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Hartman K, Schmid MW, Bodenhausen N, Bender SF, Valzano-Held AY, Schlaeppi K, van der Heijden MGA. A symbiotic footprint in the plant root microbiome. ENVIRONMENTAL MICROBIOME 2023; 18:65. [PMID: 37525294 PMCID: PMC10391997 DOI: 10.1186/s40793-023-00521-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 07/14/2023] [Indexed: 08/02/2023]
Abstract
BACKGROUND A major aim in plant microbiome research is determining the drivers of plant-associated microbial communities. While soil characteristics and host plant identity present key drivers of root microbiome composition, it is still unresolved whether the presence or absence of important plant root symbionts also determines overall microbiome composition. Arbuscular mycorrhizal fungi (AMF) and N-fixing rhizobia bacteria are widespread, beneficial root symbionts that significantly enhance plant nutrition, plant health, and root structure. Thus, we hypothesized that symbiont types define the root microbiome structure. RESULTS We grew 17 plant species from five families differing in their symbiotic associations (no symbioses, AMF only, rhizobia only, or AMF and rhizobia) in a greenhouse and used bacterial and fungal amplicon sequencing to characterize their root microbiomes. Although plant phylogeny and species identity were the most important factors determining root microbiome composition, we discovered that the type of symbioses also presented a significant driver of diversity and community composition. We found consistent responses of bacterial phyla, including members of the Acidobacteria, Chlamydiae, Firmicutes, and Verrucomicrobia, to the presence or absence of AMF and rhizobia and identified communities of OTUs specifically enriched in the different symbiotic groups. A total of 80, 75 and 57 bacterial OTUs were specific for plant species without symbiosis, plant species forming associations with AMF or plant species associating with both AMF and rhizobia, respectively. Similarly, 9, 14 and 4 fungal OTUs were specific for these plant symbiont groups. Importantly, these generic symbiosis footprints in microbial community composition were also apparent in absence of the primary symbionts. CONCLUSION Our results reveal that symbiotic associations of the host plant leaves an imprint on the wider root microbiome - which we term the symbiotype. These findings suggest the existence of a fundamental assembly principle of root microbiomes, dependent on the symbiotic associations of the host plant.
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Affiliation(s)
- Kyle Hartman
- Department of Agroecology and Environment, Plant Soil Interactions, Reckenholzstrasse 191, Agroscope, Zürich, 8046, Switzerland
| | | | - Natacha Bodenhausen
- Department of Agroecology and Environment, Plant Soil Interactions, Reckenholzstrasse 191, Agroscope, Zürich, 8046, Switzerland
- Department of Soil Sciences, Research Institute of Organic Agriculture FiBL, Frick, 5070, Switzerland
| | - S Franz Bender
- Department of Agroecology and Environment, Plant Soil Interactions, Reckenholzstrasse 191, Agroscope, Zürich, 8046, Switzerland
| | - Alain Y Valzano-Held
- Department of Agroecology and Environment, Plant Soil Interactions, Reckenholzstrasse 191, Agroscope, Zürich, 8046, Switzerland
| | - Klaus Schlaeppi
- Department of Agroecology and Environment, Plant Soil Interactions, Reckenholzstrasse 191, Agroscope, Zürich, 8046, Switzerland.
- Plant Microbe Interactions, Department of Environmental Sciences, University of Basel, Basel, 4056, Switzerland.
- Institute of Plant Sciences, Faculty of Science, University of Bern, Bern, 3013, Switzerland.
| | - Marcel G A van der Heijden
- Department of Agroecology and Environment, Plant Soil Interactions, Reckenholzstrasse 191, Agroscope, Zürich, 8046, Switzerland.
- Department of Plant and Microbial Biology, University of Zürich, Zürich, 8008, Switzerland.
