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Tkachenko OV, Evseeva NV, Kargapolova KY, Denisova AY, Pozdnyakova NN, Kulikov AA, Burygin GL. Rhizobacteria Increase the Adaptation Potential of Potato Microclones under Aeroponic Conditions. Microorganisms 2023; 11:1866. [PMID: 37513038 PMCID: PMC10385146 DOI: 10.3390/microorganisms11071866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 07/11/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
Adaptation ex vitro is strongly stressful for microplants. Plant-growth-promoting rhizobacteria (PGPR) help to increase the adaptation potential of microplants transplanted from test tubes into the natural environment. We investigated the mechanisms of antioxidant protection of PGPR-inoculated potato microclones adapting to ex vitro growth in an aeroponic system. Potato (Solanum tuberosum L. cv. Nevsky) microplants were inoculated in vitro with the bacteria Azospirillum baldaniorum Sp245 and Ochrobactrum cytisi IPA7.2. On days 1 and 7 of plant growth ex vitro, catalase and peroxidase activities in the leaves of inoculated plants were 1.5-fold higher than they were in non-inoculated plants. The activity of ascorbate peroxidase was reduced in both in vitro and ex vitro treatments, and this reduction was accompanied by a decrease in the leaf content of hydrogen peroxide and malondialdehyde. As a result, inoculation contributed to the regulation of the plant pro/antioxidant system, lowering the oxidative stress and leading to better plant survival ex vitro. This was evidenced by the higher values of measured morphological and physiological variables of the inoculated plants, as compared with the values in the control treatment. Thus, we have shown some PGPR-mediated mechanisms of potato plant protection from adverse environmental factors under aeroponic conditions.
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Affiliation(s)
- Oksana V Tkachenko
- Department of Plant Breeding, Selection, and Genetics, Faculty of Agronomy, Saratov State University of Genetics, Biotechnology and Engineering named after N.I. Vavilov, 410012 Saratov, Russia
| | - Nina V Evseeva
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Saratov Scientific Centre of the Russian Academy of Sciences (IBPPM RAS), 410049 Saratov, Russia
| | - Kristina Y Kargapolova
- Department of Plant Breeding, Selection, and Genetics, Faculty of Agronomy, Saratov State University of Genetics, Biotechnology and Engineering named after N.I. Vavilov, 410012 Saratov, Russia
| | - Alena Y Denisova
- Department of Plant Breeding, Selection, and Genetics, Faculty of Agronomy, Saratov State University of Genetics, Biotechnology and Engineering named after N.I. Vavilov, 410012 Saratov, Russia
| | - Natalia N Pozdnyakova
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Saratov Scientific Centre of the Russian Academy of Sciences (IBPPM RAS), 410049 Saratov, Russia
| | - Artem A Kulikov
- Department of Plant Breeding, Selection, and Genetics, Faculty of Agronomy, Saratov State University of Genetics, Biotechnology and Engineering named after N.I. Vavilov, 410012 Saratov, Russia
| | - Gennady L Burygin
- Department of Plant Breeding, Selection, and Genetics, Faculty of Agronomy, Saratov State University of Genetics, Biotechnology and Engineering named after N.I. Vavilov, 410012 Saratov, Russia
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Saratov Scientific Centre of the Russian Academy of Sciences (IBPPM RAS), 410049 Saratov, Russia
- Department of Organic and Bioorganic Chemistry, Institute of Chemistry, Saratov State University, 410012 Saratov, Russia
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Acosta K, Sorrels S, Chrisler W, Huang W, Gilbert S, Brinkman T, Michael TP, Lebeis SL, Lam E. Optimization of Molecular Methods for Detecting Duckweed-Associated Bacteria. Plants (Basel) 2023; 12:872. [PMID: 36840219 PMCID: PMC9965182 DOI: 10.3390/plants12040872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/05/2023] [Accepted: 02/08/2023] [Indexed: 06/18/2023]
Abstract
The bacterial colonization dynamics of plants can differ between phylogenetically similar bacterial strains and in the context of complex bacterial communities. Quantitative methods that can resolve closely related bacteria within complex communities can lead to a better understanding of plant-microbe interactions. However, current methods often lack the specificity to differentiate phylogenetically similar bacterial strains. In this study, we describe molecular strategies to study duckweed-associated bacteria. We first systematically optimized a bead-beating protocol to co-isolate nucleic acids simultaneously from duckweed and bacteria. We then developed a generic fingerprinting assay to detect bacteria present in duckweed samples. To detect specific duckweed-bacterium associations, we developed a genomics-based computational pipeline to generate bacterial strain-specific primers. These strain-specific primers differentiated bacterial strains from the same genus and enabled the detection of specific duckweed-bacterium associations present in a community context. Moreover, we used these strain-specific primers to quantify the bacterial colonization of duckweed by normalization to a plant reference gene and revealed differences in colonization levels between strains from the same genus. Lastly, confocal microscopy of inoculated duckweed further supported our PCR results and showed bacterial colonization of the duckweed root-frond interface and root interior. The molecular methods introduced in this work should enable the tracking and quantification of specific plant-microbe associations within plant-microbial communities.
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Affiliation(s)
- Kenneth Acosta
- Department of Plant Biology, Rutgers the State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Shawn Sorrels
- Department of Plant Biology, Rutgers the State University of New Jersey, New Brunswick, NJ 08901, USA
| | - William Chrisler
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, WA 99354, USA
| | - Weijuan Huang
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou 510316, China
| | - Sarah Gilbert
- Department of Plant Biology, Rutgers the State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Thomas Brinkman
- Department of Plant Biology, Rutgers the State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Todd P. Michael
- The Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Sarah L. Lebeis
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
- Plant Resilience Institute, Michigan State University, East Lansing, MI 48824, USA
| | - Eric Lam
- Department of Plant Biology, Rutgers the State University of New Jersey, New Brunswick, NJ 08901, USA
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3
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Liu T, Ren Z, Chunyu WX, Li GD, Chen X, Zhang ZTL, Sun HB, Wang M, Xie TP, Wang M, Chen JY, Zhou H, Ding ZT, Yin M. Exploration of Diverse Secondary Metabolites From Streptomyces sp. YINM00001, Using Genome Mining and One Strain Many Compounds Approach. Front Microbiol 2022; 13:831174. [PMID: 35222341 PMCID: PMC8866825 DOI: 10.3389/fmicb.2022.831174] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 01/07/2022] [Indexed: 11/24/2022] Open
Abstract
A talented endophytic bacteria strain YINM00001, which showed strong antimicrobial activity and multiple antibiotic resistances, was isolated from a Chinese medicinal herb Peperomia dindygulensis Miq. Phylogenetic analysis based on 16S rRNA gene sequences demonstrated that strain was closely related to Streptomyces anulatus NRRL B-2000T (99.93%). The complete genome of strain YINM00001 was sequenced. The RAxML phylogenomic tree also revealed that strain YINM00001 was steadily clustered on a branch with strain Streptomyces anulatus NRRL B-2000T under the 100 bootstrap values. The complete genome of strain YINM00001 consists of an 8,372,992 bp linear chromosome (71.72 mol% GC content) and a 317,781 bp circular plasmid (69.14 mol% GC content). Genome mining and OSMAC approach were carried out to investigate the biosynthetic potential of producing secondary metabolites. Fifty-two putative biosynthetic gene clusters of secondary metabolites were found, including the putative cycloheximide, dinactin, warkmycin, and anthracimycin biosynthetic gene clusters which consist with the strong antifungal and antibacterial activities exhibited by strain YINM00001. Two new compounds, peperodione (1) and peperophthalene (2), and 17 known compounds were isolated from different fermentation broth. Large amounts and high diversity of antimicrobial and/or anticancer compounds cycloheximide, dinactin, anthracimycin, and their analogs had been found as predicted before, which highlights strain YINM00001 as an ideal candidate for further biosynthetic studies and production improvement of these valuable compounds. Meanwhile, several gene clusters that were highly conserved in several sequenced actinomycetes but significantly different from known gene clusters might be silent under proceeding fermentation conditions. Further studies, such as heterologous expression and genetic modification, are needed to explore more novel compounds from this talented endophytic Streptomyces strain.
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Affiliation(s)
- Tao Liu
- School of Medicine, School of Chemical Science and Technology, Yunnan University, Kunming, China
| | - Zhen Ren
- School of Agriculture and Life Sciences, Kunming University, Kunming, China
| | - Wei-Xun Chunyu
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Gui-Ding Li
- School of Medicine, School of Chemical Science and Technology, Yunnan University, Kunming, China
| | - Xiu Chen
- School of Agriculture and Life Sciences, Kunming University, Kunming, China
| | - Zhou-Tian-Le Zhang
- School of Medicine, School of Chemical Science and Technology, Yunnan University, Kunming, China
| | - Hui-Bing Sun
- School of Medicine, School of Chemical Science and Technology, Yunnan University, Kunming, China
| | - Mei Wang
- School of Medicine, School of Chemical Science and Technology, Yunnan University, Kunming, China
| | - Tian-Peng Xie
- School of Medicine, School of Chemical Science and Technology, Yunnan University, Kunming, China
| | - Meng Wang
- School of Medicine, School of Chemical Science and Technology, Yunnan University, Kunming, China
| | - Jing-Yuan Chen
- School of Medicine, School of Chemical Science and Technology, Yunnan University, Kunming, China
| | - Hao Zhou
- School of Medicine, School of Chemical Science and Technology, Yunnan University, Kunming, China
- *Correspondence: Hao Zhou,
| | - Zhong-Tao Ding
- School of Medicine, School of Chemical Science and Technology, Yunnan University, Kunming, China
- College of Pharmacy, Dali University, Dali, China
- Zhong-Tao Ding,
| | - Min Yin
- School of Medicine, School of Chemical Science and Technology, Yunnan University, Kunming, China
- Min Yin, ;
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Cassan FD, Coniglio A, Amavizca E, Maroniche G, Cascales E, Bashan Y, de-Bashan LE. The Azospirillum brasilense type VI secretion system promotes cell aggregation, biocontrol protection against phytopathogens and attachment to the microalgae Chlorella sorokiniana. Environ Microbiol 2021; 23:6257-6274. [PMID: 34472164 DOI: 10.1111/1462-2920.15749] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 08/25/2021] [Accepted: 08/28/2021] [Indexed: 01/26/2023]
Abstract
The plant-growth-promoting bacterium Azospirillum brasilense is able to associate with the microalgae Chlorella sorokiniana. Attachment of A. brasilense increases the metabolic performances of the microalgae. Recent genome analyses have revealed that the A. brasilense Az39 genome contains two complete sets of genes encoding type VI secretion systems (T6SS), including the T6SS1 that is induced by the indole-3-acetic acid (IAA) phytohormone. The T6SS is a multiprotein machine, widespread in Gram-negative bacteria, that delivers protein effectors in both prokaryotic and eukaryotic cells. Here we show that the A. brasilense T6SS is required for Chlorella-Azospirillum synthetic mutualism. Our data demonstrate that the T6SS is an important determinant to promote production of lipids, carbohydrates and photosynthetic pigments by the microalgae. We further show that this is likely due to the role of the T6SS during the attachment stage and for the production of IAA phytohormones. Finally, we demonstrate that the A. brasilense T6SS provides antagonistic activities against a number of plant pathogens such as Agrobacterium, Pectobacterium, Dickeya and Ralstonia species in vitro, suggesting that, in addition to promoting growth, A. brasilense might confer T6SS-dependent bio-control protection to microalgae and plants against bacterial pathogens.
