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Wang Q, Yu C, Kong C, Zeng H, Yu W, Wu J. Genomics analysis of three phosphorus-dissolving bacteria isolated from Torreya grandis soil. Int Microbiol 2024; 27:361-376. [PMID: 37453003 DOI: 10.1007/s10123-023-00393-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 06/21/2023] [Accepted: 06/28/2023] [Indexed: 07/18/2023]
Abstract
With the increasingly serious problem of phosphorus deficiency in the subtropical zone, chemical fertilizers are widely used. But it pollutes the environment. Phosphorus-solubilizing microorganisms (PSMs) are referred to as a new solution to this problem. We explored the phosphorus-dissolving characteristics of PSB strains isolated from the rhizosphere soil of Torreya grandis to provide a theoretical basis for selecting the strain for managing phosphorus deficiency in subtropical soils and also provides a more sufficient theoretical basis for the utilization of PSMs. From 84 strains, three strains exhibiting high phosphorus solubility and strong IAA producing capacity were selected through a series of experiments. The phosphate-solubilizing capacity of the three selected strains W1, W74, and W83 were 339.78 mg/L, 332.57 mg/L, and 358.61 mg/L, respectively. Furthermore, W1 showed the strongest IAA secreting capacity of 8.62 mg/L, followed by W74 (7.58 mg/L), and W83 (7.59 mg/L). Determination by metabolites, it was observed that these three strains dissolved phosphorus by secreting a large amount of lactic acid, aromatic acid, and succinic acid. The genome of these PSBs were sequenced and annotated in this study. Our results revealed that PSB primarily promotes their metabolic pathway, especially carbon metabolism, to secrete plenty organic acids for dissolving insoluble phosphorus.
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Affiliation(s)
- Qi Wang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Hangzhou, China
- School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Chenliang Yu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Hangzhou, China
- School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Congcong Kong
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Hangzhou, China
- School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Hao Zeng
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Hangzhou, China
- School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Weiwu Yu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Hangzhou, China.
- School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China.
- NFGA Engineering Research Center for Torreya Grandis 'Merrillii', Zhejiang A&F University, Hangzhou, 311300, China.
| | - Jiasheng Wu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Hangzhou, China.
- School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China.
- NFGA Engineering Research Center for Torreya Grandis 'Merrillii', Zhejiang A&F University, Hangzhou, 311300, China.
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Yue J, Yang F, Xiao Y, Lin S, He Z, Wang S, Zhao J, Yuan J, Li L, Liu L. Comamonas endophytica sp. nov., a novel indole acetic acid producing endophyte isolated from bamboo in China. Int J Syst Evol Microbiol 2024; 74. [PMID: 38190243 DOI: 10.1099/ijsem.0.006217] [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] [Indexed: 01/09/2024] Open
Abstract
Two novel indole acetic acid-producing strains, 5MLIRT and D4N7, were isolated from Indosasa shibataeoides in Yongzhou, Hunan province, and Phyllostachys edulis in Hangzhou, Zhejiang province, respectively. Based on their 16S rRNA sequences, strains 5MLIRT and D4N7 were closely related to Comamonas antarcticus 16-35-5T (98.4 % sequence similarity), and the results of 92-core gene phylogenetic trees showed that strains 5MLIRT and D4N7 formed a phylogenetic lineage within the clade comprising Comamonas species. The complete genome size of strain 5MLIRT was 4.49 Mb including two plasmids, and the DNA G+C content was 66.5 mol%. The draft genome of strain D4N7 was 4.26 Mb with 66.7 mol% G+C content. The average nucleotide identity and digital DNA-DNA hybridization values among strain 5MLIRT and species in the genus Comamonas were all below the species delineation threshold. The colonies of strain 5MLIRT and D4N7 were circular with regular margins, convex, pale yellow and 1.0-2.0 mm in diameter when incubated at 30 °C for 3 days. Strains 5MLIRT and D4N7 grew optimally at 30 °C, pH 7.0 and 1.0 % NaCl. The respiratory isoprenoid quinone was ubiquinone-8. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. Polyphasic analyses indicated that strains 5MLIRT and D4N7 could be distinguished from related validly named Comamonas species and represent a novel species of the genus Comamonas, for which the name Comamonas endophytica sp. nov. is proposed. The type strain is 5MLIRT (=ACCC 62069T=GDMCC 1.2958T=JCM 35331T).
