1
|
Agunbiade VF, Fadiji AE, Agbodjato NA, Babalola OO. Isolation and Characterization of Plant-Growth-Promoting, Drought-Tolerant Rhizobacteria for Improved Maize Productivity. PLANTS (BASEL, SWITZERLAND) 2024; 13:1298. [PMID: 38794369 PMCID: PMC11125291 DOI: 10.3390/plants13101298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 02/05/2024] [Accepted: 02/20/2024] [Indexed: 05/26/2024]
Abstract
Drought is one of the main abiotic factors affecting global agricultural productivity. However, the application of bioinocula containing plant-growth-promoting rhizobacteria (PGPR) has been seen as a potential environmentally friendly technology for increasing plants' resistance to water stress. In this study, rhizobacteria strains were isolated from maize (Zea mays L.) and subjected to drought tolerance tests at varying concentrations using polyethylene glycol (PEG)-8000 and screened for plant-growth-promoting activities. From this study, 11 bacterial isolates were characterized and identified molecularly, which include Bacillus licheniformis A5-1, Aeromonas caviae A1-2, A. veronii C7_8, B. cereus B8-3, P. endophytica A10-11, B. halotolerans A9-10, B. licheniformis B9-5, B. simplex B15-6, Priestia flexa B12-4, Priestia flexa C6-7, and Priestia aryabhattai C1-9. All isolates were positive for indole-3-acetic acid (IAA), siderophore, 1-aminocyclopropane-1-carboxylate (ACC) deaminase, ammonia production, nitrogen fixation, and phosphate solubilization, but negative for hydrogen cyanide production. Aeromonas strains A1-2 and C7_8, showing the highest drought tolerance of 0.71 and 0.77, respectively, were selected for bioinoculation, singularly and combined. An increase in the above- and below-ground biomass of the maize plants at 100, 50, and 25% water-holding capacity (WHC) was recorded. Bacterial inoculants, which showed an increase in the aerial biomass of plants subjected to moderate water deficiency by up to 89%, suggested that they can be suitable candidates to enhance drought tolerance and nutrient acquisition and mitigate the impacts of water stress on plants.
Collapse
Affiliation(s)
| | | | | | - Olubukola Oluranti Babalola
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho 2735, South Africa
| |
Collapse
|
2
|
Wu N, Shi W, Liu W, Gao Z, Han L, Wang X. Differential impact of Bt-transgenic rice plantings on bacterial community in three niches over consecutive years. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 223:112569. [PMID: 34352582 DOI: 10.1016/j.ecoenv.2021.112569] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 06/11/2021] [Accepted: 07/25/2021] [Indexed: 05/26/2023]
Abstract
Transgenic-Bacillus thuringiensis (Bt) crops express insecticidal proteins, which can accumulate in plants and soil where they may influence microbial populations. The impact of Bt crops on bacterial communities has only been assessed under short-term, and results have been contradictory. Here, we analyzed the bacterial communities in three niches, rhizosphere soil (RS), root endosphere (RE) and leaf endosphere (LE), of three Bt rice and their non-Bt parental lines for three consecutive years by high-throughput sequencing. In principal coordinate analysis (PCoA) and PERMANOVA (Adonis) analysis, operational taxonomic units (OTUs) were clustered primarily by niche type and differed significantly in the RE and LE but not in the RS between each of three Bt lines compared with the non-Bt rice line, and not in each respective niche among the three Bt rice lines. The bacterial communities in the RS of different rice lines over the 3 years were clustered mainly by year rather than by lines. The differential bacterial taxa among the lines did not overlap between years, presumably because Cry proteins are rapidly degraded in the soil. A network analysis of RS bacterial communities showed that the network complexity and density for the three Bt rice lines did not decrease compared with those for the non-Bt line. In conclusion, our results demonstrated that bacterial communities differed significantly in RE and LE between Bt and non-Bt rice lines, but the differences were mild and transient, and had no adverse impact on RS over the 3 years. This study provides favorable evidence in support of the commercialization of Bt rice.