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Affiliation(s)
- Fabricio D Cassan
- Laboratorio de Fisiología Vegetal y de la interacción Planta-Microorganismo, Instituto de Investigaciones Agrobiotecnológicas (INIAB), Universidad Nacional de Río Cuarto, Córdoba, Argentina
| | - Anahí Coniglio
- Laboratorio de Fisiología Vegetal y de la interacción Planta-Microorganismo, Instituto de Investigaciones Agrobiotecnológicas (INIAB), Universidad Nacional de Río Cuarto, Córdoba, Argentina
| | - Edgar Amavizca
- Environmental Microbiology Group, Northwestern Center for Biological Research (CIBNOR), La Paz, Mexico
| | - Guillermo Maroniche
- Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata, Buenos Aires, Argentina
| | - Eric Cascales
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires, Institut de Microbiologie, Bioénergies et Biotechnologie, Aix-Marseille Université - CNRS UMR7255, Marseille, France
| | - Yoav Bashan
- Environmental Microbiology Group, Northwestern Center for Biological Research (CIBNOR), La Paz, Mexico.,The Bashan Institute of Science, Auburn, AL, USA
| | - Luz E de-Bashan
- Environmental Microbiology Group, Northwestern Center for Biological Research (CIBNOR), La Paz, Mexico.,The Bashan Institute of Science, Auburn, AL, USA.,Department of Entomology and Plant Pathology, 301 Funchess Hall, Auburn University, Auburn, AL, USA
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Hernández I, Taulé C, Pérez-Pérez R, Battistoni F, Fabiano E, Rivero D, Nápoles MC. Endophytic rhizobia promote the growth of Cuban rice cultivar. Symbiosis 2021. [DOI: 10.1007/s13199-021-00803-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Tugarova AV, Dyatlova YA, Kenzhegulov OA, Kamnev AA. Poly-3-hydroxybutyrate synthesis by different Azospirillum brasilense strains under varying nitrogen deficiency: A comparative in-situ FTIR spectroscopic analysis. Spectrochim Acta A Mol Biomol Spectrosc 2021; 252:119458. [PMID: 33601223 DOI: 10.1016/j.saa.2021.119458] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 11/23/2020] [Accepted: 01/06/2021] [Indexed: 06/12/2023]
Abstract
Monitoring of poly-3-hydroxybutyrate accumulation and changes in its relative contents in biomass of the plant-growth-promoting bacteria Azospirillum brasilense (strains Sp7, Cd and Sp245) was performed during aerobic cultivation for 1 to 8 days at various initial concentrations of bound nitrogen (0.1 to 0.5 g∙L-1 NH4Cl) in the culture medium using in-situ transmission FTIR spectroscopy. A methodology has been proposed based on calculating band areas in FTIR spectra (instead of band intensities commonly used earlier) for determining relative contents of PHB in dry bacterial biomass, using the ester ν(C=O) band as a PHB marker (in the region 1750-1720 cm-1) and amide II band of cellular proteins (at ca. 1540 cm-1). Differences in PHB accumulation levels and their changes in the course of cultivation under various trophic stress for the three strains are discussed in relation to their different ecological niches which they occupy in the rhizosphere.
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Affiliation(s)
- Anna V Tugarova
- Laboratory of Biochemistry, Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, 13 Prosp. Entuziastov, 410049 Saratov, Russia
| | - Yulia A Dyatlova
- Laboratory of Biochemistry, Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, 13 Prosp. Entuziastov, 410049 Saratov, Russia
| | - Odissey A Kenzhegulov
- Laboratory of Biochemistry, Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, 13 Prosp. Entuziastov, 410049 Saratov, Russia
| | - Alexander A Kamnev
- Laboratory of Biochemistry, Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, 13 Prosp. Entuziastov, 410049 Saratov, Russia.
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7
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Camelo A, Barreto CP, Vidal MS, Rouws JRC, da Silva Lédo FJ, Schwab S, Baldani JI. Field response of two seed propagated elephant grass genotypes to diazotrophic bacterial inoculation and in situ confocal microscopy colonization analyses. Symbiosis 2020. [DOI: 10.1007/s13199-020-00730-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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8
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Arkhipova TN, Evseeva NV, Tkachenko OV, Burygin GL, Vysotskaya LB, Akhtyamova ZA, Kudoyarova GR. Rhizobacteria Inoculation Effects on Phytohormone Status of Potato Microclones Cultivated In Vitro under Osmotic Stress. Biomolecules 2020; 10:biom10091231. [PMID: 32847137 PMCID: PMC7564303 DOI: 10.3390/biom10091231] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/12/2020] [Accepted: 08/20/2020] [Indexed: 01/16/2023] Open
Abstract
Water deficits inhibit plant growth and decrease crop productivity. Remedies are needed to counter this increasingly urgent problem in practical farming. One possible approach is to utilize rhizobacteria known to increase plant resistance to abiotic and other stresses. We therefore studied the effects of inoculating the culture medium of potato microplants grown in vitro with Azospirillum brasilense Sp245 or Ochrobactrum cytisi IPA7.2. Growth and hormone content of the plants were evaluated under stress-free conditions and under a water deficit imposed with polyethylene glycol (PEG 6000). Inoculation with either bacterium promoted the growth in terms of leaf mass accumulation. The effects were associated with increased concentrations of auxin and cytokinin hormones in the leaves and stems and with suppression of an increase in the leaf abscisic acid that PEG treatment otherwise promoted in the potato microplants. O. cytisi IPA7.2 had a greater growth-stimulating effect than A. brasilense Sp245 on stressed plants, while A. brasilense Sp245 was more effective in unstressed plants. The effects were likely to be the result of changes to the plant's hormonal balance brought about by the bacteria.
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Affiliation(s)
- Tatiana N. Arkhipova
- Ufa Institute of Biology, Ufa Federal Research Centre, Russian Academy of Sciences, Prospekt Oktyabrya, 69, 450054 Ufa, Russia; (T.N.A.); (L.B.V.); (Z.A.A.)
| | - Nina V. Evseeva
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, Prospekt Entuziastov, 13, 410049 Saratov, Russia; (N.V.E.); (G.L.B.)
| | - Oksana V. Tkachenko
- Vavilov Saratov State Agrarian University, Teatralnaya Square, 1, 410012 Saratov, Russia;
| | - Gennady L. Burygin
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, Prospekt Entuziastov, 13, 410049 Saratov, Russia; (N.V.E.); (G.L.B.)
- Vavilov Saratov State Agrarian University, Teatralnaya Square, 1, 410012 Saratov, Russia;
| | - Lidiya B. Vysotskaya
- Ufa Institute of Biology, Ufa Federal Research Centre, Russian Academy of Sciences, Prospekt Oktyabrya, 69, 450054 Ufa, Russia; (T.N.A.); (L.B.V.); (Z.A.A.)
| | - Zarina A. Akhtyamova
- Ufa Institute of Biology, Ufa Federal Research Centre, Russian Academy of Sciences, Prospekt Oktyabrya, 69, 450054 Ufa, Russia; (T.N.A.); (L.B.V.); (Z.A.A.)
| | - Guzel R. Kudoyarova
- Ufa Institute of Biology, Ufa Federal Research Centre, Russian Academy of Sciences, Prospekt Oktyabrya, 69, 450054 Ufa, Russia; (T.N.A.); (L.B.V.); (Z.A.A.)
- Correspondence: ; Tel.: +7-9191427994
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Alen’kina SA, Nikitina VE. Effect of Azospirillum Lectins on the Ascorbate Peroxidase Activity and Ascorbic Acid Content in Wheat Seedling Roots Exposed to Abiotic Stresses. APPL BIOCHEM MICRO+ 2020. [DOI: 10.1134/s0003683820020027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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10
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Shelud’ko AV, Mokeev DI, Evstigneeva SS, Filip’echeva YA, Burov AM, Petrova LP, Ponomareva EG, Katsy EI. Cell Ultrastructure in Azospirillum brasilense Biofilms. Microbiology (Reading) 2020. [DOI: 10.1134/s0026261720010142] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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11
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Evseeva NV, Tkachenko OV, Denisova AY, Burygin GL, Veselov DS, Matora LY, Shchyogolev SY. Functioning of plant-bacterial associations under osmotic stress in vitro. World J Microbiol Biotechnol 2019; 35:195. [PMID: 31784916 DOI: 10.1007/s11274-019-2778-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 11/23/2019] [Indexed: 10/25/2022]
Abstract
The search for effective plant-growth-promoting strains of rhizospheric bacteria that would ensure the resistance of plant-microbial associations to environmental stressors is essential for the design of environmentally friendly agrobiotechnologies. We investigated the interaction of potato (cv. Nevsky) microplants with the plant-growth-promoting bacteria Azospirillum brasilense Sp245 and Ochrobactrum cytisi IPA7.2 under osmotic stress in vitro. The bacteria improved the physiological and biochemical variables of the microplants, significantly increasing shoot length and root number (1.3-fold, on average). Inoculation also led a more effective recovery of the plants after stress. During repair, inoculation contributed to a decreased leaf content of malonic dialdehyde. With A. brasilense Sp245, the decrease was 1.75-fold; with O. cytisi IPA7.2, it was 1.4-fold. During repair, the shoot length, node number, and root number of the inoculated plants were greater than the control values by an average of 1.3-fold with A. brasilense Sp245 and by an average of 1.6-fold with O. cytisi IPA7.2. O. cytisi IPA7.2, previously isolated from the potato rhizosphere, protected the physiological and biochemical processes in the plants under stress and repair better than did A. brasilense Sp245. Specifically, root weight increased fivefold during repair, as compared to the noninoculated plants, while chlorophyll a content remained at the level found in the nonstressed controls. The results indicate that these bacteria can be used as components of biofertilizers. A. brasilense Sp245 has favorable prospects for use in temperate latitudes, whereas O. cytisi IPA7.2 can be successfully used in saline and drought-stressed environments.