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2
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Wolfgang A, Tack AJM, Berg G, Abdelfattah A. Reciprocal influence of soil, phyllosphere, and aphid microbiomes. ENVIRONMENTAL MICROBIOME 2023; 18:63. [PMID: 37480131 PMCID: PMC10362670 DOI: 10.1186/s40793-023-00515-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 07/06/2023] [Indexed: 07/23/2023]
Abstract
BACKGROUND The effect of soil on the plant microbiome is well-studied. However, less is known about the impact of the soil microbiome in multitrophic systems. Here we examined the effect of soil on plant and aphid microbiomes, and the reciprocal effect of aphid herbivory on the plant and soil microbiomes. We designed microcosms, which separate below and aboveground compartments, to grow oak seedlings with and without aphid herbivory in soils with three different microbiomes. We used amplicon sequencing and qPCR to characterize the bacterial and fungal communities in soils, phyllospheres, and aphids. RESULTS Soil microbiomes significantly affected the microbial communities of phyllospheres and, to a lesser extent, aphid microbiomes, indicating plant-mediated assembly processes from soil to aphids. While aphid herbivory significantly decreased microbial diversity in phyllospheres independent of soil microbiomes, the effect of aphid herbivory on the community composition in soil varied among the three soils. CONCLUSIONS This study provides experimental evidence for the reciprocal influence of soil, plant, and aphid microbiomes, with the potential for the development of new microbiome-based pest management strategies.
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Affiliation(s)
- Adrian Wolfgang
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010, Graz, Austria
| | - Ayco J M Tack
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91, Stockholm, Sweden
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010, Graz, Austria
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth-Allee 100, 14469, Potsdam, Germany
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany
| | - Ahmed Abdelfattah
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010, Graz, Austria.
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth-Allee 100, 14469, Potsdam, Germany.
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3
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Malacrinò A, Wang M, Caul S, Karley AJ, Bennett AE. Herbivory shapes the rhizosphere bacterial microbiota in potato plants. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:805-811. [PMID: 34427053 DOI: 10.1111/1758-2229.12998] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 07/23/2021] [Accepted: 07/26/2021] [Indexed: 05/04/2023]
Abstract
Plant-associated microbiomes assist their host in a variety of activities, spanning from nutrition to defence against herbivores and diseases. Previous research showed that plant-associated microbiomes shift their composition when plants are exposed to stressors, including herbivory. However, existing studies explored only single herbivore-plant combinations, whereas plants are often attacked by several different herbivores, but the effects of multiple herbivore types on the plant microbiome remain to be determined. Here, we first tested whether feeding by different herbivores (aphids, nematodes and slugs) produces a shift in the rhizosphere bacterial microbiota associated with potato plants. Then, we expanded this question asking whether the identity of the herbivore produces different effects on the rhizosphere microbial community. While we found shifts in microbial diversity and structure due to herbivory, we observed that the herbivore identity does not influence the diversity or community structure of bacteria thriving in the rhizosphere. However, a deeper analysis revealed that the herbivores differentially affected the structure of the network of microbial co-occurrences. Our results have the potential to increase our ability to predict how plant microbiomes assemble and aid our understanding of the role of plant microbiome in plant responses to biotic stress.
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Affiliation(s)
- Antonino Malacrinò
- Institute for Evolution and Biodiversity, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Mingyuan Wang
- Research Center of Horticultural Science and Engineering, Huaqiao University, Xiamen, China
| | - Sandra Caul
- Department of Ecological Sciences, The James Hutton Institute, Dundee, Scotland, UK
| | - Alison J Karley
- Department of Ecological Sciences, The James Hutton Institute, Dundee, Scotland, UK
| | - Alison E Bennett
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
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4
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Friman J, Karssemeijer PN, Haller J, de Kreek K, van Loon JJ, Dicke M. Shoot and root insect herbivory change the plant rhizosphere microbiome and affects cabbage-insect interactions through plant-soil feedback. THE NEW PHYTOLOGIST 2021; 232:2475-2490. [PMID: 34537968 PMCID: PMC9291931 DOI: 10.1111/nph.17746] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 09/09/2021] [Indexed: 05/06/2023]
Abstract
Plant-soil feedback (PSF) may influence plant-insect interactions. Although plant defense differs between shoot and root tissues, few studies have examined root-feeding insect herbivores in a PSF context. We examined here how plant growth and resistance against root-feeding Delia radicum larvae was influenced by PSF. We conditioned soil with cabbage plants that were infested with herbivores that affect D. radicum through plant-mediated effects: leaf-feeding Plutella xylostella caterpillars and Brevicoryne brassicae aphids, root-feeding D. radicum larvae, and/or added rhizobacterium Pseudomonas simiae WCS417r. We analyzed the rhizosphere microbial community, and in a second set of conspecific plants exposed to conditioned soil, we assessed growth, expression of defense-related genes, and D. radicum performance. The rhizosphere microbiome differed mainly between shoot and root herbivory treatments. Addition of Pseudomonas simiae did not influence rhizosphere microbiome composition. Plant shoot biomass, gene expression, and plant resistance against D. radicum larvae was affected by PSF in a treatment-specific manner. Soil conditioning overall reduced plant shoot biomass, Pseudomonas simiae-amended soil causing the largest growth reduction. In conclusion, shoot and root insect herbivores alter the rhizosphere microbiome differently, with consequences for growth and resistance of plants subsequently exposed to conditioned soil.
