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Sun X, Jiang C, Guo Y, Li C, Zhao W, Nie F, Liu Q. Suppression of OsSAUR2 gene expression immobilizes soil arsenic bioavailability by modulating root exudation and rhizosphere microbial assembly in rice. JOURNAL OF HAZARDOUS MATERIALS 2024; 473:134587. [PMID: 38772107 DOI: 10.1016/j.jhazmat.2024.134587] [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: 02/15/2024] [Revised: 04/27/2024] [Accepted: 05/09/2024] [Indexed: 05/23/2024]
Abstract
One of the factors influencing the behavior of arsenic (As) in environment is microbial-mediated As transformation. However, the detailed regulatory role of gene expression on the changes of root exudation, rhizosphere microorganisms, and soil As occurrence forms remains unclear. In this study, we evidence that loss-of-function of OsSAUR2 gene, a member of the SMALL AUXIN-UP RNA family in rice, results in significantly higher As uptake in roots but greatly lower As accumulation in grains via affecting the expression of OsLsi1, OsLsi2 in roots and OsABCC1 in stems. Further, the alteration of OsSAUR2 expression extensively affects the metabolomic of root exudation, and thereby leading to the variations in the composition of rhizosphere microbial communities in rice. The microbial community in the rhizosphere of Ossaur2 plants strongly immobilizes the occurrence forms of As in soil. Interestingly, Homovanillic acid (HA) and 3-Coumaric acid (CA), two differential metabolites screened from root exudation, can facilitate soil iron reduction, enhance As bioavailability, and stimulate As uptake and accumulation in rice. These findings add our further understanding in the relationship of OsSAUR2 expression with the release of root exudation and rhizosphere microbial assembly under As stress in rice, and provide potential rice genetic resources and root exudation in phytoremediation of As-contaminated paddy soil.
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Affiliation(s)
- Xueyang Sun
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou 311300, People's Republic of China
| | - Cheng Jiang
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou 311300, People's Republic of China
| | - Yao Guo
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou 311300, People's Republic of China
| | - Chunyan Li
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou 311300, People's Republic of China
| | - Wenjing Zhao
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou 311300, People's Republic of China
| | - Fanhao Nie
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou 311300, People's Republic of China
| | - Qingpo Liu
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou 311300, People's Republic of China.
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Wei F, Feng Z, Yang C, Zhao L, Zhang Y, Zhou J, Feng H, Zhu H, Xu X. Genetic control of rhizosphere microbiome of the cotton plants under field conditions. Appl Microbiol Biotechnol 2024; 108:371. [PMID: 38861165 PMCID: PMC11166756 DOI: 10.1007/s00253-024-13143-0] [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: 12/08/2023] [Revised: 03/24/2024] [Accepted: 04/09/2024] [Indexed: 06/12/2024]
Abstract
Understanding the extent of heritability of a plant-associated microbiome (phytobiome) is critically important for exploitation of phytobiomes in agriculture. Two crosses were made between pairs of cotton cultivars (Z2 and J11, L1 and Z49) with differential resistance to Verticillium wilt. F2 plants were grown in a field, together with the four parents to study the heritability of cotton rhizosphere microbiome. Amplicon sequencing was used to profile bacterial and fungal communities in the rhizosphere. F2 offspring plants of both crosses had higher average alpha diversity indices than the two parents; parents differed significantly from F2 offspring in Bray-Curtis beta diversity indices as well. Two types of data were used to study the heritability of rhizosphere microbiome: principal components (PCs) and individual top microbial operational taxonomic units (OTUs). For the L1 × Z49 cross, the variance among the F2 progeny genotypes (namely, genetic variance, VT) was significantly greater than the random variability (VE) for 12 and 34 out of top 100 fungal and bacterial PCs, respectively. For the Z2 × J11 cross, the corresponding values were 10 and 20 PCs. For 29 fungal OTUs and 10 bacterial OTUs out of the most abundant 100 OTUs, genetic variance (VT) was significantly greater than VE for the L1 × Z49 cross; the corresponding values for the Z2 × J11 cross were 24 and one. The estimated heritability was mostly in the range of 40% to 60%. These results suggested the existence of genetic control of polygenic nature for specific components of rhizosphere microbiome in cotton. KEY POINTS: • F2 offspring cotton plants differed significantly from parents in rhizosphere microbial diversity. • Specific rhizosphere components are likely to be genetically controlled by plants. • Common PCs and specific microbial groups are significant genetic components between the two crosses.
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Affiliation(s)
- Feng Wei
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, Xinjiang, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Zili Feng
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, Xinjiang, China
| | - Chuanzhen Yang
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Lihong Zhao
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Yalin Zhang
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, Xinjiang, China
| | - Jinglong Zhou
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Hongjie Feng
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, Xinjiang, China.
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China.
| | - Heqin Zhu
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, Xinjiang, China.
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China.
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Gao X, Wang S, Kong W, Li G, Zhang L, Yin X. Floristic changes and environmental drivers of soil fungi and archaea in different salt-tolerant plant communities in the intertidal habitat of coastal wetlands. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2024; 46:167. [PMID: 38592380 DOI: 10.1007/s10653-024-01951-2] [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: 11/06/2023] [Accepted: 03/08/2024] [Indexed: 04/10/2024]
Abstract
Microorganisms are crucial elements of terrestrial ecosystems, which play significant roles in improving soil physicochemical properties, providing plant growth nutrients, degrading toxic and harmful chemicals, and biogeochemical cycling. Variations in the types and quantities of root exudates among different plants greatly alter soil physicochemical properties and result in variations in the diversity, structure, and function of soil microorganisms. Not much is understood about the differences of soil fungi and archaea communities for different plant communities in coastal wetlands, and their response mechanisms to environmental changes. In this study, fungal and archaea communities in soils of Suaeda salsa, Phragmites australis, and Spartina alterniflora in the intertidal habitat of coastal wetlands were selected for research. Soil fungi and archaea were analyzed for diversity, community structure, and function using high throughput ITS and 16S rRNA gene sequencing. The study revealed significant differences in fungi and archaea's diversity and community structure in the rhizosphere soil of three plant communities. At the same time, there is no significant difference in the functional groups. SOM, TP, AP, MC, EC and SOM, TN, TP, AP, MC, EC are the primary environmental determinants affecting changes in soil fungal and archaeal communities, respectively. Variations in the diversity, community structure, and ecological functions of fungi and archaea can be used as indicators characterizing the impact of external disturbances on the soil environment, providing a theoretical foundation for the effective utilization of soil microbial resources, thereby achieving the goal of environmental protection and health promotion.
