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Wu Q, Chen Y, Dou X, Liao D, Li K, An C, Li G, Dong Z. Microbial fertilizers improve soil quality and crop yield in coastal saline soils by regulating soil bacterial and fungal community structure. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 949:175127. [PMID: 39084360 DOI: 10.1016/j.scitotenv.2024.175127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2024] [Revised: 07/19/2024] [Accepted: 07/27/2024] [Indexed: 08/02/2024]
Abstract
Salinization is a global problem affecting agricultural productivity and sustainability. The application of exogenous microbial fertilizer harbors great potential for improving saline-alkali soil conditions and increasing land productivity. Yet the responses to microbial fertilizer application rate in terms of rhizosphere soil biochemical characteristics, soil microbial community, and crop yield and their interrelationships and underlying mechanisms are still unclear. Here, we studied changes to rhizosphere soil-related variables, soil enzyme activity (catalase, sucrase, urease), microbial community diversity, and sweet sorghum (Sorghum bicolor (L.) Moench) yield under four fertilization concentration levels (0, 0.12, 0.24, and 0.36 kg m-2) in a saline-alkali ecosystem (Shandong, China). Our results showed that the best improvement effect on soil when the microbial fertilizer was applied at a rate of 0.24 kg m-2. Compared with the control (sweet sorghum + no fertilizer), it significantly increased soil organic carbon (21.50 %), available phosphorus (26.14 %), available potassium (36.30 %), and soil urease (38.46 %), while significantly reducing soil pH (2.21 %) and EC (12.04 %). Meanwhile, the yield of sweet sorghum was increased by 24.19 %. This is mainly because microbial fertilizers enhanced the diversity and the network complexity of bacterial and fungal communities, and influenced catalase (CAT), urease (UE), and sucrase (SC), thereby facilitating nutrient release in the soil, enhancing soil fertility, and indirectly influencing sweet sorghum productivity. Among them, Gemmatimonadota and Verrucomicrobiota may be the key microbial factors affecting sweet sorghum yield, while available potassium, soil urease and available phosphorus are the main soil factors. These findings provide valuable theoretical insights for preserving the health of coastal saline-alkali soils and meeting the agricultural demand for increased yield per unit of land area.
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Affiliation(s)
- Qicong Wu
- Co-Innovation Center for Soil-Water and Forest-Grass Ecological Conservation in Yellow River Basin of Shandong Higher Education Institutions, College of Forestry, Shandong Agricultural University, Tai'an 271018, China; Mountain Tai Forest Ecosystem Research Station of State Forestry and Grassland Administration, Tai'an 271018, China
| | - Yang Chen
- Co-Innovation Center for Soil-Water and Forest-Grass Ecological Conservation in Yellow River Basin of Shandong Higher Education Institutions, College of Forestry, Shandong Agricultural University, Tai'an 271018, China; Mountain Tai Forest Ecosystem Research Station of State Forestry and Grassland Administration, Tai'an 271018, China
| | - Xiaohui Dou
- Co-Innovation Center for Soil-Water and Forest-Grass Ecological Conservation in Yellow River Basin of Shandong Higher Education Institutions, College of Forestry, Shandong Agricultural University, Tai'an 271018, China; Mountain Tai Forest Ecosystem Research Station of State Forestry and Grassland Administration, Tai'an 271018, China
| | - Dongxi Liao
- Co-Innovation Center for Soil-Water and Forest-Grass Ecological Conservation in Yellow River Basin of Shandong Higher Education Institutions, College of Forestry, Shandong Agricultural University, Tai'an 271018, China; Mountain Tai Forest Ecosystem Research Station of State Forestry and Grassland Administration, Tai'an 271018, China
| | - Kaiyi Li
- Co-Innovation Center for Soil-Water and Forest-Grass Ecological Conservation in Yellow River Basin of Shandong Higher Education Institutions, College of Forestry, Shandong Agricultural University, Tai'an 271018, China; Mountain Tai Forest Ecosystem Research Station of State Forestry and Grassland Administration, Tai'an 271018, China
| | - Chunchun An
- Co-Innovation Center for Soil-Water and Forest-Grass Ecological Conservation in Yellow River Basin of Shandong Higher Education Institutions, College of Forestry, Shandong Agricultural University, Tai'an 271018, China; Mountain Tai Forest Ecosystem Research Station of State Forestry and Grassland Administration, Tai'an 271018, China
| | - Guohui Li
- Water Resources Research Institute of Shandong Province, Ji'nan 250000, China.
| | - Zhi Dong
- Co-Innovation Center for Soil-Water and Forest-Grass Ecological Conservation in Yellow River Basin of Shandong Higher Education Institutions, College of Forestry, Shandong Agricultural University, Tai'an 271018, China; Mountain Tai Forest Ecosystem Research Station of State Forestry and Grassland Administration, Tai'an 271018, China.
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Manzano-Gómez LA, Rincón-Rosales R, Flores-Felix JD, Gen-Jimenez A, Ruíz-Valdiviezo VM, Ventura-Canseco LMC, Rincón-Molina FA, Villalobos-Maldonado JJ, Rincón-Molina CI. Cost-Effective Cultivation of Native PGPB Sinorhizobium Strains in a Homemade Bioreactor for Enhanced Plant Growth. Bioengineering (Basel) 2023; 10:960. [PMID: 37627845 PMCID: PMC10451550 DOI: 10.3390/bioengineering10080960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 08/09/2023] [Accepted: 08/11/2023] [Indexed: 08/27/2023] Open
Abstract
The implementation of bioreactor systems for the production of bacterial inoculants as biofertilizers has become very important in recent decades. However, it is essential to know the bacterial growth optimal conditions to optimize the production and efficiency of bioinoculants. The aim of this work was to identify the best nutriment and mixing conditions to improve the specific cell growth rates (µ) of two PGPB (plant growth-promoting bacteria) rhizobial strains at the bioreactor level. For this purpose, the strains Sinorhizobium mexicanum ITTG-R7T and Sinorhizobium chiapanecum ITTG-S70T were previously reactivated in a PY-Ca2+ (peptone casein, yeast extract, and calcium) culture medium. Afterward, a master cell bank (MCB) was made in order to maintain the viability and quality of the strains. The kinetic characterization of each bacterial strain was carried out in s shaken flask. Then, the effect of the carbon and nitrogen sources and mechanical agitation was evaluated through a factorial design and response surface methodology (RSM) for cell growth optimization, where µ was considered a response variable. The efficiency of biomass production was determined in a homemade bioreactor, taking into account the optimal conditions obtained during the experiment conducted at the shaken flask stage. In order to evaluate the biological quality of the product obtained in the bioreactor, the bacterial strains were inoculated in common bean (Phaseolus vulgaris var. Jamapa) plants under bioclimatic chamber conditions. The maximum cell growth rate in both PGPB strains was obtained using a Y-Ca2+ (yeast extract and calcium) medium and stirred at 200 and 300 rpm. Under these growth conditions, the Sinorhizobium strains exhibited a high nitrogen-fixing capacity, which had a significant (p < 0.05) impact on the growth of the test plants. The bioreactor system was found to be an efficient alternative for the large-scale production of PGPB rhizobial bacteria, which are intended for use as biofertilizers in agriculture.
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Affiliation(s)
- Luis Alberto Manzano-Gómez
- Laboratorio de Ecología Genómica, Tecnológico Nacional de México, Instituto Tecnológico de Tuxtla Gutiérrez, Tuxtla Gutiérrez 29050, Chiapas, Mexico; (L.A.M.-G.); (R.R.-R.); (A.G.-J.); (V.M.R.-V.); (L.M.C.V.-C.); (F.A.R.-M.); (J.J.V.-M.)
