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On March 11, 2011, Japan experienced an unprecedented earthquake off the Pacific coast of Tohoku, and suffered the direct and long-term effects of the earthquake and tsunami in the area. In Fukushima prefecture, agricultural land contaminated with radioactive Cesium from the Fukushima Daiichi Nuclear Power Plant. Therefore, surface soil were removed for deconamination, and low fertility sandy soil was covered. Organic matter input is necessary to increase soil organic matter and green manure application is an effective method to improve soil fertility in the paddy field. Soil microbes and enzyme activities are sensitively responded to organic matter addition, but their dynamics on the dressed field are not well investigated. In this study, we focused on changing the microbial community, diversity and enzyme activities along with the green manure decomposition process in the sandy soil dressed paddy field in Japan. The green manure of hairy vetch and oat were harvested and incorporated in May 2020 and their decomposition process as cellulose and hemicellulose contents were determined. Soil bacterial communities were analyzed using 16S amplicon sequencing. The green manure was rapidly decomposed within the first 13 days, and they did not remain 50 days after green manure incorporation. Soil microbial biomass carbon was higher in the M treatment after GM treatment, but was not significant between treatments after 50 days. Dehydrogenase and β-glucosidase activities changed during the harvesting period, but did not correlate with GM decomposition. Microbial diversity (OTU numbers and Shannon index) also changed with GM application, but they were not associated with GM decomposition. Soil prokaryotic communities and some bacteria (Baciili and Chlorolfexi) are significantly influenced by GM treatment. However, Clostrida was not affected by GM. Mixed green manure treatment showed significantly rapid hemicellulose decomposition than other treatments. In this process, Anaerolineae were negatively correlated with the decreasing of hemicellulose in this treatment. These results showed that GM treatment affected microbial communities, and their response was active during the decomposition process.
Chol Gyu Lee; Yuko Mitsuda; Soh Sugihara; Taiichiro Ookawa; Haruo Tanaka. Effects of green manure application on soil microbial communities and activities in the decontaminated sandy soil paddy field in Fukushima, Japan. 2021, 1 .
AMA StyleChol Gyu Lee, Yuko Mitsuda, Soh Sugihara, Taiichiro Ookawa, Haruo Tanaka. Effects of green manure application on soil microbial communities and activities in the decontaminated sandy soil paddy field in Fukushima, Japan. . 2021; ():1.
Chicago/Turabian StyleChol Gyu Lee; Yuko Mitsuda; Soh Sugihara; Taiichiro Ookawa; Haruo Tanaka. 2021. "Effects of green manure application on soil microbial communities and activities in the decontaminated sandy soil paddy field in Fukushima, Japan." , no. : 1.
Anaerobic soil disinfestation (ASD) is a chemical-independent method that can reduce pathogens, such as Fusarium oxysporum. Although soil microbes play essential roles in ASD, the relationship between the microbial community structure and disinfestation efficiency remains unclear. Thus for improving our understanding of this relationship, we investigated the changes in the microbial community and pathogen density during an ASD period for 14 days in a greenhouse using three different substrates, as wheat bran, sugar-contained diatoms, and dried molasses. Soil samples were collected at 0, 3, 7, and 14 days after ASD treatment. The pathogen densities were analyzed by real-time polymerase chain reactions. Furthermore, prokaryotic community analysis was conducted by using an Illumina Miseq sequencer, and the factors related to pathogen density were statistically analyzed. The pathogen density rapidly decreased by >90% at 3 days after treatment and then slowly decreased until day 14; however the rate of decrease differed among the substrates. On the other hand, the microbial communities were altered after 3 days but recovered to their original state on day 14. The iron reduction level, microbial diversity, richness, and community structure did not correlate with pathogen density. The operational taxonomic units that drastically negatively correlated with pathogen density were Clostridia and Bacilli, both belonging to Firmicutes. This study showed that the changes in the prokaryotic community as a whole did not correlate to ASD efficiency, whereas changes in the abundance of specific microbes in the community were likely related to disinfestation efficiency.
Chol Gyu Lee; Eriko Kunitomo; Toshiya Iida; Kazuhiro Nakaho; Moriya Ohkuma. Soil prokaryotes are associated with decreasing Fusarium oxysporum density during anaerobic soil disinfestation in the tomato field. Applied Soil Ecology 2020, 155, 103632 .
AMA StyleChol Gyu Lee, Eriko Kunitomo, Toshiya Iida, Kazuhiro Nakaho, Moriya Ohkuma. Soil prokaryotes are associated with decreasing Fusarium oxysporum density during anaerobic soil disinfestation in the tomato field. Applied Soil Ecology. 2020; 155 ():103632.
Chicago/Turabian StyleChol Gyu Lee; Eriko Kunitomo; Toshiya Iida; Kazuhiro Nakaho; Moriya Ohkuma. 2020. "Soil prokaryotes are associated with decreasing Fusarium oxysporum density during anaerobic soil disinfestation in the tomato field." Applied Soil Ecology 155, no. : 103632.
