Journal of Microbiology

Journal Articles

Rhodobacteraceae are Prevalent and Ecologically Crucial Bacterial Members in Marine Biofloc Aquaculture.: Meora Rajeev, Jang-Cheon Cho; J. Microbiol. 2024;62(11):985-997. Published online November 15, 2024; DOI: https://doi.org/10.1007/s12275-024-00187-0

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Abstract: Bioflocs are microbial aggregates primarily composed of heterotrophic bacteria that play essential ecological roles in maintaining animal health, gut microbiota, and water quality in biofloc aquaculture systems. Despite the global adoption of biofloc aquaculture for shrimp and fish cultivation, our understanding of biofloc microbiota-particularly the dominant bacterial members and their ecological functions-remains limited. In this study, we employed integrated metataxonomic and metagenomic approaches to demonstrate that the family Rhodobacteraceae of Alphaproteobacteria consistently dominates the biofloc microbiota and plays essential ecological roles. We first analyzed a comprehensive metataxonomic dataset consisting of 200 16S rRNA gene amplicons collected across three Asian countries: South Korea, China, and Vietnam. Taxonomic investigation identified Rhodobacteraceae as the dominant and consistent bacterial members across the datasets. The predominance of this taxon was further validated through metagenomics approaches, including read taxonomy and read recruitment analyses. To explore the ecological roles of Rhodobacteraceae, we applied genome-centric metagenomics, reconstructing 45 metagenome-assembled genomes. Functional annotation of these genomes revealed that dominant Rhodobacteraceae genera, such as Marivita, Ruegeria, Dinoroseobacter, and Aliiroseovarius, are involved in vital ecological processes, including complex carbohydrate degradation, aerobic denitrification, assimilatory nitrate reduction, ammonium assimilation, and sulfur oxidation. Overall, our study reveals that the common practice of carbohydrate addition in biofloc aquaculture systems fosters the growth of specific heterotrophic bacterial communities, particularly Rhodobacteraceae. These bacteria contribute to maintaining water quality by removing toxic nitrogen and sulfur compounds and enhance animal health by colonizing gut microbiota and exerting probiotic effects.

Autotrophy to Heterotrophy: Shift in Bacterial Functions During the Melt Season in Antarctic Cryoconite Holes.: Aritri Sanyal, Runa Antony, Gautami Samui, Meloth Thamban; J. Microbiol. 2024;62(8):591-609. Published online May 30, 2024; DOI: https://doi.org/10.1007/s12275-024-00140-1

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Abstract: Microbes residing in cryoconite holes (debris, water, and nutrient-rich ecosystems) on the glacier surface actively participate in carbon and nutrient cycling. Not much is known about how these communities and their functions change during the summer melt-season when intense ablation and runoff alter the influx and outflux of nutrients and microbes. Here, we use high-throughput-amplicon sequencing, predictive metabolic tools and Phenotype MicroArray techniques to track changes in bacterial communities and functions in cryoconite holes in a coastal Antarctic site and the surrounding fjord, during the summer season. The bacterial diversity in cryoconite hole meltwater was predominantly composed of heterotrophs (Proteobacteria) throughout the season. The associated functional potentials were related to heterotrophic-assimilatory and -dissimilatory pathways. Autotrophic Cyanobacterial lineages dominated the debris community at the beginning and end of summer, while heterotrophic Bacteroidota- and Proteobacteria-related phyla increased during the peak melt period. Predictive functional analyses based on taxonomy show a shift from predominantly phototrophy-related functions to heterotrophic assimilatory pathways as the melt-season progressed. This shift from autotrophic to heterotrophic communities within cryoconite holes can affect carbon drawdown and nutrient liberation from the glacier surface during the summer. In addition, the flushing out and export of cryoconite hole communities to the fjord could influence the biogeochemical dynamics of the fjord ecosystem.

