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Auti AM, Narwade NP, Deshpande NM, Dhotre DP. Microbiome and imputed metagenome study of crude and refined petroleum-oil-contaminated soils: Potential for hydrocarbon degradation and plant-growth promotion. J Biosci 2019; 44:114. [PMID: 31719223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Microbial community structure of crude petroleum oil (CP)- and refined petroleum oil (RP)-contaminated soil was investigated. The taxonomical and functional diversity of such soils can be a great source of information about microbial community and genes involved in petroleum hydrocarbon (PHC) degradation. In this study, microbial diversity of soils contaminated by RP from urban biome of Pune, India, and CP from agricultural biome of Gujarat, India, were assessed by 16S rRNA amplicon sequencing on Illumina MiSeq platform. Association between the soil microbial community and the physicochemical parameters were investigated for their potential role. In RP- and CP-contaminated soils, the microbiome analysis showed Proteobacteria as most dominant phylum followed by Actinobacteria. Interestingly, Firmicutes were most prevailing in a CP-contaminated sample while they were least prevailing in RP-contaminated soils. Soil moisture content, total organic carbon and organic nitrogen content influenced the taxa diversity in these soils. Species richness was more in RP as compared to CP soils. Further prediction of metagenome using PICRUSt revealed that the RP and CP soils contain microbial communities with excellent metabolic potential for PHC degradation. Microbial community contributing to genes essential for soil health improvement and plant growth promotion was also gauged. Our analysis showed promising results for future bioaugmentation assisted phytoremediation (BAP) strategies for treating such soils.
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Affiliation(s)
- Asim M Auti
- Department of Microbiology, MES Abasaheb Garware College, Pune, India
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Microbiome and imputed metagenome study of crude and refined petroleum-oil-contaminated soils: Potential for hydrocarbon degradation and plant-growth promotion. J Biosci 2019. [DOI: 10.1007/s12038-019-9936-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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53
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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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54
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Draft Genome Sequence of Enterobacter sp. Strain AD2-3, Isolated from a Postmining Site in Benguet, Philippines. Microbiol Resour Announc 2019; 8:8/30/e00563-19. [PMID: 31346017 PMCID: PMC6658687 DOI: 10.1128/mra.00563-19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The novel strain Enterobacter sp. strain AD2-3 was isolated from postmining soil samples collected from Antamok mine in Benguet, Philippines. Here, we report a draft of its whole-genome sequence, with predicted gene inventories supporting metal tolerance, nitrogen fixation, phosphate solubilization, and indole acetic acid production.
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55
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Asaf S, Khan AL, Khan MA, Al-Harrasi A, Lee IJ. Complete genome sequencing and analysis of endophytic Sphingomonas sp. LK11 and its potential in plant growth. 3 Biotech 2018; 8:389. [PMID: 30175026 PMCID: PMC6111035 DOI: 10.1007/s13205-018-1403-z] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 08/10/2018] [Indexed: 10/28/2022] Open
Abstract
Our study aimed to elucidate the plant growth-promoting characteristics and the structure and composition of Sphingomonas sp. LK11 genome using the single molecule real-time (SMRT) sequencing technology of Pacific Biosciences. The results revealed that LK11 produces different types of gibberellins (GAs) in pure culture and significantly improves soybean plant growth by influencing endogenous GAs compared with non-inoculated control plants. Detailed genomic analyses revealed that the Sphingomonas sp. LK11 genome consists of a circular chromosome (3.78 Mbp; 66.2% G+C content) and two circular plasmids (122,975 bps and 34,160 bps; 63 and 65% G+C content, respectively). Annotation showed that the LK11 genome consists of 3656 protein-coding genes, 59 tRNAs, and 4 complete rRNA operons. Functional analyses predicted that LK11 encodes genes for phosphate solubilization and nitrate/nitrite ammonification, which are beneficial for promoting plant growth. Genes for production of catalases, superoxide dismutase, and peroxidases that confer resistance to oxidative stress in plants were also identified in LK11. Moreover, genes for trehalose and glycine betaine biosynthesis were also found in LK11 genome. Similarly, Sphingomonas spp. analysis revealed an open pan-genome and a total of 8507 genes were identified in the Sphingomonas spp. pan-genome and about 1356 orthologous genes were found to comprise the core genome. However, the number of genomes analyzed was not enough to describe complete gene sets. Our findings indicated that the genetic makeup of Sphingomonas sp. LK11 can be utilized as an eco-friendly bioresource for cleaning contaminated sites and promoting growth of plants confronted with environmental perturbations.
