscopic morphology along with analyses of 16S rRNA and pycA gene sequences. Strain PE7 showed different levels of inhibition on phytopathogens and was able to grow at variable temperatures and pH values. Strain PE7 had the ability to produce siderophores, indole-3-acetic acid (IAA), ammonia, exopolysaccharides, and 1-aminocyclopropane-1-carboxylic acid deaminase, as well as solubilize insoluble phosphate and zinc. The IAA secretion of strain PE7 showed a concentration-dependent pattern based on the concentration of l-tryptophan supplemented in the fertilizer-based culture medium. The LC-MS analysis indicates the presence of IAA in the culture filtrate of strain PE7. Treatment of the B. subtilis PE7 culture containing different metabolites, mainly IAA, significantly promoted melon growth in terms of higher growth parameters and greater plant nutrient contents compared to treatments with the culture without IAA, fertilizer, and water. The cells of B. subtilis PE7 attached to and firmly colonized the roots of the bacterized melon plants. Based on our results, B. subtilis PE7 can be utilized as a potential microbial fertilizer to substitute chemical fertilizers in sustainable agriculture.

Biofilms are widely recognized as a prominent mode of microbial growth and strategy of antimicrobial tolerance in many environments. Characteristics that are often overlooked in biofilm investigations include the examination of metabolic pathways as the assumption might be that interference with central pathways such as glycolysis would only reduce growth and thus not be meaningful. Using the Keio collection of Escherichia coli mutants, we investigated the influence of biofilm formation and planktonic growth in full-strength and diluted Luria-Bertani (LB) broths using strains with a disruption of glycolysis (Δpgi), the Entner-Doudoroff pathway (Δedd), or the pentose phosphate pathway (Δgnd). Unexpectedly, in contrast to the E. coli Keio parent strain (BW25113), planktonic growth was enhanced in full strength and diluted LB broths in the metabolic mutants. Using a microtiter biofilm assay, the E. coli parent strain showed the highest crystal violet staining. However, when analyzed by culture assays, there was an increase in biofilm populations in the mutants in comparison to the parent strain. Fluorescence microscopy showed differences in colonization patterns in the strains. Given the availability of mutant collections in many model organisms, similar metabolic studies are warranted for biofilms, given their importance in nature.

The rhizosphere is a narrow soil area directly affected by plant root exudates. Microbes inhabiting the rhizosphere have been widely studied for their beneficial effects on plant nutrition, growth, and disease prevention. Many factors affect the rhizosphere microbial composition, including plant pathogen infection. Here, we analyzed the bacterial community structure in the rhizosphere of fungi-infected Amorphophallus titanum. Soil samples were collected from rhizosphere and non-rhizosphere areas of fungi-infected A. titanum. The 16S metagenomic analysis was conducted to investigate the bacterial community of the samples by amplifying the V3-V4 region. The results showed that the phylum Firmicutes was prevalent in the rhizosphere, whereas the phyla Proteobacteria, Acidobacteria, and Actinobacteria were limited. Some major fungal genera were isolated from infected tubers and rhizosphere soil of A. titanum, including Trichoderma sp., Aspergillus sp., Perenniporia sp., and Cerrena sp. The fungal-isolate Aspergillus spp. is a well-known agricultural pest in several reports. While Cerrena sp. was reported to be pathogenic in plants, including the family of Arecaceae. Overall, the data revealed a potential relationship between fungal infections and the dominant bacterial community in the rhizosphere of A. titanum. Additionally, this research may contribute to the development of microbe-based technology to mitigate diseases in A. titanum.

Deinococcus murrayi is a bacterium isolated from hot springs in Portugal, and named after Dr. Robert G.E. Murray in recognition of his research on the genus Deinococcus. Like other Deinococcus species, D. murrayi is extremely resistant to ionizing radiation. Repair of massive DNA damage and limitation of oxidative protein damage are two important factors contributing to the robustness of Deinococcus bacteria. Here, we identify, among others, the DNA repair and oxidative stress defense proteins in D. murrayi, and highlight special features of D. murrayi. For DNA repair, D. murrayi does not contain a standalone uracil-DNA glycosylase (Ung), but it encodes a protein in which Ung is fused to a DNA photolyase domain (PhrB). UvrB and UvrD contain large insertions corresponding to inteins. One of its endonuclease III enzymes lacks a [4Fe-4S] cluster. Deinococcus murrayi possesses a homolog of the error-prone DNA polymerase IV. Concerning oxidative stress defense, D. murrayi encodes a manganese catalase in addition to a heme catalase. Its organic hydroperoxide resistance protein Ohr is atypical because the redox active cysteines are present in a CXXC motif. These and other characteristics of D. murrayi show further diversity among Deinococcus bacteria with respect to resistance-associated mechanisms.