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Affiliation(s)
- Xin Gao
- Institute of Water Ecology and Environment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Shuping Wang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Weijing Kong
- Institute of Water Ecology and Environment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China.
| | - Guowen Li
- Institute of Water Ecology and Environment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Lieyu Zhang
- Institute of Water Ecology and Environment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Xuwang Yin
- Liaoning Provincial Key Laboratory for Hydrobiology, College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023, China
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Rehneke L, Schäfer P. Symbiont effector-guided mapping of proteins in plant networks to improve crop climate stress resilience: Symbiont effectors inform highly interconnected plant protein networks and provide an untapped resource for crop climate resilience strategies. Bioessays 2024; 46:e2300172. [PMID: 38388783 DOI: 10.1002/bies.202300172] [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: 09/13/2023] [Revised: 12/21/2023] [Accepted: 01/23/2024] [Indexed: 02/24/2024]
Abstract
There is an urgent need for novel protection strategies to sustainably secure crop production under changing climates. Studying microbial effectors, defined as microbe-derived proteins that alter signalling inside plant cells, has advanced our understanding of plant immunity and microbial plant colonisation strategies. Our understanding of effectors in the establishment and beneficial outcome of plant symbioses is less well known. Combining functional and comparative interaction assays uncovered specific symbiont effector targets in highly interconnected plant signalling networks and revealed the potential of effectors in beneficially modulating plant traits. The diverse functionality of symbiont effectors differs from the paradigmatic immuno-suppressive function of pathogen effectors. These effectors provide solutions for improving crop resilience against climate stress by their evolution-driven specification in host protein targeting and modulation. Symbiont effectors represent stringent tools not only to identify genetic targets for crop breeding, but to serve as applicable agents in crop management strategies under changing environments.
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Affiliation(s)
- Laura Rehneke
- Institute of Phytopathology, Research Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - Patrick Schäfer
- Institute of Phytopathology, Research Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
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Bashyal S, Gautam CK, Müller LM. CLAVATA signaling in plant-environment interactions. PLANT PHYSIOLOGY 2024; 194:1336-1357. [PMID: 37930810 PMCID: PMC10904329 DOI: 10.1093/plphys/kiad591] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 09/15/2023] [Accepted: 09/19/2023] [Indexed: 11/08/2023]
Abstract
Plants must rapidly and dynamically adapt to changes in their environment. Upon sensing environmental signals, plants convert them into cellular signals, which elicit physiological or developmental changes that allow them to respond to various abiotic and biotic cues. Because plants can be simultaneously exposed to multiple environmental cues, signal integration between plant cells, tissues, and organs is necessary to induce specific responses. Recently, CLAVATA3/EMBRYO SURROUNDING REGION-related (CLE) peptides and their cognate CLAVATA-type receptors received increased attention for their roles in plant-environment interactions. CLE peptides are mobile signaling molecules, many of which are induced by a variety of biotic and abiotic stimuli. Secreted CLE peptides are perceived by receptor complexes on the surface of their target cells, which often include the leucine-rich repeat receptor-like kinase CLAVATA1. Receptor activation then results in cell-type and/or environment-specific responses. This review summarizes our current understanding of the diverse roles of environment-regulated CLE peptides in modulating plant responses to environmental cues. We highlight how CLE signals regulate plant physiology by fine-tuning plant-microbe interactions, nutrient homeostasis, and carbon allocation. Finally, we describe the role of CLAVATA receptors in the perception of environment-induced CLE signals and discuss how diverse CLE-CLAVATA signaling modules may integrate environmental signals with plant physiology and development.
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Affiliation(s)
- Sagar Bashyal
- Department of Biology, University of Miami, Coral Gables, FL 33146, USA
| | | | - Lena Maria Müller
- Department of Biology, University of Miami, Coral Gables, FL 33146, USA
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Malacrinò A, Böttner L, Nouere S, Huber M, Schäfer M, Xu S. Induced responses contribute to rapid adaptation of Spirodela polyrhiza to herbivory by Lymnaea stagnalis. Commun Biol 2024; 7:81. [PMID: 38200287 PMCID: PMC10781955 DOI: 10.1038/s42003-023-05706-0] [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: 07/24/2023] [Accepted: 12/13/2023] [Indexed: 01/12/2024] Open
Abstract
Herbivory-induced responses in plants are typical examples of phenotypic plasticity, and their evolution is thought to be driven by herbivory. However, direct evidence of the role of induced responses in plant adaptive evolution to herbivores is scarce. Here, we experimentally evolve populations of an aquatic plant (Spirodela polyrhiza, giant duckweed) and its native herbivore (Lymnaea stagnalis, freshwater snail), testing whether herbivory drives rapid adaptive evolution in plant populations using a combination of bioassays, pool-sequencing, metabolite analyses, and amplicon metagenomics. We show that snail herbivory drove rapid phenotypic changes, increased herbivory resistance, and altered genotype frequencies in the plant populations. Additional bioassays suggest that evolutionary changes of induced responses contributed to the rapid increase of plant resistance to herbivory. This study provides direct evidence that herbivory-induced responses in plants can be subjected to selection and have an adaptive role by increasing resistance to herbivores.
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Affiliation(s)
- Antonino Malacrinò
- Department of Agriculture, Università degli Studi Mediterranea di Reggio Calabria, Reggio Calabria, Italy.
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany.
| | - Laura Böttner
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
- Institute for Plant Biology and Biotechnology, University of Münster, Münster, Germany
| | - Sara Nouere
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Meret Huber
- Institute for Plant Biology and Biotechnology, University of Münster, Münster, Germany
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Martin Schäfer
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Shuqing Xu
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany.
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, Mainz, Germany.
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7
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Feng L, Li Q, Zhou D, Jia M, Liu Z, Hou Z, Ren Q, Ji S, Sang S, Lu S, Yu J. B. subtilis CNBG-PGPR-1 induces methionine to regulate ethylene pathway and ROS scavenging for improving salt tolerance of tomato. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:193-211. [PMID: 37812678 DOI: 10.1111/tpj.16489] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 08/10/2023] [Accepted: 09/22/2023] [Indexed: 10/11/2023]
Abstract
Soil salinity severely threatens plant growth and crop yields. The utilization of PGPR is an effective strategy for enhancing plant salt tolerance, but the mechanisms involved in this process have rarely been reported. In this study, we investigated the effects of Bacillus subtilis CNBG-PGPR-1 on improving plant salt tolerance and elucidated the molecular pathways involved. The results showed that CNBG-PGPR-1 significantly improved the cellular homeostasis and photosynthetic efficiency of leaves and reduced ion toxicity and osmotic stress caused by salt in tomato. Transcriptome analysis uncovered that CNBG-PGPR-1 enhanced plant salt tolerance through the activation of complex molecular pathways, with plant hormone signal transduction playing an important role. Comparative analysis and pharmacological experiments confirmed that the ethylene pathway was closely related to the beneficial effect of CNBG-PGPR-1 on improving plant salt tolerance. Furthermore, we found that methionine, a precursor of ethylene synthesis, significantly accumulated in response to CNBG-PGPR-1 in tomato. Exogenous L-methionine largely mimicked the beneficial effects of CNBG-PGPR-1 and activated the expression of ethylene pathway-related genes, indicating CNBG-PGPR-1 induces methionine accumulation to regulate the ethylene pathway in tomato. Finally, CNBG-PGPR-1 reduced salt-induced ROS by activating ROS scavenger-encoding genes, mainly involved in GSH metabolism and POD-related genes, which were also closely linked to methionine metabolism. Overall, our studies demonstrate that CNBG-PGPR-1-induced methionine is a key regulator in enhancing plant salt tolerance through the ethylene pathway and ROS scavenging, providing a novel understanding of the mechanism by which beneficial microbes improve plant salt tolerance.