Characterization of Marinilongibacter aquaticus gen. nov., sp. nov., a unique marine bacterium harboring four CRISPR-Cas systems in the phylum Bacteroidota: Dao-Feng Zhang , Yu-Fang Yao , Hua-Peng Xue , Zi-Yue Fu , Xiao-Mei Zhang , Zongze Shao; J. Microbiol. 2022;60(9):905-915. Published online August 1, 2022; DOI: https://doi.org/10.1007/s12275-022-2102-3

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Abstract: A novel bacterium, designated YYF0007T, was isolated from an agar-degrading co-culture. The strain was found harboring four CRISPR-Cas systems of two classes in the chromosome and subsequently subjected to a study on polyphasic taxonomy. Pairwise analyses of the 16S rRNA gene sequences indicated that strain YYF0007T had highest 16S rRNA gene sequence similarity (92.2%) to Jiulongibacter sediminis JN- 14-9T. The phylogenomic trees based on the 16S rRNA gene and 269 single-copy orthologous gene clusters (OCs) indicated that strain YYF0007T should be recognized as a novel genus of the family Spirosomaceae. The cells were Gramstain- negative, nonmotile, strictly aerobic, and straight long rods with no flagellum. Optimum growth occurred at 28°C and pH 7.0 with the presence of NaCl concentration 1.0–3.0% (w/v). The strain showed oxidase and catalase activities. The major fatty acids were C16:1ω5c, iso-C15:0 and summed feature 3 (C16:1 ω7c and/or C16:1 ω6c). The predominant isoprenoid quinone was MK-7. The complete genome size was 4.64 Mb with a DNA G + C content of 44.4%. Further typing of CRISPR-Cas systems in the family Spirosomaceae and the phylum Bacteroidota indicated that it was remarkable for strain YYF0007T featured by such a set of CRISPR-Cas systems. This trait highlights the applications of strain YYF- 0007T in studies on the evolutionary dynamics and bacterial autoimmunity of CRISPR-Cas system as a potential model. The name Marinilongibacter aquaticus gen. nov., sp. nov. is proposed, and the type strain is YYF0007T (= MCCC 1K06017T = GDMCC 1.2428T = JCM 34683T).

Characterization of staphylococcal endolysin LysSAP33 possessing untypical domain composition: Jun-Hyeok Yu , Do-Won Park , Jeong-A Lim , Jong-Hyun Park; J. Microbiol. 2021;59(9):840-847. Published online August 12, 2021; DOI: https://doi.org/10.1007/s12275-021-1242-1

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Abstract: Endolysin, a peptidoglycan hydrolase derived from bacteriophage, has been suggested as an alternative antimicrobial agent. Many endolysins on staphylococcal phages have been identified and applied extensively against Staphylococcus spp. Among them, LysK-like endolysin, a well-studied staphylococcal endolysin, accounts for most of the identified endolysins. However, relatively little interest has been paid to LysKunlike endolysin and a few of them has been characterized. An endolysin LysSAP33 encoded on bacteriophage SAP33 shared low homology with LysK-like endolysin in sequence by 41% and domain composition (CHAP-unknown CBD). A green fluorescence assay using a fusion protein for Lys- SAP33_CBD indicated that the CBD domain (157-251 aa) was bound to the peptidoglycan of S. aureus. The deletion of LysSAP33_CBD at the C-terminal region resulted in a significant decrease in lytic activity and efficacy. Compared to LysK-like endolysin, LysSAP33 retained its lytic activity in a broader range of temperature, pH, and NaCl concentrations. In addition, it showed a higher activity against biofilms than LysK-like endolysin. This study could be a helpful tool to develop our understanding of staphylococcal endolysins not belonging to LysK-like endolysins and a potential biocontrol agent against biofilms.

Reviews

Overview of bioinformatic methods for analysis of antibiotic resistome from genome and metagenome data: Kihyun Lee , Dae-Wi Kim , Chang-Jun Cha; J. Microbiol. 2021;59(3):270-280. Published online February 23, 2021; DOI: https://doi.org/10.1007/s12275-021-0652-4

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16 Citations

Abstract: Whole genome and metagenome sequencing are powerful approaches that enable comprehensive cataloging and profiling of antibiotic resistance genes at scales ranging from a single clinical isolate to ecosystems. Recent studies deal with genomic and metagenomic data sets at larger scales; therefore, designing computational workflows that provide high efficiency and accuracy is becoming more important. In this review, we summarize the computational workflows used in the research field of antibiotic resistome based on genome or metagenome sequencing. We introduce workflows, software tools, and data resources that have been successfully employed in this rapidly developing field. The workflow described in this review can be used to list the known antibiotic resistance genes from genomes and metagenomes, quantitatively profile them, and investigate the epidemiological and evolutionary contexts behind their emergence and transmission. We also discuss how novel antibiotic resistance genes can be discovered and how the association between the resistome and mobilome can be explored.