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Affiliation(s)
- Nina V Evseeva
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, 13 Prospekt Entuziastov, Saratov, Russian Federation, 410049.
| | - Oksana V Tkachenko
- Vavilov Saratov State Agrarian University, 1 Teatralnaya Ploshchad, Saratov, Russian Federation, 410012
| | - Alena Yu Denisova
- Vavilov Saratov State Agrarian University, 1 Teatralnaya Ploshchad, Saratov, Russian Federation, 410012
| | - Gennady L Burygin
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, 13 Prospekt Entuziastov, Saratov, Russian Federation, 410049.,Vavilov Saratov State Agrarian University, 1 Teatralnaya Ploshchad, Saratov, Russian Federation, 410012
| | - Dmitry S Veselov
- Ufa Institute of Biology, Russian Academy of Sciences, 69 Prospekt Oktyabrya, Ufa, Russian Federation, 450054
| | - Larisa Yu Matora
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, 13 Prospekt Entuziastov, Saratov, Russian Federation, 410049
| | - Sergei Yu Shchyogolev
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, 13 Prospekt Entuziastov, Saratov, Russian Federation, 410049
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12
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Hartmann A, Fischer D, Kinzel L, Chowdhury SP, Hofmann A, Baldani JI, Rothballer M. Assessment of the structural and functional diversities of plant microbiota: Achievements and challenges - A review. J Adv Res 2019; 19:3-13. [PMID: 31341665 PMCID: PMC6629839 DOI: 10.1016/j.jare.2019.04.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 04/23/2019] [Accepted: 04/24/2019] [Indexed: 12/28/2022] Open
Abstract
Analyses of the spatial localization and the functions of bacteria in host plant habitats through in situ identification by immunological and molecular genetic techniques combined with high resolving microscopic tools and 3D-image analysis contributed substantially to a better understanding of the functional interplay of the microbiota in plants. Among the molecular genetic methods, 16S-rRNA genes were of central importance to reconstruct the phylogeny of newly isolated bacteria and to localize them in situ. However, they usually do not allow resolution for phylogenetic affiliations below genus level. Especially, the separation of opportunistic human pathogens from plant beneficial strains, currently allocated to the same species, needs genome-based resolving techniques. Whole bacterial genome sequences allow to discriminate phylogenetically closely related strains. In addition, complete genome sequences enable strain-specific monitoring for biotechnologically relevant strains. In this mini-review we present high resolving approaches for analysis of the composition and key functions of plant microbiota, focusing on interactions of diazotrophic plant growth promoting bacteria, like Azospirillum brasilense, with non-legume host plants. Combining high resolving microscopic analyses with specific immunological detection methods and molecular genetic tools, including especially transcriptome analyses of both the bacterial and plant partners, enables new insights into key traits of beneficial bacteria-plant interactions in holobiontic systems.
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Affiliation(s)
- Anton Hartmann
- Ludwig-Maximilians-Universität (LMU) München, Faculty of Biology, Host-Microbe interactions, Großhaderner Str. 2-4, D-82152 Martinsried, Germany
| | - Doreen Fischer
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstr. 1, D-85764 Neuherberg, Munich, Germany
| | - Linda Kinzel
- Research Unit Microbe-Plant Interactions, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstr. 1, D-85764 Neuherberg, Munich, Germany
| | - Soumitra Paul Chowdhury
- Institute of Network Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstr. 1, D-85764 Neuherberg, Munich, Germany
| | - Andreas Hofmann
- EMBRAPA-Agrobiologia, Br 465, Km 07, Seropédica–RJ–CEP 23891-000, Brazil
| | - Jose Ivo Baldani
- EMBRAPA-Agrobiologia, Br 465, Km 07, Seropédica–RJ–CEP 23891-000, Brazil
| | - Michael Rothballer
- Institute of Network Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstr. 1, D-85764 Neuherberg, Munich, Germany
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Ramirez-Mata A, Pacheco MR, Moreno SJ, Xiqui-Vazquez ML, Baca BE. Versatile use of Azospirillum brasilense strains tagged with egfp and mCherry genes for the visualization of biofilms associated with wheat roots. Microbiol Res 2018; 215:155-163. [PMID: 30172303 DOI: 10.1016/j.micres.2018.07.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 07/10/2018] [Accepted: 07/18/2018] [Indexed: 11/20/2022]
Abstract
This study reports the introduction of egfp or mCherry markers to the Sp245, Sp7, and M40 wild-type strains of Azospirillum brasilense and the hhkB (encoding for a putative hybrid histidine kinase) minus mutant an isogenic strain of A. brasilense Sp245 to monitor colonization of wheat (Triticum aestivum). Two plasmids were constructed: (1) the pJMS-2 suicide plasmid derived from pSUP202 and harboring the mCherry gene expressed under the constitutive kanamycin resistance promoter to create a cis tag and (2) the broad-range plasmid pMP2449-5 that carries the mCherry gene under the lac promoter, which is derived from the plasmid pMP2444; to create the in trans tag. The stability of the plasmids encoding egfp and mCherry were confirmed in vitro for seven days of bacterial growth, and then, the A. brasilense strains harboring the plasmids were studied under nonselective conditions for adherence to seeds and, at seven or 14 days post-inoculation, for wheat root colonization. The utility of the labeled strains was proven by observation, using fluorescence microscopy and confocal laser scanning microscopy (CLSM) in wheat plants inoculated with the labeled strains and compared with the CFU g-1 for seed and wheat root. The method was suitable for observation of the in situ formation of mini-colonies, enabled visualization of bacterial colonization sites on large root fragments, and showed adherence to germinated seeds and root colonization of all strains by cell counts and direct microscopic examination. Thus, we are able to quantify the structures of the biofilms formed by each strain.
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Affiliation(s)
- Alberto Ramirez-Mata
- Centro de Investigaciones en Ciencias Microbiologicas, Benemerita Universidad Autonoma de Puebla. Edif. IC11, Ciudad Universitaria, Puebla, Puebla 72570, Mexico
| | - Miguel Ramales Pacheco
- Centro de Investigaciones en Ciencias Microbiologicas, Benemerita Universidad Autonoma de Puebla. Edif. IC11, Ciudad Universitaria, Puebla, Puebla 72570, Mexico
| | - Saul Jijon Moreno
- Centro de Investigaciones en Ciencias Microbiologicas, Benemerita Universidad Autonoma de Puebla. Edif. IC11, Ciudad Universitaria, Puebla, Puebla 72570, Mexico
| | - Maria Luisa Xiqui-Vazquez
- Centro de Investigaciones en Ciencias Microbiologicas, Benemerita Universidad Autonoma de Puebla. Edif. IC11, Ciudad Universitaria, Puebla, Puebla 72570, Mexico
| | - Beatriz E Baca
- Centro de Investigaciones en Ciencias Microbiologicas, Benemerita Universidad Autonoma de Puebla. Edif. IC11, Ciudad Universitaria, Puebla, Puebla 72570, Mexico.
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Dupuy L, Mimault M, Patko D, Ladmiral V, Ameduri B, Macdonald M, Ptashnyk M. Micromechanics of root development in soil. Curr Opin Genet Dev 2018; 51:18-25. [DOI: 10.1016/j.gde.2018.03.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 03/04/2018] [Accepted: 03/08/2018] [Indexed: 11/17/2022]
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15
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Malinich EA, Bauer CE. Transcriptome analysis of Azospirillum brasilense vegetative and cyst states reveals large-scale alterations in metabolic and replicative gene expression. Microb Genom 2018; 4. [PMID: 30058999 PMCID: PMC6159551 DOI: 10.1099/mgen.0.000200] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Several Gram-negative soil bacteria have the ability to differentiate into dormant cysts when faced with harsh environmental conditions. For example, when challenged with nutrient deprivation or desiccation, the plant-growth-promoting bacterium Azospirillum brasilense differentiates from a replicative and motile rod-shaped vegetative cell into a non-motile dormant spherical cyst. Currently, little is known about either the metabolic differences that exist between vegetative and cyst cell types, or about aspects of cyst physiology that allow dormant cells to survive harsh conditions. Here we compared transcriptomic profiles of vegetative and encysted A. brasilense. We observed that approximately one fifth of the A. brasilense transcriptome undergoes changes in expression between replicative vegetative cells and non-replicative cysts. A dramatic alteration in expression of genes involved in cell wall or cell membrane biogenesis was observed, which is congruent with changes in exopolysaccharide and lipid composition that occur between these cell types. Encysted cells also exhibited repressed mRNA abundance of genes involved in amino acid biosynthesis, ribosomal biogenesis and translation. We further observed that cysts create an anaerobic/micro-aerobic environment, as evidenced by repressed expression of oxidative phosphorylation genes coupled with increased expression of nitrate/nitrite reduction and nitrogen fixation genes.
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Affiliation(s)
| | - Carl E Bauer
- 2Department of Biochemistry, Indiana University Bloomington, Simon Hall MSB, Bloomington, IN 47405-7003, USA
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16
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Restrepo-Ortiz CX, Merbt SN, Barrero-Canossa J, Fuchs BM, Casamayor EO. Development of a 16S rRNA-targeted fluorescence in situ hybridization probe for quantification of the ammonia-oxidizer Nitrosotalea devanaterra and its relatives. Syst Appl Microbiol 2018; 41:408-413. [PMID: 29747878 DOI: 10.1016/j.syapm.2018.04.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 04/10/2018] [Accepted: 04/18/2018] [Indexed: 11/16/2022]
Abstract
The Thaumarchaeota SAGMCG-1 group and, in particular, members of the genus Nitrosotalea have high occurrence in acidic soils, the rhizosphere, groundwater and oligotrophic lakes, and play a potential role in nitrogen cycling. In this study, the specific oligonucleotide fluorescence in situ hybridization probe SAG357 was designed for this Thaumarchaeota group based on the available 16S rRNA gene sequences in databases, and included the ammonia-oxidizing species Nitrosotalea devanaterra. Cell permeabilization for catalyzed reporter deposition fluorescence in situ detection and the hybridization conditions were optimized on enrichment cultures of the target species N. devanaterra, as well as the non-target ammonia-oxidizing archaeon Nitrosopumilus maritimus. Probe specificity was improved with a competitor oligonucleotide, and fluorescence intensity and cell visualization were enhanced by the design and application of two adjacent helpers. Probe performance was tested in soil samples along a pH gradient, and counting results matched the expected in situ distributions. Probe SAG357 and the CARD-FISH protocol developed in the present study will help to improve the current understanding of the ecology and physiology of N. devanaterra and its relatives in natural environments.
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Affiliation(s)
- C X Restrepo-Ortiz
- Center of Advanced Studies of Blanes, CEAB-CSIC, Accés Cala Sant Francesc, 14, Blanes, Spain
| | - S N Merbt
- Center of Advanced Studies of Blanes, CEAB-CSIC, Accés Cala Sant Francesc, 14, Blanes, Spain
| | - J Barrero-Canossa
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, Bremen, Germany
| | - B M Fuchs
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, Bremen, Germany
| | - E O Casamayor
- Center of Advanced Studies of Blanes, CEAB-CSIC, Accés Cala Sant Francesc, 14, Blanes, Spain.
