Article
Microbiology
Xiafei Zheng, Zhongneng Yan, Chenxi Zhao, Lin He, Zhihua Lin, Minhai Liu
Summary: This study investigated the diversity, dynamics, drivers, and assembly mechanisms of total bacteria, napA, and nosZ denitrifiers in intensive shrimp aquaculture ponds. The results showed that the diversity of the total bacterial community increased over time, while the diversity of napA and nosZ bacteria remained stable. The community structure changed significantly over the culture period and multiple factors were identified as drivers of the denitrifying bacterial communities. Network analysis revealed complex co-occurrence patterns between total, napA, and nosZ bacteria, which fluctuated over time. The null model approach showed that napA and nosZ bacteria were primarily governed by deterministic processes. The findings provide important ecological insights for optimizing microbial community structure and function.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Environmental Sciences
Wei Wei, Kazuo Isobe, Yutaka Shiratori, Midori Yano, Sakae Toyoda, Keisuke Koba, Naohiro Yoshida, Haoyang Shen, Keishi Senoo
Summary: After studying with multiple methods, it was found that the overlooked denitrifying bacteria and fungi were more involved in N2O production than previously thought, and their activities varied under different fertilization practices and types. Proposed a conceptual scheme of N flow based on distinct physiological constraints among diverse NH3 oxidizers and denitrifiers to understand the environmental context-dependent N2O emission processes.
ENVIRONMENTAL POLLUTION
(2021)
Article
Soil Science
Arpita Maheshwari, Christopher M. Jones, Maren Tiemann, Sara Hallin
Summary: Agricultural soils are a major source of N2O, a potent greenhouse gas and ozone-depleting substance. The role of carbon availability in shaping the structure of N2O reducing communities in soil has not been explored. Our study shows that the effect of carbon addition on the abundance and diversity of N2O reducing genes varies with different carbon substrates in contrasting soil types, highlighting the importance of specific carbon substrates in selecting certain lineages of N2O reducers.
SOIL BIOLOGY & BIOCHEMISTRY
(2023)
Article
Biodiversity Conservation
Jun Shan, Robert A. Sanford, Joanne Chee-Sanford, Sean K. Ooi, Frank E. Loffler, Konstantinos T. Konstantinidis, Wendy H. Yang
Summary: Research has shown that Clade II N2O reducers may play important roles in controlling N2O emissions, with increasing attention in international journals over the years. However, there is confusion surrounding these two distinct groups of N2O reducers due to disciplinary silos and inconsistent nomenclature between Clade I and Clade II.
GLOBAL CHANGE BIOLOGY
(2021)
Article
Soil Science
Bing Han, Liu-Ying Mo, Yun-Ting Fang, Hong J. Di, Jun-Tao Wang, Ju-Pei Shen, Li-Mei Zhang
Summary: Denitrification and anammox are the main pathways of nitrogen loss in wet habitats, with denitrification dominating the N-2 production. The community of denitrifiers, driven by nosZ Glade I and II genes, is mainly influenced by salinity and pH, while the anammox bacteria community is mainly affected by salinity.
APPLIED SOIL ECOLOGY
(2021)
Article
Soil Science
A. Florio, M. Marechal, A. Legout, C. Creuse des Chatelliers, J. Gervaix, S. Didier, B. Zeller, X. Le Roux
Summary: The study found that tree species with BNI capacity showed higher levels of denitrification limitation by nitrate compared to species without BNI capacity, and this was correlated with potential nitrification rates and specific gene abundances. However, potential denitrification and actual N2O emissions did not directly reflect the tree BNI status.
SOIL BIOLOGY & BIOCHEMISTRY
(2021)
Article
Soil Science
Xuesong Luo, Luyang Zeng, Li Wang, Hang Qian, Chunli Hou, Shilin Wen, Boren Wang, Qiaoyun Huang, Wenli Chen
Summary: This study explored how long-term fertilization influences the community of denitrifiers in different soil aggregates by measuring denitrifier gene abundances and enzyme activities. Results showed that different genes were affected by fertilization and various environmental factors, leading to differences in nitrite reducers and N2O reducers across soil aggregate fractions. The gross and net N2O production were stimulated by swine manure fertilization, with different factors influencing their production in the soil environment.
APPLIED SOIL ECOLOGY
(2021)
Article
Engineering, Environmental
Zhi-Ling Li, Rui Cheng, Fan Chen, Xiao-Qiu Lin, Xiao-Jing Yao, Bin Liang, Cong Huang, Kai Sun, Ai-Jie Wang
Summary: The study demonstrated that sulfamethoxazole, chlortetracycline and amoxicillin have inhibitory effects on microbial denitrification performance, resulting in decreased nitrate removal efficiencies and decreased expression of important genes. Higher concentrations of antibiotics lead to stronger inhibitory effects, potentially causing changes in the abundance of denitrifying bacterial genera.
