Journal of Microbiology

Journal Article

Environmental Adaptability and Roles in Ammonia Oxidation of Aerobic Ammonia-Oxidizing Microorganisms in the Surface Sediments of East China Sea.: Wenhui Li, Yu Zhen, Yuhong Yang, Daling Wang, Hui He; J. Microbiol. 2024;62(10):845-858. Published online August 30, 2024; DOI: https://doi.org/10.1007/s12275-024-00166-5

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Abstract: This study investigated the community characteristics and environmental influencing factors of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in the surface sediments of the East China Sea. The research found no consistent pattern in the richness and diversity of AOA and AOB with respect to the distance from the shore, indicating a complex interplay of factors. The expression levels of AOA amoA gene and AOB amoA gene in the surface sediments of the East China Sea ranged from 4.49 × 10² to 2.17 × 10⁶ copies per gram of sediment and from 6.6 × 10¹ to 7.65 × 10⁴ copies per gram of sediment, respectively. Salinity (31.77 to 34.53 PSU) and nitrate concentration (1.51 to 10.12 μmol/L) were identified as key environmental factors significantly affecting the AOA community, while salinity and temperature (13.71 to 19.50 °C) were crucial for the AOB community. The study also found that AOA, dominated by the Nitrosopumilaceae family, exhibited higher gene expression levels than AOB, suggesting a more significant role in ammonia oxidation. The expression of AOB was sensitive to multiple environmental factors, indicating a responsive role in nitrogen cycles and ecosystem health. The findings contribute to a better understanding of the biogeochemical processes and ecological roles of ammonia-oxidizing microorganisms in marine sediments.

Review

Manganese Transporter Proteins in Salmonella enterica serovar Typhimurium: Nakyeong Ha , Eun-Jin Lee; J. Microbiol. 2023;61(3):289-296. Published online March 2, 2023; DOI: https://doi.org/10.1007/s12275-023-00027-7

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6 Citations

Abstract: The metal cofactors are essential for the function of many enzymes. The host restricts the metal acquisition of pathogens for their immunity and the pathogens have evolved many ways to obtain metal ions for their survival and growth. Salmonella enterica serovar Typhimurium also needs several metal cofactors for its survival, and manganese has been found to contribute to Salmonella pathogenesis. Manganese helps Salmonella withstand oxidative and nitrosative stresses. In addition, manganese affects glycolysis and the reductive TCA, which leads to the inhibition of energetic and biosynthetic metabolism. Therefore, manganese homeostasis is crucial for full virulence of Salmonella. Here, we summarize the current information about three importers and two exporters of manganese that have been identified in Salmonella. MntH, SitABCD, and ZupT have been shown to participate in manganese uptake. mntH and sitABCD are upregulated by low manganese concentration, oxidative stress, and host NRAMP1 level. mntH also contains a Mn2+- dependent riboswitch in its 5′ UTR. Regulation of zupT expression requires further investigation. MntP and YiiP have been identified as manganese efflux proteins. mntP is transcr!ptionally activated by MntR at high manganese levels and repressed its activity by MntS at low manganese levels. Regulation of yiiP requires further analysis, but it has been shown that yiiP expression is not dependent on MntS. Besides these five transporters, there might be additional transporters that need to be identified.

Journal Articles

Characterization and validation of an alternative reference bacterium Korean Pharmacopoeia Staphylococcus aureus strain: Ye Won An , Young Sill Choi , Mi-ran Yun , Chihwan Choi , Su Yeon Kim; J. Microbiol. 2022;60(2):187-191. Published online January 7, 2022; DOI: https://doi.org/10.1007/s12275-022-1335-5

