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Song Y, Spooren J, Jongekrijg CD, Manders EJHH, de Jonge R, Pieterse CMJ, Bakker PAHM, Berendsen RL. Seed tuber imprinting shapes the next-generation potato microbiome. ENVIRONMENTAL MICROBIOME 2024; 19:12. [PMID: 38383442 PMCID: PMC10882817 DOI: 10.1186/s40793-024-00553-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 01/21/2024] [Indexed: 02/23/2024]
Abstract
BACKGROUND Potato seed tubers are colonized and inhabited by soil-borne microbes, that can affect the performance of the emerging daughter plant in the next season. In this study, we investigated the intergenerational inheritance of microbiota from seed tubers to next-season daughter plants under field condition by amplicon sequencing of bacterial and fungal microbiota associated with tubers and roots, and tracked the microbial transmission from different seed tuber compartments to sprouts. RESULTS We observed that field of production and potato genotype significantly (P < 0.01) affected the composition of the seed tuber microbiome and that these differences persisted during winter storage of the seed tubers. Remarkably, when seed tubers from different production fields were planted in a single trial field, the microbiomes of daughter tubers and roots of the emerging plants could still be distinguished (P < 0.01) according to the production field of the seed tuber. Surprisingly, we found little vertical inheritance of field-unique microbes from the seed tuber to the daughter tubers and roots, constituting less than 0.2% of their respective microbial communities. However, under controlled conditions, around 98% of the sprout microbiome was found to originate from the seed tuber and had retained their field-specific patterns. CONCLUSIONS The field of production shapes the microbiome of seed tubers, emerging potato plants and even the microbiome of newly formed daughter tubers. Different compartments of seed tubers harbor distinct microbiomes. Both bacteria and fungi on seed tubers have the potential of being vertically transmitted to the sprouts, and the sprout subsequently promotes proliferation of a select number of microbes from the seed tuber. Recognizing the role of plant microbiomes in plant health, the initial microbiome of seed tubers specifically or planting materials in general is an overlooked trait. Elucidating the relative importance of the initial microbiome and the mechanisms by which the origin of planting materials affect microbiome assembly will pave the way for the development of microbiome-based predictive models that may predict the quality of seed tuber lots, ultimately facilitating microbiome-improved potato cultivation.
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Affiliation(s)
- Yang Song
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
| | - Jelle Spooren
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Casper D Jongekrijg
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Ellen J H H Manders
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Ronnie de Jonge
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Corné M J Pieterse
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Peter A H M Bakker
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Roeland L Berendsen
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
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Petrushin IS, Filinova NV, Gutnik DI. Potato Microbiome: Relationship with Environmental Factors and Approaches for Microbiome Modulation. Int J Mol Sci 2024; 25:750. [PMID: 38255824 PMCID: PMC10815375 DOI: 10.3390/ijms25020750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/12/2023] [Accepted: 01/03/2024] [Indexed: 01/24/2024] Open
Abstract
Every land plant exists in a close relationship with microbial communities of several niches: rhizosphere, endosphere, phyllosphere, etc. The growth and yield of potato-a critical food crop worldwide-highly depend on the diversity and structure of the bacterial and fungal communities with which the potato plant coexists. The potato plant has a specific part, tubers, and the soil near the tubers as a sub-compartment is usually called the "geocaulosphere", which is associated with the storage process and tare soil microbiome. Specific microbes can help the plant to adapt to particular environmental conditions and resist pathogens. There are a number of approaches to modulate the microbiome that provide organisms with desired features during inoculation. The mechanisms of plant-bacterial communication remain understudied, and for further engineering of microbiomes with particular features, the knowledge on the potato microbiome should be summarized. The most recent approaches to microbiome engineering include the construction of a synthetic microbial community or management of the plant microbiome using genome engineering. In this review, the various factors that determine the microbiome of potato and approaches that allow us to mitigate the negative impact of drought and pathogens are surveyed.
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Affiliation(s)
- Ivan S. Petrushin
- Siberian Institute of Plant Physiology and Biochemistry, Siberian Branch of the Russian Academy of Sciences, Irkutsk 664033, Russia; (N.V.F.); (D.I.G.)
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Jiao R, Wu B, Liang Z, Gao P, Gao X. GLV reveal species differences and responses to environment in alpine shrub Rosa sericea complex. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 896:166146. [PMID: 37595914 DOI: 10.1016/j.scitotenv.2023.166146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 07/20/2023] [Accepted: 08/06/2023] [Indexed: 08/20/2023]
Abstract
Plant Volatile components are an ecological adaptation mechanism of plants that can reflect species differences and environment information where it is located. The alpine shrub Rosa sericea complex consists of several allied species, which are morphologically similar and difficult to distinguish, they are typical distribution along the elevation in the Himalayas and the Transverse Ranges. We selected two typical areas to find that the different species could be distinguished by their "green leaf volatile components" (GLV) composition as well as their geographical location, and it was evident that species with glands had higher sesquiterpene content. Correlation analysis revealed the relation between volatile components and ecology factors (climate factors, soil factors, phyllospheric microorganisms). Our study adds a new perspective and basis for the environmental adaptations of different species in the alpine shrub Rosa sericea complex from a chemical ecology perspective.
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Affiliation(s)
- Ruifang Jiao
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Xingke Road 723, Guangzhou 510650, China
| | - Bohan Wu
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Zhenlong Liang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ping Gao
- Key Laboratory of Bio-Resources and Eco-Environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China.
| | - Xinfen Gao
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China.
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van der Lee TAJ, van Gent-Pelzer MPE, Jonkheer EM, Brankovics B, Houwers IM, van der Wolf JM, Bonants PJM, van Duivenbode I, Vreeburg RAM, Nas M, Smit S. An Efficient Triplex TaqMan Quantitative PCR to Detect a Blackleg-Causing Lineage of Pectobacterium brasiliense in Potato Based on a Pangenome Analysis. Microorganisms 2023; 11:2080. [PMID: 37630640 PMCID: PMC10459533 DOI: 10.3390/microorganisms11082080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 08/08/2023] [Accepted: 08/10/2023] [Indexed: 08/27/2023] Open
Abstract
P. brasiliense is an important bacterial pathogen causing blackleg (BL) in potatoes. Nevertheless, P. brasiliense is often detected in seed lots that do not develop any of the typical blackleg symptoms in the potato crop when planted. Field bioassays identified that P. brasiliense strains can be categorized into two distinct classes, some able to cause blackleg symptoms and some unable to do it. A comparative pangenomic approach was performed on 116 P. brasiliense strains, of which 15 were characterized as BL-causing strains and 25 as non-causative. In a genetically homogeneous clade comprising all BL-causing P. brasiliense strains, two genes only present in the BL-causing strains were identified, one encoding a predicted lysozyme inhibitor Lprl (LZI) and one encoding a putative Toll/interleukin-1 receptor (TIR) domain-containing protein. TaqMan assays for the specific detection of BL-causing P. brasiliense were developed and integrated with the previously developed generic P. brasiliense assay into a triplex TaqMan assay. This simultaneous detection makes the scoring more efficient as only a single tube is needed, and it is more robust as BL-causing strains of P. brasiliense should be positive for all three assays. Individual P. brasiliense strains were found to be either positive for all three assays or only for the P. brasiliense assay. In potato samples, the mixed presence of BL-causing and not BL-causing P. brasiliense strains was observed as shown by the difference in Ct value of the TaqMan assays. However, upon extension of the number of strains, it became clear that in recent years additional BL-causing lineages of P. brasiliense were detected for which additional assays must be developed.
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Affiliation(s)
- Theo A. J. van der Lee
- Biointeractions and Plant Health, Wageningen Plant Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Marga P. E. van Gent-Pelzer
- Biointeractions and Plant Health, Wageningen Plant Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Eef M. Jonkheer
- Biointeractions and Plant Health, Wageningen Plant Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Balázs Brankovics
- Biointeractions and Plant Health, Wageningen Plant Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Ilse M. Houwers
- Biointeractions and Plant Health, Wageningen Plant Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Jan M. van der Wolf
- Biointeractions and Plant Health, Wageningen Plant Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Peter J. M. Bonants
- Biointeractions and Plant Health, Wageningen Plant Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Inge van Duivenbode
- Dutch General Inspection Service (NAK), Randweg 14, 8304 AS Emmeloord, The Netherlands
| | - Robert A. M. Vreeburg
- Dutch General Inspection Service (NAK), Randweg 14, 8304 AS Emmeloord, The Netherlands
| | - Mathijs Nas
- Dutch General Inspection Service (NAK), Randweg 14, 8304 AS Emmeloord, The Netherlands
| | - Sandra Smit
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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Gharsallah H, Ksentini I, Frikha-Gargouri O, Hadj Taieb K, Ben Gharsa H, Schuster C, Chatti-Kolsi A, Triki MA, Ksantini M, Leclerque A. Exploring Bacterial and Fungal Biodiversity in Eight Mediterranean Olive Orchards ( Olea europaea L.) in Tunisia. Microorganisms 2023; 11:microorganisms11041086. [PMID: 37110509 PMCID: PMC10145363 DOI: 10.3390/microorganisms11041086] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/14/2023] [Accepted: 04/18/2023] [Indexed: 04/29/2023] Open
Abstract
A wide array of bacteria and fungi are known for their association with pests that impact the health of the olive tree. The latter presents the most economically important cultivation in Tunisia. The microbial diversity associated with olive orchards in Tunisia remains unknown and undetermined. This study investigated microbial diversity to elucidate the microbial interactions that lead to olive disease, and the bio-prospects for potential microbial biocontrol agents associated with insect pests of economic relevance for olive cultivation in the Mediterranean area. Bacterial and fungal isolation was made from soil and olive tree pests. A total of 215 bacterial and fungal strains were randomly isolated from eight different biotopes situated in Sfax (Tunisia), with different management practices. 16S rRNA and ITS gene sequencing were used to identify the microbial community. The majority of the isolated bacteria, Staphylococcus, Bacillus, Alcaligenes, and Providencia, are typical of the olive ecosystem and the most common fungi are Penicillium, Aspergillus, and Cladosporium. The different olive orchards depicted distinct communities, and exhibited dissimilar amounts of bacteria and fungi with distinct ecological functions that could be considered as promising resources in biological control.