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Affiliation(s)
- Jinjun Yue
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang 311400, PR China
| | - Fu Yang
- Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, PR China
| | - Youtie Xiao
- Hunan Jiuyishan National Nature Reserve Administration Bureau, Hunan 425603, PR China
| | - Seqiao Lin
- Hunan Jiuyishan National Nature Reserve Administration Bureau, Hunan 425603, PR China
| | - Zhengping He
- Hunan Jiuyishan National Nature Reserve Administration Bureau, Hunan 425603, PR China
| | - Siyu Wang
- Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, PR China
| | - Jiayi Zhao
- Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, PR China
| | - Jinling Yuan
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang 311400, PR China
| | - Lubin Li
- Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, PR China
| | - Lei Liu
- Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, PR China
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Sánchez-Matiz JJ, Díaz-Ariza LA. Glomeromycota associations with bamboos (Bambusoideae) worldwide, a qualitative systematic review of a promising symbiosis. PeerJ 2023; 11:e16151. [PMID: 38025720 PMCID: PMC10640841 DOI: 10.7717/peerj.16151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 08/30/2023] [Indexed: 12/01/2023] Open
Abstract
Background Around the world, bamboos are ecologically, economically, and culturally important plants, particularly in tropical regions of Asia, America, and Africa. The association of this plant group with arbuscular mycorrhizal fungi belonging to the phylum Glomeromycota is still a poorly studied field, which limits understanding of the reported ecological and physiological benefits for the plant, fungus, soil, and ecosystems under this symbiosis relationship. Methods Through a qualitative systematic review following the PRISMA framework for the collection, synthesis, and reporting of evidence, this paper presents a compilation of the research conducted on the biology and ecology of the symbiotic relationship between Glomeromycota and Bambusoideae from around the world. This review is based on academic databases enriched with documents retrieved using different online databases and the Google Scholar search engine. Results The literature search yielded over 6,000 publications, from which 18 studies were included in the present review after a process of selection and validation. The information gathered from the publications included over 25 bamboo species and nine Glomeromycota genera from eight families, distributed across five countries on two continents. Conclusion This review presents the current state of knowledge regarding the symbiosis between Glomeromycota and Bambusoideae, while reflecting on the challenges and scarcity of research on this promising association found across the world.
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Affiliation(s)
- Juan José Sánchez-Matiz
- Grupo de Investigación en Agricultura Biológica, Laboratorio de Asociaciones Suelo Planta Microorganismo, Departamento de Biología/Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, DC, Colombia
| | - Lucia Ana Díaz-Ariza
- Grupo de Investigación en Agricultura Biológica, Laboratorio de Asociaciones Suelo Planta Microorganismo, Departamento de Biología/Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, DC, Colombia
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Sriragavi G, Sangeetha M, Santhakumar M, Lokesh E, Nithyalakshmi M, Saleel CA, Balagurunathan R. Exploring Antibacterial Properties of Bioactive Compounds Isolated from Streptomyces sp. in Bamboo Rhizosphere Soil. ACS OMEGA 2023; 8:36333-36343. [PMID: 37810705 PMCID: PMC10552487 DOI: 10.1021/acsomega.3c04954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 09/04/2023] [Indexed: 10/10/2023]
Abstract
The increasing concern over multidrug resistance in pathogens has led to an ongoing search for novel antibiotics derived from soil actinobacteria. In this current investigation, actinobacteria were isolated from the rhizosphere of bamboo plants collected within the Megamalai forest of the Western Ghats in the Theni zone of Tamil Nadu, India. These actinobacteria were subjected to characterization, and their growth conditions were optimized to enhance the production of bioactive compounds. To assess antibacterial properties, the isolated Actinobacteria underwent testing using the agar plug method. The strain exhibiting notable antibacterial activity underwent further characterization through 16s rRNA gene sequencing and subsequent phylogenetic analysis. Employing response surface methodology (RSM), cultural conditions were fine-tuned. Bioactive compounds were extracted from the culture medium using ethyl acetate, and their antibacterial and antioxidant effects were evaluated through disc diffusion and DPPH radical scavenging methods, respectively. Ethyl acetate extracts were analyzed by using FT-IR and GC-MS techniques. In total, nine strains of Actinobacteria were isolated from the rhizosphere soil of bamboo. Among these, strain BS-16 displayed remarkable antibacterial activity against three strains: Staphylococcus aureus (19 mm), Bacillus subtilis (12 mm), and Streptococcus pyogenes (10 mm). This strain was identified as Streptomyces sp. The optimal conditions for bioactive compound production were determined as follows: malt extract (10 g), yeast extract (5 g), dextrose (5 g), pH 6.5, and temperature 30 °C. After a 7-day incubation period, the results showed a 6% increase in production. The ethyl acetate fraction derived from strain BS-16 exhibited dose-dependent antibacterial and antioxidant activities. FT-IR and GC-MS analyses revealed the presence of active compounds with antibacterial effects within the extract. Consequently, further investigation into the BS-16 strain holds promise for scaling up the production of bioactive compounds possessing antibacterial and antioxidant properties.