Collapse
Affiliation(s)
- Nan Wu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Wencong Shi
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, China
| | - Wenwen Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Zheng Gao
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, China
| | - Lanzhi Han
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Xifeng Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| |
Collapse
|
3
|
Zhu J, Cao A, Wu J, Fang W, Huang B, Yan D, Wang Q, Li Y. Effects of chloropicrin fumigation combined with biochar on soil bacterial and fungal communities and Fusarium oxysporum. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 220:112414. [PMID: 34126305 DOI: 10.1016/j.ecoenv.2021.112414] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 06/06/2021] [Accepted: 06/08/2021] [Indexed: 06/12/2023]
Abstract
Chloropicrin (CP) can cause long-term damage to beneficial microbes which reduces soil health. Biochar (BC) can mitigate against the effects of CP by reducing the time for beneficial microbes to recover after CP fumigation. In this study, we used Real-Time Quantitative PCR to determine the effects of different rates of BC added to CP-fumigated soil on the speed of recovery of bacteria and fungi population and on changes to gene copy number of the target pathogen Fusarium oxysporum. And then we compared the structure and composition of the beneficial microbial community in the different treatments soil by using High throughput Illumina sequencing. As the results shown, adding 1 or 3% BC after CP fumigation accelerated the recovery of bacterial and fungal populations without increasing F. oxysporum abundance. BC also promoted the recovery of beneficial bacteria Rokubacteria and Latescibacteria damaged by CP. And these two bacteria may be related to the immunity of soil to F. oxysporum. In CP-fumigated soil, BC improved the disease resistance of the soil by increasing beneficial microbes, such as Steroidobacter, Sphingomonas, Purpureocillium and Mortierella. This combination of CP and BC is a new concept that could encourages the development of a healthy and sustainable soil ecosystems while controlling plant pathogens.
Collapse
Affiliation(s)
- Jiahong Zhu
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Aocheng Cao
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jiajia Wu
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Wensheng Fang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Bin Huang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Dongdong Yan
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Qiuxia Wang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yuan Li
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| |
Collapse
|
4
|
Mitigation of Nickel Toxicity and Growth Promotion in Sesame through the Application of a Bacterial Endophyte and Zeolite in Nickel Contaminated Soil. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17238859. [PMID: 33260516 PMCID: PMC7730600 DOI: 10.3390/ijerph17238859] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 11/24/2020] [Accepted: 11/25/2020] [Indexed: 11/16/2022]
Abstract
Nickel (Ni) bioavailable fraction in the soil is of utmost importance because of its involvement in plant growth and environmental feedbacks. High concentrations of Ni in the soil environment, especially in the root zone, may retard plant growth that ultimately results in reduced plant biomass and yield. However, endophytic microorganisms have great potential to reduce the toxicity of Ni, especially when applied together with zeolite. The present research work was conducted to evaluate the potential effects of an endophytic bacterium Caulobacter sp. MN13 in combination with zeolite on the physiology, growth, quality, and yield of sesame plant under normal and Ni stressed soil conditions through possible reduction of Ni uptake. Surface sterilized sesame seeds were sown in pots filled with artificially Ni contaminated soil amended with zeolite. Results revealed that plant agronomic attributes such as shoot root dry weight, total number of pods, and 1000-grains weight were increased by 41, 45, 54, and 65%, respectively, over control treatment, with combined application of bacteria and zeolite in Ni contaminated soil. In comparison to control, the gaseous exchange parameters (CO2 assimilation rate, transpiration rate, stomatal- sub-stomatal conductance, chlorophyll content, and vapor pressure) were significantly enhanced by co-application of bacteria and zeolite ranging from 20 to 49% under Ni stress. Moreover, the combined utilization of bacteria and zeolite considerably improved water relations of sesame plant, in terms of relative water content (RWC) and relative membrane permeability (RMP) along with improvement in biochemical components (protein, ash, crude fiber, fat), and micronutrients in normal as well as in Ni contaminated soil. Moreover, the same treatment modulated the Ni-stress in plants through improvement in antioxidant enzymes (AEs) activities along with improved Ni concentration in the soil and different plant tissues. Correlation and principal component analysis (PCA) further revealed that combined application of metal-tolerant bacterium Caulobacter sp. MN13 and zeolite is the most influential strategy in alleviating Ni-induced stress and subsequent improvement in growth, yield, and physio-biochemical attributes of sesame plant.
Collapse
|
5
|
Tosi M, Gaiero J, Linton N, Mafa-Attoye T, Castillo A, Dunfield K. Bacterial Endophytes: Diversity, Functional Importance, and Potential for Manipulation. ACTA ACUST UNITED AC 2020. [DOI: 10.1007/978-981-15-6125-2_1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
|
6
|
Tosi M, Mitter EK, Gaiero J, Dunfield K. It takes three to tango: the importance of microbes, host plant, and soil management to elucidate manipulation strategies for the plant microbiome. Can J Microbiol 2020; 66:413-433. [DOI: 10.1139/cjm-2020-0085] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The world’s population is expected to grow to almost 10 billion by 2050, placing unprecedented demands on agriculture and natural resources. The risk in food security is also aggravated by climate change and land degradation, which compromise agricultural productivity. In recent years, our understanding of the role of microbial communities on ecosystem functioning, including plant-associated microbes, has advanced considerably. Yet, translating this knowledge into practical agricultural technologies is challenged by the intrinsic complexity of agroecosystems. Here, we review current strategies for plant microbiome manipulation, classifying them into three main pillars: (i) introducing and engineering microbiomes, (ii) breeding and engineering the host plant, and (iii) selecting agricultural practices that enhance resident soil and plant-associated microbial communities. In each of these areas, we analyze current trends in research, as well as research priorities and future perspectives.