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Affiliation(s)
- Julia Friman
- Laboratory of EntomologyWageningen University and ResearchDroevendaalsesteeg 1Wageningen6708 PBthe Netherlands
| | - Peter N. Karssemeijer
- Laboratory of EntomologyWageningen University and ResearchDroevendaalsesteeg 1Wageningen6708 PBthe Netherlands
| | - Julian Haller
- Laboratory of EntomologyWageningen University and ResearchDroevendaalsesteeg 1Wageningen6708 PBthe Netherlands
| | - Kris de Kreek
- Laboratory of EntomologyWageningen University and ResearchDroevendaalsesteeg 1Wageningen6708 PBthe Netherlands
| | - Joop J.A. van Loon
- Laboratory of EntomologyWageningen University and ResearchDroevendaalsesteeg 1Wageningen6708 PBthe Netherlands
| | - Marcel Dicke
- Laboratory of EntomologyWageningen University and ResearchDroevendaalsesteeg 1Wageningen6708 PBthe Netherlands
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Lewin S, Francioli D, Ulrich A, Kolb S. Crop host signatures reflected by co-association patterns of keystone Bacteria in the rhizosphere microbiota. ENVIRONMENTAL MICROBIOME 2021; 16:18. [PMID: 34641981 PMCID: PMC8513244 DOI: 10.1186/s40793-021-00387-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 09/28/2021] [Indexed: 05/28/2023]
Abstract
BACKGROUND The native crop bacterial microbiota of the rhizosphere is envisioned to be engineered for sustainable agriculture. This requires the identification of keystone rhizosphere Bacteria and an understanding on how these govern crop-specific microbiome assembly from soils. We identified the metabolically active bacterial microbiota (SSU RNA) inhabiting two compartments of the rhizosphere of wheat (Triticum aestivum L.), barley (Hordeum vulgare L.), rye (Secale cereale), and oilseed rape (Brassica napus L.) at different growth stages. RESULTS Based on metabarcoding analysis the bacterial microbiota was shaped by the two rhizosphere compartments, i.e. close and distant. Thereby implying a different spatial extent of bacterial microbiota acquirement by the cereals species versus oilseed rape. We derived core microbiota of each crop species. Massilia (barley and wheat) and unclassified Chloroflexi of group 'KD4-96' (oilseed rape) were identified as keystone Bacteria by combining LEfSe biomarker and network analyses. Subsequently, differential associations between networks of each crop species' core microbiota revealed host plant-specific interconnections for specific genera, such as the unclassified Tepidisphaeraceae 'WD2101 soil group'. CONCLUSIONS Our results provide keystone rhizosphere Bacteria derived from for crop hosts and revealed that cohort subnetworks and differential associations elucidated host species effect that was not evident from differential abundance of single bacterial genera enriched or unique to a specific plant host. Thus, we underline the importance of co-occurrence patterns within the rhizosphere microbiota that emerge in crop-specific microbiomes, which will be essential to modify native crop microbiomes for future agriculture and to develop effective bio-fertilizers.
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Affiliation(s)
- Simon Lewin
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research e.V. (ZALF), Müncheberg, Germany
| | - Davide Francioli
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research e.V. (ZALF), Müncheberg, Germany
| | - Andreas Ulrich
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research e.V. (ZALF), Müncheberg, Germany
| | - Steffen Kolb
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research e.V. (ZALF), Müncheberg, Germany.
- Thaer Institute, Faculty of Life Sciences, Humboldt University of Berlin, Berlin, Germany.