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Affiliation(s)
- Liuchun Feng
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, 210014, China
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Qi Li
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, 210014, China
| | - Dongqin Zhou
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, 210014, China
| | - Mingyun Jia
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, 210014, China
| | - Zhuangzhuang Liu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, 210014, China
| | - Zhaoqi Hou
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, 210014, China
| | - Quanjin Ren
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, 210014, China
| | - Shengdong Ji
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Shifei Sang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Shipeng Lu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, 210014, China
| | - Jinping Yu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, 210014, China
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Schillaci M, Zampieri E, Brunetti C, Gori A, Sillo F. Root transcriptomic provides insights on molecular mechanisms involved in the tolerance to water deficit in Pisum sativum inoculated with Pseudomonas sp. PLANTA 2023; 259:33. [PMID: 38160210 DOI: 10.1007/s00425-023-04310-0] [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: 09/29/2023] [Accepted: 12/04/2023] [Indexed: 01/03/2024]
Abstract
MAIN CONCLUSION Root transcriptomics and biochemical analyses in water-stressed Pisum sativum plants inoculated with Pseudomonas spp. suggested preservation of ABA-related pathway and ROS detoxification, resulting in an improved tolerance to stress. Drought already affects agriculture in large areas of the globe and, due to climate change, these areas are predicted to become increasingly unsuitable for agriculture. For several years, plant growth-promoting bacteria (PGPB) have been used to improve legume yields, but many aspects of this interaction are still unclear. To elucidate the mechanisms through which root-associated PGPB can promote plant growth in dry environments, we investigated the response of pea plants inoculated with a potentially beneficial Pseudomonas strain (PK6) and subjected to two different water regimes. Combined biometric, biochemical, and root RNA-seq analyses revealed that PK6 improved pea growth specifically under water deficit, as inoculated plants showed an increased biomass, larger leaves, and longer roots. Abscisic acid (ABA) and proline quantification, together with the transcriptome analysis, suggested that PK6-inoculated plant response to water deficit was more diversified compared to non-inoculated plants, involving alternative metabolic pathways for the detoxification of reactive oxygen species (ROS) and the preservation of the ABA stress signaling pathway. We suggest that the metabolic response of PK6-inoculated plants was more effective in their adaptation to water deprivation, leading to their improved biometric traits. Besides confirming the positive role that PGPB can have in the growth of a legume crop under adverse conditions, this study offers novel information on the mechanisms regulating plant-bacteria interaction under varying water availability. These mechanisms and the involved genes could be exploited in the future for the development of legume varieties, which can profitably grow in dry climates.
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Affiliation(s)
- Martino Schillaci
- Institute for Sustainable Plant Protection, National Research Council, Strada delle Cacce 73, Turin, Italy
| | - Elisa Zampieri
- Institute for Sustainable Plant Protection, National Research Council, Strada delle Cacce 73, Turin, Italy
| | - Cecilia Brunetti
- Institute for Sustainable Plant Protection, National Research Council, Via Madonna del Piano 10, Sesto Fiorentino, Italy
| | - Antonella Gori
- Department of Agriculture, Food, Environment and Forestry (DAGRI), University of Florence, 50019, Sesto Fiorentino, Florence, Italy
| | - Fabiano Sillo
- Institute for Sustainable Plant Protection, National Research Council, Strada delle Cacce 73, Turin, Italy.
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Park JW, Braswell WE, Kunta M. Co-Occurrence Analysis of Citrus Root Bacterial Microbiota under Citrus Greening Disease. PLANTS (BASEL, SWITZERLAND) 2023; 13:80. [PMID: 38202388 PMCID: PMC10781011 DOI: 10.3390/plants13010080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/22/2023] [Accepted: 11/23/2023] [Indexed: 01/12/2024]
Abstract
Candidatus Liberibacter asiaticus (CLas) is associated with Citrus Huanglongbing (HLB), a devastating disease in the US. Previously, we conducted a two-year-long monthly HLB survey by quantitative real-time PCR using root DNA fractions prepared from 112 field grapefruit trees grafted on sour orange rootstock. Approximately 10% of the trees remained CLas-free during the entire survey period. This study conducted 16S metagenomics using the time-series root DNA fractions, monthly prepared during twenty-four consecutive months, followed by microbial co-occurrence network analysis to investigate the microbial factors contributing to the CLas-free phenotype of the aforementioned trees. Based on the HLB status and the time when the trees were first diagnosed as CLas-positive during the survey, the samples were divided into four groups, Stage H (healthy), Stage I (early), II (mid), and III (late) samples. The 16S metagenomics data using Silva 16S database v132 revealed that HLB compromised the diversity of rhizosphere microbiota. At the phylum level, Actinobacteria and Proteobacteria were the predominant bacterial phyla, comprising >93% of total bacterial phyla, irrespective of HLB status. In addition, a temporal change in the rhizosphere microbe population was observed during a two-year-long survey, from which we confirmed that some bacterial families differently responded to HLB disease status. The clustering of the bacterial co-occurrence network data revealed the presence of a subnetwork composed of Streptomycetaceae and bacterial families with plant growth-promoting activity in Stage H and III samples. These data implicated that the Streptomycetaceae subnetwork may act as a functional unit against HLB.