The functional study of human proteins using humanized yeast: Seho Kim , Juhee Park , Taekyung Kim , Jung-Shin Lee; J. Microbiol. 2020;58(5):343-349. Published online April 27, 2020; DOI: https://doi.org/10.1007/s12275-020-0136-y

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Abstract: The functional and optimal expression of genes is crucial for survival of all living organisms. Numerous experiments and efforts have been performed to reveal the mechanisms required for the functional and optimal expression of human genes. The yeast Saccharomyces cerevisiae has evolved independently of humans for billions of years. Nevertheless, S. cerevisiae has many conserved genes and expression mechanisms that are similar to those in humans. Yeast is the most commonly used model organism for studying the function and expression mechanisms of human genes because it has a relatively simple genome structure, which is easy to manipulate. Many previous studies have focused on understanding the functions and mechanisms of human proteins using orthologous genes and biological systems of yeast. In this review, we mainly introduce two recent studies that replaced human genes and nucleosomes with those of yeast. Here, we suggest that, although yeast is a relatively small eukaryotic cell, its humanization is useful for the direct study of human proteins. In addition, yeast can be used as a model organism in a broader range of studies, including drug screening.

Journal Articles

Comparative genome analysis of the Flavobacteriales bacterium strain UJ101, isolated from the gut of Atergatis reticulatus: Jhung-Ahn Yang , Sung-Hyun Yang , Junghee Kim , Kae Kyoung Kwon , Hyun-Myung Oh; J. Microbiol. 2017;55(7):583-591. Published online June 30, 2017; DOI: https://doi.org/10.1007/s12275-017-7172-2

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6 Citations

Abstract: Here we report the comparative genomic analysis of strain UJ101 with 15 strains from the family Flavobacteriaceae, using the CGExplorer program. Flavobacteriales bacterium strain UJ101 was isolated from a xanthid crab, Atergatis reticulatus, from the East Sea near Korea. The complete genome of strain UJ101 is a 3,074,209 bp, single, circular chromosome with 30.74% GC content. While the UJ101 genome contains a number of annotated genes for many metabolic pathways, such as the Embden–Meyerhof pathway, the pentose phosphate pathway, the tricarboxylic acid (TCA) cycle, and the glyoxylate cycle, genes for the Entner-Douddoroff pathway are not found in the UJ101 genome. Overall, carbon fixation processes were absent but nitrate reduction and denitrification pathways were conserved. The UJ101 genome was compared to genomes from other marine animals (three invertebrate strains and 5 fish strains) and other marine animal- derived genera. Notable results by genome comparisons showed that UJ101 is capable of denitrification and nitrate reduction, and that biotin-thiamine pathway participation varies among marine bacteria; fish-dwelling bacteria, freeliving bacteria, invertebrate-dwelling bacteria, and strain UJ101. Pan-genome analysis of the 16 strains in this study included 7,220 non-redundant genes that covered 62% of the pan-genome. A core-genome of 994 genes was present and consisted of 8% of the genes from the pan-genome. Strain UJ101 is a symbiotic hetero-organotroph isolated from xanthid crab, and is a metabolic generalist with nitrate-reducing abilities but without the ability to synthesize biotin. There is a general tendency of UJ101 and some fish pathogens to prefer thiamine-dependent glycolysis to gluconeogenesis. Biotin and thiamine auxotrophy or prototrophy may be used as important markers in microbial community studies.

