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Hilário S, Gonçalves MFM, Matos I, Rangel LF, Sousa JA, Santos MJ, Ayra-Pardo C. Comparative genomics reveals insights into the potential of Lysinibacillus irui as a plant growth promoter. Appl Microbiol Biotechnol 2024; 108:370. [PMID: 38861018 PMCID: PMC11166776 DOI: 10.1007/s00253-024-13210-6] [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: 03/05/2024] [Revised: 05/23/2024] [Accepted: 05/28/2024] [Indexed: 06/12/2024]
Abstract
Members of the genus Lysinibacillus attract attention for their mosquitocidal, bioremediation, and plant growth-promoting abilities. Despite this interest, comprehensive studies focusing on genomic traits governing plant growth and stress resilience in this genus using whole-genome sequencing are still scarce. Therefore, we sequenced and compared the genomes of three endophytic Lysinibacillus irui strains isolated from Canary Island date palms with the ex-type strain IRB4-01. Overall, the genomes of these strains consist of a circular chromosome with an average size of 4.6 Mb and a GC content of 37.2%. Comparative analysis identified conserved gene clusters within the core genome involved in iron acquisition, phosphate solubilization, indole-3-acetic acid biosynthesis, and volatile compounds. In addition, genome analysis revealed the presence of genes encoding carbohydrate-active enzymes, and proteins that confer resistance to oxidative, osmotic, and salinity stresses. Furthermore, pathways of putative novel bacteriocins were identified in all genomes. This illustrates possible common plant growth-promoting traits shared among all strains of L. irui. Our findings highlight a rich repertoire of genes associated with plant lifestyles, suggesting significant potential for developing inoculants to enhance plant growth and resilience. This study is the first to provide insights into the overall genomic signatures and mechanisms of plant growth promotion and biocontrol in the genus Lysinibacillus. KEY POINTS: • Pioneer study in elucidating plant growth promoting in L. irui through comparative genomics. • Genome mining identified biosynthetic pathways of putative novel bacteriocins. • Future research directions to develop L. irui-based biofertilizers for sustainable agriculture.
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Affiliation(s)
- Sandra Hilário
- Interdisciplinary Centre of Marine and Environmental Research, CIIMAR, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Porto, Portugal.
- GreenUPorto, Sustainable Agrifood Production Research Centre/Inov4Agro, DGAOT, Faculty of Sciences, University of Porto, Campus de Vairão, 747, 4485-646, Vila do Conde, Portugal.
| | - Micael F M Gonçalves
- Department of Biology, Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - Inês Matos
- Interdisciplinary Centre of Marine and Environmental Research, CIIMAR, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Porto, Portugal
| | - Luis F Rangel
- Interdisciplinary Centre of Marine and Environmental Research, CIIMAR, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Porto, Portugal
| | - José A Sousa
- Interdisciplinary Centre of Marine and Environmental Research, CIIMAR, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Porto, Portugal
- Biology Department, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, FC4, 4169-007, Porto, Portugal
| | - Maria J Santos
- Interdisciplinary Centre of Marine and Environmental Research, CIIMAR, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Porto, Portugal
- Biology Department, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, FC4, 4169-007, Porto, Portugal
| | - Camilo Ayra-Pardo
- Interdisciplinary Centre of Marine and Environmental Research, CIIMAR, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Porto, Portugal.
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Sharma M, Sood G, Chauhan A. Assessment of Plant Growth Promotion Potential of Endophytic Bacterium B. subtilis KU21 Isolated from Rosmarinus officinalis. Curr Microbiol 2024; 81:207. [PMID: 38831110 DOI: 10.1007/s00284-024-03734-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 05/07/2024] [Indexed: 06/05/2024]
Abstract
The current study aimed to evaluate the plant growth-promoting (PGP) potential of endophytic strain Bacillus subtilis KU21 isolated from the roots of Rosmarinus officinalis. The strain exhibited multiple traits of plant growth promotion viz., phosphate (P) solubilization, nitrogen fixation, indole-3-acetic acid (IAA), siderophore, hydrogen cyanide (HCN), lytic enzymes production, and 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity. The isolate also exhibited antagonistic activity against phytopathogenic fungi, i.e., Fusarium oxysporum, Fusarium graminiarum, and Rhizoctonia solani. The P-solubilization activity of B. subtilis KU21 was further elucidated via detection of glucose dehydrogenase (gdh) gene involved in the production of gluconic acid which is responsible for P-solubilization. Further, B. subtilis KU21 was evaluated for in vivo growth promotion studies of tomato (test crop) under net house conditions. A remarkable increase in seed germination, plant growth parameters, nutrient acquisition, and soil quality parameters (NPK) was observed in B. subtilis KU21-treated plants over untreated control. Hence, the proposed module could be recommended for sustainable tomato production in the Northwest Himalayan region without compromising soil health and fertility.
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Affiliation(s)
- Minakshi Sharma
- Division of Soil Science and Agricultural Chemistry, Indian Agricultural Research Institute, New Delhi, India.
| | - Gaurav Sood
- Department of Soil Science and Water Management, Dr YS Parmar University of Horticulture and Forestry, Solan, Himachal Pradesh, India
| | - Anjali Chauhan
- Department of Soil Science and Water Management, Dr YS Parmar University of Horticulture and Forestry, Solan, Himachal Pradesh, India.
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Saha KK, Mandal S, Barman A, Mondal S, Chatterjee S, Mandal NC. Genomic insight of phosphate solubilization and plant growth promotion of two taxonomically distinct winter crops by Enterobacter sp. DRP3. J Appl Microbiol 2024; 135:lxae146. [PMID: 38877666 DOI: 10.1093/jambio/lxae146] [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: 12/14/2023] [Revised: 05/14/2024] [Accepted: 06/13/2024] [Indexed: 06/16/2024]
Abstract
AIMS Study of rhizospheric microbiome-mediated plant growth promotional attributes currently highlighted as a key tool for the development of suitable bio-inoculants for sustainable agriculture purposes. In this context, we have conducted a detailed study regarding the characterization of phosphate solubilizing potential by plant growth-promoting bacteria that have been isolated from the rhizosphere of a pteridophyte Dicranopteris sp., growing on the lateritic belt of West Bengal. METHODS AND RESULTS We have isolated three potent bacterial strains, namely DRP1, DRP2, and DRP3 from the rhizoids-region of Dicranopteris sp. Among the isolated strains, DRP3 is found to have the highest phosphate solubilizing potentiality and is able to produce 655.89 and 627.58 µg ml-1 soluble phosphate by solubilizing tricalcium phosphate (TCP) and Jordan rock phosphate, respectively. This strain is also able to solubilize Purulia rock phosphate moderately (133.51 µg ml-1). Whole-genome sequencing and further analysis of the studied strain revealed the presence of pyrroloquinoline quinone (PQQ)-dependent glucose dehydrogenase gdh gene along with several others that were well known for their role in phosphate solubilization. Further downstream, quantitative reverse transcriptase PCR-based expression study revealed 1.59-fold upregulation of PQQ-dependent gdh gene during the solubilization of TCP. Root colonization potential of the studied strain on two taxonomically distinct winter crops viz. Cicer arietinum and Triticum aestivum has been checked by using scanning electron microscopy. Other biochemical analyses for plant growth promotion traits including indole acetic acid production (132.02 µg ml-1), potassium solubilization (3 mg l-1), biofilm formation, and exopolymeric substances productions (1.88-2.03 µg ml-1) also has been performed. CONCLUSION This study highlighted the active involvement of PQQ-dependent gdh gene during phosphate solubilization from any Enterobacter group. Moreover, our study explored different roadmaps for sustainable farming methods and the preservation of food security without endangering soil health in the future.
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Affiliation(s)
- Kunal Kumar Saha
- Mycology and Plant Pathology Laboratory, Department of Botany, Visva Bharati, Santiniketan 731235, India
| | - Subhrangshu Mandal
- Stress Physiology and Environmental Microbiology Laboratory, Department of Botany, Visva Bharati, Santiniketan 731235, India
| | - Anik Barman
- Department of Microbiology, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata 700054, India
| | - Sangita Mondal
- Department of Biological Sciences, Bose Institute, Kolkata 700091, India
| | - Sumit Chatterjee
- Department of Biological Sciences, Bose Institute, Kolkata 700091, India
| | - Narayan Chandra Mandal
- Mycology and Plant Pathology Laboratory, Department of Botany, Visva Bharati, Santiniketan 731235, India
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Zouagui R, Zouagui H, Aurag J, Ibrahimi A, Sbabou L. Functional analysis and comparative genomics of Rahnella perminowiae S11P1 and Variovorax sp. S12S4, two plant growth-promoting rhizobacteria isolated from Crocus sativus L. (saffron) rhizosphere. BMC Genomics 2024; 25:289. [PMID: 38500021 PMCID: PMC10946135 DOI: 10.1186/s12864-024-10088-6] [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: 07/10/2023] [Accepted: 02/03/2024] [Indexed: 03/20/2024] Open
Abstract
BACKGROUND Rahnella perminowiae S11P1 and Variovorax sp. S12S4 are two plant growth-promoting rhizobacteria that were previously isolated from the rhizosphere of Crocus sativus L. (saffron), and have demonstrated interesting PGP activities and promising results when used as inoculants in field trials. To further elucidate the molecular mechanisms underlying their beneficial effects on plant growth, comprehensive genome mining of S11P1 and S12S4 and comparative genomic analysis with closely related strains were conducted. RESULTS Functional annotation of the two strains predicted a large number of genes involved in auxin and siderophore production, nitrogen fixation, sulfur metabolism, organic acid biosynthesis, pyrroloquinoline quinone production, 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, volatile organic compounds production, and polyamine biosynthesis. In addition, numerous genes implicated in plant-bacteria interactions, such as those involved in chemotaxis and quorum sensing, were predicted. Moreover, the two strains carried genes involved in bacterial fitness under abiotic stress conditions. Comparative genomic analysis revealed an open pan-genomic structure for the two strains. COG annotation showed that higher fractions of core and accessory genes were involved in the metabolism and transport of carbohydrates and amino acids, suggesting the metabolic versatility of the two strains as effective rhizosphere colonizers. Furthermore, this study reports the first comparison of Multilocus sequence analysis (MLSA) and core-based phylogenies of the Rahnella and Variovorax genera. CONCLUSIONS The present study unveils the molecular mechanisms underlying plant growth promotion and biocontrol activity of S11P1 and S12S4, and provides a basis for their further biotechnological application in agriculture.
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Affiliation(s)
- Rahma Zouagui
- Laboratory of Microbiology and Molecular Biology, Faculty of Sciences, Mohammed V University in Rabat, Rabat, Morocco
| | - Houda Zouagui
- Laboratory of Microbiology and Molecular Biology, Faculty of Sciences, Mohammed V University in Rabat, Rabat, Morocco
- Biotechnology Lab (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed V University in Rabat, Rabat, Morocco
| | - Jamal Aurag
- Laboratory of Microbiology and Molecular Biology, Faculty of Sciences, Mohammed V University in Rabat, Rabat, Morocco
| | - Azeddine Ibrahimi
- Biotechnology Lab (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed V University in Rabat, Rabat, Morocco
| | - Laila Sbabou
- Laboratory of Microbiology and Molecular Biology, Faculty of Sciences, Mohammed V University in Rabat, Rabat, Morocco.
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Abou Jaoudé R, Luziatelli F, Ficca AG, Ruzzi M. A plant's perception of growth-promoting bacteria and their metabolites. FRONTIERS IN PLANT SCIENCE 2024; 14:1332864. [PMID: 38328622 PMCID: PMC10848262 DOI: 10.3389/fpls.2023.1332864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 12/28/2023] [Indexed: 02/09/2024]
Abstract
Many recent studies have highlighted the importance of plant growth-promoting (rhizo)bacteria (PGPR) in supporting plant's development, particularly under biotic and abiotic stress. Most focus on the plant growth-promoting traits of selected strains and the latter's effect on plant biomass, root architecture, leaf area, and specific metabolite accumulation. Regarding energy balance, plant growth is the outcome of an input (photosynthesis) and several outputs (i.e., respiration, exudation, shedding, and herbivory), frequently neglected in classical studies on PGPR-plant interaction. Here, we discuss the primary evidence underlying the modifications triggered by PGPR and their metabolites on the plant ecophysiology. We propose to detect PGPR-induced variations in the photosynthetic activity using leaf gas exchange and recommend setting up the correct timing for monitoring plant responses according to the specific objectives of the experiment. This research identifies the challenges and tries to provide future directions to scientists working on PGPR-plant interactions to exploit the potential of microorganisms' application in improving plant value.
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Affiliation(s)
- Renée Abou Jaoudé
- Department for Innovation in Biological, Agrofood and Forest Systems (DIBAF), University of Tuscia, Viterbo, Italy
| | | | | | - Maurizio Ruzzi
- Department for Innovation in Biological, Agrofood and Forest Systems (DIBAF), University of Tuscia, Viterbo, Italy
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Arias RM, Heredia Abarca G, del Carmen Perea Rojas Y, de la Cruz Elizondo Y, García Guzman KY. Selection and Characterization of Phosphate-Solubilizing Fungi and Their Effects on Coffee Plantations. PLANTS (BASEL, SWITZERLAND) 2023; 12:3395. [PMID: 37836135 PMCID: PMC10574286 DOI: 10.3390/plants12193395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 09/14/2023] [Accepted: 09/20/2023] [Indexed: 10/15/2023]
Abstract
The use of phosphate-solubilizing fungi in coffee cultivation is an alternative to the use of traditional fertilizers. The objective of this study was to analyze the mechanisms involved in the phosphorus solubilization of fungal strains and to evaluate the effect of a phosphate-solubilizing strain on coffee plants. For this, phosphorus-solubilizing fungal strains were selected for evaluation of their solubilization potential and phosphatase activity. Coffee plants were inoculated in the field with a phosphate-solubilizing strain, and the soil and foliar soluble phosphorus contents, as well as coffee bean yield, were quantified. Of the 151 strains analyzed, Sagenomella diversispora, Penicillium waksmanii, and Penicillium brevicompactum showed the highest solubilization. Aspergillus niger and P. waksmanii presented the highest soluble phosphorus values; however, P. brevicompactum showed the highest phosphatase activity. The P. brevicompactum strain inoculated on the coffee plants did not favor the foliar phosphorus content but increased the soil soluble phosphorus content in two of the coffee plantations. The plants inoculated with the phosphate-solubilizing strain showed an increase in coffee bean weight on all plantations, although this increase was only significant in two of the three selected coffee plantations.