- Departamento de Investigación y Desarrollo, 3R Biotec SA de CV, Tuxtla Gutiérrez 29000, Chiapas, Mexico
| | - Reiner Rincón-Rosales
- Laboratorio de Ecología Genómica, Tecnológico Nacional de México, Instituto Tecnológico de Tuxtla Gutiérrez, Tuxtla Gutiérrez 29050, Chiapas, Mexico; (L.A.M.-G.); (R.R.-R.); (A.G.-J.); (V.M.R.-V.); (L.M.C.V.-C.); (F.A.R.-M.); (J.J.V.-M.)
| | | | - Adriana Gen-Jimenez
- Laboratorio de Ecología Genómica, Tecnológico Nacional de México, Instituto Tecnológico de Tuxtla Gutiérrez, Tuxtla Gutiérrez 29050, Chiapas, Mexico; (L.A.M.-G.); (R.R.-R.); (A.G.-J.); (V.M.R.-V.); (L.M.C.V.-C.); (F.A.R.-M.); (J.J.V.-M.)
| | - Víctor Manuel Ruíz-Valdiviezo
- Laboratorio de Ecología Genómica, Tecnológico Nacional de México, Instituto Tecnológico de Tuxtla Gutiérrez, Tuxtla Gutiérrez 29050, Chiapas, Mexico; (L.A.M.-G.); (R.R.-R.); (A.G.-J.); (V.M.R.-V.); (L.M.C.V.-C.); (F.A.R.-M.); (J.J.V.-M.)
| | - Lucia María Cristina Ventura-Canseco
- Laboratorio de Ecología Genómica, Tecnológico Nacional de México, Instituto Tecnológico de Tuxtla Gutiérrez, Tuxtla Gutiérrez 29050, Chiapas, Mexico; (L.A.M.-G.); (R.R.-R.); (A.G.-J.); (V.M.R.-V.); (L.M.C.V.-C.); (F.A.R.-M.); (J.J.V.-M.)
| | - Francisco Alexander Rincón-Molina
- Laboratorio de Ecología Genómica, Tecnológico Nacional de México, Instituto Tecnológico de Tuxtla Gutiérrez, Tuxtla Gutiérrez 29050, Chiapas, Mexico; (L.A.M.-G.); (R.R.-R.); (A.G.-J.); (V.M.R.-V.); (L.M.C.V.-C.); (F.A.R.-M.); (J.J.V.-M.)
| | - Juan José Villalobos-Maldonado
- Laboratorio de Ecología Genómica, Tecnológico Nacional de México, Instituto Tecnológico de Tuxtla Gutiérrez, Tuxtla Gutiérrez 29050, Chiapas, Mexico; (L.A.M.-G.); (R.R.-R.); (A.G.-J.); (V.M.R.-V.); (L.M.C.V.-C.); (F.A.R.-M.); (J.J.V.-M.)
| | - Clara Ivette Rincón-Molina
- Laboratorio de Ecología Genómica, Tecnológico Nacional de México, Instituto Tecnológico de Tuxtla Gutiérrez, Tuxtla Gutiérrez 29050, Chiapas, Mexico; (L.A.M.-G.); (R.R.-R.); (A.G.-J.); (V.M.R.-V.); (L.M.C.V.-C.); (F.A.R.-M.); (J.J.V.-M.)
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Islam T, Fatema, Hoque MN, Gupta DR, Mahmud NU, Sakif TI, Sharpe AG. Improvement of growth, yield and associated bacteriome of rice by the application of probiotic Paraburkholderia and Delftia. Front Microbiol 2023; 14:1212505. [PMID: 37520368 PMCID: PMC10375411 DOI: 10.3389/fmicb.2023.1212505] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 06/28/2023] [Indexed: 08/01/2023] Open
Abstract
Plant probiotic bacteria enhance growth and yield of crop plants when applied at the appropriate time and dose. Two rice probiotic bacteria, Paraburkholderia fungorum strain BRRh-4 and Delftia sp. strain BTL-M2 promote growth and yield of plants. However, no information is available on application of these two bacteria on growth, yield, and diversity and population of bacteriome in roots and rhizosphere soils of the treated rice plants. This study aimed to assess the effect of BRRh-4 and BTL-M2 application on growth, yield and bacteriome in roots and rhizosphere soil of rice under varying doses of N, P and K fertilizers. Application of BRRh-4 and BTL-M2 strains significantly (p < 0.05) increased seed germination, growth and yield of rice compared to an untreated control. Interestingly, the grain yield of rice by these bacteria with 50% less of the recommended doses of N, P, and K fertilizers were statistically similar to or better than the rice plants treated with 100% doses of these fertilizers. Targeted amplicon (16S rRNA) sequence-based analysis revealed significant differences (PERMANOVA, p = 0.00035) in alpha-diversity between the root (R) and rhizosphere soil (S) samples, showing higher diversity in the microbial ecosystem of root samples. Additionally, the bacteriome diversity in the root of rice plants that received both probiotic bacteria and chemical fertilizers were significantly higher (PERMANOVA, p = 0.0312) compared to the rice plants treated with fertilizers only. Out of 185 bacterial genera detected, Prevotella, an anaerobic and Gram-negative bacterium, was found to be the predominant genus in both rhizosphere soil and root metagenomes. However, the relative abundance of Prevotella remained two-fold higher in the rhizosphere soil metagenome (52.02%) than in the root metagenome (25.04%). The other predominant bacterial genera detected in the rice root metagenome were Bacillus (11.07%), Planctomyces (4.06%), Faecalibacterium (3.91%), Deinococcus (2.97%), Bacteroides (2.61%), and Chryseobacterium (2.30%). On the other hand, rhizosphere soil metagenome had Bacteroides (12.38%), Faecalibacterium (9.50%), Vibrio (5.94%), Roseomonas (3.40%), and Delftia (3.02%). Interestingly, we found the presence and/or abundance of specific genera of bacteria in rice associated with the application of a specific probiotic bacterium. Taken together, our results indicate that improvement of growth and yield of rice by P. fungorum strain BRRh-4 and Delftia sp. strain BTL-M2 is likely linked with modulation of diversity, structures, and signature of bacteriome in roots and rhizosphere soils. This study for the first time demonstrated that application of plant growth promoting bacteria significantly improve growth, yield and increase the diversity of bacterial community in rice.
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Affiliation(s)
- Tofazzal Islam
- Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh
| | - Fatema
- Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh
| | - M. Nazmul Hoque
- Department of Gynecology, Obstetrics and Reproductive Health, BSMRAU, Gazipur, Bangladesh
| | - Dipali Rani Gupta
- Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh
| | - Nur Uddin Mahmud
- Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh
| | - Tahsin Islam Sakif
- Lane Department of Computer Science and Electrical Engineering, West Virginia University, Morgantown, WV, United States
| | - Andrew G. Sharpe
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, Canada
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Sergio DLSV, James Michael K, Fannie Isela PC, Valeria VR, Corina HK, Luis Fernando GO, James Michael T, Sheng Yang H, Juan Jose PC. Draft genome sequence of Paraburkholderia sp . strain XV isolated from the rhizosphere of mango ( Mangifera indica L.). CURRENT RESEARCH IN MICROBIAL SCIENCES 2021; 2:100055. [PMID: 34841346 PMCID: PMC8610351 DOI: 10.1016/j.crmicr.2021.100055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/27/2021] [Accepted: 07/31/2021] [Indexed: 10/25/2022] Open
Abstract
Here, we report the draft genome of Paraburkholderia sp. XV. This strain was isolated from the rhizosphere of mango (Mangifera indica L.). Its genome consists of 9,189 coding DNA sequences, 60 tRNAs, a single copy of the 16S rRNA, 5S rRNA, and 23S rRNA gene, and 1 tmRNA. The GC content is 62.6%.