Collapse
Affiliation(s)
- Micaela Tosi
- School of Environmental Sciences, University of Guelph, Guelph, ON N1G 2W1, Canada
| | | | - Jonathan Gaiero
- School of Environmental Sciences, University of Guelph, Guelph, ON N1G 2W1, Canada
- School of Environmental Sciences, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Kari Dunfield
- School of Environmental Sciences, University of Guelph, Guelph, ON N1G 2W1, Canada
| |
Collapse
|
7
|
Alok D, Annapragada H, Singh S, Murugesan S, Singh NP. Symbiotic nitrogen fixation and endophytic bacterial community structure in Bt-transgenic chickpea (Cicer arietinum L). Sci Rep 2020; 10:5453. [PMID: 32214159 PMCID: PMC7096491 DOI: 10.1038/s41598-020-62199-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 01/10/2020] [Indexed: 01/11/2023] Open
Abstract
Symbiotic nitrogen fixation (SNF) of transgenic grain legumes might be influenced either by the site of transgene integration into the host genome or due to constitutive expression of transgenes and antibiotic-resistant marker genes. The present investigation confirmed proper nodulation of five tested Bt-chickpea events (IPCa2, IPCa4, IPCT3, IPCT10, and IPCT13) by native Mesorhizobium under field environment. Quantitative variations for nodulation traits among Bt-chickpea were determined and IPCT3 was found superior for nodule number and nodule biomass. Diversity, as well as richness indices, confirmed the changes in bacterial community structure of root and root-nodules from Bt-chickpea events IPCa2 and IPCT10. Especially, Gram-positive bacteria belonging to Firmicutes and Actinobacteria were selectively eliminated from root colonization of IPCa2. Richness indices (CHAO1 and ACE) of the root-associated bacterial community of IPCa2 was 13-14 times lesser than that of parent cv DCP92-3. Root nodule associated bacterial community of IPCT10 was unique with high diversity and richness, similar to the roots of non-Bt and Bt-chickpea. It indicated that the root nodules of IPCT10 might have lost their peculiar characteristics and recorded poor colonization of Mesorhizobium with a low relative abundance of 0.27. The impact of Bt-transgene on bacterial community structure and nodulation traits should be analyzed across the years and locations to understand and stabilize symbiotic efficiency for ecosystem sustainability.
Collapse
Affiliation(s)
- Das Alok
- Division of Plant Biotechnology, Indian Institute of Pulses Research, Kalyanpur, Kanpur, India
| | - Harika Annapragada
- Division of Basic Sciences, Indian Institute of Pulses Research, Kalyanpur, Kanpur, India
| | - Shilpa Singh
- Division of Basic Sciences, Indian Institute of Pulses Research, Kalyanpur, Kanpur, India
| | - Senthilkumar Murugesan
- Division of Basic Sciences, Indian Institute of Pulses Research, Kalyanpur, Kanpur, India.
| | - Narendra Pratap Singh
- Division of Plant Biotechnology, Indian Institute of Pulses Research, Kalyanpur, Kanpur, India
| |
Collapse
|
8
|
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.
Collapse
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
| |
Collapse
|
9
|
Berrios L, Ely B. The Isolation and Characterization of Kronos, a Novel Caulobacter Rhizosphere Phage that is Similar to Lambdoid Phages. Curr Microbiol 2019; 76:558-565. [PMID: 30810780 DOI: 10.1007/s00284-019-01656-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 02/20/2019] [Indexed: 11/29/2022]
Abstract
Despite their ubiquity, relatively few bacteriophages have been characterized. Here, we set out to explore Caulobacter bacteriophages (caulophages) in the rhizosphere and characterized Kronos, the first caulophage isolated from the rhizosphere. Kronos is a member of the Siphoviridae family since it has a long flexible tail. In addition, an analysis of the Kronos genome indicated that many of the predicted proteins were distantly related to those of bacteriophages in the lambdoid family. Consistent with this observation, we were able to demonstrate the presence of cos sites that are similar to those found at the ends of lambdoid phage genomes. Moreover, Kronos displayed a relatively rare head and tail morphology compared to other caulophages but was similar to that of the lambdoid phages. Taken together, these data indicate that Kronos is distantly related to lambdoid phages and may represent a new Siphoviridae genus.
