1
|
Csorba C, Rodić N, Antonielli L, Sessitsch A, Vlachou A, Ahmad M, Compant S, Puschenreiter M, Molin EM, Assimopoulou AN, Brader G. Soil pH, developmental stages and geographical origin differently influence the root metabolomic diversity and root-related microbial diversity of Echium vulgare from native habitats. FRONTIERS IN PLANT SCIENCE 2024; 15:1369754. [PMID: 38984162 PMCID: PMC11232435 DOI: 10.3389/fpls.2024.1369754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 06/03/2024] [Indexed: 07/11/2024]
Abstract
Improved understanding of the complex interaction between plant metabolism, environmental conditions and the plant-associated microbiome requires an interdisciplinary approach: Our hypothesis in our multiomics study posited that several environmental and biotic factors have modulating effects on the microbiome and metabolome of the roots of wild Echium vulgare plants. Furthermore, we postulated reciprocal interactions between the root metabolome and microbiome. We investigated the metabolic content, the genetic variability, and the prokaryotic microbiome in the root systems of wild E. vulgare plants at rosette and flowering stages across six distinct locations. We incorporated the assessment of soil microbiomes and the measurement of selected soil chemical composition factors. Two distinct genetic clusters were determined based on microsatellite analysis without a consistent alignment with the geographical proximity between the locations. The microbial diversity of both the roots of E. vulgare and the surrounding bulk soil exhibited significant divergence across locations, varying soil pH characteristics, and within the identified plant genetic clusters. Notably, acidophilic bacteria were characteristic inhabitants of both soil and roots under acidic soil conditions, emphasizing the close interconnectedness between these compartments. The metabolome of E. vulgare significantly differed between root samples from different developmental stages, geographical locations, and soil pH levels. The developmental stage was the dominant driver of metabolome changes, with significantly higher concentrations of sugars, pyrrolizidine alkaloids, and some of their precursors in rosette stage plant roots. Our study featured the complex dynamics between soil pH, plant development, geographical locations, plant genetics, plant metabolome and microbiome, shedding light on existing knowledge gaps.
Collapse
Affiliation(s)
- Cintia Csorba
- AIT Austrian Institute of Technology GmbH, Center for Health & Bioresources, Bioresources Unit, Tulln, Austria
| | - Nebojša Rodić
- Aristotle University of Thessaloniki, School of Chemical Engineering, Laboratory of Organic Chemistry and Center for Interdisciplinary Research and Innovation, Natural Products Research Centre of Excellence (NatPro-AUTh), Thessaloniki, Greece
| | - Livio Antonielli
- AIT Austrian Institute of Technology GmbH, Center for Health & Bioresources, Bioresources Unit, Tulln, Austria
| | - Angela Sessitsch
- AIT Austrian Institute of Technology GmbH, Center for Health & Bioresources, Bioresources Unit, Tulln, Austria
| | - Angeliki Vlachou
- Aristotle University of Thessaloniki, School of Chemical Engineering, Laboratory of Organic Chemistry and Center for Interdisciplinary Research and Innovation, Natural Products Research Centre of Excellence (NatPro-AUTh), Thessaloniki, Greece
| | - Muhammad Ahmad
- AIT Austrian Institute of Technology GmbH, Center for Health & Bioresources, Bioresources Unit, Tulln, Austria
- Department of Forest Growth, Silviculture and Genetics, Austrian Research Centre for Forests (BFW), Vienna, Austria
| | - Stéphane Compant
- AIT Austrian Institute of Technology GmbH, Center for Health & Bioresources, Bioresources Unit, Tulln, Austria
| | - Markus Puschenreiter
- Institute of Soil Research, University of Natural Resources and Life Sciences Vienna, Vienna, Austria
| | - Eva M. Molin
- AIT Austrian Institute of Technology GmbH, Center for Health & Bioresources, Bioresources Unit, Tulln, Austria
| | - Andreana N. Assimopoulou
- Aristotle University of Thessaloniki, School of Chemical Engineering, Laboratory of Organic Chemistry and Center for Interdisciplinary Research and Innovation, Natural Products Research Centre of Excellence (NatPro-AUTh), Thessaloniki, Greece
| | - Günter Brader
- AIT Austrian Institute of Technology GmbH, Center for Health & Bioresources, Bioresources Unit, Tulln, Austria
| |
Collapse
|
2
|
Wei Y, Chen S, Zhou X, Ding D, Song J, Yang S. Endophytic Microorganisms in Tomato Roots, Changes in the Structure and Function of the Community at Different Growing Stages. Microorganisms 2024; 12:1251. [PMID: 38930633 PMCID: PMC11206058 DOI: 10.3390/microorganisms12061251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 05/20/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024] Open
Abstract
This study analyzed flower bud differentiation and fruiting stages to investigate how the structure of the plant endophytic microbial community in the roots of tomatoes changes with plant senescence. Based on high-throughput sequencing technology, the diversity and relative abundance of endophytic microorganisms (bacteria and fungi) in tomato stems at different growth stages were analyzed. At the same time, based on LEfSe analysis, the differences in endophytic microorganisms in tomato stems at different growth stages were studied. Based on PICRUSt2 function prediction and FUNGuild, we predicted the functions of endophytic bacterial and fungal communities in tomato stems at different growth stages to explore potential microbial functional traits. The results demonstrated that not only different unique bacterial genera but also unique fungal genera could be found colonizing tomato roots at different growth stages. In tomato seedlings, flower bud differentiation, and fruiting stages, the functions of colonizing endophytes in tomato roots could primarily contribute to the promotion of plant growth, stress resistance, and improvement in nutrient cycling, respectively. These results also suggest that different functional endophytes colonize tomato roots at different growth stages.
Collapse
Affiliation(s)
- Yufei Wei
- Guangxi Key Laboratory of Agro-Environment and Agro-Products Safety, National Demonstration Center for Experimental Plant Science Education, Guangxi Agricultural College, Guangxi University, Nanning 530004, China; (Y.W.); (S.C.); (X.Z.); (D.D.)
| | - Siyu Chen
- Guangxi Key Laboratory of Agro-Environment and Agro-Products Safety, National Demonstration Center for Experimental Plant Science Education, Guangxi Agricultural College, Guangxi University, Nanning 530004, China; (Y.W.); (S.C.); (X.Z.); (D.D.)
| | - Xinyan Zhou
- Guangxi Key Laboratory of Agro-Environment and Agro-Products Safety, National Demonstration Center for Experimental Plant Science Education, Guangxi Agricultural College, Guangxi University, Nanning 530004, China; (Y.W.); (S.C.); (X.Z.); (D.D.)
| | - Diancao Ding
- Guangxi Key Laboratory of Agro-Environment and Agro-Products Safety, National Demonstration Center for Experimental Plant Science Education, Guangxi Agricultural College, Guangxi University, Nanning 530004, China; (Y.W.); (S.C.); (X.Z.); (D.D.)
| | - Jingjing Song
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou 535011, China
| | - Shangdong Yang
- Guangxi Key Laboratory of Agro-Environment and Agro-Products Safety, National Demonstration Center for Experimental Plant Science Education, Guangxi Agricultural College, Guangxi University, Nanning 530004, China; (Y.W.); (S.C.); (X.Z.); (D.D.)