We had developed a new pretreatment system using cow rumen fluid to improve the methane production from lignocellulosic substrates. However, the pretreatment conditions differ from the in-situ rumen environment, therefore different microbes may be involved in plant cell wall decomposition. In the current study, shotgun metagenomic analysis using MiSeq platform was performed to elucidate the bacteria which produce cellulase and hemicellulase in this pretreatment system. The rumen fluid which contained waste paper pieces (0.1% w/v) were incubated at 37°C during 120 h. The fluid samples were collected from the reactor at each time-point and analyzed for chemical properties. Rumen microbial DNA was extracted from 0-h and 60-h samples and subjected to shotgun-metagenomic analysis. After pretreatment, approximately half of cellulose and hemicellulose contents of the waste paper were decomposed and some volatile fatty acids were accumulated. Clostridia (e.g., Ruminococcus and Clostridium) were the predominant bacteria before and after 60-h pretreatment, and their relative abundance was increased during pretreatment. However, Prevotella and Fibrobacter, one of the most dominant bacteria in-situ rumen fluid, were observed less than 3% before incubation and they were decreased after pretreatment. Genes encoding cellulase and hemicellulase were mainly found in Ruminococcus, Clostridium, and Caldicellulosiruptor. Calicellulosiruptor, which had not been previously identified as the predominant genus in lignocellulose decomposition in in-situ rumen conditions, might be considered as the main fibrolytic bacterium in this system. Thus, this study demonstrated that the composition of fibrolytic bacteria in this system was greatly different from those in the in-situ rumen.
Chol Gyu Lee; Yasunori Baba; Ryoki Asano; Yasuhiro Fukuda; Chika Tada; Yutaka Nakai. Identification of bacteria involved in the decomposition of lignocellulosic biomass treated with cow rumen fluid by metagenomic analysis. Journal of Bioscience and Bioengineering 2020, 130, 137 -141.
AMA StyleChol Gyu Lee, Yasunori Baba, Ryoki Asano, Yasuhiro Fukuda, Chika Tada, Yutaka Nakai. Identification of bacteria involved in the decomposition of lignocellulosic biomass treated with cow rumen fluid by metagenomic analysis. Journal of Bioscience and Bioengineering. 2020; 130 (2):137-141.
Chicago/Turabian StyleChol Gyu Lee; Yasunori Baba; Ryoki Asano; Yasuhiro Fukuda; Chika Tada; Yutaka Nakai. 2020. "Identification of bacteria involved in the decomposition of lignocellulosic biomass treated with cow rumen fluid by metagenomic analysis." Journal of Bioscience and Bioengineering 130, no. 2: 137-141.
Understanding the community composition and diversity of arbuscular mycorrhizal fungi (AMF) in an agricultural ecosystem is important for exploiting their potential in sustainable crop production. In this study, we described the genetic diversity and community structure of indigenous AMF in rain-fed rice cultivars across six different regions in Ghana. The morphological and molecular analyses revealed a total of 15 different AMF genera isolated from rice roots. Rhizophagus and Glomus were observed to be predominant in all regions except the Ashanti region, which was dominated by the genera Scutellospora and Acaulospora. A comparison of AMF diversity among the agroecological zones revealed that Guinea Savannah had the highest diversity. Permutational Multivariate Analysis of Variance (PERMANOVA) analysis indicated that the available phosphorus (AP) in the soil was the principal determining factor for shaping the AMF community structure (p < 0.05). We report, for the first time, AMF diversity and community structure in rice roots and how communities are affected by the chemical properties of soil from different locations in Ghana.
Elsie Sarkodee-Addo; Michiko Yasuda; Chol Gyu Lee; Makoto Kanasugi; Yoshiharu Fujii; Richard Ansong Omari; Samuel Oppong Abebrese; Ralph Bam; Stella Asuming-Brempong; Khondoker Mohammad Golam Dastogeer; Shin Okazaki. Arbuscular Mycorrhizal Fungi Associated with Rice (Oryza sativa L.) in Ghana: Effect of Regional Locations and Soil Factors on Diversity and Community Assembly. Agronomy 2020, 10, 559 .
AMA StyleElsie Sarkodee-Addo, Michiko Yasuda, Chol Gyu Lee, Makoto Kanasugi, Yoshiharu Fujii, Richard Ansong Omari, Samuel Oppong Abebrese, Ralph Bam, Stella Asuming-Brempong, Khondoker Mohammad Golam Dastogeer, Shin Okazaki. Arbuscular Mycorrhizal Fungi Associated with Rice (Oryza sativa L.) in Ghana: Effect of Regional Locations and Soil Factors on Diversity and Community Assembly. Agronomy. 2020; 10 (4):559.
Chicago/Turabian StyleElsie Sarkodee-Addo; Michiko Yasuda; Chol Gyu Lee; Makoto Kanasugi; Yoshiharu Fujii; Richard Ansong Omari; Samuel Oppong Abebrese; Ralph Bam; Stella Asuming-Brempong; Khondoker Mohammad Golam Dastogeer; Shin Okazaki. 2020. "Arbuscular Mycorrhizal Fungi Associated with Rice (Oryza sativa L.) in Ghana: Effect of Regional Locations and Soil Factors on Diversity and Community Assembly." Agronomy 10, no. 4: 559.
Anaerobic soil disinfestation (ASD) is a chemical-independent method that can reduce pathogens. Although soil microbes play essential roles in ASD, the relationship between the microbial community structure and disinfestation efficiency remains unclear. To this end, we investigated changes in the microbial community and pathogen density during a period of ASD under field conditions for 14 days in a greenhouse using three different substrates. Soil samples were collected at 0, 3, 7, and 14 days after ASD treatment. The pathogen densities were analyzed by real-time polymerase chain reactions, prokaryotic community analysis was conducted using unidirectional pyrosequencing, and the factors related to pathogen density were statistically analyzed. The pathogen density rapidly decreased by >90% at 3 days after treatment and then slowly decreased until day 14, but the rate of decrease differed among the substrates. The microbial communities became altered after 3 days and recovered to their original state on day 14. The dipyridyl reaction, microbial diversity, richness, and community structure were not correlated with pathogen density. The most negatively correlated operational taxonomic units with pathogen density were Clostridia and Bacilli, both belonging to Firmicutes. These results suggested that the growth of specific microbes, but not the changes in microbial community structure, might be important for ASD disinfestation efficiency.