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6
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French E, Kaplan I, Enders L. Foliar Aphid Herbivory Alters the Tomato Rhizosphere Microbiome, but Initial Soil Community Determines the Legacy Effects. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2021. [DOI: 10.3389/fsufs.2021.629684] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Aboveground herbivory can impact the root-associated microbiome, while simultaneously different soil microbial communities influence herbivore performance. It is currently unclear how these reciprocal top-down and bottom-up interactions between plants, insects and microbes vary across different soils and over successive plant generations. In this study, we examined top-down impacts of above-ground herbivory on the rhizosphere microbiome across different soils, assessed bottom-up impacts of soil microbial community variation on herbivore performance, and evaluated their respective contributions to soil legacy effects on herbivore performance. We used Macrosiphum euphorbiae (potato aphid) and Solanum pimpinellifolium (wild tomato) to capture pre-domestication microbiome interactions with a specialist pest. First, using 16S rRNA sequencing we compared bacterial communities associated with rhizospheres of aphid-infested and uninfested control plants grown in three different soils over three time points. High aphid infestation impacted rhizosphere bacterial diversity in a soil-dependent manner, ranging from a 22% decrease to a 21% increase relative to uninfested plants and explained 6–7% of community composition differences in two of three soils. We next investigated bottom-up and soil legacy effects of aphid herbivory by growing wild tomatoes in each of the three soils and a sterilized “no microbiome” soil, infesting with aphids (phase one), then planting a second generation (phase two) of plants in the soil conditioned with aphid-infested or uninfested control plants. In the first phase, aphid performance varied across plants grown in different soil sources, ranging from a 20 to 50% increase in aphid performance compared to the “no microbiome” control soil, demonstrating a bottom-up role for soil microbial community. In the second phase, initial soil community, but not previous aphid infestation, impacted aphid performance on plants. Thus, while herbivory altered the rhizosphere microbiome in a soil community-dependent manner, the bottom-up interaction between the microbial community and the plant, not top-down effects of prior herbivore infestation, affected herbivore performance in the following plant generation. These findings suggest that the bottom-up effects of the soil microbial community play an overriding role in herbivore performance in both current and future plant generations and thus are an important target for sustainable control of herbivory in agroecosystems.
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7
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Hernández-Terán A, Navarro-Díaz M, Benítez M, Lira R, Wegier A, Escalante AE. Host genotype explains rhizospheric microbial community composition: the case of wild cotton metapopulations (Gossypium hirsutum L.) in Mexico. FEMS Microbiol Ecol 2021; 96:5850751. [PMID: 32490512 DOI: 10.1093/femsec/fiaa109] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 06/01/2020] [Indexed: 01/04/2023] Open
Abstract
The rhizosphere provides several benefits to the plant host being a strong determinant for its health, growth and productivity. Nonetheless, the factors behind the assembly of the microbial communities associated with the rhizosphere such as the role of plant genotypes are not completely understood. In this study, we tested the role that intraspecific genetic variation has in rhizospheric microbial community assemblages, using genetically distinct wild cotton populations as a model of study. We followed a common garden experiment including five wild cotton populations, controlling for plant genotypes, environmental conditions and soil microbial community inoculum, to test for microbial differences associated with genetic variation of the plant hosts. Microbial communities of the treatments were characterized by culture-independent 16S rRNA gene amplicon sequencing with Illumina MiSeq platform. We analyzed microbial community diversity (alpha and beta), and diversity structure of such communities, determined by co-occurrence networks. Results show that different plant genotypes select for different and specific microbial communities from a common inoculum. Although we found common amplicon sequence variants (ASVs) to all plant populations (235), we also found unique ASVs for different populations that could be related to potential functional role of such ASVs in the rhizosphere.
