1
|
Parnell JJ, Vintila S, Tang C, Wagner MR, Kleiner M. Evaluation of ready-to-use freezer stocks of a synthetic microbial community for maize root colonization. Microbiol Spectr 2024; 12:e0240123. [PMID: 38084978 PMCID: PMC10783020 DOI: 10.1128/spectrum.02401-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 11/06/2023] [Indexed: 01/13/2024] Open
Abstract
IMPORTANCE Synthetic communities (SynComs) are an invaluable tool to characterize and model plant-microbe interactions. Multimember SynComs approximate intricate real-world interactions between plants and their microbiome, but the complexity and time required for their construction increase enormously for each additional member added to the SynCom. Therefore, researchers who study a diversity of microbiomes using SynComs are looking for ways to simplify the use of SynComs. In this manuscript, we evaluate the feasibility of creating ready-to-use freezer stocks of a well-studied seven-member SynCom for maize roots. The frozen ready-to-use SynCom stocks work according to the principle of "just add buffer and apply to sterilized seeds or seedlings" and thus can save time applied in multiple days of laborious growing and combining of multiple microorganisms. We show that ready-to-use SynCom stocks provide comparable results to those of freshly constructed SynComs and thus allow for significant time savings when working with SynComs.
Collapse
Affiliation(s)
- J. Jacob Parnell
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
| | - Simina Vintila
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
| | - Clara Tang
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
| | - Maggie R. Wagner
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
- Kansas Biological Survey & Center for Ecological Research, University of Kansas, Lawrence, Kansas, USA
| | - Manuel Kleiner
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
| |
Collapse
|
2
|
Salvato F, Vintila S, Finkel OM, Dangl JL, Kleiner M. Evaluation of Protein Extraction Methods for Metaproteomic Analyses of Root-Associated Microbes. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:977-988. [PMID: 35876747 DOI: 10.1094/mpmi-05-22-0116-ta] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Metaproteomics is a powerful tool for the characterization of metabolism, physiology, and functional interactions in microbial communities, including plant-associated microbiota. However, the metaproteomic methods that have been used to study plant-associated microbiota are very laborious and require large amounts of plant tissue, hindering wider application of these methods. We optimized and evaluated different protein extraction methods for metaproteomics of plant-associated microbiota in two different plant species (Arabidopsis and maize). Our main goal was to identify a method that would work with low amounts of input material (40 to 70 mg) and that would maximize the number of identified microbial proteins. We tested eight protocols, each comprising a different combination of physical lysis method, extraction buffer, and cell-enrichment method on roots from plants grown with synthetic microbial communities. We assessed the performance of the extraction protocols by liquid chromatography-tandem mass spectrometry-based metaproteomics and found that the optimal extraction method differed between the two species. For Arabidopsis roots, protein extraction by beating whole roots with small beads provided the greatest number of identified microbial proteins and improved the identification of proteins from gram-positive bacteria. For maize, vortexing root pieces in the presence of large glass beads yielded the greatest number of microbial proteins identified. Based on these data, we recommend the use of these two methods for metaproteomics with Arabidopsis and maize. Furthermore, detailed descriptions of the eight tested protocols will enable future optimization of protein extraction for metaproteomics in other dicot and monocot plants. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
Collapse
Affiliation(s)
- Fernanda Salvato
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27607, U.S.A
| | - Simina Vintila
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27607, U.S.A
| | - Omri M Finkel
- Department of Biology and Howard Hughes Medical Institute, University of North Carolina, Chapel Hill, NC 27599, U.S.A
| | - Jeffery L Dangl
- Department of Biology and Howard Hughes Medical Institute, University of North Carolina, Chapel Hill, NC 27599, U.S.A
| | - Manuel Kleiner
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27607, U.S.A
| |
Collapse
|
3
|
Four species of bacteria deterministically assemble to form a stable biofilm in a millifluidic channel. NPJ Biofilms Microbiomes 2021; 7:64. [PMID: 34354076 PMCID: PMC8342524 DOI: 10.1038/s41522-021-00233-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 06/28/2021] [Indexed: 02/07/2023] Open
Abstract
Multispecies microbial adherent communities are widespread in nature and organisms, although the principles of their assembly and development remain unclear. Here, we test the possibility of establishing a simplified but relevant model of multispecies biofilm in a non-invasive laboratory setup for the real-time monitoring of community development. We demonstrate that the four chosen species (Bacillus thuringiensis, Pseudomonas fluorescens, Kocuria varians, and Rhodocyclus sp.) form a dynamic community that deterministically reaches its equilibrium after ~30 h of growth. We reveal the emergence of complexity in this simplified community as reported by an increase in spatial heterogeneity and non-monotonic developmental kinetics. Importantly, we find interspecies interactions consisting of competition for resources-particularly oxygen-and both direct and indirect physical interactions. The simplified experimental model opens new avenues to the study of adherent bacterial communities and their behavior in the context of rapid global change.
