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Knežević M, Berić T, Buntić A, Delić D, Nikolić I, Stanković S, Stajković-Srbinović O. Potential of root nodule nonrhizobial endophytic bacteria for growth promotion of Lotus corniculatus L. and Dactylis glomerata L. J Appl Microbiol 2021; 131:2929-2940. [PMID: 34003543 DOI: 10.1111/jam.15152] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 05/11/2021] [Accepted: 05/11/2021] [Indexed: 11/29/2022]
Abstract
AIMS This research aimed to isolate and characterize nonrhizobial endophytic bacteria from root nodules of Medicago sativa L. and Lotus corniculatus L. with plant growth-promoting characteristics and to test its activity in a pot experiment with acid soil. METHODS AND RESULTS Out of 44 nonrhizobial isolates, the majority exhibited indole-3-acetic acid (IAA) production; 29 produced siderophores, few isolates performed phosphate solubilization and/or produced lytic enzymes, while 30% of isolates showed notable antifungal activity. The most promising strains were identified as members of Bacillus, Pseudomonas and Serratia genera, based on 16S rRNA. Bacillus megaterium DZK1BH exhibited the overall best attributes for plant growth promotion and positively influenced the growth of L. corniculatus and Dactylis glomerata. CONCLUSIONS Root nodule endophytic B. megaterium DZK1BH could potentially be used as a biofertilizer for growing L. corniculatus L. and D. glomerata L. in acid soils, while Bacillus mojavensis L3 is a candidate for further antifungal potential investigation. SIGNIFICANCE OF IMPACT OF THE STUDY The use of root nodule endophytic bacteria with PGP traits may find its future application in organic agriculture, as their utilization could decrease the use of chemical fertilizers and pesticides and simultaneously promote plant growth, especially in soils with low production quality.
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Affiliation(s)
- M Knežević
- Department of Microbiology, Institute of Soil Science, Belgrade, Serbia
| | - T Berić
- Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - A Buntić
- Department of Microbiology, Institute of Soil Science, Belgrade, Serbia
| | - D Delić
- Department of Microbiology, Institute of Soil Science, Belgrade, Serbia
| | - I Nikolić
- Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - S Stanković
- Faculty of Biology, University of Belgrade, Belgrade, Serbia
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2
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Balázs HE, Schmid CAO, Cruzeiro C, Podar D, Szatmari PM, Buegger F, Hufnagel G, Radl V, Schröder P. Post-reclamation microbial diversity and functions in hexachlorocyclohexane (HCH) contaminated soil in relation to spontaneous HCH tolerant vegetation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 767:144653. [PMID: 33550064 DOI: 10.1016/j.scitotenv.2020.144653] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 11/24/2020] [Accepted: 12/16/2020] [Indexed: 06/12/2023]
Abstract
The toxicity, volatility and persistence of the obsolete organochlorine pesticide hexachlorocyclohexane (HCH), makes reclamation of contaminated areas a priority for the health and welfare of neighboring human communities. Microbial diversity and functions and their relation to spontaneous vegetation in post-excavation situations, are essential indicators to consider in bioaugmentation or microbe-assisted phytoremediation strategies at field scale. Our study aimed to evaluate the effects of long-term HCH contamination on soil and plant-associated microbial communities, and whether contaminated soil has the potential to act as a bacterial inoculum in post-excavation bioremediation strategies. To scrutinize the role of vegetation, the potential nitrogen fixation of free-living and symbiotic diazotrophs of the legume Lotus tenuis was assessed as a measure of nutrient cycling functions in soil under HCH contamination. Potential nitrogen fixation was generally not affected by HCH, with the exception of lower nifH gene counts in excavated contaminated rhizospheres, most probably a short-term HCH effect on early bacterial succession in this compartment. HCH shaped microbial communities in long-term contaminated bulk soil, where we identified possible HCH tolerants such as Sphingomonas and Altererythrobacter. In L. tenuis rhizosphere, microbial community composition was additionally influenced by plant growth stage. Sphingobium and Massilia were the bacterial genera characteristic for HCH contaminated rhizospheres. Long-term HCH contamination negatively affected L. tenuis growth and development. However, root-associated bacterial community composition was driven solely by plant age, with negligible HCH effect. Results showed that L. tenuis acquired possible HCH tolerant bacteria such as the Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium clade, Sphingomonas, Massilia or Pantoea which could simultaneously offer plant growth promoting (PGP) benefits for the host. Finally, we identified an inoculum with possibly HCH tolerant, PGP bacteria transferred from the contaminated bulk soil to L. tenuis roots through the rhizosphere compartment, consisting of Mesorhizobium loti, Neorhizobium galegae, Novosphingobium lindaniclasticum, Pantoea agglomerans and Lysobacter bugurensis.
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Affiliation(s)
- Helga E Balázs
- Helmholtz Zentrum München GmbH, Research Unit for Comparative Microbiome Analysis, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany; Babeş-Bolyai University, Department of Taxonomy and Ecology, 1 Kogălniceanu St., 400084 Cluj-Napoca, Romania
| | - Christoph A O Schmid
- Helmholtz Zentrum München GmbH, Research Unit for Comparative Microbiome Analysis, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Catarina Cruzeiro
- Helmholtz Zentrum München GmbH, Research Unit for Comparative Microbiome Analysis, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany.
| | - Dorina Podar
- Babeş-Bolyai University, Department of Molecular Biology and Biotechnology, 1 Kogălniceanu St., 400084 Cluj-Napoca, Romania.
| | - Paul-Marian Szatmari
- Babeş-Bolyai University, Department of Taxonomy and Ecology, 1 Kogălniceanu St., 400084 Cluj-Napoca, Romania; Biological Research Center, Botanical Garden "Vasile Fati", 16 Wesselényi Miklós St., 455200 Jibou, Romania
| | - Franz Buegger
- Helmholtz Zentrum München GmbH, Research Unit for Biochemical Plant Pathology, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany.
| | - Gudrun Hufnagel
- Helmholtz Zentrum München GmbH, Research Unit for Comparative Microbiome Analysis, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany.
| | - Viviane Radl
- Helmholtz Zentrum München GmbH, Research Unit for Comparative Microbiome Analysis, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany.
| | - Peter Schröder
- Helmholtz Zentrum München GmbH, Research Unit for Comparative Microbiome Analysis, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany.
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3
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Mukhtar A, Manzoor M, Gul I, Zafar R, Jamil HI, Niazi AK, Ali MA, Park TJ, Arshad M. Phytotoxicity of different antibiotics to rice and stress alleviation upon application of organic amendments. CHEMOSPHERE 2020; 258:127353. [PMID: 32554014 DOI: 10.1016/j.chemosphere.2020.127353] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 05/13/2020] [Accepted: 06/05/2020] [Indexed: 06/11/2023]
Abstract
Extensive use of antibiotic results in significant antibiotics pollution in the environment. Main objective of this study was to gain insight into potential impacts of antibiotics on plant physiological growth and nutritional composition, and stress alleviation through application of different organic amendments. Effects of five antibiotics (ciprofloxacin, levofloxacin, ofloxacin, amoxicillin and ampicillin) were observed in the presence of three organic amendments (rice husk, farmyard manure and poultry litter) with rice (Oryza sativa L.) as a model plant. Organic amendments were mixed with soil (@ 5 g kg-1) and after three weeks, antibiotics were applied (@10 mg kg-1) and plants were allowed to grow for four months. After which plants were harvested and physical growth parameters (root/shoot length, biomass) and nutritional composition (grain protein content, carbohydrates, phosphorous and iron) were monitored. It was observed that germination rate, seedling root/shoot length, seedling biomass and vigor index were negatively impacted. The application of organic amendments alleviated antibiotic stress on seedling dry biomass, length and vigor index by 1.8-, 3.1- and 2.5-folds, respectively as compared to the antibiotic controls. Concentrations of phosphorous, iron, carbohydrates and proteins were decreased by 5.3-, 1.3-, 1.4- and 1.6-folds upon application of antibiotics. Rice husk was the most effective treatment in case of physical growth parameters and alleviating antibiotics' induced genotoxicity. Whereas, poultry litter had the highest positive effect on nutritional composition of plants. In general, the application of organic amendments alleviated the phytotoxicity as well as genotoxicity in plants under antibiotics stress.