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Affiliation(s)
- Houda Gharsallah
- Laboratory of Improvement and Protection of Olive Tree Genetic Resources, Olive Tree Institute, University of Sfax, Sfax 3038, Tunisia
| | - Ines Ksentini
- Laboratory of Improvement and Protection of Olive Tree Genetic Resources, Olive Tree Institute, University of Sfax, Sfax 3038, Tunisia
| | - Olfa Frikha-Gargouri
- Laboratory of Biopesticides, Centre of Biotechnology of Sfax, University of Sfax, Sfax 3038, Tunisia
| | - Karama Hadj Taieb
- Laboratory of Improvement and Protection of Olive Tree Genetic Resources, Olive Tree Institute, University of Sfax, Sfax 3038, Tunisia
| | - Haifa Ben Gharsa
- Department of Biology, Technische Universität Darmstadt, 64289 Darmstadt, Germany
| | - Christina Schuster
- Department of Biology, Technische Universität Darmstadt, 64289 Darmstadt, Germany
| | - Amel Chatti-Kolsi
- Laboratory of Improvement and Protection of Olive Tree Genetic Resources, Olive Tree Institute, University of Sfax, Sfax 3038, Tunisia
| | - Mohamed Ali Triki
- Laboratory of Improvement and Protection of Olive Tree Genetic Resources, Olive Tree Institute, University of Sfax, Sfax 3038, Tunisia
| | - Mohieddine Ksantini
- Laboratory of Improvement and Protection of Olive Tree Genetic Resources, Olive Tree Institute, University of Sfax, Sfax 3038, Tunisia
| | - Andreas Leclerque
- Department of Biology, Technische Universität Darmstadt, 64289 Darmstadt, Germany
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Liu J, Zhang W, Liu Y, Zhu W, Yuan Z, Su X, Ding C. Differences in phyllosphere microbiomes among different Populus spp. in the same habitat. FRONTIERS IN PLANT SCIENCE 2023; 14:1143878. [PMID: 37063209 PMCID: PMC10098339 DOI: 10.3389/fpls.2023.1143878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 03/20/2023] [Indexed: 06/19/2023]
Abstract
INTRODUCTION The above-ground parts of terrestrial plants are collectively known as the phyllosphere. The surface of the leaf blade is a unique and extensive habitat for microbial communities. Phyllosphere bacteria are the second most closely associated microbial group with plants after fungi and viruses, and are the most abundant, occupying a dominant position in the phyllosphere microbial community. Host species are a major factor influencing the community diversity and structure of phyllosphere microorganisms. METHODS In this study, six Populus spp. were selected for study under the same site conditions and their phyllosphere bacterial community DNA fragments were paired-end sequenced using 16S ribosomal RNA (rRNA) gene amplicon sequencing. Based on the distribution of the amplicon sequence variants (ASVs), we assessed the alpha-diversity level of each sample and further measured the differences in species abundance composition among the samples, and predicted the metabolic function of the community based on the gene sequencing results. RESULTS The results revealed that different Populus spp. under the same stand conditions resulted in different phyllosphere bacterial communities. The bacterial community structure was mainly affected by the carbon and soluble sugar content of the leaves, and the leaf nitrogen, phosphorus and carbon/nitrogen were the main factors affecting the relative abundance of phyllosphere bacteria. DISCUSSION Previous studies have shown that a large proportion of the variation in the composition of phyllosphere microbial communities was explained by the hosts themselves. In contrast, leaf-borne nutrients were an available resource for bacteria living on the leaf surface, thus influencing the community structure of phyllosphere bacteria. These were similar to the conclusions obtained in this study. This study provides theoretical support for the study of the composition and structure of phyllosphere bacterial communities in woody plants and the factors influencing them.
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Affiliation(s)
- Jiaying Liu
- College of Forestry, Shenyang Agriculture University, Shenyang, China
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Weixi Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Yuting Liu
- College of Forestry, Shenyang Agriculture University, Shenyang, China
| | - Wenxu Zhu
- College of Forestry, Shenyang Agriculture University, Shenyang, China
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Research Station of Liaohe-River Plain Forest Ecosystem, Chinese Forest Ecosystem Research Network (CFERN), College of Forestry, Shenyang Agricultural University, Tieling, China
| | - Zhengsai Yuan
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Xiaohua Su
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Changjun Ding
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
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Abstract
The findings on the strategies employed by endophytic microbes have provided salient information to the researchers on the need to maximally explore them as bio-input in agricultural biotechnology. Biotic and abiotic factors are known to influence microbial recruitments from external plant environments into plant tissues. Endophytic microbes exhibit mutualism or antagonism association with host plants. The beneficial types contribute to plant growth and soil health, directly or indirectly. Strategies to enhance the use of endophytic microbes are desirable in modern agriculture, such that these microbes can be applied individually or combined as bioinoculants with bioprospecting in crop breeding systems. Scant information is available on the strategies for shaping the endophytic microbiome; hence, the need to unravel microbial strategies for yield enhancement and pathogen suppressiveness have become imperative. Therefore, this review focuses on the endophytic microbiome, mechanisms, factors influencing endophyte recruitment, and strategies for possible exploration as bioinoculants.
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Ferraboschi P, Ciceri S, Grisenti P. Applications of Lysozyme, an Innate Immune Defense Factor, as an Alternative Antibiotic. Antibiotics (Basel) 2021; 10:1534. [PMID: 34943746 PMCID: PMC8698798 DOI: 10.3390/antibiotics10121534] [Citation(s) in RCA: 105] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/03/2021] [Accepted: 12/08/2021] [Indexed: 12/18/2022] Open
Abstract
Lysozyme is a ~14 kDa protein present in many mucosal secretions (tears, saliva, and mucus) and tissues of animals and plants, and plays an important role in the innate immunity, providing protection against bacteria, viruses, and fungi. Three main different types of lysozymes are known: the c-type (chicken or conventional type), the g-type (goose type), and the i-type (invertebrate type). It has long been the subject of several applications due to its antimicrobial properties. The problem of antibiotic resistance has stimulated the search for new molecules or new applications of known compounds. The use of lysozyme as an alternative antibiotic is the subject of this review, which covers the results published over the past two decades. This review is focused on the applications of lysozyme in medicine, (the treatment of infectious diseases, wound healing, and anti-biofilm), veterinary, feed, food preservation, and crop protection. It is available from a wide range of sources, in addition to the well-known chicken egg white, and its synergism with other compounds, endowed with antimicrobial activity, are also summarized. An overview of the modified lysozyme applications is provided in the form of tables.
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Affiliation(s)
- Patrizia Ferraboschi
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Via C. Saldini 50, 20133 Milano, Italy;
| | - Samuele Ciceri
- Department of Pharmaceutical Sciences, University of Milan, Via L. Mangiagalli 25, 20133 Milano, Italy;
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Bashir I, War AF, Rafiq I, Reshi ZA, Rashid I, Shouche YS. Phyllosphere microbiome: Diversity and functions. Microbiol Res 2021; 254:126888. [PMID: 34700185 DOI: 10.1016/j.micres.2021.126888] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 09/15/2021] [Accepted: 09/30/2021] [Indexed: 12/28/2022]
Abstract
Phyllosphere or aerial surface of plants represents the globally largest and peculiar microbial habitat that inhabits diverse and rich communities of bacteria, fungi, viruses, cyanobacteria, actinobacteria, nematodes, and protozoans. These hyperdiverse microbial communities are related to the host's specific functional traits and influence the host's physiology and the ecosystem's functioning. In the last few years, significant advances have been made in unravelling several aspects of phyllosphere microbiology, including diversity and microbial community composition, dynamics, and functional interactions. This review highlights the current knowledge about the assembly, structure, and composition of phyllosphere microbial communities across spatio-temporal scales, besides functional significance of different microbial communities to the plant host and the surrounding environment. The knowledge will help develop strategies for modelling and manipulating these highly beneficial microbial consortia for furthering scientific inquiry into their interactions with the host plants and also for their useful and economic utilization.
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Affiliation(s)
- Iqra Bashir
- Department of Botany, University of Kashmir, Srinagar, 190006, Jammu and Kashmir, India.
| | - Aadil Farooq War
- Department of Botany, University of Kashmir, Srinagar, 190006, Jammu and Kashmir, India
| | - Iflah Rafiq
- Department of Botany, University of Kashmir, Srinagar, 190006, Jammu and Kashmir, India
| | - Zafar A Reshi
- Department of Botany, University of Kashmir, Srinagar, 190006, Jammu and Kashmir, India
| | - Irfan Rashid
- Department of Botany, University of Kashmir, Srinagar, 190006, Jammu and Kashmir, India
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Local Network Properties of Soil and Rhizosphere Microbial Communities in Potato Plantations Treated with a Biological Product Are Important Predictors of Crop Yield. mSphere 2021; 6:e0013021. [PMID: 34378980 PMCID: PMC8386434 DOI: 10.1128/msphere.00130-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Understanding the effectiveness and potential mechanism of action of agricultural biological products under different soil profiles and crops will allow more precise product recommendations based on local conditions and will ultimately result in increased crop yield. This study aimed to use bulk soil and rhizosphere microbial composition and structure to evaluate the potential effect of a Bacillus amyloliquefaciens inoculant (strain QST713) on potatoes and to explore its relationship with crop yield. We implemented next-generation sequencing (NGS) and bioinformatics approaches to assess the bacterial and fungal biodiversity in 185 soil samples, distributed over four different time points—from planting to harvest—from three different geographical locations in the United States. In addition to location and sampling time (which includes the difference between bulk soil and rhizosphere) as the main variables defining the microbiome composition, the microbial inoculant applied as a treatment also had a small but significant effect in fungal communities and a marginally significant effect in bacterial communities. However, treatment preserved the native communities without causing a detectable long-lasting effect on the alpha- and beta-diversity patterns after harvest. Using information about the application of the microbial inoculant and considering microbiome composition and structure data, we were able to train a Random Forest model to estimate if a bulk soil or rhizosphere sample came from a low- or high-yield block with relatively high accuracy (84.6%), concluding that the structure of fungal communities gives us more information as an estimator of potato yield than the structure of bacterial communities. IMPORTANCE Our results reinforce the notion that each cultivar on each location recruits a unique microbial community and that these communities are modulated by the vegetative growth stage of the plant. Moreover, inoculation of a Bacillus amyloliquefaciens strain QST713-based product on potatoes also changed the abundance of specific taxonomic groups and the structure of local networks in those locations where the product caused an increase in the yield. The data obtained, from in-field assays, allowed training a predictive model to estimate the yield of a certain block, identifying microbiome variables—especially those related to microbial community structure—even with a higher predictive power than the geographical location of the block (that is, the principal determinant of microbial beta-diversity). The methods described here can be replicated to fit new models in any other crop and to evaluate the effect of any agricultural input in the composition and structure of the soil microbiome.
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Compant S, Cambon MC, Vacher C, Mitter B, Samad A, Sessitsch A. The plant endosphere world - bacterial life within plants. Environ Microbiol 2020; 23:1812-1829. [PMID: 32955144 DOI: 10.1111/1462-2920.15240] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 09/11/2020] [Accepted: 09/16/2020] [Indexed: 12/23/2022]
Abstract
The plant endosphere is colonized by complex microbial communities and microorganisms, which colonize the plant interior at least part of their lifetime and are termed endophytes. Their functions range from mutualism to pathogenicity. All plant organs and tissues are generally colonized by bacterial endophytes and their diversity and composition depend on the plant, the plant organ and its physiological conditions, the plant growth stage as well as on the environment. Plant-associated microorganisms, and in particular endophytes, have lately received high attention, because of the increasing awareness of the importance of host-associated microbiota for the functioning and performance of their host. Some endophyte functions are known from mostly lab assays, genome prediction and few metagenome analyses; however, we have limited understanding on in planta activities, particularly considering the diversity of micro-environments and the dynamics of conditions. In our review, we present recent findings on endosphere environments, their physiological conditions and endophyte colonization. Furthermore, we discuss microbial functions, the interaction between endophytes and plants as well as methodological limitations of endophyte research. We also provide an outlook on needs of future research to improve our understanding on the role of microbiota colonizing the endosphere on plant traits and ecosystem functioning.