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Affiliation(s)
| | - Kremer James Michael
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA.,Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, USA
| | | | | | - Hayano-Kanashiro Corina
- Departamento de Investigaciones Científicas y Tecnológicas. Universidad de Sonora. Hermosillo, Sonora, México
| | - García-Ortega Luis Fernando
- Departamento de Ingeniería Genética, Centro de Investigación de Estudios Avanzados del IPN (CINVESTAV), Irapuato, Guanajuato, México
| | - Tiedje James Michael
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA.,Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, USA
| | - He Sheng Yang
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA.,Howard Hughes Medical Institute-Gordon and Betty Moore Foundation, Michigan State University, East Lansing, MI 48824, USA
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Zaman NR, Chowdhury UF, Reza RN, Chowdhury FT, Sarker M, Hossain MM, Akbor MA, Amin A, Islam MR, Khan H. Plant growth promoting endophyte Burkholderia contaminans NZ antagonizes phytopathogen Macrophomina phaseolina through melanin synthesis and pyrrolnitrin inhibition. PLoS One 2021; 16:e0257863. [PMID: 34591915 PMCID: PMC8483353 DOI: 10.1371/journal.pone.0257863] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 09/14/2021] [Indexed: 11/23/2022] Open
Abstract
The endophytic bacterium Burkholderia contaminans NZ was isolated from jute, which is an important fiber-producing plant. This bacterium exhibits significant growth promotion activity in in vivo pot experiments, and like other plant growth-promoting (PGP) bacteria fixes nitrogen, produces indole acetic acid (IAA), siderophore, and 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity. B. contaminans NZ is considered to exert a promising growth inhibitory effect on Macrophomina phaseolina, a phytopathogen responsible for infecting hundreds of crops worldwide. This study aimed to identify the possibility of B. contaminans NZ as a safe biocontrol agent and assess its effectiveness in suppressing phytopathogenic fungi, especially M. phaseolina. Co-culture of M. phaseolina with B. contaminans NZ on both solid and liquid media revealed appreciable growth suppression of M. phaseolina and its chromogenic aberration in liquid culture. Genome mining of B. contaminans NZ using NaPDoS and antiSMASH revealed gene clusters that displayed 100% similarity for cytotoxic and antifungal substances, such as pyrrolnitrin. GC-MS analysis of B. contaminans NZ culture extracts revealed various bioactive compounds, including catechol; 9,10-dihydro-12'-hydroxy-2'-methyl-5'-(phenylmethyl)- ergotaman 3',6',18-trione; 2,3-dihydro-3,5- dihydroxy-6-methyl-4H-pyran-4-one; 1-(1,6-Dioxooctadecyl)- pyrrolidine; 9-Octadecenamide; and 2- methoxy- phenol. These compounds reportedly exhibit tyrosinase inhibitory, antifungal, and antibiotic activities. Using a more targeted approach, an RP-HPLC purified fraction was analyzed by LC-MS, confirming the existence of pyrrolnitrin in the B. contaminans NZ extract. Secondary metabolites, such as catechol and ergotaman, have been predicted to inhibit melanin synthesis in M. phaseolina. Thus, B. contaminans NZ appears to inhibit phytopathogens by apparently impairing melanin synthesis and other potential biochemical pathways, exhibiting considerable fungistatic activity.
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Affiliation(s)
- Nazia R. Zaman
- Molecular Biology Laboratory, Department of Biochemistry and Molecular Biology, Faculty Biological Sciences, University of Dhaka, Dhaka, Bangladesh
| | - Umar F. Chowdhury
- Molecular Biology Laboratory, Department of Biochemistry and Molecular Biology, Faculty Biological Sciences, University of Dhaka, Dhaka, Bangladesh
| | - Rifath N. Reza
- Molecular Biology Laboratory, Department of Biochemistry and Molecular Biology, Faculty Biological Sciences, University of Dhaka, Dhaka, Bangladesh
| | - Farhana T. Chowdhury
- Molecular Biology Laboratory, Department of Biochemistry and Molecular Biology, Faculty Biological Sciences, University of Dhaka, Dhaka, Bangladesh
| | - Mrinmoy Sarker
- NSU Genome Research Institute (NGRI), Department of Biochemistry and Microbiology, North South University, Dhaka, Bangladesh
| | - Muhammad M. Hossain
- NSU Genome Research Institute (NGRI), Department of Biochemistry and Microbiology, North South University, Dhaka, Bangladesh
| | - Md. Ahedul Akbor
- Institute of National Analytical Research and Service (INARS), Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, Bangladesh
| | - Al Amin
- Molecular Biology Laboratory, Department of Biochemistry and Molecular Biology, Faculty Biological Sciences, University of Dhaka, Dhaka, Bangladesh
| | - Mohammad Riazul Islam
- Molecular Biology Laboratory, Department of Biochemistry and Molecular Biology, Faculty Biological Sciences, University of Dhaka, Dhaka, Bangladesh
| | - Haseena Khan
- Molecular Biology Laboratory, Department of Biochemistry and Molecular Biology, Faculty Biological Sciences, University of Dhaka, Dhaka, Bangladesh
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Barrera-Galicia GC, Peniche-Pavía HA, Peña-Cabriales JJ, Covarrubias SA, Vera-Núñez JA, Délano-Frier JP. Metabolic Footprints of Burkholderia Sensu Lato Rhizosphere Bacteria Active against Maize Fusarium Pathogens. Microorganisms 2021; 9:microorganisms9102061. [PMID: 34683382 PMCID: PMC8538949 DOI: 10.3390/microorganisms9102061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/20/2021] [Accepted: 09/24/2021] [Indexed: 11/16/2022] Open
Abstract
Consistent with their reported abundance in soils, several Burkholderia sensu lato strains were isolated from the rhizosphere of maize plants cultivated at different sites in central México. Comparative analysis of their 16S rRNA gene sequences permitted their separation into three distinctive clades, which were further subdivided into six other clusters by their close resemblance to (1) Trinickia dinghuensis; (2) Paraburkholderia kirstenboschensis, P. graminis, P. dilworthii and P. rhynchosiae; (3) B. gladioli; (4) B. arboris; (5) B. contaminans, or (6) B. metallica representative species. Direct confrontation assays revealed that these strains inhibited the growth of pathogenic Fusarium oxysporum f. sp. radicis-lycopersici, and F. verticillioides within a roughly 3-55% inhibition range. The use of a DIESI-based non-targeted mass spectroscopy experimental strategy further indicated that this method is an option for rapid determination of the pathogen inhibitory capacity of Burkholderia sensu lato strains based solely on the analysis of their exometabolome. Furthermore, it showed that the highest anti-fungal activity observed in B. contaminans and B. arboris was associated with a distinctive abundance of certain m/z ions, some of which were identified as components of the ornbactin and pyochelin siderophores. These results highlight the chemical diversity of Burkholderia sensu lato bacteria and suggest that their capacity to inhibit the Fusarium-related infection of maize in suppressive soils is associated with siderophore synthesis.
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Affiliation(s)
- Guadalupe C. Barrera-Galicia
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Irapuato, Irapuato 36824, Guanajuato, Mexico; (G.C.B.-G.); (H.A.P.-P.); (J.J.P.-C.)
| | - Héctor A. Peniche-Pavía
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Irapuato, Irapuato 36824, Guanajuato, Mexico; (G.C.B.-G.); (H.A.P.-P.); (J.J.P.-C.)
| | - Juan José Peña-Cabriales
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Irapuato, Irapuato 36824, Guanajuato, Mexico; (G.C.B.-G.); (H.A.P.-P.); (J.J.P.-C.)
| | - Sergio A. Covarrubias
- Área de Ciencias de la Salud, Ciudad Universitaria Campus Siglo XXI, Universidad Autónoma de Zacatecas, Zacatecas 98160, Zacatecas, Mexico; (S.A.C.); (J.A.V.-N.)
| | - José A. Vera-Núñez
- Área de Ciencias de la Salud, Ciudad Universitaria Campus Siglo XXI, Universidad Autónoma de Zacatecas, Zacatecas 98160, Zacatecas, Mexico; (S.A.C.); (J.A.V.-N.)
| | - John P. Délano-Frier
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Irapuato, Irapuato 36824, Guanajuato, Mexico; (G.C.B.-G.); (H.A.P.-P.); (J.J.P.-C.)
- Correspondence: ; Tel.: +52-462-623-9600
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Gonçalves-Dias J, Stetter MG. PopAmaranth: A population genetic genome browser for grain amaranths and their wild relatives. G3-GENES GENOMES GENETICS 2021; 11:6208888. [PMID: 33822034 PMCID: PMC8495932 DOI: 10.1093/g3journal/jkab103] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 03/07/2021] [Indexed: 12/15/2022]
Abstract
The combination of genomic, physiological, and population genetic research has accelerated the understanding and improvement of numerous crops. For non-model crops the lack of interdisciplinary research hinders their improvement. Grain amaranth is an ancient nutritious pseudocereal that has been domesticated three times in different regions of the Americas. We present and employ PopAmaranth, a population genetic genome browser, which provides an accessible representation of the genetic variation of the three grain amaranth species (A. hypochondriacus, A. cruentus, and A. caudatus) and two wild relatives (A. hybridus and A. quitensis) along the A. hypochondriacus reference sequence. We performed population-scale diversity and selection analysis from whole-genome sequencing data of 88 curated genetically and taxonomically unambiguously classified accessions. We employ the platform to show that genetic diversity in the water stress-related MIF1 gene declined during amaranth domestication and provide evidence for convergent saponin reduction between amaranth and quinoa. PopAmaranth is available through amaranthGDB at amaranthgdb.org/popamaranth.html.