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Affiliation(s)
- Rosa María Arias
- Instituto de Ecología A. C., Carretera Antigua a Coatepec, No. 351. Col. El Haya, Xalapa 91070, Veracruz, Mexico;
| | - Gabriela Heredia Abarca
- Instituto de Ecología A. C., Carretera Antigua a Coatepec, No. 351. Col. El Haya, Xalapa 91070, Veracruz, Mexico;
| | - Yamel del Carmen Perea Rojas
- Centro de Investigación en Micologia Aplicada, Universidad Veracruzana Médicos No. 5, U.H. del Bosque, Xalapa-Enríquez 91017, Veracruz, Mexico;
| | - Yadeneyro de la Cruz Elizondo
- Facultad de Biología, Universidad Veracruzana, Campus Xalapa, Circuito Gonzalo Aguirre Beltrán s/n. CP Zona Universitaria, Xalapa 91090, Mexico;
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Volke DC, Gurdo N, Milanesi R, Nikel PI. Time-resolved, deuterium-based fluxomics uncovers the hierarchy and dynamics of sugar processing by Pseudomonas putida. Metab Eng 2023; 79:159-172. [PMID: 37454792 DOI: 10.1016/j.ymben.2023.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/30/2023] [Accepted: 07/13/2023] [Indexed: 07/18/2023]
Abstract
Pseudomonas putida, a microbial host widely adopted for metabolic engineering, processes glucose through convergent peripheral pathways that ultimately yield 6-phosphogluconate. The periplasmic gluconate shunt (PGS), composed by glucose and gluconate dehydrogenases, sequentially transforms glucose into gluconate and 2-ketogluconate. Although the secretion of these organic acids by P. putida has been extensively recognized, the mechanism and spatiotemporal regulation of the PGS remained elusive thus far. To address this challenge, we adopted a dynamic 13C- and 2H-metabolic flux analysis strategy, termed D-fluxomics. D-fluxomics demonstrated that the PGS underscores a highly dynamic metabolic architecture in glucose-dependent batch cultures of P. putida, characterized by hierarchical carbon uptake by the PGS throughout the cultivation. Additionally, we show that gluconate and 2-ketogluconate accumulation and consumption can be solely explained as a result of the interplay between growth rate-coupled and decoupled metabolic fluxes. As a consequence, the formation of these acids in the PGS is inversely correlated to the bacterial growth rate-unlike the widely studied overflow metabolism of Escherichia coli and yeast. Our findings, which underline survival strategies of soil bacteria thriving in their natural environments, open new avenues for engineering P. putida towards efficient, sugar-based bioprocesses.
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Affiliation(s)
- Daniel C Volke
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark.
| | - Nicolas Gurdo
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Riccardo Milanesi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126, Milano, Italy
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark.
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Zuzolo D, Ranauda MA, Maisto M, Tartaglia M, Prigioniero A, Falzarano A, Marotta G, Sciarrillo R, Guarino C. The rootstock shape microbial diversity and functionality in the rhizosphere of Vitis vinifera L. cultivar Falanghina. FRONTIERS IN PLANT SCIENCE 2023; 14:1205451. [PMID: 37645461 PMCID: PMC10461393 DOI: 10.3389/fpls.2023.1205451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 07/24/2023] [Indexed: 08/31/2023]
Abstract
The rhizosphere effect occurring at the root-soil interface has increasingly been shown to play a key role in plant fitness and soil functionality, influencing plants resilience. Here, for the first time, we investigated whether the rootstock genotype on which Vitis vinifera L. cultivar Falanghina is grafted can influence the rhizosphere microbiome. Specifically, we evaluated to which extent the 5BB and 1103P rootstocks are able to shape microbial diversity of rhizosphere environment. Moreover, we explored the potential function of microbial community and its shift under plant genotype influence. We investigated seven vineyards subjected to the same pedo-climatic conditions, similar age, training system and management and collected twelve rhizosphere soil samples for metagenomic analyses and composite soil samples for physical-chemical properties. In this study, we used 16S rRNA gene-based metagenomic analysis to investigate the rhizosphere bacterial diversity and composition. Liner discriminant analysis effect size (LEFSe) was conducted for metagenomic biomarker discovery. The functional composition of sampled communities was determined using PICRUSt, which is based on marker gene sequencing profiles. Soil analyses involved the determination of texture, pH, Cation Exchange Capacity (CSC), Organic Carbon (OC), electrical conductivity (EC), calcium (Ca), magnesium (Mg), potassium (K) content, Phosphorous (P), nitrogen (N). The latter revealed that soil features were quite homogenous. The metagenomic data showed that the bacterial alpha-diversity (Observed OTUs) significantly increased in 1103P rhizosphere microbiota. Irrespective of cultivar, Pseudomonadota was the dominant phylum, followed by Actinomycetota > Bacteroidota > Thermoproteota. However, Actinomycetota was the major marker phyla differentiating the rhizosphere microbial communities associated with the different rootstock types. At the genus level, several taxa belonging to Actinomycetota and Alphaproteobacteria classes were enriched in 1103P genotype rhizosphere. Investigating the potential functional profile, we found that most key enzyme-encoding genes involved in N cycling were significantly more abundant in 5BB rootstock rhizosphere soil. However, we found that 1103P rhizosphere was enriched in genes involved in C cycle and Plant Growth Promotion (PGP) functionality. Our results suggest that the different rootstocks not only recruit specific bacterial communities, but also specific functional traits within the same environment.
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Affiliation(s)
- Daniela Zuzolo
- Department of Science and Technologies, University of Sannio, Benevento, Italy
| | | | - Maria Maisto
- Department of Science and Technologies, University of Sannio, Benevento, Italy
| | - Maria Tartaglia
- Department of Science and Technologies, University of Sannio, Benevento, Italy
| | | | | | - Giuseppe Marotta
- Department of Law, Economics, Management and Quantitative Methods (DEMM), University of Sannio, Benevento, Italy
| | - Rosaria Sciarrillo
- Department of Science and Technologies, University of Sannio, Benevento, Italy
| | - Carmine Guarino
- Department of Science and Technologies, University of Sannio, Benevento, Italy
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Liu S, Zeng J, Yu H, Wang C, Yang Y, Wang J, He Z, Yan Q. Antimony efflux underpins phosphorus cycling and resistance of phosphate-solubilizing bacteria in mining soils. THE ISME JOURNAL 2023:10.1038/s41396-023-01445-6. [PMID: 37270585 DOI: 10.1038/s41396-023-01445-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 05/14/2023] [Accepted: 05/24/2023] [Indexed: 06/05/2023]
Abstract
Microorganisms play crucial roles in phosphorus (P) turnover and P bioavailability increases in heavy metal-contaminated soils. However, microbially driven P-cycling processes and mechanisms of their resistance to heavy metal contaminants remain poorly understood. Here, we examined the possible survival strategies of P-cycling microorganisms in horizontal and vertical soil samples from the world's largest antimony (Sb) mining site, which is located in Xikuangshan, China. We found that total soil Sb and pH were the primary factors affecting bacterial community diversity, structure and P-cycling traits. Bacteria with the gcd gene, encoding an enzyme responsible for gluconic acid production, largely correlated with inorganic phosphate (Pi) solubilization and significantly enhanced soil P bioavailability. Among the 106 nearly complete bacterial metagenome-assembled genomes (MAGs) recovered, 60.4% carried the gcd gene. Pi transportation systems encoded by pit or pstSCAB were widely present in gcd-harboring bacteria, and 43.8% of the gcd-harboring bacteria also carried the acr3 gene encoding an Sb efflux pump. Phylogenetic and potential horizontal gene transfer (HGT) analyses of acr3 indicated that Sb efflux could be a dominant resistance mechanism, and two gcd-harboring MAGs appeared to acquire acr3 through HGT. The results indicated that Sb efflux could enhance P cycling and heavy metal resistance in Pi-solubilizing bacteria in mining soils. This study provides novel strategies for managing and remediating heavy metal-contaminated ecosystems.
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Affiliation(s)
- Shengwei Liu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, 510006, China
| | - Jiaxiong Zeng
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, 510006, China
| | - Huang Yu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, 510006, China
| | - Cheng Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, 510006, China
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, 100084, Beijing, China
| | - Jianjun Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, 510006, China
| | - Qingyun Yan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, 510006, China.
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Wang G, Jin Z, George TS, Feng G, Zhang L. Arbuscular mycorrhizal fungi enhance plant phosphorus uptake through stimulating hyphosphere soil microbiome functional profiles for phosphorus turnover. THE NEW PHYTOLOGIST 2023; 238:2578-2593. [PMID: 36694293 DOI: 10.1111/nph.18772] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 01/17/2023] [Indexed: 05/19/2023]
Abstract
The extraradical hyphae of arbuscular mycorrhizal (AM) fungi are colonized by different bacteria in natural and agricultural systems, but the mechanisms by which AM fungi interact with the hyphosphere soil microbiome and influence soil organic phosphorus (P) mobilization remain unclear. We grew Medicago in two-compartment microcosms, inoculated with Rhizophagus irregularis, or not, in the root compartment and set up P treatments (without P, with P addition as KH2 PO4 or nonsoluble phytate) in the hyphal compartment. We studied the processes of soil P turnover and characterized the microbiome functional profiles for P turnover in the hyphosphere soil by metagenomic sequencing. Compared with the bulk soil, the hyphosphere soil of R. irregularis was inhabited by a specific bacterial community and their functional profiles for P turnover was stimulated. At the species level, the shift in hyphosphere soil microbiome was characterized by the recruitment of the genome bin2.39 harbouring both gcd and phoD genes and genome bin2.97 harbouring the phoD gene, which synergistically drove nonsoluble phytate mobilization in the hyphosphere soil. Our results suggest that AM fungi recruits a specific hyphosphere soil microbiome and stimulated their functional profiles for P turnover to enhance utilization of phytate.
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Affiliation(s)
- Guiwei Wang
- College of Resources and Environmental Sciences, MOE Key Laboratory of Plant-Soil Interactions, National Academy of Agriculture Green Development, China Agricultural University, Beijing, 100193, China
| | - Zexing Jin
- College of Resources and Environmental Sciences, MOE Key Laboratory of Plant-Soil Interactions, National Academy of Agriculture Green Development, China Agricultural University, Beijing, 100193, China
| | | | - Gu Feng
- College of Resources and Environmental Sciences, MOE Key Laboratory of Plant-Soil Interactions, National Academy of Agriculture Green Development, China Agricultural University, Beijing, 100193, China
| | - Lin Zhang
- College of Resources and Environmental Sciences, MOE Key Laboratory of Plant-Soil Interactions, National Academy of Agriculture Green Development, China Agricultural University, Beijing, 100193, China
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Elizabeth George S, Wan Y. Microbial functionalities and immobilization of environmental lead: Biogeochemical and molecular mechanisms and implications for bioremediation. JOURNAL OF HAZARDOUS MATERIALS 2023; 457:131738. [PMID: 37285788 DOI: 10.1016/j.jhazmat.2023.131738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 05/26/2023] [Accepted: 05/28/2023] [Indexed: 06/09/2023]
Abstract
The increasing environmental and human health concerns about lead in the environment have stimulated scientists to search for microbial processes as innovative bioremediation strategies for a suite of different contaminated media. In this paper, we provide a compressive synthesis of existing research on microbial mediated biogeochemical processes that transform lead into recalcitrant precipitates of phosphate, sulfide, and carbonate, in a genetic, metabolic, and systematics context as they relate to application in both laboratory and field immobilization of environmental lead. Specifically, we focus on microbial functionalities of phosphate solubilization, sulfate reduction, and carbonate synthesis related to their respective mechanisms that immobilize lead through biomineralization and biosorption. The contributions of specific microbes, both single isolates or consortia, to actual or potential applications in environmental remediation are discussed. While many of the approaches are successful under carefully controlled laboratory conditions, field application requires optimization for a host of variables, including microbial competitiveness, soil physical and chemical parameters, metal concentrations, and co-contaminants. This review challenges the reader to consider bioremediation approaches that maximize microbial competitiveness, metabolism, and the associated molecular mechanisms for future engineering applications. Ultimately, we outline important research directions to bridge future scientific research activities with practical applications for bioremediation of lead and other toxic metals in environmental systems.
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Affiliation(s)
- S Elizabeth George
- US EPA Office of Research and Development, Center for Environmental Measurement and Modeling, Gulf Ecosystem Measurement and Modeling Division, One Sabine Island Drive, Gulf Breeze, FL 32561, USA
| | - Yongshan Wan
- US EPA Office of Research and Development, Center for Environmental Measurement and Modeling, Gulf Ecosystem Measurement and Modeling Division, One Sabine Island Drive, Gulf Breeze, FL 32561, USA.