Collapse
Affiliation(s)
- Louis Berrios
- Department of Biological Sciences, University of South Carolina, Columbia, SC, 29208, USA
| | - Bert Ely
- Department of Biological Sciences, University of South Carolina, Columbia, SC, 29208, USA.
| |
Collapse
|
10
|
Metagenomic analyses of bacterial endophytes associated with the phyllosphere of a Bt maize cultivar and its isogenic parental line from South Africa. World J Microbiol Biotechnol 2017; 33:80. [PMID: 28341909 DOI: 10.1007/s11274-017-2249-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 03/16/2017] [Indexed: 10/19/2022]
Abstract
Genetic modification of maize with Bacillus thuringiensis (Bt) cry proteins may predispose shifts in the bacterial endophytes' community associated with maize shoots. In this study, the diversity of bacterial endophytes associated with a Bt maize genotype (Mon810) and its isogenic non-transgenic parental line were investigated at pre-flowering (50 days) and post-flowering (90 days) developmental stages. PCR-DGGE and high throughput sequencing on the Illumina MiSeq sequencer were used to characterize bacterial 16S rRNA gene diversity in leaves, stems, seeds and tassels. PCR-DGGE profile revealed similarity as well as differences between bacterial communities of shoots in both cultivars and at both developmental stages. A total of 1771 operational taxonomic units (OTUs) were obtained from the MiSeq and assigned into 14 phyla, 27 classes, 58 orders, 116 families and 247 genera. Differences in alpha and beta diversity measures of OTUs between the phyllospheres of both genotypes were not significant (P > .05) at all developmental stages. In all cultivars, OTU diversity reduced with plant development. OTUs belonging to the phyla Proteobacteria were dominant in all maize phyllospheres. The class Gammaproteobacteria was dominant in Bt maize while, Alphaproteobacteria and Actinobacteria were dominant in non-Bt maize phyllospheres. Differences in the abundance of some genera, including Acidovorax, Burkerholderia, Brachybacterium, Enterobacter and Rhodococcus, whose species are known beneficial endophytes were observed between cultivars. Hierarchical cluster analysis further suggests that the bacterial endophyte communities of both maize genotypes associate differently (are dissimilar). Overall, the results suggest that bacterial endophytes community differed more across developmental stages than between maize genotypes.
Collapse
|
11
|
Foster ZSL, Sharpton TJ, Grünwald NJ. Metacoder: An R package for visualization and manipulation of community taxonomic diversity data. PLoS Comput Biol 2017; 100:1738-50. [PMID: 28222096 DOI: 10.3732/ajb.1200572] [Citation(s) in RCA: 236] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 03/07/2017] [Accepted: 02/10/2017] [Indexed: 05/20/2023] Open
Abstract
Community-level data, the type generated by an increasing number of metabarcoding studies, is often graphed as stacked bar charts or pie graphs that use color to represent taxa. These graph types do not convey the hierarchical structure of taxonomic classifications and are limited by the use of color for categories. As an alternative, we developed metacoder, an R package for easily parsing, manipulating, and graphing publication-ready plots of hierarchical data. Metacoder includes a dynamic and flexible function that can parse most text-based formats that contain taxonomic classifications, taxon names, taxon identifiers, or sequence identifiers. Metacoder can then subset, sample, and order this parsed data using a set of intuitive functions that take into account the hierarchical nature of the data. Finally, an extremely flexible plotting function enables quantitative representation of up to 4 arbitrary statistics simultaneously in a tree format by mapping statistics to the color and size of tree nodes and edges. Metacoder also allows exploration of barcode primer bias by integrating functions to run digital PCR. Although it has been designed for data from metabarcoding research, metacoder can easily be applied to any data that has a hierarchical component such as gene ontology or geographic location data. Our package complements currently available tools for community analysis and is provided open source with an extensive online user manual.
Collapse
Affiliation(s)
- Zachary S L Foster
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Thomas J Sharpton
- Department of Microbiology, Oregon State University, Corvallis, Oregon, United States of America
- Department of Statistics, Oregon State University, Corvallis, Oregon, United States of America
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America
| | - Niklaus J Grünwald
- Horticultural Crops Research Laboratory, USDA-ARS, Corvallis, Oregon, United States of America
| |
Collapse
|
12
|
Sun C, Geng L, Wang M, Shao G, Liu Y, Shu C, Zhang J. No adverse effects of transgenic maize on population dynamics of endophytic Bacillus subtilis strain B916-gfp. Microbiologyopen 2016; 6. [PMID: 27666942 PMCID: PMC5300882 DOI: 10.1002/mbo3.404] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 08/18/2016] [Accepted: 08/23/2016] [Indexed: 11/12/2022] Open
Abstract
Endophytic bacterial communities play a key role in promoting plant growth and combating plant diseases. However, little is known about their population dynamics in plant tissues and bulk soil, especially in transgenic crops. This study investigated the colonization of transgenic maize harboring the Bacillus thuringiensis (Bt) cry1Ah gene by Bacillus subtilis strain B916‐gfp present in plant tissues and soil. Bt and nontransgenic maize were inoculated with B916‐gfp by seed soaking, or root irrigation under both laboratory greenhouse and field conditions. During the growing season, B916‐gfp colonized transgenic as well as nontransgenic plants by both inoculation methods. No differences were observed in B916‐gfp population size between transgenic and nontransgenic plants, except at one or two time points in the roots and stems that did not persist over the examination period. Furthermore, planting transgenic maize did not affect the number of B916‐gfp in bulk soil in either laboratory or field trials. These results indicate that transgenic modification of maize with the cry1Ah gene has no influence on colonization by the endophytic bacteria B916‐gfp present in the plant and in bulk soil.