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Affiliation(s)
| | - Markus G Stetter
- Dept. of Plant Sciences, University of Cologne, Cologne, Germany.,Cluster of Excellence on Plant Sciences, University of Cologne, Cologne, Germany
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Nunes RDO, Domiciano Abrahão G, de Sousa Alves W, Aparecida de Oliveira J, César Sousa Nogueira F, Pasqualoto Canellas L, Lopes Olivares F, Benedeta Zingali R, Soares MR. Quantitative proteomic analysis reveals altered enzyme expression profile in Zea mays roots during the early stages of colonization by Herbaspirillum seropedicae. Proteomics 2021; 21:e2000129. [PMID: 33570822 DOI: 10.1002/pmic.202000129] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 11/09/2022]
Abstract
The use of plant growth-promoting bacteria as agricultural inoculants of plants should be encouraged because of their prominent role in biological nitrogen fixation, the increase of nutrient uptake by roots, abiotic stress mitigation, and disease control. The complex mechanisms underlying the association between plant and beneficial bacteria have been increasingly studied, and proteomic tools can expand our perception regarding the fundamental molecular processes modulated by the interaction. In this study, we investigated the changes in protein expression in maize roots in response to treatment with the endophytic diazotrophic Herbaspirillum seropedicae and the activities of enzymes related to nitrogen metabolism. To identify maize proteins whose expression levels were altered in the presence of bacteria, a label-free quantitative proteomic approach was employed. Using this approach, we identified 123 differentially expressed proteins, of which 34 were upregulated enzymes, in maize roots cultivated with H. seropedicae. The maize root colonization of H. seropedicae modulated the differential expression of enzymes involved in the stress response, such as peroxidases, phenylalanine ammonia-lyase, and glutathione transferase. The differential protein profile obtained in the inoculated roots reflects the effect of colonization on plant growth and development compared with control plants.
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Affiliation(s)
- Rosane de Oliveira Nunes
- Departamento de Bioquímica/Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Giselli Domiciano Abrahão
- Departamento de Bioquímica/Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Wilber de Sousa Alves
- Departamento de Ensino Médio e Técnico, Centro Federal de Educação Tecnológica Celso Suckow da Fonseca, Rio de Janeiro, Brazil
| | - Jaqueline Aparecida de Oliveira
- Núcleo de Desenvolvimento de Insumos Biológicos para Agricultura, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Fábio César Sousa Nogueira
- Laboratório de Proteômica/LADETEC, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.,Unidade de Proteômica, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Luciano Pasqualoto Canellas
- Núcleo de Desenvolvimento de Insumos Biológicos para Agricultura, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Fábio Lopes Olivares
- Núcleo de Desenvolvimento de Insumos Biológicos para Agricultura, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Russolina Benedeta Zingali
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Márcia Regina Soares
- Departamento de Bioquímica/Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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9
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Hsu SH, Shen MW, Chen JC, Lur HS, Liu CT. The Photosynthetic Bacterium Rhodopseudomonas palustris Strain PS3 Exerts Plant Growth-Promoting Effects by Stimulating Nitrogen Uptake and Elevating Auxin Levels in Expanding Leaves. FRONTIERS IN PLANT SCIENCE 2021; 12:573634. [PMID: 33613595 PMCID: PMC7889516 DOI: 10.3389/fpls.2021.573634] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 01/13/2021] [Indexed: 05/11/2023]
Abstract
Rhodopseudomonas palustris strain PS3, a phototrophic bacterium, was originally isolated from a paddy field located in Taipei city, Taiwan, and showed positive effects on the growth of leafy vegetables. The aim of this study was to clarify the mechanism of the beneficial effects exerted by PS3 on plants. An ineffective R. palustris strain, YSC3, isolated from a paddy field located in Yilan County, was used as the negative control for comparative analyses. We cultivated non-heading Chinese cabbage (Brassica rapa var. chinensis) in 1/2 strength Hoagland hydroponic solution, in which nitrate is the main nitrogen source. We evaluated various plant physiological responses to inoculation with different bacterial inoculants. The N use efficiency (NUE) of PS3-inoculated plants was dramatically higher than that of YSC3-inoculated plants. The nitrate uptake efficiency (NUpE) was significantly elevated in plants treated with PS3; however, no excess nitrate accumulation was observed in leaves. We also noticed that the endogenous indole-3-acetic acid (IAA) levels as well as the cell division rate in the leaves of PS3-inoculated plants were significantly higher than those in the leaves of YSC3-inoculated plants. We examined the bacterial transcription of some genes during root colonization, and found that the expression level of IAA synthesis related gene MAO was almost the same between these two strains. It suggests that the elevated endogenous IAA in the PS3-inoculated plants was not directly derived from the exogenous IAA produced by this bacterium. Taken together, we deduced that PS3 inoculation could promote plant growth by enhancing nitrate uptake and stimulating the accumulation of endogenous auxin in young expanding leaves to increase the proliferation of leaf cells during leaf development.
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Affiliation(s)
- Shu-Hua Hsu
- Department of Agronomy, National Taiwan University, Taipei, Taiwan
| | - Meng-Wei Shen
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Jen-Chih Chen
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Huu-Sheng Lur
- Department of Agronomy, National Taiwan University, Taipei, Taiwan
- *Correspondence: Huu-Sheng Lur,
| | - Chi-Te Liu
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
- *Correspondence: Huu-Sheng Lur,
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10
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Javazmi L, Low T, Ash G, Young A. Investigation of slow release of urea from biodegradable single- and double-layered hollow nanofibre yarns. Sci Rep 2020; 10:19619. [PMID: 33184334 PMCID: PMC7665195 DOI: 10.1038/s41598-020-76395-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 10/22/2020] [Indexed: 11/17/2022] Open
Abstract
Urea is the most common form of nitrogenous fertiliser. Recently, research has focused on the development of delivery systems to prolong fertiliser release and prevent fertiliser loss through leaching and volatilization. This study investigates and compares single- and double-layered hollow nanofibrous yarns as novel delivery systems to encapsulate and release urea. Single-layered hollow poly l-lactic acid (PLLA) nanofibre yarns loaded with urea fertiliser were fabricated using a customized electrospinning. Double-layered hollow nanofibre yarns were produced by electrospinning polyhydroxybutyrate (PHB) nanofibres as an outer layer, with urea-impregnated PLLA nanofibres as the inner layer. Scanning electron microscopy (SEM) with an energy-dispersive spectroscopy (EDS) was used to characterize the morphology of hollow electrospun nanofibre yarns. A total nitrogen instrument (TNM-1) was used to study the urea release from single- and double-layered hollow nanofibres yarn in water. A Carbon:Nitrogen (CN) elemental analyser determined encapsulated nitrogen in PLLA nanofibres samples. Results indicated that urea-impregnated double-layered hollow nanofibre yarns significantly started nitrogen releasing at much lower amount during first 12 h compared to single-layered hollow nanofibre yarns (P value = 0.000). In conclusion, double-layered hollow nanofibre yarn has potential as an effective alternative to current methods for the slow release of fertilisers and other plant-required chemicals.