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Affiliation(s)
- Ayesha Mukhtar
- Institute of Environmental Sciences and Engineering, School of Civil and Environmental Engineering, National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Maria Manzoor
- Institute of Environmental Sciences and Engineering, School of Civil and Environmental Engineering, National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Iram Gul
- Institute of Environmental Sciences and Engineering, School of Civil and Environmental Engineering, National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Rabeea Zafar
- Institute of Environmental Sciences and Engineering, School of Civil and Environmental Engineering, National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Hira Imam Jamil
- Institute of Environmental Sciences and Engineering, School of Civil and Environmental Engineering, National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Adnan Khan Niazi
- Centre for Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan
| | - Muhammad Arif Ali
- Department of Soil Science, Faculty of Agriculture and Technology, Bahauddin Zakariya University, Multan, Pakistan
| | - Tae Jung Park
- Department of Chemistry, Chung-Ang University, Seoul, Republic of Korea
| | - Muhammad Arshad
- Institute of Environmental Sciences and Engineering, School of Civil and Environmental Engineering, National University of Sciences and Technology (NUST), Islamabad, Pakistan.
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4
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Hansen BL, Pessotti RDC, Fischer MS, Collins A, El-Hifnawi L, Liu MD, Traxler MF. Cooperation, Competition, and Specialized Metabolism in a Simplified Root Nodule Microbiome. mBio 2020; 11:e01917-20. [PMID: 32843548 PMCID: PMC7448283 DOI: 10.1128/mbio.01917-20] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 07/20/2020] [Indexed: 01/01/2023] Open
Abstract
Microbiomes associated with various plant structures often contain members with the potential to make specialized metabolites, e.g., molecules with antibacterial, antifungal, or siderophore activities. However, when and where microbes associated with plants produce specialized metabolites, and the potential role of these molecules in mediating intramicrobiome interactions, is not well understood. Root nodules of legume plants are organs devoted to hosting symbiotic bacteria that fix atmospheric nitrogen and have recently been shown to harbor a relatively simple accessory microbiome containing members with the ability to produce specialized metabolites in vitro On the basis of these observations, we sought to develop a model nodule microbiome system for evaluating specialized microbial metabolism in planta Starting with an inoculum derived from field-grown Medicago sativa nodules, serial passaging through gnotobiotic nodules yielded a simplified accessory community composed of four members: Brevibacillus brevis, Paenibacillus sp., Pantoea agglomerans, and Pseudomonas sp. Some members of this community exhibited clear cooperation in planta, while others were antagonistic and capable of disrupting cooperation between other partners. Using matrix-assisted laser desorption ionization-imaging mass spectrometry, we found that metabolites associated with individual taxa had unique distributions, indicating that some members of the nodule community were spatially segregated. Finally, we identified two families of molecules produced by B. brevisin planta as the antibacterial tyrocidines and a novel set of gramicidin-type molecules, which we term the britacidins. Collectively, these results indicate that in addition to nitrogen fixation, legume root nodules are likely also sites of active antimicrobial production.
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Affiliation(s)
- Bridget L Hansen
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA
| | - Rita de Cassia Pessotti
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA
| | - Monika S Fischer
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA
| | - Alyssa Collins
- Department of Molecular and Cellular Biology, University of California, Berkeley, Berkeley, California, USA
| | - Laila El-Hifnawi
- Department of Molecular and Cellular Biology, University of California, Berkeley, Berkeley, California, USA
| | - Mira D Liu
- Department of Chemistry, University of California, Berkeley, Berkeley, California, USA
| | - Matthew F Traxler
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA
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5
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Kumar A, Dubey A. Rhizosphere microbiome: Engineering bacterial competitiveness for enhancing crop production. J Adv Res 2020; 24:337-352. [PMID: 32461810 PMCID: PMC7240055 DOI: 10.1016/j.jare.2020.04.014] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 04/15/2020] [Accepted: 04/25/2020] [Indexed: 12/29/2022] Open
Abstract
Plants in nature are constantly exposed to a variety of abiotic and biotic stresses which limits their growth and production. Enhancing crop yield and production to feed exponentially growing global population in a sustainable manner by reduced chemical fertilization and agrochemicals will be a big challenge. Recently, the targeted application of beneficial plant microbiome and their cocktails to counteract abiotic and biotic stress is gaining momentum and becomes an exciting frontier of research. Advances in next generation sequencing (NGS) platform, gene editing technologies, metagenomics and bioinformatics approaches allows us to unravel the entangled webs of interactions of holobionts and core microbiomes for efficiently deploying the microbiome to increase crops nutrient acquisition and resistance to abiotic and biotic stress. In this review, we focused on shaping rhizosphere microbiome of susceptible host plant from resistant plant which comprises of specific type of microbial community with multiple potential benefits and targeted CRISPR/Cas9 based strategies for the manipulation of susceptibility genes in crop plants for improving plant health. This review is significant in providing first-hand information to improve fundamental understanding of the process which helps in shaping rhizosphere microbiome.
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Affiliation(s)
- Ashwani Kumar
- Metagenomics and Secretomics Research Laboratory, Department of Botany, Dr. Harisingh Gour University (A Central University), Sagar 470003, M.P., India
| | - Anamika Dubey
- Metagenomics and Secretomics Research Laboratory, Department of Botany, Dr. Harisingh Gour University (A Central University), Sagar 470003, M.P., India
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6
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Moccia K, Willems A, Papoulis S, Flores A, Forister ML, Fordyce JA, Lebeis SL. Distinguishing nutrient-dependent plant driven bacterial colonization patterns in alfalfa. ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 12:70-77. [PMID: 31775178 DOI: 10.1111/1758-2229.12815] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 11/21/2019] [Accepted: 11/22/2019] [Indexed: 05/23/2023]
Abstract
To understand factors that influence the assembly of microbial communities, we inoculated Medicago sativa with a series of nested bacterial synthetic communities and grew plants in distinct nitrogen concentrations. Two isolates in our eight-member synthetic community, Williamsia sp. R60 and Pantoea sp. R4, consistently dominate community structure across nitrogen regimes. While Pantoea sp. R4 consistently colonizes plants to a higher degree compared to the other six organisms across each community and each nutrient level, Williamsia sp. R60 exhibits nutrient specific colonization differences. Williamsia sp. R60 is more abundant in plants grown at higher nitrogen concentrations, but exhibits the opposite trend when no plant is present, indicating plant-driven influence over colonization. Our research discovered unique, repeatable colonization phenotypes for individual microbes during plant microbiome assembly, and identified alterations caused by the host plant, microbes, and available nutrients.
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Affiliation(s)
- Katherine Moccia
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee
| | - Andrew Willems
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee
| | - Spiridon Papoulis
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee
| | - Alicia Flores
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee
| | | | - James A Fordyce
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, Tennessee
| | - Sarah L Lebeis
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee
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7
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Esposito-Polesi NP. Contaminação versus manifestação endofítica: implicações no cultivo in vitro de plantas. RODRIGUÉSIA 2020. [DOI: 10.1590/2175-7860202071072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Resumo A cultura de tecidos vegetais é imprescindível à propagação e multiplicação uniforme de plantas, à conservação de germoplasma, a programas de melhoramento e à transformação genética. Essa técnica tem exigido, cada vez mais, estudos que colaborem com o entendimento dos mecanismos envolvidos no crescimento dos microrganismos nos meios de cultivo, bem como as relações que eles estabelecem com a planta hospedeira. Dessa maneira, a presente revisão pretende esclarecer esses questionamentos e promover a distinção entre contaminação e manifestação endofítica que ocorrem no cultivo in vitro por diferentes causas. Tal distinção permite diminuir o pânico que se instala quando do seu aparecimento, além de auxiliar na adoção de medidas de prevenção e/ou controle desses eventos sem que haja descartes desnecessários de material de alto valor comercial e genético.