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Joshi S, Gangola S, Jaggi V, Sahgal M. Functional characterization and molecular fingerprinting of potential phosphate solubilizing bacterial candidates from Shisham rhizosphere. Sci Rep 2023; 13:7003. [PMID: 37117212 PMCID: PMC10147649 DOI: 10.1038/s41598-023-33217-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 04/10/2023] [Indexed: 04/30/2023] Open
Abstract
Phosphate solubilizing bacteria (PSB) are important role players in plant growth promotion. In the present study, we aimed to screen the functionally active phosphate solubilizing bacteria (PSB) associated with Dalbergia sissoo Roxb. (Shisham) from different provenances. Screening for phosphate solubilization was done on Pikovskaya's agar, and 18 bacteria positive for the tri-calcium phosphate (Ca3(PO4)2 solubilization showing visible dissolution halo zones were identified. All 18 isolates showed zinc solubilization, indole acetic acid (IAA), siderophore, and hydrogen cyanide (HCN) production. The morphological and biochemical characterization with 16S rDNA gene-based phylogenetic analysis identified bacterial strains as belonging to the genus Pseudomonas, Klebsiella, Streptomyces, Pantoea, Kitasatospora, Micrococcus, and Staphylococcus. Among all the isolates, one of the isolates named L4, from Lacchiwala region was the most efficient P solubilizer with a high P solubilization index (4.75 ± 0.06) and quantitative P solubilization activity (891.38 ± 18.55 μg mL-1). The validation of phosphate solubilization activity of PSB isolates was done by amplification of the Pyrroloquinoline quinone (PQQ) genes, pqqA and pqqC. Based on this study, we have selected the bacterial strains which are efficient phosphate solubilizers and could be economical and eco-friendly in plant growth promotion, disease suppression, as an antioxidant, and for subsequent enhancement of yield.
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Affiliation(s)
- Samiksha Joshi
- School of Agriculture, Graphic Era Hill University, Bhimtal, 263136, India
| | - Saurabh Gangola
- School of Agriculture, Graphic Era Hill University, Bhimtal, 263136, India
| | - Vandana Jaggi
- Department of Microbiology, GB Pant University of Agriculture and Technology, Pantnagar, 263145, India
| | - Manvika Sahgal
- Department of Microbiology, GB Pant University of Agriculture and Technology, Pantnagar, 263145, India.
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Ahmad SA, Naqvi TA, Munis MFH, Javed MT, Chaudhary HJ. Biodegradation of monocrotophos by Brucella intermedia Msd2 isolated from cotton plant. World J Microbiol Biotechnol 2023; 39:141. [PMID: 37000294 DOI: 10.1007/s11274-023-03575-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 03/09/2023] [Indexed: 04/01/2023]
Abstract
Widespread and inadequate use of Monocrotophos has led to several environmental issues. Biodegradation is an ecofriendly method used for detoxification of toxic monocrotophos. In the present study, Msd2 bacterial strain was isolated from the cotton plant growing in contaminated sites of Sahiwal, Pakistan. Msd2 is capable of utilizing the monocrotophos (MCP) organophosphate pesticide as its sole carbon source for growth. Msd2 was identified as Brucella intermedia on the basis of morphology, biochemical characterization and 16S rRNA sequencing. B. intermedia showed tolerance of MCP up to 100 ppm. The presence of opd candidate gene for pesticide degradation, gives credence to B. intermedia as an effective bacterium to degrade MCP. Screening of the B. intermedia strain Msd2 for plant growth promoting activities revealed its ability to produce ammonia, exopolysaccharides, catalase, amylase and ACC-deaminase, and phosphorus, zinc and potassium solubilization. The optimization of the growth parameters (temperatures, shaking rpm, and pH level) of the MCP-degrading isolate was carried out in minimal salt broth supplemented with MCP. The optimal pH, temperature, and rpm for Msd2 growth were observed as pH 6, 35 °C, and 120 rpm, respectively. Based on optimization results, batch degradation experiment was performed. Biodegradation of MCP by B. intermedia was monitored using HPLC and recorded 78% degradation of MCP at 100 ppm concentration within 7 days of incubation. Degradation of MCP by Msd2 followed the first order reaction kinetics. Plant growth promoting and multi-stress tolerance ability of Msd2 was confirmed by molecular analysis. It is concluded that Brucella intermedia strain Msd2 could be beneficial as potential biological agent for an effective bioremediation for polluted environments.
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Affiliation(s)
- Siti Aqlima Ahmad
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, UPM 43400 Serdang, Selangor, Malaysia
| | - Tatheer Alam Naqvi
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad Campus, Abbottabad, Pakistan
| | | | - Muhammad Tariq Javed
- Department of Botany, Government College University, Faisalabad, 38000, Pakistan
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Ali N, Swarnkar MK, Veer R, Kaushal P, Pati AM. Temperature-induced modulation of stress-tolerant PGP genes bioprospected from Bacillus sp. IHBT-705 associated with saffron ( Crocus sativus) rhizosphere: A natural -treasure trove of microbial biostimulants. FRONTIERS IN PLANT SCIENCE 2023; 14:1141538. [PMID: 36923125 PMCID: PMC10009223 DOI: 10.3389/fpls.2023.1141538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 02/14/2023] [Indexed: 06/18/2023]
Abstract
There is a renewed interest in sustainable agriculture wherein novel plant growth-promoting rhizobacteria (PGPR) are being explored for developing efficient biostimulants. The key requirement of a microbe to qualify as a good candidate for developing a biostimulant is its intrinsic plant growth-promoting (PGP) characteristics. Though numerous studies have been conducted to assess the beneficial effects of PGPRs on plant growth under normal and stressed conditions but not much information is available on the characterization of intrinsic traits of PGPR under stress. Here, we focused on understanding how temperature stress impacts the functionality of key stress tolerant and PGP genes of Bacillus sp. IHBT-705 isolated from the rhizosphere of saffron (Crocus sativus). To undertake the study, Bacillus sp. IHBT-705 was grown under varied temperature regimes, their PGP traits were assessed from very low to very high-temperature range and the expression trend of targeted stress tolerant and PGP genes were analyzed. The results illustrated that Bacillus sp. IHBT-705 is a stress-tolerant PGPR as it survived and multiplied in temperatures ranging from 4°C-50°C, tolerated a wide pH range (5-11), withstood high salinity (8%) and osmolarity (10% PEG). The PGP traits varied under different temperature regimes indicating that temperature influences the functionality of PGP genes. This was further ascertained through whole genome sequencing followed by gene expression analyses wherein certain genes like cspB, cspD, hslO, grpE, rimM, trpA, trpC, trpE, fhuC, fhuD, acrB5 were found to be temperature sensitive while, cold tolerant (nhaX and cspC), heat tolerant (htpX) phosphate solubilization (pstB1), siderophore production (fhuB and fhuG), and root colonization (xerC1 and xerC2) were found to be highly versatile as they could express well both under low and high temperatures. Further, the biostimulant potential was checked through a pot study on rice (Oryza sativa), wherein the application of Bacillus sp. IHBT-705 improved the length of shoots, roots, and number of roots over control. Based on the genetic makeup, stress tolerance potential, retention of PGP traits under stress, and growth-promoting potential, Bacillus sp. IHBT-705 could be considered a good candidate for developing biostimulants.
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Affiliation(s)
- Nilofer Ali
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Mohit Kumar Swarnkar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
| | - Raj Veer
- Incubatee at Chief Minister Startup Scheme, Shimla, India
| | - Priya Kaushal
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
| | - Aparna Maitra Pati
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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Garneau L, Beauregard PB, Roy S. Deciphering the role of non- Frankia nodular endophytes in alder through in vitro and genomic characterization. Can J Microbiol 2023; 69:72-87. [PMID: 36288604 DOI: 10.1139/cjm-2022-0073] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Endophytic bacterial populations are well-positioned to provide benefits to their host plants such as nutrient acquisition and plant hormone level manipulation. Actinorhizal plants such as alders are well known for their microbial symbioses that allow them to colonize harsh environments whether natural or anthropized. Although the nitrogen-fixing actinobacterium Frankia sp. is the main endophyte found in alder root nodules, other bacterial genera, whose roles remain poorly defined, inhabit this niche. In this study, we isolated a diverse panel of non-Frankia nodular endophytes (NFNE). Some NFNE were isolated from alders grown from surface-sterilized seeds and maintained in sterile conditions, suggesting these may have been seed-borne. In vitro testing of 24 NFNE revealed some possessed putative plant growth promotion traits. Their genomes were also sequenced to identify genes related to plant growth promotion traits. This study highlights the complexity of the alder nodular microbial community. It paves the way for further understanding of the biology of nodules and could help improve land reclamation practices that involve alders.
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Affiliation(s)
- Louis Garneau
- Centre SÈVE, Département de biologie, Faculté des Sciences, Université de Sherbrooke, 2500 boulevard de l'Université, Sherbrooke, Québec, Canada, J1K 2R1
| | - Pascale B Beauregard
- Centre SÈVE, Département de biologie, Faculté des Sciences, Université de Sherbrooke, 2500 boulevard de l'Université, Sherbrooke, Québec, Canada, J1K 2R1
| | - Sébastien Roy
- Centre SÈVE, Département de biologie, Faculté des Sciences, Université de Sherbrooke, 2500 boulevard de l'Université, Sherbrooke, Québec, Canada, J1K 2R1
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Genome insights into the plant growth-promoting bacterium Saccharibacillus brassicae ATSA2 T. AMB Express 2023; 13:9. [PMID: 36680648 PMCID: PMC9867790 DOI: 10.1186/s13568-023-01514-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 01/09/2023] [Indexed: 01/22/2023] Open
Abstract
Endophytes can facilitate the improvement of plant growth and health in agriculturally important crops, yet their genomes and secondary metabolites remain largely unexplored. We previously isolated Saccharibacillus brassicae strain ATSA2T from surface-sterilized seeds of kimchi cabbage and represented a novel species of the genus Saccharibacillus. In this study, we evaluated the plant growth-promoting (PGP) effect of strain ATSA2T in kimchi cabbage, bok choy, and pepper plants grown in soils. We found a significant effect on the shoot and root biomass, and chlorophyll contents following strain ATSA2T treatment. Strain ATSA2T displayed PGP traits such as indole acetic acid (IAA, 62.9 μg/mL) and siderophore production, and phosphate solubilization activity. Furthermore, genome analysis of this strain suggested the presence of gene clusters involved in iron acquisition (fhuABD, afuABC, fbpABC, and fepCDG) and phosphate solubilization (pstABCHS, phoABHLU, and phnCDEP) and other phytohormone biosynthesis genes, including indole-3-acetic acid (trpABCDEFG), in the genome. Interestingly, the secondary metabolites cerecidin, carotenoid, siderophore (staphylobactin), and bacillaene underlying plant growth promotion were found in the whole genome via antiSMASH analysis. Overall, physiological testing and genome analysis data provide comprehensive insights into plant growth-promoting mechanisms, suggesting the relevance of strain ATSA2T in agricultural biotechnology.
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Sanchez-Gonzalez ME, Mora-Herrera ME, Wong-Villarreal A, De La Portilla-López N, Sanchez-Paz L, Lugo J, Vaca-Paulín R, Del Aguila P, Yañez-Ocampo G. Effect of pH and Carbon Source on Phosphate Solubilization by Bacterial Strains in Pikovskaya Medium. Microorganisms 2022; 11:microorganisms11010049. [PMID: 36677341 PMCID: PMC9866999 DOI: 10.3390/microorganisms11010049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/13/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Phosphate-solubilizing bacteria (PSB) transform precipitated inorganic phosphorus into soluble orthophosphates. This study evaluated the efficiency of tricalcium and iron phosphate solubilization in Pikovskaya medium using five bacterial strains (A1, A2, A3, A5, and A6) cultured in acidic and alkaline pH levels. The bacterial strain that proved to be more efficient for P solubilization and was tolerant to pH variations was selected for assessing bacterial growth and P solubilization with glucose and sucrose in the culture medium. The bacterial strains were identified through 16S rRNA gene sequencing as Pseudomonas libanensis A1, Pseudomonas libanensis (A2), Bacillus pumilus (A3), Pseudomonas libanensis (A5), and Bacillus siamensis (A6). These five bacterial strains grew, tolerated pH changes, and solubilized inorganic phosphorus. The bacterial strain A3 solubilized FePO4 (4 mg L-1) and Ca3(PO4)2 (50 mg L-1). P solubilization was assayed with glucose and sucrose as carbon sources for A3 (Bacillus pumilus MN100586). After four culture days, Ca3(PO4)2 was solubilized, reaching 246 mg L-1 with sucrose in culture media. Using glucose as a carbon source, FePO4 was solubilized and reached 282 mg L-1 in six culture days. Our findings were: Pseudomonas libanensis, and Bacillus siamensis, as new bacteria, can be reported as P solubilizers with tolerance to acidic or alkaline pH levels. The bacterial strain B. pumilus grew using two sources of inorganic phosphorus and carbon, and it tolerated pH changes. For that reason, it is an ideal candidate for inorganic phosphorus solubilization and future production as a biofertilizer.