Chol Gyu Lee; Eriko Kunitomo; Toshiya Iida; Kazuhiro Nakaho; Moriya Ohkuma. Soil prokaryotes associated with decreasing pathogen density during anaerobic soil disinfestation. 2019, 774810 .
AMA StyleChol Gyu Lee, Eriko Kunitomo, Toshiya Iida, Kazuhiro Nakaho, Moriya Ohkuma. Soil prokaryotes associated with decreasing pathogen density during anaerobic soil disinfestation. . 2019; ():774810.
Chicago/Turabian StyleChol Gyu Lee; Eriko Kunitomo; Toshiya Iida; Kazuhiro Nakaho; Moriya Ohkuma. 2019. "Soil prokaryotes associated with decreasing pathogen density during anaerobic soil disinfestation." , no. : 774810.
Anaerobic soil disinfestation (ASD) is a chemical-independent fumigation method used for reducing the abundance of pathogens at soil depths of Betaproteobacteria and Clostridia were significantly increased in well-disinfested fields. Overall, 25 operational taxonomic units (OTUs) were specifically increased in various well-disinfested soils and 18 OTUs belonged to phylogenetically diversified Clostridia. Other OTUs belonged to aerobic bacteria and were not previously detected in sample collected from ASD-treated fields. The results showed that the changes to the prokaryotic communities did not affect ASD efficiency, whereas changes in the abundance of specific microbes in the community were related to disinfestation.
Chol Gyu Lee; Toshiya Iida; Eriko Matsuda; Kayo Yoshida; Masato Kawabe; Masayuki Maeda; Yasunori Muramoto; Hideki Watanabe; Yoko Otani; Kazhiro Nakaho; Moriya Ohkuma; Eriko Matusda; Kazuhiro Nakaho. Comparison of prokaryotic communities among fields exhibiting different disinfestation effects by anaerobic soil disinfestation. 2019, 596825 .
AMA StyleChol Gyu Lee, Toshiya Iida, Eriko Matsuda, Kayo Yoshida, Masato Kawabe, Masayuki Maeda, Yasunori Muramoto, Hideki Watanabe, Yoko Otani, Kazhiro Nakaho, Moriya Ohkuma, Eriko Matusda, Kazuhiro Nakaho. Comparison of prokaryotic communities among fields exhibiting different disinfestation effects by anaerobic soil disinfestation. . 2019; ():596825.
Chicago/Turabian StyleChol Gyu Lee; Toshiya Iida; Eriko Matsuda; Kayo Yoshida; Masato Kawabe; Masayuki Maeda; Yasunori Muramoto; Hideki Watanabe; Yoko Otani; Kazhiro Nakaho; Moriya Ohkuma; Eriko Matusda; Kazuhiro Nakaho. 2019. "Comparison of prokaryotic communities among fields exhibiting different disinfestation effects by anaerobic soil disinfestation." , no. : 596825.
Previously, pretreatment of plant biomass using rumen fluid systems was developed to decompose cell wall. However, microbes which involved in plant cell wall decomposition in this system have not been identified, because the conditions of this system are different from the in situ rumen environment. We investigated the bacteria involved in the decomposition of cellulose and hemicellulose in a waste paper with the rumen pretreatment system using shotgun metagenomic analysis with next generation sequencing. After pretreatment of waste paper, about a half of the cellulose and hemicellulose content was decomposed. Genes encoding for cellulase and hemicellulase were mainly found to belonging to Ruminococcus, Clostridium, and Exiguobacterium. This study shows that Clostridium and Exiguobacterium, which have not been identified as predominant genus involved in cellulose and hemicellulose decomposition, might be categorized as the main fibrolytic bacteria in this system.
Chol Gyu Lee; Yasunori Baba; Ryoki Asano; Yasuhiro Fukuda; Chika Tada; Yutaka Nakai. Identification of bacteria involved in the decomposition of lignocellulosic biomass treated with cow rumen fluid by metagenomic analysis. 2019, 570374 .
AMA StyleChol Gyu Lee, Yasunori Baba, Ryoki Asano, Yasuhiro Fukuda, Chika Tada, Yutaka Nakai. Identification of bacteria involved in the decomposition of lignocellulosic biomass treated with cow rumen fluid by metagenomic analysis. . 2019; ():570374.
Chicago/Turabian StyleChol Gyu Lee; Yasunori Baba; Ryoki Asano; Yasuhiro Fukuda; Chika Tada; Yutaka Nakai. 2019. "Identification of bacteria involved in the decomposition of lignocellulosic biomass treated with cow rumen fluid by metagenomic analysis." , no. : 570374.
Fungi play an essential role in recovering the quality and fertility of soil. There is a limited understating of the complex response of fungal diversity to different organic materials in clay loam soil. Here, we report the response of soil fungi toward the short-term application of manure (M), sugarcane straw (S), and sugarcane straw plus manure (MS), including no organic material control (CK) at two different time points (50 and 100 days after application). Illumina sequencing was used to examine the fungal communities. Our results reveal a significant shift among the soil fungal community structure associated with each organic material application. After both time points, amendments—especially M and MS—decreased the fungal richness and stimulated the copiotrophic fungal group (Ascomycota) compared to the control soil (CK) and S-amended soil. On the contrary, as compared to the M and MS-amended soils, the CK and S-amended soils at both time points increased the fungal richness and stimulated the oligotrophic fungal groups. Organic material use, especially M and MS, showed variable results regarding pathogenic fungi enhancing the abundance of Lophodermium and Cercophora and decreasing Fusarium. Concerning the abundance of plant-beneficial fungi, Mortierella was reduced, and Podospora was increased by M and MS input. FUNGuild showed that the amendment of organic materials efficiently declined the abundance of endophytes and plant pathogens, but also enhanced the animal pathogens in terms of abundance with respect to CK at two time points. This study could be useful to provide a novel understanding of the management of soil-borne pathogens by organic amendments for the sustainable production of short-term crops.