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Affiliation(s)
- Stéphane Compant
- Center for Health and Bioresources, Bioresources Unit, Konrad Lorenz Straße 24, AIT Austrian Institute of Technology, Tulln, A-3430, Austria
| | | | | | - Birgit Mitter
- Center for Health and Bioresources, Bioresources Unit, Konrad Lorenz Straße 24, AIT Austrian Institute of Technology, Tulln, A-3430, Austria
| | - Abdul Samad
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, G1V4C7, Canada
| | - Angela Sessitsch
- Center for Health and Bioresources, Bioresources Unit, Konrad Lorenz Straße 24, AIT Austrian Institute of Technology, Tulln, A-3430, Austria
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Rai PK, Kim KH, Lee SS, Lee JH. Molecular mechanisms in phytoremediation of environmental contaminants and prospects of engineered transgenic plants/microbes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 705:135858. [PMID: 31846820 DOI: 10.1016/j.scitotenv.2019.135858] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 11/21/2019] [Accepted: 11/28/2019] [Indexed: 05/06/2023]
Abstract
Concerns about emerging environmental contaminants have been growing along with industrialization and urbanization around the globe. Among various options for remediating these contaminants, phytotechnology is suggested as a feasible option to maintain the environmental sustainability. The recent advances in phytoremediation, genetic/molecular/omics/metabolic engineering, and nanotechnology are opening new paths for efficient treatment of emerging organic/inorganic contaminants. In this respect, elucidation of molecular mechanisms and genetic engineering of hyperaccumulator plants is expected to enhance remediation of environmental contaminants. This review was organized to offer valuable insights into the molecular mechanisms of phytoremediation and the prospects of transgenic hyperaccumulators with enhanced stress tolerance to diverse contaminants such as heavy metals and metalloids, xenobiotics, explosives, poly aromatic hydrocarbons (PAHs), petroleum hydrocarbons, pesticides, and nanoparticles. The roles of genoremediation and nanoparticles in augmenting the phytoremediation technology are also described in an interrelated framework with biotechnological prospects (e.g., plant molecular nano-farming). Finally, political debate on the preferential use of crops versus non-crop hyperaccumulators in genoremediation, limitations of transgenics in phytotechnologies, and their public acceptance issues are discussed in the policy framework.
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Affiliation(s)
- Prabhat Kumar Rai
- Department of Environmental Science, Mizoram University, Aizawl 796004, India
| | - Ki-Hyun Kim
- Department of Civil and Environmental Engineering, Hanyang University, Seoul 04763, Republic of Korea.
| | - Sang Soo Lee
- Department of Environmental Engineering, Yonsei University, Wonju 26494, Republic of Korea.
| | - Jin-Hong Lee
- Department of Environmental Engineering, Chungnam National University, Daejeon 34148, Republic of Korea
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13
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Nerva L, Pagliarani C, Pugliese M, Monchiero M, Gonthier S, Gullino ML, Gambino G, Chitarra W. Grapevine Phyllosphere Community Analysis in Response to Elicitor Application against Powdery Mildew. Microorganisms 2019; 7:microorganisms7120662. [PMID: 31817902 PMCID: PMC6956034 DOI: 10.3390/microorganisms7120662] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 11/26/2019] [Accepted: 12/05/2019] [Indexed: 12/23/2022] Open
Abstract
The reduction of antimicrobial treatments and mainly the application of environmentally friendly compounds, such as resistance elicitors, is an impelling challenge to undertake more sustainable agriculture. We performed this research to study the effectiveness of non-conventional compounds in reducing leaf fungal attack and to investigate whether they influence the grape phyllosphere. Pathogenicity tests were conducted on potted Vitis vinifera "Nebbiolo" and "Moscato" cultivars infected with the powdery mildew agent (Erysiphe necator) and treated with three elicitors. Differences in the foliar microbial community were then evaluated by community-level physiological profiling by using BiologTM EcoPlates, high throughput sequencing of the Internal Transcribed Spacer (ITS) region, and RNA sequencing for the viral community. In both cultivars, all products were effective as they significantly reduced pathogen development. EcoPlate analysis and ITS sequencing showed that the microbial communities were not influenced by the alternative compound application, confirming their specific activity as plant defense elicitors. Nevertheless, "Moscato" plants were less susceptible to the disease and presented different phyllosphere composition, resulting in a richer viral community, when compared with the "Nebbiolo" plants. The observed effect on microbial communities pointed to the existence of distinct genotype-specific defense mechanisms independently of the elicitor application.
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Affiliation(s)
- Luca Nerva
- Research Centre for Viticulture and Enology, Council for Agricultural Research and Economics (CREA-VE), Via XXVIII Aprile 26, 31015 Conegliano, Italy
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Strada delle Cacce 73, 10135 Torino, Italy; (C.P.); (S.G.); (G.G.)
- Correspondence: (L.N.); (W.C.); Tel.: +39-04-3845-6712 (W.C.); Fax: +39-04-3845-0773 (W.C.)
| | - Chiara Pagliarani
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Strada delle Cacce 73, 10135 Torino, Italy; (C.P.); (S.G.); (G.G.)
| | - Massimo Pugliese
- Centre of Competence for the Innovation in the Agro-Environmental Sector (AGROINNOVA), University of Torino, Largo Paolo Braccini 2, 10095 Grugliasco (TO), Italy; (M.P.); (M.L.G.)
- Department of Agricultural, Forest and Food Sciences (DISAFA), University of Torino, Largo Paolo Braccini 2, 10095 Grugliasco (TO), Italy
| | | | - Solène Gonthier
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Strada delle Cacce 73, 10135 Torino, Italy; (C.P.); (S.G.); (G.G.)
- Biocomputing and Modelling Department, National Institute of Applied Sciences, INSA Lyon, 69621 Villeurbanne cedex, France
| | - Maria Lodovica Gullino
- Centre of Competence for the Innovation in the Agro-Environmental Sector (AGROINNOVA), University of Torino, Largo Paolo Braccini 2, 10095 Grugliasco (TO), Italy; (M.P.); (M.L.G.)
- Department of Agricultural, Forest and Food Sciences (DISAFA), University of Torino, Largo Paolo Braccini 2, 10095 Grugliasco (TO), Italy
| | - Giorgio Gambino
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Strada delle Cacce 73, 10135 Torino, Italy; (C.P.); (S.G.); (G.G.)
| | - Walter Chitarra
- Research Centre for Viticulture and Enology, Council for Agricultural Research and Economics (CREA-VE), Via XXVIII Aprile 26, 31015 Conegliano, Italy
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Strada delle Cacce 73, 10135 Torino, Italy; (C.P.); (S.G.); (G.G.)
- Correspondence: (L.N.); (W.C.); Tel.: +39-04-3845-6712 (W.C.); Fax: +39-04-3845-0773 (W.C.)
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14
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Buchholz F, Antonielli L, Kostić T, Sessitsch A, Mitter B. The bacterial community in potato is recruited from soil and partly inherited across generations. PLoS One 2019; 14:e0223691. [PMID: 31703062 PMCID: PMC6839881 DOI: 10.1371/journal.pone.0223691] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 09/25/2019] [Indexed: 01/18/2023] Open
Abstract
Strong efforts have been made to understand the bacterial communities in potato plants and the rhizosphere. Research has focused on the effect of the environment and plant genotype on bacterial community structures and dynamics, while little is known about the origin and assembly of the bacterial community, especially in potato tubers. The tuber microbiota, however, may be of special interest as it could play an important role in crop quality, such as storage stability. Here, we used 16S rRNA gene amplicon sequencing to study the bacterial communities that colonize tubers of different potato cultivars commonly used in Austrian potato production over three generations and grown in different soils. Statistical analysis of sequencing data showed that the bacterial community of potato tubers has changed over generations and has become more similar to the soil bacterial community, while the impact of the potato cultivar on the bacterial assemblage has lost significance over time. The communities in different tuber parts did not differ significantly, while the soil bacterial community showed significant differences to the tuber microbiota composition. Additionally, the presence of OTUs in subsequent tuber generation points to vertical transmission of a subset of the tuber microbiota. Four OTUs were common to all tuber generations and all potato varieties. In summary, we conclude that the microbiota of potato tubers is recruited from the soil largely independent from the plant variety. Furthermore, the bacterial assemblage in potato tubers consists of bacteria transmitted from one tuber generation to the next and bacteria recruited from the soil.
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Affiliation(s)
- Franziska Buchholz
- Center for Health & Bioresources, Bioresources Unit, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Livio Antonielli
- Center for Health & Bioresources, Bioresources Unit, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Tanja Kostić
- Center for Health & Bioresources, Bioresources Unit, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Angela Sessitsch
- Center for Health & Bioresources, Bioresources Unit, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Birgit Mitter
- Center for Health & Bioresources, Bioresources Unit, AIT Austrian Institute of Technology GmbH, Tulln, Austria
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15
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Mediterranean Native Leguminous Plants: A Reservoir of Endophytic Bacteria with Potential to Enhance Chickpea Growth under Stress Conditions. Microorganisms 2019; 7:microorganisms7100392. [PMID: 31557944 PMCID: PMC6843138 DOI: 10.3390/microorganisms7100392] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 09/17/2019] [Accepted: 09/24/2019] [Indexed: 01/22/2023] Open
Abstract
Bacterial endophytes, a subset of a plant’s microbiota, can facilitate plant growth by a number of different mechanisms. The aims of this study were to assess the diversity and functionality of endophytic bacterial strains from internal root tissues of native legume species grown in two distinct sites in South of Portugal and to evaluate their ability to promote plant growth. Here, 122 endophytic bacterial isolates were obtained from 12 different native legume species. Most of these bacteria possess at least one of the plant growth-promoting features tested in vitro, with indole acetic acid production being the most common feature among the isolates followed by the production of siderophores and inorganic phosphate solubilization. The results of in planta experiments revealed that co-inoculation of chickpea plants with specific endophytic bacteria along with N2-fixing symbionts significantly improved the total biomass of chickpea plants, in particular when these plants were grown under saline conditions. Altogether, this study revealed that Mediterranean native legume species are a reservoir of plant growth-promoting bacteria, that are also tolerant to salinity and to toxic levels of Mn. Thus, these bacterial endophytes are well adapted to common constraints present in soils of this region which constitutes important factors to consider in the development of bacterial inoculants for stressful conditions in the Mediterranean region.
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16
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Gupta S, Pandey S. Unravelling the biochemistry and genetics of ACC deaminase-An enzyme alleviating the biotic and abiotic stress in plants. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.plgene.2019.100175] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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17
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Wang Y, Zhang W, Ding C, Zhang B, Huang Q, Huang R, Su X. Endophytic Communities of Transgenic Poplar Were Determined by the Environment and Niche Rather Than by Transgenic Events. Front Microbiol 2019; 10:588. [PMID: 30972046 PMCID: PMC6445066 DOI: 10.3389/fmicb.2019.00588] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 03/07/2019] [Indexed: 11/13/2022] Open
Abstract
Microbial communities associated with plants represent key determinants of plant health, survival, and growth. However, a good understanding of the structural composition of the bacterial and fungal microbiome present in different plant tissues and growing environments, especially in transgenic woody plants, is required. In the present study, we hypothesized that environmental conditions, ecological niches, and transgenic events could influence the community structure of plant-associated microorganisms (bacterial and fungal endophytes). We sampled the root and stem endospheres of field-grown transgenic and non-transgenic poplar trees (Populus alba × P. berolinensis) and applied 16S rRNA and internal transcribed spacer amplicon Illumina MiSeq sequencing to determine the bacterial and fungal communities associated with the different plant habitats and tissues. We found that actinobacteria, proteobacteria, bacteroidetes, and firmicutes were the dominant endophytic bacteria, and the fungal community was dominated by dothideomycetes, agaricomycetes, leotiomycetes, and sordariomycetes. In conclusion, transgenic events did not affect the endophytic bacterial and fungal diversity of poplar trees. The bacterial and fungal community structure depends on the pH and the soil organic matter content. Each plant tissue represents a unique ecological niche for the microbial communities. Finally, we identified the indicator operational taxonomic units (OTUs) and core microbiome associated with the different plant tissues of Populus and different environmental conditions. The results provide a basis for further study of host-microbial interactions with the identified abundant OTUs of Populus.