Collapse
|
4
|
Abstract
Hybrids account for nearly all commercially planted varieties of maize and many other crop plants because crosses between inbred lines of these species produce first-generation [F1] offspring that greatly outperform their parents. The mechanisms underlying this phenomenon, called heterosis or hybrid vigor, are not well understood despite over a century of intensive research. The leading hypotheses-which focus on quantitative genetic mechanisms (dominance, overdominance, and epistasis) and molecular mechanisms (gene dosage and transcriptional regulation)-have been able to explain some but not all of the observed patterns of heterosis. Abiotic stressors are known to impact the expression of heterosis; however, the potential role of microbes in heterosis has largely been ignored. Here, we show that heterosis of root biomass and other traits in maize is strongly dependent on the belowground microbial environment. We found that, in some cases, inbred lines perform as well by these criteria as their F1 offspring under sterile conditions but that heterosis can be restored by inoculation with a simple community of seven bacterial strains. We observed the same pattern for seedlings inoculated with autoclaved versus live soil slurries in a growth chamber and for plants grown in steamed or fumigated versus untreated soil in the field. In a different field site, however, soil steaming increased rather than decreased heterosis, indicating that the direction of the effect depends on community composition, environment, or both. Together, our results demonstrate an ecological phenomenon whereby soil microbes differentially impact the early growth of inbred and hybrid maize.
Collapse
|
5
|
Kamal KY, Khodaeiaminjan M, Yahya G, El-Tantawy AA, Abdel El-Moneim D, El-Esawi MA, Abd-Elaziz MAA, Nassrallah AA. Modulation of cell cycle progression and chromatin dynamic as tolerance mechanisms to salinity and drought stress in maize. PHYSIOLOGIA PLANTARUM 2021; 172:684-695. [PMID: 33159351 DOI: 10.1111/ppl.13260] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 10/12/2020] [Accepted: 10/28/2020] [Indexed: 05/14/2023]
Abstract
Salinity and drought are the major abiotic stresses that disturb several aspects of maize plants growth at the cellular level, one of these aspects is cell cycle machinery. In our study, we dissected the molecular alterations and downstream effectors of salinity and drought stress on cell cycle regulation and chromatin remodeling. Effects of salinity and drought stress were determined on maize seedlings using 200 mM NaCl (induced salinity stress), and 250 mM mannitol (induced drought stress) treatments, then cell cycle progression and chromatin remodeling dynamics were investigated. Seedlings displayed severe growth defects, including inhibition of root growth. Interestingly, stress treatments induced cell cycle arrest in S-phase with extensive depletion of cyclins B1 and A1. Further investigation of gene expression profiles of cell cycle regulators showed the downregulation of the CDKA, CDKB, CYCA, and CYCB. These results reveal the direct link between salinity and drought stress and cell cycle deregulation leading to a low cell proliferation rate. Moreover, abiotic stress alters chromatin remodeling dynamic in a way that directs the cell cycle arrest. We observed low DNA methylation patterns accompanied by dynamic histone modifications that favor chromatin decondensation. Also, the high expression of DNA topoisomerase 2, 6 family was detected as consequence of DNA damage. In conclusion, in response to salinity and drought stress, maize seedlings exhibit modulation of cell cycle progression, resulting in the cell cycle arrest through chromatin remodeling.
Collapse
Affiliation(s)
- Khaled Y Kamal
- Agronomy Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
- Redox Biology and Cell Signaling Laboratory, Department of Health and Kinesiology, Graduate Faculty of Nutrition, Texas A&M University, Texas, USA
| | - Mortaza Khodaeiaminjan
- Department of Molecular Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Olomouc, The Czech Republic
| | - Galal Yahya
- Microbiology and Immunology Department, Faculty of Pharmacy, Zagazig University, Zagazig, Egypt
- Department of Molecular Genetics, Faculty of Biology, Technical University of Kaiserslautern, Kaiserslautern, Germany
| | - Ahmed A El-Tantawy
- Ornamental Horticulture Department, Faculty of Agriculture, Cairo University, Cairo, Egypt
| | - Diaa Abdel El-Moneim
- Department of Plant production (Genetic branch), Faculty of Environmental and Agricultural Sciences, Arish University, Arish, Egypt
| | | | - Mohamed A A Abd-Elaziz
- Maize Research Department, Field Crops Research Institute, Agriculture Research Center, Giza, Egypt
| | - Amr A Nassrallah
- Biochemistry Department, Faculty of Agriculture, Cairo University, Cairo, Egypt
| |
Collapse
|