| |
Collapse
|
3
|
Liu S, Pan Y, Jin X, Zhao S, Xu X, Chen Y, Shen Z, Chen C. A novel Biochar-PGPB strategy for simultaneous soil remediation and safe vegetable production. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 356:124254. [PMID: 38815893 DOI: 10.1016/j.envpol.2024.124254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 05/08/2024] [Accepted: 05/25/2024] [Indexed: 06/01/2024]
Abstract
There is currently increasing pressure on agriculture to simultaneously remediate soil and ensure safe agricultural production. In this study, we investigate the potential of a novel combination of biochar and plant growth-promoting bacteria (PGPB) as a promising approach. Two types of biochar, corn stover and rice husk-derived, were used in combination with a PGPB strain, Bacillus sp. PGP5, to remediate Cd and Pb co-contaminated soil and enhance lettuce performance. The contaminated soil was pre-incubated with biochar prior to PGP5 inoculation. The combined application of biochar and PGPB reduced the diethylenetriaminepentaacetic acid (DTPA) -extractable Cd and Pb concentrations in the soil by 46.45%-55.96% and 42.08%-44.83%, respectively. Additionally, this combined application increased lettuce yield by 23.37%-65.39% and decreased Cd and Pb concentrations in the edible parts of the lettuce by 57.39%-68.04% and 13.57%-32.50%. The combined application showed a better promotion on lettuce growth by facilitating chlorophyll synthesis and reducing oxidative stress. These demonstrated a synergistic effect between biochar and PGPB. Furthermore, our study elucidated the specific role of the biochar-PGPB combination in soil microbial communities. Biochar application promoted the survival of PGP5 in the soil. The impact of biochar or PGPB on microbial communities was found to be most significant in the early stage, while the development of plants had a greater influence on rhizosphere microbial communities in later stage. Plants showed a tendency to recruit plant-associated microbes, such as Cyanobacteria, to facilitate growth processes. Notably, the combined application of biochar and PGPB expedited the assembly of microbial communities, enabling them more closely with the rhizosphere microbial communities in late stage of plant development and thus enhancing their effects on promoting plant growth. This study highlights the "accelerating" advantage of the biochar-PGPB combination in the assembly of rhizosphere microbiomes and offers a new strategy for simultaneous soil remediation and safe agricultural production.
Collapse
Affiliation(s)
- Sijia Liu
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Yiwen Pan
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Xinjie Jin
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, Zhejiang, China
| | - Shangjun Zhao
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Xiaohong Xu
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Yahua Chen
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China; Jiangsu Collaborative Innovation Centre for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Zhenguo Shen
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China; Jiangsu Collaborative Innovation Centre for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Chen Chen
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China; Jiangsu Collaborative Innovation Centre for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
| |
Collapse
|
4
|
Ding S, Liang Y, Wang M, Hu R, Song Z, Xu X, Zheng L, Shen Z, Chen C. Less is more: A new strategy combining nanomaterials and PGPB to promote plant growth and phytoremediation in contaminated soil. JOURNAL OF HAZARDOUS MATERIALS 2024; 469:134110. [PMID: 38522194 DOI: 10.1016/j.jhazmat.2024.134110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 02/28/2024] [Accepted: 03/21/2024] [Indexed: 03/26/2024]
Abstract
Novel combination strategies of nanomaterials (NMs) and plant growth-promoting bacteria (PGPB) may facilitate soil remediation and plant growth. However, the efficiency of the NM-PGPB combination and interactions among NMs, PGPB, and plants are still largely unknown. We used multiwalled carbon nanotubes (MWCNTs) and zero-valent iron (nZVI) combined with Bacillus sp. PGP5 to enhance the phytoremediation efficiency of Solanum nigrum on heavy metal (HM)-contaminated soil. The NM-PGPB combination showed the best promoting effect on plant growth, which also had synergistic effects on the bioaccumulation of HMs in S. nigrum. The MWCNT-PGP5 combination increased the Cd, Pb, and Zn removal efficiency of S. nigrum by 62.03%, 69.44%, and 61.31%, respectively. The underlining causes of improved plant growth and phytoremediation by NMs-PGPB combination were further elucidated. NM application promoted PGPB survival in soil. Compared with each single application, the combined application minimized disturbance to plant transcription levels and rhizosphere microbial community, resulting in the best performance on soil remediation and plant growth. The NM-PGPB-induced changes in the microbial community and root gene expression were necessary for plant growth promotion. This work reveals the "less is more" advantage of the NM-PGPB combination in soil remediation, providing a new strategy for soil management.
Collapse
Affiliation(s)
- Shifeng Ding
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yinping Liang
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Mingshuo Wang
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Ruoning Hu
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhengguo Song
- Department of Materials and Environmental Engineering, Shantou University, Shantou 515063, Guangdong, China
| | - Xiaohong Xu
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Luqing Zheng
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; Jiangsu Collaborative Innovation Centre for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhenguo Shen
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; Jiangsu Collaborative Innovation Centre for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Chen Chen
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; Jiangsu Collaborative Innovation Centre for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, China.
| |
Collapse
|
5
|
Dixon MM, Afkairin A, Davis JG, Chitwood-Brown J, Buchanan CM, Ippolito JA, Manter DK, Vivanco JM. Tomato domestication rather than subsequent breeding events reduces microbial associations related to phosphorus recovery. Sci Rep 2024; 14:9934. [PMID: 38689014 PMCID: PMC11061195 DOI: 10.1038/s41598-024-60775-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 04/26/2024] [Indexed: 05/02/2024] Open
Abstract
Legacy phosphorus (P) is a reservoir of sparingly available P, and its recovery could enhance sustainable use of nonrenewable mineral fertilizers. Domestication has affected P acquisition, but it is unknown if subsequent breeding efforts, like the Green Revolution (GR), had a similar effect. We examined how domestication and breeding events altered P acquisition by growing wild, traditional (pre-GR), and modern (post-GR) tomato in soil with legacy P but low bioavailable P. Wild tomatoes, particularly accession LA0716 (Solanum pennellii), heavily cultured rhizosphere P solubilizers, suggesting reliance on microbial associations to acquire P. Wild tomato also had a greater abundance of other putatively beneficial bacteria, including those that produce chelating agents and antibiotic compounds. Although wild tomatoes had a high abundance of these P solubilizers, they had lower relative biomass and greater P stress factor than traditional or modern tomato. Compared to wild tomato, domesticated tomato was more tolerant to P deficiency, and both cultivated groups had a similar rhizosphere bacterial community composition. Ultimately, this study suggests that while domestication changed tomato P recovery by reducing microbial associations, subsequent breeding processes have not further impacted microbial P acquisition mechanisms. Selecting microbial P-related traits that diminished with domestication may therefore increase legacy P solubilization.