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Affiliation(s)
- Yanbo Wang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.,Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Beijing, China
| | - Weixi Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.,Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Beijing, China
| | - Changjun Ding
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.,Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Beijing, China
| | - Bingyu Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.,Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Beijing, China
| | - Qinjun Huang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.,Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Beijing, China
| | - Rongfeng Huang
- Institute of Biotechnology, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaohua Su
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.,Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Beijing, China.,Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
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18
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Diversity and Functionality of Culturable Endophytic Bacterial Communities in Chickpea Plants. PLANTS 2019; 8:plants8020042. [PMID: 30769814 PMCID: PMC6409739 DOI: 10.3390/plants8020042] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 02/01/2019] [Accepted: 02/12/2019] [Indexed: 11/16/2022]
Abstract
The aims of this study were to isolate, identify and characterize culturable endophytic bacteria from chickpea (Cicer arietinum L.) roots grown in different soils. In addition, the effects of rhizobial inoculation, soil and stress on the functionality of those culturable endophytic bacterial communities were also investigated. Phylogenetic analysis based on partial 16S rRNA gene sequences revealed that the endophytic bacteria isolated in this work belong to the phyla Proteobacteria, Firmicutes and Actinobacteria, with Enterobacter and Pseudomonas being the most frequently observed genera. Production of indoleacetic acid and ammonia were the most widespread plant growth-promoting features, while antifungal activity was relatively rare among the isolates. Despite the fact that the majority of bacterial endophytes were salt- and Mn-tolerant, the isolates obtained from soil with Mn toxicity were generally more Mn-tolerant than those obtained from the same soil amended with dolomitic limestone. Several associations between an isolate's genus and specific plant growth-promoting mechanisms were observed. The data suggest that soil strongly impacts the Mn tolerance of endophytic bacterial communities present in chickpea roots while rhizobial inoculation induces significant changes in terms of isolates' plant growth-promoting abilities. In addition, this study also revealed chickpea-associated endophytic bacteria that could be exploited as sources with potential application in agriculture.
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19
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Escobar Rodríguez C, Mitter B, Antonielli L, Trognitz F, Compant S, Sessitsch A. Roots and Panicles of the C4 Model Grasses Setaria viridis (L). and S. pumila Host Distinct Bacterial Assemblages With Core Taxa Conserved Across Host Genotypes and Sampling Sites. Front Microbiol 2018; 9:2708. [PMID: 30483233 PMCID: PMC6240606 DOI: 10.3389/fmicb.2018.02708] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 10/23/2018] [Indexed: 01/22/2023] Open
Abstract
Virtually all studied plant tissues are internally inhabited by endophytes. Due to their relevance for plant growth and health, bacterial microbiota of crop plants have been broadly studied. In plant microbiome research the root is the most frequently addressed environment, whereas the ecology of microbiota associated with reproductive organs still demands investigation. In this work, we chose the model grasses Setaria viridis and Setaria pumila to better understand the drivers shaping bacterial communities associated with panicles (representing a reproductive organ) as compared to those associated with roots. We collected wild individuals of both grass species from 20 different locations across Austria and investigated the bacterial assemblages within roots and ripe grain-harboring panicles by 16S rRNA gene-based Illumina sequencing. Furthermore, plant samples were subjected to genotyping by genetic diversity-focused Genotyping by Sequencing. Overall, roots hosted more diverse microbiota than panicles. Both the plant organ and sampling site significantly shaped the root and panicle-associated microbiota, whereas the host genotype only affected root communities. In terms of community structure, root-specific assemblages were highly diverse and consisted of conserved bacterial taxa. In contrast, panicle-specific communities were governed by Gammaproteobacteria, were less diverse and highly origin-dependent. Among OTUs found in both plant tissues, relative abundances of Gammaproteobacteria were higher in panicles, whereas Rhizobiales dominated root communities. We further identified core and non-core taxa within samples of both Setaria species. Non-core taxa included members of the Saccharibacteria and Legionelalles, while core communities encompassed eleven OTUs of seven bacterial orders, together with a set of ten panicle-enriched OTUs. These communities were widespread across root and panicle samples from all locations, hinting toward an evolved form of mutualism through potential vertical transmission of these taxa within Setaria species.
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Affiliation(s)
- Carolina Escobar Rodríguez
- Bioresources Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Vienna, Austria
| | - Birgit Mitter
- Bioresources Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Vienna, Austria
| | - Livio Antonielli
- Bioresources Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Vienna, Austria
| | - Friederike Trognitz
- Bioresources Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Vienna, Austria
| | - Stéphane Compant
- Bioresources Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Vienna, Austria
| | - Angela Sessitsch
- Bioresources Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Vienna, Austria
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20
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Correa-Galeote D, Bedmar EJ, Arone GJ. Maize Endophytic Bacterial Diversity as Affected by Soil Cultivation History. Front Microbiol 2018; 9:484. [PMID: 29662471 PMCID: PMC5890191 DOI: 10.3389/fmicb.2018.00484] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 02/28/2018] [Indexed: 11/20/2022] Open
Abstract
The bacterial endophytic communities residing within roots of maize (Zea mays L.) plants cultivated by a sustainable management in soils from the Quechua maize belt (Peruvian Andes) were examined using tags pyrosequencing spanning the V4 and V5 hypervariable regions of the 16S rRNA. Across four replicate libraries, two corresponding to sequences of endophytic bacteria from long time maize-cultivated soils and the other two obtained from fallow soils, 793 bacterial sequences were found that grouped into 188 bacterial operational taxonomic units (OTUs, 97% genetic similarity). The numbers of OTUs in the libraries from the maize-cultivated soils were significantly higher than those found in the libraries from fallow soils. A mean of 30 genera were found in the fallow soil libraries and 47 were in those from the maize-cultivated soils. Both alpha and beta diversity indexes showed clear differences between bacterial endophytic populations from plants with different soil cultivation history and that the soils cultivated for long time requires a higher diversity of endophytes. The number of sequences corresponding to main genera Sphingomonas, Herbaspirillum, Bradyrhizobium and Methylophilus in the maize-cultivated libraries were statistically more abundant than those from the fallow soils. Sequences of genera Dyella and Sreptococcus were significantly more abundant in the libraries from the fallow soils. Relative abundance of genera Burkholderia, candidatus Glomeribacter, Staphylococcus, Variovorax, Bacillus and Chitinophaga were similar among libraries. A canonical correspondence analysis of the relative abundance of the main genera showed that the four libraries distributed in two clearly separated groups. Our results suggest that cultivation history is an important driver of endophytic colonization of maize and that after a long time of cultivation of the soil the maize plants need to increase the richness of the bacterial endophytes communities.
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Affiliation(s)
- David Correa-Galeote
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Agencia Estatal Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Eulogio J Bedmar
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Agencia Estatal Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Gregorio J Arone
- Department of Agricultural Sciences, National University of Huancavelica, Huancavelica, Peru
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Quambusch M, Winkelmann T. Bacterial Endophytes in Plant Tissue Culture: Mode of Action, Detection, and Control. Methods Mol Biol 2018; 1815:69-88. [PMID: 29981114 DOI: 10.1007/978-1-4939-8594-4_4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Endophytic bacteria have been increasingly in the focus of research projects during the last decade. This has changed the view on bacteria in plant tissue culture and led to the differentiation between artificially introduced contaminations and naturally occurring endophytes with neutral, negative, or positive impact on the plant propagation process. This review chapter gives an overview on recent findings about the impact that bacteria have on the plant physiology in general and during micropropagation. Additionally, methods for the detection and identification of bacteria in plant tissue are described and, finally, suggestions of how to deal with bacterial endophytes in in vitro culture are given.
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Affiliation(s)
- Mona Quambusch
- Abteilung Waldgenressourcen, Nordwestdeutsche Forstliche Versuchsanstalt, Hann. Münden, Germany.
| | - Traud Winkelmann
- Institut für Gartenbauliche Produktionssysteme, Leibniz Universität Hannover, Hannover, Germany
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22
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Hussain SS, Mehnaz S, Siddique KHM. Harnessing the Plant Microbiome for Improved Abiotic Stress Tolerance. PLANT MICROBIOME: STRESS RESPONSE 2018. [DOI: 10.1007/978-981-10-5514-0_2] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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23
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Khan MS, Sadat SU, Jan A, Munir I. Impact of Transgenic Brassica napus Harboring the Antifungal Synthetic Chitinase (NiC) Gene on Rhizosphere Microbial Diversity and Enzyme Activities. FRONTIERS IN PLANT SCIENCE 2017; 8:1307. [PMID: 28791039 PMCID: PMC5524829 DOI: 10.3389/fpls.2017.01307] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 07/12/2017] [Indexed: 06/07/2023]
Abstract
Transgenic Brassica napus harboring the synthetic chitinase (NiC) gene exhibits broad-spectrum antifungal resistance. As the rhizosphere microorganisms play an important role in element cycling and nutrient transformation, therefore, biosafety assessment of NiC containing transgenic plants on soil ecosystem is a regulatory requirement. The current study is designed to evaluate the impact of NiC gene on the rhizosphere enzyme activities and microbial community structure. The transgenic lines with the synthetic chitinase gene (NiC) showed resistance to Alternaria brassicicola, a common disease causing fungal pathogen. The rhizosphere enzyme analysis showed no significant difference in the activities of fivesoil enzymes: alkalyine phosphomonoestarase, arylsulphatase, β-glucosidase, urease and sucrase between the transgenic and non-transgenic lines of B. napus varieties, Durr-e-NIFA (DN) and Abasyne-95 (AB-95). However, varietal differences were observed based on the analysis of molecular variance. Some individual enzymes were significantly different in the transgenic lines from those of non-transgenic but the results were not reproducible in the second trail and thus were considered as environmental effect. Genotypic diversity of soil microbes through 16S-23S rRNA intergenic spacer region amplification was conducted to evaluate the potential impact of the transgene. No significant diversity (4% for bacteria and 12% for fungal) between soil microbes of NiC B. napus and the non-transgenic lines was found. However, significant varietal differences were observed between DN and AB-95 with 79% for bacterial and 54% for fungal diversity. We conclude that the NiC B. napus lines may not affect the microbial enzyme activities and community structure of the rhizosphere soil. Varietal differences might be responsible for minor changes in the tested parameters.