Identification and characterization of a new agar-degrading strain with the novel properties of saccharides inhibition and nitrogen fixation: Hao Wu , Guiguang Chen , Yaxi Bian , Wei Zeng , Bihong Sun , Zhiqun Liang; J. Microbiol. 2017;55(6):475-482. Published online May 28, 2017; DOI: https://doi.org/10.1007/s12275-017-6464-x

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Abstract: In this study, a new agar-degrading strain was isolated from soil with agar as a sole carbon source and energy. Based on its morphological, physiological, biochemical characterization and 16S rDNA sequence, the strain was identified as Strep-tomyces lavendulae UN-8. The extracellular agarase activity reached 0.03 U/ml after fermentation in shake flask (250 ml), which was close to other reported non-marine micro-organisms. Furthermore, it is interesting that the growth of UN-8 would be inhibited by glucose (40 g/L) and maltose (40 g/L) with the inhibitory rate of 100% and 70%, respec-tively. Besides, UN-8 could be grown on the solid medium without any nitrogen sources, then the possible nitrogen fix-ation gene nifU was cloned from its genomic DNA. The de-duced amino acid sequence of nifU has high similarity (98%) with nitrogen fixation protein NifU from Streptomyces sp. NRRL S-104 (KJY22454.1) and Streptomyces sp. NRRL F-4428 (KJK52526.1) based on NCBI blast. It is suggested that the nifU gene of UN-8 also encoded nitrogen fixation protein NifU. These results provided some new information for the further understanding of agar-degrading strain.

Requirement of the isocitrate lyase gene ICL1 for VPS41-mediated starvation response in Cryptococcus neoformans: Zhe Xu , Yafei Zhi , Jianzhang Dong , Benfeng Lin , Di Ye , Xiaoguang Liu; J. Microbiol. 2016;54(7):487-491. Published online June 28, 2016; DOI: https://doi.org/10.1007/s12275-016-6177-6

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Abstract: Cryptococcus neoformans is a major cause of fungal meningitis in individuals with impaired immunity. Our previous studies have shown that the VPS41 gene plays a critical role in the survival of Cryptococcus neoformans under nitrogen starvation; however, the molecular mechanisms underlying VPS41-mediated starvation response remain to be elucidated. In the present study, we show that, under nitrogen starvation, VPS41 strongly enhanced ICL1 expression in C. neoformans and that overexpression of ICL1 in the vps41 mutant dramatically suppressed its defects in starvation response due to the loss of VPS41 function. Moreover, targeted deletion of ICL1 resulted in a dramatic decline in viability of C. neoformans cells under nitrogen deprivation. Taken together, our data suggest a model in which VPS41 up-regulates ICL1 expression, directly or indirectly, to promote survival of C. neoformans under nitrogen starvation.

Characterization of MocR, a GntR-like transcriptional regulator, in Bradyrhizobium japonicum: its impact on motility, biofilm formation, and soybean nodulation: May Nyan Taw , Hae-In Lee , Sang-Ho Lee , Woo-Suk Chang; J. Microbiol. 2015;53(8):518-525. Published online July 31, 2015; DOI: https://doi.org/10.1007/s12275-015-5313-z

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9 Citations

Abstract: Bradyrhizobium japonicum is a Gram-negative soil bacterium that can fix nitrogen into ammonia by developing a symbiotic relationship with the soybean plant. MocR proteins make up a subfamily of GntR superfamily, one of the most widely distributed and prolific groups of the helix-turn-helix transcription factors. In this study, we constructed a mutant strain for mocR (blr6977) to investigate its role in cellular processes and symbiosis in B. japonicum. Although growth rate and morphology of the mutant were indistinguishable from those of the wild type, the mutant showed significant differences in motility and attachment (i.e., biofilm formation) from the wild type. The mutant displayed a decrease in biofilm formation, but was more motile than the wild type. The inactivation of mocR did not affect the number of nodules on soybean roots, but caused delayed nodulation. Delayed nodulation intrigued us to study competitiveness of the mutant infecting soybeans. The mutant was less competitive than the wild type, indicating that delayed nodulation might be due to competitiveness. Gene expressions of other MocR subfamily members were also compared between the wild type and mutant strains. None of the mocR-like genes examined in this study were differentially expressed between both strains.