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Affiliation(s)
- Leila Javazmi
- School of Mechanical and Mechatronic Engineering, University of Southern Queensland, Toowoomba, Australia. .,Centre for Crop Health, University of Southern Queensland, Toowoomba, Australia.
| | - Tobias Low
- School of Mechanical and Mechatronic Engineering, University of Southern Queensland, Toowoomba, Australia
| | - Gavin Ash
- Centre for Crop Health, University of Southern Queensland, Toowoomba, Australia
| | - Anthony Young
- Centre for Crop Health, University of Southern Queensland, Toowoomba, Australia.,School of Agriculture and Food Sciences, The University of Queensland, Brisbane, Australia
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11
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Malviya MK, Li CN, Solanki MK, Singh RK, Htun R, Singh P, Verma KK, Yang LT, Li YR. Comparative analysis of sugarcane root transcriptome in response to the plant growth-promoting Burkholderia anthina MYSP113. PLoS One 2020; 15:e0231206. [PMID: 32267863 PMCID: PMC7141665 DOI: 10.1371/journal.pone.0231206] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 03/18/2020] [Indexed: 12/23/2022] Open
Abstract
The diazotrophic Burkholderia anthina MYSP113 is a vital plant growth-promoting bacteria and sugarcane root association. The present study based on a detailed analysis of sugarcane root transcriptome by using the HiSeq-Illumina platform in response to the strain MYSP113. The bacterium was initially isolated from the rhizosphere of sugarcane. To better understand biological, cellular, and molecular mechanisms, a de novo transcriptomic assembly of sugarcane root was performed. HiSeq-Illumina platformwas employed for the sequencing of an overall of 16 libraries at a 2×100 bp configuration. Differentially expressed genes (DEGs) analysis identified altered gene expression in 370 genes (total of 199 up-regulated genes and 171 down-regulated genes). Deciphering the huge datasets, concerning the functioning and production of biological systems, a high throughput genome sequencing analysis was attempted with Gene ontology functional analyses and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. The report revealed a total of 148930 unigenes. 70414 (47.28%) of them were annotated successfully to Gene Ontology (GO) terms. 774 at 45 days, 4985 of 30 days and 15 days of 6846 terms were significantly regulated. GO analysis revealed that many genes involved in the metabolic, oxidation-reduction process and biological regulatory processes in response to strain MYSP113 and significantly enriched as compare to the control. Moreover, KEGG enriched results show that differentially expressed genes were classified into different pathway categories involved in various processes, such as nitrogen metabolism, plant hormone signal transduction, etc. The sample correlation analyses could help examine the similarity at the gene expression level. The reliability of the observed differential gene expression patterns was validated with quantitative real-time PCR (qRT-PCR). Additionally, plant enzymes activities such as peroxidase and superoxide dismutase were significantly increased in plant roots after the inoculation of strain MYSP113. The results of the research may help in understanding the plant growth-promoting rhizobacteria and plant interaction.
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Affiliation(s)
- Mukesh Kumar Malviya
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
- Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, Guangxi, China
| | - Chang-Ning Li
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Manoj Kumar Solanki
- Department of Food Quality & Safety, Institute for Post-Harvest and Food Sciences, The Volcani Center, Agricultural Research Organization, Rishon LeZion, Israel
| | - Rajesh Kumar Singh
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
- Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, Guangxi, China
| | - Reemon Htun
- Department of Biotechnology, Mandalay Technological University, Mandalay, Myanmar
| | - Pratiksha Singh
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
- Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, Guangxi, China
| | - Krishan K. Verma
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
- Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, Guangxi, China
| | - Li-Tao Yang
- College of Agriculture, Guangxi University, Nanning, Guangxi, China
| | - Yang-Rui Li
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
- College of Agriculture, Guangxi University, Nanning, Guangxi, China
- * E-mail:
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12
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Bhatt K, Maheshwari DK. Bacillus megaterium Strain CDK25, a Novel Plant Growth Promoting Bacterium Enhances Proximate Chemical and Nutritional Composition of Capsicum annuum L. FRONTIERS IN PLANT SCIENCE 2020; 11:1147. [PMID: 32849705 PMCID: PMC7406793 DOI: 10.3389/fpls.2020.01147] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 07/14/2020] [Indexed: 05/21/2023]
Abstract
The present study aimed to scrutinize the effect of different cow dung bacterial treatments on the nutritional value of Capsicum annuum L. Among all treatments, seeds inoculated with Bacillus megaterium (CDK25) showed significant enhancement in various proximate constituents viz., crude fiber (3.31%), crude protein (3.84%), and ash (2.53%) as compared to control. Likewise, significant increase in different nutrient contents viz., Ca (16.26 mg/100 g), Mg (17.37 mg/100 g), P (11.91 mg/100 g), K (0.47 mg/100 g), Fe (1.37 mg/100 g), and Zn (0.21 mg/100 g) was recorded over the control. Principal component analysis data depicts a positive correlation between different treatments with variables, validating enhancement in nutritional constituents by B. megaterium (CDK25) treatment. The study suggests the application of "B. megaterium" for achieving the persistent potential for augmenting and boosting up plant biological, functional, and nutritional assets, thereby enhancing the overall edible quality of C. annuum L. along with weathering of soil minerals.
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13
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Abstract
Burkholderia bacteria are multifaceted organisms that are ecologically and metabolically diverse. The Burkholderia genus has gained prominence because it includes human pathogens; however, many strains are nonpathogenic and have desirable characteristics such as beneficial plant associations and degradation of pollutants. The diversity of the Burkholderia genus is reflected within the large genomes that feature multiple replicons. Burkholderia genomes encode a plethora of natural products with potential therapeutic relevance and biotechnological applications. This review highlights Burkholderia as an emerging source of natural products. An overview of the taxonomy of the Burkholderia genus, which is currently being revised, is provided. We then present a curated compilation of natural products isolated from Burkholderia sensu lato and analyze their characteristics in terms of biosynthetic class, discovery method, and bioactivity. Finally, we describe and discuss genome characteristics and highlight the biosynthesis of a select number of natural products that are encoded in unusual biosynthetic gene clusters. The availability of >1000 Burkholderia genomes in public databases provides an opportunity to realize the genetic potential of this underexplored taxon for natural product discovery.
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Affiliation(s)
- Sylvia Kunakom
- Department of Medicinal Chemistry and Pharmacognosy and Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Alessandra S. Eustáquio
- Department of Medicinal Chemistry and Pharmacognosy and Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
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14
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Delivery of Inoculum of Rhizophagus irregularis via Seed Coating in Combination with Pseudomonas libanensis for Cowpea Production. AGRONOMY-BASEL 2019. [DOI: 10.3390/agronomy9010033] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Cowpea (Vigna unguiculata L. Walp) is an important legume grown primarily in semi-arid area. Its production is generally inhibited by various abiotic and biotic stresses. The use of beneficial microorganisms (e.g., plant growth promoting bacteria (PGPB) and arbuscular mycorrhizal fungi (AMF)) can enhance agricultural production, as these microorganisms can improve soil fertility and plant tolerance to environmental stresses, thus enhancing crop yield in an eco-friendly manner. Application of PGPB and AMF in large scale agriculture needs to be improved. Thus, the use of seed coating could be an efficient mechanism for placement of inocula into soils. The aim of this study was to evaluate the effects of the AMF Rhizophagus irregularis BEG140 and the PGPB Pseudomonas libanensis TR1 alone or in combination on the biomass and physiological traits of cowpea. Four treatments were set: (i) non-inoculated control; (ii) PGPB; (iii) AMF applied via seed coating; and (iv) PGPB + AMF applied via seed coating. Cowpea plants inoculated via seed coating with R. irregularis and those inoculated with R. irregularis + P. libanensis showed root mycorrhizal colonization of 21.7% and 24.2%, respectively. PGPB P. libanensis was efficient in enhancing plant biomass and seed yield. There was no benefit of single (AMF) or dual (PGPB + AMF) inoculation on plant growth or seed yield. The application of beneficial soil microorganisms can be a viable approach for sustainable cowpea production in precision agriculture scenarios.
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15
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Cheng L, Zhou Q, Yu B. Responses and roles of roots, microbes, and degrading genes in rhizosphere during phytoremediation of petroleum hydrocarbons contaminated soil. INTERNATIONAL JOURNAL OF PHYTOREMEDIATION 2019; 21:1161-1169. [PMID: 31099253 DOI: 10.1080/15226514.2019.1612841] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Rhizodegradation performed by plant roots and the associated bacteria is one of the major mechanisms that contribute to removal of petroleum hydrocarbons (PHCs) during phytoremediation. In this study, the pot-culture experiment using wild ornamental Hylotelephium spectabile (Boreau) H. Ohba was designed to explore responses and roles of roots, microbes, and degrading genes in the rhizodegradation process. Results showed that PHCs degradation rate by phytoremediation was up to 37.6-53.3% while phytoaccumulation accounted for a low proportion, just at 0.3-13.3%. A total of 37 phyla were classified through the high throughput sequencing, among which Proteobacteria, Actinobacteria, and Acidobacteria were the three most dominant phyla, accounting for >60% of the phylum frequency. The selective enrichment of PHC degraders with high salt-tolerance, including Alcanivorax and Bacteroidetes, was induced. Generally, relative abundance of the PHC degrading genes increased significantly with an increase in PHCs concentrations, and the gene copy number in the phytoremediation group was 1.46-14.44 times as much as that in the unplanted controls. Overall, the presence of PHCs and plant roots showed a stimulating effect on the development of specific degraders containing PHC degrading genes, and correspondingly, a biodegradation-beneficial community structure had been constructed to contribute to PHCs degradation in the rhizosphere.