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Affiliation(s)
- Govindaraj Sriragavi
- Actinobacterial
Research Laboratory, Department of Microbiology, Periyar University, Salem 636011, Tamilnadu, India
| | - Murthy Sangeetha
- Actinobacterial
Research Laboratory, Department of Microbiology, Periyar University, Salem 636011, Tamilnadu, India
| | - Munusamy Santhakumar
- Actinobacterial
Research Laboratory, Department of Microbiology, Periyar University, Salem 636011, Tamilnadu, India
| | - Elumalai Lokesh
- Actinobacterial
Research Laboratory, Department of Microbiology, Periyar University, Salem 636011, Tamilnadu, India
| | - Mohanam Nithyalakshmi
- Actinobacterial
Research Laboratory, Department of Microbiology, Periyar University, Salem 636011, Tamilnadu, India
| | - Chanduveetil Ahamed Saleel
- Department
of Mechanical Engineering, College of Engineering, King Khalid University, P.O. Box 394, Abha 61421, Saudi Arabia
| | - Ramasamy Balagurunathan
- Actinobacterial
Research Laboratory, Department of Microbiology, Periyar University, Salem 636011, Tamilnadu, India
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Liang S, Wang SN, Zhou LL, Sun S, Zhang J, Zhuang LL. Combination of Biochar and Functional Bacteria Drives the Ecological Improvement of Saline-Alkali Soil. PLANTS (BASEL, SWITZERLAND) 2023; 12:284. [PMID: 36678996 PMCID: PMC9864812 DOI: 10.3390/plants12020284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/04/2023] [Accepted: 01/06/2023] [Indexed: 06/17/2023]
Abstract
The addition of functional bacteria (FB) is low-cost and is widely applied in saline-alkali soil remediation, which may gradually become ineffective due to inter-specific competition with indigenous bacteria. To improve the adaptability of FB, the target FB strains were isolated from local saline-alkali soil, and the combined effects of FB and biochar were explored. The results showed that FB isolated from local soil showed better growth than the purchased strains under high saline-alkali conditions. However, the indigenous community still weakened the function of added FB. Biochar addition provided a specific niche and increased the relative abundance of FB, especially for Proteobacteria and Bacteroidota. As a result, the co-addition of 10% biochar and FB significantly increased the soil available phosphorus (AP) by 74.85% and available nitrogen (AN) by 114.53%. Zea Mays's growth (in terms of height) was enhanced by 87.92% due to the decreased salinity stress and extra nutrients provided.
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Affiliation(s)
- Shuang Liang
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science & Engineering, Shandong University, Qingdao 266237, China
| | - Sheng-Nan Wang
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science & Engineering, Shandong University, Qingdao 266237, China
| | - Lu-Lu Zhou
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science & Engineering, Shandong University, Qingdao 266237, China
| | - Shuo Sun
- Baiyangdian Basin Eco-environmental Support Center, Shijiazhuang 050000, China
| | - Jian Zhang
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science & Engineering, Shandong University, Qingdao 266237, China
- College of Safety and Environmental Engineering, Shandong University of Science and Technology, Qingdao 266590, China
| | - Lin-Lan Zhuang
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science & Engineering, Shandong University, Qingdao 266237, China
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Chen P, Wan W. Rare alkaline phosphatase-harboring bacteria mediate organic phosphorus mineralization during swine manure composting. BIORESOURCE TECHNOLOGY 2023; 368:128335. [PMID: 36403913 DOI: 10.1016/j.biortech.2022.128335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/10/2022] [Accepted: 11/13/2022] [Indexed: 06/16/2023]
Abstract
Deciphering ecological functions of alkaline phosphatase (phoD)-harboring bacteria in composting systems is crucial but poorly understood. High-throughput sequencing, gene quantification, and statistical analyses were applied to investigate effects of abundance and diversity of phoD-harboring bacteria (PHB) on phosphorus availability during swine manure composting. Results showed that available phosphorus notably increased from 0.5 to 1.43 g kg-1, and physicochemical properties and enzyme activities affected PHB community composition. Phylogenetic signals of PHB responded notably to temperature and phosphorus components, and stochasticity (94.2 %) dominated community assembly. Abundance and diversity of PHB directly and indirectly influenced phosphorus availability, and rare PHB mediated organic phosphorus mineralization. A phosphate-solubilizing bacterium (PSB) Pseudomonas sp. WWJ-22 isolated from compost displayed good efficiency in mineralizing lecithin, demonstrating the highest phosphorus-solubilizing level of 116.3 mg L-1. This study highlights ecological roles of PHB on phosphorus availability and provides a potential PSB candidate for composting.