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Affiliation(s)
- Ma. Esther Sanchez-Gonzalez
- Laboratory of Edaphology and Environment, Faculty of Sciences, Autonomous University of the State of Mexico, Toluca 50000, Mexico
| | - Martha E. Mora-Herrera
- Tenancingo Universitary Center, Autonomous University of the State of Mexico, Toluca 50000, Mexico
| | | | - Nadia De La Portilla-López
- Laboratory of Edaphology and Environment, Faculty of Sciences, Autonomous University of the State of Mexico, Toluca 50000, Mexico
| | - Laura Sanchez-Paz
- Laboratory of Edaphology and Environment, Faculty of Sciences, Autonomous University of the State of Mexico, Toluca 50000, Mexico
| | - Jorge Lugo
- Laboratory of Edaphology and Environment, Faculty of Sciences, Autonomous University of the State of Mexico, Toluca 50000, Mexico
| | - Rocio Vaca-Paulín
- Laboratory of Edaphology and Environment, Faculty of Sciences, Autonomous University of the State of Mexico, Toluca 50000, Mexico
| | - Pedro Del Aguila
- Laboratory of Edaphology and Environment, Faculty of Sciences, Autonomous University of the State of Mexico, Toluca 50000, Mexico
| | - Gustavo Yañez-Ocampo
- Laboratory of Edaphology and Environment, Faculty of Sciences, Autonomous University of the State of Mexico, Toluca 50000, Mexico
- Correspondence: ; Tel.: +52-722-2262-300
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Transcriptome Profiling Analysis of Phosphate-Solubilizing Mechanism of Pseudomonas Strain W134. Microorganisms 2022; 10:microorganisms10101998. [PMID: 36296274 PMCID: PMC9609647 DOI: 10.3390/microorganisms10101998] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/22/2022] [Accepted: 09/30/2022] [Indexed: 11/24/2022] Open
Abstract
Phosphate-solubilizing bacteria (PSB) can alleviate available phosphorus deficiency without causing environmental pollution, unlike chemical phosphate fertilizers. However, the phosphate solubilization mechanisms of PSB are still unclear. Transcriptome sequencing was used to analyze the expression patterns of differential expressed genes (DEGs) of the phosphate-solubilizing bacterium W134 under the conditions of soluble phosphorus (group A), insoluble phosphorus (group B), and lacking phosphorus (group C). Nine DEGs in three different groups were detected by quantitative real-time polymerase chain reaction (qRT-PCR). Then, high performance liquid chromatography (HPLC) was applied to detect the concentrations and composition of organic acids. Compared with group A, Gene Ontology (GO) annotation showed that the cluster of W134 DEGs in groups B and C were basically the same. Besides, the results of enrichment Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway indicated that genes in the Citrate cycle (TCA cycle) pathway closely related to organic acid production were significantly upregulated. The qRT-PCR results were almost consistent with the expression trends of the transcriptome data. The HPLC results showed that the formic acid, ascorbic acid, acetic acid, citric acid, and succinic acid concentrations were significantly increased in group B and C (p < 0.05), while the contents of lactic acid and malic acid were significantly increased in group B (p < 0.05). The above results provided further validation that the upregulated genes should be related to W134 secretion of organic acids. Our study revealed several potential candidate genes and tried to explain phosphate solubilization mechanisms. This provides a new insight for calcareous reclaimed soil, and it will reduce the need of chemical phosphate fertilizers to promote environmentally friendly agriculture.
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Muster C, Leiva D, Morales C, Grafe M, Schloter M, Carú M, Orlando J. Peltigera frigida Lichens and Their Substrates Reduce the Influence of Forest Cover Change on Phosphate Solubilizing Bacteria. Front Microbiol 2022; 13:843490. [PMID: 35836424 PMCID: PMC9275751 DOI: 10.3389/fmicb.2022.843490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Accepted: 05/30/2022] [Indexed: 11/17/2022] Open
Abstract
Phosphorus (P) is one of the most critical macronutrients in forest ecosystems. More than 70 years ago, some Chilean Patagonian temperate forests suffered wildfires and the subsequent afforestation with foreign tree species such as pines. Since soil P turnover is interlinked with the tree cover, this could influence soil P content and bioavailability. Next to soil microorganisms, which are key players in P transformation processes, a vital component of Patagonian temperate forest are lichens, which represent microbial hotspots for bacterial diversity. In the present study, we explored the impact of forest cover on the abundance of phosphate solubilizing bacteria (PSB) from three microenvironments of the forest floor: Peltigera frigida lichen thallus, their underlying substrates, and the forest soil without lichen cover. We expected that the abundance of PSB in the forest soil would be strongly affected by the tree cover composition since the aboveground vegetation influences the edaphic properties; but, as P. frigida has a specific bacterial community, lichens would mitigate this impact. Our study includes five sites representing a gradient in tree cover types, from a mature forest dominated by the native species Nothofagus pumilio, to native second-growth forests with a gradual increase in the presence of Pinus contorta in the last sites. In each site, we measured edaphic parameters, P fractions, and the bacterial potential to solubilize phosphate by quantifying five specific marker genes by qPCR. The results show higher soluble P, labile mineral P, and organic matter in the soils of the sites with a higher abundance of P. contorta, while most of the molecular markers were less abundant in the soils of these sites. Contrarily, the abundance of the molecular markers in lichens and substrates was less affected by the tree cover type. Therefore, the bacterial potential to solubilize phosphate is more affected by the edaphic factors and tree cover type in soils than in substrates and thalli of P. frigida lichens. Altogether, these results indicate that the microenvironments of lichens and their substrates could act as an environmental buffer reducing the influence of forest cover composition on bacteria involved in P turnover.
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Affiliation(s)
- Cecilia Muster
- Laboratory of Microbial Ecology, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Diego Leiva
- Institute of Biology, University of Graz, Graz, Austria
| | - Camila Morales
- Laboratory of Microbial Ecology, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Martin Grafe
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, Germany
| | - Michael Schloter
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, Germany
| | - Margarita Carú
- Laboratory of Microbial Ecology, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Julieta Orlando
- Laboratory of Microbial Ecology, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago, Chile
- *Correspondence: Julieta Orlando,
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Pangenome analyses of Bacillus pumilus, Bacillus safensis, and Priestia megaterium exploring the plant-associated features of bacilli strains isolated from canola. Mol Genet Genomics 2022; 297:1063-1079. [PMID: 35612623 DOI: 10.1007/s00438-022-01907-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 05/05/2022] [Indexed: 12/11/2022]
Abstract
Previous genome mining of the strains Bacillus pumilus 7PB, Bacillus safensis 1TAz, 8Taz, and 32PB, and Priestia megaterium 16PB isolated from canola revealed differences in the profile of antimicrobial biosynthetic genes when compared to the species type strains. To evaluate not only the similarities among B. pumilus, B. safensis, and P. megaterium genomes but also the specificities found in the canola bacilli, we performed comparative genomic analyses through the pangenome evaluation of each species. Besides that, other genome features were explored, especially focusing on plant-associated and biotechnological characteristics. The combination of the genome metrics Average Nucleotide Identity and digital DNA-DNA hybridization formulas 1 and 3 adopting the universal thresholds of 95 and 70%, respectively, was suitable to verify the identification of strains from these groups. On average, core genes corresponded to 45%, 52%, and 34% of B. pumilus, B. safensis, and P. megaterium open pangenomes, respectively. Many genes related to adaptations to plant-associated lifestyles were predicted, especially in the Bacillus genomes. These included genes for acetoin production, polyamines utilization, root exudate chemoreceptors, biofilm formation, and plant cell-wall degrading enzymes. Overall, we could observe that strains of these species exhibit many features in common, whereas most of their variable genome portions have features yet to be uncovered. The observed antifungal activity of canola bacilli might be a result of the synergistic action of secondary metabolites, siderophores, and chitinases. Genome analysis confirmed that these species and strains have biotechnological potential to be used both as agricultural inoculants or hydrolases producers. Up to our knowledge, this is the first work that evaluates the pangenome features of P. megaterium.
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Postmortem Skeletal Microbial Community Composition and Function in Buried Human Remains. mSystems 2022; 7:e0004122. [PMID: 35353006 PMCID: PMC9040591 DOI: 10.1128/msystems.00041-22] [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] [Indexed: 11/20/2022] Open
Abstract
Bones and teeth can provide a lasting resource to identify human remains following decomposition. Bone can support dynamic communities of micro- and macroscopic scavengers and incidental taxa, which influence the preservation of bone over time. Previously we identified key microbial taxa associated with survivability of DNA in bones of surface-decomposed human remains, observing high intra- and interindividual variation. Here we characterized the postmortem bone microbiome of skeletal remains in a multi-individual burial to better understand subsurface bone colonization and preservation. To understand microbial community origins and assembly, 16S rRNA amplicon sequences from 256 bone and 27 soil samples were compared to bone from individuals who decomposed on the ground surface, and human gut sequences from the American Gut Project. Untargeted metabolomics was applied to a subset of 41 bone samples from buried remains to examine potential microbe–metabolite interactions and infer differences related to community functionality. Results show that postmortem bone microbial communities are distinct from those of the oxic surface soils and the human gut. Microbial communities from surface-deposited bone and shallow buried bone were more similar to those from soils, while bones recovered from saturated areas deeper in the grave showed increased similarity with human gut samples with higher representation of anaerobic taxa, suggesting that the depositional environment affected the established bone microbiome. Correlations between metabolites and microbes indicate that phosphate solubilization is likely an important mechanism of microbially mediated skeletal degradation. This research expands our knowledge of microbial bone colonizers, including colonizers important in a burial environment. IMPORTANCE Understanding the microbes that colonize and degrade bone has important implications for preservation of skeletal elements and identification of unknown human remains. Current research on the postmortem bone microbiome is limited and largely focuses on archaeological or marine contexts. Our research expands our understanding of bone microbiomes in buried remains by characterizing the taxonomic and metabolic diversity of microbes that are colonizing bone after a 4-year postmortem burial interval and examines the potential impact of microbial colonization on human skeletal DNA preservation. Our results indicate that the postmortem bone microbiome is distinct from the human gut and soil. Evidence from combined metabolomic and amplicon sequencing analysis suggests that Pseudomonas and phosphate solubilization likely play a role in skeletal degradation. This work provides important insight into the types and activities of microbes controlling the preservation of buried skeletal remains.
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22
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Uroz S, Picard L, Turpault MP. Recent progress in understanding the ecology and molecular genetics of soil mineral weathering bacteria. Trends Microbiol 2022; 30:882-897. [PMID: 35181182 DOI: 10.1016/j.tim.2022.01.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 01/24/2022] [Accepted: 01/25/2022] [Indexed: 12/31/2022]
Abstract
Mineral weathering bacteria play essential roles in nutrient cycling and plant nutrition. However, we are far from having a comprehensive view of the factors regulating their distribution and the molecular mechanisms involved. In this review, we highlight the extrinsic factors (i.e., nutrient availability, carbon source) and the intrinsic properties of minerals explaining the distribution and functioning of these functional communities. We also present and discuss the progress made in understanding the molecular mechanisms and genes that are used by bacteria during the mineral weathering process, or regulated during their interaction with minerals, that have been recently unraveled by omics approaches.
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Affiliation(s)
- Stephane Uroz
- Université de Lorraine, INRAE, UMR1136 'Interactions Arbres-Microorganismes', F-54280 Champenoux, France; INRAE, UR1138 'Biogéochimie des Ecosystèmes Forestiers', F-54280 Champenoux, France.
| | - Laura Picard
- Université de Lorraine, INRAE, UMR1136 'Interactions Arbres-Microorganismes', F-54280 Champenoux, France; INRAE, UR1138 'Biogéochimie des Ecosystèmes Forestiers', F-54280 Champenoux, France
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Msimbira LA, Naamala J, Antar M, Subramanian S, Smith DL. Effect of Microbial Cell-Free Supernatants Extracted From a Range of pH Levels on Corn (Zea mays L.) and Tomato (Solanum lycopersicum L.) Seed Germination and Seedling Growth. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2022. [DOI: 10.3389/fsufs.2022.789335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The negative effects of more extreme pH conditions (soil acidity and alkalinity) are increasingly challenging crop production. Managing acidity and alkalinity in soils has been achieved through techniques such as the use of lime, afforestation, tillage, and addition of organic matter. The use of microbes to address this challenge is new and could increase agroecosystem sustainability while helping plants survive more extreme acidity and alkalinity, among other stresses. Use of plant growth promoting microbes (PGPM) has recently gained attention as these microbes afford plants several benefits, including nutrient acquisition and stress tolerance, both biotic and abiotic. Several methods of microbe application have been developed, all intended to maximize the benefits of plant-microbial interactions. The current study assessed the potential of changing microbial culture pH during production, followed by removal of cells to produce supernatant that enhances plant growth, specifically under acidity and alkalinity stresses. The study included L. helveticus. (EL2006H) and B. subtilis (EB2004S) which were cultured at three pH levels (5, 7, and 8) incubated for 24–48 h then centrifuged at 12 000 g to remove the cells. The cell-free supernatants obtained were used for seed germination and early seedling growth assays. The results indicated significant increase in seed germination rate, for both corn and tomato, compared to experimental controls. Supernatants produced at pH 5, for both strains, had greater effect than those produced at pHs 7 and 8. Similarly, the positive effect of these supernatants was observed in seedling growth as increased root length and volume. Their results indicate that there is potential in stressing microbes below or above optimum pH (~7) to induce production and excretion of favorable materials into the growth medium, as was evident in this study. To the best of our knowledge this would be the first attempt to look at this pH change to increase potential benefits related to plant growth promotion by microbes. It was interesting to learn that using the CFS of microbes cultured at pH 5 increased germination rate and seedling growth. These results provide an initial indication that support broadened research into PGPM under pH stressed conditions.
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Ding Y, Yi Z, Fang Y, He S, Li Y, He K, Zhao H, Jin Y. Multi-Omics Reveal the Efficient Phosphate-Solubilizing Mechanism of Bacteria on Rocky Soil. Front Microbiol 2021; 12:761972. [PMID: 34956124 PMCID: PMC8696128 DOI: 10.3389/fmicb.2021.761972] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 11/22/2021] [Indexed: 12/13/2022] Open
Abstract
Phosphate-solubilizing bacteria (PSB) can alleviate available phosphorus (AP)-deficiency without causing environmental pollution like chemical phosphate fertilizers. However, the research and application of PSB on the barren rocky soil is very rare. We screened six PSB from sweetpotato rhizosphere rocky soil. Among them, Ochrobactrum haematophilum FP12 showed the highest P-solubilizing ability of 1,085.00 mg/L at 7 days, which was higher than that of the most reported PSB. The assembled genome of PSB FP12 was 4.92 Mb with P-solubilizing and plant growth-promoting genes. In an AP-deficient environment, according to transcriptome and metabolomics analysis, PSB FP12 upregulated genes involved in gluconic acid synthesis and the tricarboxylic acid cycle, and increased the concentration of gluconic acid and malic acid, which would result in the enhanced P-solubilizing ability. Moreover, a series of experiments in the laboratory and field confirmed the efficient role of the screened PSB on significantly increasing AP in the barren rocky soil and promoting sweetpotato yield. So, in this study, we screened highly efficient PSB, especially suitable for the barren rocky soil, and explored the P-solubilizing mechanism. The research will reduce the demand for chemical phosphate fertilizers and promote the environment-friendly agricultural development.
