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Zhang Y, Wang B, Wang G, Zheng Z, Chen Y, Li O, Peng Y, Hu X. Acidification induce chemical and microbial variation in tea plantation soils and bacterial degradation of the key acidifying phenolic acids. Arch Microbiol 2024; 206:239. [PMID: 38689148 DOI: 10.1007/s00203-024-03858-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 01/16/2024] [Accepted: 01/22/2024] [Indexed: 05/02/2024]
Abstract
Camellia sinensis is an important economic plant grown in southern subtropical hilly areas, especially in China, mainly for the production of tea. Soil acidification is a significant cause of the reduction of yield and quality and continuous cropping obstacles in tea plants. Therefore, chemical and microbial properties of tea growing soils were investigated and phenolic acid-degrading bacteria were isolated from a tea plantation. Chemical and ICP-AES investigations showed that the soils tested were acidic, with pH values of 4.05-5.08, and the pH negatively correlated with K (p < 0.01), Al (p < 0.05), Fe and P. Aluminum was the highest (47-584 mg/kg) nonessential element. Based on high-throughput sequencing, a total of 34 phyla and 583 genera were identified in tea plantation soils. Proteobacteria and Acidobacteria were the main dominant phyla and the highest abundance of Acidobacteria was found in three soils, with nearly 22% for the genus Gp2. Based on the functional abundance values, general function predicts the highest abundance, while the abundance of amino acids and carbon transport and metabolism were higher in soils with pH less than 5. According to Biolog Eco Plate™ assay, the soil microorganisms utilized amino acids well, followed by polymers and phenolic acids. Three strains with good phenolic acid degradation rates were obtained, and they were identified as Bacillus thuringiensis B1, Bacillus amyloliquefaciens B2 and Bacillus subtilis B3, respectively. The three strains significantly relieved the inhibition of peanut germination and growth by ferulic acid, p-coumaric acid, p-hydroxybenzoic acid, cinnamic acid, and mixed acids. Combination of the three isolates showed reduced relief of the four phenolic acids due to the antagonist of B2 against B1 and B3. The three phenolic acid degradation strains isolated from acidic soils display potential in improving the acidification and imbalance in soils of C. sinensis.
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Affiliation(s)
- Yuhan Zhang
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, 928 Second Avenue, Hangzhou, 310018, People's Republic of China
| | - Binjie Wang
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, 928 Second Avenue, Hangzhou, 310018, People's Republic of China
| | - Guiwei Wang
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, 928 Second Avenue, Hangzhou, 310018, People's Republic of China
| | - Zhisheng Zheng
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, 928 Second Avenue, Hangzhou, 310018, People's Republic of China
| | - Ying Chen
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, 928 Second Avenue, Hangzhou, 310018, People's Republic of China
| | - Ou Li
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, 928 Second Avenue, Hangzhou, 310018, People's Republic of China
| | - Yulong Peng
- Zunyi Branch of Guizhou Provincial Tobacco Company, Zunyi, 563000, People's Republic of China
| | - Xiufang Hu
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, 928 Second Avenue, Hangzhou, 310018, People's Republic of China.
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Luo W, Zhang Q, Wang P, Luo J, She C, Guo X, Yuan J, Sun Y, Guo R, Li Z, Liu J, Tao J. Unveiling the impacts moso bamboo invasion on litter and soil properties: A meta-analysis. Sci Total Environ 2024; 909:168532. [PMID: 37972783 DOI: 10.1016/j.scitotenv.2023.168532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 11/05/2023] [Accepted: 11/10/2023] [Indexed: 11/19/2023]
Abstract
Moso bamboo invasion potentially alters litter, soil properties and soil microbial communities in forest ecosystems. However, the overall direction and magnitude of this alteration at a large spatial scale remain unclear. Here, we conducted a meta-analysis of 72 experimental studies on the impact of moso bamboo invasion on litter, soil physicochemical properties, and soil microbial communities. Overall, the moso bamboo invasion increased litter decomposition, soil pH, and NH4+-N, while concurrently leading to a decrease in soil bulk density, soil electrical conductivity, soil TN: TP ratio, soil NO3--N, and available potassium. Moreover, we observed that the invasion significantly enhanced soil microbial biomass nitrogen, fungal ACE diversity index, fungal biomass, and bacterial Shannon diversity index, while decreasing the ratio of Gram-positive to Gram-negative bacteria and the biomass of Gram-positive bacteria. Furthermore, we identified the primary factors influencing specific soil properties and microbial community responses to moso bamboo invasion. Specifically, the response of NH4+-N, NO3--N, soil bulk density, fungal diversity and pH were found to be primarily influenced by climatic factors (mean annual temperature, mean annual precipitation), topographic factors (aspect), and invasion stage, respectively. In addition, we further revealed a close relationship between soil physicochemical properties and microbial communities during moso bamboo invasion. Specifically, the response of soil microbial biomass nitrogen was positively correlated with the responses of soil organic nitrogen and total nitrogen content, Gram-positive bacteria biomass was positively correlated with soil total nitrogen but negatively correlated with soil pH. Meanwhile, soil bacterial diversity showed a significant positive correlation with soil pH but exhibited a negative correlation with soil SOC. Our study suggests that macro-climatic conditions, local microenvironment, and invasion stage co-regulate the important effects of moso bamboo invasion on litter, soil physicochemical properties, and microbial communities.