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Affiliation(s)
- Alejandra Hernández-Terán
- Laboratorio Nacional de Ciencias de la Sostenibilidad (LANCIS), Instituto de Ecología, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico.,Programa de Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Marcelo Navarro-Díaz
- Laboratorio Nacional de Ciencias de la Sostenibilidad (LANCIS), Instituto de Ecología, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico.,Programa de Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Mariana Benítez
- Laboratorio Nacional de Ciencias de la Sostenibilidad (LANCIS), Instituto de Ecología, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico.,Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Rafael Lira
- Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, 54090, Mexico City, Mexico
| | - Ana Wegier
- Jardín Botánico, Instituto de Biología, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Ana E Escalante
- Laboratorio Nacional de Ciencias de la Sostenibilidad (LANCIS), Instituto de Ecología, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
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8
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Hereira-Pacheco SE, Navarro-Noya YE, Dendooven L. The root endophytic bacterial community of Ricinus communis L. resembles the seeds community more than the rhizosphere bacteria independent of soil water content. Sci Rep 2021; 11:2173. [PMID: 33500437 PMCID: PMC7838207 DOI: 10.1038/s41598-021-81551-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 10/20/2020] [Indexed: 01/25/2023] Open
Abstract
Rhizosphere and root endophytic bacteria are crucial for plant development, but the question remains if their composition is similar and how environmental conditions, such as water content, affect their resemblance. Ricinus communis L., a highly drought resistant plant, was used to study how varying soil water content affected the bacterial community in uncultivated, non-rhizosphere and rhizosphere soil, and in its roots. Additionally, the bacterial community structure was determined in the seeds of R. communis at the onset of the experiment. Plants were cultivated in soil at three different watering regimes, i.e. 50% water holding capacity (WHC) or adjusted to 50% WHC every two weeks or every month. Reducing the soil water content strongly reduced plant and root dry biomass and plant development, but had little effect on the bacterial community structure. The bacterial community structure was affected significantly by cultivation of R. communis and showed large variations over time. After 6 months, the root endophytic bacterial community resembled that in the seeds more than in the rhizosphere. It was found that water content had only a limited effect on the bacterial community structure and the different bacterial groups, but R. communis affected the bacterial community profoundly.
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Affiliation(s)
| | - Yendi E Navarro-Noya
- Cátedras CONACYT, Centro Tlaxcala de Biología de La Conducta, Universidad Autónoma de Tlaxcala, Tlaxcala, Mexico
| | - Luc Dendooven
- Laboratory of Soil Ecology, Cinvestav, Mexico City, Mexico.
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9
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Pongsilp N, Nimnoi P. Inoculation of Ensifer fredii strain LP2/20 immobilized in agar results in growth promotion and alteration of bacterial community structure of Chinese kale planted soil. Sci Rep 2020; 10:15857. [PMID: 32985587 PMCID: PMC7522984 DOI: 10.1038/s41598-020-72986-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 09/09/2020] [Indexed: 12/20/2022] Open
Abstract
In our former research, we succeeded in using agar, alginate, and perlite as immobilization materials to maintain long-term survival of the inoculant, Ensifer fredii LP2/20, in a controlled glasshouse. Therefore the information on the establishment and activity of the inoculant to promote plant growth under field conditions, the effects of the inoculant on the soil microbial communities and specific microbial taxa, and the association between the inoculant and soil elements merit further studies. Here, we found that agar was the most suitable material that supported the establishment of the inoculant under field conditions. RNA-based analysis showed that E. fredii LP2/20 immobilized in agar was still metabolically active at day 50 after being introduced into soil. Inoculation of E. fredii LP2/20 immobilized in agar conferred the highest plant dry weight (up to 89.94%) and all plant elements including total N (9.55%), P (17.94%), K (68.42%), Ca (39.77%), Mg (30.76%), Fe (29.85%), and Zn (22.44%). Inoculation of E. fredii LP2/20 immobilized in agar increased soil chemicals including soil organic matter (99.02%), total N (272.48%), P (31.75%), K (52.74%), Fe (51.06%), and Zn (63.10%). High-throughput next-generation sequencing of bacterial 16S rRNA amplicons showed that the Proteobacteria, Acidobacteria, Bacteroidetes, and Firmicutes were dominant phyla in Chinese kale field soil. Inoculation of E. fredii LP2/20 significantly affected the soil bacterial community structure by decreasing total bacterial richness and diversity. The numbers of alpha- and gamma-Proteobacteria were significantly increased while the number of delta-Proteobacteria was significantly decreased due to E. fredii LP2/20 establishment. Soil total P, K, and Ca and soil pH were the important factors that shaped the soil bacterial community composition.
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Affiliation(s)
- Neelawan Pongsilp
- Department of Microbiology, Faculty of Science, Silpakorn University, Nakhon Pathom, 7300, Thailand
| | - Pongrawee Nimnoi
- Department of Microbiology, Faculty of Liberal Arts and Science, Kasetsart University, Nakhon Pathom, 73140, Thailand.