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17
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Ren Z, Tang S, Jiang Y, Jiang M, Zheng S, Liu W, Yang Z, Sang S, Chen Z, Xia T, Yin M. High-Throughput Sequencing Analysis of Endophytic Bacteria Diversity in Fruits of White and Red Pitayas from Three Different Origins. Pol J Microbiol 2018; 67:27-35. [DOI: 10.5604/01.3001.0011.6139] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/26/2017] [Indexed: 01/08/2023] Open
Abstract
Pitaya contains various types of polyphenols, flavonoid and vitamins which are beneficial for health and it is among the most important commercial tropical fruits worldwide. Endophytic bacteria might be beneficial for plant growth and yield. However, bacterial diversity in pitaya is poorly characterized. In this study, fruits of white and red pitayas from three different origins (Thailand, Vietnam and China) were chosen for endophytic bacteria diversity investigation by using Illumina HiSeq second-generation high-throughput sequencing technology. Large number of endophytic bacteria were detected and 22 phyla, 56 classes, 81 orders, 122 families and 159 genera were identified. Endophytic bacteria diversity was uneven among pitaya fruits from different origins and bacteria structure was different between white pitaya group and red pitaya group. Phylum Bacteroidetes, classes Bacteroidia and Coriobacteriia, orders Bacteroidales and Coriobacteriales, families Prevotellaceae, Bacteroidaceae, Ruminococcaceae, Paraprevotellaceae, Rikenellaceae, Alcaligenaceae and Coriobacteriaceae, genera Prevotella, Bacteroides, Roseburia, Faecalibacterium and Sutterella were statistically significant different species (P < 0.05) between white and red pitayas. These findings might be useful for growth improvement, fruit preservation and processing of different pitaya species from different origins.
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Affiliation(s)
- Zhen Ren
- School of Agriculture, Kunming University, Kunming, Yunnan, China
| | - Shukun Tang
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, Yunnan, China
| | - Yi Jiang
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, Yunnan, China
| | - Mingxing Jiang
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, Yunnan, China
| | - Shangyong Zheng
- School of Medicine, Yunnan University, Kunming, Yunnan, China
| | - Wenjing Liu
- School of Medicine, Yunnan University, Kunming, Yunnan, China
| | - Zhili Yang
- School of Medicine, Yunnan University, Kunming, Yunnan, China
| | - Shuping Sang
- School of Medicine, Yunnan University, Kunming, Yunnan, China
| | - Zebin Chen
- School of Agriculture, Kunming University, Kunming, Yunnan, China
| | - Tiyuan Xia
- School of Agriculture, Kunming University, Kunming, Yunnan, China
| | - Min Yin
- School of Medicine, Yunnan University, Kunming, Yunnan, China
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Abstract
Bacteria of the genus Azospirillum comprise 15 species to date, with A. brasilense the best studied species in the genus. Azospirillum are soil bacteria able to promote the growth of plants from 113 species spanning 35 botanical families. These non-pathogenic and beneficial bacteria are ubiquitous in soils and inhabit the roots of diverse plants. These bacteria are microaerophilic, able to fix nitrogen under free-living conditions, motile, and able to navigate in gradients of various chemicals, including oxygen. These physiological traits are used to isolate these soil bacteria from soil and plant root samples, providing isolates that can be used for studying microbial physiology and plant growth promotion. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- Gladys Alexandre
- Biochemistry & Cellular and Molecular Biology, The University of Tennessee, Knoxville, Tennessee
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19
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Santos ARS, Etto RM, Furmam RW, Freitas DLD, Santos KFDN, Souza EMD, Pedrosa FDO, Ayub RA, Steffens MBR, Galvão CW. Labeled Azospirillum brasilense wild type and excretion-ammonium strains in association with barley roots. Plant Physiol Biochem 2017; 118:422-426. [PMID: 28711791 DOI: 10.1016/j.plaphy.2017.07.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 06/20/2017] [Accepted: 07/03/2017] [Indexed: 06/07/2023]
Abstract
Soil bacteria colonization in plants is a complex process, which involves interaction between many bacterial characters and plant responses. In this work, we labeled Azospirillum brasilense FP2 (wild type) and HM053 (excretion-ammonium) strains by insertion of the reporter gene gusA-kanamycin into the dinitrogenase reductase coding gene, nifH, and evaluated bacteria colonization in barley (Hordeum vulgare). In addition, we determined inoculation effect based on growth promotion parameters. We report an uncommon endophytic behavior of A. brasilense Sp7 derivative inside the root hair cells of barley and highlight the promising use of A. brasilense HM053 as plant growth-promoting bacterium.
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Affiliation(s)
| | - Rafael Mazer Etto
- Department of Chemistry, Universidade Estadual de Ponta Grossa, Ponta Grossa, Paraná, Brazil
| | - Rafaela Wiegand Furmam
- Department of Structural and Molecular Biology and Genetics, Universidade Estadual de Ponta Grossa, Ponta Grossa, Paraná, Brazil
| | - Denis Leandro de Freitas
- Department of Structural and Molecular Biology and Genetics, Universidade Estadual de Ponta Grossa, Ponta Grossa, Paraná, Brazil
| | | | - Emanuel Maltempi de Souza
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Fábio de Oliveira Pedrosa
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Ricardo Antônio Ayub
- Department of Phytotechny and Phytosanitary, Universidade Estadual de Ponta Grossa, Ponta Grossa, Paraná, Brazil
| | | | - Carolina Weigert Galvão
- Department of Structural and Molecular Biology and Genetics, Universidade Estadual de Ponta Grossa, Ponta Grossa, Paraná, Brazil.
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Wang D, Xu A, Elmerich C, Ma LZ. Biofilm formation enables free-living nitrogen-fixing rhizobacteria to fix nitrogen under aerobic conditions. ISME J 2017; 11:1602-1613. [PMID: 28338674 DOI: 10.1038/ismej.2017.30] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Revised: 12/26/2016] [Accepted: 01/22/2017] [Indexed: 12/14/2022]
Abstract
The multicellular communities of microorganisms known as biofilms are of high significance in agricultural setting, yet it is largely unknown about the biofilm formed by nitrogen-fixing bacteria. Here we report the biofilm formation by Pseudomonas stutzeri A1501, a free-living rhizospheric bacterium, capable of fixing nitrogen under microaerobic and nitrogen-limiting conditions. P. stutzeri A1501 tended to form biofilm in minimal media, especially under nitrogen depletion condition. Under such growth condition, the biofilms formed at the air-liquid interface (termed as pellicles) and the colony biofilms on agar plates exhibited nitrogenase activity in air. The two kinds of biofilms both contained large ovoid shape 'cells' that were multiple living bacteria embedded in a sac of extracellular polymeric substances (EPSs). We proposed to name such large 'cells' as A1501 cyst. Our results suggest that the EPS, especially exopolysaccharides enabled the encased bacteria to fix nitrogen while grown under aerobic condition. The formation of A1501 cysts was reversible in response to the changes of carbon or nitrogen source status. A1501 cyst formation depended on nitrogen-limiting signaling and the presence of sufficient carbon sources, yet was independent of an active nitrogenase. The pellicles formed by Azospirillum brasilense, another free-living nitrogen-fixing rhizobacterium, which also exhibited nitrogenase activity and contained the large EPS-encapsuled A1501 cyst-like 'cells'. Our data imply that free-living nitrogen-fixing bacteria could convert the easy-used carbon sources to exopolysaccharides in order to enable nitrogen fixation in a natural aerobic environment.
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Affiliation(s)
- Di Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Anming Xu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | | | - Luyan Z Ma
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
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21
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Ellison MA, McMahon MB, Bonde MR, Palmer CL, Luster DG. In situ hybridization for the detection of rust fungi in paraffin embedded plant tissue sections. Plant Methods 2016; 12:37. [PMID: 27471544 PMCID: PMC4964054 DOI: 10.1186/s13007-016-0137-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 07/19/2016] [Indexed: 05/20/2023]
Abstract
BACKGROUND Rust fungi are obligate pathogens with multiple life stages often including different spore types and multiple plant hosts. While individual rust pathogens are often associated with specific plants, a wide range of plant species are infected with rust fungi. To study the interactions between these important pathogenic fungi and their host plants, one must be able to differentiate fungal tissue from plant tissue. This can be accomplished using the In situ hybridization (ISH) protocol described here. RESULTS To validate reproducibility using the ISH protocol, samples of Chrysanthemum × morifolium infected with Puccinia horiana, Gladiolus × hortulanus infected with Uromyces transversalis and Glycine max infected with Phakopsora pachyrhizi were tested alongside uninfected leaf tissue samples. The results of these tests show that this technique clearly distinguishes between rust pathogens and their respective host plant tissues. CONCLUSIONS This ISH protocol is applicable to rust fungi and potentially other plant pathogenic fungi as well. It has been shown here that this protocol can be applied to pathogens from different genera of rust fungi with no background staining of plant tissue. We encourage the use of this protocol for the study of plant pathogenic fungi in paraffin embedded sections of host plant tissue.
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Affiliation(s)
- Mitchell A. Ellison
- Department of Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Michael B. McMahon
- USDA-ARS Foreign Disease-Weed Science Research Unit, Ft. Detrick, MD USA
| | - Morris R. Bonde
- USDA-ARS Foreign Disease-Weed Science Research Unit, Ft. Detrick, MD USA
| | | | - Douglas G. Luster
- USDA-ARS Foreign Disease-Weed Science Research Unit, Ft. Detrick, MD USA
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Glassner H, Zchori-Fein E, Compant S, Sessitsch A, Katzir N, Portnoy V, Yaron S. Characterization of endophytic bacteria from cucurbit fruits with potential benefits to agriculture in melons (Cucumis melo L.). FEMS Microbiol Ecol 2015; 91:fiv074. [PMID: 26183916 DOI: 10.1093/femsec/fiv074] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/09/2015] [Indexed: 11/14/2022] Open
Abstract
Endophytes are microorganisms that mainly colonize vegetative parts, but are also found in reproductive and disseminating organs, and may have beneficial characteristics. To identify microorganisms associated with the agriculturally important family, Cucurbitaceae, endophytes were initially determined in fruits of Cucumis melo Reticulatus Group 'Dulce' by a cultivation-independent approach based on fluorescence in situ hybridization using double labeling of oligonucleotide probes. Alpha-, Beta-, Gammaproteobacteria, Firmicutes and Actinobacteria were localized inside the fruits. Culturable bacteria were further isolated and identified from fruit tissues of 'Dulce', from fruits of other cultivated and wild-field-grown Cucurbitaceae, and from wild fruits growing under natural conditions. Low densities of culturable bacteria were detected in the investigated fruits, especially in four out of the five wild species, regardless of their growing environment. Substantial differences were observed between the wild and cultivated cucurbit taxa in regard to the number of colonized fruits as well as the type of endophytes. Bacillus was the most dominant genus of endophytes colonizing fruits of Cucurbitaceae. The antagonistic effects of isolated endophytes were assessed against cucurbit disease agents in dual-culture assays. Several bacterial isolates exhibited antagonistic properties against the tested plant pathogens. The identified bacteria may be useful for protecting plants not only in the field, but also for post-harvest.