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Abstract: The National Culture Collection of Pathogens (NCCP) is a microbial resource bank in Korea that collects pathogen resources causing infectious disease in human and distributes them for research and education. The NCCP bank attempts to discover strains with various characteristics and specific purposes to provide diverse resources to researchers. Staphylococcus aureus American Type Culture Collection (ATCC) 6538P is used as a reference strain in the microbial assay for antibiotics in the Korean and in the United States Pharmacopoeias. We aimed to analyze domestically isolated microbial resources from the NCCP to replace the S. aureus reference strain. Staphylococcus aureus strains were identified using matrix- assisted laser desorption/ionization time-of-flight mass spectrometry and the VITEK-2 system and characterized by multilocus sequence typing, 16S rRNA sequencing, and antibiotic susceptibility testing. Several candidate strains had similar characteristics as the reference strain. Among them, the nucleotide sequence of the 16S rRNA region of NCCP 16830 was 100% identical to that of the reference strain; it was sensitive to six types of antibiotics and showed results most similar to the reference strain. A validity evaluation was conducted using the cylinder-plate method. NCCP 16830 presented valid results and had the same performance as ATCC 6538P; therefore, it was selected as an alternative candidate strain.

Comparative genomics analysis of Pediococcus acidilactici species: Zhenzhen Li , Qi Song , Mingming Wang , Junli Ren , Songling Liu , Shancen Zhao; J. Microbiol. 2021;59(6):573-583. Published online May 15, 2021; DOI: https://doi.org/10.1007/s12275-021-0618-6

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15 Citations

Abstract: Pediococcus acidilactici is a reliable bacteriocin producer and a promising probiotic species with wide application in the food and health industry. However, the underlying genetic features of this species have not been analyzed. In this study, we performed a comprehensive comparative genomic analysis of 41 P. acidilactici strains from various ecological niches. The bacteriocin production of 41 strains were predicted and three kinds of bacteriocin encoding genes were identified in 11 P. acidilactici strains, namely pediocin PA-1, enterolysin A, and colicin-B. Moreover, whole-genome analysis showed a high genetic diversity within the population, mainly related to a large proportion of variable genomes, mobile elements, and hypothetical genes obtained through horizontal gene transfer. In addition, comparative genomics also facilitated the genetic explanation of the adaptation for host environment, which specify the protection mechanism against the invasion of foreign DNA (i.e. CRISPR/Cas locus), as well as carbohydrate fermentation. The 41 strains of P. acidilactici can metabolize a variety of carbon sources, which enhances the adaptability of this species and survival in different environments. This study evaluated the antibacterial ability, genome evolution, and ecological flexibility of P. acidilactici from the perspective of genetics and provides strong supporting evidence for its industrial development and application.

Garden microbiomes of Apterostigma dentigerum and Apterostigma pilosum fungus-growing ants (Hymenoptera: Formicidae): Cely T. González , Kristin Saltonstall , Hermógenes Fernández-Marín; J. Microbiol. 2019;57(10):842-851. Published online August 3, 2019; DOI: https://doi.org/10.1007/s12275-019-8639-0

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Abstract: Fungus-growing ants share a complex symbiosis with microbes, including fungal mutualists, antibiotic-producing bacteria, and fungal pathogens. The bacterial communities associated with this symbiosis are poorly understood but likely play important roles in maintaining the health and function of fungal gardens. We studied bacterial communities in gardens of two Apterostigma species, A. dentigerum, and A. pilosum, using next-generation sequencing to evaluate differences between the two ant species, their veiled and no-veiled fungal garden types, and across three collection locations. We also compared different parts of nests to test for homogeneity within nests. Enterobacteriaceae dominated gardens of both species and common OTUs were shared across both species and nest types. However, differences in community diversity were detected between ant species, and in the communities of A. dentigerum veiled and no-veiled nests within sites. Apterostigma pilosum had a higher proportion of Phyllobacteriaceae and differed from A. dentigerum in the proportions of members of the order Clostridiales. Within A. dentigerum, nests with veiled and no-veiled fungus gardens had similar taxonomic profiles but differed in the relative abundance of some groups, with veiled gardens having more Rhodospirillaceae and Hyphomicrobiaceae, and no-veiled having more Xanthomonadaceae and certain genera in the Enterobacteriaceae C. However, bacterial communities in Apterostigma fungal gardens are highly conserved and resemble those of the nests of other attine ants with dominant taxa likely playing a role in biomass degradation and defense. Further work is required to understand and explain how bacterial community composition of fungus-growing nests is maintained.