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Affiliation(s)
- Mohammad S. Khan
- Genomics and Bioinformatics Laboratory, Institute of Biotechnology and Genetic Engineering (IBGE), Faculty of Crop Production Sciences, University of AgriculturePeshawar, Pakistan
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24
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Barnawal D, Pandey S, Bharti N, Pandey A, Ray T, Singh S, Chanotiya C, Kalra A. ACC deaminase-containing plant growth-promoting rhizobacteria protect Papaver somniferum
from downy mildew. J Appl Microbiol 2017; 122:1286-1298. [DOI: 10.1111/jam.13417] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 01/27/2017] [Accepted: 02/07/2017] [Indexed: 11/30/2022]
Affiliation(s)
- D. Barnawal
- Microbial Technology Department; CSIR-Central Institute of Medicinal and Aromatic Plants; Lucknow Uttar Pradesh India
| | - S.S. Pandey
- Microbial Technology Department; CSIR-Central Institute of Medicinal and Aromatic Plants; Lucknow Uttar Pradesh India
| | - N. Bharti
- Microbial Technology Department; CSIR-Central Institute of Medicinal and Aromatic Plants; Lucknow Uttar Pradesh India
| | - A. Pandey
- Microbial Technology Department; CSIR-Central Institute of Medicinal and Aromatic Plants; Lucknow Uttar Pradesh India
| | - T. Ray
- Microbial Technology Department; CSIR-Central Institute of Medicinal and Aromatic Plants; Lucknow Uttar Pradesh India
| | - S. Singh
- Microbial Technology Department; CSIR-Central Institute of Medicinal and Aromatic Plants; Lucknow Uttar Pradesh India
| | - C.S. Chanotiya
- Central Instrument Facility; CSIR-Central Institute of Medicinal and Aromatic Plants; Lucknow Uttar Pradesh India
| | - A. Kalra
- Microbial Technology Department; CSIR-Central Institute of Medicinal and Aromatic Plants; Lucknow Uttar Pradesh India
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25
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Feng NX, Yu J, Zhao HM, Cheng YT, Mo CH, Cai QY, Li YW, Li H, Wong MH. Efficient phytoremediation of organic contaminants in soils using plant-endophyte partnerships. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 583:352-368. [PMID: 28117167 DOI: 10.1016/j.scitotenv.2017.01.075] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 01/11/2017] [Accepted: 01/12/2017] [Indexed: 05/20/2023]
Abstract
Soil pollution with organic contaminants is one of the most intractable environmental problems today, posing serious threats to humans and the environment. Innovative strategies for remediating organic-contaminated soils are critically needed. Phytoremediation, based on the synergistic actions of plants and their associated microorganisms, has been recognized as a powerful in situ approach to soil remediation. Suitable combinations of plants and their associated endophytes can improve plant growth and enhance the biodegradation of organic contaminants in the rhizosphere and/or endosphere, dramatically expediting the removal of organic pollutants from soils. However, for phytoremediation to become a more widely accepted and predictable alternative, a thorough understanding of plant-endophyte interactions is needed. Many studies have recently been conducted on the mechanisms of endophyte-assisted phytoremediation of organic contaminants in soils. In this review, we highlight the superiority of organic pollutant-degrading endophytes for practical applications in phytoremediation, summarize alternative strategies for improving phytoremediation, discuss the fundamental mechanisms of endophyte-assisted phytoremediation, and present updated information regarding the advances, challenges, and new directions in the field of endophyte-assisted phytoremediation technology.
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Affiliation(s)
- Nai-Xian Feng
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, School of Environment, Jinan University, Guangzhou 510632, China
| | - Jiao Yu
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, School of Environment, Jinan University, Guangzhou 510632, China
| | - Hai-Ming Zhao
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, School of Environment, Jinan University, Guangzhou 510632, China
| | - Yu-Ting Cheng
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, School of Environment, Jinan University, Guangzhou 510632, China
| | - Ce-Hui Mo
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, School of Environment, Jinan University, Guangzhou 510632, China.
| | - Quan-Ying Cai
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, School of Environment, Jinan University, Guangzhou 510632, China
| | - Yan-Wen Li
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, School of Environment, Jinan University, Guangzhou 510632, China
| | - Hui Li
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, School of Environment, Jinan University, Guangzhou 510632, China
| | - Ming-Hung Wong
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, School of Environment, Jinan University, Guangzhou 510632, China; Consortium on Health, Environment, Education and Research (CHEER), Department of Science and Environmental Studies, The Education University of Hong Kong, Tai Po, Hong Kong, China
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Functional and phylogenetic diversity of cultivable rhizobacterial endophytes of sorghum [Sorghum bicolor (L.) Moench]. Antonie van Leeuwenhoek 2017; 110:925-943. [PMID: 28353092 DOI: 10.1007/s10482-017-0864-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 03/21/2017] [Indexed: 10/19/2022]
Abstract
A diverse group of bacteria colonize the exo- and endo-rhizospheres of sorghum and play a critical role in its tolerance to drought and other abiotic stresses. Two hundred and eighty endophytic bacteria were isolated from the surface-sterilized roots of four sorghum cultivars that were grown on three soil types at three different phenological stages of growth. The isolates were subjected to in vitro screening for their plant growth promoting traits. Out of 280 isolates, 70 could produce Indole 3-Acetic Acid (IAA), 28 showed N-fixation, 28 could solubilize phosphate, 24 had ACC deaminase activity and 13 isolates were able to produce siderophores. Functional diversity grouping of the isolates indicated one isolate having five PGP traits and two isolates having four PGP traits; two and 29 isolates having three and two PGP traits, respectively. Among the thirty-four isolates that possessed multiple PGP traits, 19 and 17 isolates were able to produce significant quantities of IAA in the presence and absence of L-tryptophan, an inducer. Eight isolates possessed high levels of ACC deaminase activity. PCR-RFLP of the 16Sr RNA gene revealed a distinct clustering and considerable genetic diversity among these functionally characterized isolates. The 16S rRNA gene based identification of the isolates of single and multiple PGP traits revealed phylogenetic dominance of Firmicutes; Acinetobacter, Bacillus, Enterobacter, Geobacillus, Lysinibacillus, Microbacterium, Ochrobactrum, Paenibacillus and Pseudomonas were the major genera present in the endo-rhizosphere of sorghum. Results of this study are constructive in selection of effective rhizobacterial endophytes or consortia for drought stress alleviation in sorghum.
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Zimmermann J, Musyoki MK, Cadisch G, Rasche F. Biocontrol agent Fusarium oxysporum f.sp. strigae has no adverse effect on indigenous total fungal communities and specific AMF taxa in contrasting maize rhizospheres. FUNGAL ECOL 2016; 23:1-10. [PMID: 27721900 PMCID: PMC5045157 DOI: 10.1016/j.funeco.2016.05.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
We studied the effects of Fusarium oxysporum f.sp. strigae (Fos), a soil-borne biocontrol agent (BCA) against Striga hermonthica, on total fungal and arbuscular mycorrhizal fungal (AMF) taxa in rhizospheres of maize in both clayey and sandy soil. Effects of Fos-BCA ‘Foxy-2’ were evaluated against (1) S. hermonthica presence, and (2) organic fertilization with Tithonia diversifolia residues at 14, 28 and 42 d after ‘Foxy-2’ inoculation, via DNA-based quantitative PCR and TRFLP fingerprinting. In both soils, ‘Foxy-2’ occasionally promoted total fungal abundance, while the community composition was mainly altered by T. diversifolia and S. hermonthica. Notably, ‘Foxy-2’ stimulated AMF Gigaspora margarita abundance, while G. margarita was suppressed by S. hermonthica. Total fungal and AMF abundance were promoted by T. diversifolia residues. In conclusion, ‘Foxy-2’ resulted in no adverse effects on indigenous rhizosphere fungal communities substantiating its environmental safety as BCA against S. hermonthica. ‘Foxy-2’ promoted AMF Gigaspora margarita abundance. Total fungal abundance was only transiently stimulated by ‘Foxy-2’. Contrastingly, G. margarita abundance was suppressed by Striga hermonthica. ‘Foxy-2’ induced only a minor alteration of fungal community composition. ‘Foxy-2’ effects were generally superimposed by organic fertilization.
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Affiliation(s)
- Judith Zimmermann
- Institute of Agricultural Sciences in the Tropics (Hans-Ruthenberg-Institute), University of Hohenheim, Stuttgart, Germany
| | - Mary K Musyoki
- Institute of Agricultural Sciences in the Tropics (Hans-Ruthenberg-Institute), University of Hohenheim, Stuttgart, Germany
| | - Georg Cadisch
- Institute of Agricultural Sciences in the Tropics (Hans-Ruthenberg-Institute), University of Hohenheim, Stuttgart, Germany
| | - Frank Rasche
- Institute of Agricultural Sciences in the Tropics (Hans-Ruthenberg-Institute), University of Hohenheim, Stuttgart, Germany
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Communities of endophytic microorganisms in different developmental stages from a local variety as well as transgenic and conventional isogenic hybrids of maize. World J Microbiol Biotechnol 2016; 32:189. [PMID: 27696288 DOI: 10.1007/s11274-016-2149-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2015] [Accepted: 09/24/2016] [Indexed: 01/06/2023]
Abstract
The diversity of endophytic microorganisms may change due to the genotype of the host plant and its phenological stage. In this study we evaluated the effect of phenological stage, transgenes and genetic composition of maize on endophytic bacterial and fungal communities. The maize populations were composed of a local variety named Rosado (RS) and three isogenic hybrids. One isogenic hybrid was not genetically modified (NGM). Another hybrid (Hx) contained the transgenes cry1F and pat (T1507 event), which provide resistance to insects of the order Lepidoptera and tolerance to the glufosinate-ammonium herbicide, respectively. The third hybrid (Hxrr) contained the transgene cp4 epsps (NK603 event) combined with the transgenes cry1F and pat (T1507 event), which allow tolerance to the Roundup Ready herbicide, besides the characteristics of Hx. Evaluation of the foliar tissue was done through PCR-DGGE analysis, with specific primers for bacteria and fungi within four phenological stages of maize. The endophytic bacteria were only clustered by phenological stages; the structure of the fungal community was clustered by maize genotypes in each phenological stage. The fungal community from the local variety RS was different from the three hybrids (NGM, Hx and Hxrr) within the four evaluated stages. In the reproductive stage, the fungal community from the two transgenic hybrids (Hx and Hxrr) were separated, and the Hxrr was different from NGM, in the two field experiments. This research study showed that the genetic composition of the maize populations, especially the presence of transgenes, is the determining factor for the changes detected in the endophytic fungal community of maize leaves.
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Romão-Dumaresq AS, Dourado MN, Fávaro LCDL, Mendes R, Ferreira A, Araújo WL. Diversity of Cultivated Fungi Associated with Conventional and Transgenic Sugarcane and the Interaction between Endophytic Trichoderma virens and the Host Plant. PLoS One 2016; 11:e0158974. [PMID: 27415014 PMCID: PMC4944904 DOI: 10.1371/journal.pone.0158974] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 06/24/2016] [Indexed: 12/23/2022] Open
Abstract
Plant-associated fungi are considered a vast source for biotechnological processes whose potential has been poorly explored. The interactions and diversity of sugarcane, one of the most important crops in Brazil, have been rarely studied, mainly concerning fungal communities and their interactions with transgenic plants. Taking this into consideration, the purpose of this study was, based on culture dependent strategy, to determine the structure and diversity of the fungal community (root endophytes and rhizosphere) associated with two varieties of sugarcane, a non-genetically modified (SP80-1842) variety and its genetically modified counterpart (IMI-1, expressing imazapyr herbicide resistance). For this, the sugarcane varieties were evaluated in three sampling times (3, 10 and 17 months after planting) under two crop management (weeding and herbicide treatments). In addition, a strain of Trichoderma virens, an endophyte isolated from sugarcane with great potential as a biological control, growth promotion and enzyme production agent, was selected for the fungal-plant interaction assays. The results of the isolation, characterization and evaluation of fungal community changes showed that the sugarcane fungal community is composed of at least 35 different genera, mostly in the phylum Ascomycota. Many genera are observed at very low frequencies among a few most abundant genera, some of which were isolated from specific plant sites (e.g., the roots or the rhizosphere). An assessment of the possible effects upon the fungal community showed that the plant growth stage was the only factor that significantly affected the community's structure. Moreover, if transgenic effects are present, they may be minor compared to other natural sources of variation. The results of interaction studies using the Green fluorescent protein (GFP)-expressing T. virens strain T.v.223 revealed that this fungus did not promote any phenotypic changes in the host plant and was found mostly in the roots where it formed a dense mycelial cover and was able to penetrate the intercellular spaces of the root epidermis upper layers. The ability of T. virens to colonize plant roots suggests a potential for protecting plant health, inhibiting pathogens or inducing systemic resistance.