Muhammad Tayyab; Waqar Islam; Chol Gyu Lee; Ziqin Pang; Farghama Khalil; Sheng Lin; Wenxiong Lin; Hua Zhang. Short-Term Effects of Different Organic Amendments on Soil Fungal Composition. Sustainability 2019, 11, 198 .
AMA StyleMuhammad Tayyab, Waqar Islam, Chol Gyu Lee, Ziqin Pang, Farghama Khalil, Sheng Lin, Wenxiong Lin, Hua Zhang. Short-Term Effects of Different Organic Amendments on Soil Fungal Composition. Sustainability. 2019; 11 (1):198.
Chicago/Turabian StyleMuhammad Tayyab; Waqar Islam; Chol Gyu Lee; Ziqin Pang; Farghama Khalil; Sheng Lin; Wenxiong Lin; Hua Zhang. 2019. "Short-Term Effects of Different Organic Amendments on Soil Fungal Composition." Sustainability 11, no. 1: 198.
Chol Gyu Lee; Shizuo Suzuki; Kazuyuki Inubushi. Temperature sensitivity of anaerobic labile soil organic carbon decomposition in brackish marsh. Soil Science and Plant Nutrition 2018, 64, 443 -448.
AMA StyleChol Gyu Lee, Shizuo Suzuki, Kazuyuki Inubushi. Temperature sensitivity of anaerobic labile soil organic carbon decomposition in brackish marsh. Soil Science and Plant Nutrition. 2018; 64 (4):443-448.
Chicago/Turabian StyleChol Gyu Lee; Shizuo Suzuki; Kazuyuki Inubushi. 2018. "Temperature sensitivity of anaerobic labile soil organic carbon decomposition in brackish marsh." Soil Science and Plant Nutrition 64, no. 4: 443-448.
Here, we report the draft genome sequence of Tepidibacter mesophilus strain JCM 16806 T , which was isolated from an oil field. It is composed of 3,310,272 bp and contains 3,160 protein-coding genes, 8 5S rRNAs, 3 16S rRNAs, and 69 tRNAs.
Chol Gyu Lee; Masahiro Yuki; Toshiya Iida; Kazuhiro Nakaho; Moriya Ohkuma. Draft Genome Sequence of Tepidibacter mesophilus Strain JCM 16806 T Isolated from Soil Polluted by Crude Oil in China. Genome Announcements 2017, 5, e01308-17 .
AMA StyleChol Gyu Lee, Masahiro Yuki, Toshiya Iida, Kazuhiro Nakaho, Moriya Ohkuma. Draft Genome Sequence of Tepidibacter mesophilus Strain JCM 16806 T Isolated from Soil Polluted by Crude Oil in China. Genome Announcements. 2017; 5 (47):e01308-17.
Chicago/Turabian StyleChol Gyu Lee; Masahiro Yuki; Toshiya Iida; Kazuhiro Nakaho; Moriya Ohkuma. 2017. "Draft Genome Sequence of Tepidibacter mesophilus Strain JCM 16806 T Isolated from Soil Polluted by Crude Oil in China." Genome Announcements 5, no. 47: e01308-17.
The characterization of microbial communities that promote or suppress soil-borne pathogens is important for controlling plant diseases. We compared prokaryotic communities in soil with or without the signs of tomato bacterial wilt caused by Ralstonia solanacearum. Soil samples were collected from a greenhouse at two different depths because this pathogen is present in deep soil. We used samples from sites in which we detected phcA, a key gene regulating R. solanacearum pathogenicity. The pyrosequencing of prokaryotic 16S rRNA sequences in four soil samples without disease symptoms but with phcA and in two soil samples with disease symptoms indicated that community richness was not significantly different between these two soils; however, microbial diversity in the lower soil layer was higher in soil samples without disease symptoms but with phcA. A difference in prokaryotic community structures between soil samples with and without bacterial wilt was only observed in the upper soil layer despite apparent similarities in the communities at the phylum level. Proteobacteria, Acidobacteria, Chloroflexi, Verrucomicrobia, and several Archaea were more abundant in soil samples without disease symptoms, whereas taxa in another eight phyla were more abundant in soil samples with disease symptoms. Furthermore, some prokaryotic taxa were abundant specifically in the lower layer of soil, regardless of whether disease was present. These prokaryotic taxa may suppress or accelerate the pathogenesis of bacterial wilt and are good targets for future studies on disease control.
Chol Gyu Lee; Toshiya Iida; Yasuhiro Inoue; Yasunori Muramoto; Hideki Watanabe; Kazuhiro Nakaho; Moriya Ohkuma. Prokaryotic Communities at Different Depths between Soils with and without Tomato Bacterial Wilt but Pathogen-Present in a Single Greenhouse. Microbes and Environments 2017, 32, 118 -124.