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Affiliation(s)
- Hanoch Glassner
- Faculty of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa 32000, Israel ARO, Dept. of Entomology, Newe Ya'ar Research Center 30095, Israel
| | | | - Stéphane Compant
- AIT Austrian Institute of Technology GmbH, Department of Health & Environment, Bioresources Unit, Konrad-Lorenz-Strasse 24, A-3430, Tulln, Austria
| | - Angela Sessitsch
- AIT Austrian Institute of Technology GmbH, Department of Health & Environment, Bioresources Unit, Konrad-Lorenz-Strasse 24, A-3430, Tulln, Austria
| | - Nurit Katzir
- ARO, Agricultural Research Organization, Dept. of Vegetable Crops, Newe Ya'ar Research Center 30095, Israel
| | - Vitaly Portnoy
- ARO, Agricultural Research Organization, Dept. of Vegetable Crops, Newe Ya'ar Research Center 30095, Israel
| | - Sima Yaron
- Faculty of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa 32000, Israel
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23
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Dazzo F, Niccum B. Use of CMEIAS Image Analysis Software to Accurately Compute Attributes of Cell Size, Morphology, Spatial Aggregation and Color Segmentation that Signify in Situ Ecophysiological Adaptations in Microbial Biofilm Communities. Computation 2015; 3:72-98. [DOI: 10.3390/computation3010072] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Hou X, McMillan M, Coumans JVF, Poljak A, Raftery MJ, Pereg L. Cellular responses during morphological transformation in Azospirillum brasilense and Its flcA knockout mutant. PLoS One 2014; 9:e114435. [PMID: 25502569 PMCID: PMC4264754 DOI: 10.1371/journal.pone.0114435] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 11/10/2014] [Indexed: 01/25/2023] Open
Abstract
FlcA is a response regulator controlling flocculation and the morphological transformation of Azospirillum cells from vegetative to cyst-like forms. To understand the cellular responses of Azospirillum to conditions that cause morphological transformation, proteins differentially expressed under flocculation conditions in A. brasilense Sp7 and its flcA knockout mutant were investigated. Comparison of 2-DE protein profiles of wild-type (Sp7) and a flcA deletion mutant (Sp7-flcAΔ) revealed a total of 33 differentially expressed 2-DE gel spots, with 22 of these spots confidently separated to allow protein identification. Analysis of these spots by liquid chromatography-tandem mass spectrometry (LC-MS/MS) and MASCOT database searching identified 48 proteins (≥10% emPAI in each spot). The functional characteristics of these proteins included carbon metabolism (beta-ketothiolase and citrate synthase), nitrogen metabolism (Glutamine synthetase and nitric oxide synthase), stress tolerance (superoxide dismutase, Alkyl hydroperoxidase and ATP-dependent Clp protease proteolytic subunit) and morphological transformation (transducer coupling protein). The observed differences between Sp7 wild-type and flcA− strains enhance our understanding of the morphological transformation process and help to explain previous phenotypical observations. This work is a step forward in connecting the Azospirillum phenome and genome.
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Affiliation(s)
- Xingsheng Hou
- School of Science and Technology, University of New England, Armidale, New South Wales, Australia
- Department of Microbiology and Immunology, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Mary McMillan
- School of Science and Technology, University of New England, Armidale, New South Wales, Australia
| | - Joëlle V. F. Coumans
- School of Science and Technology, University of New England, Armidale, New South Wales, Australia
- School of Rural Medicine, University of New England, Armidale, New South Wales, Australia
| | - Anne Poljak
- Bioanalytical Mass Spectrometry Facility, Analytical Centre, University of New South Wales, Sydney, New South Wales, Australia
- The School of Medical Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Mark J. Raftery
- Bioanalytical Mass Spectrometry Facility, Analytical Centre, University of New South Wales, Sydney, New South Wales, Australia
| | - Lily Pereg
- School of Science and Technology, University of New England, Armidale, New South Wales, Australia
- * E-mail: mailto:
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25
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Farrar K, Bryant D, Cope-Selby N. Understanding and engineering beneficial plant-microbe interactions: plant growth promotion in energy crops. Plant Biotechnol J 2014; 12:1193-206. [PMID: 25431199 PMCID: PMC4265282 DOI: 10.1111/pbi.12279] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 08/22/2014] [Accepted: 10/09/2014] [Indexed: 05/16/2023]
Abstract
Plant production systems globally must be optimized to produce stable high yields from limited land under changing and variable climates. Demands for food, animal feed, and feedstocks for bioenergy and biorefining applications, are increasing with population growth, urbanization and affluence. Low-input, sustainable, alternatives to petrochemical-derived fertilizers and pesticides are required to reduce input costs and maintain or increase yields, with potential biological solutions having an important role to play. In contrast to crops that have been bred for food, many bioenergy crops are largely undomesticated, and so there is an opportunity to harness beneficial plant-microbe relationships which may have been inadvertently lost through intensive crop breeding. Plant-microbe interactions span a wide range of relationships in which one or both of the organisms may have a beneficial, neutral or negative effect on the other partner. A relatively small number of beneficial plant-microbe interactions are well understood and already exploited; however, others remain understudied and represent an untapped reservoir for optimizing plant production. There may be near-term applications for bacterial strains as microbial biopesticides and biofertilizers to increase biomass yield from energy crops grown on land unsuitable for food production. Longer term aims involve the design of synthetic genetic circuits within and between the host and microbes to optimize plant production. A highly exciting prospect is that endosymbionts comprise a unique resource of reduced complexity microbial genomes with adaptive traits of great interest for a wide variety of applications.
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Affiliation(s)
- Kerrie Farrar
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth UniversityAberystwyth, UK
- *Correspondence (Tel +0044 (0)1970 823097; fax 0044 (0)1970 828357; email )
| | - David Bryant
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth UniversityAberystwyth, UK
| | - Naomi Cope-Selby
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth UniversityAberystwyth, UK
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Thiebaut F, Rojas CA, Grativol C, Motta MR, Vieira T, Regulski M, Martienssen RA, Farinelli L, Hemerly AS, Ferreira PCG. Genome-wide identification of microRNA and siRNA responsive to endophytic beneficial diazotrophic bacteria in maize. BMC Genomics 2014; 15:766. [PMID: 25194793 PMCID: PMC4168055 DOI: 10.1186/1471-2164-15-766] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Accepted: 08/22/2014] [Indexed: 11/10/2022] Open
Abstract
Background Small RNA (sRNA) has been described as a regulator of gene expression. In order to understand the role of maize sRNA (Zea mays – hybrid UENF 506-8) during association with endophytic nitrogen-fixing bacteria, we analyzed the sRNA regulated by its association with two diazotrophic bacteria, Herbaspirillum seropedicae and Azospirillum brasilense. Results Deep sequencing analysis was done with RNA extracted from plants inoculated with H. seropedicae, allowing the identification of miRNA and siRNA. A total of 25 conserved miRNA families and 15 novel miRNAs were identified. A dynamic regulation in response to inoculation was also observed. A hypothetical model involving copper-miRNA is proposed, emphasizing the fact that the up-regulation of miR397, miR398, miR408 and miR528, which is followed by inhibition of their targets, can facilitate association with diazotrophic bacteria. Similar expression patterns were observed in samples inoculated with A. brasilense. Moreover, novel miRNA and siRNA were classified in the Transposable Elements (TE) database, and an enrichment of siRNA aligned with TE was observed in the inoculated samples. In addition, an increase in 24-nt siRNA mapping to genes was observed, which was correlated with an increase in methylation of the coding regions and a subsequent reduction in transcription. Conclusion Our results show that maize has RNA-based silencing mechanisms that can trigger specific responses when plants interact with beneficial endophytic diazotrophic bacteria. Our findings suggest important roles for sRNA regulation in maize, and probably in other plants, during association with diazotrophic bacteria, emphasizing the up-regulation of Cu-miRNA. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-766) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Paulo C G Ferreira
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Cidade Universitária, Avenida Carlos Chagas Filho, 373, CCS, Bl,L-29ss, Rio de Janeiro RJ 21941-599, Brazil.
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Niranjana SR, Hariprasad P. Understanding the Mechanism Involved in PGPR-Mediated Growth Promotion and Suppression of Biotic and Abiotic Stress in Plants. Fungal Biol 2014. [DOI: 10.1007/978-1-4939-1188-2_3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Abstract
Microbial bioaggregates and biofilms are hydrated three-dimensional structures of cells and extracellular polymeric substances (EPS). Microbial communities associated with interfaces and the samples thereof may come from natural, technical, and medical habitats. For imaging such complex microbial communities confocal laser scanning microscopy (CLSM) is the method of choice. CLSM allows flexible mounting and noninvasive three-dimensional sectioning of hydrated, living, as well as fixed samples. For this purpose a broad range of objective lenses is available having different working distance and resolution. By means of CLSM the signals detected may originate from reflection, autofluorescence, reporter genes/fluorescence proteins, fluorochromes binding to specific targets, or other probes conjugated with fluorochromes. Recorded datasets can be used not only for visualization but also for semiquantitative analysis. As a result CLSM represents a very useful tool for imaging of microbiological samples in combination with other analytical techniques.
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Affiliation(s)
- Thomas R Neu
- Department of River Ecology, Helmholtz Centre for Environmental Research-UFZ, Brueckstrasse 3a, 39114, Magdeburg, Germany,
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Kurzbaum E, Kirzhner F, Armon R. A hydroponic system for growing gnotobiotic vs. sterile plants to study phytoremediation processes. Int J Phytoremediation 2014; 16:267-274. [PMID: 24912223 DOI: 10.1080/15226514.2013.773278] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
In some phytoremediation studies it is desirable to separate and define the specific contribution of plants and root-colonizing bacteria towards contaminant removal. Separating the influence of plants and associated bacteria is a difficult task for soil root environments. Growing plants hydroponically provides more control over the biological factors in contaminant removal. In this study, a hydroponic system was designed to evaluate the role of sterile plant roots, rhizodeposition, and root-associated bacteria in the removal of a model contaminant, phenol. A strain of Pseudomonas pseudoalcaligenes that grows on phenol was inoculated onto plant roots. The introduced biofilm persisted in the root zone and promoted phenol removal over non-augmented controls. These findings indicate that this hydroponic system can be a valuable tool for phytoremediation studies that investigate the effects of biotic and abiotic factors on pollution remediation.