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8
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Ou T, Xu WF, Wang F, Strobel G, Zhou ZY, Xiang ZH, Liu J, Xie J. A Microbiome Study Reveals Seasonal Variation in Endophytic Bacteria Among different Mulberry Cultivars. Comput Struct Biotechnol J 2019; 17:1091-1100. [PMID: 31452862 PMCID: PMC6702411 DOI: 10.1016/j.csbj.2019.07.018] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 07/26/2019] [Accepted: 07/27/2019] [Indexed: 12/24/2022] Open
Abstract
Knowledge of seasonal shifts in the bacterial community composition among different mulberry (Morus L.) cultivars will facilitate to develop the biocontrol phytopathogens strategy using endophytic bacteria. The present study investigated the endophytic bacterial communities of four mulberry cultivars that have different resistance to mulberry fruit sclerotiniosis using Illumina-based sequencing of the 16S rRNA gene fragment in spring and autumn. The results indicated that spring samples harbor higher bacterial operational taxonomic units (OTUs), α-diversity, and bacterial community complexity in comparison with autumn samples. The taxonomic composition analysis showed that the majority of endophytes were composed of Proteobacteria (genus level: Methylobaterium) and Actinobacteria in spring, while sequences classified as Proteobacteria (genus level: Pantoea and Pseudomonas) were abundant in autumn. Analysis of β-diversity also revealed endophytic bacteria were divided into two main groups by season. By comparison among different mulberry cultivars, we found that Pantoea, Methylobaterium, and Pseudomonas were the three major bacterial genera in all cultivars, while their relative abundances varied with cultivars and appeared no obvious relationship with resistance level of mulberry fruit sclerotiniosis. The complex correlation of the endophytic communities in susceptible mulberry cultivars was higher than that of the resistant cultivars. Overall, the findings suggested that season plays a key role in determining the mulberry endophytic bacterial communities, followed by host cultivar, and Proteobacteria was the predominant phylum in both seasons and different mulberry cultivars. Season played a key role in determining mulberry endophytic bacterial communities. Mulberry endophytic bacterial variation was not obviously related with cultivars. Mulberry recruited beneficial endophytes as potential biocontrol agents.
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Affiliation(s)
- Ting Ou
- State Key Laboratory of Silkworm Genome Biology, College of Biotechnology, Southwest University, Chongqing 400715, China.,Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, College of Biotechnology, Southwest University, Chongqing 400715, China
| | - Wei-Fang Xu
- State Key Laboratory of Silkworm Genome Biology, College of Biotechnology, Southwest University, Chongqing 400715, China.,Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, College of Biotechnology, Southwest University, Chongqing 400715, China
| | - Fei Wang
- State Key Laboratory of Silkworm Genome Biology, College of Biotechnology, Southwest University, Chongqing 400715, China.,Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, College of Biotechnology, Southwest University, Chongqing 400715, China
| | - Gary Strobel
- Department of Plant Sciences, Montana State University, Bozeman, MT 59717, USA
| | - Ze-Yang Zhou
- State Key Laboratory of Silkworm Genome Biology, College of Biotechnology, Southwest University, Chongqing 400715, China.,Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, College of Biotechnology, Southwest University, Chongqing 400715, China.,College of Life Science, Chongqing Normal University, Chongqing 400047, China
| | - Zhong-Huai Xiang
- State Key Laboratory of Silkworm Genome Biology, College of Biotechnology, Southwest University, Chongqing 400715, China.,Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, College of Biotechnology, Southwest University, Chongqing 400715, China
| | - Jia Liu
- Chongqing Key Laboratory of Economic Plant Biotechnology, College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, Chongqing 402160, China
| | - Jie Xie
- State Key Laboratory of Silkworm Genome Biology, College of Biotechnology, Southwest University, Chongqing 400715, China.,Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, College of Biotechnology, Southwest University, Chongqing 400715, China
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9
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Fagorzi C, Checcucci A, diCenzo GC, Debiec-Andrzejewska K, Dziewit L, Pini F, Mengoni A. Harnessing Rhizobia to Improve Heavy-Metal Phytoremediation by Legumes. Genes (Basel) 2018; 9:genes9110542. [PMID: 30413093 PMCID: PMC6266702 DOI: 10.3390/genes9110542] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 11/05/2018] [Accepted: 11/06/2018] [Indexed: 12/15/2022] Open
Abstract
Rhizobia are bacteria that can form symbiotic associations with plants of the Fabaceae family, during which they reduce atmospheric di-nitrogen to ammonia. The symbiosis between rhizobia and leguminous plants is a fundamental contributor to nitrogen cycling in natural and agricultural ecosystems. Rhizobial microsymbionts are a major reason why legumes can colonize marginal lands and nitrogen-deficient soils. Several leguminous species have been found in metal-contaminated areas, and they often harbor metal-tolerant rhizobia. In recent years, there have been numerous efforts and discoveries related to the genetic determinants of metal resistance by rhizobia, and on the effectiveness of such rhizobia to increase the metal tolerance of host plants. Here, we review the main findings on the metal resistance of rhizobia: the physiological role, evolution, and genetic determinants, and the potential to use native and genetically-manipulated rhizobia as inoculants for legumes in phytoremediation practices.
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Affiliation(s)
- Camilla Fagorzi
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy.
| | - Alice Checcucci
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy.
| | - George C diCenzo
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy.
| | - Klaudia Debiec-Andrzejewska
- Laboratory of Environmental Pollution Analysis, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland.
| | - Lukasz Dziewit
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland.
| | - Francesco Pini
- Department of Agri-food Production and Environmental Science, University of Florence, 50144 Florence, Italy.
| | - Alessio Mengoni
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy.
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10
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Isolation and diversity of culturable rhizobacteria associated with economically important crops and uncultivated plants in Québec, Canada. Syst Appl Microbiol 2018; 41:629-640. [DOI: 10.1016/j.syapm.2018.06.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 06/26/2018] [Indexed: 11/19/2022]
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11
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Kang W, Xu L, Jiang Z, Shi S. Genetic diversity and symbiotic efficiency difference of endophytic rhizobia of Medicago sativa. Can J Microbiol 2018; 65:68-83. [PMID: 30273494 DOI: 10.1139/cjm-2018-0158] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Research on rhizobium diversity has paved the way for diversification of rhizobial germplasm resources. Seventy-three endophytic bacterial isolates were collected from seven tissues of five alfalfa cultivars in three geographic locations in Gansu, China. Restriction fragment length polymorphism (RFLP) fingerprinting of 16S rRNA and analysis of concatenated sequence of three housekeeping genes (atpD, glnII, and recA) and two symbiotic genes (nodC and nifH) were used for strain identification. Results showed that the endophytic strains were genetically diverse at different taxonomic levels, and Ensifer meliloti (31) and Agrobacterium radiobacter (12) are common Medicago sativa endophytic bacteria in Gansu, China. The nifH genes (97%-98% sequence identity) of E. meliloti strains were more diverse than the nodC genes (99%-100% sequence identity), even though the strains evolved from a common ancestor. The degree of dispersion of symbiotic phenotypes of E. meliloti strains on M. sativa 'Gannong No. 3', 'Gannong No. 9', and 'Qingshui' was much less than that on M. sativa 'Longzhong' and 'WL168HQ'. This suggested that the symbiotic efficiency of E. meliloti strains on the former three alfalfa cultivars was similar but on the latter two was discrepant. Their symbiotic efficiency differed primarily according to alfalfa cultivars and, to a lesser extent, to the tested strains, indicating the difference in the sensitivity of different alfalfa cultivars to rhizobial strains.
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Affiliation(s)
- Wenjuan Kang
- a College of Grassland Science, Gansu Agricultural University, Lanzhou 730070, P.R. China
| | - Lin Xu
- b College of Agriculture and Biotechnology, Hexi University, Zhangye 734000, P.R. China
| | - Zhehao Jiang
- a College of Grassland Science, Gansu Agricultural University, Lanzhou 730070, P.R. China
| | - Shangli Shi
- a College of Grassland Science, Gansu Agricultural University, Lanzhou 730070, P.R. China.,c Key Laboratory of Grassland Ecosystem of Ministry of Education, Lanzhou 730070, P.R. China
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12
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Xue S, Biondi EG. Coordination of symbiosis and cell cycle functions in Sinorhizobium meliloti. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1862:691-696. [PMID: 29783033 DOI: 10.1016/j.bbagrm.2018.05.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 05/11/2018] [Accepted: 05/17/2018] [Indexed: 10/16/2022]
Abstract
The symbiotic nitrogen fixing species Sinorhizobium meliloti represents a remarkable model system for the class Alphaproteobacteria, which includes genera such as Caulobacter, Agrobacterium and Brucella. It is capable of living free in the soil, and is also able to establish a complex symbiosis with leguminous plants, during which its cell cycle program is completely rewired presumably due, at least in part, to the action of peptides secreted by the plant. Here we will discuss how the cell cycle regulation works in S. meliloti and the kinds of molecular mechanisms that take place during the infection. We will focus on the complex regulation of the master regulator of the S. meliloti cell cycle, the response regulator CtrA, discussing its implication in symbiosis.