AMA StyleChol Gyu Lee, Toshiya Iida, Yasuhiro Inoue, Yasunori Muramoto, Hideki Watanabe, Kazuhiro Nakaho, Moriya Ohkuma. Prokaryotic Communities at Different Depths between Soils with and without Tomato Bacterial Wilt but Pathogen-Present in a Single Greenhouse. Microbes and Environments. 2017; 32 (2):118-124.
Chicago/Turabian StyleChol Gyu Lee; Toshiya Iida; Yasuhiro Inoue; Yasunori Muramoto; Hideki Watanabe; Kazuhiro Nakaho; Moriya Ohkuma. 2017. "Prokaryotic Communities at Different Depths between Soils with and without Tomato Bacterial Wilt but Pathogen-Present in a Single Greenhouse." Microbes and Environments 32, no. 2: 118-124.
Biocontrol agents (BCA) effectively suppress soil-borne disease symptoms using natural antagonistic prokaryotes or eukaryotes. The main issue associated with the application of BCA is that disease reduction effects are unstable under different field conditions. In order to identify potentially effective BCA among several fields, we compared prokaryotic and eukaryotic communities in soil with and without tomato bacterial wilt from three different fields, each of which had the same field management and similar soil characteristics. Soil samples were collected from three fields and two depths because bacterial wilt pathogens were present in soil at a depth greater than 40 cm. We classified soil samples based on the presence or absence of the bacterial phcA gene, a key gene for bacterial wilt pathogenicity and tomato disease symptoms. Pyrosequencing of the prokaryotic 16S rRNA gene and eukaryotic internal transcribed spacer region sequences showed that the diversity and richness of the communities mostly did not correlate with disease symptoms. Prokaryotic and eukaryotic community structures were affected more by regional differences than the appearance of disease. Several prokaryotes and eukaryotes were more abundant in soil that lacked disease symptoms, and eight prokaryotes and one eukaryote of this group were commonly detected among the three fields. Some of these taxa were not previously found in disease-suppressive soil. Our results suggest that several prokaryotes and eukaryotes control plant disease symptoms.
Chol Gyu Lee; Toshiya Iida; Yohei Uwagaki; Yoko Otani; Kazuhiro Nakaho; Moriya Ohkuma. Comparison of Prokaryotic and Eukaryotic Communities in Soil Samples with and without Tomato Bacterial Wilt Collected from Different Fields. Microbes and Environments 2017, 32, 376 -385.
AMA StyleChol Gyu Lee, Toshiya Iida, Yohei Uwagaki, Yoko Otani, Kazuhiro Nakaho, Moriya Ohkuma. Comparison of Prokaryotic and Eukaryotic Communities in Soil Samples with and without Tomato Bacterial Wilt Collected from Different Fields. Microbes and Environments. 2017; 32 (4):376-385.
Chicago/Turabian StyleChol Gyu Lee; Toshiya Iida; Yohei Uwagaki; Yoko Otani; Kazuhiro Nakaho; Moriya Ohkuma. 2017. "Comparison of Prokaryotic and Eukaryotic Communities in Soil Samples with and without Tomato Bacterial Wilt Collected from Different Fields." Microbes and Environments 32, no. 4: 376-385.
Plant residues are one of the main sources of soil organic matter in paddy fields, and elucidation of the bacterial communities decomposing plant residues was important to understand their function and roles, as the microbial decomposition of plant residues is linked to soil fertility. We conducted a DNA stable isotope probing (SIP) experiment to elucidate the bacterial community assimilating 13-carbon (13C) derived from plant residue under an anoxic soil condition. In addition, we compared the bacterial community with that under the oxic soil condition, which was elucidated in our previous study (Lee et al. in Soil Biol Biochem 43:814–822, 2011). We used the 13C-labeled dried rice callus cells as a model of rice plant residue. A paddy field soil was incubated with unlabeled and 13C-labeled callus cells. DNA extracted from the soils was subjected to buoyant density gradient centrifugation to fractionate 13C-enriched DNA. Then, polymerase chain reaction (PCR) and denaturing gradient gel electrophoresis (DGGE) analysis of bacterial 16S rDNA band patterns and band sequencing method were used to evaluate bacterial community. DGGE analysis showed that the band patterns in the 13C-enriched fractions were distinctly changed over time, while the changes in the community structure before fractionation were minor. Sequencing of the 13C-labeled DGGE bands revealed that Clostridia were a major group in the bacterial communities incorporating the callus-derived carbon although Gram-negative bacteria, and Actinobacteria also participated in the carbon flow from the callus under the anoxic condition. The proportion of Gram-negative bacteria and Actinobacteria increased on 14 days after the onset of incubation, suggesting that the callus was decomposed by diverse bacterial members on this phase. When the bacterial groups incorporating the 13C were compared between under anoxic and oxic soil conditions, the composition was largely different under the two opposite conditions. However, some members of Gram-negative bacteria were commonly found under the anoxic and oxic soil conditions. The majority of bacterial members assimilating the callus carbon was Clostridia in the soil under anoxic conditions. However, several Gram-negative bacterial members, such as Acidobacteria, Bacteroidetes, and Proteobacteria, also participated in the decomposition of callus under anoxic soil conditions. Our study showed that carbon flow into the diverse bacterial members during the callus decomposition and the distinctiveness of the bacterial communities was formed under the anoxic and oxic soil conditions.
Chol Gyu Lee; Takeshi Watanabe; Susumu Asakawa. Bacterial community incorporating carbon derived from plant residue in an anoxic non-rhizosphere soil estimated by DNA-SIP analysis. Journal of Soils and Sediments 2016, 17, 1084 -1091.