Community structures and genomic features of undesirable white colony-forming yeasts on fermented vegetables: Joon Yong Kim , Juseok Kim , In-Tae Cha , Min Young Jung , Hye Seon Song , Yeon Bee Kim , Changsu Lee , Seung-Yeon Kang , Jin-Woo Bae , Yoon-E Choi , Tae-Woon Kim , Seong Woon Roh; J. Microbiol. 2019;57(1):30-37. Published online October 25, 2018; DOI: https://doi.org/10.1007/s12275-019-8487-y

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21 Citations

Abstract: White colony-forming yeasts (WCFYs) often appear in fermented foods, depending on the storage method. Despite the ongoing research on fermented foods, the community and genome features of WCFYs have not been well studied. In this study, the community structures of WCFYs on fermented vegetables (kimchi) prepared with various raw materials were investigated using deep sequencing. Only eight operational taxonomic units (OTUs) were detected, indicating that the community structure of WCFYs on kimchi is very simple. The five most abundant OTUs represented Pichia kluyveri, Yarrowia lipolytica, Candida sake, Hanseniaspora uvarum, and Kazachstania servazzii. Using a culture-dependent
method
, 41 strains representing the five major OTUs were isolated from the surface of the food samples. Whole genomes of the five major yeast strains were sequenced and annotated. The total genome length for the strains ranged from 8.97 Mbp to 21.32 Mbp. This is the first study to report genome sequences of the two yeasts Pichia kluyveri and Candida sake. Genome analysis indicated that each yeast strain had core metabolic pathways such as oxidative phosphorylation; purine metabolism; glycolysis/gluconeogenesis; aminoacyl- tRNA biosynthesis; citrate cycle; but strain specific pathways were also found. In addition, no toxin or antimicrobial resistance genes were identified. Our study provides genome information for five WCFY strains that may highlight their potential beneficial or harmful metabolic effects in fermented vegetables.

Vertical distribution of bacterial community is associated with the degree of soil organic matter decomposition in the active layer of moist acidic tundra: Hye Min Kim , Min Jin Lee , Ji Young Jung , Chung Yeon Hwang , Mincheol Kim , Hee-Myong Ro , Jongsik Chun , Yoo Kyung Lee; J. Microbiol. 2016;54(11):713-723. Published online October 29, 2016; DOI: https://doi.org/10.1007/s12275-016-6294-2

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54 Citations

Abstract: The increasing temperature in Arctic tundra deepens the active layer, which is the upper layer of permafrost soil that experiences repeated thawing and freezing. The increasing of soil temperature and the deepening of active layer seem to affect soil microbial communities. Therefore, information on soil microbial communities at various soil depths is essential to understand their potential responses to climate change in the active layer soil. We investigated the community structure of soil bacteria in the active layer from moist acidic tundra in Council, Alaska. We also interpreted their relationship with some relevant soil physicochemical characteristics along soil depth with a fine scale (5 cm depth interval). The bacterial community structure was found to change along soil depth. The relative abundances of Acidobacteria, Gammaproteobacteria, Planctomycetes, and candidate phylum WPS-2 rapidly decreased with soil depth, while those of Bacteroidetes, Chloroflexi, Gemmatimonadetes, and candidate AD3 rapidly increased. A structural shift was also found in the soil bacterial communities around 20 cm depth, where two organic (upper Oi and lower Oa) horizons are subdivided. The quality and the decomposition degree of organic matter might have influenced the bacterial community structure. Besides the organic matter quality, the vertical distribution of bacterial communities was also found to be related to soil pH and total phosphorus content. This study showed the vertical change of bacterial community in the active layer with a fine scale resolution and the possible influence of the quality of soil organic matter on shaping bacterial community structure.