Collapse
Affiliation(s)
- Mary M Dixon
- Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, CO, USA
| | - Antisar Afkairin
- Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, CO, USA
| | - Jessica G Davis
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
| | - Jessica Chitwood-Brown
- Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, CO, USA
| | - Cassidy M Buchanan
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
| | - James A Ippolito
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
- United States Department of Agriculture-Agricultural Research Service, Soil Management and Sugar Beet Research, Fort Collins, CO, USA
| | - Daniel K Manter
- School of Environment and Natural Resources, The Ohio State University, Columbus, OH, USA
| | - Jorge M Vivanco
- Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, CO, USA.
| |
Collapse
|
6
|
Berruto CA, Demirer GS. Engineering agricultural soil microbiomes and predicting plant phenotypes. Trends Microbiol 2024:S0966-842X(24)00043-X. [PMID: 38429182 DOI: 10.1016/j.tim.2024.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 02/02/2024] [Accepted: 02/06/2024] [Indexed: 03/03/2024]
Abstract
Plant growth-promoting rhizobacteria (PGPR) can improve crop yields, nutrient use efficiency, plant tolerance to stressors, and confer benefits to future generations of crops grown in the same soil. Unlocking the potential of microbial communities in the rhizosphere and endosphere is therefore of great interest for sustainable agriculture advancements. Before plant microbiomes can be engineered to confer desirable phenotypic effects on their plant hosts, a deeper understanding of the interacting factors influencing rhizosphere community structure and function is needed. Dealing with this complexity is becoming more feasible using computational approaches. In this review, we discuss recent advances at the intersection of experimental and computational strategies for the investigation of plant-microbiome interactions and the engineering of desirable soil microbiomes.
Collapse
Affiliation(s)
- Chiara A Berruto
- Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Gozde S Demirer
- Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA.
| |
Collapse
|
7
|
Kimotho RN, Maina S. Unraveling plant-microbe interactions: can integrated omics approaches offer concrete answers? JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1289-1313. [PMID: 37950741 PMCID: PMC10901211 DOI: 10.1093/jxb/erad448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 11/08/2023] [Indexed: 11/13/2023]
Abstract
Advances in high throughput omics techniques provide avenues to decipher plant microbiomes. However, there is limited information on how integrated informatics can help provide deeper insights into plant-microbe interactions in a concerted way. Integrating multi-omics datasets can transform our understanding of the plant microbiome from unspecified genetic influences on interacting species to specific gene-by-gene interactions. Here, we highlight recent progress and emerging strategies in crop microbiome omics research and review key aspects of how the integration of host and microbial omics-based datasets can be used to provide a comprehensive outline of complex crop-microbe interactions. We describe how these technological advances have helped unravel crucial plant and microbial genes and pathways that control beneficial, pathogenic, and commensal plant-microbe interactions. We identify crucial knowledge gaps and synthesize current limitations in our understanding of crop microbiome omics approaches. We highlight recent studies in which multi-omics-based approaches have led to improved models of crop microbial community structure and function. Finally, we recommend holistic approaches in integrating host and microbial omics datasets to achieve precision and efficiency in data analysis, which is crucial for biotic and abiotic stress control and in understanding the contribution of the microbiota in shaping plant fitness.
Collapse
Affiliation(s)
- Roy Njoroge Kimotho
- Hebei Key Laboratory of Soil Ecology, Key Laboratory of Agricultural Water Resources, Centre for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Solomon Maina
- Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, New South Wales 2568, Australia
| |
Collapse
|
8
|
Chavarro-Carrero EA, Snelders NC, Torres DE, Kraege A, López-Moral A, Petti GC, Punt W, Wieneke J, García-Velasco R, López-Herrera CJ, Seidl MF, Thomma BPHJ. The soil-borne white root rot pathogen Rosellinia necatrix expresses antimicrobial proteins during host colonization. PLoS Pathog 2024; 20:e1011866. [PMID: 38236788 PMCID: PMC10796067 DOI: 10.1371/journal.ppat.1011866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 11/27/2023] [Indexed: 01/22/2024] Open
Abstract
Rosellinia necatrix is a prevalent soil-borne plant-pathogenic fungus that is the causal agent of white root rot disease in a broad range of host plants. The limited availability of genomic resources for R. necatrix has complicated a thorough understanding of its infection biology. Here, we sequenced nine R. necatrix strains with Oxford Nanopore sequencing technology, and with DNA proximity ligation we generated a gapless assembly of one of the genomes into ten chromosomes. Whereas many filamentous pathogens display a so-called two-speed genome with more dynamic and more conserved compartments, the R. necatrix genome does not display such genome compartmentalization. It has recently been proposed that fungal plant pathogens may employ effectors with antimicrobial activity to manipulate the host microbiota to promote infection. In the predicted secretome of R. necatrix, 26 putative antimicrobial effector proteins were identified, nine of which are expressed during plant colonization. Two of the candidates were tested, both of which were found to possess selective antimicrobial activity. Intriguingly, some of the inhibited bacteria are antagonists of R. necatrix growth in vitro and can alleviate R. necatrix infection on cotton plants. Collectively, our data show that R. necatrix encodes antimicrobials that are expressed during host colonization and that may contribute to modulation of host-associated microbiota to stimulate disease development.
Collapse
Affiliation(s)
- Edgar A. Chavarro-Carrero
- Laboratory of Phytopathology, Wageningen University & Research, Wageningen, The Netherlands
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
| | - Nick C. Snelders
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
- Theoretical Biology & Bioinformatics Group, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - David E. Torres
- Laboratory of Phytopathology, Wageningen University & Research, Wageningen, The Netherlands
- Theoretical Biology & Bioinformatics Group, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Anton Kraege
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
| | - Ana López-Moral
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
| | - Gabriella C. Petti
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
| | - Wilko Punt
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
| | - Jan Wieneke
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
| | - Rómulo García-Velasco
- Laboratory of Phytopathology, Tenancingo University Center, Autonomous University of the State of Mexico, Tenancingo, State of Mexico, Mexico
| | - Carlos J. López-Herrera
- CSIC, Instituto de Agricultura Sostenible, Dept. Protección de Cultivos, C/Alameda del Obispo s/n, Córdoba, Spain
| | - Michael F. Seidl
- Theoretical Biology & Bioinformatics Group, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Bart P. H. J. Thomma
- Laboratory of Phytopathology, Wageningen University & Research, Wageningen, The Netherlands
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
| |
Collapse
|
9
|
Shankar N, Shetty P, Melo TC, Kesseli R. Multi-Generation Ecosystem Selection of Rhizosphere Microbial Communities Associated with Plant Genotype and Biomass in Arabidopsis thaliana. Microorganisms 2023; 11:2932. [PMID: 38138075 PMCID: PMC10745315 DOI: 10.3390/microorganisms11122932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 12/01/2023] [Accepted: 12/01/2023] [Indexed: 12/24/2023] Open
Abstract
The role of the microbiome in shaping the host's phenotype has emerged as a critical area of investigation, with implications in ecology, evolution, and host health. The complex and dynamic interactions involving plants and their diverse rhizospheres' microbial communities are influenced by a multitude of factors, including but not limited to soil type, environment, and plant genotype. Understanding the impact of these factors on microbial community assembly is key to yielding host-specific and robust benefits for plants, yet it remains challenging. Here, we conducted an artificial ecosystem selection experiment for eight generations of Arabidopsis thaliana Ler and Cvi to select soil microbiomes associated with a higher or lower biomass of the host. This resulted in divergent microbial communities shaped by a complex interplay between random environmental variations, plant genotypes, and biomass selection pressures. In the initial phases of the experiment, the genotype and the biomass selection treatment had modest but significant impacts. Over time, the plant genotype and biomass treatments gained more influence, explaining ~40% of the variation in the microbial community's composition. Furthermore, a genotype-specific association of plant-growth-promoting rhizobacterial taxa, Labraceae with Ler and Rhizobiaceae with Cvi, was observed under selection for high biomass.