AMA StyleChol Gyu Lee, Takeshi Watanabe, Susumu Asakawa. Bacterial community incorporating carbon derived from plant residue in an anoxic non-rhizosphere soil estimated by DNA-SIP analysis. Journal of Soils and Sediments. 2016; 17 (4):1084-1091.
Chicago/Turabian StyleChol Gyu Lee; Takeshi Watanabe; Susumu Asakawa. 2016. "Bacterial community incorporating carbon derived from plant residue in an anoxic non-rhizosphere soil estimated by DNA-SIP analysis." Journal of Soils and Sediments 17, no. 4: 1084-1091.
The minirhizotron technique is a non-destructive method to evaluate fine roots, which converts two-dimensional image data to three- dimensional root biomass data. Recently, conversion factors in soils at 10-cm depth intervals successfully estimated fine root biomass using image data from the minirhizotron method. However, this technique was conducted only at one forest site and did not consider different vegetation types. Therefore, the objective of this study was to verify a method for calibration of minirhizotron data with the core sampling values obtained by direct measurement of root biomass in wetland ecosystems among three vegetation types. Evaluations by minirhizotron technique and soil-core sampling were made at 30-cm soil depth in a cool-temperate brackish marsh in northern Japan. Linear regression was examined between root volume and weight of fine roots in soil core samples, and the fine root biomass on minirhizotron tubes was calculated from their length and diameter. The technique was well adapted for vegetation types dominated by Phragmites australis, Juncus yokoscensis, and Miscanthus sinensis and Cirsium inundatum. Compared with the fine root biomass estimated by the core sampling method, fine root biomass estimated by the minirhizotron method was overestimated in the 0–10-cm layer. Further, we determined conversion factors based on the ratio of the fine root biomass by the core sampling method to that by the minirhizotron tubes. Estimation of the fine root biomass using the conversion factors for each 10-cm soil depth was well adapted in P. australis vegetation and J. yokoscensis vegetation types as a forest ecosystem; meanwhile, M. sinensis and C. inundatum vegetation types were not well adapted. This study suggests that the minirhizotron technique is available to estimate fine root biomass of single-species dominated vegetation in the brackish marsh using conversion factors for each 10-cm depth.
Chol Gyu Lee; Shizuo Suzuki; Kyotaro Noguchi; Kazuyuki Inubushi. Estimation of fine root biomass using a minirhizotron technique among three vegetation types in a cool-temperate brackish marsh. Soil Science and Plant Nutrition 2016, 62, 465 -470.
AMA StyleChol Gyu Lee, Shizuo Suzuki, Kyotaro Noguchi, Kazuyuki Inubushi. Estimation of fine root biomass using a minirhizotron technique among three vegetation types in a cool-temperate brackish marsh. Soil Science and Plant Nutrition. 2016; 62 (5-6):465-470.
Chicago/Turabian StyleChol Gyu Lee; Shizuo Suzuki; Kyotaro Noguchi; Kazuyuki Inubushi. 2016. "Estimation of fine root biomass using a minirhizotron technique among three vegetation types in a cool-temperate brackish marsh." Soil Science and Plant Nutrition 62, no. 5-6: 465-470.
An aerobic, methane-oxidizing bacterium (strain RS11D-PrT) was isolated from rice rhizosphere. Cells of strain RS11D-PrT were Gram-stain-negative, motile rods with a single polar flagellum and contained an intracytoplasmic membrane system typical of type I methanotrophs. The strain utilized methane and methanol as sole carbon and energy sources. It could grow at 20–37 °C (optimum 31–33 °C), at pH 6.8–7.4 (range 5.5–9.0) and with 0–0.2 % (w/v) NaCl (there was no growth at above 0.5 % NaCl). pmoA and mmoX genes were present. The ribulose monophosphate and/or ribulose bisphosphate pathways were used for carbon assimilation. Results of sequence analysis of 16S rRNA genes showed that strain RS11D-PrT is related closely to the genera Methylococcus, Methylocaldum, Methyloparacoccus and Methylogaea in the family Methylococcaceae. The similarity was low (94.6 %) between strain RS11D-PrT and the most closely related type strain (Methyloparacoccus murrellii R-49797T). The DNA G+C content was 64.1 mol%. Results of phylogenetic analysis of the pmoA gene and chemotaxonomic data regarding the major cellular fatty acids (C16 : 1ω7c, C16 : 0 and C14 : 0) and the major respiratory quinone (MQ-8) also indicated the affiliation of strain RS11D-PrT to the Methylococcus–Methylocaldum–Methyloparacoccus–Methylogaea clade. On the basis of phenotypic, genotypic and phylogenetic characteristics, strain RS11D-PrT is considered to represent a novel genus and species within the family Methylococcaceae, for which the name Methylomagnum ishizawai gen. nov., sp. nov. is proposed. The type strain is RS11D-PrT ( = JCM 18894T = NBRC 109438T = DSM 29768T = KCTC 4681T).
Ashraf Khalifa; Chol Gyu Lee; Takuya Ogiso; Chihoko Ueno; Dayéri Dianou; Toyoko Demachi; Arata Katayama; Susumu Asakawa. Methylomagnum ishizawai gen. nov., sp. nov., a mesophilic type I methanotroph isolated from rice rhizosphere. International Journal of Systematic and Evolutionary Microbiology 2015, 65, 3527 -3534.
AMA StyleAshraf Khalifa, Chol Gyu Lee, Takuya Ogiso, Chihoko Ueno, Dayéri Dianou, Toyoko Demachi, Arata Katayama, Susumu Asakawa. Methylomagnum ishizawai gen. nov., sp. nov., a mesophilic type I methanotroph isolated from rice rhizosphere. International Journal of Systematic and Evolutionary Microbiology. 2015; 65 (10):3527-3534.