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Schmidt H, Eickhorst T. Detection and quantification of native microbial populations on soil-grown rice roots by catalyzed reporter deposition-fluorescencein situhybridization. FEMS Microbiol Ecol 2013; 87:390-402. [DOI: 10.1111/1574-6941.12232] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Revised: 08/08/2013] [Accepted: 09/21/2013] [Indexed: 02/05/2023] Open
Affiliation(s)
- Hannes Schmidt
- Soil Microbial Ecology; University of Bremen; Bremen Germany
| | - Thilo Eickhorst
- Soil Microbial Ecology; University of Bremen; Bremen Germany
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Madhaiyan M, Peng N, Te NS, Hsin I C, Lin C, Lin F, Reddy C, Yan H, Ji L. Improvement of plant growth and seed yield in Jatropha curcas by a novel nitrogen-fixing root associated Enterobacter species. Biotechnol Biofuels 2013; 6:140. [PMID: 24083555 PMCID: PMC3879406 DOI: 10.1186/1754-6834-6-140] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Accepted: 09/26/2013] [Indexed: 05/13/2023]
Abstract
BACKGROUND Jatropha curcas L. is an oil seed producing non-leguminous tropical shrub that has good potential to be a fuel plant that can be cultivated on marginal land. Due to the low nutrient content of the targeted plantation area, the requirement for fertilizer is expected to be higher than other plants. This factor severely affects the commercial viability of J. curcas. RESULTS We explored the feasibility to use endophytic nitrogen-fixing bacteria that are native to J. curcas to improve plant growth, biomass and seed productivity. We demonstrated that a novel N-fixing endophyte, Enterobacter sp. R4-368, was able to colonize in root and stem tissues and significantly promoted early plant growth and seed productivity of J. curcas in sterilized and non-sterilized soil. Inoculation of young seedling led to an approximately 57.2% increase in seedling vigour over a six week period. At 90 days after planting, inoculated plants showed an average increase of 25.3%, 77.7%, 27.5%, 45.8% in plant height, leaf number, chlorophyll content and stem volume, respectively. Notably, inoculation of the strain led to a 49.0% increase in the average seed number per plant and 20% increase in the average single seed weight when plants were maintained for 1.5 years in non-sterilized soil in pots in the open air. Enterobacter sp. R4-368 cells were able to colonize root tissues and moved systemically to stem tissues. However, no bacteria were found in leaves. Promotion of plant growth and leaf nitrogen content by the strain was partially lost in nifH, nifD, nifK knockout mutants, suggesting the presence of other growth promoting factors that are associated with this bacterium strain. CONCLUSION Our results showed that Enterobacter sp. R4-368 significantly promoted growth and seed yield of J. curcas. The application of the strains is likely to significantly improve the commercial viability of J. curcas due to the reduced fertilizer cost and improved oil yield.
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Affiliation(s)
- Munusamy Madhaiyan
- Biomaterials and Biocatalysts Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Republic of Singapore
| | - Ni Peng
- Biomaterials and Biocatalysts Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Republic of Singapore
| | - Ngoh Si Te
- Biomaterials and Biocatalysts Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Republic of Singapore
| | - Cheng Hsin I
- Biomaterials and Biocatalysts Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Republic of Singapore
| | - Cai Lin
- Biomaterials and Biocatalysts Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Republic of Singapore
| | - Fu Lin
- Biomaterials and Biocatalysts Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Republic of Singapore
| | - Chalapathy Reddy
- Joil Pte Ltd, 1 Research Link National University of Singapore, Singapore 117604, Republic of Singapore
| | - Hong Yan
- Joil Pte Ltd, 1 Research Link National University of Singapore, Singapore 117604, Republic of Singapore
| | - Lianghui Ji
- Biomaterials and Biocatalysts Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Republic of Singapore
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Sigida EN, Fedonenko YP, Shashkov AS, Zdorovenko EL, Konnova SA, Ignatov VV, Knirel YA. Structural studies of the O-specific polysaccharide(s) from the lipopolysaccharide of Azospirillum brasilense type strain Sp7. Carbohydr Res 2013; 380:76-80. [DOI: 10.1016/j.carres.2013.07.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Revised: 07/25/2013] [Accepted: 07/27/2013] [Indexed: 12/20/2022]
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Serrato RV, Meneses CHSG, Vidal MS, Santana-Filho AP, Iacomini M, Sassaki GL, Baldani JI. Structural studies of an exopolysaccharide produced by Gluconacetobacter diazotrophicus Pal5. Carbohydr Polym 2013; 98:1153-9. [PMID: 23987457 DOI: 10.1016/j.carbpol.2013.07.025] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Revised: 06/27/2013] [Accepted: 07/09/2013] [Indexed: 11/15/2022]
Abstract
Gluconacetobacter diazotrophicus is a nitrogen-fixing bacterium that has been found colonizing several plants. This acid-tolerant bacterium produces phytohormones that promote plant growth and is also able to grow in high-sugar concentrations. It has been demonstrated that exopolysaccharides (EPS), which are produced by strain Pal5 of G. diazotrophicus, play an important role in plant infection. We have investigated the structure of the EPS, which was produced by a strain of Pal5 grown in liquid medium containing mannitol as the sole carbon source. The results reveal an EPS with Glc, Gal, Man in a molar ratio of 6:3:1, respectively. NMR spectroscopy and chemical derivatization have revealed that the EPS structure has 4-O-substituted units of β-glucose, 3-O-substituted units of β-galactose and 2-O-substituted units of α-mannose. Glucose and galactose units linked at C6 were also found. The structure proposed herein is different from EPS produced by other species of Gluconacetobacter published to date.
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Affiliation(s)
- Rodrigo V Serrato
- Setor Litoral, Universidade Federal do Paraná - UFPR, Rua Jaguariaíva 512, 83260-000 Matinhos, PR, Brazil.
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Straub D, Rothballer M, Hartmann A, Ludewig U. The genome of the endophytic bacterium H. frisingense GSF30(T) identifies diverse strategies in the Herbaspirillum genus to interact with plants. Front Microbiol 2013; 4:168. [PMID: 23825472 PMCID: PMC3695564 DOI: 10.3389/fmicb.2013.00168] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 06/03/2013] [Indexed: 01/14/2023] Open
Abstract
The diazotrophic, bacterial endophyte Herbaspirillum frisingense GSF30T has been identified in biomass grasses grown in temperate climate, including the highly nitrogen-efficient grass Miscanthus. Its genome was annotated and compared with related Herbaspirillum species from diverse habitats, including H. seropedicae, and further well-characterized endophytes. The analysis revealed that Herbaspirillum frisingense lacks a type III secretion system that is present in some related Herbaspirillum grass endophytes. Together with the lack of components of the type II secretion system, the genomic inventory indicates distinct interaction scenarios of endophytic Herbaspirillum strains with plants. Differences in respiration, carbon, nitrogen and cell wall metabolism among Herbaspirillum isolates partially correlate with their different habitats. Herbaspirillum frisingense is closely related to strains isolated from the rhizosphere of phragmites and from well water, but these lack nitrogen fixation and metabolism genes. Within grass endophytes, the high diversity in their genomic inventory suggests that even individual plant species provide distinct, highly diverse metabolic niches for successful endophyte-plant associations.
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Affiliation(s)
- Daniel Straub
- Institut für Kulturpflanzenwissenschaften, Ernährungsphysiologie der Kulturpflanzen (340h), Universität Hohenheim Stuttgart, Germany
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Weerasekara ML, Ryuda N, Miyamoto H, Okumura T, Ueno D, Inoue K, Someya T. Double-color fluorescence in situ hybridization (FISH) for the detection of Bacillus anthracis spores in environmental samples with a novel permeabilization protocol. J Microbiol Methods 2013; 93:177-84. [PMID: 23523967 DOI: 10.1016/j.mimet.2013.03.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2013] [Revised: 03/10/2013] [Accepted: 03/10/2013] [Indexed: 11/22/2022]
Abstract
For anti-bioterrorism measures against the use of Bacillus anthracis, a double-color fluorescence in situ hybridization (FISH) is proposed, for the rapid and specific detection of B. anthracis. The probes were designed based on the differences in 16S and 23S rRNA genes of B. cereus group. A new permeabilization protocol was developed to enhance the permeability of FISH probes into B. anthracis spores. The highest detection rate (90.8 ± 0.69) of B. anthracis spores by FISH was obtained with successive incubation steps with 50% ethanol at 80 °C, a mixture of SDS/DTT solution (10mg/ml SDS, 50mM DTT) at 65 °C and finally in a lysozyme solution (20mg/ml) at 37 °C for 30 min each. This protocol was evaluated for the detection of B. anthracis spores in soil and air samples after adding formalin-fixed spores at different densities. The results have proven the success of double-color FISH in detecting B. anthracis spores in air samples in the range of 10(3) spores/m(3) and above. Conversely, for detecting B. anthracis spores in a soil sample, the lowest detection limit was found to be 10(7) spores/g dry soils. These results confirm the applicability of the developed permeabilization protocol, combined with the double-color FISH technique in specific detection of B. anthracis in soil and air samples.
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Wisniewski-Dyé F, Lozano L, Acosta-Cruz E, Borland S, Drogue B, Prigent-Combaret C, Rouy Z, Barbe V, Herrera AM, González V, Mavingui P. Genome Sequence of Azospirillum brasilense CBG497 and Comparative Analyses of Azospirillum Core and Accessory Genomes provide Insight into Niche Adaptation. Genes (Basel) 2012; 3:576-602. [PMID: 24705077 PMCID: PMC3899980 DOI: 10.3390/genes3040576] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Revised: 08/24/2012] [Accepted: 09/13/2012] [Indexed: 11/29/2022] Open
Abstract
Bacteria of the genus Azospirillum colonize roots of important cereals and grasses, and promote plant growth by several mechanisms, notably phytohormone synthesis. The genomes of several Azospirillum strains belonging to different species, isolated from various host plants and locations, were recently sequenced and published. In this study, an additional genome of an A. brasilense strain, isolated from maize grown on an alkaline soil in the northeast of Mexico, strain CBG497, was obtained. Comparative genomic analyses were performed on this new genome and three other genomes (A. brasilense Sp245, A. lipoferum 4B and Azospirillum sp. B510). The Azospirillum core genome was established and consists of 2,328 proteins, representing between 30% to 38% of the total encoded proteins within a genome. It is mainly chromosomally-encoded and contains 74% of genes of ancestral origin shared with some aquatic relatives. The non-ancestral part of the core genome is enriched in genes involved in signal transduction, in transport and in metabolism of carbohydrates and amino-acids, and in surface properties features linked to adaptation in fluctuating environments, such as soil and rhizosphere. Many genes involved in colonization of plant roots, plant-growth promotion (such as those involved in phytohormone biosynthesis), and properties involved in rhizosphere adaptation (such as catabolism of phenolic compounds, uptake of iron) are restricted to a particular strain and/or species, strongly suggesting niche-specific adaptation.
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Affiliation(s)
- Florence Wisniewski-Dyé
- Université de Lyon, UMR 5557 CNRS, USC 1193 INRA, VetAgro Sup Ecologie Microbienne, Villeurbanne 69622, France.
| | - Luis Lozano
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, AP565-A Cuernavaca, Morelos 62210, México.
| | - Erika Acosta-Cruz
- Université de Lyon, UMR 5557 CNRS, USC 1193 INRA, VetAgro Sup Ecologie Microbienne, Villeurbanne 69622, France.
| | - Stéphanie Borland
- Université de Lyon, UMR 5557 CNRS, USC 1193 INRA, VetAgro Sup Ecologie Microbienne, Villeurbanne 69622, France.
| | - Benoît Drogue
- Université de Lyon, UMR 5557 CNRS, USC 1193 INRA, VetAgro Sup Ecologie Microbienne, Villeurbanne 69622, France.
| | - Claire Prigent-Combaret
- Université de Lyon, UMR 5557 CNRS, USC 1193 INRA, VetAgro Sup Ecologie Microbienne, Villeurbanne 69622, France.
| | - Zoé Rouy
- Laboratoire d'Analyse Bioinformatique en Génomique et Métabolisme CNRS UMR8030, France.
| | - Valérie Barbe
- Institut de Génomique, CEA, Génoscope, 2 rue Gaston Crémieux, 91057 Evry, France.
| | - Alberto Mendoza Herrera
- Centro de Biotecnología Genómica, Instituto politécnico Nacional, 88710 Reynosa, Tamaulipas, México.
| | - Victor González
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, AP565-A Cuernavaca, Morelos 62210, México.
| | - Patrick Mavingui
- Université de Lyon, UMR 5557 CNRS, USC 1193 INRA, VetAgro Sup Ecologie Microbienne, Villeurbanne 69622, France.