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Affiliation(s)
- Sajjad Asaf
- Natural and Medical Sciences Research Center, University of Nizwa, 616 Nizwa, Oman
| | - Abdul Latif Khan
- Natural and Medical Sciences Research Center, University of Nizwa, 616 Nizwa, Oman
| | - Muhammad Aaqil Khan
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566 Republic of Korea
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, 616 Nizwa, Oman
| | - In-Jung Lee
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566 Republic of Korea
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56
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Lo KJ, Lin SS, Lu CW, Kuo CH, Liu CT. Whole-genome sequencing and comparative analysis of two plant-associated strains of Rhodopseudomonas palustris (PS3 and YSC3). Sci Rep 2018; 8:12769. [PMID: 30143697 PMCID: PMC6109142 DOI: 10.1038/s41598-018-31128-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 08/13/2018] [Indexed: 11/14/2022] Open
Abstract
Rhodopseudomonas palustris strains PS3 and YSC3 are purple non-sulfur phototrophic bacteria isolated from Taiwanese paddy soils. PS3 has beneficial effects on plant growth and enhances the uptake efficiency of applied fertilizer nutrients. In contrast, YSC3 has no significant effect on plant growth. The genomic structures of PS3 and YSC3 are similar; each contains one circular chromosome that is 5,269,926 or 5,371,816 bp in size, with 4,799 or 4,907 protein-coding genes, respectively. In this study, a large class of genes involved in chemotaxis and motility was identified in both strains, and genes associated with plant growth promotion, such as nitrogen fixation-, IAA synthesis- and ACC deamination-associated genes, were also identified. We noticed that the growth rate, the amount of biofilm formation, and the relative expression levels of several chemotaxis-associated genes were significantly higher for PS3 than for YSC3 upon treatment with root exudates. These results indicate that PS3 responds better to the presence of plant hosts, which may contribute to the successful interactions of PS3 with plant hosts. Moreover, these findings indicate that the existence of gene clusters associated with plant growth promotion is required but not sufficient for a bacterium to exhibit phenotypes associated with plant growth promotion.
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Affiliation(s)
- Kai-Jiun Lo
- Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan
| | - Shih-Shun Lin
- Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan.,Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 115, Taiwan.,Center of Biotechnology, National Taiwan University, Taipei, 106, Taiwan.,National Center for High-Performance Computing, National Applied Research Laboratories, Hsinchu, 300, Taiwan
| | - Chia-Wei Lu
- Center for Shrimp Disease Control and Genetic Improvement, National Cheng Kung University, Tainan, 701, Taiwan
| | - Chih-Horng Kuo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 115, Taiwan. .,Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung Hsing University and Academia Sinica, Taipei, 115, Taiwan. .,Graduate Institute of Biotechnology, National Chung Hsing University, Taichung City, 402, Taiwan.
| | - Chi-Te Liu
- Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan. .,Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 115, Taiwan.
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57
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Kotoky R, Rajkumari J, Pandey P. The rhizosphere microbiome: Significance in rhizoremediation of polyaromatic hydrocarbon contaminated soil. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2018; 217:858-870. [PMID: 29660711 DOI: 10.1016/j.jenvman.2018.04.022] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 03/22/2018] [Accepted: 04/05/2018] [Indexed: 06/08/2023]
Abstract
Microbial communities are an essential part of plant rhizosphere and participate in the functioning of plants, including rhizoremediation of petroleum contaminants. Rhizoremediation is a promising technology for removal of polyaromatic hydrocarbons based on interactions between plants and microbiome in the rhizosphere. Root exudation in the rhizosphere provides better nutrient uptake for rhizosphere microbiome, and therefore it is considered to be one of the major factors of microbial community function in the rhizosphere that plays a key role in the enhanced PAH biodegradation. Although the importance of the rhizosphere microbiome for plant growth has been widely recognized, the interactions between microbiome and plant roots in the process of rhizosphere mediated remediation of PAH still needs attention. Most of the current researches target PAH degradation by plant or single microorganism, separately, whereas the interactions between plants and whole microbiome are overlooked and its role has been ignored. This review summarizes recent knowledge of PAH degradation in the rhizosphere in the process of plant-microbiome interactions based on emerging omics approaches such as metagenomics, metatranscriptomics, metabolomics and metaproteomics. These omics approaches with combinations to bioinformatics tools provide us a better understanding in integrated activity patterns between plants and rhizosphere microbes, and insight into the biochemical and molecular modification of the meta-organisms (plant-microbiome) to maximize rhizoremediation activity. Moreover, a better understanding of the interactions could lead to the development of techniques to engineer rhizosphere microbiome for better hydrocarbon degradation.