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Affiliation(s)
- Jong-Won Park
- Citrus Center, Texas A&M University-Kingsville, 312 N. International Blvd., Weslaco, TX 78599, USA
| | - W. Evan Braswell
- Insect Management and Molecular Diagnostic Laboratory, USDA APHIS PPQ S&T, Edinburg, TX 78541, USA
| | - Madhurababu Kunta
- Citrus Center, Texas A&M University-Kingsville, 312 N. International Blvd., Weslaco, TX 78599, USA
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10
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Chee-Sanford JC, Connor LM. Comparison of microbial community assemblages in the rhizosphere of three Amaranthus spp. PLoS One 2023; 18:e0294966. [PMID: 38019804 PMCID: PMC10686429 DOI: 10.1371/journal.pone.0294966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 11/10/2023] [Indexed: 12/01/2023] Open
Abstract
Weed management remains a major challenge in cropping systems worldwide, with rising interest in ecological based approaches that can be integrated with herbicide use. Soil microbial communities may play important, yet undiscovered, roles in weed success. Little is known about the rhizosphere communities associated with weeds like Amaranthus, commonly known as pigweeds, and considered some of the most problematic weeds in agricultural systems. In a greenhouse experiment that allowed controlled plant growth conditions and a high number of individual plant specimens to analyze for statistical robustness (n = 8 per species), we show that specific bacterial assemblages form in the rhizospheres of A. retroflexus L. (redroot pigweed), A. palmeri S. Watson (Palmer amaranth), and A. tuberculatus (Moq.) J. D. Sauer (waterhemp). Using a relatively rapid and easy approach of T-RFLP community profiling of the 16S rRNA genes, distinct assemblages corresponded to plant species (PERMANOVA F = 14.776, p = 0.001), and further within each species, similar communities (F = 11.449, p = 0.001) were associated with three rhizosphere soil fractions taken in increasing distances away from the root tissue. These results provide the first solid basis for distinct plant-microbe relationships within three closely related Amaranthus species, warranting closer examination of the identities and function of the microorganisms that appear to be selectively recruited from the extant soil community. More intensive efforts to obtain the microbial taxonomic identities via sequencing are underway that can lead to further detailed studies to elucidate important functional plant-microbe interactions that may associate with weed success. Such data provides underlying key information that may ultimately exploit weed-microbe interactions in development of new integrated weed control tactics.
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Hou M, Zhao X, Wang Y, Lv X, Chen Y, Jiao X, Sui Y. Pedogenesis of typical zonal soil drives belowground bacterial communities of arable land in the Northeast China Plain. Sci Rep 2023; 13:14555. [PMID: 37666914 PMCID: PMC10477331 DOI: 10.1038/s41598-023-41401-0] [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: 03/09/2023] [Accepted: 08/25/2023] [Indexed: 09/06/2023] Open
Abstract
Belowground bacterial communities play essential roles in maintaining ecosystem multifunction, while our understanding of how and why their distribution patterns and community compositions may change with the distinct pedogenetic conditions of different soil types is still limited. Here, we evaluated the roles of soil physiochemical properties and biotic interactions in driving belowground bacterial community composition across three typical zonal soil types, including black calcium soil (QS), typical black soil (HL) and dark brown soil (BQL), with distinct pedogenesis on the Northeast China Plain. Changes in soil bacterial diversity and community composition in these three zonal soil types were strongly correlated with soil pedogenetic features. SOC concentrations in HL were higher than in QS and BQL, but bacterial diversity was low, and the network structure revealed greater stability and connectivity. The composition of the bacterial community correlated significantly with soil pH in QS but with soil texture in BQL. The bacterial co-occurrence network of HL had higher density and clustering coefficients but lower edges, and different keystone species of networks were also detected. This work provides a basic understanding of the driving mechanisms responsible for belowground bacterial biodiversity and distribution patterns over different pedogenetic conditions in agroecosystems.
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Affiliation(s)
- Meng Hou
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 150081, Harbin, People's Republic of China
- University of Chinese Academy of Sciences, 100049, Beijing, People's Republic of China
| | - Xiaorui Zhao
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 150081, Harbin, People's Republic of China
| | - Yao Wang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 150081, Harbin, People's Republic of China
- University of Chinese Academy of Sciences, 100049, Beijing, People's Republic of China
| | - Xuemei Lv
- College of Modern Agriculture and Eco-Environment, Heilongjiang University, 150080, Harbin, People's Republic of China
| | - Yimin Chen
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 150081, Harbin, People's Republic of China
| | - Xiaoguang Jiao
- College of Modern Agriculture and Eco-Environment, Heilongjiang University, 150080, Harbin, People's Republic of China.
| | - Yueyu Sui
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 150081, Harbin, People's Republic of China.
- University of Chinese Academy of Sciences, 100049, Beijing, People's Republic of China.
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12
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Gómez JM, González-Megías A, Armas C, Narbona E, Navarro L, Perfectti F. The role of phenotypic plasticity in shaping ecological networks. Ecol Lett 2023; 26 Suppl 1:S47-S61. [PMID: 37840020 DOI: 10.1111/ele.14192] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 01/16/2023] [Accepted: 02/15/2023] [Indexed: 10/17/2023]
Abstract
Plasticity-mediated changes in interaction dynamics and structure may scale up and affect the ecological network in which the plastic species are embedded. Despite their potential relevance for understanding the effects of plasticity on ecological communities, these effects have seldom been analysed. We argue here that, by boosting the magnitude of intra-individual phenotypic variation, plasticity may have three possible direct effects on the interactions that the plastic species maintains with other species in the community: may expand the interaction niche, may cause a shift from one interaction niche to another or may even cause the colonization of a new niche. The combined action of these three factors can scale to the community level and eventually expresses itself as a modification in the topology and functionality of the entire ecological network. We propose that this causal pathway can be more widespread than previously thought and may explain how interaction niches evolve quickly in response to rapid changes in environmental conditions. The implication of this idea is not solely eco-evolutionary but may also help to understand how ecological interactions rewire and evolve in response to global change.