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Affiliation(s)
- Aline Silva Romão-Dumaresq
- Department of Genetics, Escola Superior de Agricultura “Luiz de Queiroz”(ESALQ), University of São Paulo, São Paulo, Brazil
| | - Manuella Nóbrega Dourado
- Department of Genetics, Escola Superior de Agricultura “Luiz de Queiroz”(ESALQ), University of São Paulo, São Paulo, Brazil
- Laboratory of Molecular Biology and Microbial Ecology, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Léia Cecilia de Lima Fávaro
- Department of Genetics, Escola Superior de Agricultura “Luiz de Queiroz”(ESALQ), University of São Paulo, São Paulo, Brazil
- Brazilian Agricultural Research Corporation, Embrapa Agroenergy, Brasília, Distrito Federal, Brazil
| | - Rodrigo Mendes
- Department of Genetics, Escola Superior de Agricultura “Luiz de Queiroz”(ESALQ), University of São Paulo, São Paulo, Brazil
- Brazilian Agricultural Research Corporation, Embrapa Environment, Jaguariuna, São Paulo, Brazil
| | - Anderson Ferreira
- Department of Genetics, Escola Superior de Agricultura “Luiz de Queiroz”(ESALQ), University of São Paulo, São Paulo, Brazil
- Brazilian Agricultural Research Corporation, Embrapa Agrosilvopastoral, Sinop, Mato Grosso, Brazil
| | - Welington Luiz Araújo
- Department of Genetics, Escola Superior de Agricultura “Luiz de Queiroz”(ESALQ), University of São Paulo, São Paulo, Brazil
- Laboratory of Molecular Biology and Microbial Ecology, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
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Hardoim PR, van Overbeek LS, Berg G, Pirttilä AM, Compant S, Campisano A, Döring M, Sessitsch A. The Hidden World within Plants: Ecological and Evolutionary Considerations for Defining Functioning of Microbial Endophytes. Microbiol Mol Biol Rev 2015; 79:293-320. [PMID: 26136581 PMCID: PMC4488371 DOI: 10.1128/mmbr.00050-14] [Citation(s) in RCA: 1058] [Impact Index Per Article: 117.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
All plants are inhabited internally by diverse microbial communities comprising bacterial, archaeal, fungal, and protistic taxa. These microorganisms showing endophytic lifestyles play crucial roles in plant development, growth, fitness, and diversification. The increasing awareness of and information on endophytes provide insight into the complexity of the plant microbiome. The nature of plant-endophyte interactions ranges from mutualism to pathogenicity. This depends on a set of abiotic and biotic factors, including the genotypes of plants and microbes, environmental conditions, and the dynamic network of interactions within the plant biome. In this review, we address the concept of endophytism, considering the latest insights into evolution, plant ecosystem functioning, and multipartite interactions.
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Affiliation(s)
- Pablo R. Hardoim
- Centre of Marine Sciences, University of Algarve, Faro, Portugal
| | | | - Gabriele Berg
- Institute for Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | | | - Stéphane Compant
- Department of Health and Environment, Bioresources Unit, Austrian Institute of Technology GmbH, Tulln, Austria
| | - Andrea Campisano
- Sustainable Agro-Ecosystems and Bioresources Department, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, TN, Italy
| | | | - Angela Sessitsch
- Department of Health and Environment, Bioresources Unit, Austrian Institute of Technology GmbH, Tulln, Austria
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Turrini A, Sbrana C, Giovannetti M. Belowground environmental effects of transgenic crops: a soil microbial perspective. Res Microbiol 2015; 166:121-31. [DOI: 10.1016/j.resmic.2015.02.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Revised: 01/21/2015] [Accepted: 02/17/2015] [Indexed: 10/23/2022]
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Sessitsch A, Mitter B. 21st century agriculture: integration of plant microbiomes for improved crop production and food security. Microb Biotechnol 2014; 8:32-3. [PMID: 25545820 PMCID: PMC4321367 DOI: 10.1111/1751-7915.12180] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 09/08/2014] [Indexed: 01/09/2023] Open
Affiliation(s)
- Angela Sessitsch
- Health & Environment Department, Bioresources Unit, AIT Austrian Institute of Technology GmbH, Konrad-Lorenz-straße 24, 3430, Tulln, Austria
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Johnston-Monje D, Mousa WK, Lazarovits G, Raizada MN. Impact of swapping soils on the endophytic bacterial communities of pre-domesticated, ancient and modern maize. BMC PLANT BIOLOGY 2014; 14:233. [PMID: 25227492 PMCID: PMC4189167 DOI: 10.1186/s12870-014-0233-3] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 08/27/2014] [Indexed: 05/03/2023]
Abstract
BACKGROUND Endophytes are microbes that live within plants such as maize (corn, Zea mays L.) without causing disease. It is generally assumed that most endophytes originate from soil. If this is true, then as humans collected, domesticated, bred and migrated maize globally from its native Mexico, they moved the species away from its native population of endophyte donors. The migration of maize persists today, as breeders collect wild and exotic seed (as sources of diverse alleles) from sites of high genetic diversity in Mexico for breeding programs on distant soils. When transported to new lands, it is unclear whether maize permits only selective colonization of microbes from the Mexican soils on which it co-evolved, tolerates shifts in soil-derived endophytes, or prevents colonization of soil-based microbes in favour of seed-transmitted microbes. To test these hypotheses, non-sterilized seeds of three types of maize (pre-domesticated-Mexican, ancient-Mexican, modern-temperate) were planted side-by-side on indigenous Mexican soil, Canadian temperate soil or sterilized sand. The impact of these soil swaps on founder bacterial endophyte communities was tested using 16S-rDNA profiling, culturing and microbial trait phenotyping. RESULTS Multivariate analysis showed that bacterial 16S-rDNA TRFLP profiles from young, surface-sterilized maize plants were more similar when the same host genotype was grown on the different soils than when different maize genotypes were grown on the same soil. There appeared to be two reasons for this result. First, the largest fraction of bacterial 16S-signals from soil-grown plants was shared with parental seeds and/or plants grown on sterilized sand, suggesting significant inheritance of candidate endophytes. The in vitro activities of soil-derived candidate endophytes could be provided by bacteria that were isolated from sterile sand grown plants. Second, many non-inherited 16S-signals from sibling plants grown on geographically-distant soils were shared with one another, suggesting maize can select microbes with similar TRFLP peak sizes from diverse soils. Wild, pre-domesticated maize did not possess more unique 16S-signals when grown on its native Mexican soil than on Canadian soil, pointing against long-term co-evolutionary selection. The modern hybrid did not reject more soil-derived 16S-signals than did ancestral maize, pointing against such rejection as a mechanism that contributes to yield stability across environments. A minor fraction of 16S-signals was uniquely associated with any one soil. CONCLUSION Within the limits of TRFLP profiling, the candidate bacterial endophyte populations of pre-domesticated, ancient and modern maize are partially buffered against the effects of geographic migration --- from a Mexican soil associated with ancestral maize, to a Canadian soil associated with modern hybrid agriculture. These results have implications for understanding the effects of domestication, migration, ex situ seed conservation and modern breeding, on the microbiome of one of the world's most important food crops.
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Affiliation(s)
- David Johnston-Monje
- />Department of Plant Agriculture, University of Guelph, 50 Stone Road, Guelph, ON N1G 2W1 Canada
- />A&L Biologicals, Agroecology Research Services Centre, 2136 Jetstream Road, London, ON N5V 3P5 Canada
| | - Walaa Kamel Mousa
- />Department of Plant Agriculture, University of Guelph, 50 Stone Road, Guelph, ON N1G 2W1 Canada
- />Department of Pharmacognosy, Mansoura University, Mansoura, 35516 Egypt
| | - George Lazarovits
- />A&L Biologicals, Agroecology Research Services Centre, 2136 Jetstream Road, London, ON N5V 3P5 Canada
| | - Manish N Raizada
- />Department of Plant Agriculture, University of Guelph, 50 Stone Road, Guelph, ON N1G 2W1 Canada
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Khan MU, Sessitsch A, Harris M, Fatima K, Imran A, Arslan M, Shabir G, Khan QM, Afzal M. Cr-resistant rhizo- and endophytic bacteria associated with Prosopis juliflora and their potential as phytoremediation enhancing agents in metal-degraded soils. FRONTIERS IN PLANT SCIENCE 2014; 5:755. [PMID: 25610444 PMCID: PMC4284999 DOI: 10.3389/fpls.2014.00755] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 12/09/2014] [Indexed: 05/04/2023]
Abstract
Prosopis juliflora is characterized by distinct and profuse growth even in nutritionally poor soil and environmentally stressed conditions and is believed to harbor some novel heavy metal-resistant bacteria in the rhizosphere and endosphere. This study was performed to isolate and characterize Cr-resistant bacteria from the rhizosphere and endosphere of P. juliflora growing on the tannery effluent contaminated soil. A total of 5 and 21 bacterial strains were isolated from the rhizosphere and endosphere, respectively, and were shown to tolerate Cr up to 3000 mg l(-1). These isolates also exhibited tolerance to other toxic heavy metals such as, Cd, Cu, Pb, and Zn, and high concentration (174 g l(-1)) of NaCl. Moreover, most of the isolated bacterial strains showed one or more plant growth-promoting activities. The phylogenetic analysis of the 16S rRNA gene showed that the predominant species included Bacillus, Staphylococcus and Aerococcus. As far as we know, this is the first report analyzing rhizo- and endophytic bacterial communities associated with P. juliflora growing on the tannery effluent contaminated soil. The inoculation of three isolates to ryegrass (Lolium multiflorum L.) improved plant growth and heavy metal removal from the tannery effluent contaminated soil suggesting that these bacteria could enhance the establishment of the plant in contaminated soil and also improve the efficiency of phytoremediation of heavy metal-degraded soils.