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Schmidt H, Eickhorst T, Tippkötter R. Evaluation of tyramide solutions for an improved detection and enumeration of single microbial cells in soil by CARD-FISH. J Microbiol Methods 2012; 91:399-405. [PMID: 23022442 DOI: 10.1016/j.mimet.2012.09.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Revised: 09/17/2012] [Accepted: 09/17/2012] [Indexed: 11/28/2022]
Abstract
Several tyramide solutions were evaluated for the application of fluorescence in situ hybridization with catalyzed reporter deposition (CARD-FISH) in soil. Fluorescently labeled tyramide solutions were synthesized and compared to commercially available tyramides for the detection and quantification of single microbial cells. Among the tyramide solutions tested, a succinimidyl ester of fluorescein diluted with dimethylformamide containing iodophenolboronic acid (SFX-DMF-IPBA) gave the best results, yielding highly reproducible cell numbers and detection rates of archaea and bacteria along with negligible non-specific signals. The addition of organic and inorganic compounds to the amplification reagents had a positive impact on the detection of prokaryotic cells. The applicability of SFX-DMF-IPBA for CARD-FISH in soil was further evaluated in soils of different texture. Cell numbers and detection rates of bacteria and archaea remained on a high level independent of the clay or organic matter content. Based on the results obtained in this study, the choice of the tyramide solution used for CARD-FISH has a significant influence on the detection and quantification of single microbial cells in soil. Therefore, we suggest the application of the presented tyramide signal amplification procedure including the tyramide solution SFX-DMF-IPBA for comprehensive CARD-FISH studies investigating the abundance and spatial distribution of soil microorganisms.
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Wisniewski-Dyé F, Borziak K, Khalsa-Moyers G, Alexandre G, Sukharnikov LO, Wuichet K, Hurst GB, McDonald WH, Robertson JS, Barbe V, Calteau A, Rouy Z, Mangenot S, Prigent-Combaret C, Normand P, Boyer M, Siguier P, Dessaux Y, Elmerich C, Condemine G, Krishnen G, Kennedy I, Paterson AH, González V, Mavingui P, Zhulin IB. Azospirillum genomes reveal transition of bacteria from aquatic to terrestrial environments. PLoS Genet 2011; 7:e1002430. [PMID: 22216014 DOI: 10.1371/journal.pgen.1002430] [Citation(s) in RCA: 124] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2011] [Accepted: 11/02/2011] [Indexed: 12/20/2022] Open
Abstract
Fossil records indicate that life appeared in marine environments ∼3.5 billion years ago (Gyr) and transitioned to terrestrial ecosystems nearly 2.5 Gyr. Sequence analysis suggests that “hydrobacteria” and “terrabacteria” might have diverged as early as 3 Gyr. Bacteria of the genus Azospirillum are associated with roots of terrestrial plants; however, virtually all their close relatives are aquatic. We obtained genome sequences of two Azospirillum species and analyzed their gene origins. While most Azospirillum house-keeping genes have orthologs in its close aquatic relatives, this lineage has obtained nearly half of its genome from terrestrial organisms. The majority of genes encoding functions critical for association with plants are among horizontally transferred genes. Our results show that transition of some aquatic bacteria to terrestrial habitats occurred much later than the suggested initial divergence of hydro- and terrabacterial clades. The birth of the genus Azospirillum approximately coincided with the emergence of vascular plants on land. Genome sequencing and analysis of plant-associated beneficial soil bacteria Azospirillum spp. reveals that these organisms transitioned from aquatic to terrestrial environments significantly later than the suggested major Precambrian divergence of aquatic and terrestrial bacteria. Separation of Azospirillum from their close aquatic relatives coincided with the emergence of vascular plants on land. Nearly half of the Azospirillum genome has been acquired horizontally, from distantly related terrestrial bacteria. The majority of horizontally acquired genes encode functions that are critical for adaptation to the rhizosphere and interaction with host plants.
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Meneses CHSG, Rouws LFM, Simoes-Araujo JL, Vidal MS, Baldani JI. Exopolysaccharide production is required for biofilm formation and plant colonization by the nitrogen-fixing endophyte Gluconacetobacter diazotrophicus. Mol Plant Microbe Interact 2011; 24:1448-1458. [PMID: 21809982 DOI: 10.1094/mpmi-05-11-0127] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The genome of the endophytic diazotrophic bacterial species Gluconacetobacter diazotrophicus PAL5 (PAL5) revealed the presence of a gum gene cluster. In this study, the gumD gene homologue, which is predicted to be responsible for the first step in exopolysaccharide (EPS) production, was insertionally inactivated and the resultant mutant (MGD) was functionally studied. The mutant MGD presented normal growth and nitrogen (N(2)) fixation levels but did not produce EPS when grown on different carbon sources. MGD presented altered colony morphology on soft agar plates (0.3% agar) and was defective in biofilm formation on glass wool. Most interestingly, MGD was defective in rice root surface attachment and in root surface and endophytic colonization. Genetic complementation reverted all mutant phenotypes. Also, the addition of EPS purified from culture supernatants of the wild-type strain PAL5 to the mutant MGD was effective in partially restoring wild-type biofilm formation and plant colonization. These data provide strong evidence that the PAL5 gumD gene is involved in EPS biosynthesis and that EPS biosynthesis is required for biofilm formation and plant colonization. To our knowledge, this is the first report of a role of EPS in the endophytic colonization of graminaceous plants by a nitrogen-fixing bacterium.
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de-Bashan LE, Schmid M, Rothballer M, Hartmann A, Bashan Y. CELL-CELL INTERACTION IN THE EUKARYOTE-PROKARYOTE MODEL OF THE MICROALGAE CHLORELLA VULGARIS AND THE BACTERIUM AZOSPIRILLUM BRASILENSE IMMOBILIZED IN POLYMER BEADS(1). J Phycol 2011; 47:1350-9. [PMID: 27020359 DOI: 10.1111/j.1529-8817.2011.01062.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Cell-cell interaction in the eukaryote-prokaryote model of the unicellular, freshwater microalga Chlorella vulgaris Beij. and the plant growth-promoting bacterium Azospirillum brasilense, when jointly immobilized in small polymer alginate beads, was evaluated by quantitative fluorescence in situ hybridization (FISH) combined with SEM. This step revealed significant changes, with an increase in the populations of both partners, cluster (mixed colonies) mode of colonization of the bead by the two microorganisms, increase in the size of microalgae-bacterial clusters, movement of the motile bacteria cells toward the immotile microalgae cells within solid matrix, and formation of firm structures among the bacteria, microalgae cells, and the inert matrix that creates a biofilm. This biofilm was sufficiently strong to keep the two species attached to each other, even after eliminating the alginate support. This study showed that the common structural phenotypic interaction of Azospirillum with roots of higher plants, via fibrils and sheath material, is also formed and maintained during the interaction of this bacterium with the surface of rootless single-cell microalgae.
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Affiliation(s)
- Luz E de-Bashan
- Environmental Microbiology Group, Northwestern Center for Biological Research (CIBNOR), Mar Bermejo 195, Col. Playa Palo de Santa Rita, La Paz, B.C.S. 23090, Mexico The Bashan Foundation, 3740 NW Harrison Blvd., Corvallis, Oregon 97330, USAHelmholtz Zentrum München, German Research Centre for Environmental Health, Department of Microbe-Plant Interactions, Ingolstaedter Landstrasse 1, D-85764 Neuherberg, Germany Environmental Microbiology Group, Northwestern Center for Biological Research (CIBNOR), Mar Bermejo 195, Col. Playa Palo de Santa Rita, La Paz, B.C.S. 23090, Mexico The Bashan Foundation, 3740 NW Harrison Blvd., Corvallis, Oregon 97330, USA
| | - Michael Schmid
- Environmental Microbiology Group, Northwestern Center for Biological Research (CIBNOR), Mar Bermejo 195, Col. Playa Palo de Santa Rita, La Paz, B.C.S. 23090, Mexico The Bashan Foundation, 3740 NW Harrison Blvd., Corvallis, Oregon 97330, USAHelmholtz Zentrum München, German Research Centre for Environmental Health, Department of Microbe-Plant Interactions, Ingolstaedter Landstrasse 1, D-85764 Neuherberg, Germany Environmental Microbiology Group, Northwestern Center for Biological Research (CIBNOR), Mar Bermejo 195, Col. Playa Palo de Santa Rita, La Paz, B.C.S. 23090, Mexico The Bashan Foundation, 3740 NW Harrison Blvd., Corvallis, Oregon 97330, USA
| | - Michael Rothballer
- Environmental Microbiology Group, Northwestern Center for Biological Research (CIBNOR), Mar Bermejo 195, Col. Playa Palo de Santa Rita, La Paz, B.C.S. 23090, Mexico The Bashan Foundation, 3740 NW Harrison Blvd., Corvallis, Oregon 97330, USAHelmholtz Zentrum München, German Research Centre for Environmental Health, Department of Microbe-Plant Interactions, Ingolstaedter Landstrasse 1, D-85764 Neuherberg, Germany Environmental Microbiology Group, Northwestern Center for Biological Research (CIBNOR), Mar Bermejo 195, Col. Playa Palo de Santa Rita, La Paz, B.C.S. 23090, Mexico The Bashan Foundation, 3740 NW Harrison Blvd., Corvallis, Oregon 97330, USA
| | - Anton Hartmann
- Environmental Microbiology Group, Northwestern Center for Biological Research (CIBNOR), Mar Bermejo 195, Col. Playa Palo de Santa Rita, La Paz, B.C.S. 23090, Mexico The Bashan Foundation, 3740 NW Harrison Blvd., Corvallis, Oregon 97330, USAHelmholtz Zentrum München, German Research Centre for Environmental Health, Department of Microbe-Plant Interactions, Ingolstaedter Landstrasse 1, D-85764 Neuherberg, Germany Environmental Microbiology Group, Northwestern Center for Biological Research (CIBNOR), Mar Bermejo 195, Col. Playa Palo de Santa Rita, La Paz, B.C.S. 23090, Mexico The Bashan Foundation, 3740 NW Harrison Blvd., Corvallis, Oregon 97330, USA
| | - Yoav Bashan
- Environmental Microbiology Group, Northwestern Center for Biological Research (CIBNOR), Mar Bermejo 195, Col. Playa Palo de Santa Rita, La Paz, B.C.S. 23090, Mexico The Bashan Foundation, 3740 NW Harrison Blvd., Corvallis, Oregon 97330, USAHelmholtz Zentrum München, German Research Centre for Environmental Health, Department of Microbe-Plant Interactions, Ingolstaedter Landstrasse 1, D-85764 Neuherberg, Germany Environmental Microbiology Group, Northwestern Center for Biological Research (CIBNOR), Mar Bermejo 195, Col. Playa Palo de Santa Rita, La Paz, B.C.S. 23090, Mexico The Bashan Foundation, 3740 NW Harrison Blvd., Corvallis, Oregon 97330, USA
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Covarrubias SA, de-Bashan LE, Moreno M, Bashan Y. Alginate beads provide a beneficial physical barrier against native microorganisms in wastewater treated with immobilized bacteria and microalgae. Appl Microbiol Biotechnol 2011; 93:2669-80. [DOI: 10.1007/s00253-011-3585-8] [Citation(s) in RCA: 150] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Revised: 08/19/2011] [Accepted: 09/15/2011] [Indexed: 11/28/2022]
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Affiliation(s)
| | | | - Martin Kratzmeier
- Liquid Phase Analysis Division, Agilent Technologies, Hewlett-Packard-Strasse 8, 76337 Waldbronn, Germany
| | - Ewa M. Goldys
- Macquarie University, North Ryde 2109 NSW, Australia
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de-Bashan LE, Hernandez JP, Bashan Y, Maier R. Bacillus pumilus ES4: candidate plant growth-promoting bacterium to enhance establishment of plants in mine tailings. Environ Exp Bot 2010; 69:343-352. [PMID: 25009362 PMCID: PMC4084739 DOI: 10.1016/j.envexpbot.2010.04.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Three plant growth-promoting bacteria (PGPB; Bacillus pumilus ES4, B. pumilus RIZO1, and Azospirillum brasilense Cd) were tested for their ability to enhance plant growth and development of the native Sonoran Desert shrub quailbush (Atriplex lentiformis) and for their effect on the native bacterial community in moderately acidic, high-metal content (AHMT) and in neutral, low metal content natural tailings (NLMT) in controlled greenhouse experiments. Inoculation of quailbush with all three PGPB significantly enhanced plant growth parameters, such as germination, root length, dry weight of shoots and roots, and root/shoot ratio in both types of tailings. The effect of inoculation on the indigenous bacterial community by the most successful PGPB Bacillus pumilus ES4 was evaluated by denaturating gradient gel electrophoresis (PCR-DGGE) fingerprinting and root colonization was followed by specific fluorescent in situ hybridization (FISH). Inoculation with this strain significantly changed the bacterial community over a period of 60 days. FISH analysis showed that the preferred site of colonization was the root tips and root elongation area. This study shows that inoculation of native perennial plants with PGPB can be used for developing technologies for phytostabilizing mine tailings.