Collapse
Affiliation(s)
- Nachiket Shankar
- Department of Biology, University of Massachusetts, Boston, MA 02125, USA (R.K.)
| | - Prateek Shetty
- Institute of Plant Biology, Biological Research Centre, 6726 Szeged, Hungary;
| | - Tatiana C. Melo
- Department of Biology, University of Massachusetts, Boston, MA 02125, USA (R.K.)
| | - Rick Kesseli
- Department of Biology, University of Massachusetts, Boston, MA 02125, USA (R.K.)
| |
Collapse
|
10
|
Byers AK, Condron LM, O'Callaghan M, Waller L, Dickie IA, Wakelin SA. Plant species identity and plant-induced changes in soil physicochemistry-but not plant phylogeny or functional traits - shape the assembly of the root-associated soil microbiome. FEMS Microbiol Ecol 2023; 99:fiad126. [PMID: 37816673 PMCID: PMC10589101 DOI: 10.1093/femsec/fiad126] [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: 05/21/2023] [Revised: 10/02/2023] [Accepted: 10/06/2023] [Indexed: 10/12/2023] Open
Abstract
The root-associated soil microbiome contributes immensely to support plant health and performance against abiotic and biotic stressors. Understanding the processes that shape microbial assembly in root-associated soils is of interest in microbial ecology and plant health research. In this study, 37 plant species were grown in the same soil mixture for 10 months, whereupon the root-associated soil microbiome was assessed using amplicon sequencing. From this, the contribution of direct and indirect plant effects on microbial assembly was assessed. Plant species and plant-induced changes in soil physicochemistry were the most significant factors that accounted for bacterial and fungal community variation. Considering that all plants were grown in the same starting soil mixture, our results suggest that plants, in part, shape the assembly of their root-associated soil microbiome via their effects on soil physicochemistry. With the increase in phylogenetic ranking from plant species to class, we observed declines in the degree of community variation attributed to phylogenetic origin. That is, plant-microbe associations were unique to each plant species, but the phylogenetic associations between plant species were not important. We observed a large degree of residual variation (> 65%) not accounted for by any plant-related factors, which may be attributed to random community assembly.
Collapse
Affiliation(s)
- Alexa-Kate Byers
- Bioprotection Aotearoa, Lincoln University, PO Box 85084, Lincoln 7647, New Zealand
| | - Leo M Condron
- Bioprotection Aotearoa, Lincoln University, PO Box 85084, Lincoln 7647, New Zealand
| | | | - Lauren Waller
- Biosecurity New Zealand, Ministry for Primary Industries, 34-38 Bowen Street, PO Box 2526, Wellington 6140, New Zealand
| | - Ian A Dickie
- Bioprotection Aotearoa, School of Biological Sciences, University of Canterbury, PO Box 4800, Christchurch 8140, New Zealand
| | - Steve A Wakelin
- Ecology and Environment, Scion Research Ltd, 10 Kyle Street, Riccarton, Christchurch 8011, Canterbury, New Zealand
| |
Collapse
|
11
|
Liu X, Wang Y, Han L, Xia Y, Xie J. A virus induces alterations in root morphology while exerting minimal effects on the rhizosphere and endosphere microorganisms in rice. FEMS Microbiol Ecol 2023; 99:fiad113. [PMID: 37742208 DOI: 10.1093/femsec/fiad113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/11/2023] [Accepted: 09/19/2023] [Indexed: 09/26/2023] Open
Abstract
The highly destructive southern rice black-streaked dwarf virus (SRBSDV) causes significant losses in rice production. To understand its impact on rice root, we studied fibrous root development and root microbiota variation (rhizosphere and endosphere) after SRBSDV infection. SRBSDV infection reduced the number and length of fibrous roots in rice. Interestingly, the rhizosphere had higher bacterial diversity and abundance at the initial (0 days) and 30-day postinfection stages, while 30-day-old roots showed increased diversity and abundance. However, there were no significant differences in microbiota diversity between infected and noninfected rice plants. The major rhizosphere microbiota included Proteobacteria, Bacteroidota, Acidobacteriota, and Planctomycetota, comprising about 80% of the community. The endosphere was dominated by Proteobacteria and Cyanobacteria, constituting over 90%, with Bacteroidota as the next most prominent group. Further, we identified differentially expressed genes related to plant-pathogen interactions, plant hormone signal, and ABC transporters, potentially affecting root morphology. Notably, specific bacteria (e.g. Inquilinus and Actinoplanes) showed correlations with these pathways. In conclusion, SRBSDV primarily influences root growth through host metabolism, rather than exerting direct effects on the root microbiota. These insights into the interactions among the pathogen, rice plant, and associated microbiota could have implications for managing SRBSDV's detrimental effects on rice production.
Collapse
Affiliation(s)
- Xuewei Liu
- School of Life Sciences, Genetic Engineering Research Center, Chongqing University, Daxuecheng South Road No. 55, Shapingba District 401331, Chongqing, China
- Chongqing Engineering Research Center for Fungal Insecticides, Daxuecheng South Road No. 55, Shapingba District 401331, Chongqing, China
- Key Laboratory of Gene Function and Regulation Technology under Chongqing Municipal Education Commission, Daxuecheng South Road No. 55, Shapingba District 401331, Chongqing, China
| | - Yirong Wang
- School of Life Sciences, Genetic Engineering Research Center, Chongqing University, Daxuecheng South Road No. 55, Shapingba District 401331, Chongqing, China
- Chongqing Engineering Research Center for Fungal Insecticides, Daxuecheng South Road No. 55, Shapingba District 401331, Chongqing, China
- Key Laboratory of Gene Function and Regulation Technology under Chongqing Municipal Education Commission, Daxuecheng South Road No. 55, Shapingba District 401331, Chongqing, China
| | - Lijuan Han
- School of Life Sciences, Genetic Engineering Research Center, Chongqing University, Daxuecheng South Road No. 55, Shapingba District 401331, Chongqing, China
- Chongqing Engineering Research Center for Fungal Insecticides, Daxuecheng South Road No. 55, Shapingba District 401331, Chongqing, China
- Key Laboratory of Gene Function and Regulation Technology under Chongqing Municipal Education Commission, Daxuecheng South Road No. 55, Shapingba District 401331, Chongqing, China
| | - Yuxian Xia
- School of Life Sciences, Genetic Engineering Research Center, Chongqing University, Daxuecheng South Road No. 55, Shapingba District 401331, Chongqing, China
- Chongqing Engineering Research Center for Fungal Insecticides, Daxuecheng South Road No. 55, Shapingba District 401331, Chongqing, China
- Key Laboratory of Gene Function and Regulation Technology under Chongqing Municipal Education Commission, Daxuecheng South Road No. 55, Shapingba District 401331, Chongqing, China
| | - Jiaqin Xie
- School of Life Sciences, Genetic Engineering Research Center, Chongqing University, Daxuecheng South Road No. 55, Shapingba District 401331, Chongqing, China
- Chongqing Engineering Research Center for Fungal Insecticides, Daxuecheng South Road No. 55, Shapingba District 401331, Chongqing, China
- Key Laboratory of Gene Function and Regulation Technology under Chongqing Municipal Education Commission, Daxuecheng South Road No. 55, Shapingba District 401331, Chongqing, China
| |
Collapse
|
12
|
Garrido-Sanz D, Čaušević S, Vacheron J, Heiman CM, Sentchilo V, van der Meer JR, Keel C. Changes in structure and assembly of a species-rich soil natural community with contrasting nutrient availability upon establishment of a plant-beneficial Pseudomonas in the wheat rhizosphere. MICROBIOME 2023; 11:214. [PMID: 37770950 PMCID: PMC10540321 DOI: 10.1186/s40168-023-01660-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 08/31/2023] [Indexed: 09/30/2023]
Abstract
BACKGROUND Plant-beneficial bacterial inoculants are of great interest in agriculture as they have the potential to promote plant growth and health. However, the inoculation of the rhizosphere microbiome often results in a suboptimal or transient colonization, which is due to a variety of factors that influence the fate of the inoculant. To better understand the fate of plant-beneficial inoculants in complex rhizosphere microbiomes, composed by hundreds of genotypes and multifactorial selection mechanisms, controlled studies with high-complexity soil microbiomes are needed. RESULTS We analysed early compositional changes in a taxa-rich natural soil bacterial community under both exponential nutrient-rich and stationary nutrient-limited growth conditions (i.e. growing and stable communities, respectively) following inoculation with the plant-beneficial bacterium Pseudomonas protegens in a bulk soil or a wheat rhizosphere environment. P. protegens successfully established under all conditions tested and was more abundant in the rhizosphere of the stable community. Nutrient availability was a major factor driving microbiome composition and structure as well as the underlying assembly processes. While access to nutrients resulted in communities assembled mainly by homogeneous selection, stochastic processes dominated under the nutrient-deprived conditions. We also observed an increased rhizosphere selection effect under nutrient-limited conditions, resulting in a higher number of amplicon sequence variants (ASVs) whose relative abundance was enriched. The inoculation with P. protegens produced discrete changes, some of which involved other Pseudomonas. Direct competition between Pseudomonas strains partially failed to replicate the observed differences in the microbiome and pointed to a more complex interaction network. CONCLUSIONS The results of this study show that nutrient availability is a major driving force of microbiome composition, structure and diversity in both the bulk soil and the wheat rhizosphere and determines the assembly processes that govern early microbiome development. The successful establishment of the inoculant was facilitated by the wheat rhizosphere and produced discrete changes among other members of the microbiome. Direct competition between Pseudomonas strains only partially explained the microbiome changes, indicating that indirect interactions or spatial distribution in the rhizosphere or soil interface may be crucial for the survival of certain bacteria. Video Abstract.