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Affiliation(s)
- Rhitu Kotoky
- Department of Microbiology, Assam University, Silchar, 788011, India
| | - Jina Rajkumari
- Department of Microbiology, Assam University, Silchar, 788011, India
| | - Piyush Pandey
- Department of Microbiology, Assam University, Silchar, 788011, India.
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58
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Andrés-Barrao C, Lafi FF, Alam I, de Zélicourt A, Eida AA, Bokhari A, Alzubaidy H, Bajic VB, Hirt H, Saad MM. Complete Genome Sequence Analysis of Enterobacter sp. SA187, a Plant Multi-Stress Tolerance Promoting Endophytic Bacterium. Front Microbiol 2017; 8:2023. [PMID: 29163376 PMCID: PMC5664417 DOI: 10.3389/fmicb.2017.02023] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 10/04/2017] [Indexed: 11/13/2022] Open
Abstract
Enterobacter sp. SA187 is an endophytic bacterium that has been isolated from root nodules of the indigenous desert plant Indigofera argentea. SA187 could survive in the rhizosphere as well as in association with different plant species, and was able to provide abiotic stress tolerance to Arabidopsis thaliana. The genome sequence of SA187 was obtained by using Pacific BioScience (PacBio) single-molecule sequencing technology, with average coverage of 275X. The genome of SA187 consists of one single 4,429,597 bp chromosome, with an average 56% GC content and 4,347 predicted protein coding DNA sequences (CDS), 153 ncRNA, 7 rRNA, and 84 tRNA. Functional analysis of the SA187 genome revealed a large number of genes involved in uptake and exchange of nutrients, chemotaxis, mobilization and plant colonization. A high number of genes were also found to be involved in survival, defense against oxidative stress and production of antimicrobial compounds and toxins. Moreover, different metabolic pathways were identified that potentially contribute to plant growth promotion. The information encoded in the genome of SA187 reveals the characteristics of a dualistic lifestyle of a bacterium that can adapt to different environments and promote the growth of plants. This information provides a better understanding of the mechanisms involved in plant-microbe interaction and could be further exploited to develop SA187 as a biological agent to improve agricultural practices in marginal and arid lands.
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Affiliation(s)
- Cristina Andrés-Barrao
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Feras F Lafi
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.,Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Intikhab Alam
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Axel de Zélicourt
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Abdul A Eida
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Ameerah Bokhari
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Hanin Alzubaidy
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Vladimir B Bajic
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Heribert Hirt
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Maged M Saad
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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59
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Belbahri L, Chenari Bouket A, Rekik I, Alenezi FN, Vallat A, Luptakova L, Petrovova E, Oszako T, Cherrad S, Vacher S, Rateb ME. Comparative Genomics of Bacillus amyloliquefaciens Strains Reveals a Core Genome with Traits for Habitat Adaptation and a Secondary Metabolites Rich Accessory Genome. Front Microbiol 2017; 8:1438. [PMID: 28824571 PMCID: PMC5541019 DOI: 10.3389/fmicb.2017.01438] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Accepted: 07/17/2017] [Indexed: 12/04/2022] Open
Abstract
The Gram positive, non-pathogenic endospore-forming soil inhabiting prokaryote Bacillus amyloliquefaciens is a plant growth-promoting rhizobacterium. Bacillus amyloliquefaciens processes wide biocontrol abilities and numerous strains have been reported to suppress diverse bacterial, fungal and fungal-like pathogens. Knowledge about strain level biocontrol abilities is warranted to translate this knowledge into developing more efficient biocontrol agents and bio-fertilizers. Ever-expanding genome studies of B. amyloliquefaciens are showing tremendous increase in strain-specific new secondary metabolite clusters which play key roles in the suppression of pathogens and plant growth promotion. In this report, we have used genome mining of all sequenced B. amyloliquefaciens genomes to highlight species boundaries, the diverse strategies used by different strains to promote plant growth and the diversity of their secondary metabolites. Genome composition of the targeted strains suggest regions of genomic plasticity that shape the structure and function of these genomes and govern strain adaptation to different niches. Our results indicated that B. amyloliquefaciens: (i) suffer taxonomic imprecision that blurs the debate over inter-strain genome diversity and dynamics, (ii) have diverse strategies to promote plant growth and development, (iii) have an unlocked, yet to be delimited impressive arsenal of secondary metabolites and products, (iv) have large number of so-called orphan gene clusters, i.e., biosynthetic clusters for which the corresponding metabolites are yet unknown, and (v) have a dynamic pan genome with a secondary metabolite rich accessory genome.