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Affiliation(s)
- Yanqiang Ding
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Zhuolin Yi
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Yang Fang
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Sulan He
- Sweetpotato Institute, Nanchong Academy of Agricultural Sciences, Nanchong, China
| | - Yuming Li
- Sweetpotato Institute, Nanchong Academy of Agricultural Sciences, Nanchong, China
| | - Kaize He
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Hai Zhao
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Yanling Jin
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
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Rizvi A, Ahmed B, Khan MS, Umar S, Lee J. Psychrophilic Bacterial Phosphate-Biofertilizers: A Novel Extremophile for Sustainable Crop Production under Cold Environment. Microorganisms 2021; 9:2451. [PMID: 34946053 PMCID: PMC8704983 DOI: 10.3390/microorganisms9122451] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 11/23/2021] [Accepted: 11/24/2021] [Indexed: 11/18/2022] Open
Abstract
Abiotic stresses, including low-temperature environments, adversely affect the structure, composition, and physiological activities of soil microbiomes. Also, low temperatures disturb physiological and metabolic processes, leading to major crop losses worldwide. Extreme cold temperature habitats are, however, an interesting source of psychrophilic and psychrotolerant phosphate solubilizing bacteria (PSB) that can ameliorate the low-temperature conditions while maintaining their physiological activities. The production of antifreeze proteins and expression of stress-induced genes at low temperatures favors the survival of such organisms during cold stress. The ability to facilitate plant growth by supplying a major plant nutrient, phosphorus, in P-deficient soil is one of the novel functional properties of cold-tolerant PSB. By contrast, plants growing under stress conditions require cold-tolerant rhizosphere bacteria to enhance their performance. To this end, the use of psychrophilic PSB formulations has been found effective in yield optimization under temperature-stressed conditions. Most of the research has been done on microbial P biofertilizers impacting plant growth under normal cultivation practices but little attention has been paid to the plant growth-promoting activities of cold-tolerant PSB on crops growing in low-temperature environments. This scientific gap formed the basis of the present manuscript and explains the rationale for the introduction of cold-tolerant PSB in competitive agronomic practices, including the mechanism of solubilization/mineralization, release of biosensor active biomolecules, molecular engineering of PSB for increasing both P solubilizing/mineralizing efficiency, and host range. The impact of extreme cold on the physiological activities of plants and how plants overcome such stresses is discussed briefly. It is time to enlarge the prospects of psychrophilic/psychrotolerant phosphate biofertilizers and take advantage of their precious, fundamental, and economical but enormous plant growth augmenting potential to ameliorate stress and facilitate crop production to satisfy the food demands of frighteningly growing human populations. The production and application of cold-tolerant P-biofertilizers will recuperate sustainable agriculture in cold adaptive agrosystems.
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Affiliation(s)
- Asfa Rizvi
- Department of Botany, School of Chemical and Life Sciences, Jamia Hamdard, Hamdard Nagar, New Delhi 110062, India; (A.R.); (S.U.)
| | - Bilal Ahmed
- School of Chemical Engineering, Yeungnam University, Gyeongsan 38541, Korea
| | - Mohammad Saghir Khan
- Department of Agricultural Microbiology, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh 202002, India;
| | - Shahid Umar
- Department of Botany, School of Chemical and Life Sciences, Jamia Hamdard, Hamdard Nagar, New Delhi 110062, India; (A.R.); (S.U.)
| | - Jintae Lee
- School of Chemical Engineering, Yeungnam University, Gyeongsan 38541, Korea
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Mei C, Chretien RL, Amaradasa BS, He Y, Turner A, Lowman S. Characterization of Phosphate Solubilizing Bacterial Endophytes and Plant Growth Promotion In Vitro and in Greenhouse. Microorganisms 2021; 9:microorganisms9091935. [PMID: 34576829 PMCID: PMC8469958 DOI: 10.3390/microorganisms9091935] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/03/2021] [Accepted: 09/09/2021] [Indexed: 11/16/2022] Open
Abstract
Phosphate is one of the most important nutrients for plant growth and development, and only 0.1% of the phosphate in soils is available to plants. Currently, the use of excess phosphate fertilizer has caused surface and ground water pollution and water eutrophication, resulting in algal blooms in lakes and oceans. Therefore, it is imperative to explore alternative ways to solve these problems for sustainable agricultural production and improvement of soil fertility, while protecting the environment. Microorganisms from the rhizosphere and within plants are able to solubilize insoluble soil phosphate, making it available to plants. Five high phosphate solubilizing bacteria from our bacterial endophyte library were chosen for this study and identified as Pantoea vagans IALR611, Pseudomonas psychrotolerans IALR632, Bacillus subtilis IALR1033, Bacillus safensis IALR1035 and Pantoea agglomerans IALR1325. All five bacteria significantly promoted tall fescue growth in vitro. Greenhouse experiments showed that IALR1325 significantly promoted pepper and tomato growth, and IALR632 was the best in promoting tomato growth. In addition, all these bacteria had extracellular acid phosphatase and phytase activities. One of the mechanisms for phosphate solubilization by bacteria is pH reduction caused by gluconic acid production. Our results indicate that P. agglomerans IALR1325 is a promising bacterium for future applications.
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Genome Mining and Comparative Genome Analysis Revealed Niche-Specific Genome Expansion in Antibacterial Bacillus pumilus Strain SF-4. Genes (Basel) 2021; 12:genes12071060. [PMID: 34356076 PMCID: PMC8303946 DOI: 10.3390/genes12071060] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 05/13/2021] [Accepted: 05/21/2021] [Indexed: 01/21/2023] Open
Abstract
The present study reports the isolation of antibacterial exhibiting Bacillus pumilus (B. pumilus) SF-4 from soil field. The genome of this strain SF-4 was sequenced and analyzed to acquire in-depth genomic level insight related to functional diversity, evolutionary history, and biosynthetic potential. The genome of the strain SF-4 harbor 12 Biosynthetic Gene Clusters (BGCs) including four Non-ribosomal peptide synthetases (NRPSs), two terpenes, and one each of Type III polyketide synthases (PKSs), hybrid (NRPS/PKS), lipopeptide, β-lactone, and bacteriocin clusters. Plant growth-promoting genes associated with de-nitrification, iron acquisition, phosphate solubilization, and nitrogen metabolism were also observed in the genome. Furthermore, all the available complete genomes of B. pumilus strains were used to highlight species boundaries and diverse niche adaptation strategies. Phylogenetic analyses revealed local diversification and indicate that strain SF-4 is a sister group to SAFR-032 and 150a. Pan-genome analyses of 12 targeted strains showed regions of genome plasticity which regulate function of these strains and proposed direct strain adaptations to specific habitats. The unique genome pool carries genes mostly associated with “biosynthesis of secondary metabolites, transport, and catabolism” (Q), “replication, recombination and repair” (L), and “unknown function” (S) clusters of orthologous groups (COG) categories. Moreover, a total of 952 unique genes and 168 exclusively absent genes were prioritized across the 12 genomes. While newly sequenced B. pumilus SF-4 genome consists of 520 accessory, 59 unique, and seven exclusively absent genes. The current study demonstrates genomic differences among 12 B. pumilus strains and offers comprehensive knowledge of the respective genome architecture which may assist in the agronomic application of this strain in future.
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The Influence of Soil Fertilization on the Distribution and Diversity of Phosphorus Cycling Genes and Microbes Community of Maize Rhizosphere Using Shotgun Metagenomics. Genes (Basel) 2021; 12:genes12071022. [PMID: 34209356 PMCID: PMC8306440 DOI: 10.3390/genes12071022] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 06/23/2021] [Accepted: 06/28/2021] [Indexed: 11/25/2022] Open
Abstract
Biogeochemical cycling of phosphorus in the agro-ecosystem is mediated by soil microbes. These microbes regulate the availability of phosphorus in the soil. Little is known about the response of functional traits of phosphorus cycling microbes in soil fertilized with compost manure (derived from domestic waste and plant materials) or inorganic nitrogen fertilizers at high and low doses. We used a metagenomics investigation study to understand the changes in the abundance and distribution of microbial phosphorus cycling genes in agricultural farmlands receiving inorganic fertilizers (120 kg N/ha, 60 kg N/ha) or compost manure (8 tons/ha, 4 tons/ha), and in comparison with the control. Soil fertilization with high level of compost (Cp8) or low level of inorganic nitrogen (N1) fertilizer have nearly similar effects on the rhizosphere of maize plants in promoting the abundance of genes involved in phosphorus cycle. Genes such as ppk involved in polyphosphate formation and pstSABC (for phosphate transportation) are highly enriched in these treatments. These genes facilitate phosphorus immobilization. At a high dose of inorganic fertilizer application or low compost manure treatment, the phosphorus cycling genes were repressed and the abundance decreased. The bacterial families Bacillaceae and Carnobacteriaceae were very abundant in the high inorganic fertilizer (N2) treated soil, while Pseudonocardiaceae, Clostridiaceae, Cytophagaceae, Micromonosporaceae, Thermomonosporaceae, Nocardiopsaceae, Sphaerobacteraceae, Thermoactinomycetaceae, Planococcaceae, Intrasporangiaceae, Opitutaceae, Acidimicrobiaceae, Frankiaceae were most abundant in Cp8. Pyrenophora, Talaromyces, and Trichophyton fungi were observed to be dominant in Cp8 and Methanosarcina, Methanobrevibacter, Methanoculleus, and Methanosphaera archaea have the highest percentage occurrence in Cp8. Moreover, N2 treatment, Cenarchaeum, Candidatus Nitrososphaera, and Nitrosopumilus were most abundant among fertilized soils. Our findings have brought to light the basis for the manipulation of rhizosphere microbial communities and their genes to improve availability of phosphorus as well as phosphorus cycle regulation in agro-ecosystems.
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Wang S, Zhao Z, Ge S, Peng B, Zhang K, Hu M, Mai W, Tian C. Root Morphology and Rhizosphere Characteristics Are Related to Salt Tolerance of Suaeda salsa and Beta vulgaris L. FRONTIERS IN PLANT SCIENCE 2021; 12:677767. [PMID: 34234797 PMCID: PMC8255919 DOI: 10.3389/fpls.2021.677767] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 05/24/2021] [Indexed: 06/13/2023]
Abstract
Halophytes are capable of resisting salinity, and their root system is the part in direct contact with the saline soil environment. The aim of this study was to compare the responses of root morphology and rhizosphere characteristics to salinity between a halophyte, Suaeda salsa (suaeda), and a glycophyte, Beta vulgaris L. (sugar beet). The soil salt content was set to four levels (0.7, 1.2, 1.7, and 2.7%) by NaCl-treated plants. We investigated the soil pH, EC, nutrients and soil, plant ion (Na+, Cl-, K+, and Mg2+) concentration to evaluate the rhizospheric processes, and salt tolerance of suaeda by the root mat method. The highest biomass was in the 1.2% salt level for suaeda and in the 0.7% salt level for sugar beet. The root length and root surface area of suaeda showed similar trends to biomass, but the root diameter decreased by 11.5-17.9% with higher salinity. The Na+, Cl-, and K+ accumulations in the shoot of suaeda displayed higher than that in sugar beet, while the Mg2+ accumulation was lower in suaeda than that in sugar beet. High salinity resulted in increased pH and EC values in the rhizosphere for suaeda, but lower values of these parameters for sugar beet. Under high salinity, the Olsen phosphorus content was 0.50 g·kg-1 and 0.99 g·kg-1 higher in the rhizosphere than in the non-rhizosphere for suaeda and sugar beet. We concluded that the two species [halophyte, Suaeda salsa (suaeda), and a glycophyte, B. vulgaris L. (sugar beet)] showed diverse approaches for nutrient absorption under salinity stress. Suaeda altered its root morphology (smaller root diameter and longer roots) under salt stress to increase the root surface area, while sugar beet activated rhizospheric processes to take up more nutrients.
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Affiliation(s)
- Shoule Wang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhenyong Zhao
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Shaoqing Ge
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Bin Peng
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ke Zhang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Mingfang Hu
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Wenxuan Mai
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Changyan Tian
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
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30
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Amini Hajiabadi A, Mosleh Arani A, Ghasemi S, Rad MH, Etesami H, Shabazi Manshadi S, Dolati A. Mining the rhizosphere of halophytic rangeland plants for halotolerant bacteria to improve growth and yield of salinity-stressed wheat. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 163:139-153. [PMID: 33845330 DOI: 10.1016/j.plaphy.2021.03.059] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 03/30/2021] [Indexed: 06/12/2023]
Abstract
In this study, the effects of three halotolerant rhizobacterial isolates AL, HR, and SB, which are able to grow at a salinity level of 1600 mM NaCl, with multiple plant growth promoting (PGP) traits on some seed and forage quality attributes, and vegetative, reproductive, biochemical and physiological characteristics of wheat plant irrigated with saline water (0, 40, 80, and 160 mM NaCl) were investigated. The ability of halotolerant bacterial isolates to produce PGP traits was affected by salinity levels, depending upon the bacterial isolates. Salinity stress significantly affected the yield, quality, and growth of wheat by modifying the morpho-physiological and biochemical traits of the exposed plants. However, all three bacterial isolates, especially isolate AL, significantly improved the biochemical (an increase in K+/Na+ ratio by 55%, plant P content by 50%, and plant Ca content by 31%), morphological (an increase in stem dry weight by 52%, root dry weight by 44%, spike dry weight by 34%, and grain dry weight by 43%), and physiological (an increase in leaf proline content by 50% and total phenol in leaf by 42%) attributes of wheat and aided the plant to tolerate salinity stress in contrast to un-inoculated plant. Plants inoculated with bacterial isolates showed significantly improved seed amylose by 36%, leaf crude protein by 30%, leaf metabolic energy by 37%, and leaf water-soluble sugar content by 34%. Among the measured PGP and plant attributes, bacterial auxin and plant K content were of key importance in increasing reproductive performance of wheat. The bacterial isolates AL, HR, and SB were identified as Bacillus safensis, B. pumilus, and Zhihengliuella halotolerans, respectively, based on 16 S rDNA sequence. The study reveals that application of halotolerant plant growth-promoting rhizobacteria isolated from halophytic rangeland plants can be a cost effective and ecological sustainable method to improve wheat productivity, especially the attributes related to seed and forage quality, under salinity stress conditions.
