Microbes and Environments最新文献

Microbial community structures in mesophilic and low-temperature anammox and partial nitrification-anammox reactors were exami-ned by a 16S rRNA-gene amplicon sequencing ana-lysis. The anammox bacterium, Jettenia sp., was dominant, and nitrifying bacteria, including Nitrosomonas sp. (aerobic ammonia-oxidizing bacterium) and Nitrospira sp., (nitrite-oxidizing bacterium) coexisted in the bioreactors. Core coexisting bacteria, such as Sulfurisoma sp. and Zeimonas sp., showed oxygen-scavenging and NO₃^- reduction potentials. Sulfurisoma-related bacteria are distributed across wastewater treatment plants worldwide, particularly in denitrification systems. These results underscore the ecological and functional importance of microbial consortia in enhancing nitrogen removal efficiency.

We herein exami-ned the effects of soil flooding treatments on the occupancy of adzuki bean-nodulated bradyrhizobia and how changes in its occupancy affects adzuki bean growth. Microcosms containing mixtures of four different strains were prepared and incubated under flooded and non-flooded conditions. These microcosms were then used to cultivate adzuki bean in culture pots. After assessing the growth parameters of the plants, nodules collected from the roots were analyzed to assess occupancy rates. Be31, which exhibited a similar restriction fragment length polymorphism (RFLP) pattern in the 16S-23S rRNA gene ITS region to Bradyrhizobium elkanii USDA 31, was dominant overall. However, its occupancy declined under flooded conditions, while the occupancy of Bd110, similar to Bradyrhizobium diazoefficiens USDA 110^T, increased. Furthermore, a non-metric multidimensional scaling anal-ysis showed that adzuki bean-nodulated bradyrhizobial communities were affected by changes in Bd110 and Be31 occupancies due to soil flooding. In terms of growth, shoot length and shoot dry weight generally increased in cultivars where Bd110 occupancy surpassed that of Be31 under flooding. A correlation anal-ysis revealed that Bd110 occupancy correlated with shoot dry weight. These results suggest that increased Bd110 occupancy through soil flooding enhanced adzuki bean growth. However, alternative methods need to be considered in order to more effectively regulate Be31 occupancy.

Clostridium spp. are anaerobic, Gram-positive, spore-forming bacteria comprising more than 150 species, some of which are important pathogens of humans and animals. Members of this genus have been isolated from a number of environments, but are rarely found in the atmosphere. In the present study, we exami-ned culturable airborne Clostridium spp. and clarified their pathogenicity. We obtained 19 culturable Clostridium isolates from size-fractionated samples collected at a suburban site in Toyama, central Japan. Culturable Clostridium spp. were detected in particles larger than 1.1‍ ‍μm, and the size distribution peaked at 2.1-3.3‍ ‍μm, corresponding to the spore size of Clostridium spp. More Clostridium spp. were detected in coarse particles >2.1‍ ‍μm not only by culture methods, but also by 16S rRNA gene amplicon sequencing. Whole-genome sequencing (WGS) identified seven Clostridium species, among which Clostridium perfringens was predominant. Moreover, WGS revealed that C. perfringens isolates harbored many virulence and antibiotic resistance genes with the potential to cause gas gangrene. The detection and characterization of potential airborne pathogens are crucial for preventing the spread of diseases caused by these pathogens. To the best of our knowledge, this is the first study to demonstrate that anaerobic Clostridium spp. may be transported under aerobic conditions in the atmosphere and pose potential risks to human health.