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Affiliation(s)
- Shuanghong Xue
- Aix Marseille University, CNRS, IMM, LCB, 13009 Marseille, France
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Igiehon NO, Babalola OO. Rhizosphere Microbiome Modulators: Contributions of Nitrogen Fixing Bacteria towards Sustainable Agriculture. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2018; 15:ijerph15040574. [PMID: 29570619 PMCID: PMC5923616 DOI: 10.3390/ijerph15040574] [Citation(s) in RCA: 105] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 03/03/2018] [Accepted: 03/19/2018] [Indexed: 02/05/2023]
Abstract
Rhizosphere microbiome which has been shown to enhance plant growth and yield are modulated or influenced by a few environmental factors such as soil type, plant cultivar, climate change and anthropogenic activities. In particular, anthropogenic activity, such as the use of nitrogen-based chemical fertilizers, is associated with environmental destruction and this calls for a more ecofriendly strategy to increase nitrogen levels in agricultural land. This feat is attainable by harnessing nitrogen-fixing endophytic and free-living rhizobacteria. Rhizobium, Pseudomonas, Azospirillum and Bacillus, have been found to have positive impacts on crops by enhancing both above and belowground biomass and could therefore play positive roles in achieving sustainable agriculture outcomes. Thus, it is necessary to study this rhizosphere microbiome with more sophisticated culture-independent techniques such as next generation sequencing (NGS) with the prospect of discovering novel bacteria with plant growth promoting traits. This review is therefore aimed at discussing factors that can modulate rhizosphere microbiome with focus on the contributions of nitrogen fixing bacteria towards sustainable agricultural development and the techniques that can be used for their study.
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Affiliation(s)
- Nicholas Ozede Igiehon
- Food Security and Safety Niche, Faculty of Natural and Agricultural Science, Private Mail Bag X2046, North West University, Mmabatho 2735, South Africa.
| | - Olubukola Oluranti Babalola
- Food Security and Safety Niche, Faculty of Natural and Agricultural Science, Private Mail Bag X2046, North West University, Mmabatho 2735, South Africa.
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15
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López JL, Alvarez F, Príncipe A, Salas ME, Lozano MJ, Draghi WO, Jofré E, Lagares A. Isolation, taxonomic analysis, and phenotypic characterization of bacterial endophytes present in alfalfa (Medicago sativa) seeds. J Biotechnol 2018; 267:55-62. [DOI: 10.1016/j.jbiotec.2017.12.020] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 11/27/2017] [Accepted: 12/19/2017] [Indexed: 10/18/2022]
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Sheehan LM, Caswell CC. An account of evolutionary specialization: the AbcR small RNAs in the Rhizobiales. Mol Microbiol 2017; 107:24-33. [PMID: 29076560 DOI: 10.1111/mmi.13869] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/21/2017] [Indexed: 01/26/2023]
Abstract
The AbcR small RNAs (sRNAs) are a fascinating example of two highly conserved sRNAs that differ tremendously at the functional level among organisms. From their transcriptional activation to their regulatory capabilities, the AbcR sRNAs exhibit varying characteristics in three well-studied bacteria belonging to the Rhizobiales order: the plant symbiont Sinorhizobium meliloti, the plant pathogen Agrobacterium tumefaciens, and the animal pathogen Brucella abortus. This review outlines the similarities and differences of the AbcR sRNAs between each of these organisms, and discusses reasons as to why this group of sRNAs has diverged in their genetic organization and regulatory functions across species. In the end, this review will shed light on how regulatory systems, although seemingly conserved among bacteria, can vary based on the environmental niche and lifestyle of an organism.
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Affiliation(s)
- Lauren M Sheehan
- Department of Biomedical Sciences and Pathobiology, VA-MD College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, USA
| | - Clayton C Caswell
- Department of Biomedical Sciences and Pathobiology, VA-MD College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, USA
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Suhaimi NSM, Goh SY, Ajam N, Othman RY, Chan KG, Thong KL. Diversity of microbiota associated with symptomatic and non-symptomatic bacterial wilt-diseased banana plants determined using 16S rRNA metagenome sequencing. World J Microbiol Biotechnol 2017; 33:168. [PMID: 28828756 DOI: 10.1007/s11274-017-2336-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 08/18/2017] [Indexed: 10/19/2022]
Abstract
Banana is one of the most important fruits cultivated in Malaysia, and it provides many health benefits. However, bacterial wilt disease, which attacks bananas, inflicts major losses on the banana industry in Malaysia. To understand the complex interactions of the microbiota of bacterial wilt-diseased banana plants, we first determined the bacterial communities residing in the pseudostems of infected (symptomatic) and diseased-free (non-symptomatic) banana plants. We characterized the associated microorganisms using the targeted 16S rRNA metagenomics sequencing on the Illumina MiSeq platform. Taxonomic classifications revealed 17 and nine known bacterial phyla in the tissues of non-symptomatic and symptomatic plants, respectively. Cyanobacteria and Proteobacteria (accounted for more than 99% of the 16S rRNA gene fragments) were the two most abundant phyla in both plants. The five major genera found in both plant samples were Ralstonia, Sphingomonas, Methylobacterium, Flavobacterium, and Pseudomonas. Ralstonia was more abundant in symptomatic plant (59% out of the entire genera) as compared to those in the non-symptomatic plant (only 36%). Our data revealed that 102 bacterial genera were only assigned to the non-symptomatic plant. Overall, this study indicated that more diverse and abundant microbiota were associated with the non-symptomatic bacterial wilt-diseased banana plant as compared to the symptomatic plant. The higher diversity of endophytic microbiota in the non-symptomatic banana plant could be an indication of pathogen suppression which delayed or prevented the disease expression. This comparative study of the microbiota in the two plant conditions might provide caveats for potential biological control strategies.
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Affiliation(s)
| | - Share-Yuan Goh
- Genetics and Molecular Biology Unit, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Noni Ajam
- Microbiology Unit, Institute of Biological Sciences, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Rofina Yasmin Othman
- Microbiology Unit, Institute of Biological Sciences, University of Malaya, 50603, Kuala Lumpur, Malaysia.,Centre for Research in Biotechnology for Agriculture (CEBAR), Research Management and Innovation Complex, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Kok-Gan Chan
- Genetics and Molecular Biology Unit, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Kwai Lin Thong
- Microbiology Unit, Institute of Biological Sciences, University of Malaya, 50603, Kuala Lumpur, Malaysia.
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Hegazi NA, Sarhan MS, Fayez M, Patz S, Murphy BR, Ruppel S. Plant-fed versus chemicals-fed rhizobacteria of Lucerne: Plant-only teabags culture media not only increase culturability of rhizobacteria but also recover a previously uncultured Lysobacter sp., Novosphingobium sp. and Pedobacter sp. PLoS One 2017; 12:e0180424. [PMID: 28686606 PMCID: PMC5501534 DOI: 10.1371/journal.pone.0180424] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 06/15/2017] [Indexed: 11/19/2022] Open
Abstract
In an effort to axenically culture the previously uncultivable populations of the rhizobacteria of Lucerne (Medicago sativa L.), we propose plant-only teabags culture media to mimic the nutritional matrix available in the rhizosphere. Here, we show that culture media prepared from Lucerne powder teabags substantially increased the cultivability of Lucerne rhizobacteria compared with a standard nutrient agar, where we found that the cultivable populations significantly increased by up to 60% of the total bacterial numbers as estimated by Quantitative Real-time Polymerase Chain Reaction (qRT-PCR). Cluster analysis of 16S rDNA Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis (PCR-DGGE) of cultivable Colony-Forming Units (CFUs) revealed a more distinct composition and separation of bacterial populations recovered on the plant-only teabags culture media than those developed on a standard nutrient agar. Further, the new plant medium gave preference to the micro-symbiont Sinorhizobium meliloti, and succeeded in isolating a number of not-yet-cultured bacteria, most closely matched to Novosphingobium sp., Lysobacter sp. and Pedobacter sp. The present study may encourage other researchers to consider moving from the well-established standard culture media to the challenging new plant-only culture media. Such a move may reveal previously hidden members of rhizobacteria, and help to further explore their potential environmental impacts.
