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Sato Y, Miwa T, Inaba T, Akachi T, Tanaka E, Hori T, Murofushi K, Takagi H, Futamata H, Aoyagi T, Habe H. Microbially produced fertilizer provides rhizobacteria to hydroponic tomato roots by forming beneficial biofilms. Appl Microbiol Biotechnol 2023; 107:7365-7374. [PMID: 37773217 DOI: 10.1007/s00253-023-12794-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 09/08/2023] [Accepted: 09/13/2023] [Indexed: 10/01/2023]
Abstract
Hydroponic cultivation of Solanum lycopersicum (tomato) is important, and high tomato production depends on the use of nitrogen and phosphate fertilizers. We had developed a microbial fertilizer (MF), which is mainly composed of nitrate. To investigate the effect of MF on plant growth, hydroponic tomato was grown with MF or commercial inorganic fertilizer (IF), and the microbiomes of the rhizosphere and the liquid phase were analyzed by confocal microscopy and high-throughput sequencing. Plant biomass and biofilm formation were increased by growth in MF compared to IF. The microbial community structures of tomato roots and hydroponic water differed between the two conditions, and three operational taxonomic units (OTUs) dominated in plants grown with MF. The three OTUs were related to Rudaea spp., Chitinophaga spp., and Stenotrophobacter terrae, which are reported to be disease-suppressive epiphytic or endophytic microbes of plant roots. Because these three OTUs also predominated in the MF itself, they were likely provided to the rhizosphere or endophytic environments of tomato roots via hydroponic water. KEY POINTS: • Microbial fertilizer for hydroponic growth enhanced biofilm formation on tomato root. • Microbial fertilizer contains tomato-root epiphytic or endophytic microbes. • Microbial fertilizer provided beneficial microbes to the rhizosphere and endophytic environments of tomato roots via hydroponic water.
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Affiliation(s)
- Yuya Sato
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba West, 16-1 Onogawa, Tsukuba, Ibaraki, 305-8569, Japan.
| | - Teruhiko Miwa
- Department of Eco-Farm, IAI Incorporated, 577-1 Obane, Shimizu, Shizuoka, 424-0103, Japan
| | - Tomohiro Inaba
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba West, 16-1 Onogawa, Tsukuba, Ibaraki, 305-8569, Japan
| | - Takuto Akachi
- Department of Eco-Farm, IAI Incorporated, 577-1 Obane, Shimizu, Shizuoka, 424-0103, Japan
| | - Eiji Tanaka
- Department of Eco-Farm, IAI Incorporated, 577-1 Obane, Shimizu, Shizuoka, 424-0103, Japan
| | - Tomoyuki Hori
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba West, 16-1 Onogawa, Tsukuba, Ibaraki, 305-8569, Japan
| | - Keita Murofushi
- Department of Environment and Energy, Industrial Research Institute of Shizuoka Prefecture, 2078 Makigaya, Aoi-Ku, Shizuoka, Shizuoka, 421-1298, Japan
| | - Hiroshi Takagi
- Numazu Technical Support Center, Industrial Research Institute of Shizuoka Prefecture, 3981-1 Ohoka, Numazu, Shizuoka, 410-0022, Japan
| | - Hiroyuki Futamata
- Department of Applied Chemistry and Biochemical Engineering, Graduate School of Engineering, Shizuoka University, 3-5-1 Johoku, Naka-Ku, Hamamatsu, Shizuoka, 432-8561, Japan
| | - Tomo Aoyagi
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba West, 16-1 Onogawa, Tsukuba, Ibaraki, 305-8569, Japan
| | - Hiroshi Habe
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba West, 16-1 Onogawa, Tsukuba, Ibaraki, 305-8569, Japan.
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Huang J, Gao K, Yang L, Lu Y. Successional action of Bacteroidota and Firmicutes in decomposing straw polymers in a paddy soil. ENVIRONMENTAL MICROBIOME 2023; 18:76. [PMID: 37838745 PMCID: PMC10576277 DOI: 10.1186/s40793-023-00533-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 10/06/2023] [Indexed: 10/16/2023]
Abstract
BACKGROUND Decomposition of plant biomass is vital for carbon cycling in terrestrial ecosystems. In waterlogged soils including paddy fields and natural wetlands, plant biomass degradation generates the largest natural source of global methane emission. However, the intricate process of plant biomass degradation by diverse soil microorganisms remains poorly characterized. Here we report a chemical and metagenomic investigation into the mechanism of straw decomposition in a paddy soil. RESULTS The chemical analysis of 16-day soil microcosm incubation revealed that straw decomposition could be divided into two stages based on the dynamics of methane, short chain fatty acids, dissolved organic carbon and monosaccharides. Metagenomic analysis revealed that the relative abundance of glucoside hydrolase (GH) encoding genes for cellulose decomposition increased rapidly during the initial stage (3-7 days), while genes involved in hemicellulose decomposition increased in the later stage (7-16 days). The increase of cellulose GH genes in initial stage was derived mainly from Firmicutes while Bacteroidota contributed mostly to the later stage increase of hemicellulose GH genes. Flagella assembly genes were prevalent in Firmicutes but scarce in Bacteroidota. Wood-Ljungdahl pathway (WLP) was present in Firmicutes but not detected in Bacteroidota. Overall, Bacteroidota contained the largest proportion of total GHs and the highest number of carbohydrate active enzymes gene clusters in our paddy soil metagenomes. The strong capacity of the Bacteroidota phylum to degrade straw polymers was specifically attributed to Bacteroidales and Chitinophagales orders, the latter has not been previously recognized. CONCLUSIONS This study revealed a collaborating sequential contribution of microbial taxa and functional genes in the decomposition of straw residues in a paddy soil. Firmicutes with the property of mobility, WLP and cellulose decomposition could be mostly involved in the initial breakdown of straw polymers, while Bacteroidota became abundant and possibly responsible for the decomposition of hemicellulosic polymers during the later stage.
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Affiliation(s)
- Junjie Huang
- College of Urban and Environmental Sciences, Peking University, No. 5, Yiheyuan Road, Haidian District, Beijing, 100871, China
| | - Kailin Gao
- College of Urban and Environmental Sciences, Peking University, No. 5, Yiheyuan Road, Haidian District, Beijing, 100871, China
| | - Lu Yang
- College of Urban and Environmental Sciences, Peking University, No. 5, Yiheyuan Road, Haidian District, Beijing, 100871, China
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs/Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Yahai Lu
- College of Urban and Environmental Sciences, Peking University, No. 5, Yiheyuan Road, Haidian District, Beijing, 100871, China.
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