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Affiliation(s)
- Lassaad Belbahri
- Laboratory of Soil Biology, University of NeuchatelNeuchatel, Switzerland.,NextBiotechAgareb, Tunisia
| | - Ali Chenari Bouket
- NextBiotechAgareb, Tunisia.,Graduate School of Life and Environmental Sciences, Osaka Prefecture UniversitySakai, Japan.,Young Researchers and Elite Club, Tabriz Branch, Islamic Azad UniversityTabriz, Iran
| | | | | | - Armelle Vallat
- Neuchâtel Platform of Analytical Chemistry, Institute of Chemistry, University of NeuchâtelNeuchâtel, Switzerland
| | - Lenka Luptakova
- NextBiotechAgareb, Tunisia.,Department of Biology and Genetics, Institute of Biology, Zoology and Radiobiology, University of Veterinary Medicine and PharmacyKosice, Slovakia
| | - Eva Petrovova
- Institute of Anatomy, University of Veterinary Medicine and PharmacyKosice, Slovakia
| | | | | | | | - Mostafa E Rateb
- School of Science and Sport, University of the West of ScotlandPaisley, United Kingdom
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60
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Hao DC, Xiao PG. Rhizosphere Microbiota and Microbiome of Medicinal Plants: From Molecular Biology to Omics Approaches. CHINESE HERBAL MEDICINES 2017. [DOI: 10.1016/s1674-6384(17)60097-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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61
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Cross-compatibility evaluation of plant growth promoting rhizobacteria of coconut and cocoa on yield and rhizosphere properties of vegetable crops. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2017. [DOI: 10.1016/j.bcab.2016.11.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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62
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Cipriano MAP, Lupatini M, Lopes-Santos L, da Silva MJ, Roesch LFW, Destéfano SAL, Freitas SS, Kuramae EE. Lettuce and rhizosphere microbiome responses to growth promoting Pseudomonas species under field conditions. FEMS Microbiol Ecol 2016; 92:fiw197. [PMID: 27660605 DOI: 10.1093/femsec/fiw197] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/21/2016] [Indexed: 11/13/2022] Open
Abstract
Plant growth promoting rhizobacteria are well described and recommended for several crops worldwide. However, one of the most common problems in research into them is the difficulty in obtaining reproducible results. Furthermore, few studies have evaluated plant growth promotion and soil microbial community composition resulting from bacterial inoculation under field conditions. Here we evaluated the effect of 54 Pseudomonas strains on lettuce (Lactuca sativa) growth. The 12 most promising strains were phylogenetically and physiologically characterized for plant growth-promoting traits, including phosphate solubilization, hormone production and antagonism to pathogen compounds, and their effect on plant growth under farm field conditions. Additionally, the impact of beneficial strains on the rhizospheric bacterial community was evaluated for inoculated plants. The strains IAC-RBcr4 and IAC-RBru1, with different plant growth promoting traits, improved lettuce plant biomass yields up to 30%. These two strains also impacted rhizosphere bacterial groups including Isosphaera and Pirellula (phylum Planctomycetes) and Acidothermus, Pseudolabrys and Singusphaera (phylum Actinobacteria). This is the first study to demonstrate consistent results for the effects of Pseudomonas strains on lettuce growth promotion for seedlings and plants grown under tropical field conditions.