Collapse
Affiliation(s)
- Daniel Garrido-Sanz
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland.
| | - Senka Čaušević
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Jordan Vacheron
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Clara M Heiman
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Vladimir Sentchilo
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Jan Roelof van der Meer
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Christoph Keel
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland.
| |
Collapse
|
13
|
Schultz CR, Johnson M, Wallace JG. Effects of Inbreeding on Microbial Community Diversity of Zea mays. Microorganisms 2023; 11:microorganisms11040879. [PMID: 37110300 PMCID: PMC10145435 DOI: 10.3390/microorganisms11040879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/14/2023] [Accepted: 03/28/2023] [Indexed: 03/31/2023] Open
Abstract
Heterosis, also known as hybrid vigor, is the basis of modern maize production. The effect of heterosis on maize phenotypes has been studied for decades, but its effect on the maize-associated microbiome is much less characterized. To determine the effect of heterosis on the maize microbiome, we sequenced and compared the bacterial communities of inbred, open pollinated, and hybrid maize. Samples covered three tissue types (stalk, root, and rhizosphere) in two field experiments and one greenhouse experiment. Bacterial diversity was more affected by location and tissue type than genetic background for both within-sample (alpha) and between-sample (beta) diversity. PERMANOVA analysis similarly showed that tissue type and location had significant effects on the overall community structure, whereas the intraspecies genetic background and individual plant genotypes did not. Differential abundance analysis identified only 25 bacterial ASVs that significantly differed between inbred and hybrid maize. Predicted metagenome content was inferred with Picrust2, and it also showed a significantly larger effect of tissue and location than genetic background. Overall, these results indicate that the bacterial communities of inbred and hybrid maize are often more similar than they are different and that non-genetic effects are generally the largest influences on the maize microbiome.
Collapse
|
14
|
Runge P, Ventura F, Kemen E, Stam R. Distinct Phyllosphere Microbiome of Wild Tomato Species in Central Peru upon Dysbiosis. MICROBIAL ECOLOGY 2023; 85:168-183. [PMID: 35041070 PMCID: PMC9849306 DOI: 10.1007/s00248-021-01947-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 12/15/2021] [Indexed: 06/14/2023]
Abstract
Plants are colonized by myriads of microbes across kingdoms, which affect host development, fitness, and reproduction. Hence, plant microbiomes have been explored across a broad range of host species, including model organisms, crops, and trees under controlled and natural conditions. Tomato is one of the world's most important vegetable crops; however, little is known about the microbiota of wild tomato species. To obtain insights into the tomato microbiota occurring in natural environments, we sampled epiphytic microbes from leaves of four tomato species, Solanum habrochaites, S. corneliomulleri, S. peruvianum, and S. pimpinellifolium, from two geographical locations within the Lima region of Peru over 2 consecutive years. Here, a high-throughput sequencing approach was applied to investigate microbial compositions including bacteria, fungi, and eukaryotes across tomato species and geographical locations. The phyllosphere microbiome composition varies between hosts and location. Yet, we identified persistent microbes across tomato species that form the tomato microbial core community. In addition, we phenotypically defined healthy and dysbiotic samples and performed a downstream analysis to reveal the impact on microbial community structures. To do so, we compared microbial diversities, unique OTUs, relative abundances of core taxa, and microbial hub taxa, as well as co-occurrence network characteristics in healthy and dysbiotic tomato leaves and found that dysbiosis affects the phyllosphere microbial composition in a host species-dependent manner. Yet, overall, the present data suggests an enrichment of plant-promoting microbial taxa in healthy leaves, whereas numerous microbial taxa containing plant pathogens occurred in dysbiotic leaves.Concluding, we identify the core phyllosphere microbiome of wild tomato species, and show that the overall phyllosphere microbiome can be impacted by sampling time point, geographical location, host genotype, and plant health. Future studies in these components will help understand the microbial contribution to plant health in natural systems and can be of use in cultivated tomatoes.
Collapse
Affiliation(s)
- Paul Runge
- Department of Microbial Interactions, IMIT/ZMBP, University of Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, 50829, Köln, Germany
| | - Freddy Ventura
- Plant Pathology and Bacteriology, International Potato Centre, Avenida La Molina 1895, La Molina, Lima, Peru
| | - Eric Kemen
- Department of Microbial Interactions, IMIT/ZMBP, University of Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany
| | - Remco Stam
- Chair of Phytopathology, TUM School of Life Science, Emil-Ramann-Str. 2, 85354, Freising-Weihenstephan, Germany.