Chicago/Turabian StyleAshraf Khalifa; Chol Gyu Lee; Takuya Ogiso; Chihoko Ueno; Dayéri Dianou; Toyoko Demachi; Arata Katayama; Susumu Asakawa. 2015. "Methylomagnum ishizawai gen. nov., sp. nov., a mesophilic type I methanotroph isolated from rice rhizosphere." International Journal of Systematic and Evolutionary Microbiology 65, no. 10: 3527-3534.
Chol Gyu Lee; Takeshi Watanabe; Jun Murase; Susumu Asakawa; Makoto Kimura. Growth of methanogens in an oxic soil microcosm: Elucidation by a DNA-SIP experiment using 13C-labeled dried rice callus. Applied Soil Ecology 2012, 58, 37 -44.
AMA StyleChol Gyu Lee, Takeshi Watanabe, Jun Murase, Susumu Asakawa, Makoto Kimura. Growth of methanogens in an oxic soil microcosm: Elucidation by a DNA-SIP experiment using 13C-labeled dried rice callus. Applied Soil Ecology. 2012; 58 ():37-44.
Chicago/Turabian StyleChol Gyu Lee; Takeshi Watanabe; Jun Murase; Susumu Asakawa; Makoto Kimura. 2012. "Growth of methanogens in an oxic soil microcosm: Elucidation by a DNA-SIP experiment using 13C-labeled dried rice callus." Applied Soil Ecology 58, no. : 37-44.
Cyanobacteria play an important role in maintaining soil fertility in rice fields. Some cyanobacterial members can grow heterotrophically under dark conditions, which might be an important trait for the survival of cyanobacteria during the drained period after harvest. This study aimed to elucidate the heterotrophic growth of cyanobacteria and the microbial loop mediated by cyanophages (cyanobacteria-cyanophages-dissolved organic carbon) in soil using carbon-13 (13C)-labeled dried callus cells as a model material of plant residues. This study used the stable isotope probing (SIP) method coupled with denaturing gradient gel electrophoresis (DGGE). Although heterotrophic growth of cyanobacteria in soil was not observed, the phage-mediated microbial loop in the transformation of callus carbon was elucidated from the detection of 13C-labeled g20 genes in the heaviest fractions (buoyant density: 1.754 g mL−1). The closest relatives of eleven sequenced DGGE bands from the heaviest fractions were uncultured cyanophage g20 clones that had been obtained from rice field soils in Japan. Proliferation of bacteriophages having cyanophage-related g20 genes with no detectable heterotrophic growth of cyanobacteria strongly indicates that bacteriophages having these g20 genes infected bacteria other than cyanobacteria.
Chol Gyu Lee; Takeshi Watanabe; Yuichi Fujita; Susumu Asakawa; Makoto Kimura. Heterotrophic growth of cyanobacteria and phage-mediated microbial loop in soil: Examination by stable isotope probing (SIP) method. Soil Science and Plant Nutrition 2012, 58, 161 -168.
AMA StyleChol Gyu Lee, Takeshi Watanabe, Yuichi Fujita, Susumu Asakawa, Makoto Kimura. Heterotrophic growth of cyanobacteria and phage-mediated microbial loop in soil: Examination by stable isotope probing (SIP) method. Soil Science and Plant Nutrition. 2012; 58 (2):161-168.
Chicago/Turabian StyleChol Gyu Lee; Takeshi Watanabe; Yuichi Fujita; Susumu Asakawa; Makoto Kimura. 2012. "Heterotrophic growth of cyanobacteria and phage-mediated microbial loop in soil: Examination by stable isotope probing (SIP) method." Soil Science and Plant Nutrition 58, no. 2: 161-168.
Incorporation of plant residues into soil brings about nitrification when ammonification of organic nitrogen derived from plant residues proceeds. In the present study, we traced carbon flow into ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) during decomposition of plant residues in a soil, by isotope 13 carbon (13C)-DNA stable isotope probing and denaturing gradient gel electrophoresis (DGGE) analysis of amoA genes encoding ammonia monooxygenase subunit A. Unlabeled (12C) and 13C-labeled dried rice (Oryza sativa) callus (Oryza sativa L. cv. Yukihikari) was used as a model plant residue. The soil with or without the dried rice callus was aerobically incubated with 55% of maximum water holding capacity for 56 days. DGGE analysis of AOB and AOA communities showed that the band patterns of the callus-treated soil gradually changed during incubation and was distinctly different from the no-callus treatment (control) after 28 and 42 days of incubation, respectively. Subsequent analysis after isopycnic centrifugation of the soil DNA showed that 13C-enriched AOB clones were obtained at 14 and 28 days, whereas 13C-enriched AOA clones were found at 28 days of incubation. The AOB community consisted of members of clusters 1, 9 and 11 and other members of Nitrosospira spp., of which most of the 13C-enriched clones were affiliated with clusters 1 and 9. The AOA community mostly belonged to the clusters consisting of clones obtained mainly from terrestrial environments. The 13C-enriched AOA clones were all closely related to “Nitrososphaera viennensis” and Candidatus Nitrososphaera gargensis. Our study showed that carbon derived from the dried rice callus flowed into both the AOB and AOA communities in the aerobically incubated soil during decomposition.
Takeshi Watanabe; Chol Gyu Lee; Jun Murase; Susumu Asakawa; Makoto Kimura. Carbon flow into ammonia-oxidizing bacteria and archaea during decomposition of13C-labeled plant residues in soil. Soil Science and Plant Nutrition 2011, 57, 775 -785.