Research Support, Non-U.S. Gov'ts

Role of the extracytoplasmic function sigma factor CarQ in oxidative response of Bradyrhizobium japonicum: Anchana Thaweethawakorn , Dylan Parks , Jae-Seong So , Woo-Suk Chang; J. Microbiol. 2015;53(8):526-534. Published online July 31, 2015; DOI: https://doi.org/10.1007/s12275-015-5308-9

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Abstract: As a nitrogen-fixing bacterium, Bradyrhizobium japonicum can establish a symbiotic relationship with the soybean plant (Glycine max). To be a successful symbiont, B. japonicum must deal with plant defense responses, such as an oxidative burst. Our previous functional genomics study showed that carQ (bll1028) encoding extracytoplasmic function (ECF) sigma factor was highly expressed (107.8-fold induction) under oxidative stress. Little is known about the underlying mechanisms of how CarQ responds to oxidative stress. In this study, a carQ knock-out mutant was constructed using site-specific mutagenesis to identify the role of carQ in the oxidative response of B. japonicum. The carQ mutant showed a longer generation time than the wild type and exhibited significantly decreased survival at 10 mM H2O2 for 10 min of exposure. Surprisingly, there was no significant difference in expression of oxidative stress-responsive genes such as katG and sod between the wild type and carQ mutant. The mutant also showed a significant increase in susceptibility to H2O2 compared to the wild type in the zone inhibition assay. Nodulation phenotypes of the carQ mutant were distinguishable compared to those of the wild type, including lower numbers of nodules, decreased nodule dry weight, decreased plant dry weight, and a lower nitrogen fixation capability. Moreover, desiccation of mutant cells also resulted in significantly lower percent of survival in both early (after 4 h) and late (after 24 h) desiccation periods. Taken together, this information will provide an insight into the role of the ECF sigma factor in B. japonicum to deal with a plant-derived oxidative burst.

Analysis of the Abilities of Endophytic Bacteria Associated with Banana Tree Roots to Promote Plant Growth: Leandro Fernandes Andrade , Gleika Larisse Oliveira Dorasio de Souza , Silvia Nietsche , Adelica Aparecida Xavier , Marcia Regina Costa , Acleide Maria Santos Cardoso , Marlon Cristian Toledo Pereira , Débora Francine Gomes Silva Pereira; J. Microbiol. 2014;52(1):27-34. Published online January 4, 2014; DOI: https://doi.org/10.1007/s12275-014-3019-2

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61 Citations

Abstract: A total of 40 endophytic bacterial isolates obtained from banana tree roots were characterized for their biotechnological potential for promoting banana tree growth. All isolates had at least one positive feature. Twenty isolates were likely diazotrophs and formed pellicles in nitrogen-free culture medium, and 67% of these isolates belonged to the genus Bacillus sp. The isolates EB-04, EB-169, EB-64, and EB-144 had N fixation abilities as measured by the Kjeldahl method and by an acetylene reduction activity assay. Among the 40 isolates, 37.5% were capable of solubilizing inorganic phosphate and the isolates EB-47 and EB-64 showed the highest solubilization capacity. The isolate EB-53 (Lysinibacillus sp.) had a high solubilization index, whereas 73% of the isolates had low solubilization indices. The synthesis of indole-3- acetic acid (IAA) in the presence of L-tryptophan was detected in 40% of the isolates. The isolate EB-40 (Bacillus sp.) produced the highest amount of IAA (47.88 μg/ml) in medium supplemented with L-tryptophan and was able to synthesize IAA in the absence of L-tryptophan. The isolates EB-126 (Bacillus subtilis) and EB-47 (Bacillus sp.) were able to simultaneously fix nitrogen, solubilize phosphate and produce IAA in vitro. The results of this study demonstrated that the isolates analyzed here had diverse abilities and all have the potential to be used as growth-promoting microbial inoculants for banana trees.

Saccharomyces cerevisiae Can Secrete Sapp1p Proteinase of Candida parapsilosis But Cannot Use It for Efficient Nitrogen Acquisition: Zuzana Vinterová , Václava Bauerová , Ji&# , Hana Sychrová , Olga Hru&# , Iva Pichová; J. Microbiol. 2013;51(3):336-344. Published online June 28, 2013; DOI: https://doi.org/10.1007/s12275-013-2422-4