| |
Collapse
|
15
|
Chang J, Tian L, Leite MFA, Sun Y, Shi S, Xu S, Wang J, Chen H, Chen D, Zhang J, Tian C, Kuramae EE. Nitrogen, manganese, iron, and carbon resource acquisition are potential functions of the wild rice Oryza rufipogon core rhizomicrobiome. MICROBIOME 2022; 10:196. [PMID: 36419170 PMCID: PMC9682824 DOI: 10.1186/s40168-022-01360-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 08/31/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND The assembly of the rhizomicrobiome, i.e., the microbiome in the soil adhering to the root, is influenced by soil conditions. Here, we investigated the core rhizomicrobiome of a wild plant species transplanted to an identical soil type with small differences in chemical factors and the impact of these soil chemistry differences on the core microbiome after long-term cultivation. We sampled three natural reserve populations of wild rice (i.e., in situ) and three populations of transplanted in situ wild rice grown ex situ for more than 40 years to determine the core wild rice rhizomicrobiome. RESULTS Generalized joint attribute modeling (GJAM) identified a total of 44 amplicon sequence variants (ASVs) composing the core wild rice rhizomicrobiome, including 35 bacterial ASVs belonging to the phyla Actinobacteria, Chloroflexi, Firmicutes, and Nitrospirae and 9 fungal ASVs belonging to the phyla Ascomycota, Basidiomycota, and Rozellomycota. Nine core bacterial ASVs belonging to the genera Haliangium, Anaeromyxobacter, Bradyrhizobium, and Bacillus were more abundant in the rhizosphere of ex situ wild rice than in the rhizosphere of in situ wild rice. The main ecological functions of the core microbiome were nitrogen fixation, manganese oxidation, aerobic chemoheterotrophy, chemoheterotrophy, and iron respiration, suggesting roles of the core rhizomicrobiome in improving nutrient resource acquisition for rice growth. The function of the core rhizosphere bacterial community was significantly (p < 0.05) shaped by electrical conductivity, total nitrogen, and available phosphorus present in the soil adhering to the roots. CONCLUSION We discovered that nitrogen, manganese, iron, and carbon resource acquisition are potential functions of the core rhizomicrobiome of the wild rice Oryza rufipogon. Our findings suggest that further potential utilization of the core rhizomicrobiome should consider the effects of soil properties on the abundances of different genera. Video Abstract.
Collapse
Affiliation(s)
- Jingjing Chang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, Jilin, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Department of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, 6708 PB, Wageningen, the Netherlands
| | - Lei Tian
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, Jilin, China
| | - Marcio F A Leite
- Department of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, 6708 PB, Wageningen, the Netherlands
- Ecology and Biodiversity, Institute of Environmental Biology, Utrecht University, 3584 CH, Utrecht, the Netherlands
| | - Yu Sun
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, Jilin, China
| | - Shaohua Shi
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, Jilin, China
| | - Shangqi Xu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, Jilin, China
| | - Jilin Wang
- Jiangxi Super-rice Research and Development Center, National Engineering Laboratory for Rice, Nanchang, China
| | - Hongping Chen
- Jiangxi Super-rice Research and Development Center, National Engineering Laboratory for Rice, Nanchang, China
| | - Dazhou Chen
- Jiangxi Super-rice Research and Development Center, National Engineering Laboratory for Rice, Nanchang, China
| | - Jianfeng Zhang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Chunjie Tian
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, Jilin, China.
| | - Eiko E Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, 6708 PB, Wageningen, the Netherlands.
- Ecology and Biodiversity, Institute of Environmental Biology, Utrecht University, 3584 CH, Utrecht, the Netherlands.
| |
Collapse
|
16
|
Orozco-Mosqueda MDC, Fadiji AE, Babalola OO, Glick BR, Santoyo G. Rhizobiome engineering: Unveiling complex rhizosphere interactions to enhance plant growth and health. Microbiol Res 2022; 263:127137. [PMID: 35905581 DOI: 10.1016/j.micres.2022.127137] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 06/17/2022] [Accepted: 07/13/2022] [Indexed: 12/13/2022]
Abstract
Crop plants are affected by a series of inhibitory environmental and biotic factors that decrease their growth and production. To counteract these adverse effects, plants work together with the microorganisms that inhabit their rhizosphere, which is part of the soil influenced by root exudates. The rhizosphere is a microecosystem where a series of complex interactions takes place between the resident microorganisms (rhizobiome) and plant roots. Therefore, this study analyzes the dynamics of plant-rhizobiome communication, the role of exudates (diffusible and volatile) as a factor in stimulating a diverse rhizobiome, and the differences between rhizobiomes of domesticated crops and wild plants. The study also analyzes different strategies to decipher the rhizobiome through both classical cultivation techniques and the so-called "omics" sciences. In addition, the rhizosphere engineering concept and the two general strategies to manipulate the rhizobiome, i.e., top down and bottom up engineering have been revisited. In addition, recent studies on the effects on the indigenous rhizobiome of inoculating plants with foreign strains, the impact on the endobiome, and the collateral effects on plant crops are discussed. Finally, understanding of the complex rhizosphere interactions and the biological repercussions of rhizobiome engineering as essential steps for improving plant growth and health is proposed, including under adverse conditions.
Collapse
Affiliation(s)
| | - Ayomide Emmanuel Fadiji
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho 2735, South Africa
| | - Olubukola Oluranti Babalola
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho 2735, South Africa
| | - Bernard R Glick
- Department of Biology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Gustavo Santoyo
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mich 58030, Mexico.
| |
Collapse
|
17
|
Rotoni C, Leite MFA, Pijl A, Kuramae EE. Rhizosphere microbiome response to host genetic variability: a trade-off between bacterial and fungal community assembly. FEMS Microbiol Ecol 2022; 98:6590037. [PMID: 35595468 DOI: 10.1093/femsec/fiac061] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 05/13/2022] [Accepted: 05/17/2022] [Indexed: 11/14/2022] Open
Abstract
Rhizosphere microbial community composition is strongly influenced by plant species and cultivar. However, our understanding of the impact of plant cultivar genetic variability on microbial assembly composition remains limited. Here, we took advantage of vegetatively propagated chrysanthemum (Chrysanthemum indicum L.) as a plant model and induced roots in five commercial cultivars: Barolo, Chic, Chic 45, Chic Cream, and Haydar. We observed strong rhizosphere selection for the bacterial community but weaker selection for the fungal community. The genetic distance between cultivars explained 42.83% of the total dissimilarity between the bacteria selected by the different cultivars. By contrast, rhizosphere fungal selection was not significantly linked to plant genetic dissimilarity. Each chrysanthemum cultivar selected unique bacterial and fungal genera in the rhizosphere. We also observed a trade-off in the rhizosphere selection of bacteria and fungi in which the cultivar with the strongest selection of fungal communities showed the weakest bacterial selection. Finally, bacterial and fungal family taxonomic groups consistently selected by all cultivars were identified (bacteria Chitinophagaceae, Beijerinckiaceae, and Acidobacteriaceae and fungi Pseudeurotiaceae and Chrysozymaceae). Taken together, our findings suggest that chrysanthemum cultivars select distinct rhizosphere microbiomes and share a common core of microbes partially explained by the genetic dissimilarity between cultivars.