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Affiliation(s)
- Nabil A. Hegazi
- Environmental Studies and Research Unit (ESRU), Department of Microbiology, Faculty of Agriculture, Cairo University, Giza, Egypt
- * E-mail:
| | - Mohamed S. Sarhan
- Environmental Studies and Research Unit (ESRU), Department of Microbiology, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Mohamed Fayez
- Environmental Studies and Research Unit (ESRU), Department of Microbiology, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Sascha Patz
- Leibniz Institute of Vegetable and Ornamental Crops Großbeeren/ Erfurt e.V. (IGZ), Großbeeren, Germany
| | - Brian R. Murphy
- Department of Botany, School of Natural Sciences, Trinity College Dublin, Dublin, Ireland
| | - Silke Ruppel
- Leibniz Institute of Vegetable and Ornamental Crops Großbeeren/ Erfurt e.V. (IGZ), Großbeeren, Germany
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Yaish MW, Al-Lawati A, Jana GA, Vishwas Patankar H, Glick BR. Impact of Soil Salinity on the Structure of the Bacterial Endophytic Community Identified from the Roots of Caliph Medic (Medicago truncatula). PLoS One 2016; 11:e0159007. [PMID: 27391592 PMCID: PMC4938511 DOI: 10.1371/journal.pone.0159007] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2016] [Accepted: 06/24/2016] [Indexed: 12/02/2022] Open
Abstract
In addition to being a forage crop, Caliph medic (Medicago truncatula) is also a model legume plant and is used for research focusing on the molecular characterization of the interaction between rhizobia and plants. However, the endophytic microbiome in this plant is poorly defined. Endophytic bacteria play a role in supplying plants with the basic requirements necessary for growth and development. Moreover, these bacteria also play a role in the mechanism of salinity stress adaptation in plants. As a prelude to the isolation and utilization of these bacteria in Caliph medic farming, 41 bacterial OTUs were identified in this project from within the interior of the roots of this plant by pyrosequencing of the small ribosomal subunit gene (16S rDNA) using a cultivation-independent approach. In addition, the differential abundance of these bacteria was studied following exposure of the plants to salinity stress. About 29,064 high-quality reads were obtained from the sequencing of six libraries prepared from control and salinity-treated tissues. Statistical analysis revealed that the abundance of ~70% of the OTUs was significantly (p ≤ 0.05) altered in roots that were exposed to salinity stress. Sequence analysis showed a similarity between some of the identified species and other, known, growth-promoting bacteria, marine and salt-stressed soil-borne bacteria, and nitrogen-fixing bacterial isolates. Determination of the amendments to the bacterial community due to salinity stress in Caliph medic provides a crucial step toward developing an understanding of the association of these endophytes, under salt stress conditions, in this model plant. To provide direct evidence regarding their growth promoting activity, a group of endophytic bacteria were isolated from inside of plant roots using a cultivation-dependent approach. Several of these isolates were able to produce ACC-deaminase, ammonia and IAA; and to solubilize Zn+2 and PO4-3. This data is consistent with the predicted occurrence (based on cultivation-independent techniques) of these bacteria and provides some insight into the importance of the endophytic bacteria in Caliph medic when grown under normal and saline conditions.
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Affiliation(s)
- Mahmoud W. Yaish
- Department of Biology, College of Science, Sultan Qaboos University, Muscat, Oman
- * E-mail:
| | - Abbas Al-Lawati
- Department of Biology, College of Science, Sultan Qaboos University, Muscat, Oman
| | - Gerry Aplang Jana
- Department of Biology, College of Science, Sultan Qaboos University, Muscat, Oman
| | | | - Bernard R. Glick
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
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Jiang YF, Ling J, Dong JD, Chen B, Zhang YY, Zhang YZ, Wang YS. Illumina-based analysis the microbial diversity associated with Thalassia hemprichii in Xincun Bay, South China Sea. ECOTOXICOLOGY (LONDON, ENGLAND) 2015; 24:1548-1556. [PMID: 26092035 DOI: 10.1007/s10646-015-1511-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 06/08/2015] [Indexed: 06/04/2023]
Abstract
In order to increase our understanding of the microbial diversity associated with seagrass Thalassia hemprichii in Xincun Bay, South China Sea, 16S rRNA gene was identified by highthrough sequencing method. Bacteria associated with seagrass T. hemprichii belonged to 37 phyla, 99 classes. The diversity of bacteria associated with seagrass was similar among the geographically linked coastal locations of Xincun Bay. Proteobacteria was the dominant bacteria and the α-proteobacteria had adapted to the seagrass ecological niche. As well, α-proteobacteria and Pseudomonadales were associated microflora in seagrass meadows, but the interaction between the bacteria and plant is needed to further research. Burkholderiales and Verrucomicrobiae indicated the influence of the bay from anthropogenic activities. Further, Cyanobacteria could imply the difference of the nutrient conditions in the sites. γ-proteobacteria, Desulfobacterales and Pirellulales played a role in the cycle of sulfur, organic mineralization and meadow ecosystem, respectively. In addition, the less abundance bacteria species have key functions in the seagrass meadows, but there is lack knowledge of the interaction of the seagrass and less abundance bacteria species. Microbial communities can response to surroundings and play key functions in the biochemical cycle.
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Affiliation(s)
- Yu-Feng Jiang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya, 572000, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Juan Ling
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya, 572000, China
| | - Jun-De Dong
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
- Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya, 572000, China.
| | - Biao Chen
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya, 572000, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yan-Ying Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya, 572000, China
| | - Yuan-Zhou Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya, 572000, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - You-Shao Wang
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
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Endophytic bacterial communities associated with two explant sources of Eucalyptus benthamii Maiden & Cambage. World J Microbiol Biotechnol 2015; 31:1737-46. [PMID: 26377625 DOI: 10.1007/s11274-015-1924-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 08/11/2015] [Indexed: 10/23/2022]
Abstract
Micropropagation has been applied in the recovery and rejuvenation of adult trees, which is achieved by various subcultures in the multiplication phase. This strategy has brought questions about the endophytic microbiota associated with these plants along its manipulation. Therefore, the aim of this study was to evaluate the composition of the endophytic bacterial communities associated with two explants sources [the canopy branches (CB) and the trunk base of the tree (TB)] under prolonged in vitro cultivation. In addition we analyzed the bacterial community dynamic along the subcultures in different micropropagation phases. Bacterial DNA was extracted from samples of mini-stumps (in vivo) from CB and TB and in micro-stumps produced by in vitro cultivations of these explants sources--both originated from one single matrix plant of Eucalyptus benthamii. In vitro establishment occurred in two dates and the evaluation of endophytic bacterial communities was made in vivo and in vitro samples (on 10th, 13th and 16th subcultures), when elongated shoots and roots were analyzed. Analysis was performed by PCR-DGGE based on the V6 region of ribosomal gene 16S rDNA. Bands profiles showed differences in communities between in vivo and in vitro samples, and also distinctions of communities assessed in the subcultures, elongated and rooted samples. Distinctions in the composition of endophytic bacterial communities were greater in CB micro-stumps. These results indicate a differential colonization of explants by endophytic bacteria, with predominance of common (ever-present) endophytes in TB samples and casual, here named opportunistic, in CB samples.