Dominant genera of cyanobacteria in Lake Taihu and their relationships with environmental factors: Lijun Feng , Shiyou Liu , Wenxian Wu , Jiawen Ma , Pei Li , Hailing Xu , Na Li , Yaoyu Feng; J. Microbiol. 2016;54(7):468-476. Published online June 28, 2016; DOI: https://doi.org/10.1007/s12275-016-6037-4

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Abstract: Cyanobacterial blooms in freshwaters have become one of the most widespread of environmental problems and threaten water resources worldwide. Previous studies on cyanobacteria in Lake Taihu often collected samples from one site (like Meiliang Bay or Zhushan Bay) and focused on the variation in patterns or abundance of Microcystis during the blooming season. However, the distribution of cyanobacteria in Lake Taihu shows differing pattern in various seasons. In this study, water samples were collected monthly for one year at five sites in Lake Taihu with different trophic status and a physicochemical analysis and denaturing gradient gel electrophoresis (DGGE) were conducted. DGGE fingerprint analysis showed that Microcystis (7/35 bands) and Synechococcus (12/35 bands) were the two most dominant genera present during the study period at all five sites. Cyanobium (3/35 bands) was the third most common genus which has seldom been previously reported in Lake Taihu. Redundancy analysis (RDA) indicated that the cyanobacterial community structure was significantly correlated with NO3 --N, CODMn, and NH4 +-N in the winter and spring, whereas it was correlated with water temperature in the summer and autumn. Limiting the nutrient input (especially of N and C loading) in Lake Taihu would be a key factor in controlling the growth of different genera of cyanobacteria.

Molecular diversity and distribution of indigenous arbuscular mycorrhizal communities colonizing roots of two different winter cover crops in response to their root proliferation: Masao Higo , Katsunori Isobe , Yusuke Miyazawa , Yukiya Matsuda , Rhae A. Drijber , Yoichi Torigoe; J. Microbiol. 2016;54(2):86-97. Published online February 2, 2016; DOI: https://doi.org/10.1007/s12275-016-5379-2

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Abstract: A clear understanding of how crop root proliferation affects the distribution of the spore abundance of arbuscular mycorrhizal fungi (AMF) and the composition of AMF communities in agricultural fields is imperative to identify the potential roles of AMF in winter cover crop rotational systems. Toward this goal, we conducted a field trial using wheat (Triticum aestivum L.) or red clover (Trifolium pratense L.) grown during the winter season. We conducted a molecular analysis to compare the diversity and distribution of AMF communities in roots and spore abundance in soil cropped with wheat and red clover. The AMF spore abundance, AMF root colonization, and abundance of root length were investigated at three different distances from winter crops (0 cm, 7.5 cm, and 15 cm), and differences in these variables were found between the two crops. The distribution of specific AMF communities and variables responded to the two winter cover crops. The majority of Glomerales phylotypes were common to the roots of both winter cover crops, but Gigaspora phylotypes in Gigasporales were found only in red clover roots. These
results
also demonstrated that the diversity of the AMF colonizing the roots did not significantly change with the three distances from the crop within each rotation but was strongly influenced by the host crop identity. The distribution of specific AMF phylotypes responded to the presence of wheat and red clover roots, indicating that the host crop identity was much more important than the proliferation of crop roots in determining the diversity of the AMF communities.

Research Support, Non-U.S. Gov't

Effect of Long-Term Different Fertilization on Bacterial Community Structures and Diversity in Citrus Orchard Soil of Volcanic Ash: Jae Ho Joa , Hang Yeon Weon , Hae Nam Hyun , Young Chull Jeun , Sang Wook Koh; J. Microbiol. 2014;52(12):995-1001. Published online November 29, 2014; DOI: https://doi.org/10.1007/s12275-014-4129-6

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32 Citations

Abstract: This study was conducted to assess bacterial species richness, diversity and community distribution according to different fertilization regimes for 16 years in citrus orchard soil of volcanic ash. Soil samples were collected and analyzed from Compost (cattle manure, 2,000 kg/10a), 1/2 NPK+compost (14-20-14+2,000 kg/10a), NPK+compost (28-40-28+2,000 kg/10a), NPK (28-40-28 kg/10a), 3 NPK (84-120-84 kg/10a), and Control (no fertilization) plot which have been managed in the same manners with compost and different amount of chemical fertilization. The range of pyrosequencing reads and OTUs were 4,687–7,330 and 1,790–3,695, respectively. Species richness estimates such as Ace, Chao1, and Shannon index were higher in 1/2 NPK+compost than other treatments, which were 15,202, 9,112, 7.7, respectively. Dominant bacterial groups at level of phylum were Proteobacteria, Acidobacteria, and Actinobacteria. Those were occupied at 70.9% in 1/2 NPK+compost. Dominant bacterial groups at level of genus were Pseudolabrys, Bradyrhizobium, and Acidobacteria. Those were distributed at 14.4% of a total of bacteria in Compost. Soil pH displayed significantly closely related to bacterial species richness estimates such as Ace, Chao1 (p<0.05) and Shannon index (p<0.01). However, it showed the negative correlation with exchangeable aluminum contents (p<0.05). In conclusion, diversity of bacterial community in citrus orchard soil was affected by fertilization management, soil pH changes and characteristics of volcanic ash.