Acinetobacter baumannii is an opportunistic pathogen known for causing hospital-acquired infections. The natural habitat includes soil, water, sewage, and drains, but it is also detected in infected individuals' blood, pus, and respiratory pathways. Due to its resilient nature, it is known to be a causative agent for outbreaks. Therefore, it is crucial to understand the genetic similarity between clinical and environmental isolates. The study aimed to find the genetic relationships between clinical and environmental isolates using PCR-based typing methods such as enterobacterial repetitive intergenic consensus sequence PCR (ERIC-PCR), random amplified polymorphic DNA (RAPD), and repetitive extragenic palindromic sequence-based PCR (Rep-PCR). Additionally, outer membrane protein (OMP) and whole cell protein (WCP) profiles were also used. The PCR-based methods, ERIC-PCR and Rep-PCR, showed decreased genetic similarity between clinical and environmental isolates (66% and 58%, respectively). However, RAPD showed relatively higher genetic similarity (91%). The OMP and WCP profiles showed varied banding patterns between the clinical and environmental isolates in the 29-43 kDa region. The PCR-based methods proved to be a reliable and reproducible technique. The OMP and WCP profiles, though not as discriminatory as the molecular typing methods, could help identify the most and least commonly occurring protein bands and thus help in typing clinical and environmental A. baumannii isolates.

The family Deinococcaceae exhibits exceptional radiation resistance and possesses all the necessary traits for surviving in radiation-exposed environments. Their survival strategy involves the coupling of metabolic and DNA repair functions, resulting in an extraordinarily efficient homologous repair of DNA double-strand breaks (DSBs) caused by radiation or desiccation. The keys to their survival lie in the hyperaccumulation of manganous (Mn²⁺)-metabolite antioxidants that protect their DNA repair proteins under extreme oxidative stress and the persistent structural linkage by Holliday junctions of their multiple genome copies per cell that facilitates DSB repair. This coupling of metabolic and DNA repair functions has made polyploid Deinococcus bacteria a useful tool in environmental biotechnology, radiobiology, aging, and planetary protection. The review highlights the groundbreaking contributions of the late Robert G.E. Murray to the field of Deinococcus research and the emergent paradigm-shifting discoveries that revolutionized our understanding of radiation survivability and oxidative stress defense, demonstrating that the proteome, rather than the genome, is the primary target responsible for survivability. These discoveries have led to the commercial development of irradiated vaccines using Deinococcus Mn-peptide antioxidants and have significant implications for various fields.

The genus Robertmurraya was created by my group in 2020 to recognize the contributions of Dr. Robert G.E. Murray to the field of prokaryotic taxonomy. This manuscript updates the information regarding this genus. In addition to the seven Robertmurraya species with validly published names, the work presented here shows that two species with effectively published names, "Bacillus yapensis" and "Bacillus dakarensis", and an uncharacterized Bacillus sp. Y1 are also affiliated with this genus. Based on these results, reclassification of "Bacillus yapensis" as a novel species Robertmurraya yapensis sp. nov. is proposed. It is also suggested that "Bacillus dakarensis", for which strains are not available from culture collections, should also be recognized as "Robertmurraya dakarensis". This article also reflects on the serendipitous way I came to know Dr. Murray and his extensive interactions with me and strong support for our work for more than 10 years. Dr. Murray also introduced me and our work to his friend and contemporary Dr. Peter Sneath, who like him also contributed extensively to the field of prokaryotic taxonomy. This introduction led to a fruitful collaboration with Dr. Sneath leading to a joint publication describing the use of the Character Compatibility approach to molecular sequence data.