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Affiliation(s)
| | - Asghar Mosleh Arani
- Department of Environmental Sciences, Faculty of Natural Resources, Yazd University, Yazd, Iran.
| | - Somayeh Ghasemi
- Department of Soil Sciences, Faculty of Natural Resources, Yazd University, Yazd, Iran
| | - Mohammad Hadi Rad
- Forest and Rangeland Division, Yazd Agricultural and Natural Resource Research and Education Center, Yazd, Iran
| | - Hassan Etesami
- Department of Soil Science, University of Tehran, Karaj, Iran.
| | | | - Ali Dolati
- Faculty of Mathematics, Department of Statistics, Yazd University, Yazd, Iran
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31
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Alemneh AA, Cawthray GR, Zhou Y, Ryder MH, Denton MD. Ability to produce indole acetic acid is associated with improved phosphate solubilising activity of rhizobacteria. Arch Microbiol 2021; 203:3825-3837. [PMID: 33997908 DOI: 10.1007/s00203-021-02364-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/28/2021] [Accepted: 05/07/2021] [Indexed: 10/21/2022]
Abstract
Indole acetic acid (IAA) can upregulate genes encoding enzymes responsible for the synthesis of carboxylates involved in phosphorus (P) solubilisation. Here, we investigated whether IAA and its precursor affect the P-solubilising activity of rhizobacteria. A total of 841 rhizobacteria were obtained using taxonomically selective and enrichment isolation methods. Phylogenetic analysis revealed 15 genera of phosphate solubilising bacteria (PSB) capable of producing a wide range of IAA concentrations between 4.1 and 67.2 µg mL-1 in vitro. Addition of L-tryptophan to growth media improved the P-solubilising activity of PSB that were able to produce IAA greater than 20 µg mL-1. This effect was connected to the drop of pH and release of a high concentration of carboxylates, comprising α-ketoglutarate, cis-aconitate, citrate, malate and succinate. An increase in production of organic acids rather than IAA production per se appears to result in the improved P solubilisation in PSB.
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Affiliation(s)
- Anteneh Argaw Alemneh
- School of Agriculture, Food and Wine, The University of Adelaide, Glen Osmond, SA, 5064, Australia.,China-Australia Joint Laboratory for Soil Ecological Health and Remediation, The University of Adelaide, Glen Osmond, SA, 5064, Australia
| | - Gregory R Cawthray
- School of Biological Sciences, The University of Western Australia, 35 Stirling Hwy, Crawley, Perth, WA, 6009, Australia
| | - Yi Zhou
- School of Agriculture, Food and Wine, The University of Adelaide, Glen Osmond, SA, 5064, Australia. .,China-Australia Joint Laboratory for Soil Ecological Health and Remediation, The University of Adelaide, Glen Osmond, SA, 5064, Australia.
| | - Maarten H Ryder
- School of Agriculture, Food and Wine, The University of Adelaide, Glen Osmond, SA, 5064, Australia.,China-Australia Joint Laboratory for Soil Ecological Health and Remediation, The University of Adelaide, Glen Osmond, SA, 5064, Australia
| | - Matthew D Denton
- School of Agriculture, Food and Wine, The University of Adelaide, Glen Osmond, SA, 5064, Australia.,China-Australia Joint Laboratory for Soil Ecological Health and Remediation, The University of Adelaide, Glen Osmond, SA, 5064, Australia
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Aasfar A, Bargaz A, Yaakoubi K, Hilali A, Bennis I, Zeroual Y, Meftah Kadmiri I. Nitrogen Fixing Azotobacter Species as Potential Soil Biological Enhancers for Crop Nutrition and Yield Stability. Front Microbiol 2021; 12:628379. [PMID: 33717018 PMCID: PMC7947814 DOI: 10.3389/fmicb.2021.628379] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 02/05/2021] [Indexed: 12/20/2022] Open
Abstract
Biological nitrogen fixation (BNF) refers to a microbial mediated process based upon an enzymatic "Nitrogenase" conversion of atmospheric nitrogen (N2) into ammonium readily absorbable by roots. N2-fixing microorganisms collectively termed as "diazotrophs" are able to fix biologically N2 in association with plant roots. Specifically, the symbiotic rhizobacteria induce structural and physiological modifications of bacterial cells and plant roots into specialized structures called nodules. Other N2-fixing bacteria are free-living fixers that are highly diverse and globally widespread in cropland. They represent key natural source of nitrogen (N) in natural and agricultural ecosystems lacking symbiotic N fixation (SNF). In this review, the importance of Azotobacter species was highlighted as both important free-living N2-fixing bacteria and potential bacterial biofertilizer with proven efficacy for plant nutrition and biological soil fertility. In addition, we described Azotobacter beneficial plant promoting traits (e.g., nutrient use efficiency, protection against phytopathogens, phytohormone biosynthesis, etc.). We shed light also on the agronomic features of Azotobacter that are likely an effective component of integrated plant nutrition strategy, which contributes positively to sustainable agricultural production. We pointed out Azotobacter based-biofertilizers, which possess unique characteristics such as cyst formation conferring resistance to environmental stresses. Such beneficial traits can be explored profoundly for the utmost aim to research and develop specific formulations based on inoculant Azotobacter cysts. Furthermore, Azotobacter species still need to be wisely exploited in order to address specific agricultural challenges (e.g., nutrient deficiencies, biotic and abiotic constraints) taking into consideration several variables including their biological functions, synergies and multi-trophic interactions, and biogeography and abundance distribution.
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Affiliation(s)
- Abderrahim Aasfar
- Green Biotechnology Laboratory, Moroccan Foundation for Advanced Science, Innovation and Research (MAScIR), Rabat Design Centre, Rabat, Morocco.,Laboratory of Health Sciences and Technologies, High Institute of Health Sciences, Hassan 1st University, Settat, Morocco
| | - Adnane Bargaz
- AgroBioSciences-Microbiome, Laboratory of Plant-Microbe Interactions, Mohammed VI Polytechnic University, Ben Guerir, Morocco
| | - Kaoutar Yaakoubi
- Green Biotechnology Laboratory, Moroccan Foundation for Advanced Science, Innovation and Research (MAScIR), Rabat Design Centre, Rabat, Morocco
| | - Abderraouf Hilali
- Laboratory of Health Sciences and Technologies, High Institute of Health Sciences, Hassan 1st University, Settat, Morocco
| | - Iman Bennis
- Green Biotechnology Laboratory, Moroccan Foundation for Advanced Science, Innovation and Research (MAScIR), Rabat Design Centre, Rabat, Morocco
| | | | - Issam Meftah Kadmiri
- Green Biotechnology Laboratory, Moroccan Foundation for Advanced Science, Innovation and Research (MAScIR), Rabat Design Centre, Rabat, Morocco.,AgroBioSciences-Microbiome, Laboratory of Plant-Microbe Interactions, Mohammed VI Polytechnic University, Ben Guerir, Morocco
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33
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Muleta A, Tesfaye K, Haile Selassie TH, Cook DR, Assefa F. Phosphate solubilization and multiple plant growth promoting properties of Mesorhizobium species nodulating chickpea from acidic soils of Ethiopia. Arch Microbiol 2021; 203:2129-2137. [PMID: 33611634 DOI: 10.1007/s00203-021-02189-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 12/19/2020] [Accepted: 02/04/2021] [Indexed: 11/24/2022]
Abstract
The main purpose of this study was to screen and select strains from seven Mesorhizobium spp. for efficient phosphate solubilizing and other plant growth-promoting traits. Mesorhizobium species were tested for their ability to dissolve inorganic phosphate sources and multiple plant growth-promoting attributes. From a total of 62 Mesorhizobium strains, 47(76%) strains formed clear zones with an average PSI of 1.9-2.7 on Pikovskaya's agar plate. The selected strains also released soluble phosphorus [125-150 P (µgml-1)] from tri-calcium phosphate and low level of phosphorous i.e., 15.4 µg/ml and 14.5 µg/ml from inorganic ferrous and aluminum phosphates, respectively, in a liquid medium after 4 days of incubation. The release of soluble P was significantly (P < 0.01) correlated with a drop in pH of the medium. Moreover, screening for multiple plant growth-promoting attributes showed that 40, 28, 26, 21, and 38% of the strains were capable of producing indole-3-acetic acid, hydrogen cyanide, siderophores, ACC deaminase, and antagonism against Fusarium oxysporum f.sp. ciceris under in vitro conditions. The Mesorhizobium strains were endowed with the presence of ACC deaminase which was rarely reported elsewhere. All taken together, the acidic soils harbor numerous and more diverse phosphate solubilizing and plant growth-promoting Mesorhizobium spp. However, greenhouse and field conditions can be further studied within the context of improving chickpea production in Ethiopia.
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Affiliation(s)
- Atsede Muleta
- Department of Microbial Cellular and Molecular Biology, Addis Ababa University, P.O. Box 1176, Addis Ababa, Ethiopia.
| | - Kassahun Tesfaye
- Institutes of Biotechnology, Addis Ababa University, P.O. Box 1176, Addis Ababa, Ethiopia
| | | | - Douglas R Cook
- Department of Plant Pathology, University of California Davis, One Shields Ave, Davis, CA, 956168680, USA
| | - Fassil Assefa
- Department of Microbial Cellular and Molecular Biology, Addis Ababa University, P.O. Box 1176, Addis Ababa, Ethiopia
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Maldonado S, Rodríguez A, Ávila B, Morales P, González MP, Araya Angel JPA, Olalde V, Bravo J, Jana C, Sierra C, Stoll A. Enhanced Crop Productivity and Sustainability by Using Native Phosphate Solubilizing Rhizobacteria in the Agriculture of Arid Zones. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2020. [DOI: 10.3389/fsufs.2020.607355] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The importance of phosphate solubilizing rhizobacteria (PSB) has been well-document as an option for enhancing sustainable agriculture. As a particular group of plant growth promoting rhizobacteria (PGPR), PSB play an important role in the soil phosphorus cycle, increasing the bioavailability for growth and plant development. This study analyses the plant growth promoting effects of 5 strains (BN0009, BN0013, BN0015, BN0024, and BN0035) out of 180 isolated from Jarava frigida (Phil.) F.Rojas (Poaceae), a native grass from the Andean Atacama desert from North of Chile. The five bacterial isolated (BN strains) were identified as non-pathogenic Erwinia sp. and show a high phosphate solubilization capacity for Ca(PO4) ranging from 608.9 to 781.4 mg/L. Strains IAA production varies between 23.5 and 35.9 mg/L, siderophores, phosphatase (alkaline and acid) production was also observed, but none of the five isolated presented antagonism against plant pathogens Botrytis sp. and Sclerotinia sp. All isolates enhanced seed germination in Lactuca sativa and Solanum lycopersicum (excepting BN009). Additionally, all strains stimulated the early root elongation and seedling development in lettuce and tomato. Pot experiments displayed that BN0015, BN0024, and BN0035 significantly promote plant growth regarding root and leaf area, root and leaf weight, as well as leaf number compared with non-treated plants. In a field experiment with lettuce and two fertilization treatments (50 and 100% of the recommended crop fertilization), BN0024 application improved crop productivity compared to respective control. P content in plants with bacterial inoculations increased significantly compared to control in either fertilization treatment, suggesting an improved nutrient uptake. Also, lettuce with 50% fertilization and inoculation with BN0024 equate productivity with the control 100% fertilization. Finally, we discuss these results in the context of applicability to enhance the agroecosystem productivity in arid and semiarid zones.
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Ribeiro IDA, Volpiano CG, Vargas LK, Granada CE, Lisboa BB, Passaglia LMP. Use of Mineral Weathering Bacteria to Enhance Nutrient Availability in Crops: A Review. FRONTIERS IN PLANT SCIENCE 2020; 11:590774. [PMID: 33362817 PMCID: PMC7759553 DOI: 10.3389/fpls.2020.590774] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 11/26/2020] [Indexed: 05/19/2023]
Abstract
Rock powders are low-cost potential sources of most of the nutrients required by higher plants for growth and development. However, slow dissolution rates of minerals represent an obstacle to the widespread use of rock powders in agriculture. Rhizosphere processes and biological weathering may further enhance mineral dissolution since the interaction between minerals, plants, and bacteria results in the release of macro- and micronutrients into the soil solution. Plants are important agents in this process acting directly in the mineral dissolution or sustaining a wide diversity of weathering microorganisms in the root environment. Meanwhile, root microorganisms promote mineral dissolution by producing complexing ligands (siderophores and organic acids), affecting the pH (via organic or inorganic acid production), or performing redox reactions. Besides that, a wide variety of rhizosphere bacteria and fungi could also promote plant development directly, synergistically contributing to the weathering activity performed by plants. The inoculation of weathering bacteria in soil or plants, especially combined with the use of crushed rocks, can increase soil fertility and improve crop production. This approach is more sustainable than conventional fertilization practices, which may contribute to reducing climate change linked to agricultural activity. Besides, it could decrease the dependency of developing countries on imported fertilizers, thus improving local development.