JOURNAL OF HAZARDOUS MATERIALS
(2021)
Article
Biotechnology & Applied Microbiology
Yuan Gao, Magnus overlie Arntzen, Morten Kjos, Lars R. Bakken, Asa Frostegard
Summary: Rhizobia living as microsymbionts inside nodules have stable access to carbon substrates, while surviving as free-living bacteria in soil. Many rhizobia can denitrify and switch to anaerobic respiration under low oxygen tension. The cellular machinery regulating this transition is relatively well known, but more information is needed about the regulation in starved organisms. Rating: 8 out of 10.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Environmental Sciences
Ke Ding, Linge Xu, Yulin Chen, Wenxuan Li, Xiaoli Chai, Xiaohu Dai, Boran Wu
Summary: This study found that polyhydroxyalkanoates (PHAs) have advantages in screening specific denitrifying bacteria compared with other carbon sources like glucose and sodium acetate. The microbial community screened by PHA was identified, and the environmental functions of these bacteria were analyzed. PHA improved denitrification efficiency by increasing the expression of key enzymes and accelerating the assimilation rate of nitrate. Mechanistic insights into the PHA-enhanced denitrification capacity of the microbial community can provide novel options for eutrophic surface water remediation.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Environmental Sciences
Da-won Lee, Yongtae Ahn, Kalimuthu Pandi, Joonhong Park, Seong-Teak Yun, Min Jang, Jaeyoung Choi
Summary: The study evaluated the denitrification potential in nitrate contaminated bedrock aquifers by injecting different carbon sources, among which acetate was identified as the optimum electron donor for microbial metabolic processes. The injection of acetate activated biological heterotrophic denitrification in the groundwater, leading to a significant nitrate reduction rate and an increase in the ratio of denitrification bacteria.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Article
Ecology
Debasish Saha, Jason P. Kaye, Arnab Bhowmik, Mary Ann Bruns, John M. Wallace, Armen R. Kemanian
Summary: Soil fertility in organic agriculture is dependent on microbial cycling of nutrients from legume cover crops and animal manure, but the labile carbon and nitrogen in these inputs can lead to increased nitrous oxide emissions. Our research shows that managing the rate and timing of organic input additions, as well as preventing the co-location of legume cover crops and manure, could help mitigate N2O emissions.
ECOLOGICAL APPLICATIONS
(2021)
Article
Agronomy
Nguyen Van Sinh, Risako Kato, Doan Thi Truc Linh, Nguyen Thi Kim Phuong, Koki Toyota
Summary: Biochar has the potential to improve soil properties and ecological functions, but it can also negatively impact soil organisms. This study found that the application of biochar at different rates and types had significant effects on the composition and abundance of soil nematode communities.
Article
Engineering, Environmental
Toshikazu Suenaga, Takumi Ota, Kohei Oba, Kentaro Usui, Toshiki Sako, Tomoyuki Hori, Shohei Riya, Masaaki Hosomi, Kartik Chandran, Susanne Lackner, Barth F. Smets, Akihiko Terada
Summary: This study investigated the phylogeny of resident N2O-reducing bacteria in an anammox microbial community and quantified individually the processes of N2O production and consumption. The results showed that N2O-reducing bacteria primarily belonged to Burkholderiaceae and Chloroflexus genera, and other less abundant strains in Rhodoferax, Azospirillum, Lautropia, and Bdellovibrio also likely acted as N2O sinks. The study also introduced a novel N-15 tracer method to quantify N2O production and consumption rates, providing insights into the potential N2O-reducing activity in anammox-based processes.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2021)
Article
Microbiology
Daniele Cabral Michel, Elaine Martins da Costa, Amanda Azarias Guimaraes, Teotonio Soares de Carvalho, Polyane Santos de Castro Caputo, Anne Willems, Fatima Maria de Souza Moreira
Summary: A new nitrogen-fixing bacterial strain, named Bradyrhizobium campsiandrae, was isolated from nodules of Campsiandra laurilifolia in the Amazon region of Brazil. Through multiple analyses, it was determined to be a new species closely related to other Bradyrhizobium species.
ARCHIVES OF MICROBIOLOGY
(2021)
Review
Microbiology
Cristina Sanchez, Kiwamu Minamisawa
FRONTIERS IN MICROBIOLOGY
(2019)
Editorial Material
Plant Sciences
Brett James Ferguson, Kiwamu Minamisawa, Nacira Belen Munoz, Hon-Ming Lam
FRONTIERS IN PLANT SCIENCE
(2019)
Article
Microbiology
Sawa Wasai-Hara, Kiwamu Minamisawa, Sylvie Cloutier, Eden S. P. Bromfield
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2020)
Article
Microbiology
Maria Luisa T. Mason, Baby Lyn T. De Guzman, Akihiro Yamamoto, Yuichi Saeki
Summary: The study evaluated the performance of indigenous Bradyrhizobia strains in soybean cultivation, with B. elkanii IS-2 identified as the most efficient for Philippines cultivars and B. diazoefficiens SK-5 for Japanese and Brazilian cultivars. Positive correlation was found between symbiotic efficiency and nitrogenase activity, indicating efficient N-fixation by indigenous strains. This research provides insights for soybean inoculation in the Philippines.