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Affiliation(s)
- Lijuan Cheng
- Key Laboratory of Pollution Processes and Environmental Criteria/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, Ministry of Education, College of Environmental Science and Engineering, Nankai University , Tianjin , China
- College of Geography and Tourism, Chongqing Normal University , Chongqing , China
| | - Qixing Zhou
- Key Laboratory of Pollution Processes and Environmental Criteria/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, Ministry of Education, College of Environmental Science and Engineering, Nankai University , Tianjin , China
| | - Binbin Yu
- College of Environmental Science and Engineering, Yangzhou University , Yangzhou , China
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16
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Lade SB, Román C, Cueto-Ginzo AI, Serrano L, Sin E, Achón MA, Medina V. Host-specific proteomic and growth analysis of maize and tomato seedlings inoculated with Azospirillum brasilense Sp7. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 129:381-393. [PMID: 29945074 DOI: 10.1016/j.plaphy.2018.06.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 06/16/2018] [Accepted: 06/16/2018] [Indexed: 05/26/2023]
Abstract
Azospirillum brasilense Sp7 (Sp7) is a diazotrophic, free-living plant growth-promoting rhizobacterium (PGPR) that is increasingly used for its ability to reduce stress and improve nutrient uptake by plants. To test the hypothesis that Sp7 interacts differently with the primary metabolism in C3 and C4 plants, differential proteomics were employed to study weekly protein expression in Sp7-treated maize (Zea mays cv. B73) and tomato (Solanum lycopersicum cv. Boludo) seedlings. Plant and root growth parameters were also monitored. Protein changes were most striking at the four-leaf stage (T1) for both species. Proteins related to metabolism and redox homeostasis were most abundant in tomato at T1, but later, plants experienced inhibited Calvin-Benson (CB) cycle and chloroplast development, indicating that photosynthetic proteins were damaged by reactive oxygen species (ROS). In maize, Sp7 first increased ROS-scavenging enzymes and decreased those related to metabolism, which ultimately reduced photoinhibition at later sampling times. Overall, the early interaction with maize is more complex and beneficial because the photosynthetic aparatus is protected by the C4 mechanism, thereby improving the interaction of the PGPR with maize. Better seedling emergence and vigor were observed in inoculated maize compared to tomato. This study provides an integrated perspective on the Sp7 strain-specific interactions with young C3 and C4 plants to modulate primary metabolism and photosynthesis.
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Affiliation(s)
- Sarah Boyd Lade
- Department of Plant Production and Forestry Science, University of Lleida - Agrotecnio Center, Lleida, Spain.
| | - Carla Román
- Department of Plant Production and Forestry Science, University of Lleida - Agrotecnio Center, Lleida, Spain
| | - Ana Isabel Cueto-Ginzo
- Department of Plant Production and Forestry Science, University of Lleida - Agrotecnio Center, Lleida, Spain
| | - Luis Serrano
- Department of Plant Production and Forestry Science, University of Lleida - Agrotecnio Center, Lleida, Spain
| | - Ester Sin
- Department of Plant Production and Forestry Science, University of Lleida - Agrotecnio Center, Lleida, Spain
| | - Maria Angels Achón
- Department of Plant Production and Forestry Science, University of Lleida - Agrotecnio Center, Lleida, Spain
| | - Vicente Medina
- Department of Plant Production and Forestry Science, University of Lleida - Agrotecnio Center, Lleida, Spain
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17
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Batista BD, Lacava PT, Ferrari A, Teixeira-Silva NS, Bonatelli ML, Tsui S, Mondin M, Kitajima EW, Pereira JO, Azevedo JL, Quecine MC. Screening of tropically derived, multi-trait plant growth- promoting rhizobacteria and evaluation of corn and soybean colonization ability. Microbiol Res 2018; 206:33-42. [PMID: 29146258 DOI: 10.1016/j.micres.2017.09.007] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Accepted: 09/18/2017] [Indexed: 01/10/2023]
Abstract
The present study assessed the plant growth-promoting (PGP) traits and diversity of culturable rhizobacteria associated with guarana (Paullinia cupana), a typical tropical plant. Ninety-six bacteria were isolated, subjected to biochemical tests, and identified by partial or total 16S rDNA sequencing. Proteobacteria and Firmicutes were the dominant rhizospheric phyla found, and Burkholderia and Bacillus were the most abundant genera. Thirteen strains exhibited the four PGP traits evaluated, and most of them belonged to the genus Burkholderia. Two multi-trait PGP strains, RZ2MS9 (Bacillus sp.) and RZ2MS16 (Burkholderia ambifaria), expressively promoted corn and soybean growth under greenhouse conditions. Compared to the non-inoculated control, increases in corn root dry weight of 247.8 and 136.9% were obtained with RZ2MS9 and RZ2MS16 inoculation, respectively, at 60days after seeding. The dry weights of corn and soybean shoots were significantly higher than those of non-inoculated plants, showing increases of more than 47% for both strains and crops. However, soybean root dry weight did not increased after bacterial inoculation with either strain. The colonization behavior of RZ2MS16 was assessed using GFP-labeling combined with fluorescence microscopy and a cultivation-based approach for quantification. RZ2MS16:gfp was able to colonize the roots and shoots of corn and soybean, revealing an endophytic behavior.
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Affiliation(s)
- Bruna Durante Batista
- Department of Genetics, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, - SP, Brazil
| | - Paulo Teixeira Lacava
- Department of Morphology and Pathology, Center for Biological and Health Sciences, Federal University of São Carlos, São Carlos, - SP, Brazil
| | - Andrea Ferrari
- Department of Genetics, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, - SP, Brazil
| | - Natalia Sousa Teixeira-Silva
- Department of Genetics, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, - SP, Brazil
| | - Maria Letícia Bonatelli
- Department of Genetics, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, - SP, Brazil
| | - Sarina Tsui
- Department of Genetics, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, - SP, Brazil
| | - Mateus Mondin
- Department of Genetics, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, - SP, Brazil
| | - Elliot Watanabe Kitajima
- Department of Plant Pathology and Nematology, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, - SP, Brazil
| | | | - João Lúcio Azevedo
- Department of Genetics, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, - SP, Brazil
| | - Maria Carolina Quecine
- Department of Genetics, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, - SP, Brazil.
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18
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Simonetti E, Roberts IN, Montecchia MS, Gutierrez-Boem FH, Gomez FM, Ruiz JA. A novel Burkholderia ambifaria strain able to degrade the mycotoxin fusaric acid and to inhibit Fusarium spp. growth. Microbiol Res 2017; 206:50-59. [PMID: 29146260 DOI: 10.1016/j.micres.2017.09.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 09/07/2017] [Accepted: 09/20/2017] [Indexed: 02/05/2023]
Abstract
Fusaric acid (FA) is a fungal metabolite produced by several Fusarium species responsible for wilts and root rot diseases of a great variety of plants. Bacillus spp. and Pseudomonas spp. have been considered as promising biocontrol agents against phytopathogenic Fusarium spp., however it has been demonstrated that FA negatively affects growth and production of some antibiotics in these bacteria. Thus, the capability to degrade FA would be a desirable characteristic in bacterial biocontrol agents of Fusarium wilt. Taking this into account, bacteria isolated from the rhizosphere of barley were screened for their ability to use FA as sole carbon and energy source. One strain that fulfilled this requirement was identified according to sequence analysis of 16S rRNA, gyrB and recA genes as Burkholderia ambifaria. This strain, designated T16, was able to grow with FA as sole carbon, nitrogen and energy source and also showed the ability to detoxify FA in barley seedlings. This bacterium also exhibited higher growth rate, higher cell densities, longer survival, higher levels of indole-3-acetic acid (IAA) production, enhanced biofilm formation and increased resistance to different antibiotics when cultivated in Luria Bertani medium at pH 5.3 compared to pH 7.3. Furthermore, B. ambifaria T16 showed distinctive plant growth-promoting features, such as siderophore production, phosphate-solubilization, 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, in vitro antagonism against Fusarium spp. and improvement of grain yield when inoculated to barley plants grown under greenhouse conditions. This strain might serve as a new source of metabolites or genes for the development of novel FA-detoxification systems.