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Maida I, Chiellini C, Mengoni A, Bosi E, Firenzuoli F, Fondi M, Fani R. Antagonistic interactions between endophytic cultivable bacterial communities isolated from the medicinal plantEchinacea purpurea. Environ Microbiol 2015; 18:2357-65. [DOI: 10.1111/1462-2920.12911] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 05/15/2015] [Accepted: 05/16/2015] [Indexed: 11/28/2022]
Affiliation(s)
- Isabel Maida
- Department of Biology; University of Florence; Via Madonna del Piano 6 Sesto Fiorentino Florence I-50019 Italy
| | - Carolina Chiellini
- Department of Biology; University of Florence; Via Madonna del Piano 6 Sesto Fiorentino Florence I-50019 Italy
- CRA-ABP Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria; Centro di ricerca per l'Agrobiologia e la Pedologia; Piazza M. D'Azeglio 30 Firenze FI 50121 Italy
| | - Alessio Mengoni
- Department of Biology; University of Florence; Via Madonna del Piano 6 Sesto Fiorentino Florence I-50019 Italy
| | - Emanuele Bosi
- Department of Biology; University of Florence; Via Madonna del Piano 6 Sesto Fiorentino Florence I-50019 Italy
| | - Fabio Firenzuoli
- Center for Integrative Medicine; Careggi University Hospital; University of Florence; Florence Italy
| | - Marco Fondi
- Department of Biology; University of Florence; Via Madonna del Piano 6 Sesto Fiorentino Florence I-50019 Italy
| | - Renato Fani
- Department of Biology; University of Florence; Via Madonna del Piano 6 Sesto Fiorentino Florence I-50019 Italy
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Khalifa AYZ, Alsyeeh AM, Almalki MA, Saleh FA. Characterization of the plant growth promoting bacterium, Enterobacter cloacae MSR1, isolated from roots of non-nodulating Medicago sativa. Saudi J Biol Sci 2015; 23:79-86. [PMID: 26858542 PMCID: PMC4705252 DOI: 10.1016/j.sjbs.2015.06.008] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 06/04/2015] [Accepted: 06/10/2015] [Indexed: 11/25/2022] Open
Abstract
The aim of the present study was to characterize the endophytic bacterial strain designated MSR1 that was isolated from inside the non-nodulating roots of Medicago sativa after surface-sterilization. MSR1 was identified as Enterobacter cloacae using both 16S rDNA gene sequence analysis and API20E biochemical identification system (Biomerieux, France). Furthermore, this bacterium was characterized using API50CH kit (Biomerieux, France) and tested for antibacterial activities against some food borne pathogens. The results showed that E. cloacae consumed certain carbohydrates such as glycerol, d-xylose, d-maltose and esculin melibiose as a sole carbon source and certain amino acids such as arginine, tryptophan ornithine as nitrogen source. Furthermore, MSR1 possessed multiple plant-growth promoting characteristics; phosphate solubility, production of phytohormones acetoin and bioactive compounds. Inoculation of Pisum sativum with MSR1 significantly improved the growth parameters (the length and dry weight) of this economically important grain legume compared to the non-treated plants. To our knowledge, this is the first report addressing E. cloacae which exist in roots of alfalfa growing in Al-Ahsaa region. The results confirmed that E. cloacae exhibited traits for plant growth promoting and could be developed as an eco-friendly biofertilizer for P. sativum and probably for other important plant species in future.
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Affiliation(s)
- Ashraf Y Z Khalifa
- Biological Sciences Department, College of Science, King Faisal University, Saudi Arabia; Botany and Microbiology Department, Faculty of Science, University of Beni-Suef, Beni-Suef, Egypt
| | - Abdel-Moneium Alsyeeh
- Biological Sciences Department, College of Science, King Faisal University, Saudi Arabia
| | - Mohammed A Almalki
- Biological Sciences Department, College of Science, King Faisal University, Saudi Arabia
| | - Farag A Saleh
- Department of Food Science and Nutrition, College of Agricultural and Food Sciences, King Faisal University, Saudi Arabia; Department of Special Food and Nutrition, Food Technology Research Institute, Agricultural Research Center, Giza, Egypt
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Exploring the dynamics of bacterial community composition in soil: the pan-bacteriome approach. Antonie van Leeuwenhoek 2015; 107:785-97. [PMID: 25563635 DOI: 10.1007/s10482-014-0372-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 12/26/2014] [Indexed: 10/24/2022]
Abstract
We performed a longitudinal study (repeated observations of the same sample over time) to investigate both the composition and structure of temporal changes of bacterial community composition in soil mesocosms, subjected to three different treatments (water and 5 or 25 mg kg(-1) of dried soil Cd(2+)). By analogy with the pan genome concept, we identified a core bacteriome and an accessory bacteriome. Resident taxa were assigned to the core bacteriome, while occasional taxa were assigned to the accessory bacteriome. Core and accessory bacteriome represented roughly 35 and 50 % of the taxa detected, respectively, and were characterized by different taxonomic signatures from phylum to genus level while 15 % of the taxa were found to be unique to a particular sample. In particular, the core bacteriome was characterized by higher abundance of members of Planctomycetes, Actinobacteria, Verrucomicrobia and Acidobacteria, while the accessory bacteriome included more members of Firmicutes, Clamydiae and Proteobacteria, suggesting potentially different responses to environmental changes of members from these phyla. We conclude that the pan-bacteriome model may be a useful approach to gain insight for modeling bacterial community structure and inferring different abilities of bacteria taxa.
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Zhang JJ, Lu YC, Yang H. Chemical modification and degradation of atrazine in Medicago sativa through multiple pathways. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2014; 62:9657-9668. [PMID: 25226578 DOI: 10.1021/jf503221c] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Atrazine is a member of the triazine herbicide family intensively used to control weeds for crop production. In this study, atrazine residues and its degraded products in alfalfa (Medicago sativa) were characterized using UPLC-TOF-MS/MS. Most of atrazine absorbed in plants was found as chemically modified derivatives like deisopropylated atrazine (DIA), dehydrogenated atrazine (DHA), or methylated atrazine (MEA), and some atrazine derivatives were conjugated through different functional groups such as sugar, glutathione, and amino acids. Interestingly, the specific conjugates DHA+hGSH (homoglutathione) and MEA-HCl+hGSH in alfalfa were detected. These results suggest that atrazine in alfalfa can be degraded through different pathways. The increased activities of glycosyltransferase and glutathione S-transferase were determined to support the atrazine degradation models. The outcome of the work uncovered the detailed mechanism for the residual atrazine accumulation and degradation in alfalfa and will help to evaluate whether the crop is suitable to be cultivated in the atrazine-polluted soil.
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Affiliation(s)
- Jing Jing Zhang
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University , Nanjing 210095, China
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Antibiotic resistance differentiates Echinacea purpurea endophytic bacterial communities with respect to plant organs. Res Microbiol 2014; 165:686-94. [PMID: 25283726 DOI: 10.1016/j.resmic.2014.09.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 09/23/2014] [Accepted: 09/23/2014] [Indexed: 11/24/2022]
Abstract
Recent findings have shown that antibiotic resistance is widespread in multiple environments and multicellular organisms, as plants, harboring rich and complex bacterial communities, could be hot spot for emergence of antibiotic resistances as a response to bioactive molecules production by members of the same community. Here, we investigated a panel of 137 bacterial isolates present in different organs of the medicinal plant Echinacea purpurea, aiming to evaluate if different plant organs harbor strains with different antibiotic resistance profiles, implying then the presence of different biological interactions in the communities inhabiting different plant organs. Data obtained showed a large antibiotic resistance variability among strains, which was strongly related to the different plant organs (26% of total variance, P < 0.0001). Interestingly this uneven antibiotic resistance pattern was present also when a single genus (Pseudomonas), ubiquitous in all organs, was analyzed and no correlation of antibiotic resistance pattern with genomic relatedness among strains was found. In conclusion, we speculate that antibiotic resistance patterns are tightly linked to the type of plant organ under investigation, suggesting the presence of differential forms of biological interaction in stem/leaves, roots and rhizosphere.