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Affiliation(s)
- Muhammad U. Khan
- Environmental Biotechnology Division, National Institute for Biotechnology and Genetic EngineeringFaisalabad, Pakistan
| | - Angela Sessitsch
- Bioresources Unit, Austrian Institute of Technology GmbHTulln, Austria
| | - Muhammad Harris
- Environmental Biotechnology Division, National Institute for Biotechnology and Genetic EngineeringFaisalabad, Pakistan
| | - Kaneez Fatima
- Environmental Biotechnology Division, National Institute for Biotechnology and Genetic EngineeringFaisalabad, Pakistan
| | - Asma Imran
- Environmental Biotechnology Division, National Institute for Biotechnology and Genetic EngineeringFaisalabad, Pakistan
| | - Muhammad Arslan
- Environmental Biotechnology Division, National Institute for Biotechnology and Genetic EngineeringFaisalabad, Pakistan
- Earth Sciences Department, King Fahd University of Petroleum and MineralsDhahran, Saudi Arabia
| | - Ghulam Shabir
- Environmental Biotechnology Division, National Institute for Biotechnology and Genetic EngineeringFaisalabad, Pakistan
| | - Qaiser M. Khan
- Environmental Biotechnology Division, National Institute for Biotechnology and Genetic EngineeringFaisalabad, Pakistan
| | - Muhammad Afzal
- Environmental Biotechnology Division, National Institute for Biotechnology and Genetic EngineeringFaisalabad, Pakistan
- *Correspondence: Muhammad Afzal, Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, PO Box 577, Jhang Road, Faisalabad 38000, Pakistan e-mail: ;
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Sessitsch A, Kuffner M, Kidd P, Vangronsveld J, Wenzel WW, Fallmann K, Puschenreiter M. The role of plant-associated bacteria in the mobilization and phytoextraction of trace elements in contaminated soils. SOIL BIOLOGY & BIOCHEMISTRY 2013; 60:182-194. [PMID: 23645938 PMCID: PMC3618436 DOI: 10.1016/j.soilbio.2013.01.012] [Citation(s) in RCA: 310] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Revised: 01/04/2013] [Accepted: 01/13/2013] [Indexed: 05/04/2023]
Abstract
Phytoextraction makes use of trace element-accumulating plants that concentrate the pollutants in their tissues. Pollutants can be then removed by harvesting plants. The success of phytoextraction depends on trace element availability to the roots and the ability of the plant to intercept, take up, and accumulate trace elements in shoots. Current phytoextraction practises either employ hyperaccumulators or fast-growing high biomass plants; the phytoextraction process may be enhanced by soil amendments that increase trace element availability in the soil. This review will focus on the role of plant-associated bacteria to enhance trace element availability in the rhizosphere. We report on the kind of bacteria typically found in association with trace element - tolerating or - accumulating plants and discuss how they can contribute to improve trace element uptake by plants and thus the efficiency and rate of phytoextraction. This enhanced trace element uptake can be attributed to a microbial modification of the absorptive properties of the roots such as increasing the root length and surface area and numbers of root hairs, or by increasing the plant availability of trace elements in the rhizosphere and the subsequent translocation to shoots via beneficial effects on plant growth, trace element complexation and alleviation of phytotoxicity. An analysis of data from literature shows that effects of bacterial inoculation on phytoextraction efficiency are currently inconsistent. Some key processes in plant-bacteria interactions and colonization by inoculated strains still need to be unravelled more in detail to allow full-scale application of bacteria assisted phytoremediation of trace element contaminated soils.
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Affiliation(s)
- Angela Sessitsch
- AIT Austrian Institute of Technology GmbH, Bioresources Unit, A-3430 Tulln, Austria
| | - Melanie Kuffner
- AIT Austrian Institute of Technology GmbH, Bioresources Unit, A-3430 Tulln, Austria
| | - Petra Kidd
- Instituto de Investigaciones Agrobiológicas de Galicia (IIAG), CSIC, Apdo. 122, 15780 Santiago de Compostela, Spain
| | - Jaco Vangronsveld
- Hasselt University, Centre for Environmental Sciences, B-3590 Diepenbeek, Belgium
| | - Walter W. Wenzel
- University of Natural Resources and Life Sciences Vienna, Department of Forest and Soil Sciences, A-3430 Tulln, Austria
| | - Katharina Fallmann
- AIT Austrian Institute of Technology GmbH, Bioresources Unit, A-3430 Tulln, Austria
- University of Natural Resources and Life Sciences Vienna, Department of Forest and Soil Sciences, A-3430 Tulln, Austria
| | - Markus Puschenreiter
- University of Natural Resources and Life Sciences Vienna, Department of Forest and Soil Sciences, A-3430 Tulln, Austria
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36
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Mitter B, Brader G, Afzal M, Compant S, Naveed M, Trognitz F, Sessitsch A. Advances in Elucidating Beneficial Interactions Between Plants, Soil, and Bacteria. ADVANCES IN AGRONOMY 2013:381-445. [PMID: 0 DOI: 10.1016/b978-0-12-407685-3.00007-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
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Microbial rescue to plant under habitat-imposed abiotic and biotic stresses. Appl Microbiol Biotechnol 2012; 96:1137-55. [DOI: 10.1007/s00253-012-4429-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2012] [Revised: 09/07/2012] [Accepted: 09/10/2012] [Indexed: 12/27/2022]
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Phylogenetic diversity of bacterial endophytes of Panax notoginseng with antagonistic characteristics towards pathogens of root-rot disease complex. Antonie Van Leeuwenhoek 2012; 103:299-312. [PMID: 22987248 DOI: 10.1007/s10482-012-9810-3] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Accepted: 09/06/2012] [Indexed: 10/27/2022]
Abstract
Endophytes play an important role in protection of host plants from infection by phytopathogens. Endophytic bacteria were isolated from five different parts (root, stem, petiole, leaf and seed) of Panax notoginseng and evaluated for antagonistic activity against Fusarium oxysporum, Ralstonia sp. and Meloidogyne hapla, three major pathogens associated with root-rot disease complex of P. notoginseng. From 1000 endophytic bacterial strains evaluated in vitro, 104 strains exhibited antagonistic properties against at least one of these three pathogens. Phylogenetic analyses of their 16S rRNA gene sequences showed that these 104 antagonistic bacteria belong to four clusters: Firmicutes, Proteobacteria, Actinobacteria and Bacteroidetes/Chlorobi. Members of the Firmicutes, in particular the Bacillus spp., were predominant in all analyzed tissues. The root was the main reservoir for antagonistic bacteria. Of the 104 antagonists, 51 strains showed antagonistic activities to one pathogen only, while 43 and 10 displayed the activities towards two and all three pathogens, respectively. The most dominant species in all tissues were Bacillus amyloliquefaciens subsp. plantarum and Bacillus methylotrophicus, which were represented by eight strains with broad antagonistic spectrum to the all three test pathogens of root-rot disease complex of P. notoginseng.
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Pancher M, Ceol M, Corneo PE, Longa CMO, Yousaf S, Pertot I, Campisano A. Fungal endophytic communities in grapevines (Vitis vinifera L.) respond to crop management. Appl Environ Microbiol 2012; 78:4308-17. [PMID: 22492448 PMCID: PMC3370515 DOI: 10.1128/aem.07655-11] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2011] [Accepted: 03/28/2012] [Indexed: 11/20/2022] Open
Abstract
We studied the distribution of fungal endophytes of grapevine (Vitis vinifera L.) plants in a subalpine area of northern Italy, where viticulture is of high economic relevance. We adopted both cultivation-based and cultivation-independent approaches to address how various anthropic and nonanthropic factors shape microbial communities. Grapevine stems were harvested from several locations considering organic and integrated pest management (IPM) and from the cultivars Merlot and Chardonnay. Cultivable fungi were isolated and identified by internal-transcribed-spacer sequence analysis, using a novel colony-PCR method, to amplify DNA from fungal specimens. The composition of fungal communities was assessed using a cultivation-independent approach, automated ribosomal intergenic spacer analysis (ARISA). Multivariate statistical analysis of both culture-dependent and culture-independent data sets was convergent and indicated that fungal endophytic communities in grapevines from organically managed farms were different from those from farms utilizing IPM. Fungal communities in plants of cv. Merlot and cv. Chardonnay overlapped when analyzed using culture-dependent approaches but could be partially resolved using ARISA fingerprinting.
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Affiliation(s)
- Michael Pancher
- Sustainable Agro-Ecosystems and Bioresources Department, IASMA Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
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Prischl M, Hackl E, Pastar M, Pfeiffer S, Sessitsch A. Genetically modified Bt maize lines containing cry3Bb1, cry1A105 or cry1Ab2 do not affect the structure and functioning of root-associated endophyte communities. APPLIED SOIL ECOLOGY 2012. [PMID: 0 DOI: 10.1016/j.apsoil.2011.12.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
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Wellner S, Lodders N, Kämpfer P. Diversity and biogeography of selected phyllosphere bacteria with special emphasis on Methylobacterium spp. Syst Appl Microbiol 2011; 34:621-30. [PMID: 22000032 DOI: 10.1016/j.syapm.2011.08.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2011] [Revised: 08/17/2011] [Accepted: 08/23/2011] [Indexed: 11/26/2022]
Abstract
On the basis of cultivation-dependent (isolation on mineral salt medium supplemented with 0.5% methanol) and -independent (DGGE analysis) methods, we investigated the influence of the host plant species Trifolium repens and Cerastium holosteoides, three geographic locations and the land-use types meadow, mown pasture and pasture on the abundance and community composition of selected phyllosphere bacteria with emphasis on Methylobacterium species. Methylobacterium abundance was significantly higher on leaves of T. repens (mean value 2.0×10(7) CFU PPFM per g leaf) than on leaves of C. holosteoides (mean value 2.0×10(6) CFU per g leaf). Leaves from the sampling site Schorfheide-Chorin showed slightly lower Methylobacterium numbers than leaves of the other sampling sites. Land-use and sampling period had no consistent influence on Methylobacterium community size. Methylobacterium community composition was very similar over both sampling periods, all three sampling sites, all land-use types and both plant species. Moreover, no relationship between geographic and genetic distance was observed. Community composition of selected Proteobacteria was influenced by plant species, geographic location and land-use. Often, differences in community composition could be observed between meadows, mown pastures and pastures but not between different kinds of meadows (cutted once versus three times) and mown pastures (fertilized versus non-fertilized). The results also indicate, that whether there are differences between land-use types or not strongly depends on the investigated host plant species and ecosystem. Besides Methylobacterium, representatives of Methylophilus were detected. The results indicate that Methylobacterium species are generally abundant and stable members of the phyllosphere community whereas other genera occur more occasionally, and that Methylobacterium clearly dominates the methylotrophic phyllosphere community.
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Affiliation(s)
- S Wellner
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
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Yousaf S, Afzal M, Reichenauer TG, Brady CL, Sessitsch A. Hydrocarbon degradation, plant colonization and gene expression of alkane degradation genes by endophytic Enterobacter ludwigii strains. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2011; 159:2675-83. [PMID: 21700373 DOI: 10.1016/j.envpol.2011.05.031] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2011] [Revised: 05/17/2011] [Accepted: 05/28/2011] [Indexed: 05/06/2023]
Abstract
The genus Enterobacter comprises a range of beneficial plant-associated bacteria showing plant growth promotion. Enterobacter ludwigii belongs to the Enterobacter cloacae complex and has been reported to include human pathogens but also plant-associated strains with plant beneficial capacities. To assess the role of Enterobacter endophytes in hydrocarbon degradation, plant colonization, abundance and expression of CYP153 genes in different plant compartments, three plant species (Italian ryegrass, birdsfoot trefoil and alfalfa) were grown in sterile soil spiked with 1% diesel and inoculated with three endophytic E. ludwigii strains. Results showed that all strains were capable of hydrocarbon degradation and efficiently colonized the rhizosphere and plant interior. Two strains, ISI10-3 and BRI10-9, showed highest degradation rates of diesel fuel up to 68% and performed best in combination with Italian ryegrass and alfalfa. All strains expressed the CYP153 gene in all plant compartments, indicating an active role in degradation of diesel in association with plants.