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Affiliation(s)
- Igor Daniel Alves Ribeiro
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Camila Gazolla Volpiano
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Luciano Kayser Vargas
- Laboratório de Microbiologia Agrícola, Departamento de Diagnóstico e Pesquisa Agropecuária, Secretaria Estadual da Agricultura, Pecuária e Desenvolvimento Rural, Porto Alegre, Brazil
| | | | - Bruno Brito Lisboa
- Laboratório de Microbiologia Agrícola, Departamento de Diagnóstico e Pesquisa Agropecuária, Secretaria Estadual da Agricultura, Pecuária e Desenvolvimento Rural, Porto Alegre, Brazil
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Cell-Free Supernatants of Plant Growth-Promoting Bacteria: A Review of Their Use as Biostimulant and Microbial Biocontrol Agents in Sustainable Agriculture. SUSTAINABILITY 2020. [DOI: 10.3390/su12239917] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Plant growth-promoting bacteria (PGPB) afford plants several advantages (i.e., improvement of nutrient acquisition, growth, and development; induction of abiotic and biotic stress tolerance). Numerous PGPB strains have been isolated and studied over the years. However, only a few of them are available on the market, mainly due to the failed bacterial survival within the formulations and after application inside agroecosystems. PGPB strains with these challenging limitations can be used for the formulation of cell-free supernatants (CFSs), broth cultures processed through several mechanical and physical processes for cell removal. In the scientific literature there are diverse reviews and updates on PGPB in agriculture. However, no review deals with CFSs and the CFS metabolites obtainable by PGPB. The main objective of this review is to provide useful information for future research on CFSs as biostimulant and biocontrol agents in sustainable agriculture. Studies on CFS agricultural applications, both for biostimulant and biocontrol applications, have been reviewed, presenting limitations and advantages. Among the 109 articles selected and examined, the Bacillus genus seems to be the most promising due to the numerous articles that support its biostimulant and biocontrol potentialities. The present review underlines that research about this topic needs to be encouraged; evidence so far obtained has demonstrated that PGPB could be a valid source of secondary metabolites useful in sustainable agriculture.
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Genitsaris S, Stefanidou N, Leontidou K, Matsi T, Karamanoli K, Mellidou I. Bacterial Communities in the Rhizosphere and Phyllosphere of Halophytes and Drought-Tolerant Plants in Mediterranean Ecosystems. Microorganisms 2020; 8:E1708. [PMID: 33142812 PMCID: PMC7692439 DOI: 10.3390/microorganisms8111708] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 10/29/2020] [Accepted: 10/30/2020] [Indexed: 12/23/2022] Open
Abstract
The aim of the study was to investigate the bacterial community diversity and structure by means of 16S rRNA gene high-throughput amplicon sequencing, in the rhizosphere and phyllosphere of halophytes and drought-tolerant plants in Mediterranean ecosystems with different soil properties. The locations of the sampled plants included alkaline, saline-sodic soils, acidic soils, and the volcanic soils of Santorini Island, differing in soil fertility. Our results showed high bacterial richness overall with Proteobacteria and Actinobacteria dominating in terms of OTUs number and indicated that variable bacterial communities differed depending on the plant's compartment (rhizosphere and phyllosphere), the soil properties and location of sampling. Furthermore, a shared pool of generalist bacterial taxa was detected independently of sampling location, plant species, or plant compartment. We conclude that the rhizosphere and phyllosphere of native plants in stressed Mediterranean ecosystems consist of common bacterial assemblages contributing to the survival of the plant, while at the same time the discrete soil properties and environmental pressures of each habitat drive the development of a complementary bacterial community with a distinct structure for each plant and location. We suggest that this trade-off between generalist and specialist bacterial community is tailored to benefit the symbiosis with the plant.
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Affiliation(s)
- Savvas Genitsaris
- Department of Ecology, School of Biology, Aristotle University of Thessaloniki, 54 124 Thessaloniki, Greece
| | - Natassa Stefanidou
- Department of Botany, School of Biology, Aristotle University of Thessaloniki, 54 124 Thessaloniki, Greece
| | - Kleopatra Leontidou
- Laboratory of Agricultural Chemistry, School of Agriculture, Aristotle University of Thessaloniki, 54 124 Thessaloniki, Greece
| | - Theodora Matsi
- Soil Science Laboratory, School of Agriculture, Aristotle University of Thessaloniki, 54 124 Thessaloniki, Greece
| | - Katerina Karamanoli
- Laboratory of Agricultural Chemistry, School of Agriculture, Aristotle University of Thessaloniki, 54 124 Thessaloniki, Greece
| | - Ifigeneia Mellidou
- Laboratory of Agricultural Chemistry, School of Agriculture, Aristotle University of Thessaloniki, 54 124 Thessaloniki, Greece
- Institute of Plant Breeding and Genetic Resources, HAO ELGO-DEMETER, 57 001 Thermi, Greece
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Meng D, Liu YL, Gu PF, Fan XY, Huang ZS, Ji Y, Li WM, Du ZJ, Li Q. Chelativorans xinjiangense sp. nov., a novel bacterial species isolated from soil in Xinjiang, China. Arch Microbiol 2020; 203:693-699. [PMID: 33037888 DOI: 10.1007/s00203-020-02064-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 08/24/2020] [Accepted: 09/30/2020] [Indexed: 11/28/2022]
Abstract
A novel Gram-strain-negative, beige-pigmented, aerobic, rod-shaped, non-flagellated and non-gliding bacterium, designated strain lm93T, was isolated from rhizosphere soil of Alhagi sparsifolia obtained from Alar city, located in Xinjiang province, China. Growth optimally occurred at 30 °C, pH 6.5-7.5, and 0-2% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain lm93T belonged to the genus Chelativorans, with highest sequence similarity to Chelativorans multitrophicus DSM 9103T (96.9%). Genome sequencing revealed a genome size of 5 689 708 bp and a G + C content of 64.3 mol%. The ANI, POCP and the dDDH between strain lm93T and C. multitrophicus DSM 9103T were 76.4%, 54.8% and 0.8%, respectively. The prediction result of secondary metabolites based on genome showed that the strain lm93T contained one cluster of bacteriocin, one cluster of terpene production, two clusters of ectoine production, one cluster of non-ribosomal peptide synthetase, one cluster of type I polyketide synthases, three clusters of homoserine lactone production, one cluster of N-acetylglutaminylglutamine amide production and one cluster of phosphonate production. The major respiratory quinone was Q-10. The major fatty acids were C19:0 cyclo ω8c, iso-C17:0 and summed feature 8 (C18:1 ω6c and/or C18:1 ω7c) and its polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, two unidentified aminophospholipids, aminoglycolipid, three unknown lipids and diphosphatidylglycerol. On the basis of these data, strain lm93T is considered to represent a novel species of the genus Chelativorans, for which the name Chelativorans xinjiangense sp. nov. is proposed. The type strain is lm93T (= KCTC 72857T = CCTCC AB2019376T).
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Affiliation(s)
- Dong Meng
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, People's Republic of China
| | - Yu-Ling Liu
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, People's Republic of China
| | - Peng-Fei Gu
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, People's Republic of China
| | - Xiang-Yu Fan
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, People's Republic of China
| | - Zhao-Song Huang
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, People's Republic of China
| | - Yan Ji
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, People's Republic of China
| | - Wei-Min Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China. .,Key Laboratory for Northern Urban, Agriculture of Ministry of Agriculture and Rural Affairs, Beijing University of Agriculture, Beijing, 102206, People's Republic of China.
| | - Zong-Jun Du
- Marine College, Shandong University, Weihai, 264209, People's Republic of China
| | - Qiang Li
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, People's Republic of China.
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YAÑEZ-OCAMPO GUSTAVO, MORA-HERRERA MARTHAE, WONG-VILLARREAL ARNOLDO, DE LA PAZ-OSORIO DENISSEM, DE LA PORTILLA-LÓPEZ NADIA, LUGO JORGE, VACA-PAULÍN ROCIO, DEL ÁGUILA PEDRO. Isolated Phosphate-Solubilizing Soil Bacteria Promotes In vitro Growth of Solanum tuberosum L. Pol J Microbiol 2020; 69:357-365. [PMID: 33574865 PMCID: PMC7810110 DOI: 10.33073/pjm-2020-039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 08/14/2020] [Accepted: 08/15/2020] [Indexed: 11/29/2022] Open
Abstract
The capacity of four bacterial strains isolated from productive soil potato fields to solubilize tricalcium phosphate on Pikovskaya agar or in a liquid medium was evaluated. A bacterial strain was selected to evaluate in vitro capacity of plant-growth promotion on Solanum tuberosum L. culture. Bacterial strain A3 showed the highest value of phosphate solubilization, reaching a 20 mm-diameter halo and a concentration of 350 mg/l on agar and in a liquid medium, respectively. Bacterial strain A3 was identified by 16S rDNA analysis as Bacillus pumilus with 98% identity; therefore, it is the first report for Bacillus pumilus as phosphate solubilizer. Plant-growth promotion assayed by in vitro culture of potato microplants showed that the addition of bacterial strain A3 increased root and stems length after 28 days. It significantly increased stem length by 79.3%, and duplicated the fresh weight of control microplants. In this paper, results reported regarding phosphorus solubilization and growth promotion under in vitro conditions represent a step forward in the use of innocuous bacterial strain biofertilizer on potato field cultures.
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Affiliation(s)
- GUSTAVO YAÑEZ-OCAMPO
- Laboratory of Edaphology and Environment, Faculty of Sciences, Autonomous University of the State of Mexico, Toluca, Mexico
| | - MARTHA E. MORA-HERRERA
- Tenancingo Universitary Center, Autonomous University of the State of Mexico, Toluca, Mexico
| | | | - DENISSE M. DE LA PAZ-OSORIO
- Laboratory of Edaphology and Environment, Faculty of Sciences, Autonomous University of the State of Mexico, Toluca, Mexico
| | - NADIA DE LA PORTILLA-LÓPEZ
- Laboratory of Edaphology and Environment, Faculty of Sciences, Autonomous University of the State of Mexico, Toluca, Mexico
| | - JORGE LUGO
- Laboratory of Edaphology and Environment, Faculty of Sciences, Autonomous University of the State of Mexico, Toluca, Mexico
| | - ROCIO VACA-PAULÍN
- Laboratory of Edaphology and Environment, Faculty of Sciences, Autonomous University of the State of Mexico, Toluca, Mexico
| | - PEDRO DEL ÁGUILA
- Laboratory of Edaphology and Environment, Faculty of Sciences, Autonomous University of the State of Mexico, Toluca, Mexico
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Tee HS, Waite D, Payne L, Middleditch M, Wood S, Handley KM. Tools for successful proliferation: diverse strategies of nutrient acquisition by a benthic cyanobacterium. THE ISME JOURNAL 2020; 14:2164-2178. [PMID: 32424245 PMCID: PMC7367855 DOI: 10.1038/s41396-020-0676-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 04/23/2020] [Accepted: 05/01/2020] [Indexed: 12/28/2022]
Abstract
Freshwater cyanobacterial blooms have increased worldwide, channeling organic carbon into these systems, and threatening animal health through the production of cyanotoxins. Both toxic and nontoxic Microcoleus proliferations usually occur when there are moderate concentrations of dissolved inorganic nitrogen, but when phosphorus is scarce. In order to understand how Microcoleus establishes thick biofilms (or mats) on riverbeds under phosphorus-limiting conditions, we collected Microcoleus-dominated biofilms over a 19-day proliferation event for proteogenomics. A single pair of nitrogen-dependent Microcoleus species were consistently present in relatively high abundance, although each followed a unique metabolic trajectory. Neither possessed anatoxin gene clusters, and only very low concentrations of anatoxins (~2 µg kg-1) were detected, likely originating from rarer Microcoleus species also present. Proteome allocations were dominated by photosynthesizing cyanobacteria and diatoms, and data indicate biomass was actively recycled by Bacteroidetes and Myxococcales. Microcoleus likely acquired nutrients throughout the proliferation event by uptake of nitrate, urea, and inorganic and organic phosphorus. Both species also harbored genes that could be used for inorganic phosphate solubilization with pyrroloquinoline quinone cofactors produced by cohabiting Proteobacteria. Results indicate that Microcoleus are equipped with diverse mechanisms for nitrogen and phosphorus acquisition, enabling them to proliferate and out-compete others in low-phosphorus waters.
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Affiliation(s)
- H S Tee
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - D Waite
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - L Payne
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - M Middleditch
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - S Wood
- Cawthron Institute, Nelson, New Zealand
| | - K M Handley
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.
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Mining Saline Soils to Manifest Plant Stress-Alleviating Halophilic Bacteria. Curr Microbiol 2020; 77:2265-2278. [PMID: 32468180 DOI: 10.1007/s00284-020-02028-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 05/13/2020] [Indexed: 10/24/2022]
Abstract
The connection between soil and microbes plays a critical role in soil health and quality and can be elastic with the application of soil amendments and/or crop rotations. Inappropriate management of soil and application of impermissible levels of fertilizers ruptures the overriding connection between the soil and microbes. This is currently evidenced in the degraded soils (i.e., saline soils of India) which are caused by modern agricultural practices. Reclamation of saline soils with a saturated package of practices and conventional breeding methods requires biological intervention. Shortfall of nutrients is one of the chief constraints for plant growth in salt-affected soils. In the present investigation, we have observed an arsenal of fifty halophilic bacteria carrying an absolute requirement of 3% NaCl for solubilizing the insoluble minerals (ZnCO3, ZnO, Mica and tri-calcium phosphate) under in vitro conditions; however, increasing the amount of NaCl over and above resulted in loss of solubilization capacity. Of the isolates solubilizing zinc carbonate and zinc oxide at 3% NaCl concentration, there were 29 isolates; at 10% concentration, 10 isolates were positive for the presence of zinc carbonate. At 3% NaCl concentration, HB-5 showed 23.16 mm zinc carbonate solubilization, HB-20 showed 13.3 mm Zinc oxide solubilization, and HB-7 showed 13.4 mm tri-calcium phosphate solubilization. Mica solubilization was peaked at 6% NaCl and maximum solubilization was observed in HB-27 (18.03 mm). When compared to the zinc carbonate solubilization, zinc oxide solubilization was slow to reach desired levels. Solubilization lasted for up to 9 days and ceased thereafter in all the tests. Eight elite isolates were identified as Bacillus albus, Bacillus safensis, Pseudomonas stutzeri (2), Lysinibacillus sphaericus, Staphylococcus xylosus, and Bacillus cereus (2) based on 16S rRNA analysis.