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Affiliation(s)
- José M Gómez
- Estación Experimental de Zonas Áridas (EEZA-CSIC), Almería, Spain
- Research Unit Modeling Nature, Universidad de Granada, Granada, Spain
| | - Adela González-Megías
- Research Unit Modeling Nature, Universidad de Granada, Granada, Spain
- Departamento de Zoología, Universidad de Granada, Granada, Spain
| | - Cristina Armas
- Estación Experimental de Zonas Áridas (EEZA-CSIC), Almería, Spain
| | - Eduardo Narbona
- Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide, Sevilla, Spain
| | - Luis Navarro
- Departamento de Biología Vegetal y Ciencias del Suelo, Universidad de Vigo, Vigo, Spain
| | - Francisco Perfectti
- Research Unit Modeling Nature, Universidad de Granada, Granada, Spain
- Departamento de Genética, Universidad de Granada, Granada, Spain
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13
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Kaval A, Yılmaz H, Tunca Gedik S, Yıldız Kutman B, Kutman ÜB. The Fungal Root Endophyte Serendipita indica ( Piriformospora indica) Enhances Bread and Durum Wheat Performance under Boron Toxicity at Both Vegetative and Generative Stages of Development through Mechanisms Unrelated to Mineral Homeostasis. BIOLOGY 2023; 12:1098. [PMID: 37626984 PMCID: PMC10452518 DOI: 10.3390/biology12081098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 07/27/2023] [Accepted: 08/02/2023] [Indexed: 08/27/2023]
Abstract
While the importance of beneficial soil microorganisms for soil health and crop performance has been receiving ever-increasing attention, Serendipita indica has been widely studied as a fungal root endophyte with significant potential for increasing the stress tolerance of host plants. Boron (B) toxicity as an adverse soil condition is particularly prevalent in arid and semi-arid regions and threatens crop production. Studies on S. indica-wheat symbiosis are limited, and effects of S. indica on crops have never been reported in the context of B toxicity. Here, two pot experiments were conducted under greenhouse conditions to investigate the effects of S. indica on the growth and yield parameters of bread (Triticum aestivum) and durum wheat (Triticum durum) grown at different levels of B toxicity in native vs. sterilized soil, and parameters related to root colonization, membrane damage, oxidative stress, chlorophyll, and mineral nutrition were measured to elucidate the physiological mechanisms of damage and benefit. Boron toxicity decreased early vegetative growth and grain yield, but it did not affect the straw dry weight of mature plants, whereas S. indica significantly enhanced the vegetative growth, straw dry weight, and the grain number of both wheat species. Membrane damage as demonstrated by increased lipid peroxidation and relative electrolyte leakage was caused by B toxicity and alleviated by S. indica. The benefits provided by S. indica could not be attributed to any significant changes in tissue concentrations of B or other minerals such as phosphorus. Soil sterilization generally improved plant performance but it did not consistently strengthen or weaken the effects of S. indica. The presented results suggest that S. indica may be used as an effective microbial inoculant to enhance wheat growth under adverse soil conditions such as B toxicity through mechanisms that are possibly unrelated to mineral homeostasis.
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Affiliation(s)
- Ali Kaval
- Institute of Biotechnology, Gebze Technical University, Gebze 41400, Kocaeli, Türkiye (B.Y.K.)
| | - Halil Yılmaz
- Department of Molecular Biology and Genetics, Gebze Technical University, Gebze 41400, Kocaeli, Türkiye; (H.Y.); (S.T.G.)
| | - Sedef Tunca Gedik
- Department of Molecular Biology and Genetics, Gebze Technical University, Gebze 41400, Kocaeli, Türkiye; (H.Y.); (S.T.G.)
| | - Bahar Yıldız Kutman
- Institute of Biotechnology, Gebze Technical University, Gebze 41400, Kocaeli, Türkiye (B.Y.K.)
| | - Ümit Barış Kutman
- Institute of Biotechnology, Gebze Technical University, Gebze 41400, Kocaeli, Türkiye (B.Y.K.)
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14
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Osborne R, Rehneke L, Lehmann S, Roberts J, Altmann M, Altmann S, Zhang Y, Köpff E, Dominguez-Ferreras A, Okechukwu E, Sergaki C, Rich-Griffin C, Ntoukakis V, Eichmann R, Shan W, Falter-Braun P, Schäfer P. Symbiont-host interactome mapping reveals effector-targeted modulation of hormone networks and activation of growth promotion. Nat Commun 2023; 14:4065. [PMID: 37429856 DOI: 10.1038/s41467-023-39885-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 06/27/2023] [Indexed: 07/12/2023] Open
Abstract
Plants have benefited from interactions with symbionts for coping with challenging environments since the colonisation of land. The mechanisms of symbiont-mediated beneficial effects and similarities and differences to pathogen strategies are mostly unknown. Here, we use 106 (effector-) proteins, secreted by the symbiont Serendipita indica (Si) to modulate host physiology, to map interactions with Arabidopsis thaliana host proteins. Using integrative network analysis, we show significant convergence on target-proteins shared with pathogens and exclusive targeting of Arabidopsis proteins in the phytohormone signalling network. Functional in planta screening and phenotyping of Si effectors and interacting proteins reveals previously unknown hormone functions of Arabidopsis proteins and direct beneficial activities mediated by effectors in Arabidopsis. Thus, symbionts and pathogens target a shared molecular microbe-host interface. At the same time Si effectors specifically target the plant hormone network and constitute a powerful resource for elucidating the signalling network function and boosting plant productivity.
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Affiliation(s)
- Rory Osborne
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
- School of Biosciences, University of Birmingham, Edgbaston, B15 2TT, UK
| | - Laura Rehneke
- Institute of Phytopathology, Research Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, 35392, Giessen, Germany
| | - Silke Lehmann
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
- Laboratory of Biotechnology and Marine Chemistry LBCM, EA3884, IUEM, Southern Brittany University, 56000, Vannes, France
| | - Jemma Roberts
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Melina Altmann
- Institute of Network Biology, Molecular Targets and Therapeutics Center, Helmholtz Munich, 85764, Munich-Neuherberg, Germany
| | - Stefan Altmann
- Institute of Network Biology, Molecular Targets and Therapeutics Center, Helmholtz Munich, 85764, Munich-Neuherberg, Germany
| | - Yingqi Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Eva Köpff
- Institute of Molecular Botany, Ulm University, 89069, Ulm, Germany
| | | | - Emeka Okechukwu
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Chrysi Sergaki
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | | | - Vardis Ntoukakis
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Ruth Eichmann
- Institute of Phytopathology, Research Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, 35392, Giessen, Germany
| | - Weixing Shan
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Pascal Falter-Braun
- Institute of Network Biology, Molecular Targets and Therapeutics Center, Helmholtz Munich, 85764, Munich-Neuherberg, Germany.
- Microbe-Host Interactions, Faculty of Biology, Ludwig-Maximilians-University München, 82152, Planegg-Martinsried, Germany.
| | - Patrick Schäfer
- Institute of Phytopathology, Research Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, 35392, Giessen, Germany.