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Affiliation(s)
- Sohail Yousaf
- AIT Austrian Institute of Technology GmbH, Bioresources Unit, A-2444 Seibersdorf, Austria
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Nikolic B, Schwab H, Sessitsch A. Metagenomic analysis of the 1-aminocyclopropane-1-carboxylate deaminase gene (acdS) operon of an uncultured bacterial endophyte colonizing Solanum tuberosum L. Arch Microbiol 2011; 193:665-76. [PMID: 21523387 DOI: 10.1007/s00203-011-0703-z] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2010] [Revised: 02/16/2011] [Accepted: 03/29/2011] [Indexed: 01/08/2023]
Abstract
Deamination of the ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC) is a key plant-beneficial trait found in many plant growth-promoting bacteria. In this study, we analysed ACC deaminase genes (acdS) of bacterial endophytes colonizing field-grown potato plants. PCR analysis revealed the presence of two types of acdS genes, the dominant one showing high homology to an acdS gene derived from Pseudomonas fluorescens. Construction, functional screening and sequence analysis of metagenomic libraries revealed clones containing the acdS gene identified in the PCR library. Sequence analysis of one metagenomic clone identified the entire acdS operon of an uncultivated endophyte and revealed that the acdS gene is coupled upstream with an acdR transcriptional regulator gene as previously found in P. putida strain UW4 (Grichko and Glick 2000). However, in-silico analysis of 195 fully sequenced, acdS-containing bacterial genomes revealed that the majority of strains, including numerous strains belonging to the genus Pseudomonas, do not contain an acdR regulatory gene in the vicinity of the acdS gene or elsewhere in the genome. The acdR (+)-acdS (+) operon was exclusively found in several Alpha- and Betaproteobacteria most prominently in the genus Burkholderia.
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Afzal M, Yousaf S, Reichenauer TG, Kuffner M, Sessitsch A. Soil type affects plant colonization, activity and catabolic gene expression of inoculated bacterial strains during phytoremediation of diesel. JOURNAL OF HAZARDOUS MATERIALS 2011; 186:1568-75. [PMID: 21216097 DOI: 10.1016/j.jhazmat.2010.12.040] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2010] [Accepted: 12/09/2010] [Indexed: 05/06/2023]
Abstract
The combined use of plants and associated microorganisms has great potential for cleaning up soils contaminated with petroleum hydrocarbons. Apart from environmental conditions the physicochemical properties of the soil are the main factors influencing the survival and activity of an inoculated strain as well as the growth of plants. This study examined the effect of different soil types (sandy, loamy sand and loam) on the survival, gene abundance and catabolic gene expression of two inoculated strains (Pseudomonas sp. strain ITRI53 and Pantoea sp. strain BTRH79) in the rhizosphere and shoot interior of Italian ryegrass vegetated in diesel contaminated soils. High colonization, gene abundance and expression in loamy soils were observed. By contrast, low colonization, gene abundance and absence of gene expression in sandy soil were found. The highest levels of genes expression and hydrocarbon degradation were seen in loamy soil that had been inoculated with BTRH79 and were significantly higher compared to those in other soils. A positive correlation was observed between gene expression and hydrocarbon degradation indicating that catabolic gene expression is necessary for contaminant degradation. These results suggest that soil type influences the bacterial colonization and microbial activities and subsequently the efficiency of contaminant degradation.
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Affiliation(s)
- Muhammad Afzal
- AIT Austrian Institute of Technology GmbH, Department of Health and Environment, A-2444 Seibersdorf, Austria
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Lamarche J, Stefani FO, Séguin A, Hamelin RC. Impact of endochitinase-transformed white spruce on soil fungal communities under greenhouse conditions. FEMS Microbiol Ecol 2011; 76:199-208. [DOI: 10.1111/j.1574-6941.2011.01041.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Diallo S, Crépin A, Barbey C, Orange N, Burini JF, Latour X. Mechanisms and recent advances in biological control mediated through the potato rhizosphere. FEMS Microbiol Ecol 2011; 75:351-64. [DOI: 10.1111/j.1574-6941.2010.01023.x] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Yousaf S, Andria V, Reichenauer TG, Smalla K, Sessitsch A. Phylogenetic and functional diversity of alkane degrading bacteria associated with Italian ryegrass (Lolium multiflorum) and Birdsfoot trefoil (Lotus corniculatus) in a petroleum oil-contaminated environment. JOURNAL OF HAZARDOUS MATERIALS 2010; 184:523-532. [PMID: 20851515 DOI: 10.1016/j.jhazmat.2010.08.067] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2010] [Revised: 08/18/2010] [Accepted: 08/19/2010] [Indexed: 05/06/2023]
Abstract
Twenty-six different plant species were analyzed regarding their performance in soil contaminated with petroleum oil. Two well-performing species, Italian ryegrass (Lolium multiflorum var. Taurus), Birdsfoot trefoil (Lotus corniculatus var. Leo) and the combination of these two plants were selected to study the ecology of plant-associated, culturable alkane-degrading bacteria. Hydrocarbon degrading bacteria were isolated from the rhizosphere, root interior and shoot interior and subjected to the analysis of 16S rRNA gene, the 16S and 23S rRNA intergenic spacer region and alkane hydroxylase genes. Furthermore, we investigated whether alkane hydroxylase genes are plasmid located. Higher numbers of culturable, alkane-degrading bacteria were associated with Italian ryegrass, which were also characterized by a higher diversity, particularly in the plant interior. Only half of the isolated bacteria hosted known alkane hydroxylase genes (alkB and cytochrome P153-like). Degradation genes were found both on plasmids as well as in the chromosome. In regard to application of plants for rhizodegradation, where support of numerous degrading bacteria is essential for efficient break-down of pollutants, Italian ryegrass seems to be more appropriate than Birdsfoot trefoil.
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Affiliation(s)
- Sohail Yousaf
- Bioresources Unit, AIT Austrian Institute of Technology GmbH, A-2444 Seibersdorf, Austria
| | - Verania Andria
- Bioresources Unit, AIT Austrian Institute of Technology GmbH, A-2444 Seibersdorf, Austria
| | - Thomas G Reichenauer
- Unit of Environmental Resources & Technologies, AIT Austrian Institute of Technology GmbH, A-2444 Seibersdorf, Austria
| | - Kornelia Smalla
- Julius Kühn-Institut - Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen Diagnostics, D-38104 Braunschweig, Germany
| | - Angela Sessitsch
- Bioresources Unit, AIT Austrian Institute of Technology GmbH, A-2444 Seibersdorf, Austria.
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Hunter PJ, Hand P, Pink D, Whipps JM, Bending GD. Both leaf properties and microbe-microbe interactions influence within-species variation in bacterial population diversity and structure in the lettuce (Lactuca Species) phyllosphere. Appl Environ Microbiol 2010; 76:8117-25. [PMID: 20952648 PMCID: PMC3008232 DOI: 10.1128/aem.01321-10] [Citation(s) in RCA: 128] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2010] [Accepted: 10/07/2010] [Indexed: 11/20/2022] Open
Abstract
Morphological and chemical differences between plant genera influence phyllosphere microbial populations, but the factors driving within-species variation in phyllosphere populations are poorly understood. Twenty-six lettuce accessions were used to investigate factors controlling within-species variation in phyllosphere bacterial populations. Morphological and physiochemical characteristics of the plants were compared, and bacterial community structure and diversity were investigated using terminal restriction fragment length polymorphism (T-RFLP) profiling and 16S rRNA gene clone libraries. Plant morphology and levels of soluble carbohydrates, calcium, and phenolic compounds (which have long been associated with plant responses to biotic stress) were found to significantly influence bacterial community structure. Clone libraries from three representative accessions were found to be significantly different in terms of both sequence differences and the bacterial genera represented. All three libraries were dominated by Pseudomonas species and the Enterobacteriaceae family. Significant differences in the relative proportions of genera in the Enterobacteriaceae were detected between lettuce accessions. Two such genera (Erwinia and Enterobacter) showed significant variation between the accessions and revealed microbe-microbe interactions. We conclude that both leaf surface properties and microbial interactions are important in determining the structure and diversity of the phyllosphere bacterial community.
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Affiliation(s)
- Paul J Hunter
- Warwick HRI, University of Warwick, Wellesbourne, Warwick CV35 9EF, United Kingdom.
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Yousaf S, Ripka K, Reichenauer TG, Andria V, Afzal M, Sessitsch A. Hydrocarbon degradation and plant colonization by selected bacterial strains isolated from Italian ryegrass and birdsfoot trefoil. J Appl Microbiol 2010; 109:1389-401. [PMID: 20522148 DOI: 10.1111/j.1365-2672.2010.04768.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AIMS To assess the degradation potential and plant colonization capacity of four alkane-degrading strains (ITSI10, ITRI15, ITRH76 and BTRH79) in combination with birdsfoot trefoil and Italian ryegrass and to evaluate the diversity of indigenous alkane-degrading soil bacteria in the rhizo- and endosphere. METHODS AND RESULTS Contaminated soil was prepared by spiking agricultural soil with 10 g diesel fuel per kg soil. Italian ryegrass (Lolium multiflorum var. Taurus) and birdsfoot trefoil (Lotus corniculatus var. Leo) were inoculated with four alkane-degrading strains. Hydrocarbon degradation (up to 57%) was observed in all inoculated treatments of vegetated and unvegetated samples. Italian ryegrass in combination with compost and BTRH79 showed highest degradation, while birdsfoot trefoil performed best with compost and strain ITSI10. Cultivation-based as well as cultivation-independent analysis showed that both strains were competitive colonizers. CONCLUSIONS The combination between vegetation, inoculation with well-performing degrading bacteria and compost amendment was an efficient approach to reduce hydrocarbon contamination. Two Pantoea sp. strains, ITSI10 and BTRH79, established well in the plant environment despite the presence of a variety of other, indigenous alkane-degrading bacteria. SIGNIFICANCE AND IMPACT OF THE STUDY This study suggests that the application of degrading bacterial strains, which are able to compete with the native microflora and to tightly associate with plants, are promising candidates to be used for phytoremediation applications.
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Affiliation(s)
- S Yousaf
- AIT Austrian Institute of Technology GmbH, Bioresources Unit, Seibersdorf, Austria
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Compant S, van der Heijden MGA, Sessitsch A. Climate change effects on beneficial plant-microorganism interactions. FEMS Microbiol Ecol 2010; 73:197-214. [PMID: 20528987 DOI: 10.1111/j.1574-6941.2010.00900.x] [Citation(s) in RCA: 133] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
It is well known that beneficial plant-associated microorganisms may stimulate plant growth and enhance resistance to disease and abiotic stresses. The effects of climate change factors such as elevated CO(2), drought and warming on beneficial plant-microorganism interactions are increasingly being explored. This now makes it possible to test whether some general patterns occur and whether different groups of plant-associated microorganisms respond differently or in the same way to climate change. Here, we review the results of 135 studies investigating the effects of climate change factors on beneficial microorganisms and their interaction with host plants. The majority of studies showed that elevated CO(2) had a positive influence on the abundance of arbuscular and ectomycorrhizal fungi, whereas the effects on plant growth-promoting bacteria and endophytic fungi were more variable. In most cases, plant-associated microorganisms had a beneficial effect on plants under elevated CO(2). The effects of increased temperature on beneficial plant-associated microorganisms were more variable, positive and neutral, and negative effects were equally common and varied considerably with the study system and the temperature range investigated. Moreover, numerous studies indicated that plant growth-promoting microorganisms (both bacteria and fungi) positively affected plants subjected to drought stress. Overall, this review shows that plant-associated microorganisms are an important factor influencing the response of plants to climate change.
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Affiliation(s)
- Stéphane Compant
- AIT Austrian Institute of Technology GmbH, Bioresources Unit, Seibersdorf, Austria
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