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10
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Al-Quwaie DAH. Bacterial community dynamics with rhizosphere of Calotropis procera and Senna alexandrina desert plants in Saudi Arabia. Bioinformation 2020; 16:567-578. [PMID: 33214744 PMCID: PMC7649021 DOI: 10.6026/97320630016567] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 06/12/2020] [Indexed: 12/30/2022] Open
Abstract
It is of interest to study the rhizobacteria associated with two different desert wild plants, e.g., Calotropis procera and Senna alexandrina compared with bulk soil sample in order to identify signatures of microbes in rhizospheres of the two plants and detect influence of soil microbiome in drawing soil architecture. Analysis of deep sequencing microbial dataset indicated occurrence of 296,642 sequence tags assigned 5,210 OTUs (operational taxonomic units). Species richness in control sample was higher than those of either plant's rhizosphere, while microbial abundance was lower. Principal coordinate analysis (PCoA) plot indicated complete separation of microbiome diversity among groups. Abundances of Pseudomonas stutzeri and Virgibacillus koreensis increased in the rhizosphere of C. procera compared with that of S. alexandrina, while those of Streptococcus sobrinus, Veillonella parvula and unassigned species of Sphingomonas genus increased in rhizosphere of S. alexandrina. Unassigned species of genera Marinobacter, Porticoccus and Alcanivorax only exist in rhizosphere microbiome of C. procera, while unassigned species of genus Pseudomonas only exists in rhizosphere microbiome of Senna alexandrina. High abundances of the two microbes Pseudomonas stutzeri and Virgibacillus koreensis in rhizosphere of C. procera allow the plant to grow well under both normal and saline condition. Also, Marinobacter, Porticoccus and Alcanivorax genera only exist in rhizosphere microbiome of C. procera. These microbes produce siderophores that protect plant from pathogens. Data shows that C. procera might be more protected from microbial pathogens compared with S. alexandrina. The differential abundances or exclusive presence of soil microbes reflect the ability of plant species to survive under biotic and abiotic stresses. Results imply that rhizospheric microbes can be used as biomarkers of plant growth rate and the ability to survive under harsh conditions.
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Affiliation(s)
- Diana AH Al-Quwaie
- Department of Biological Sciences, Rabigh College of Science and Arts, King Abdulaziz University (KAU), Rabigh, Saudi Arabia
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11
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Randall KC, Brennan F, Clipson N, Creamer RE, Griffiths BS, Storey S, Doyle E. An Assessment of Climate Induced Increase in Soil Water Availability for Soil Bacterial Communities Exposed to Long-Term Differential Phosphorus Fertilization. Front Microbiol 2020; 11:682. [PMID: 32477279 PMCID: PMC7242630 DOI: 10.3389/fmicb.2020.00682] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 03/24/2020] [Indexed: 11/13/2022] Open
Abstract
The fate of future food productivity depends primarily upon the health of soil used for cultivation. For Atlantic Europe, increased precipitation is predicted during both winter and summer months. Interactions between climate change and the fertilization of land used for agriculture are therefore vital to understand. This is particularly relevant for inorganic phosphorus (P) fertilization, which already suffers from resource and sustainability issues. The soil microbiota are a key indicator of soil health and their functioning is critical to plant productivity, playing an important role in nutrient acquisition, particularly when plant available nutrients are limited. A multifactorial, mesocosm study was established to assess the effects of increased soil water availability and inorganic P fertilization, on spring wheat biomass, soil enzymatic activity (dehydrogenase and acid phosphomonoesterase) and soil bacterial community assemblages. Our results highlight the significance of the spring wheat rhizosphere in shaping soil bacterial community assemblages and specific taxa under a moderate soil water content (60%), which was diminished under a higher level of soil water availability (80%). In addition, an interaction between soil water availability and plant presence overrode a long-term bacterial sensitivity to inorganic P fertilization. Together this may have implications for developing sustainable P mobilization through the use of the soil microbiota in future. Spring wheat biomass grown under the higher soil water regime (80%) was reduced compared to the constant water regime (60%) and a reduction in yield could be exacerbated in the future when grown in cultivated soil that have been fertilized with inorganic P. The potential feedback mechanisms for this need now need exploration to understand how future management of crop productivity may be impacted.