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15
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Li Y, Wang C, Zheng L, Ma W, Li M, Guo Z, Zhao Q, Zhang K, Liu R, Liu Y, Tian Z, Bai Y, Zhong Y, Liao H. Natural variation of GmRj2/Rfg1 determines symbiont differentiation in soybean. Curr Biol 2023; 33:2478-2490.e5. [PMID: 37301200 DOI: 10.1016/j.cub.2023.05.037] [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: 01/28/2023] [Revised: 04/17/2023] [Accepted: 05/16/2023] [Indexed: 06/12/2023]
Abstract
Symbiotic nitrogen fixation (SNF) provides much of the N utilized by leguminous plants throughout growth and development. Legumes may simultaneously establish symbiosis with different taxa of microbial symbionts. Yet, the mechanisms used to steer associations toward symbionts that are most propitious across variations in soil types remain mysterious. Here, we demonstrate that GmRj2/Rfg1 is responsible for regulating symbiosis with multiple taxa of soybean symbionts. In our experiments, the GmRj2/Rfg1SC haplotype favored association with Bradyrhizobia, which is mostly distributed in acid soils, whereas the GmRj2/Rfg1HH haplotype and knockout mutants of GmRj2/Rfg1SC associated equally with Bradyrhizobia and Sinorhizobium. Association between GmRj2/Rfg1 and NopP, furthermore, appeared to be involved in symbiont selection. Furthermore, geographic distribution analysis of 1,821 soybean accessions showed that GmRj2/Rfg1SC haplotypes were enriched in acidic soils where Bradyrhizobia were the dominant symbionts, whereas GmRj2/Rfg1HH haplotypes were most prevalent in alkaline soils dominated by Sinorhizobium, and neutral soils harbored no apparent predilections toward either haplotype. Taken together, our results suggest that GmRj2/Rfg1 regulates symbiosis with different symbionts and is a strong determinant of soybean adaptability across soil regions. As a consequence, the manipulation of the GmRj2/Rfg1 genotype or application of suitable symbionts according to the haplotype at the GmRj2/Rfg1 locus might be suitable strategies to explore for increasing soybean yield through the management of SNF.
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Affiliation(s)
- Yanjun Li
- Root Biology Center, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Cunhu Wang
- Root Biology Center, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Lei Zheng
- Root Biology Center, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Wenjing Ma
- Root Biology Center, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Mingjia Li
- Root Biology Center, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zilong Guo
- Root Biology Center, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Qingsong Zhao
- Root Biology Center, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Kefei Zhang
- Root Biology Center, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ran Liu
- Root Biology Center, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yucheng Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Bai
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yongjia Zhong
- Root Biology Center, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Hong Liao
- Root Biology Center, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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16
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Esmaeilzadeh-Salestani K, Tohidfar M, Ghanbari Moheb Seraj R, Khaleghdoust B, Keres I, Marawne H, Loit E. Transcriptome profiling of barley in response to mineral and organic fertilizers. BMC PLANT BIOLOGY 2023; 23:261. [PMID: 37193945 DOI: 10.1186/s12870-023-04263-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 05/04/2023] [Indexed: 05/18/2023]
Abstract
BACKGROUND Nitrogen is very important for crop yield and quality. Crop producers face the challenge of reducing the use of mineral nitrogen while maintaining food security and other ecosystem services. The first step towards understanding the metabolic responses that could be used to improve nitrogen use efficiency is to identify the genes that are up- or downregulated under treatment with different forms and rates of nitrogen. We conducted a transcriptome analysis of barley (Hordeum vulgare L.) cv. Anni grown in a field experiment in 2019. The objective was to compare the effects of organic (cattle manure) and mineral nitrogen (NH4NO3; 0, 40, 80 kg N ha-1) fertilizers on gene activity at anthesis (BBCH60) and to associate the genes that were differentially expressed between treatment groups with metabolic pathways and biological functions. RESULTS The highest number of differentially expressed genes (8071) was found for the treatment with the highest mineral nitrogen rate. This number was 2.6 times higher than that for the group treated with a low nitrogen rate. The lowest number (500) was for the manure treatment group. Upregulated pathways in the mineral fertilizer treatment groups included biosynthesis of amino acids and ribosomal pathways. Downregulated pathways included starch and sucrose metabolism when mineral nitrogen was supplied at lower rates and carotenoid biosynthesis and phosphatidylinositol signaling at higher mineral nitrogen rates. The organic treatment group had the highest number of downregulated genes, with phenylpropanoid biosynthesis being the most significantly enriched pathway for these genes. Genes involved in starch and sucrose metabolism and plant-pathogen interaction pathways were enriched in the organic treatment group compared with the control treatment group receiving no nitrogen input. CONCLUSION These findings indicate stronger responses of genes to mineral fertilizers, probably because the slow and gradual decomposition of organic fertilizers means that less nitrogen is provided. These data contribute to our understanding of the genetic regulation of barley growth under field conditions. Identification of pathways affected by different nitrogen rates and forms under field conditions could help in the development of more sustainable cropping practices and guide breeders to create varieties with low nitrogen input requirements.
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Affiliation(s)
- Keyvan Esmaeilzadeh-Salestani
- Chair of Crop Science and Plant Biology, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Fr. R.Kreutzwaldi 1, 51014, Tartu, Estonia.
| | - Masoud Tohidfar
- Department of Cell and Molecular Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Rahele Ghanbari Moheb Seraj
- Department of Horticultural Sciences, Faculty of Agriculture and Natural Resources, University of Mohaghegh Ardabili, Ardabil, Iran
| | - Banafsheh Khaleghdoust
- Chair of Crop Science and Plant Biology, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Fr. R.Kreutzwaldi 1, 51014, Tartu, Estonia
| | - Indrek Keres
- Chair of Crop Science and Plant Biology, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Fr. R.Kreutzwaldi 1, 51014, Tartu, Estonia
| | - Hashem Marawne
- Department of Cell and Molecular Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Evelin Loit
- Chair of Crop Science and Plant Biology, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Fr. R.Kreutzwaldi 1, 51014, Tartu, Estonia
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17
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Liu Q, Cheng L, Nian H, Jin J, Lian T. Linking plant functional genes to rhizosphere microbes: a review. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:902-917. [PMID: 36271765 PMCID: PMC10106864 DOI: 10.1111/pbi.13950] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 10/09/2022] [Accepted: 10/16/2022] [Indexed: 05/04/2023]
Abstract
The importance of rhizomicrobiome in plant development, nutrition acquisition and stress tolerance is unquestionable. Relevant plant genes corresponding to the above functions also regulate rhizomicrobiome construction. Deciphering the molecular regulatory network of plant-microbe interactions could substantially contribute to improving crop yield and quality. Here, the plant gene-related nutrient uptake, biotic and abiotic stress resistance, which may influence the composition and function of microbial communities, are discussed in this review. In turn, the influence of microbes on the expression of functional plant genes, and thereby plant growth and immunity, is also reviewed. Moreover, we have specifically paid attention to techniques and methods used to link plant functional genes and rhizomicrobiome. Finally, we propose to further explore the molecular mechanisms and signalling pathways of microbe-host gene interactions, which could potentially be used for managing plant health in agricultural systems.