AMA StyleTakeshi Watanabe, Chol Gyu Lee, Jun Murase, Susumu Asakawa, Makoto Kimura. Carbon flow into ammonia-oxidizing bacteria and archaea during decomposition of13C-labeled plant residues in soil. Soil Science and Plant Nutrition. 2011; 57 (6):775-785.
Chicago/Turabian StyleTakeshi Watanabe; Chol Gyu Lee; Jun Murase; Susumu Asakawa; Makoto Kimura. 2011. "Carbon flow into ammonia-oxidizing bacteria and archaea during decomposition of13C-labeled plant residues in soil." Soil Science and Plant Nutrition 57, no. 6: 775-785.
The microbial decomposition of plant residue is a central part of the carbon cycle in soil ecosystems. Here, we explored the microeukaryotic community responsible for the uptake of plant residue carbon in a rice field soil through DNA-based stable-isotope probing (SIP) using dried rice callus labelled with 13C as a model substrate. Molecular fingerprinting with PCR-DGGE showed that the total eukaryotic community in soil under drained (upland) conditions distinctly changed within 3 days after the callus was applied and stable thereafter. The predominant group of eukaryotes that incorporated callus carbon were fungi affiliated with the Mucoromycotina (Mortierella), Ascomycota (Galactomyces, Eleutherascus, Gibberella and Fusarium) and Zoopagomycotina (Syncephalis). ‘Fungus-like’ protists such as Pythium (stramenopiles) and Polymyxa (Cercozoa) were also involved in carbon flow from the callus. Some of these fungi and ‘fungus-like’ protists took up soil organic matter with time, which suggested a priming effect of the callus on the eukaryotic community. Our results demonstrated the usefulness of SIP not only to trace the carbon flow from fresh organic matter but also to study the effect of fresh organic matter on the utilization of soil organic matter by the microbial community.
Jun Murase; Manami Shibata; Chol Gyu Lee; Takeshi Watanabe; Susumu Asakawa; Makoto Kimura. Incorporation of plant residue-derived carbon into the microeukaryotic community in a rice field soil revealed by DNA stable-isotope probing. FEMS Microbiology Ecology 2011, 79, 371 -379.
AMA StyleJun Murase, Manami Shibata, Chol Gyu Lee, Takeshi Watanabe, Susumu Asakawa, Makoto Kimura. Incorporation of plant residue-derived carbon into the microeukaryotic community in a rice field soil revealed by DNA stable-isotope probing. FEMS Microbiology Ecology. 2011; 79 (2):371-379.
Chicago/Turabian StyleJun Murase; Manami Shibata; Chol Gyu Lee; Takeshi Watanabe; Susumu Asakawa; Makoto Kimura. 2011. "Incorporation of plant residue-derived carbon into the microeukaryotic community in a rice field soil revealed by DNA stable-isotope probing." FEMS Microbiology Ecology 79, no. 2: 371-379.
Although root cap cells are an important substrate for microorganisms in the rhizosphere, little attention has been paid to the decomposition of sloughed root cap cells by microorganisms. This study used rice plant callus cells grown on medium containing 13C-labelled glucose as a model material for rice plant root cap cells. Harvested 13C-labelled callus cells (78 atom % 13C) were subjected to decomposition in an aerobic soil microcosm for 56 days. The low cellulose and lignin levels and the disaggregated nature of the callus cells indicated that these cells were an appropriate model material for root cap cells. DNA was extracted from a soil incubated with 12C- and 13C-callus cells and subjected to buoyant density gradient centrifugation to identify bacterial species that assimilated carbon from the callus cells. The stability of the total bacterial communities during the incubation was estimated. Many DGGE bands in light fractions of soil incubated with 13C-callus cells were weaker in intensity than those from soil incubated with 12C-callus cells, and those bands were shifted to heavier fractions after 13C-callus treatment. 13C-labelled DNA was detected from Day 3 onwards, and the DGGE bands in the heavy fractions were most numerous on Day 21. DGGE bands from heavy and light fractions were sequenced, revealing more than 70% of callus- C incorporating bacteria were Gram-negative, predominantly α-Proteobacteria, β-Proteobacteria, γ-Proteobacteria, Sphingobacteria and Actinobacteria. These species were phylogenetically distinct from the bacteria reported to be present during plant residue decomposition and resident in rice roots. This study indicates that root cap cells are decomposed by specific bacterial species in the rhizosphere, and that these species augment the diversity of rhizospheric bacterial communities.
Yong Li; Chol Gyu Lee; Takeshi Watanabe; Jun Murase; Susumu Asakawa; Makoto Kimura. Identification of microbial communities that assimilate substrate from root cap cells in an aerobic soil using a DNA-SIP approach. Soil Biology and Biochemistry 2011, 43, 1928 -1935.
AMA StyleYong Li, Chol Gyu Lee, Takeshi Watanabe, Jun Murase, Susumu Asakawa, Makoto Kimura. Identification of microbial communities that assimilate substrate from root cap cells in an aerobic soil using a DNA-SIP approach. Soil Biology and Biochemistry. 2011; 43 (9):1928-1935.
Chicago/Turabian StyleYong Li; Chol Gyu Lee; Takeshi Watanabe; Jun Murase; Susumu Asakawa; Makoto Kimura. 2011. "Identification of microbial communities that assimilate substrate from root cap cells in an aerobic soil using a DNA-SIP approach." Soil Biology and Biochemistry 43, no. 9: 1928-1935.