Collapse
Affiliation(s)
- Cristina Rotoni
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands.,Ecology and Biodiversity, Institute of Environmental Biology, Utrecht University, Utrecht, Netherlands
| | - Marcio F A Leite
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands.,Ecology and Biodiversity, Institute of Environmental Biology, Utrecht University, Utrecht, Netherlands
| | - Agata Pijl
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - Eiko E Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands.,Ecology and Biodiversity, Institute of Environmental Biology, Utrecht University, Utrecht, Netherlands
| |
Collapse
|
18
|
Soil Origin and Plant Genotype Modulate Switchgrass Aboveground Productivity and Root Microbiome Assembly. mBio 2022; 13:e0007922. [PMID: 35384699 PMCID: PMC9040762 DOI: 10.1128/mbio.00079-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Switchgrass (Panicum virgatum) is a model perennial grass for bioenergy production that can be productive in agricultural lands that are not suitable for food production. There is growing interest in whether its associated microbiome may be adaptive in low- or no-input cultivation systems. However, the relative impact of plant genotype and soil factors on plant microbiome and biomass are a challenge to decouple. To address this, a common garden greenhouse experiment was carried out using six common switchgrass genotypes, which were each grown in four different marginal soils collected from long-term bioenergy research sites in Michigan and Wisconsin. We characterized the fungal and bacterial root communities with high-throughput amplicon sequencing of the ITS and 16S rDNA markers, and collected phenological plant traits during plant growth, as well as soil chemical traits. At harvest, we measured the total plant aerial dry biomass. Significant differences in richness and Shannon diversity across soils but not between plant genotypes were found. Generalized linear models showed an interaction between soil and genotype for fungal richness but not for bacterial richness. Community structure was also strongly shaped by soil origin and soil origin × plant genotype interactions. Overall, plant genotype effects were significant but low. Random Forest models indicate that important factors impacting switchgrass biomass included NO3−, Ca2+, PO43−, and microbial biodiversity. We identified 54 fungal and 52 bacterial predictors of plant aerial biomass, which included several operational taxonomic units belonging to Glomeraceae and Rhizobiaceae, fungal and bacterial lineages that are involved in provisioning nutrients to plants.
Collapse
|
19
|
Tyagi R, Pradhan S, Bhattacharjee A, Dubey S, Sharma S. Management of abiotic stresses by microbiome-based engineering of the rhizosphere. J Appl Microbiol 2022; 133:254-272. [PMID: 35352450 DOI: 10.1111/jam.15552] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 02/27/2022] [Accepted: 03/22/2022] [Indexed: 11/30/2022]
Abstract
Abiotic stresses detrimentally affect both plant and soil health, threatening food security in an ever-increasing world population. Sustainable agriculture is necessary to augment crop yield with simultaneous management of stresses. Limitations of conventional bioinoculants has shifted the focus on more effective alternatives. With the realisation of the potential of rhizospheric microbiome engineering in enhancing plant's fitness under stresses, efforts have accelerated in this direction. Though still in its infancy, microbiome-based engineering has gained popularity because of its advantages over microbe-based approach. This review briefly presents major abiotic stresses afflicting arable land, followed by introduction to the conventional approach of microbe-based enhancement of plant attributes and stress mitigation with its inherent limitations. It then focusses on the significance of rhizospheric microbiome, and harnessing its potential by its strategic engineering for stress management. Further, success stories related to two major approaches of microbiome engineering (generation of synthetic microbial community/consortium, and host-mediated artificial selection) pertaining to stress management have been critically presented. Together with bringing forth the challenges associated with wide application of rhizospheric microbiome engineering in agriculture, the review proposes the adoption of combinatorial scheme for the same, bringing together ecological and reductionist approaches for improvised sustainable agricultural practices.
Collapse
Affiliation(s)
- Rashi Tyagi
- Department of Biochemical Engineering and, Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi
| | - Salila Pradhan
- Department of Biochemical Engineering and, Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi
| | - Annapurna Bhattacharjee
- Department of Biochemical Engineering and, Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi
| | - Shubham Dubey
- Department of Biochemical Engineering and, Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi
| | - Shilpi Sharma
- Department of Biochemical Engineering and, Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi
| |
Collapse
|
20
|
Abstract
Coffee is one of the most important commodities in the global market. Of the 130 species of Coffea, only Coffea arabica and Coffea canephora are actually cultivated on a large scale. Despite the economic and social importance of coffee, little research has been done on the coffee tree microbiome. To assess the structure and function of the rhizosphere microbiome, we performed a deep shotgun metagenomic sequencing of the rhizospheres of five different species, C. arabica, C. canephora, Coffea stenophylla, Coffea racemosa, and Coffea liberica. Our findings indicated that C. arabica and C. stenophylla have different microbiomes, while no differences were detected between the other Coffea species. The core rhizosphere microbiome comprises genera such as Streptomyces, Mycobacterium, Bradyrhizobium, Burkholderia, Sphingomonas, Penicillium, Trichoderma, and Rhizophagus, several of which are potential plant-beneficial microbes. Streptomyces and mycorrhizal fungi dominate the microbial communities. The concentration of sucrose in the rhizosphere seems to influence fungal communities, and the concentration of caffeine/theobromine has little effect on the microbiome. We also detected a possible relationship between drought tolerance in Coffea and known growth-promoting microorganisms. The results provide important information to guide future studies of the coffee tree microbiome to improve plant production and health. IMPORTANCE The microbiome has been identified as a fundamental factor for the maintenance of plant health, helping plants to fight diseases and the deleterious effects of abiotic stresses. Despite this, in-depth studies of the microbiome have been limited to a few species, generally with a short life cycle, and perennial species have mostly been neglected. The coffee tree microbiome, on the other hand, has gained interest in recent years as Coffea trees are perennial tropical species of enormous importance, especially for developing countries. A better understanding of the microorganisms associated with coffee trees can help to mitigate the deleterious effects of climate change on the crop, improving plant health and making the system more sustainable.
Collapse
|
21
|
Ajilogba CF, Olanrewaju OS, Babalola OO. Plant Growth Stage Drives the Temporal and Spatial Dynamics of the Bacterial Microbiome in the Rhizosphere of Vigna subterranea. Front Microbiol 2022; 13:825377. [PMID: 35250941 PMCID: PMC8891599 DOI: 10.3389/fmicb.2022.825377] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 01/10/2022] [Indexed: 11/23/2022] Open
Abstract
Bambara groundnut (BGN) is an underutilized legume commonly found in sub-Saharan Africa. It thrives in marginal soils and is resistant to drought stress. Several studies have been carried out on the nutritional properties of BGN, but very little is known about the effects of plant growth changes and development on rhizosphere bacterial dynamics and function. This study reports on the bacterial dynamics and function in the bulk and rhizosphere soils of BGN at different growth stages (vegetative, flowering, pod-filling, and maturation stages). Aside from the maturation stage that shows distinct community structure from the other growth stages, results obtained showed no significant differences in bacterial community structure among the other growth stages. At a closer level, Actinobacteria, Proteobacteria, and Acidobacteria were dominant in rhizosphere soils at all growth stages. The bulk soil had the least average phyla abundance, while the maturity stage was characterized by the highest average phyla abundance. Rubrobacter, Acidobacterium, and Skermanella were the most predominant genus. It was observed from the analysis of operational taxonomic units that there was significant change in the bacterial structure of the rhizosphere with a higher abundance of potential plant growth-promoting rhizobacteria, at the different growth stages, which include the genera Bacillus and Acidobacterium. Biomarker analysis revealed 7 and 4 highly significant bacterial biomarkers by linear discriminant analysis effect size and random forest analysis at the maturation stage, respectively. The results obtained in this study demonstrated that the bacterial communities of BGN rhizosphere microbiome dynamics and function are influenced by the plant’s growth stages.