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Affiliation(s)
- Ester Simonetti
- Instituto de Investigaciones en Biociencias Agrícolas y Ambientales, Universidad de Buenos Aires, CONICET, FAUBA. Av. San Martín 4453, C1417DSE, Ciudad Autónoma de Buenos Aires, Argentina
| | - Irma N Roberts
- Instituto de Investigaciones en Biociencias Agrícolas y Ambientales, Universidad de Buenos Aires, CONICET, FAUBA. Av. San Martín 4453, C1417DSE, Ciudad Autónoma de Buenos Aires, Argentina.
| | - Marcela S Montecchia
- Instituto de Investigaciones en Biociencias Agrícolas y Ambientales, Universidad de Buenos Aires, CONICET, FAUBA. Av. San Martín 4453, C1417DSE, Ciudad Autónoma de Buenos Aires, Argentina
| | - Flavio H Gutierrez-Boem
- Instituto de Investigaciones en Biociencias Agrícolas y Ambientales, Universidad de Buenos Aires, CONICET, FAUBA. Av. San Martín 4453, C1417DSE, Ciudad Autónoma de Buenos Aires, Argentina
| | - Federico M Gomez
- Instituto de Investigaciones en Biociencias Agrícolas y Ambientales, Universidad de Buenos Aires, CONICET, FAUBA. Av. San Martín 4453, C1417DSE, Ciudad Autónoma de Buenos Aires, Argentina
| | - Jimena A Ruiz
- Instituto de Investigaciones en Biociencias Agrícolas y Ambientales, Universidad de Buenos Aires, CONICET, FAUBA. Av. San Martín 4453, C1417DSE, Ciudad Autónoma de Buenos Aires, Argentina.
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Dingjan T, Imberty A, Pérez S, Yuriev E, Ramsland PA. Molecular Simulations of Carbohydrates with a Fucose-Binding Burkholderia ambifaria Lectin Suggest Modulation by Surface Residues Outside the Fucose-Binding Pocket. Front Pharmacol 2017; 8:393. [PMID: 28680402 PMCID: PMC5478714 DOI: 10.3389/fphar.2017.00393] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Accepted: 06/06/2017] [Indexed: 12/22/2022] Open
Abstract
Burkholderia ambifaria is an opportunistic respiratory pathogen belonging to the Burkholderia cepacia complex, a collection of species responsible for the rapidly fatal cepacia syndrome in cystic fibrosis patients. A fucose-binding lectin identified in the B. ambifaria genome, BambL, is able to adhere to lung tissue, and may play a role in respiratory infection. X-ray crystallography has revealed the bound complex structures for four fucosylated human blood group epitopes (blood group B, H type 1, H type 2, and Lex determinants). The present study employed computational approaches, including docking and molecular dynamics (MD), to extend the structural analysis of BambL-oligosaccharide complexes to include four additional blood group saccharides (A, Lea, Leb, and Ley) and a library of blood-group-related carbohydrates. Carbohydrate recognition is dominated by interactions with fucose via a hydrogen-bonding network involving Arg15, Glu26, Ala38, and Trp79 and a stacking interaction with Trp74. Additional hydrogen bonds to non-fucose residues are formed with Asp30, Tyr35, Thr36, and Trp74. BambL recognition is dominated by interactions with fucose, but also features interactions with other parts of the ligands that may modulate specificity or affinity. The detailed computational characterization of the BambL carbohydrate-binding site provides guidelines for the future design of lectin inhibitors.
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Affiliation(s)
- Tamir Dingjan
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash UniversityMelbourne, VIC, Australia
| | - Anne Imberty
- Centre de Recherches sur les Macromolécules Végétales, Centre National de la Recherche Scientifique UPR5301, Université Grenoble AlpesGrenoble, France
| | - Serge Pérez
- Département de Pharmacochimie Moléculaire, Centre National de la Recherche Scientifique, UMR5063, Université Grenoble AlpesGrenoble, France
| | - Elizabeth Yuriev
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash UniversityMelbourne, VIC, Australia
| | - Paul A Ramsland
- School of Science, RMIT UniversityMelbourne, VIC, Australia.,Department of Surgery Austin Health, University of MelbourneMelbourne, VIC, Australia.,Department of Immunology, Central Clinical School, Monash UniversityMelbourne, VIC, Australia.,Burnet InstituteMelbourne, VIC, Australia
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20
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De Gregorio PR, Michavila G, Ricciardi Muller L, de Souza Borges C, Pomares MF, Saccol de Sá EL, Pereira C, Vincent PA. Beneficial rhizobacteria immobilized in nanofibers for potential application as soybean seed bioinoculants. PLoS One 2017; 12:e0176930. [PMID: 28472087 PMCID: PMC5417607 DOI: 10.1371/journal.pone.0176930] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 04/19/2017] [Indexed: 11/18/2022] Open
Abstract
Seed inoculation with plant growth promoting rhizobacteria (PGPR) is an ideal tool to supply the soil with a high density of beneficial microorganisms. However, maintaining viable microorganisms is a major problem during seed treatment and storage. In this work, an evaluation was made of the effect of bacterial immobilization in nanofibers on the stability (viability and maintenance of beneficial properties) of two potential PGPR, Pantoea agglomerans ISIB55 and Burkholderia caribensis ISIB40. Moreover, the impact of soybean seed coating with nanofiber-immobilized rhizobacteria on bacterial survival during seed storage and on germination and plant growth parameters was determined. Bacterial nanoimmobilization and subsequent seed coating with nanofiber-immobilized rhizobacteria were carried out by electrospinning. The results demonstrate that this technique successfully immobilized P. agglomerans ISIB55 and B. caribensis ISIB40 because it did not affect the viability or beneficial properties of either rhizobacteria. Seed coating with nanofiber-immobilized rhizobacteria improved P. agglomerans ISIB55 and B. caribensis ISIB40 survival on seeds stored for 30 days and contributed to the successful colonization of both bacteria on the plant root. Moreover, seed coating with P. agglomerans ISIB55 increased germination, length and dry weight of the root. Furthermore, seed coating with B. caribensis ISIB40 increased leaf number and dry weight of the shoot. Therefore, the technique applied in the present work to coat seeds with nanofiber-immobilized PGPR could be considered a promising eco-friendly approach to improve soybean production using a microbial inoculant.