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Donnarumma F, Bazzicalupo M, Blažinkov M, Mengoni A, Sikora S, Babić KH. Biogeography of Sinorhizobium meliloti nodulating alfalfa in different Croatian regions. Res Microbiol 2014; 165:508-16. [DOI: 10.1016/j.resmic.2014.06.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 06/11/2014] [Indexed: 11/16/2022]
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Isolation and characterization of an endophytic bacterium, Bacillus megaterium BMN1, associated with root-nodules of Medicago sativa L. growing in Al-Ahsaa region, Saudi Arabia. ANN MICROBIOL 2014. [DOI: 10.1007/s13213-014-0946-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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Guerriero G, Legay S, Hausman JF. Alfalfa Cellulose synthase gene expression under abiotic stress: a Hitchhiker's guide to RT-qPCR normalization. PLoS One 2014; 9:e103808. [PMID: 25084115 PMCID: PMC4118957 DOI: 10.1371/journal.pone.0103808] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 07/07/2014] [Indexed: 01/22/2023] Open
Abstract
Abiotic stress represents a serious threat affecting both plant fitness and productivity. One of the promptest responses that plants trigger following abiotic stress is the differential expression of key genes, which enable to face the adverse conditions. It is accepted and shown that the cell wall senses and broadcasts the stress signal to the interior of the cell, by triggering a cascade of reactions leading to resistance. Therefore the study of wall-related genes is particularly relevant to understand the metabolic remodeling triggered by plants in response to exogenous stresses. Despite the agricultural and economical relevance of alfalfa (Medicago sativa L.), no study, to our knowledge, has addressed specifically the wall-related gene expression changes in response to exogenous stresses in this important crop, by monitoring the dynamics of wall biosynthetic gene expression. We here identify and analyze the expression profiles of nine cellulose synthases, together with other wall-related genes, in stems of alfalfa plants subjected to different abiotic stresses (cold, heat, salt stress) at various time points (e.g. 0, 24, 72 and 96 h). We identify 2 main responses for specific groups of genes, i.e. a salt/heat-induced and a cold/heat-repressed group of genes. Prior to this analysis we identified appropriate reference genes for expression analyses in alfalfa, by evaluating the stability of 10 candidates across different tissues (namely leaves, stems, roots), under the different abiotic stresses and time points chosen. The results obtained confirm an active role played by the cell wall in response to exogenous stimuli and constitute a step forward in delineating the complex pathways regulating the response of plants to abiotic stresses.
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Affiliation(s)
- Gea Guerriero
- Department Environment and Agro-biotechnologies (EVA), Centre de Recherche Public, Gabriel Lippmann, Belvaux, Luxembourg
| | - Sylvain Legay
- Department Environment and Agro-biotechnologies (EVA), Centre de Recherche Public, Gabriel Lippmann, Belvaux, Luxembourg
| | - Jean-Francois Hausman
- Department Environment and Agro-biotechnologies (EVA), Centre de Recherche Public, Gabriel Lippmann, Belvaux, Luxembourg
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Linking Bacterial Endophytic Communities to Essential Oils: Clues from Lavandula angustifolia Mill. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2014; 2014:650905. [PMID: 24971151 PMCID: PMC4058287 DOI: 10.1155/2014/650905] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Accepted: 04/29/2014] [Indexed: 12/04/2022]
Abstract
Endophytic bacteria play a crucial role in plant life and are also drawing much attention for their capacity to produce bioactive compounds of relevant biotechnological interest. Here we present the characterisation of the cultivable endophytic bacteria of Lavandula angustifolia Mill.—a species used since antiquity for its therapeutic properties—since the production of bioactive metabolites from medical plants may reside also in the activity of bacterial endophytes through their direct production, PGPR activity on host, and/or elicitation of plant metabolism. Lavender tissues are inhabited by a tissue specific endophytic community dominated by Proteobacteria, highlighting also their difference from the rhizosphere environment where Actinobacteria and Firmicutes are also found. Leaves' endophytic community resulted as the most diverse from the other ecological niches. Overall, the findings reported here suggest: (i) the existence of different entry points for the endophytic community, (ii) its differentiation on the basis of the ecological niche variability, and (iii) a two-step colonization process for roots endophytes. Lastly, many isolates showed a strong inhibition potential against human pathogens and the molecular characterization demonstrated also the presence of not previously described isolates that may constitute a reservoir of bioactive compounds relevant in the field of pathogen control, phytoremediation, and human health.
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Bacci G, Pagoto E, Passaponti M, Vannocci P, Ugolini A, Mengoni A. Composition of supralittoral sediments bacterial communities in a Mediterranean island. ANN MICROBIOL 2014. [DOI: 10.1007/s13213-014-0829-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Jackson CR, Randolph KC, Osborn SL, Tyler HL. Culture dependent and independent analysis of bacterial communities associated with commercial salad leaf vegetables. BMC Microbiol 2013; 13:274. [PMID: 24289725 PMCID: PMC4219373 DOI: 10.1186/1471-2180-13-274] [Citation(s) in RCA: 131] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Accepted: 11/26/2013] [Indexed: 02/01/2023] Open
Abstract
Background Plants harbor a diverse bacterial community, both as epiphytes on the plant surface and as endophytes within plant tissue. While some plant-associated bacteria act as plant pathogens or promote plant growth, others may be human pathogens. The aim of the current study was to determine the bacterial community composition of organic and conventionally grown leafy salad vegetables at the point of consumption using both culture-dependent and culture-independent methods. Results Total culturable bacteria on salad vegetables ranged from 8.0 × 103 to 5.5 × 108 CFU g-1. The number of culturable endophytic bacteria from surface sterilized plants was significantly lower, ranging from 2.2 × 103 to 5.8 × 105 CFU g-1. Cultured isolates belonged to six major bacterial phyla, and included representatives of Pseudomonas, Pantoea, Chryseobacterium, and Flavobacterium. Eleven different phyla and subphyla were identified by culture-independent pyrosequencing, with Gammaproteobacteria, Betaproteobacteria, and Bacteroidetes being the most dominant lineages. Other bacterial lineages identified (e.g. Firmicutes, Alphaproteobacteria, Acidobacteria, and Actinobacteria) typically represented less than 1% of sequences obtained. At the genus level, sequences classified as Pseudomonas were identified in all samples and this was often the most prevalent genus. Ralstonia sequences made up a greater portion of the community in surface sterilized than non-surface sterilized samples, indicating that it was largely endophytic, while Acinetobacter sequences appeared to be primarily associated with the leaf surface. Analysis of molecular variance indicated there were no significant differences in bacterial community composition between organic versus conventionally grown, or surface-sterilized versus non-sterilized leaf vegetables. While culture-independent pyrosequencing identified significantly more bacterial taxa, the dominant taxa from pyrosequence data were also detected by traditional culture-dependent methods. Conclusions The use of pyrosequencing allowed for the identification of low abundance bacteria in leaf salad vegetables not detected by culture-dependent methods. The presence of a range of bacterial populations as endophytes presents an interesting phenomenon as these microorganisms cannot be removed by washing and are thus ingested during salad consumption.
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Affiliation(s)
- Colin R Jackson
- Department of Biology, The University of Mississippi, University 38677, USA.
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Bacci G, Bazzicalupo M, Benedetti A, Mengoni A. StreamingTrim 1.0: a Java software for dynamic trimming of 16S rRNA sequence data from metagenetic studies. Mol Ecol Resour 2013; 14:426-34. [PMID: 24128146 DOI: 10.1111/1755-0998.12187] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Accepted: 10/07/2013] [Indexed: 12/29/2022]
Abstract
Next-generation sequencing technologies are extensively used in the field of molecular microbial ecology to describe taxonomic composition and to infer functionality of microbial communities. In particular, the so-called barcode or metagenetic applications that are based on PCR amplicon library sequencing are very popular at present. One of the problems, related to the utilization of the data of these libraries, is the analysis of reads quality and removal (trimming) of low-quality segments, while retaining sufficient information for subsequent analyses (e.g. taxonomic assignment). Here, we present StreamingTrim, a DNA reads trimming software, written in Java, with which researchers are able to analyse the quality of DNA sequences in fastq files and to search for low-quality zones in a very conservative way. This software has been developed with the aim to provide a tool capable of trimming amplicon library data, retaining as much as taxonomic information as possible. This software is equipped with a graphical user interface for a user-friendly usage. Moreover, from a computational point of view, StreamingTrim reads and analyses sequences one by one from an input fastq file, without keeping anything in memory, permitting to run the computation on a normal desktop PC or even a laptop. Trimmed sequences are saved in an output file, and a statistics summary is displayed that contains the mean and standard deviation of the length and quality of the whole sequence file. Compiled software, a manual and example data sets are available under the BSD-2-Clause License at the GitHub repository at https://github.com/GiBacci/StreamingTrim/.