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Affiliation(s)
- Matheus A P Cipriano
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
- Agronomic Institute of Campinas (IAC), Campinas, São Paulo, Brazil
| | - Manoeli Lupatini
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | | | | | - Luiz F W Roesch
- Federal University of Pampa, São Gabriel, Rio Grande do Sul, Brazil
| | | | - Sueli S Freitas
- Agronomic Institute of Campinas (IAC), Campinas, São Paulo, Brazil
| | - Eiko E Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
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63
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Microbially Mediated Plant Salt Tolerance and Microbiome-based Solutions for Saline Agriculture. Biotechnol Adv 2016; 34:1245-1259. [PMID: 27587331 DOI: 10.1016/j.biotechadv.2016.08.005] [Citation(s) in RCA: 157] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 08/26/2016] [Accepted: 08/26/2016] [Indexed: 01/15/2023]
Abstract
Soil salinization adversely affects plant growth and has become one of the major limiting factors for crop productivity worldwide. The conventional approach, breeding salt-tolerant plant cultivars, has often failed to efficiently alleviate the situation. In contrast, the use of a diverse array of microorganisms harbored by plants has attracted increasing attention because of the remarkable beneficial effects of microorganisms on plants. Multiple advanced '-omics' technologies have enabled us to gain insights into the structure and function of plant-associated microbes. In this review, we first focus on microbe-mediated plant salt tolerance, in particular on the physiological and molecular mechanisms underlying root-microbe symbiosis. Unfortunately, when introducing such microbes as single strains to soils, they are often ineffective in improving plant growth and stress tolerance, largely due to competition with native soil microbial communities and limited colonization efficiency. Rapid progress in rhizosphere microbiome research has revived the belief that plants may benefit more from association with interacting, diverse microbial communities (microbiome) than from individual members in a community. Understanding how a microbiome assembles in the continuous compartments (endosphere, rhizoplane, and rhizosphere) will assist in predicting a subset of core or minimal microbiome and thus facilitate synthetic re-construction of microbial communities and their functional complementarity and synergistic effects. These developments will open a new avenue for capitalizing on the cultivable microbiome to strengthen plant salt tolerance and thus to refine agricultural practices and production under saline conditions.
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64
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Liu W, Wang Q, Hou J, Tu C, Luo Y, Christie P. Whole genome analysis of halotolerant and alkalotolerant plant growth-promoting rhizobacterium Klebsiella sp. D5A. Sci Rep 2016; 6:26710. [PMID: 27216548 PMCID: PMC4877636 DOI: 10.1038/srep26710] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 05/09/2016] [Indexed: 11/09/2022] Open
Abstract
This research undertook the systematic analysis of the Klebsiella sp. D5A genome and identification of genes that contribute to plant growth-promoting (PGP) traits, especially genes related to salt tolerance and wide pH adaptability. The genome sequence of isolate D5A was obtained using an Illumina HiSeq 2000 sequencing system with average coverages of 174.7× and 200.1× using the paired-end and mate-pair sequencing, respectively. Predicted and annotated gene sequences were analyzed for similarity with the Kyoto Encyclopedia of Genes and Genomes (KEGG) enzyme database followed by assignment of each gene into the KEGG pathway charts. The results show that the Klebsiella sp. D5A genome has a total of 5,540,009 bp with 57.15% G + C content. PGP conferring genes such as indole-3-acetic acid (IAA) biosynthesis, phosphate solubilization, siderophore production, acetoin and 2,3-butanediol synthesis, and N2 fixation were determined. Moreover, genes putatively responsible for resistance to high salinity including glycine-betaine synthesis, trehalose synthesis and a number of osmoregulation receptors and transport systems were also observed in the D5A genome together with numerous genes that contribute to pH homeostasis. These genes reveal the genetic adaptation of D5A to versatile environmental conditions and the effectiveness of the isolate to serve as a plant growth stimulator.
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Affiliation(s)
- Wuxing Liu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Qingling Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Jinyu Hou
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Chen Tu
- Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
| | - Yongming Luo
- Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
| | - Peter Christie
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
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65
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Li Z, Chang S, Ye S, Chen M, Lin L, Li Y, Li S, An Q. Differentiation of 1-aminocyclopropane-1-carboxylate (ACC) deaminase from its homologs is the key for identifying bacteria containing ACC deaminase. FEMS Microbiol Ecol 2015; 91:fiv112. [PMID: 26362924 DOI: 10.1093/femsec/fiv112] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/07/2015] [Indexed: 01/28/2023] Open
Abstract
1-Aminocyclopropane-1-carboxylate (ACC) deaminase-mediated reduction of ethylene generation in plants under abiotic stresses is a key mechanism by which bacteria can promote plant growth. Misidentification of ACC deaminase and the ACC deaminase structure gene (acdS) can lead to overestimation of the number of bacteria containing ACC deaminase and their function in ecosystems. Previous non-specific amplification of acdS homologs has led to an overestimation of the horizontal transfer of acdS genes. Here, we designed consensus-degenerate hybrid oligonucleotide primers (acdSf3, acdSr3 and acdSr4) based on differentiating the key residues in ACC deaminases from those of homologs for specific amplification of partial acdS genes. PCR amplification, sequencing and phylogenetic analysis identified acdS genes from a wide range of proteobacteria and actinobacteria. PCR amplification and a genomic search did not find the acdS gene in bacteria belonging to Pseudomonas stutzeri or in the genera Enterobacter, Klebsiella or Bacillus. We showed that differentiating the acdS gene and ACC deaminase from their homologs was crucial for the molecular identification of bacteria containing ACC deaminase and for understanding the evolution of the acdS gene. We provide an effective method for screening and identifying bacteria containing ACC deaminase.