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Abstract: Secreted aspartic proteinase Sapp1p of Candida parapsilosis represents one of the factors contributing to the pathogenicity of the fungus. The proteinase is synthesized as an inactive pre-pro-enzyme, but only processed Sapp1p is secreted into extracellular space. We constructed a plasmid containing the SAPP1 coding sequence under control of the ScGAL1 promoter and used it for proteinase expression in a Saccharomyces cerevisiae kex2Δ mutant. Because Sapp1p maturation depends on cleavage by Kex2p proteinase, the kex2Δ mutant secreted only the pro-form of Sapp1p. Characterization of this secreted proteinase form revealed that the Sapp1p signal peptide consists of 23 amino acids. Additionally, we prepared a plasmid with the SAPP1 coding sequence under control of its authentic CpSAPP1 promoter, which contains two GATAA motifs. While in C. parapsilosis SAPP1 expression is repressed by good low molecular weight nitrogen sources (e.g., ammonium ions), S. cerevisiae cells harboring this plasmid secreted a low concentration of active proteinase regardless of the type of nitrogen source used. Quantitative real-time PCR analysis of a set of genes related to nitrogen metabolism and uptake (GAT1, GLN3, STP2, GAP1, OPT1, and PTR2) obtained from S. cerevisiae cells transformed with either plasmid encoding SAPP1 under control of its own promoter or empty vector and cultivated in media containing various nitrogen sources also suggested that SAPP1 expression can be connected with the S. cerevisiae regulatory network. However, this regulation occurs in a different manner than in C. parapsilosis.

Enhancement of Butanol Tolerance and Butanol Yield in Clostridium acetobutylicum Mutant NT642 Obtained by Nitrogen Ion Beam Implantation: Xiao-Bo Liu , Qiu-Ya Gu , Xiao-Bin Yu , Wei Luo; J. Microbiol. 2012;50(6):1024-1028. Published online December 30, 2012; DOI: https://doi.org/10.1007/s12275-012-2289-9

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29 Citations

Abstract: As a promising alternative biofuel, biobutanol can be produced through acetone/butanol/ethanol (ABE) fermentation. Currently, ABE fermentation is still a small-scale industry due to its low production and high input cost. Moreover, butanol toxicity to the Clostridium fermentation host limits the accumulation of butanol in the fermentation broth. The wild-type Clostridium acetobutylicum D64 can only produce about 13 g butanol/L and tolerates less than 2% (v/v) butanol. To improve the tolerance of C. acetobutylicum D64 for enhancing the production of butanol, nitrogen ion beam implantation was employed and finally five mutants with enhanced butanol tolerance were obtained. Among these, the most butanol tolerant mutant C. acetobutylicum NT642 can tolerate above 3% (v/v) butanol while the wide-type strain can only withstand 2% (v/v). In batch fermentation, the production of butanol and ABE yield of C. acetobutylicum NT642 was 15.4 g/L and 22.3 g/L, respectively, which were both higher than those of its parental strain and the other mutants using corn or cassava as substrate. Enhancing butanol tolerance is a great precondition for obtaining a hyperyield producer. Nitrogen ion beam implantation could be a promising biotechnology to improve butanol tolerance and production of the host strain C. acetobutylicum.

The Impacts of Excessive Nitrogen Additions on Enzyme Activities and Nutrient Leaching in Two Contrasting Forest Soils: Haryun Kim , Hojeong Kang; J. Microbiol. 2011;49(3):369-375. Published online June 30, 2011; DOI: https://doi.org/10.1007/s12275-011-0421-x

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28 Citations

Abstract: Nitrogen (N) deposition has increased dramatically worldwide, which may affect forest soils in various ways. In this study, we conducted a short-term manipulation experiment of N addition on two types of forest soils (urban and rural soils) found in Korea. N addition significantly decreased phenol oxidase activities in urban soil samples; however, it did not affect those in rural soils. Furthermore, N addition did not change β-glucosidase and N-acetylglucosaminidase activities, except for β-glucosidase activities in the O layer of rural soils. Changes in microbial biomass and general activity (dehydrogenase activity) were not induced by N addition, except for dehydrogenase in the A layer of urban soils. Although N addition did not change the extractable soil nutrients, organic matter, and water contents significantly, it enhanced nutrient leaching and resulted in lower pH leachate. These results suggest that excessive N addition to forest soils may induce nutrient leaching in the long-term. Overall results of our study also suggest that N addition may induce retardation of organic matter decomposition in soils; however, such a response may depend on the intensity of previous exposure to N deposition.

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