Article
Plant Sciences
Yoshikazu Nitawaki, Hayato Kitabayashi, Maria Luisa Tabing Mason, Akihiro Yamamoto, Yuichi Saeki
Summary: The study examined the impact of different salinity levels on soybean growth and nodulation by various rhizobia strains. Results showed that different rhizobia strains had varying effects on soybean growth and nodulation under salt-stress conditions, with a positive relationship observed between soybean growth and symbiotic efficiency of bradyrhizobia.
SOIL SCIENCE AND PLANT NUTRITION
(2021)
Article
Ecology
Haruka Arashida, Haruka Odake, Masayuki Sugawara, Ryota Noda, Kaori Kakizaki, Satoshi Ohkubo, Hisayuki Mitsui, Shusei Sato, Kiwamu Minamisawa
Summary: Symbiosis between organisms influences evolution through adaptive changes in genome architectures. Interactions between soybeans and Bradyrhizobium involve IS-mediated duplications and deletions on symbiosis islands, with host plants selecting mutualistic variants from the pool of rhizobial populations. Homologous recombination between direct IS copies provides a natural mechanism for generating deletions and duplications in symbiosis islands.
Article
Microbiology
Shintaro Hara, Naohisa Wada, Sliver Sung-Yun Hsiao, Meng Zhang, Zhihua Bao, Yoshiyuki Iizuka, Der-Chuen Lee, Shusei Sato, Sen-Lin Tang, Kiwamu Minamisawa
Summary: This study demonstrates that type II methanotrophs in the root tissues of paddy rice perform methane oxidation and nitrogen fixation simultaneously at the single-cell level. The findings provide direct evidence of the activities of methanotrophs in root tissues, suggesting that they may provide fixed nitrogen to root systems or depend on different microenvironmental niches.
Article
Agronomy
Israel M. Guanzon, Maria Luisa T. Mason, Purisima P. Juico, Fernan T. Fiegalan
Summary: This study assessed the presence of soil microorganisms in lahar-laden soils and found some beneficial microbes for crop production.
ACTA AGRICULTURAE SCANDINAVICA SECTION B-SOIL AND PLANT SCIENCE
(2023)
Review
Biochemistry & Molecular Biology
Kiwamu Minamisawa
Summary: This mini-review highlights the potential of bacterial nitrogen fixation to mitigate greenhouse gas emissions in soybean and rice fields. It discusses the role of rhizobia in reducing nitrous oxide emissions and the use of methane-oxidizing bacteria to fix nitrogen and reduce methane emissions. By utilizing symbiotic nitrogen fixation, it is possible to mitigate GHG emissions while supporting sustainable agriculture.
BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY
(2023)
Article
Biotechnology & Applied Microbiology
Kazuyuki Okazaki, Hirohito Tsurumaru, Megumi Hashimoto, Hiroyuki Takahashi, Takashi Okubo, Takuji Ohwada, Kiwamu Minamisawa, Seishi Ikeda
Summary: The study showed distinct differences in bacterial community structures between above-ground and below-ground tissues of sugar beet, with above-ground tissues being more tightly clustered. By analyzing 16S rRNA gene sequence data of clone libraries and isolate collections, 44 potential plant growth-promoting bacteria were identified, with eight isolates demonstrating growth-promoting effects on sugar beet seedlings in inoculation tests. Seven genera were newly identified as PGPBs for sugar beet at the genus level, extending the potential for developing novel biofertilizers.
MICROBES AND ENVIRONMENTS
(2021)
Article
Horticulture
Md Hafizur Rahman Hafiz, Ahsanul Salehin, Fumihiko Adachi, Masayuki Omichi, Yuichi Saeki, Akihiro Yamamoto, Shohei Hayashi, Kazuhito Itoh
Summary: The distribution of soybean-nodulating rhizobia varies in different climate conditions, with Bradyrhizobium japonicum dominating in the northern areas and B. elkanii dominating in the southern areas. Temperature-dependent proliferation in soil and infection are both key factors influencing the distribution of these rhizobia in different regions.
Article
Biotechnology & Applied Microbiology
Arthur Fernandes Siqueira, Masayuki Sugawara, Haruka Arashida, Kiwamu Minamisawa, Cristina Sanchez
MICROBES AND ENVIRONMENTS
(2020)
Article
Biotechnology & Applied Microbiology
Sawa Wasai-Hara, Shintaro Hara, Takashi Morikawa, Masayuki Sugawara, Hideto Takami, Junich Yoneda, Tsuyoshi Tokunaga, Kiwamu Minamisawa
MICROBES AND ENVIRONMENTS
(2020)