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Affiliation(s)
- Weixue Luo
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, Chongqing Key Laboratory of Plant Ecology and Resources Research in Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing, China; Chongqing Jinfo Mountain Karst Ecosystem National Observation and Research Station, Southwest University, Chongqing, China.
| | - Qingyu Zhang
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, Chongqing Key Laboratory of Plant Ecology and Resources Research in Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing, China
| | - Peng Wang
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, Chongqing Key Laboratory of Plant Ecology and Resources Research in Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing, China
| | - Jie Luo
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, Chongqing Key Laboratory of Plant Ecology and Resources Research in Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing, China
| | - Chunyan She
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, Chongqing Key Laboratory of Plant Ecology and Resources Research in Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing, China
| | - Xuman Guo
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, Chongqing Key Laboratory of Plant Ecology and Resources Research in Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing, China
| | - Jiajia Yuan
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, Chongqing Key Laboratory of Plant Ecology and Resources Research in Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing, China
| | - Yuhong Sun
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, Chongqing Key Laboratory of Plant Ecology and Resources Research in Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing, China
| | - Ruming Guo
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, Chongqing Key Laboratory of Plant Ecology and Resources Research in Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing, China
| | - Zongfeng Li
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, Chongqing Key Laboratory of Plant Ecology and Resources Research in Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing, China; Chongqing Jinfo Mountain Karst Ecosystem National Observation and Research Station, Southwest University, Chongqing, China.
| | - Jinchun Liu
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, Chongqing Key Laboratory of Plant Ecology and Resources Research in Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing, China; Chongqing Jinfo Mountain Karst Ecosystem National Observation and Research Station, Southwest University, Chongqing, China.
| | - Jianping Tao
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, Chongqing Key Laboratory of Plant Ecology and Resources Research in Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing, China; Chongqing Jinfo Mountain Karst Ecosystem National Observation and Research Station, Southwest University, Chongqing, China.
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Kang K, Chong H, Ning K. Meta-Prism 2.0: Enabling algorithm and web server for ultra-fast, memory-efficient, and accurate analysis among millions of microbial community samples. Gigascience 2022; 11:6651347. [PMID: 35902093 PMCID: PMC9334027 DOI: 10.1093/gigascience/giac073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 05/02/2022] [Accepted: 06/27/2022] [Indexed: 11/28/2022] Open
Abstract
Background Microbial community samples have been accumulating at a speed faster than ever, with hundreds of thousands of samples been sequenced each year. Mining such a huge amount of multisource heterogeneous data is becoming an increasingly difficult challenge, so efficient and accurate compare and search of samples is in urgent need: faced with millions of samples in the data repository, traditional sample comparison and search approaches fall short in speed and accuracy. Findings Here we proposed Meta-Prism 2.0, a microbial community sample analysis method that has pushed the time and memory efficiency to a new limit without compromising accuracy. Based on sparse data structure, time-saving instruction pipeline, and SIMD optimization, Meta-Prism 2.0 has enabled ultra-fast, memory-efficient, flexible, and accurate search among millions of samples. Meta-Prism 2.0 was put to test on several data sets, with the largest containing 1 million samples. Results show that Meta-Prism 2.0’s 0.00001-s per sample pair compare speed and 8-GB memory needs for searching against 1 million samples have made it one of the most efficient sample analysis methods. Additionally, Meta-Prism 2.0 can achieve accuracy comparable with or better than other contemporary methods. Third, Meta-Prism 2.0 can precisely identify the original biome for samples, thus enabling sample source tracking. Finally, we have provided a web server for fast search of microbial community samples online. Conclusions In summary, Meta-Prism 2.0 has changed the resource-intensive sample search scheme to an effective procedure, which could be conducted by researchers every day even on a laptop, for insightful sample search, similarity analysis, and knowledge discovery. Meta-Prism 2.0 can be accessed at https://github.com/HUST-NingKang-Lab/Meta-Prism-2.0, and the web server can be accessed at https://hust-ningkang-lab.github.io/Meta-Prism-2.0/.
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Affiliation(s)
- Kai Kang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China.,Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Hui Chong
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Kang Ning
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
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Jin Y, Fang Z, Zhou X. Variation of soil bacterial communities in a chronosequence of citrus orchard. ANN MICROBIOL 2022; 72. [DOI: 10.1186/s13213-022-01681-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Purpose
Soil microorganisms are vital for soil ecosystems through bioconversion of soil nutrients and maintenance of soil fertility to promoting the growth and development of citrus. However, understanding of how different planting years affect the soil bacterial community structures as related to nutrient availability in citrus orchards is limited.
Methods
Here, Illumina MiSeq technology was used to investigate changes in bacterial community structures with different ages of citrus orchards that were 2, 5, 10, 15, and 18 years old.
Results
The data showed that (1) soil bacterial community structures changed over the different growth stages of citrus orchards. With the extension of plantation age, the microbial diversity of citrus orchards increased gradually so that it was highest in 10-year-old citrus plantations but then decreased where the diversity of 18-year-old citrus ages was significantly lower than that of 10 and 15-year-old ones. Proteobacteria, Actinobacteria, Acidobacteria, and Chloroflexi were the four dominant phyla in soil of citrus orchards, accounting for 30.85%, 24.89%, 14.27%, and 14.05% of the total soil bacterial communities, respectively. (2) Soil bacterial community structures in different succession stages were affected by soil pH and nutrients, in particular available potassium (AK).
Conclusion
This study advances the understanding of soil microbiota of orchards and their interactions related to environmental factors in citrus orchard, which will improve our ability to promote the function of soil bacteria, so as to improve soil pH and reduce potassium (K) fertilizer input and improve the fruit quality.
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