Research Support, U.S. Gov't, Non-P.H.S.

Functional Shifts in Unvegetated, Perhumid, Recently-Deglaciated Soils Do Not Correlate with Shifts in Soil Bacterial Community Composition: Sarah R. Sattin , Cory C. Cleveland , Eran Hood , Sasha C. Reed , Andrew J. King , Steven K. Schmidt , Michael S. Robeson , Nataly Ascarrunz , Diana R. Nemergut; J. Microbiol. 2009;47(6):673-681. Published online February 4, 2010; DOI: https://doi.org/10.1007/s12275-009-0194-7

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73 Citations

Abstract: Past work in recently deglaciated soils demonstrates that microbial communities undergo shifts prior to plant colonization. To date, most studies have focused on relatively ‘long’ chronosequences with the ability to sample plant-free sites over at least 50 years of development. However, some recently deglaciated soils feature rapid plant colonization and questions remain about the relative rate of change in the microbial community in the unvegetated soils of these chronosequences. Thus, we investigated the forelands of the Mendenhall Glacier near Juneau, AK, USA, where plants rapidly establish. We collected unvegetated samples representing soils that had been ice-free for 0, 1, 4, and 8 years. Total nitrogen (N) ranged from 0.00~0.14 mg/g soil, soil organic carbon pools ranged from 0.6~2.3 mg/g soil, and both decreased in concentration between the 0 and 4 yr soils. Biologically available phosphorus (P) and pH underwent similar dynamics. However, both pH and available P increased in the 8 yr soils. Nitrogen fixation was nearly undetectable in the most recently exposed soils, and increased in the 8 yr soils to ~5 ng N fixed/cm2/h, a trend that was matched by the activity of the soil N-cycling enzymes urease and β-1,4-N-acetyl-glucosaminidase. 16S rRNA gene clone libraries revealed no significant differences between the 0 and 8 yr soils; however, 8 yr soils featured the presence of cyanobacteria, a division wholly absent from the 0 yr soils. Taken together, our results suggest that microbes are consuming allochtonous organic matter sources in the most recently exposed soils. Once this carbon source is depleted, a competitive advantage may be ceded to microbes not reliant on in situ nutrient sources.

Research Support, Non-U.S. Gov't

Dominance of Endospore-forming Bacteria on a Rotating Activated Bacillus Contactor Biofilm for Advanced Wastewater Treatment: Seong Joo Park , Jerng Chang Yoon , Kwang-Soo Shin , Eung Ho Kim , Soobin Yim , Yeon-Je Cho , Gi Moon Sung , Dong-Geun Lee , Seung Bum Kim , Dong-Uk Lee , Sung-Hoon Woo , Ben Koopman; J. Microbiol. 2007;45(2):113-121.; DOI: https://doi.org/2525 [pii]