Collapse
Affiliation(s)
- Caroline Fadeke Ajilogba
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, South Africa
- Agricultural Research Council, Natural Resources and Engineering, Division of Agrometeorology, Pretoria, South Africa
| | - Oluwaseyi Samuel Olanrewaju
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, South Africa
| | - Olubukola Oluranti Babalola
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, South Africa
- *Correspondence: Olubukola Oluranti Babalola,
| |
Collapse
|
22
|
Gupta R, Elkabetz D, Leibman-Markus M, Jami E, Bar M. Cytokinin-microbiome interactions regulate developmental functions. ENVIRONMENTAL MICROBIOME 2022; 17:2. [PMID: 35033189 PMCID: PMC8760676 DOI: 10.1186/s40793-022-00397-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 01/05/2022] [Indexed: 05/30/2023]
Abstract
BACKGROUND The interaction of plants with the complex microbial networks that inhabit them is important for plant health. While the reliance of plants on their microbial inhabitants for defense against invading pathogens is well documented, the acquisition of data concerning the relationships between plant developmental stage or aging, and microbiome assembly, is still underway. The plant hormone cytokinin (CK) regulates various plant growth and developmental processes. Here, examining the relationships between plant development and microbiome assembly, we observed developmental-age dependent changes in the phyllopshere microbiome. We show that age-related shifts in microbiome content vary based on content of, or sensitivity to, CK. RESULTS We found a developmental age associated decline in microbial richness and diversity, accompanied by a decline in the presence of growth promoting and resistance inducing Bacilli in the phyllosphere. This decline was absent from CK-rich or CK-hypersensitive genotypes. Bacillus isolates we obtained from CK rich genotypes were found to alter the expression of developmental genes to support morphogenesis and alter the leaf developmental program when applied to seedlings, and enhance yield and agricultural productivity when applied to mature plants. CONCLUSIONS Our results support the notion that CK supports developmental functions in part via the bacterial community.
Collapse
Affiliation(s)
- Rupali Gupta
- Department of Plant Pathology and Weed Research, Plant Protection Institute, Agricultural Research Organization, Volcani Institute, Rishon LeZion, Israel
| | - Dorin Elkabetz
- Department of Plant Pathology and Weed Research, Plant Protection Institute, Agricultural Research Organization, Volcani Institute, Rishon LeZion, Israel
- Department of Plant Pathology and Microbiology, Hebrew University of Jerusalem, Rehovot, Israel
| | - Meirav Leibman-Markus
- Department of Plant Pathology and Weed Research, Plant Protection Institute, Agricultural Research Organization, Volcani Institute, Rishon LeZion, Israel
| | - Elie Jami
- Department of Ruminant Science, Animal Science Institute, Agricultural Research Organization, Volcani Institute, Rishon LeZion, Israel
| | - Maya Bar
- Department of Plant Pathology and Weed Research, Plant Protection Institute, Agricultural Research Organization, Volcani Institute, Rishon LeZion, Israel.
| |
Collapse
|
23
|
Santoyo G. How plants recruit their microbiome? New insights into beneficial interactions. J Adv Res 2021; 40:45-58. [PMID: 36100333 PMCID: PMC9481936 DOI: 10.1016/j.jare.2021.11.020] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 11/25/2021] [Accepted: 11/30/2021] [Indexed: 01/07/2023] Open
Abstract
Plant-microbiome interaction occurs at the rhizosphere, endosphere, and phyllosphere. Root exudates can favor the recruitment of a beneficial microbiome in the rhizosphere. Plant topology and phytochemistry influence the recruitment of the phyllosphere microbiome. Diverse plant strategies selectively recruit beneficial microbiomes. Multiple plant mechanisms displace potential pathogens from the rhizosphere. The beneficial microbiome helps plants to recruit other beneficial microbiota.
Background Research on beneficial mechanisms by plant-associated microbiomes, such as plant growth stimulation and protection from plant pathogens, has gained considerable attention over the past decades; however, the mechanisms used by plants to recruit their microbiome is largely unknown. Aim of Review Here, we review the latest studies that have begun to reveal plant strategies in selectively recruiting beneficial microbiomes, and how they manage to exclude potential pathogens. Key Scientific concepts of Review: We examine how plants attract beneficial microbiota from the main areas of interaction, such as the rhizosphere, endosphere, and phyllosphere, and demonstrate that such process occurs by producing root exudates, and recognizing molecules produced by the beneficial microbiota or distinguishing pathogens using specific receptors, or by triggering signals that support plant-microbiome homeostasis. Second, we analyzed the main environmental or biotic factors that modulate the structure and successional dynamics of microbial communities. Finally, we review how the associated microbiome is capable of engaging with other synergistic microbes, hence providing an additional element of selection. Collectively, this study reveals the importance of understanding the complex network of plant interactions, which will improve the understanding of bioinoculant application in agriculture, based on a microbiome that interacts efficiently with plant organs under different environmental conditions.
Collapse
Affiliation(s)
- Gustavo Santoyo
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, 58030 Morelia, Mexico.
| |
Collapse
|
24
|
Rolli E, Vergani L, Ghitti E, Patania G, Mapelli F, Borin S. 'Cry-for-help' in contaminated soil: a dialogue among plants and soil microbiome to survive in hostile conditions. Environ Microbiol 2021; 23:5690-5703. [PMID: 34139059 PMCID: PMC8596516 DOI: 10.1111/1462-2920.15647] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/25/2021] [Accepted: 06/16/2021] [Indexed: 12/20/2022]
Abstract
An open question in environmental ecology regards the mechanisms triggered by root chemistry to drive the assembly and functionality of a beneficial microbiome to rapidly adapt to stress conditions. This phenomenon, originally described in plant defence against pathogens and predators, is encompassed in the ‘cry‐for‐help’ hypothesis. Evidence suggests that this mechanism may be part of the adaptation strategy to ensure the holobiont fitness in polluted environments. Polychlorinated biphenyls (PCBs) were considered as model pollutants due to their toxicity, recalcitrance and poor phyto‐extraction potential, which lead to a plethora of phytotoxic effects and rise environmental safety concerns. Plants have inefficient detoxification processes to catabolize PCBs, even leading to by‐products with a higher toxicity. We propose that the ‘cry‐for‐help’ mechanism could drive the exudation‐mediated recruitment and sustainment of the microbial services for PCBs removal, exerted by an array of anaerobic and aerobic microbial degrading populations working in a complex metabolic network. Through this synergistic interaction, the holobiont copes with the soil contamination, releasing the plant from the pollutant stress by the ecological services provided by the boosted metabolism of PCBs microbial degraders. Improving knowledge of root chemistry under PCBs stress is, therefore, advocated to design rhizoremediation strategies based on plant microbiome engineering.
Collapse
Affiliation(s)
- Eleonora Rolli
- Department of Food, Environmental and Nutritional Sciences, DeFENS, University of Milan, Via Celoria 2, Milan, 20133, Italy
| | - Lorenzo Vergani
- Department of Food, Environmental and Nutritional Sciences, DeFENS, University of Milan, Via Celoria 2, Milan, 20133, Italy
| | - Elisa Ghitti
- Department of Food, Environmental and Nutritional Sciences, DeFENS, University of Milan, Via Celoria 2, Milan, 20133, Italy
| | - Giovanni Patania
- Department of Food, Environmental and Nutritional Sciences, DeFENS, University of Milan, Via Celoria 2, Milan, 20133, Italy
| | - Francesca Mapelli
- Department of Food, Environmental and Nutritional Sciences, DeFENS, University of Milan, Via Celoria 2, Milan, 20133, Italy
| | - Sara Borin
- Department of Food, Environmental and Nutritional Sciences, DeFENS, University of Milan, Via Celoria 2, Milan, 20133, Italy
| |
Collapse
|