Ascetosporeans are parasitic protists of invertebrates. A deep sequencing ana-lysis of species within the orders Mikrocytida, Paramyxida, and Haplosporida using metagenomic approaches revealed that their mitochondria were functionally reduced and their organellar genomes were lacking. Ascetosporeans belonging to the order Paradinida have not been sequenced, and the nature of their mitochondria remains unclear. We herein established two cultures of Paradinida and conducted DNA and RNA sequencing ana-lyses. The results obtained indicate that mitochondrial function in paradinids was not reduced and their organellar genomes were retained. In contrast, their mitochondrial genomes were involved in massive A-to-I and C-to-U substitution types of RNA editing. All edits in protein-coding genes were nonsynonymous substitutions, and likely had a restorative function against negative mutations. Furthermore, we detected possible sequences of DYW type of pentatricopeptide repeat (PPR-DYW) protein and a homologue of adenosine deaminase acting on RNA (ADAR-like), which are key enzymes for C-to-U and A-to-I substitutions, respectively. An immunofluorescence ana-lysis showed that ADAR-like of paradinids may specifically localize within mitochondria. These results expand our knowledge of the diversity and complexity of organellar RNA editing phenomena.

Many plant pathogenic bacteria regulate the expression of virulence factors via N-acylhomoserine lactone (AHL), a quorum-sensing signaling compound. When numerous spore-forming bacteria were isolated from a natural environment, Priestia megaterium was the dominant species, and some P. megaterium strains exhibited AHL-degrading activity. The results of a HPLC ana-lysis of AHL degradation products demonstrated that P. megaterium degraded AHL by AHL lactonase, which hydrolyzes the lactone ring of AHL. The novel AHL lactonase gene, aiiB, was found in the whole genome sequence of AHL-degrading P. megaterium. The relationship between the presence of aiiB and AHL-degrading activity in P. megaterium strains revealed that P. megaterium may be classified into three AHL degradation groups: Group 1 (with AHL-degrading activity and aiiB), Group 2 (with neither AHL-degrading activity nor aiiB), and Group 3 (without AHL-degrading activity, but with aiiB). A comparative genome ana-lysis suggested that aiiB was obtained or missed by a non-transpositional event during the process of evolution in P. megaterium. The amino acid sequences of AiiB in Group 1 and 3 strains were almost identical, and Escherichia coli harboring aiiB from Groups 1 and 3 exhibited high AHL-degrading activity. Although the AHL-degrading activity of Group 3 strains was markedly weaker than that of Group 1 strains, they degraded AHL in a long-term incubation. Based on the present results, Group 1 and 3 strains, the genomes of which contain aiiB, may reduce potato maceration activity under the control of AHL-mediated quorum sensing in P. carotovorum subsp. carotovorum NBRC 12380.

Soybean (Glycine max) is one of the most important crops worldwide. Root nodule symbiosis between soybean and rhizobia has been extensively exami-ned due to its significance for agricultural productivity and environmental sustainability. Recent advances have enhanced our understanding of the soybean genotypes known as the Rj/rj genotypes, which play a critical role in regulating root nodule symbiosis. Furthermore, the function of rhizobium-secreted proteins, termed effectors, in eliciting specific responses in soybean Rj/rj genotypes has been elucidated. This review summarizes the involvement of soybean Rj/rj genotypes and their corresponding root nodule bacterial effectors in the regulation of nodule formation. We also discussed the potential for manipulating root nodule symbiosis by applying Rj/rj genotypes in soybean breeding programs, which may enhance nitrogen fixation efficiency and subsequently reduce the need for chemical fertilizers and greenhouse gas emissions from agricultural land.

Frankia, a nitrogen-fixing actinobacterium, forms a unique multicellular structure known as a vesicle that is dedicated to nitrogen fixation. The vesicle is surrounded by a thick hopanoid lipid envelope that acts as a barrier against oxygen penetration, preventing nitrogenase inactivation. Five mutants produced a similar number of vesicles to the wild type; however, they failed to fix N₂. The thickness of vesicle envelopes was reduced in all five mutants, and the oxygen concentration increased inside the vesicles of four mutants. Therefore, these mutants were unable to fix N₂ due to the inactivation of nitrogenase caused by oxygen penetration into the vesicles.