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Affiliation(s)
- Kate C Randall
- School of Biology and Environmental Science, Earth Institute, University College Dublin, Dublin, Ireland.,School of Life Sciences, University of Essex, Colchester, United Kingdom
| | - Fiona Brennan
- Teagasc Environment Research Centre, Wexford, Ireland
| | - Nicholas Clipson
- School of Biology and Environmental Science, Earth Institute, University College Dublin, Dublin, Ireland
| | - Rachel E Creamer
- Teagasc Environment Research Centre, Wexford, Ireland.,Soil Biology Group, Wageningen University & Research, Wageningen, Netherlands
| | - Bryan S Griffiths
- Teagasc Environment Research Centre, Wexford, Ireland.,SRUC, Crop & Soil Systems Research Group, Edinburgh, United Kingdom
| | - Sean Storey
- School of Biology and Environmental Science, Earth Institute, University College Dublin, Dublin, Ireland
| | - Evelyn Doyle
- School of Biology and Environmental Science, Earth Institute, University College Dublin, Dublin, Ireland
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Ishizawa H, Kuroda M, Inoue D, Morikawa M, Ike M. Community dynamics of duckweed-associated bacteria upon inoculation of plant growth-promoting bacteria. FEMS Microbiol Ecol 2020; 96:5843272. [DOI: 10.1093/femsec/fiaa101] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Accepted: 05/22/2020] [Indexed: 01/05/2023] Open
Abstract
ABSTRACT
Plant growth-promoting bacteria (PGPB) have recently been demonstrated as a promising agent to improve wastewater treatment and biomass production efficiency of duckweed hydrocultures. With a view to their reliable use in aqueous environments, this study analysed the plant colonization dynamics of PGPB and the ecological consequences for the entire duckweed-associated bacterial community. A PGPB strain, Aquitalea magnusonii H3, was inoculated to duckweed at different cell densities or timings in the presence of three environmental bacterial communities. The results showed that strain H3 improved duckweed growth by 11.7–32.1% in five out of nine experiments. Quantitative-PCR and amplicon sequencing analyses showed that strain H3 successfully colonized duckweed after 1 and 3 d of inoculation in all cultivation tests. However, it significantly decreased in number after 7 d, and similar bacterial communities were observed on duckweed regardless of H3 inoculation. Predicted metagenome analysis suggested that genes related to bacterial chemotactic motility and surface attachment systems are consistently enriched through community assembly on duckweed. Taken together, strain H3 dominantly colonized duckweed for a short period and improved duckweed growth. However, the inoculation of the PGPB did not have a lasting impact due to the strong resilience of the natural duckweed microbiome.
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Affiliation(s)
- Hidehiro Ishizawa
- Division of Sustainable Energy and Environmental Engineering, Graduate School of Engineering, Osaka University , 2-1 Suita, Osaka, Japan
| | - Masashi Kuroda
- Division of Sustainable Energy and Environmental Engineering, Graduate School of Engineering, Osaka University , 2-1 Suita, Osaka, Japan
| | - Daisuke Inoue
- Division of Sustainable Energy and Environmental Engineering, Graduate School of Engineering, Osaka University , 2-1 Suita, Osaka, Japan
| | - Masaaki Morikawa
- Division of Biosphere Science, Graduate School of Environmental Science, Hokkaido University, N10 W5 Sapporo, Hokkaido, Japan
| | - Michihiko Ike
- Division of Sustainable Energy and Environmental Engineering, Graduate School of Engineering, Osaka University , 2-1 Suita, Osaka, Japan
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13
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Rowen E, Tooker JF. Fertilizing Corn With Manure Decreases Caterpillar Performance but Increases Slug Damage. ENVIRONMENTAL ENTOMOLOGY 2020; 49:141-150. [PMID: 31778537 DOI: 10.1093/ee/nvz145] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Indexed: 06/10/2023]
Abstract
Many farmers use manure as an alternative to inorganic fertilizer. Previous research has shown that manure can decrease plant susceptibility to herbivores, but the mechanisms remain unclear. To determine how manure affects herbivore performance in a greenhouse setting, we fertilized corn with stacked cow manure or an equivalent amount of NPK fertilizer and measured caterpillar development, plant nutritional content, and defenses. After 4 wk of growth, we allowed fall armyworm (Spodoptera frugiperda) or black cutworm (Agrotis ipsilon) caterpillars to feed on these plants for 6 d. Compared to inorganic fertilizer, manure reduced mass-gain of black cutworm caterpillars and smaller fall armyworms. We paired this greenhouse experiment with a 3-yr field experiment, which incorporated a wheat cover-crop treatment crossed with the two fertilizer treatments in a 2 × 2 factorial design. We measured plant damage early in the season from naturally occurring herbivores and measured neonate fall armyworm performance on field-collected leaf tissue. In 2017, corn in manure-fertilized plots sustained more herbivore damage, primarily driven by a higher incidence of slug damage. Fall armyworm performance, however, was lower on leaves collected from manure-fertilized plants. In contrast to previous studies, we did not find increased micronutrients or enhanced defenses in manure treated plants. While manure can offer resistance to some herbivores, our results suggest that this resistance can be overshadowed by habitat conditions.