Collapse
Affiliation(s)
- Chongsi Sun
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lili Geng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Meiling Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Gaoxiang Shao
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yongfeng Liu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Science, Nanjing, China
| | - Changlong Shu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jie Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| |
Collapse
|
13
|
Singh AK, Dubey SK. Current trends in Bt crops and their fate on associated microbial community dynamics: a review. PROTOPLASMA 2016; 253:663-681. [PMID: 26560114 DOI: 10.1007/s00709-015-0903-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 10/19/2015] [Accepted: 10/21/2015] [Indexed: 06/05/2023]
Abstract
Cry protein expressing insect-resistant trait is mostly deployed to control major devastating pests and minimize reliance on the conventional pesticides. However, the ethical and environmental issues are the major constraints in their acceptance, and consequently, the cultivation of genetically modified (GM) crops has invited intense debate. Since root exudates of Bacillus thuringiensis (Bt) crops harbor the insecticidal protein, there is a growing concern about the release and accumulation of soil-adsorbed Cry proteins and their impact on non-target microorganisms and soil microbial processes. This review pertains to reports from the laboratory studies and field trials to assess the Bt toxin proteins in soil microbes and the processes determining the soil quality in conjunction with the existing hypothesis and molecular approaches to elucidate the risk posed by the GM crops. Ecological perturbations hinder the risk aspect of soil microbiota in response to GM crops. Therefore, extensive research based on in vivo and interpretation of results using high-throughput techniques such as NGS on risk assessment are imperative to evaluate the impact of Bt crops to resolve the controversy related to their commercialization. But more studies are needed on the risk associated with stacked traits. Such studies would strengthen our knowledge about the plant-microbe interactions.
Collapse
Affiliation(s)
| | - Suresh Kumar Dubey
- Department of Botany, Banaras Hindu University, Varanasi, 221005, India.
| |
Collapse
|
14
|
Pii Y, Borruso L, Brusetti L, Crecchio C, Cesco S, Mimmo T. The interaction between iron nutrition, plant species and soil type shapes the rhizosphere microbiome. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2016; 99:39-48. [PMID: 26713550 DOI: 10.1016/j.plaphy.2015.12.002] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 11/30/2015] [Accepted: 12/01/2015] [Indexed: 05/07/2023]
Abstract
Plant-associated microorganisms can stimulate plants growth and influence both crops yield and quality by nutrient mobilization and transport. Therefore, rhizosphere microbiome appears to be one of the key determinants of plant health and productivity. The roots of plants have the ability to influence its surrounding microbiology, the rhizosphere microbiome, through the creation of specific chemical niches in the soil mediated by the release of phytochemicals (i.e. root exudates) that depends on several factors, such as plants genotype, soil properties, plant nutritional status, climatic conditions. In the present research, two different crop species, namely barley and tomato, characterized by different strategies for Fe acquisition, have been grown in the RHIZOtest system using either complete or Fe-free nutrient solution to induce Fe starvation. Afterward, plants were cultivated for 6 days on two different calcareous soils. Total DNA was extracted from rhizosphere and bulk soil and 454 pyrosequencing technology was applied to V1-V3 16S rRNA gene region. Approximately 5000 sequences were obtained for each sample. The analysis of the bacterial population confirmed that the two bulk soils showed a different microbial community. The presence of the two plant species, as well as the nutritional status (Fe-deficiency and Fe-sufficiency), could promote a differentiation of the rhizosphere microbiome, as highlighted by non-metric multidimensional scaling (NMDS) analysis. Alphaproteobacteria, Actinobacteria, Chloracidobacteria, Thermoleophilia, Betaproteobacteria, Saprospirae, Gemmatimonadetes, Gammaproteobacteria, Acidobacteria were the most represented classes in all the samples analyzed even though their relative abundance changed as a function of the soil, plant species and nutritional status. To our knowledge, this research demonstrate for the first time that different plants species with a diverse nutritional status can promote the development of a peculiar rhizosphere microbiome, depending on the growth substrate.