Flooded rice fields are a major source of atmospheric methane, a strong greenhouse gas second only to carbon dioxide. Rice roots are one of the most important hotspots for methane oxidation in rice fields. However, limited information is available on the physiological and genomic characteristics of methane-oxidizing bacteria (MOB) inhabiting rice roots. In the present study, we isolated MOB from rice roots and characterized the strains phenotypically and genomically. We obtained 100 MOB-enriched cultures from the roots of three rice cultivars (Oryza sativa L. subsp. japonica cv. Nipponbare, O. sativa L. subsp. indica cv. Muha, and Tupa 121-3), in which twelve MOB isolates, two Methylomonas sp., three Methylocystis sp., and seven Methylosinus sp., were successfully purified. They showed different morphological features (types of flagellation) and colony formation potentials within the same group in some cases. A genome sequencing ana-lysis revealed variations in the number of genes or the clusters of methane monooxygenase, methanol dehydrogenase, and nitrogenase. The number of plasmid DNAs also differed among the strains. Four strains belonging to the genus Methylomonas or Methylocystis represented putative novel species based on their phenotypic and genotypic characteristics. The present study largely expanded the eco-collection of MOB cultures inhabiting rice fields and rice roots.

Phytophthora root and stem rot (PRSR) caused by Phytophthora sojae is a major concern for global soybean production. To identify a bacterial biocontrol agent against PRSR, 73 rhizobacterial strains were isolated from wild and cultivated legumes and screened for their protective activities against PRSR in pot experiments. Strain GVv1 was selected for its consistent protective effect through repeated pot experiments. The protective effect of this strain was similar to that of the fungicide mancozeb-metalaxyl. A dual-culture assay showed that GVv1 produced antifungal metabolites effective against P. sojae. To evaluate the potential adaptability of GVv1 to the soybean rhizosphere environment, its growth was exami-ned in soybean root exudates and nutrient medium, both supplemented with daidzein, an antimicrobial isoflavone secreted by soybean roots. GVv1 proliferated using soybean root exudates and had sufficient tolerance to daidzein to colonize the soybean rhizosphere. The plant growth-promoting effect of GVv1 on soybean plants was also investigated. GVv1 significantly increased shoot and root dry weights, indicating its plant growth-promoting activity. In vitro assays showed that GVv1 produced indole-3-acetic acid, siderophores, and 1-aminocyclopropane-1-carboxylate deaminase and solubilized insoluble phosphates. A taxonogenomic ana-lysis of the draft genome identified GVv1 as Enterobacter pseudoroggenkampii with high similarity (98.32% average nucleotide identity) to E. pseudoroggenkampii strain 155092^T. To the best of our knowledge, this is the first study to report the biocontrol and plant growth-promoting activities of E. pseudoroggenkampii.

Over the past 10 centuries, sake brewing methods have been developed in stages, including doburoku, mizumoto, kimoto, yamahaimoto, and sokujyomoto. Mizumoto-sake is considered the oldest prototype. The brewing process involves lactic acid fermentation and multiple parallel saccharification and alcoholic fermentation by indigenous microbes, which has been operated based on a sense of craftsmanship. The processes involved lead to the creation of extreme conditions characterized by low pH levels and high alcohol concentrations. The characteristic feature of mizumoto-sake is that it begins with fermentation by indigenous lactic acid bacteria to produce acidic water for yeasts to ferment alcohol by inhibiting the growth of undesirable microbes. In the present study, we investigated changes in the microbial community and the transition of metabolites that affect taste and flavor during processes from the initiation of mizumoto-sake brewing to the final product. In the lactic acid fermentation phase, bacteria, including those in the genera Lactococcus, Leuconostoc, and Lactobacillus, produced lactic acid and contributed to the production of acidic water (pH of approximately 4) called soyashimizu. A heating process, known as "Anka", which increased the brewing temperature, then switched the relative abundance of 18S rRNA from 75.0% Pichia to 72.3% Saccharomycetaceae. Alcohol fermentation was accelerated by the Saccharomyces family (relative abundance: 89.8%), reaching alcohol concentrations >15%.