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Abstract: The bacterial diversity inherent to the biofilm community structure of a modified rotating biological contactor wastewater treatment process, referred to as the Rotating Activated Bacillus Contactor (RABC) process, was characterized in this study, via both culture-dependent and culture-independent methods. On the basis of culture-dependent methods, Bacillus sp. were found to exist in large numbers on the biofilm (6.5% of the heterotrophic bacteria) and the microbial composition of the biofilms was quite simple. Only three phyla were identified-namely, the Proteobacteria, the Actinobacteria (High G+C Gram-positive bacteria), and the Firmicutes (Low G+C Gram-positive bacteria). The culture-independent partial 16S rDNA sequence analysis revealed a considerably more diverse microbial composition within the biofilms. A total of eight phyla were recovered in this case, three of which were major groups: the Firmicutes (43.9%), the Proteobacteria (28.6%), and the Bacteroidetes (17.6%). The remaining five phyla were minor groups: the Planctomycetes (4.4%), the Chlorobi (2.2%), the Actinobacteria (1.1%), the Nitrospirae (1.1%), and the Verrucomicrobia (1.1%). The two most abundant genera detected were the endospore-forming bacteria (31.8%), Clostridium and Bacillus, both of which are members of the Firmicutes phylum. This finding indicates that these endospore-forming bacteria successfully colonized and dominated the RABC process biofilms. Many of the colonies or clones recovered from the biofilms evidenced significantly high homology in the 16S rDNA sequences of bacteria stored in databases associated with advanced wastewater treatment capabilities, including nitrification and denitrification, phosphorus accumulation, the removal of volatile odors, and the removal of chlorohydrocarbons or heavy metals. The microbial community structures observed in the biofilms were found to correlate nicely with the enhanced performance of advanced wastewater treatment protocols.

Review

Effects of Elevated Atmospheric CO_2 Concentrations on Soil Microorganisms: Chris Freeman , Seon-Young Kim , Seung-Hoon Lee , Hojeong Kang; J. Microbiol. 2004;42(4):267-277.; DOI: https://doi.org/2111 [pii]

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Abstract: Effects of elevated CO_2 on soil microorganisms are known to be mediated by various interactions with plants, for which such effects are relatively poorly documented. In this review, we summarize and synthesize results from studies assessing impacts of elevated CO_2 on soil ecosystems, focusing primarily on plants and a variety the of microbial processes. The processes considered include changes in microbial biomass of C and N, microbial number, respiration rates, organic matter decomposition, soil enzyme activities, microbial community composition, and functional groups of bacteria mediating trace gas emission such as methane and nitrous oxide. Elevated CO_2 in atmosphere may enhance certain microbial processes such as CH_4 emission from wetlands due to enhanced carbon supply from plants. However, responses of extracellular enzyme activities and microbial community structure are still controversy, because interferences with other factors such as the types of plants, nutrient availabilitial in soil, soil types, analysis methods, and types of CO_2 fumigation systems are not fully understood.

Research Support, Non-U.S. Gov't

Monitoring of Bacterial Community in a Coniferous Forest Soil After a Wildfire: Ok-Sun Kim , Jae-Jun Yoo , Dong-Hun Lee , Tae-Seok Ahn , Hong-Gyu Song; J. Microbiol. 2004;42(4):278-284.; DOI: https://doi.org/2110 [pii]

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Abstract: Changes in the soil bacterial community of a coniferous forest were analyzed to assess microbial responses to wildfire. Soil samples were collected from three different depths in lightly and severely burned areas, as well as a nearby unburned control area. Direct bacterial counts ranged from 3.3-22.6 x10^8 cells/(g . soil). In surface soil, direct bacterial counts of unburned soil exhibited a great degree of fluctuation. Those in lightly burned soil changed less, but no significant variation was observed in the severely burned soil. The fluctuations of direct bacterial count were less in the middle and deep soil layers. The structure of the bacterial community was analyzed via the fluorescent in situ hybridization method. The number of bacteria detected with the eubacteria-targeted probe out of the direct bacterial count varied from 30.3 to 84.7%, and these ratios were generally higher in the burned soils than in the unburned control soils. In the surface unburned soil, the ratios of [alpha]-, [beta]- and [gamma]-proteobacteria, Cytophaga-Flavobacterium group, and other eubacteria groups to total eubacteria were 9.9, 10.6, 15.5, 9.0, and 55.0%, respectively, and these ratios were relatively stable. The ratios of [alpha]-, [beta]- and [gamma]-proteobacteria, and Cytophaga-Flavobacterium group to total eubacteria increased immediately after the wildfire, and the other eubacterial proportions decreased in the surface and middle layer soils. By way of contrast, the composition of the 5 groups of eubacteria in the subsurface soil exhibited no significant fluctuations during the entire period. The total bacterial population and bacterial community structure disturbed by wildfire soon began to recover, and original levels seemed to be restored 3 months after the wildfire.

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