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Affiliation(s)
- Peng Chen
- Key Laboratory of Aquatic Botany and Watershed Ecology Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, PR China; Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, Chinese Academy of Sciences & Hubei Province, Wuhan 430074, PR China
| | - Wenjie Wan
- Key Laboratory of Aquatic Botany and Watershed Ecology Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, PR China; Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, Chinese Academy of Sciences & Hubei Province, Wuhan 430074, PR China.
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He D, Wan W. Distribution of Culturable Phosphate-Solubilizing Bacteria in Soil Aggregates and Their Potential for Phosphorus Acquisition. Microbiol Spectr 2022; 10:e0029022. [PMID: 35536021 PMCID: PMC9241762 DOI: 10.1128/spectrum.00290-22] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 04/21/2022] [Indexed: 11/22/2022] Open
Abstract
Deciphering distribution patterns of phosphate-solubilizing bacteria (PSB) and phosphorus-cycling-related genes in soils is important to evaluate phosphorus (P) transformation. However, the linkage between PSB number and P-cycling-related gene abundance in soils, especially soil aggregates, remains largely unknown. Here, we estimated the numbers of PSB and abundances of P-cycling-related genes (i.e., gcd and bpp) in soil aggregates under different fertilization regimes as well as P-solubilizing performance and plant-growth-promoting ability of PSB. We found that tricalcium phosphate-solubilizing bacteria, phytate-degrading bacteria, and gcd and bpp abundances were more abundant in silt plus clay (silt+clay; <53 μm) than in macroaggregate (250 to 2000 μm) and microaggregate (53 to 250 μm). Fertilization treatment and aggregate fractionation showed distinct effects on PSB number and P-cycling-related gene abundance. We found significantly negative correlation between gcd gene abundance and tricalcium phosphate-solubilizing bacterial number (Col-CaP) and dramatically positive correlation between bpp gene abundance and phytate-degrading bacterial number (Col-Phy). P fractions were responsible for PSB number and P-cycling-related gene abundance. The isolated Pseudomonas sp. strain PSB-2 and Arthrobacter sp. strain PSB-5 exhibited good performances for solubilizing tricalcium phosphate. The inoculation of Pseudomonas sp. PSB-2 could significantly enhance plant fresh weight, plant dry weight, and plant height. Our results emphasized distinct distribution characteristics of PSB and P-cycling-related genes in soil aggregates and deciphered a close linkage between PSB number and P-cycling-related gene abundance. Our findings might guide the isolation of PSB from agricultural soils and provide a candidate plant-growth-promoting bacterium for agro-ecosystems. IMPORTANCE Phosphate-solubilizing bacteria are responsible for inorganic P solubilization and organic P mineralization. Elucidating the linkage between phosphate-solubilizing bacterial number and P-cycling-related gene abundance is important to isolate plant-growth-promoting bacteria for agro-ecosystems. Our findings reveal differentiating strategies of phosphate-solubilizing bacteria in soil aggregates, and the deciphered P fractions show strong effects on distribution patterns of phosphate-solubilizing bacteria and P-cycling-related genes. Additionally, we isolated phosphate-solubilizing bacteria with good plant-growth-promoting ability. This study enriches our knowledge of P cycling in soil aggregates and might guide the production and management of farmland.
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Affiliation(s)
- Donglan He
- College of Life Science, South-Central University for Nationalities, Wuhan, People’s Republic of China
| | - Wenjie Wan
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, People’s Republic of China
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, People’s Republic of China
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