Collapse
Affiliation(s)
- Youry Pii
- Faculty of Science and Technology, Free University of Bolzano, Piazza Università 5, I-39100 Bolzano, Italy.
| | - Luigimaria Borruso
- Faculty of Science and Technology, Free University of Bolzano, Piazza Università 5, I-39100 Bolzano, Italy
| | - Lorenzo Brusetti
- Faculty of Science and Technology, Free University of Bolzano, Piazza Università 5, I-39100 Bolzano, Italy
| | - Carmine Crecchio
- Department of Soil, Plant and Food Sciences, University of Bari "Aldo Moro", via Amendola 165/A, I-70126 Bari, Italy
| | - Stefano Cesco
- Faculty of Science and Technology, Free University of Bolzano, Piazza Università 5, I-39100 Bolzano, Italy
| | - Tanja Mimmo
- Faculty of Science and Technology, Free University of Bolzano, Piazza Università 5, I-39100 Bolzano, Italy
| |
Collapse
|
15
|
Schmidt JE, Bowles TM, Gaudin ACM. Using Ancient Traits to Convert Soil Health into Crop Yield: Impact of Selection on Maize Root and Rhizosphere Function. FRONTIERS IN PLANT SCIENCE 2016; 7:373. [PMID: 27066028 PMCID: PMC4811947 DOI: 10.3389/fpls.2016.00373] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2016] [Accepted: 03/11/2016] [Indexed: 05/21/2023]
Abstract
The effect of domestication and modern breeding on aboveground traits in maize (Zea mays) has been well-characterized, but the impact on root systems and the rhizosphere remain unclear. The transition from wild ecosystems to modern agriculture has focused on selecting traits that yielded the largest aboveground production with increasing levels of crop management and nutrient inputs. Root morphology, anatomy, and ecophysiological processes may have been affected by the substantial environmental and genetic shifts associated with this transition. As a result, root and rhizosphere traits that allow more efficient foraging and uptake in lower synthetic input environments might have been lost. The development of modern maize has led to a shift in microbiome community composition, but questions remain as to the dynamics and drivers of this change during maize evolution and its implications for resource acquisition and agroecosystem functioning under different management practices. Better understanding of how domestication and breeding affected root and rhizosphere microbial traits could inform breeding strategies, facilitate the sourcing of favorable alleles, and open new frontiers to improve resource use efficiency through greater integration of root development and ecophysiology with agroecosystem functioning.
Collapse
Affiliation(s)
- Jennifer E. Schmidt
- Department of Plant Sciences, University of California at DavisDavis, CA, USA
| | - Timothy M. Bowles
- Department of Natural Resources and the Environment, University of New HampshireDurham, NH, USA
| | - Amélie C. M. Gaudin
- Department of Plant Sciences, University of California at DavisDavis, CA, USA
- *Correspondence: Amélie C. M. Gaudin
| |
Collapse
|
16
|
Akhtar SS, Andersen MN, Naveed M, Zahir ZA, Liu F. Interactive effect of biochar and plant growth-promoting bacterial endophytes on ameliorating salinity stress in maize. FUNCTIONAL PLANT BIOLOGY : FPB 2015; 42:770-781. [PMID: 32480720 DOI: 10.1071/fp15054] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 04/24/2015] [Indexed: 06/11/2023]
Abstract
The objective of this work was to study the interactive effect of biochar and plant growth-promoting endophytic bacteria containing 1-aminocyclopropane-1-carboxylate deaminase and exopolysaccharide activity on mitigating salinity stress in maize (Zea mays L.). The plants were grown in a greenhouse under controlled conditions, and were subjected to separate or combined treatments of biochar (0% and 5%, w/w) and two endophytic bacterial strains (Burkholderia phytofirmans (PsJN) and Enterobacter sp. (FD17)) and salinity stress. The results indicated that salinity significantly decreased the growth of maize, whereas both biochar and inoculation mitigated the negative effects of salinity on maize performance either by decreasing the xylem Na+ concentration ([Na+]xylem) uptake or by maintaining nutrient balance within the plant, especially when the two treatments were applied in combination. Moreover, in biochar-amended saline soil, strain FD17 performed significantly better than did PsJN in reducing [Na+]xylem. Our results suggested that inoculation of plants with endophytic baterial strains along with biochar amendment could be an effective approach for sustaining crop production in salt-affected soils.