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Affiliation(s)
- Qi Liu
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Lang Cheng
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Hai Nian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Jian Jin
- Northeast Institute of Geography and AgroecologyChinese Academy of SciencesHarbinChina
- Department of Animal, Plant and Soil Sciences, Centre for AgriBioscienceLa Trobe UniversityBundooraVictoriaAustralia
| | - Tengxiang Lian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of AgricultureSouth China Agricultural UniversityGuangzhouChina
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18
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de Vries F, Lau J, Hawkes C, Semchenko M. Plant-soil feedback under drought: does history shape the future? Trends Ecol Evol 2023:S0169-5347(23)00054-X. [PMID: 36973124 DOI: 10.1016/j.tree.2023.03.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 03/02/2023] [Accepted: 03/03/2023] [Indexed: 03/29/2023]
Abstract
Plant-soil feedback (PSF) is widely recognised as a driver of plant community composition, but understanding of its response to drought remains in its infancy. Here, we provide a conceptual framework for the role of drought in PSF, considering plant traits, drought severity, and historical precipitation over ecological and evolutionary timescales. Comparing experimental studies where plants and microbes do or do not share a drought history (through co-sourcing or conditioning), we hypothesise that plants and microbes with a shared drought history experience more positive PSF under subsequent drought. To reflect real-world responses to drought, future studies need to explicitly include plant-microbial co-occurrence and potential co-adaptation and consider the precipitation history experienced by both plants and microbes.
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Affiliation(s)
- Franciska de Vries
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands.
| | - Jennifer Lau
- Department of Biology and Environmental Resilience Institute, Indiana University, IN, USA
| | - Christine Hawkes
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA
| | - Marina Semchenko
- Institute of Ecology and Earth Sciences, University of Tartu, Liivi 2, 50409 Tartu, Estonia
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19
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Zhou H, Hua J, Zhang J, Luo S. Negative Interactions Balance Growth and Defense in Plants Confronted with Herbivores or Pathogens. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:12723-12732. [PMID: 36165611 DOI: 10.1021/acs.jafc.2c04218] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Plants have evolved a series of defensive mechanisms against pathogens and herbivores, but the defense response always leads to decreases in growth or reproduction, which has serious implications for agricultural production. Growth and defense are negatively regulated not only through metabolic consumption but also through the antagonism of different phytohormones, such as jasmonic acid (JA) and salicylic acid (SA). Meanwhile, plants can limit the expression of defensive metabolites to reduce the costs of defense by producing constitutive defenses such as glandular trichomes or latex and accumulating specific metabolites, determining the activation of plant defense or the maintenance of plant growth. Interestingly, plant defense pathways might be prepared in advance which may be transmitted to descendants. Plants can also use external organisms to protect themselves, thus minimizing the costs of defense. In addition, plant relatives exhibit cooperation to deal with pathogens and herbivores, which is also a way to regulate growth and defense.
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Affiliation(s)
- Huiwen Zhou
- Key Laboratory of Biological Invasions and Global Changes, College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, Liaoning Province, China
| | - Juan Hua
- Key Laboratory of Biological Invasions and Global Changes, College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, Liaoning Province, China
| | - Jiaming Zhang
- Key Laboratory of Biological Invasions and Global Changes, College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, Liaoning Province, China
| | - Shihong Luo
- Key Laboratory of Biological Invasions and Global Changes, College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, Liaoning Province, China
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20
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Wang Y, Wang X, Sun S, Jin C, Su J, Wei J, Luo X, Wen J, Wei T, Sahu SK, Zou H, Chen H, Mu Z, Zhang G, Liu X, Xu X, Gram L, Yang H, Wang E, Liu H. GWAS, MWAS and mGWAS provide insights into precision agriculture based on genotype-dependent microbial effects in foxtail millet. Nat Commun 2022; 13:5913. [PMID: 36207301 PMCID: PMC9546826 DOI: 10.1038/s41467-022-33238-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 09/09/2022] [Indexed: 11/09/2022] Open
Abstract
Genetic and environmental factors collectively determine plant growth and yield. In the past 20 years, genome-wide association studies (GWAS) have been conducted on crops to decipher genetic loci that contribute to growth and yield, however, plant genotype appears to be insufficient to explain the trait variations. Here, we unravel the associations between genotypic, phenotypic, and rhizoplane microbiota variables of 827 foxtail millet cultivars by an integrated GWAS, microbiome-wide association studies (MWAS) and microbiome genome-wide association studies (mGWAS) method. We identify 257 rhizoplane microbial biomarkers associated with six key agronomic traits and validated the microbial-mediated growth effects on foxtail millet using marker strains isolated from the field. The rhizoplane microbiota composition is mainly driven by variations in plant genes related to immunity, metabolites, hormone signaling and nutrient uptake. Among these, the host immune gene FLS2 and transcription factor bHLH35 are widely associated with the microbial taxa of the rhizoplane. We further uncover a plant genotype-microbiota interaction network that contributes to phenotype plasticity. The microbial-mediated growth effects on foxtail millet are dependent on the host genotype, suggesting that precision microbiome management could be used to engineer high-yielding cultivars in agriculture systems.
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Grants
- Statens Naturvidenskabelige Forskningsrad (Danish National Science Foundation)
- This research was supported by the Funding of Joint Research on Agricultural Variety Improvement of Henan Province (No. 2022010401, H. Z.), the Major Science and Technology Projects of Yunnan Province (Digitalization, development and application of biotic resource, No. 860 202002AA100007, H. L.), the National Science Foundation (32088102, 31730103, 31825003, E. W.), the Specialty Industry for Key Research and Development Program in Shanxi Academy of Agricultural Sciences (No. YCX2019T01, Z. M.) and Key R&D Program of ShanXi Province (No. 201903D211003, Z. M.). This work was also supported by China National GeneBank (CNGB), Key Laboratory of Genomics, Ministry of Agriculture, BGI-Shenzhen.
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Affiliation(s)
- Yayu Wang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Xiaolin Wang
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Shuai Sun
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
- BGI-Qingdao, Qingdao, 266555, China
| | - Canzhi Jin
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jianmu Su
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Jinpu Wei
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Xinyue Luo
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jiawen Wen
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Tong Wei
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Sunil Kumar Sahu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Hongfeng Zou
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Hongyun Chen
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Zhixin Mu
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Taiyuan, 030031, China
| | - Gengyun Zhang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Xin Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Xun Xu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, 518083, China
| | - Lone Gram
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, 2800 Kgs, Lyngby, Denmark
| | - Huanming Yang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Ertao Wang
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China.
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin, 150040, China.