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Affiliation(s)
- Zhengyi Li
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Siping Chang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Shuting Ye
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Mingyue Chen
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Li Lin
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Yuanyuan Li
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Shuying Li
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Qianli An
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
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Kõiv V, Roosaare M, Vedler E, Kivistik PA, Toppi K, Schryer DW, Remm M, Tenson T, Mäe A. Microbial population dynamics in response to Pectobacterium atrosepticum infection in potato tubers. Sci Rep 2015; 5:11606. [PMID: 26118792 PMCID: PMC4484245 DOI: 10.1038/srep11606] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 05/28/2015] [Indexed: 12/23/2022] Open
Abstract
Endophytes are microbes and fungi that live inside plant tissues without damaging the host. Herein we examine the dynamic changes in the endophytic bacterial community in potato (Solanum tuberosum) tuber in response to pathogenic infection by Pectobacterium atrosepticum, which causes soft rot in numerous economically important crops. We quantified community changes using both cultivation and next-generation sequencing of the 16S rRNA gene and found that, despite observing significant variability in both the mass of macerated tissue and structure of the endophytic community between individual potato tubers, P. atrosepticum is always taken over by the endophytes during maceration. 16S rDNA sequencing revealed bacteria from the phyla Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes, Fusobacteria, Verrucomicrobia, Acidobacteria, TM7, and Deinococcus-Thermus. Prior to infection, Propionibacterium acnes is frequently among the dominant taxa, yet is out competed by relatively few dominant taxa as the infection proceeds. Two days post-infection, the most abundant sequences in macerated potato tissue are Gammaproteobacteria. The most dominant genera are Enterobacter and Pseudomonas. Eight days post-infection, the number of anaerobic pectolytic Clostridia increases, probably due to oxygen depletion. These results demonstrate that the pathogenesis is strictly initiated by the pathogen (sensu stricto) and proceeds with a major contribution from the endophytic community.
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Affiliation(s)
- Viia Kõiv
- Institute of Molecular and Cell Biology, University of Tartu, 23 Riia Street, Tartu 51010, Estonia
| | - Märt Roosaare
- Institute of Molecular and Cell Biology, University of Tartu, 23 Riia Street, Tartu 51010, Estonia
| | - Eve Vedler
- Institute of Molecular and Cell Biology, University of Tartu, 23 Riia Street, Tartu 51010, Estonia
| | - Paula Ann Kivistik
- Estonian Genome Center, University of Tartu, Riia 23 B, 51010 Tartu, Estonia
| | - Kristel Toppi
- Institute of Molecular and Cell Biology, University of Tartu, 23 Riia Street, Tartu 51010, Estonia
| | - David W Schryer
- Institute of Technology, University of Tartu, 1 Nooruse Street, Tartu 50411, Estonia
| | - Maido Remm
- Institute of Molecular and Cell Biology, University of Tartu, 23 Riia Street, Tartu 51010, Estonia
| | - Tanel Tenson
- Institute of Technology, University of Tartu, 1 Nooruse Street, Tartu 50411, Estonia
| | - Andres Mäe
- Institute of Molecular and Cell Biology, University of Tartu, 23 Riia Street, Tartu 51010, Estonia
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Alkema W, Boekhorst J, Wels M, van Hijum SAFT. Microbial bioinformatics for food safety and production. Brief Bioinform 2015; 17:283-92. [PMID: 26082168 PMCID: PMC4793891 DOI: 10.1093/bib/bbv034] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Indexed: 12/14/2022] Open
Abstract
In the production of fermented foods, microbes play an important role. Optimization of fermentation processes or starter culture production traditionally was a trial-and-error approach inspired by expert knowledge of the fermentation process. Current developments in high-throughput 'omics' technologies allow developing more rational approaches to improve fermentation processes both from the food functionality as well as from the food safety perspective. Here, the authors thematically review typical bioinformatics techniques and approaches to improve various aspects of the microbial production of fermented food products and food safety.
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