Collapse
Affiliation(s)
- Saqib Saleem Akhtar
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Højbakkegård Allé 13, DK-2630 Tåstrup, Denmark
| | - Mathias Neumann Andersen
- Sino-Danish Center for Education and Research, 3 Zhongguancun South 1st Alley, Haidian District, 100190 Beijing, China
| | - Muhammad Naveed
- Institute of Soil and Environmental Sciences, University of Agriculture, Faisalabad-38040, Pakistan
| | - Zahir Ahmad Zahir
- Institute of Soil and Environmental Sciences, University of Agriculture, Faisalabad-38040, Pakistan
| | - Fulai Liu
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Højbakkegård Allé 13, DK-2630 Tåstrup, Denmark
| |
Collapse
|
17
|
da Silva DAF, Cotta SR, Vollú RE, Jurelevicius DDA, Marques JM, Marriel IE, Seldin L. Endophytic microbial community in two transgenic maize genotypes and in their near-isogenic non-transgenic maize genotype. BMC Microbiol 2014; 14:332. [PMID: 25540019 PMCID: PMC4327796 DOI: 10.1186/s12866-014-0332-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2014] [Accepted: 12/17/2014] [Indexed: 11/23/2022] Open
Abstract
Background Despite all the benefits assigned to the genetically modified plants, there are still no sufficient data available in literature concerning the possible effects on the microbial communities associated with these plants. Therefore, this study was aimed at examining the effects of the genetic modifications of two transgenic maize genotypes (MON810 – expressing the insecticidal Bt-toxin and TC1507 – expressing the insecticidal Bt-toxin and the herbicide resistance PAT [phosphinothricin-N-acetyltransferase]) on their endophytic microbial communities, in comparison to the microbial community found in the near-isogenic non-transgenic maize (control). Results The structure of the endophytic communities (Bacteria, Archaea and fungi) and their composition (Bacteria) were evaluated by denaturing gradient gel electrophoresis (DGGE) and the construction of clone libraries, respectively. DGGE analysis and the clone libraries of the bacterial community showed that genotype TC1507 slightly differed from the other two genotypes. Genotype TC1507 showed a higher diversity within its endophytic bacterial community when compared to the other genotypes. Although some bacterial genera were found in all genotypes, such as the genera Burkholderia, Achromobacer and Stenotrophomonas, some were unique to genotype TC1507. Moreover, OTUs associated with Enterobacter predominated only in TC1507 clone libraries. Conclusion The endophytic bacterial community of the maize genotype TC1507 differed from the communities of the maize genotype MON810 and of their near-isogenic parental genotypes (non-Bt or control). The differences observed among the maize genotypes studied may be associated with insertion of the gene coding for the protein PAT present only in the transgenic genotype TC1507.
Collapse
Affiliation(s)
| | - Simone Raposo Cotta
- Departamento de Ciências do Solo, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, São Paulo, Brazil.
| | - Renata Estebanez Vollú
- Universidade Federal do Rio de Janeiro, Instituto de Microbiologia Paulo de Góes, Rio de Janeiro, RJ, Brazil.
| | | | - Joana Montezano Marques
- Universidade Federal do Rio de Janeiro, Instituto de Microbiologia Paulo de Góes, Rio de Janeiro, RJ, Brazil.
| | - Ivanildo Evódio Marriel
- EMBRAPA/CNPMS- Empresa Brasileira de Pesquisa Agropecuária, Centro Nacional de Pesquisas de Milho e Sorgo, Sete Lagoas, MG, Brazil.
| | - Lucy Seldin
- Universidade Federal do Rio de Janeiro, Instituto de Microbiologia Paulo de Góes, Rio de Janeiro, RJ, Brazil. .,Laboratório de Genética Microbiana, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Centro de Ciências da Saúde, Bloco I, Ilha do Fundão, Rio de Janeiro, RJ, CEP 21941-590, Brazil.
| |
Collapse
|
18
|
Rukarwa RJ, Mukasa SB, Odongo B, Ssemakula G, Ghislain M. Identification of relevant non-target organisms exposed to weevil-resistant Bt sweetpotato in Uganda. 3 Biotech 2014; 4:217-226. [PMID: 28324435 PMCID: PMC4026458 DOI: 10.1007/s13205-013-0153-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Accepted: 07/01/2013] [Indexed: 11/26/2022] Open
Abstract
Assessment of the impact of transgenic crops on non-target organisms (NTO) is a prerequisite to their release into the target environment for commercial use. Transgenic sweetpotato varieties expressing Cry proteins (Bt sweetpotato) are under development to provide effective protection against sweetpotato weevils (Coleoptera) which cause severe economic losses in sub-Saharan Africa. Like any other pest control technologies, genetically engineered crops expressing insecticidal proteins need to be evaluated to assess potential negative effects on non-target organisms that provide important services to the ecosystem. Beneficial arthropods in sweetpotato production systems can include pollinators, decomposers, and predators and parasitoids of the target insect pest(s). Non-target arthropod species commonly found in sweetpotato fields that are related taxonomically to the target pests were identified through expert consultation and literature review in Uganda where Bt sweetpotato is expected to be initially evaluated. Results indicate the presence of few relevant non-target Coleopterans that could be affected by Coleopteran Bt sweetpotato varieties: ground, rove and ladybird beetles. These insects are important predators in sweetpotato fields. Additionally, honeybee (hymenoptera) is the main pollinator of sweetpotato and used for honey production. Numerous studies have shown that honeybees are unaffected by the Cry proteins currently deployed which are homologous to those of the weevil-resistant Bt sweetpotato. However, because of their feeding behaviour, Bt sweetpotato represents an extremely low hazard due to negligible exposure. Hence, we conclude that there is good evidence from literature and expert opinion that relevant NTOs in sweetpotato fields are unlikely to be affected by the introduction of Bt sweetpotato in Uganda.