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Affiliation(s)
- Priscilla Romina De Gregorio
- Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET-UNT and Instituto de Química Biológica "Dr. Bernabé Bloj", Facultad de Bioquímica, Química y Farmacia, UNT. Chacabuco 461, San Miguel de Tucumán, Tucumán, Argentina
| | - Gabriela Michavila
- Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET-UNT and Instituto de Química Biológica "Dr. Bernabé Bloj", Facultad de Bioquímica, Química y Farmacia, UNT. Chacabuco 461, San Miguel de Tucumán, Tucumán, Argentina
| | | | - Clarissa de Souza Borges
- Departamento de Solos, Faculdade de Agronomia, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves, 7712, Porto Alegre, RS, Brazil
| | - María Fernanda Pomares
- Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET-UNT and Instituto de Química Biológica "Dr. Bernabé Bloj", Facultad de Bioquímica, Química y Farmacia, UNT. Chacabuco 461, San Miguel de Tucumán, Tucumán, Argentina
| | - Enilson Luiz Saccol de Sá
- Departamento de Solos, Faculdade de Agronomia, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves, 7712, Porto Alegre, RS, Brazil
| | - Claudio Pereira
- Tecnano Produtos e Serviços Ltda, Rua Washington Luiz, 675, Porto Alegre, RS, Brazil
| | - Paula Andrea Vincent
- Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET-UNT and Instituto de Química Biológica "Dr. Bernabé Bloj", Facultad de Bioquímica, Química y Farmacia, UNT. Chacabuco 461, San Miguel de Tucumán, Tucumán, Argentina
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21
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Shang C, Chen A, Chen G, Li H, Guan S, He J. Microbial Biofertilizer Decreases Nicotine Content by Improving Soil Nitrogen Supply. Appl Biochem Biotechnol 2017; 181:1-14. [PMID: 27439003 DOI: 10.1007/s12010-016-2195-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 07/13/2016] [Indexed: 12/07/2022]
Abstract
Biofertilizers have been widely used in many countries for their benefit to soil biological and physicochemical properties. A new microbial biofertilizer containing Phanerochaete chrysosporium and Bacillus thuringiensis was prepared to decrease nicotine content in tobacco leaves by regulating soil nitrogen supply. Soil NO3--N, NH4+-N, nitrogen supply-related enzyme activities, and nitrogen accumulation in plant leaves throughout the growing period were investigated to explore the mechanism of nicotine reduction. The experimental results indicated that biofertilizer can reduce the nicotine content in tobacco leaves, with a maximum decrement of 16-18 % in mature upper leaves. In the meantime, the total nitrogen in mature lower and middle leaves increased with the application of biofertilizer, while an opposite result was observed in upper leaves. Protein concentration in leaves had similar fluctuation to that of total nitrogen in response to biofertilizer. NO3--N content and nitrate reductase activity in biofertilizer-amended soil increased by 92.3 and 42.2 %, respectively, compared to those in the control, whereas the NH4+-N and urease activity decreased by 37.8 and 29.3 %, respectively. Nitrogen uptake was improved in the early growing stage, but this phenomenon was not observed during the late growth period. Nicotine decrease is attributing to the adjustment of biofertilizer in soil nitrogen supply and its uptake in tobacco, which result in changes of nitrogen content as well as its distribution in tobacco leaves. The application of biofertilizer containing P. chrysosporium and B. thuringiensis can reduce the nicotine content and improve tobacco quality, which may provide some useful information for tobacco cultivation.
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Affiliation(s)
- Cui Shang
- College of Resources and Environment, Hunan Agricultural University, Changsha, 410128, People's Republic of China
| | - Anwei Chen
- College of Resources and Environment, Hunan Agricultural University, Changsha, 410128, People's Republic of China.
| | - Guiqiu Chen
- College of Environmental Science and Engineering, Hunan University, Changsha, People's Republic of China.
| | - Huanke Li
- College of Environmental Science and Engineering, Hunan University, Changsha, People's Republic of China
| | - Song Guan
- College of Environmental Science and Engineering, Hunan University, Changsha, People's Republic of China
| | - Jianmin He
- College of Environmental Science and Engineering, Hunan University, Changsha, People's Republic of China
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22
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de Almeida Lopes KB, Carpentieri-Pipolo V, Oro TH, Stefani Pagliosa E, Degrassi G. Culturable endophytic bacterial communities associated with field-grown soybean. J Appl Microbiol 2016; 120:740-55. [PMID: 26744016 DOI: 10.1111/jam.13046] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 11/25/2015] [Accepted: 12/28/2015] [Indexed: 12/21/2022]
Abstract
AIMS Assess the diversity of the culturable endophytic bacterial population associated with transgenic and nontransgenic soybean grown in field trial sites in Brazil and characterize them phenotypically and genotypically focusing on characteristics related to plant growth promotion. METHODS AND RESULTS Endophytic bacteria were isolated from roots, stems and leaves of soybean cultivars (nontransgenic (C) and glyphosate-resistant (GR) transgenic soybean), including the isogenic BRS133 and BRS245RR. Significant differences were observed in bacterial densities in relation to genotype and tissue from which the isolates were obtained. The highest number of bacteria was observed in roots and in GR soybean. Based on characteristics related to plant growth promotion, 54 strains were identified by partial 16S rRNA sequence analysis, with most of the isolates belonging to the species Enterobacter ludwigii and Variovorax paradoxus. Among the isolates, 44·4% were able to either produce indoleacetic acid (IAA) or solubilize phosphates, and 9·2% (all from GR soybean) presented both plant growth-promoting activities. CONCLUSIONS The results from this study indicate that the abundance of endophytic bacterial communities of soybean differs between cultivars and in general it was higher in the transgenic cultivars than in nontransgenic cultivars. BRS 245 RR exhibited no significant difference in abundance compared to nontransgenic BRS133. This suggests that the impact of the management used in the GR soybean fields was comparable with the impacts of some enviromental factors. However, the bacterial endophytes associated to GR and nontransgenic soybean were different. The soybean-associated bacteria showing characteristics related to plant growth promotion were identified as belonging to the species Pantoea agglomerans and Variovorax paradoxus. SIGNIFICANCE AND IMPACT OF THE STUDY Our study demonstrated differences concerning compostion of culturable endophytic bacterial population in nontransgenic and transgenic soybean.
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Affiliation(s)
- K B de Almeida Lopes
- Agronomy Department, Post Graduation Program in Agronomy, Londrina State University, Londrina, PR, Brazil
| | | | - T H Oro
- Agronomy Department, Post Graduation Program in Agronomy, Londrina State University, Londrina, PR, Brazil
| | - E Stefani Pagliosa
- Agronomy Department, Post Graduation Program in Agronomy, Londrina State University, Londrina, PR, Brazil
| | - G Degrassi
- Industrial Biotechnology Group, International Center for Genetic Engineering and Biotechnology, Trieste, Italy
- IBioBA-ICGEB, Polo Cientifico Tecnologico, Buenos Aires, Argentina
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De Meyer SE, Fabiano E, Tian R, Van Berkum P, Seshadri R, Reddy T, Markowitz V, Ivanova N, Pati A, Woyke T, Howieson J, Kyrpides N, Reeve W. High-quality permanent draft genome sequence of the Parapiptadenia rigida-nodulating Burkholderia sp. strain UYPR1.413. Stand Genomic Sci 2015. [PMID: 26203342 PMCID: PMC4511699 DOI: 10.1186/s40793-015-0018-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Burkholderia sp. strain UYPR1.413 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from a root nodule of Parapiptadenia rigida collected at the Angico plantation, Mandiyu, Uruguay, in December 2006. A survey of symbionts of P. rigida in Uruguay demonstrated that this species is nodulated predominantly by Burkholderia microsymbionts. Moreover, Burkholderia sp. strain UYPR1.413 is a highly efficient nitrogen fixing symbiont with this host. Currently, the only other sequenced isolate to fix with this host is Cupriavidus sp. UYPR2.512. Therefore, Burkholderia sp. strain UYPR1.413 was selected for sequencing on the basis of its environmental and agricultural relevance to issues in global carbon cycling, alternative energy production, and biogeochemical importance, and is part of the GEBA-RNB project. Here we describe the features of Burkholderia sp. strain UYPR1.413, together with sequence and annotation. The 10,373,764 bp high-quality permanent draft genome is arranged in 336 scaffolds of 342 contigs, contains 9759 protein-coding genes and 77 RNA-only encoding genes.
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Affiliation(s)
- Sofie E De Meyer
- Centre for Rhizobium Studies, Murdoch University, Murdoch, WA, Australia
| | - Elena Fabiano
- Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Rui Tian
- Centre for Rhizobium Studies, Murdoch University, Murdoch, WA, Australia
| | - Peter Van Berkum
- Soybean Genomics and improvement laboratory Bldg 006, BARC-West USDA ARS, 10300 Baltimore Blvd, Beltsville 20705, MD, USA
| | | | - Tbk Reddy
- DOE Joint Genome Institute, Walnut Creek, CA, USA
| | - Victor Markowitz
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Amrita Pati
- DOE Joint Genome Institute, Walnut Creek, CA, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, CA, USA
| | - John Howieson
- Centre for Rhizobium Studies, Murdoch University, Murdoch, WA, Australia
| | - Nikos Kyrpides
- DOE Joint Genome Institute, Walnut Creek, CA, USA ; Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Wayne Reeve
- Centre for Rhizobium Studies, Murdoch University, Murdoch, WA, Australia
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