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Affiliation(s)
- Elizabeth Rowen
- Department of Entomology, The Pennsylvania State University, University Park, PA
| | - John F Tooker
- Department of Entomology, The Pennsylvania State University, University Park, PA
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O’Brien FJM, Almaraz M, Foster MA, Hill AF, Huber DP, King EK, Langford H, Lowe MA, Mickan BS, Miller VS, Moore OW, Mathes F, Gleeson D, Leopold M. Soil Salinity and pH Drive Soil Bacterial Community Composition and Diversity Along a Lateritic Slope in the Avon River Critical Zone Observatory, Western Australia. Front Microbiol 2019; 10:1486. [PMID: 31312189 PMCID: PMC6614384 DOI: 10.3389/fmicb.2019.01486] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 06/14/2019] [Indexed: 01/25/2023] Open
Abstract
Soils are crucial in regulating ecosystem processes, such as nutrient cycling, and supporting plant growth. To a large extent, these functions are carried out by highly diverse and dynamic soil microbiomes that are in turn governed by numerous environmental factors including weathering profile and vegetation. In this study, we investigate geophysical and vegetation effects on the microbial communities of iron-rich lateritic soils in the highly weathered landscapes of Western Australia (WA). The study site was a lateritic hillslope in southwestern Australia, where gradual erosion of the duricrust has resulted in the exposure of the different weathering zones. High-throughput amplicon sequencing of the 16S rRNA gene was used to investigate soil bacterial community diversity, composition and functioning. We predicted that shifts in the microbial community would reflect variations in certain edaphic properties associated with the different layers of the lateritic profile and vegetation cover. Our results supported this hypothesis, with electrical conductivity, pH and clay content having the strongest correlation with beta diversity, and many of the differentially abundant taxa belonging to the phyla Actinobacteria and Proteobacteria. Soil water repellence, which is associated with Eucalyptus vegetation, also affected beta diversity. This enhanced understanding of the natural system could help to improve future crop management in WA since the physicochemical properties of the agricultural soils in this region are inherited from laterites via the weathering and pedogenesis processes.
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Affiliation(s)
| | - Maya Almaraz
- National Center for Ecological Analysis and Synthesis, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Melissa A. Foster
- U.S. Bureau of Reclamation, Denver Federal Center, Denver, CO, United States
| | - Alice F. Hill
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Boulder, CO, United States
| | - David P. Huber
- Department of Biological Sciences, Idaho State University, Pocatello, ID, United States
| | - Elizabeth K. King
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | - Harry Langford
- Department of Geography, The University of Sheffield, Sheffield, United Kingdom
| | - Mary-Anne Lowe
- UWA School of Agriculture and Environment, The University of Western Australia, Crawley, WA, Australia
| | - Bede S. Mickan
- UWA School of Agriculture and Environment, The University of Western Australia, Crawley, WA, Australia
| | - Valerie S. Miller
- Department of Renewable Resources, University of Alberta, Edmonton, AB, Canada
| | - Oliver W. Moore
- School of Earth and Environment, University of Leeds, Leeds, United Kingdom
| | - Falko Mathes
- UWA School of Agriculture and Environment, The University of Western Australia, Crawley, WA, Australia
| | - Deirdre Gleeson
- UWA School of Agriculture and Environment, The University of Western Australia, Crawley, WA, Australia
| | - Matthias Leopold
- UWA School of Agriculture and Environment, The University of Western Australia, Crawley, WA, Australia
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