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Affiliation(s)
- G Bacci
- Department of Biology, University of Florence, via Madonna del Piano 6, Firenze, I-50019, Italy; Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Centro di Ricerca per lo Studio delle Relazioni tra Pianta e Suolo (CRA-RPS), Via della Navicella 2/4, Roma, I-00184, Italy
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Bogino P, Abod A, Nievas F, Giordano W. Water-limiting conditions alter the structure and biofilm-forming ability of bacterial multispecies communities in the alfalfa rhizosphere. PLoS One 2013; 8:e79614. [PMID: 24223979 PMCID: PMC3817132 DOI: 10.1371/journal.pone.0079614] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Accepted: 09/26/2013] [Indexed: 11/18/2022] Open
Abstract
Biofilms are microbial communities that adhere to biotic or abiotic surfaces and are enclosed in a protective matrix of extracellular compounds. An important advantage of the biofilm lifestyle for soil bacteria (rhizobacteria) is protection against water deprivation (desiccation or osmotic effect). The rhizosphere is a crucial microhabitat for ecological, interactive, and agricultural production processes. The composition and functions of bacterial biofilms in soil microniches are poorly understood. We studied multibacterial communities established as biofilm-like structures in the rhizosphere of Medicago sativa (alfalfa) exposed to 3 experimental conditions of water limitation. The whole biofilm-forming ability (WBFA) for rhizospheric communities exposed to desiccation was higher than that of communities exposed to saline or nonstressful conditions. A culture-dependent ribotyping analysis indicated that communities exposed to desiccation or saline conditions were more diverse than those under the nonstressful condition. 16S rRNA gene sequencing of selected strains showed that the rhizospheric communities consisted primarily of members of the Actinobacteria and α- and γ-Proteobacteria, regardless of the water-limiting condition. Our findings contribute to improved understanding of the effects of environmental stress factors on plant-bacteria interaction processes and have potential application to agricultural management practices.
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Affiliation(s)
- Pablo Bogino
- Departamento de Biología Molecular, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba, Argentina
| | - Ayelén Abod
- Departamento de Biología Molecular, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba, Argentina
| | - Fiorela Nievas
- Departamento de Biología Molecular, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba, Argentina
| | - Walter Giordano
- Departamento de Biología Molecular, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba, Argentina
- * E-mail:
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Galardini M, Pini F, Bazzicalupo M, Biondi EG, Mengoni A. Replicon-dependent bacterial genome evolution: the case of Sinorhizobium meliloti. Genome Biol Evol 2013; 5:542-58. [PMID: 23431003 PMCID: PMC3622305 DOI: 10.1093/gbe/evt027] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Many bacterial species, such as the alphaproteobacterium Sinorhizobium meliloti, are characterized by open pangenomes and contain multipartite genomes consisting of a chromosome and other large-sized replicons, such as chromids, megaplasmids, and plasmids. The evolutionary forces in both functional and structural aspects that shape the pangenome of species with multipartite genomes are still poorly understood. Therefore, we sequenced the genomes of 10 new S. meliloti strains, analyzed with four publicly available additional genomic sequences. Results indicated that the three main replicons present in these strains (a chromosome, a chromid, and a megaplasmid) partly show replicon-specific behaviors related to strain differentiation. In particular, the pSymB chromid was shown to be a hot spot for positively selected genes, and, unexpectedly, genes resident in the pSymB chromid were also found to be more widespread in distant taxa than those located in the other replicons. Moreover, through the exploitation of a DNA proximity network, a series of conserved “DNA backbones” were found to shape the evolution of the genome structure, with the rest of the genome experiencing rearrangements. The presented data allow depicting a scenario where the pSymB chromid has a distinctive role in intraspecies differentiation and in evolution through positive selection, whereas the pSymA megaplasmid mostly contributes to structural fluidity and to the emergence of new functions, indicating a specific evolutionary role for each replicon in the pangenome evolution.
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Affiliation(s)
- Marco Galardini
- Department of Biology, University of Firenze, Firenze, Italy
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Lin W, Wu L, Lin S, Zhang A, Zhou M, Lin R, Wang H, Chen J, Zhang Z, Lin R. Metaproteomic analysis of ratoon sugarcane rhizospheric soil. BMC Microbiol 2013; 13:135. [PMID: 23773576 PMCID: PMC3687580 DOI: 10.1186/1471-2180-13-135] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2013] [Accepted: 05/30/2013] [Indexed: 11/13/2022] Open
Abstract
Background The current study was undertaken to elucidate the mechanism of yield decline in ratoon sugarcane using soil metaproteomics combined with community level physiological profiles (CLPP) analysis. Results The available stalk number, stalk diameter, single stalk weight and theoretical yield of ratoon cane (RS) were found to be significantly lower than those of plant cane (NS). The activities of several carbon, nitrogen and phosphorus processing enzymes, including invertase, peroxidase, urease and phosphomonoesterase were found to be significantly lower in RS soil than in NS soil. BIOLOG analysis indicated a significant decline in average well-color development (AWCD), Shannon’s diversity and evenness indices in RS soil as compared to NS soil. To profile the rhizospheric metaproteome, 109 soil protein spots with high resolution and repeatability were successfully identified. These proteins were found to be involved in carbohydrate/energy, amino acid, protein, nucleotide, auxin and secondary metabolisms, membrane transport, signal transduction and resistance, etc. Comparative metaproteomics analysis revealed that 38 proteins were differentially expressed in the RS soil as compared to the control soil or NS soil. Among these, most of the plant proteins related to carbohydrate and amino acid metabolism and stress response were up-regulated in RS soil. Furthermore, several microbial proteins related to membrane transport and signal transduction were up-regulated in RS soil. These proteins were speculated to function in root colonization by microbes. Conclusions Our experiments revealed that sugarcane ratooning practice induced significant changes in the soil enzyme activities, the catabolic diversity of microbial community, and the expression level of soil proteins. They influenced the biochemical processes in the rhizosphere ecosystem and mediated the interactions between plants and soil microbes.
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Affiliation(s)
- Wenxiong Lin
- Key Laboratory of Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, P R China.
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Bapaume L, Reinhardt D. How membranes shape plant symbioses: signaling and transport in nodulation and arbuscular mycorrhiza. FRONTIERS IN PLANT SCIENCE 2012; 3:223. [PMID: 23060892 PMCID: PMC3464683 DOI: 10.3389/fpls.2012.00223] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Accepted: 09/14/2012] [Indexed: 05/19/2023]
Abstract
As sessile organisms that cannot evade adverse environmental conditions, plants have evolved various adaptive strategies to cope with environmental stresses. One of the most successful adaptations is the formation of symbiotic associations with beneficial microbes. In these mutualistic interactions the partners exchange essential nutrients and improve their resistance to biotic and abiotic stresses. In arbuscular mycorrhiza (AM) and in root nodule symbiosis (RNS), AM fungi and rhizobia, respectively, penetrate roots and accommodate within the cells of the plant host. In these endosymbiotic associations, both partners keep their plasma membranes intact and use them to control the bidirectional exchange of signaling molecules and nutrients. Intracellular accommodation requires the exchange of symbiotic signals and the reprogramming of both interacting partners. This involves fundamental changes at the level of gene expression and of the cytoskeleton, as well as of organelles such as plastids, endoplasmic reticulum (ER), and the central vacuole. Symbiotic cells are highly compartmentalized and have a complex membrane system specialized for the diverse functions in molecular communication and nutrient exchange. Here, we discuss the roles of the different cellular membrane systems and their symbiosis-related proteins in AM and RNS, and we review recent progress in the analysis of membrane proteins involved in endosymbiosis.
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Affiliation(s)
| | - Didier Reinhardt
- Department of Biology, University of FribourgFribourg, Switzerland
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