Collapse
Affiliation(s)
- R J Rukarwa
- School of Agricultural Sciences, Makerere University, P.O. Box 7062, Kampala, Uganda.
| | - S B Mukasa
- School of Agricultural Sciences, Makerere University, P.O. Box 7062, Kampala, Uganda
| | - B Odongo
- African Institute for Capacity Development, P.O. Box 46179, Nairobi GPO, 00100, Kenya
| | - G Ssemakula
- National Crop Resources Research Institute (NaCRRI), P.O. Box 7084, Namulonge, Kampala, Uganda
| | - M Ghislain
- International Potato Center, P.O. Box 25171, Nairobi, 00603, Kenya
| |
Collapse
|
19
|
Ondreičková K, Mihálik D, Ficek A, Hudcovicová M, Kraic J, Drahovská H. Impact of Genetically Modified Maize on the Genetic Diversity of Rhizosphere Bacteria: a Two-Year Study in Slovakia. POLISH JOURNAL OF ECOLOGY 2014. [DOI: 10.3161/104.062.0107] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
20
|
Generic and functional diversity in endophytic actinomycetes from wild Compositae plant species at South Sinai - Egypt. Res Microbiol 2013; 164:761-9. [PMID: 23541473 DOI: 10.1016/j.resmic.2013.03.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2013] [Accepted: 03/14/2013] [Indexed: 11/22/2022]
Abstract
The diversity of culturable endophytic actinomycetes associated with wild Compositae plants is scantily explored. In this study, one hundred and thirty one endophytic actinobacteria were isolated from ten Compositae plant species collected from South Sinai in Egypt. Microscopic and chemotaxonomic investigation of the isolates indicated fourteen genera. Rare genera, such as Microtetraspora, and Intrasporangium, which have never been previously reported to be endophytic, were identified. Each plant species accommodated between three to eight genera of actinobacteria and unidentified strains were recovered from seven plant species. The generic diversity analysis of endophytic assemblages grouped the plant species into three main clusters, representing high, moderate and low endophytic diversity. The endophytes showed high functional diversity, based on forty four catabolic and plant growth promotion traits; providing some evidence that such traits could represent key criteria for successful residence of endophytes in the endosphere. Stress-tolerance traits were more predictive measure of functional diversity differences between the endophyte assemblages (Shannon's index, p = 0.01). The results indicate a potential prominent role of endophytes for their hosts and emphasize the potency of plant endosphere as a habitat for actinobacteria with promising future applications.
Collapse
|
21
|
Scientific Opinion on an application from Pioneer Hi‐Bred International and Dow AgroSciences LLC (EFSA‐GMO‐NL‐2005‐23) for placing on the market of genetically modified maize 59122 for food and feed uses, import, processing and cultivation under Regulation (EC) No 1829/2003. EFSA J 2013. [DOI: 10.2903/j.efsa.2013.3135] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
|
22
|
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]
|
23
|
Buiatti M, Christou P, Pastore G. The application of GMOs in agriculture and in food production for a better nutrition: two different scientific points of view. GENES AND NUTRITION 2012; 8:255-70. [PMID: 23076994 PMCID: PMC3639326 DOI: 10.1007/s12263-012-0316-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Accepted: 08/03/2012] [Indexed: 12/21/2022]
Abstract
This commentary is a face-to-face debate between two almost opposite positions regarding the application of genetic engineering in agriculture and food production. Seven questions on the potential benefits of the application of genetic engineering in agriculture and on the potentially adverse impacts on the environment and human health were posed to two scientists: one who is sceptical about the use of GMOs in Agriculture, and one who views GMOs as an important tool for quantitatively and qualitatively improving food production.
Collapse
Affiliation(s)
- M Buiatti
- University of Florence, Florence, Italy,
| | | | | |
Collapse
|