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Affiliation(s)
- Luz E. de-Bashan
- Department of Soil, Water and Environmental Science, University of Arizona, Tucson, Arizona, USA
- Environmental Microbiology Group, Northwestern Center for Biological Research (CIBNOR), La Paz, B.C.S., Mexico
| | - Juan-Pablo Hernandez
- Environmental Microbiology Group, Northwestern Center for Biological Research (CIBNOR), La Paz, B.C.S., Mexico
| | - Yoav Bashan
- Department of Soil, Water and Environmental Science, University of Arizona, Tucson, Arizona, USA
- Environmental Microbiology Group, Northwestern Center for Biological Research (CIBNOR), La Paz, B.C.S., Mexico
| | - Raina Maier
- Department of Soil, Water and Environmental Science, University of Arizona, Tucson, Arizona, USA
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Kurzbaum E, Kirzhner F, Sela S, Zimmels Y, Armon R. Efficiency of phenol biodegradation by planktonic Pseudomonas pseudoalcaligenes (a constructed wetland isolate) vs. root and gravel biofilm. Water Res 2010; 44:5021-5031. [PMID: 20705318 DOI: 10.1016/j.watres.2010.07.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2010] [Revised: 06/10/2010] [Accepted: 07/08/2010] [Indexed: 05/29/2023]
Abstract
In the last two decades, constructed wetland systems gained increasing interest in wastewater treatment and as such have been intensively studied around the world. While most of the studies showed excellent removal of various pollutants, the exact contribution, in kinetic terms, of its particular components (such as: root, gravel and water) combined with bacteria is almost nonexistent. In the present study, a phenol degrader bacterium identified as Pseudomonas pseudoalcaligenes was isolated from a constructed wetland, and used in an experimental set-up containing: plants and gravel. Phenol removal rate by planktonic and biofilm bacteria (on sterile Zea mays roots and gravel surfaces) was studied. Specific phenol removal rates revealed significant advantage of planktonic cells (1.04 × 10(-9) mg phenol/CFU/h) compared to root and gravel biofilms: 4.59 × 10(-11)-2.04 × 10(-10) and 8.04 × 10(-11)-4.39 × 10(-10) (mg phenol/CFU/h), respectively. In batch cultures, phenol biodegradation kinetic parameters were determined by biomass growth rates and phenol removal as a function of time. Based on Haldane equation, kinetic constants such as μ(max) = 1.15/h, K(s) = 35.4 mg/L and K(i) = 198.6 mg/L fit well phenol removal by P. pseudoalcaligenes. Although P. pseudoalcaligenes planktonic cells showed the highest phenol removal rate, in constructed wetland systems and especially in those with sub-surface flow, it is expected that surface associated microorganisms (biofilms) will provide a much higher contribution in phenol and other organics removal, due to greater bacterial biomass. Factors affecting the performance of planktonic vs. biofilm bacteria in sub-surface flow constructed wetlands are further discussed.
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Affiliation(s)
- Eyal Kurzbaum
- Faculty of Civil & Environmental Engineering, Division of Environmental, Water & Agricultural Engineering, Technion-Israel Institute of Technology, Haifa 32000, Israel
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Xiao CH, Tang H, Pu LJ, Sun DM, Ma JZ, Yu M, Duan RS. Diversity of nitrogenase (nifH) genes pool in soybean field soil after continuous and rotational cropping. J Basic Microbiol 2010; 50:373-9. [PMID: 20473958 DOI: 10.1002/jobm.200900317] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Diazotrophs diversity in soybean is a topic requiring thorough investigation since the previous researches have focused on only rice, forest, grass, water, etc. In this research, iron-only nitrogenase nifH gene was as genetic marker. PCR-RFLP was used to investigate the difference of diazotrophs community diversity in the soil from the continuous cropping (CC) (the 5-yr tilling of soybean) and the rotational cropping (RC) (soybean-corn) soils in the northeast of China. A total of 36 isolates were genetically characterized. Most of the isolates closely related to Azospirillum and Azotobacter. Eighty-six unique nifH gene sequences were obtained by cloning of the respective PCR products in two soil samples. It was found that the diversity of nifH genes in CC changed obviously compared with RC. Phylogenetic analysis indicated that most of the clones clustered together in a high homogeneity with some sequence retrieved from environmental representatives. The sequence diversity of nifH genes was high and the members of the Alphaproteobacteria were predominant in both samples. The experimental study also revealed the two non-proteobacterial diazotrophs, firmicutes and euryarchaeota. Through this study, it can be assumed that different tillage perhaps affected the nifH gene-containing population diversity.
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Affiliation(s)
- C H Xiao
- Subject of Physiology and Ecology, College of Life Science, Heilongjiang August First Land Reclamation University, Daqing, China
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Seneviratne G, Weerasekara MLMAW, Seneviratne KACN, Zavahir JS, Kecskés ML, Kennedy IR. Importance of Biofilm Formation in Plant Growth Promoting Rhizobacterial Action. Plant Growth and Health Promoting Bacteria 2010. [DOI: 10.1007/978-3-642-13612-2_4] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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Kurzbaum E, Zimmels Y, Armon R. Isolation of a Halotolerant Streptomyces sp. from a Constructed Wetland that Biodegrade Phenol and Various Biopolymers. ACTA ACUST UNITED AC 2010; 24:31-8. [DOI: 10.3209/saj.saj240201] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Rinaudi LV, González JE. The low-molecular-weight fraction of exopolysaccharide II from Sinorhizobium meliloti is a crucial determinant of biofilm formation. J Bacteriol 2009; 191:7216-24. [PMID: 19783627 DOI: 10.1128/JB.01063-09] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Sinorhizobium meliloti is a soil bacterium that elicits the formation of root organs called nodules on its host plant, Medicago sativa. Inside these structures, the bacteria are able to convert atmospheric nitrogen into ammonia, which is then used by the plant as a nitrogen source. The synthesis by S. meliloti of at least one exopolysaccharide, succinoglycan or EPS II, is essential for a successful symbiosis. While exopolysaccharide-deficient mutants induce the formation of nodules, they fail to invade them, and as a result, no nitrogen fixation occurs. Interestingly, the low-molecular-weight fractions of these exopolysaccharides are the symbiotically active forms, and it has been suggested that they act as signals to the host plant to initiate infection thread formation. In this work, we explored the role of these rhizobial exopolysaccharides in biofilm formation and their importance in the symbiotic relationship with the host. We showed that the ExpR/Sin quorum-sensing system controls biofilm formation in S. meliloti through the production of EPS II, which provides the matrix for the development of structured and highly organized biofilms. Moreover, the presence of the low-molecular-weight fraction of EPS II is vital for biofilm formation, both in vitro and in vivo. This is the first report where the symbiotically active fraction of EPS II is shown to be a critical factor for biofilm formation and root colonization. Thus, the ability of S. meliloti to properly attach to root surfaces and form biofilms conferred by the synthesis of exopolysaccharides may embody the main function of these symbiotically essential molecules.
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Mulyukin AL, Suzina NE, Pogorelova AY, Antonyuk LP, Duda VI, El-Registan GI. Diverse morphological types of dormant cells and conditions for their formation in Azospirillum brasilense. Microbiology (Reading) 2009. [DOI: 10.1134/s0026261709010056] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Iverson SL, Maier RM. Effects of compost on colonization of roots of plants grown in metalliferous mine tailings, as examined by fluorescence in situ hybridization. Appl Environ Microbiol 2009; 75:842-7. [PMID: 19047384 DOI: 10.1128/AEM.01434-08] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The relationship between compost amendment, plant biomass produced, and bacterial root colonization as measured by fluorescence in situ hybridization was examined following plant growth in mine tailings. Mine tailings can remain devoid of vegetation for decades after deposition due to a combination of factors that include heavy metal toxicity, low pH, poor substrate structure and water-holding capacity, and a severely impacted heterotrophic microbial community. Research has shown that plant establishment, a desired remedial objective to reduce eolian and water erosion of such tailings, is enhanced by organic matter amendment and is correlated with significant increases in rhizosphere populations of neutrophilic heterotrophic bacteria. Results show that for the acidic metalliferous tailings tested in this study, compost amendment was associated with significantly increased bacterial colonization of roots and increased production of plant biomass. In contrast, for a Vinton control soil, increased compost had no effect on root colonization and resulted only in increased plant biomass at high levels of compost amendment. These data suggest that the positive association between compost amendment and root colonization is important in the stressed mine tailings environment where root colonization may enhance both microbial and plant survival and growth.
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