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42
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Evolution of Microbial Composition and Enzymatic Activities during the Composting of Textile Waste. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10113758] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The production of stable and mature compost often depends on the performance of microbes and their enzymatic activity. Environmental and nutritional conditions influence the characteristics of microbial communities and, therefore, the dynamics of major metabolic activities. Using three waste mixtures (textile waste mixed with either green, paper, or cardboard waste), the maturity of the compost produced was assessed by following the physico-chemical parameters and enzymatic activities provided by the microorganisms that were identified using next-generation sequencing (NGS). Among the three mixtures used, it was found that the two best mixtures showed C/N ratios of 16.30 and 16.96, total nitrogen of 1.37 and 1.39%, cellulase activities of 50.62 and 52.67 Ug−1, acid phosphatase activities of 38.81 and 68.77 Ug−1, and alkaline phosphatase activities of 51.12 and 56.86 Ug−1. In addition, several lignocellulosic species, together with those that are able to solubilize phosphate, were identified. Among those known for cellulase and acid/alkaline phosphatase activities, bacteria belonging to the Proteobacteria, Bacteroidetes, Actinobacteria, and Firmicutes phyla were shown. The presence of species belonging to the Ascomycota and Basidiomycota phyla of Fungi, which are known for their ability to produce cellulase and acid/alkaline phosphatases, was demonstrated. These findings provide a basis for the production of stable and mature compost based on textile waste.
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43
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Ding LJ, Cui HL, Nie SA, Long XE, Duan GL, Zhu YG. Microbiomes inhabiting rice roots and rhizosphere. FEMS Microbiol Ecol 2020; 95:5420819. [PMID: 30916760 DOI: 10.1093/femsec/fiz040] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 03/26/2019] [Indexed: 11/12/2022] Open
Abstract
Land plants directly contact soil through their roots. An enormous diversity of microbes dwelling in root-associated zones, including endosphere (inside root), rhizoplane (root surface) and rhizosphere (soil surrounding the root surface), play essential roles in ecosystem functioning and plant health. Rice is a staple food that feeds over 50% of the global population. Its root is a unique niche, which is often characterized by an oxic region (e.g. the rhizosphere) surrounded by anoxic bulk soil. This oxic-anoxic interface has been recognized as a pronounced hotspot that supports dynamic biogeochemical cycles mediated by various functional microbial groups. Considering the significance of rice production upon global food security and the methane budget, novel insights into how the overall microbial community (i.e. the microbiome) of the rice root system influences ecosystem functioning is the key to improving crop health and sustainable productivity of paddy ecosystems, and alleviating methane emissions. This mini-review summarizes the current understanding of microbial diversity of rice root-associated compartments to some extent, especially the rhizosphere, and makes a comparison of rhizosphere microbial community structures between rice and other crops/plants. Moreover, this paper describes the interactions between root-related microbiomes and rice plants, and further discusses the key factors shaping the rice root-related microbiomes.
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Affiliation(s)
- Long-Jun Ding
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Hui-Ling Cui
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - San-An Nie
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian Province, China
| | - Xi-En Long
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, Fujian Province, China
| | - Gui-Lan Duan
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yong-Guan Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, Fujian Province, China
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44
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Mowafy AM. Biological leaching of rare earth elements. World J Microbiol Biotechnol 2020; 36:61. [PMID: 32285218 DOI: 10.1007/s11274-020-02838-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 04/06/2020] [Indexed: 12/24/2022]
Abstract
The distinctive physico-chemical features of rare earth elements (REEs) have led to an increase in demand by the global market due to their multiple uses in industrial, medical and agricultural implementations. However, the scarcity of REEs and the harsh eco-unfriendly leaching processes from primary sources beside obliviousness to their recycling from secondary sources, together with the geopolitical situation, have created the need to develop a more sustainable mining strategy. Therefore, there is a growing interest in bio-hydrometallurgy, which may contribute to the scavenging of these strategic elements from low-grade resources in an environmentally friendly and economically feasible way as with copper and gold. Several prokaryotes and eukaryotes show the ability to leach REEs, however, the success in employing these microorganisms or their products in this process relays on several biotic and abiotic factors. This review focuses on the differences made by microorganisms in REEs leaching and fundamentally explains microbes-REEs interaction.
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Affiliation(s)
- Amr M Mowafy
- Botany Department, Faculty of Science, Mansoura University, Mansoura, 35516, Egypt.
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45
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Liang JL, Liu J, Jia P, Yang TT, Zeng QW, Zhang SC, Liao B, Shu WS, Li JT. Novel phosphate-solubilizing bacteria enhance soil phosphorus cycling following ecological restoration of land degraded by mining. ISME JOURNAL 2020; 14:1600-1613. [PMID: 32203124 PMCID: PMC7242446 DOI: 10.1038/s41396-020-0632-4] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 03/02/2020] [Accepted: 03/10/2020] [Indexed: 01/10/2023]
Abstract
Little is known about the changes in soil microbial phosphorus (P) cycling potential during terrestrial ecosystem management and restoration, although much research aims to enhance soil P cycling. Here, we used metagenomic sequencing to analyse 18 soil microbial communities at a P-deficient degraded mine site in southern China where ecological restoration was implemented using two soil ameliorants and eight plant species. Our results show that the relative abundances of key genes governing soil microbial P-cycling potential were higher at the restored site than at the unrestored site, indicating enhancement of soil P cycling following restoration. The gcd gene, encoding an enzyme that mediates inorganic P solubilization, was predominant across soil samples and was a major determinant of bioavailable soil P. We reconstructed 39 near-complete bacterial genomes harboring gcd, which represented diverse novel phosphate-solubilizing microbial taxa. Strong correlations were found between the relative abundance of these genomes and bioavailable soil P, suggesting their contributions to the enhancement of soil P cycling. Moreover, 84 mobile genetic elements were detected in the scaffolds containing gcd in the 39 genomes, providing evidence for the role of phage-related horizontal gene transfer in assisting soil microbes to acquire new metabolic potential related to P cycling.
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Affiliation(s)
- Jie-Liang Liang
- Institute of Ecological Science and Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China
| | - Jun Liu
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Pu Jia
- Institute of Ecological Science and Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China
| | - Tao-Tao Yang
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Qing-Wei Zeng
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Sheng-Chang Zhang
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Bin Liao
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Wen-Sheng Shu
- Institute of Ecological Science and Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China
| | - Jin-Tian Li
- Institute of Ecological Science and Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China. .,School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China.
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Luziatelli F, Ficca AG, Cardarelli M, Melini F, Cavalieri A, Ruzzi M. Genome Sequencing of Pantoea agglomerans C1 Provides Insights into Molecular and Genetic Mechanisms of Plant Growth-Promotion and Tolerance to Heavy Metals. Microorganisms 2020; 8:microorganisms8020153. [PMID: 31979031 PMCID: PMC7074716 DOI: 10.3390/microorganisms8020153] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Revised: 01/03/2020] [Accepted: 01/20/2020] [Indexed: 11/20/2022] Open
Abstract
Distinctive strains of Pantoea are used as soil inoculants for their ability to promote plant growth. Pantoea agglomerans strain C1, previously isolated from the phyllosphere of lettuce, can produce indole-3-acetic acid (IAA), solubilize phosphate, and inhibit plant pathogens, such as Erwinia amylovora. In this paper, the complete genome sequence of strain C1 is reported. In addition, experimental evidence is provided on how the strain tolerates arsenate As (V) up to 100 mM, and on how secreted metabolites like IAA and siderophores act as biostimulants in tomato cuttings. The strain has a circular chromosome and two prophages for a total genome of 4,846,925-bp, with a DNA G+C content of 55.2%. Genes related to plant growth promotion and biocontrol activity, such as those associated with IAA and spermidine synthesis, solubilization of inorganic phosphate, acquisition of ferrous iron, and production of volatile organic compounds, siderophores and GABA, were found in the genome of strain C1. Genome analysis also provided better understanding of the mechanisms underlying strain resistance to multiple toxic heavy metals and transmission of these genes by horizontal gene transfer. Findings suggested that strain C1 exhibits high biotechnological potential as plant growth-promoting bacterium in heavy metal polluted soils.
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Affiliation(s)
- Francesca Luziatelli
- Department for Innovation in Biological, Agrofood and Forest systems (DIBAF), University of Tuscia, via C. de Lellis, snc, I-01100 Viterbo, Italy; (F.L.); (A.G.F.)
| | - Anna Grazia Ficca
- Department for Innovation in Biological, Agrofood and Forest systems (DIBAF), University of Tuscia, via C. de Lellis, snc, I-01100 Viterbo, Italy; (F.L.); (A.G.F.)
| | | | - Francesca Melini
- CREA Research Centre for Food and Nutrition, Via Ardeatina 546, I-00178 Rome, Italy;
| | - Andrea Cavalieri
- Department of Plant and Environmental Sciences, University of Copenhagen, DK–1871 Frederiksberg, Denmark;
| | - Maurizio Ruzzi
- Department for Innovation in Biological, Agrofood and Forest systems (DIBAF), University of Tuscia, via C. de Lellis, snc, I-01100 Viterbo, Italy; (F.L.); (A.G.F.)
- Correspondence: ; Tel.: +39-0761-357-317
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Complete Genome Sequence of the Plant Growth-Promoting Bacterium Hartmannibacter diazotrophicus Strain E19 T. Int J Genomics 2019; 2019:7586430. [PMID: 31583244 PMCID: PMC6754898 DOI: 10.1155/2019/7586430] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 08/05/2019] [Accepted: 08/13/2019] [Indexed: 11/17/2022] Open
Abstract
Strain E19T described as Hartmannibacter diazotrophicus gen. nov. sp. nov. was isolated from the rhizosphere of Plantago winteri from a natural salt meadow in a nature protection area. Strain E19T is a plant growth-promoting rhizobacterium able to colonize the rhizosphere of barley and to promote its growth only under salt stress conditions. To gain insights into the genetic bases of plant growth promotion and its lifestyle at the rhizosphere under salty conditions, we determined the complete genome sequence using two complementary sequencing platforms (Ilumina MiSeq and PacBio RSII). The E19T genome comprises one circular chromosome and one plasmid containing several genes involved in salt adaptation and genes related to plant growth-promoting traits under salt stress. Based on previous experiments, ACC deaminase activity was identified as a main mechanism of E19T to promote plant growth under salt stress. Interestingly, no genes classically reported to encode for ACC deaminase activity are present. In general, the E19T genome provides information to confirm, discover, and better understand many of its previously evaluated traits involved in plant growth promotion under salt stress. Furthermore, the complete E19T genome sequence helps to define its previously reported unclear 16S rRNA gene-based phylogenetic affiliation. Hartmannibacter forms a distinct subcluster with genera Methylobrevis, Pleomorphomonas, Oharaeibacter, and Mongoliimonas subclustered with genera belonging to Rhizobiales.
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Roberts DP, Mattoo AK. Sustainable Crop Production Systems and Human Nutrition. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2019. [DOI: 10.3389/fsufs.2019.00072] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
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Regulatory rewiring through global gene regulations by PhoB and alarmone (p)ppGpp under various stress conditions. Microbiol Res 2019; 227:126309. [PMID: 31421713 DOI: 10.1016/j.micres.2019.126309] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 07/23/2019] [Accepted: 08/02/2019] [Indexed: 12/14/2022]
Abstract
The phosphorus availability in soil ranged from <0.01 to 1 ppm and found limiting for the utilization by plants. Hence, phosphate solubilizing bacteria (PSB) proficiently fulfill the phosphorus requirement of plants in an eco-friendly manner. The PSB encounter dynamic and challenging environmental conditions viz., high temperature, osmotic, acid, and climatic changes often hamper their activity and proficiency. The modern trend is shifting from isolation of the PSB to their genetic potentials and genome annotation not only for their better performance in the field trials but also to study their ability to cope up with stresses. In order to withstand environmental stress, bacteria need to restructure its metabolic network to ensure its survival. Pi starving condition response regulator (PhoB) and the mediator of stringent stress response alarmone (p)ppGpp known to regulate the global regulatory network of bacteria to provide balanced physiology under various stress condition. The current review discusses the global regulation and crosstalk of genes involved in phosphorus homeostasis, solubilization, and various stress response to fine tune the bacterial physiology. The knowledge of these network crosstalk help bacteria to respond efficiently to the challenging environmental parameters, and their physiological plasticity lead us to develop proficient long-lasting consortia for plant growth promotion.
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Camacho-Montealegre CM, Rodrigues EM, Tótola MR. Microbial diversity and bioremediation of rhizospheric soils from Trindade Island - Brazil. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2019; 236:358-364. [PMID: 30739041 DOI: 10.1016/j.jenvman.2019.02.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 01/17/2019] [Accepted: 02/02/2019] [Indexed: 06/09/2023]
Abstract
Pristine environments may harbor complex microbial communities with metabolic potential for use in bioremediation of organic pollutants. This study aimed to evaluate crude oil biodegradation by microbial communities present in rhizospheric soils of Bulbostylis nesiotis and Cyperus atlanticus on Trindade Island and the compositional structure of these communities. After 60 days under aerobic conditions, Total Petroleum Hydrocarbon biodegradation ranged from 66 to 75%, depending on the plant species and the origin of the soil samples. There was no response of petroleum biodegradation to fertilization with N:P:K (80:160:80 mg dm-3). Soil contamination with crude oil did not necessarily reduce microbial diversity. The richness and diversity increased in contaminated soils in some specific situations. We conclude that microbial communities from pristine soils have the ability to remove hydrocarbons through biodegradation and that Bulbostylis nesiotis and Cyperus atlanticus inhabiting Trindade Island harbor rhizospheric microbial communities with potential for application in rhizoremediation.
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Affiliation(s)
- Celia Marcela Camacho-Montealegre
- Laboratório de Biotecnologia e Biodiversidade para o Meio Ambiente, Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Edmo Montes Rodrigues
- Laboratório de Biotecnologia e Biodiversidade para o Meio Ambiente, Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil.
| | - Marcos Rogério Tótola
- Laboratório de Biotecnologia e Biodiversidade para o Meio Ambiente, Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil.
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