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21
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El-Saadony MT, Saad AM, Soliman SM, Salem HM, Ahmed AI, Mahmood M, El-Tahan AM, Ebrahim AAM, Abd El-Mageed TA, Negm SH, Selim S, Babalghith AO, Elrys AS, El-Tarabily KA, AbuQamar SF. Plant growth-promoting microorganisms as biocontrol agents of plant diseases: Mechanisms, challenges and future perspectives. FRONTIERS IN PLANT SCIENCE 2022; 13:923880. [PMID: 36275556 PMCID: PMC9583655 DOI: 10.3389/fpls.2022.923880] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 08/24/2022] [Indexed: 05/14/2023]
Abstract
Plant diseases and pests are risk factors that threaten global food security. Excessive chemical pesticide applications are commonly used to reduce the effects of plant diseases caused by bacterial and fungal pathogens. A major concern, as we strive toward more sustainable agriculture, is to increase crop yields for the increasing population. Microbial biological control agents (MBCAs) have proved their efficacy to be a green strategy to manage plant diseases, stimulate plant growth and performance, and increase yield. Besides their role in growth enhancement, plant growth-promoting rhizobacteria/fungi (PGPR/PGPF) could suppress plant diseases by producing inhibitory chemicals and inducing immune responses in plants against phytopathogens. As biofertilizers and biopesticides, PGPR and PGPF are considered as feasible, attractive economic approach for sustainable agriculture; thus, resulting in a "win-win" situation. Several PGPR and PGPF strains have been identified as effective BCAs under environmentally controlled conditions. In general, any MBCA must overcome certain challenges before it can be registered or widely utilized to control diseases/pests. Successful MBCAs offer a practical solution to improve greenhouse crop performance with reduced fertilizer inputs and chemical pesticide applications. This current review aims to fill the gap in the current knowledge of plant growth-promoting microorganisms (PGPM), provide attention about the scientific basis for policy development, and recommend further research related to the applications of PGPM used for commercial purposes.
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Affiliation(s)
- Mohamed T. El-Saadony
- Department of Agricultural Microbiology, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Ahmed M. Saad
- Department of Biochemistry, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Soliman M. Soliman
- Department of Internal Medicine and Infectious Diseases, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
| | - Heba M. Salem
- Department of Poultry Diseases, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
| | - Alshaymaa I. Ahmed
- Department of Agricultural Microbiology, Faculty of Agriculture, Beni-Suef University, Beni-Suef, Egypt
| | - Mohsin Mahmood
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province, Hainan University, Haikou, China
| | - Amira M. El-Tahan
- Plant Production Department, Arid Lands Cultivation Research Institute, The City of Scientific Research and Technological Applications, Alexandria, Egypt
| | - Alia A. M. Ebrahim
- Jiangsu Key Laboratory for Microbes and Genomics, School, of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Taia A. Abd El-Mageed
- Department of Soils and Water, Faculty of Agriculture, Fayoum University, Fayoum, Egypt
| | - Shaimaa H. Negm
- Department of Home Economic, Specific Education Faculty, Port Said University, Port Said, Egypt
| | - Samy Selim
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka, Saudi Arabia
| | - Ahmad O. Babalghith
- Medical Genetics Department, College of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Ahmed S. Elrys
- Soil Science Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Khaled A. El-Tarabily
- Department of Biology, College of Science, United Arab Emirates University, Al-Ain, United Arab Emirates
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al-Ain, United Arab Emirates
- Harry Butler Institute, Murdoch University, Murdoch, WA, Australia
| | - Synan F. AbuQamar
- Department of Biology, College of Science, United Arab Emirates University, Al-Ain, United Arab Emirates
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22
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The Microbially Extended Phenotype of Plants, a Keystone against Abiotic Stress. THE EUROBIOTECH JOURNAL 2022. [DOI: 10.2478/ebtj-2022-0017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Abstract
Background: Climate change affects every region across the globe with heterogeneous effects on local temperatures and precipitation patterns. In plants, sessile organisms, climate change imposes more drastic effects leading to loss of yield or even death. However, plants establish mutualistic interactions with microorganisms that boost plant tolerance against abiotic stresses or strengthen the plant immune system against pathogens, thus, enhancing their survival and fitness. Moreover, in the wild, microbial endophytes provide important ecosystem services.
Purpose and scope: Little we know about the mechanisms of response against the adverse effects of climate change on natural populations of wild plants and even less about the potential role played by microbial biostimulants. In this article, we review the effects of biostimulants on plant responses against abiotic stresses, with a particular focus on the role of mycorrhizas and leaf endophytes.
Results: We have reviewed the effects of the main abiotic stresses in plants, the mechanisms that plants use to face these abiotic challenges, and the interaction plant-biostimulant-abiotic stress, highlighting the primary responses and parameters to evaluate different plant responses.
Conclusion: Abiotic stresses can check the phenotypic plasticity of plants and also trigger a complex and heterogeneous array of responses to face different abiotic stresses, and beneficial microorganisms do play an essential role in enhancing such responses. Our laboratory has initiated a project to characterise microbial populations associated with plants from wild areas and analyse their potential role in aiding the plants to cope with abiotic stresses.
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23
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Upadhyay SK, Srivastava AK, Rajput VD, Chauhan PK, Bhojiya AA, Jain D, Chaubey G, Dwivedi P, Sharma B, Minkina T. Root Exudates: Mechanistic Insight of Plant Growth Promoting Rhizobacteria for Sustainable Crop Production. Front Microbiol 2022; 13:916488. [PMID: 35910633 PMCID: PMC9329127 DOI: 10.3389/fmicb.2022.916488] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 06/09/2022] [Indexed: 12/18/2022] Open
Abstract
The breaking silence between the plant roots and microorganisms in the rhizosphere affects plant growth and physiology by impacting biochemical, molecular, nutritional, and edaphic factors. The components of the root exudates are associated with the microbial population, notably, plant growth-promoting rhizobacteria (PGPR). The information accessible to date demonstrates that PGPR is specific to the plant's roots. However, inadequate information is accessible for developing bio-inoculation/bio-fertilizers for the crop in concern, with satisfactory results at the field level. There is a need to explore the perfect candidate PGPR to meet the need for plant growth and yield. The functions of PGPR and their chemotaxis mobility toward the plant root are triggered by the cluster of genes induced by the components of root exudates. Some reports have indicated the benefit of root exudates in plant growth and productivity, yet a methodical examination of rhizosecretion and its consequences in phytoremediation have not been made. In the light of the afore-mentioned facts, in the present review, the mechanistic insight and recent updates on the specific PGPR recruitment to improve crop production at the field level are methodically addressed.
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Affiliation(s)
- Sudhir K. Upadhyay
- Department of Environmental Science, V.B.S. Purvanchal University, Jaunpur, India
| | | | - Vishnu D. Rajput
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, Russia
| | - Prabhat K. Chauhan
- Department of Environmental Science, V.B.S. Purvanchal University, Jaunpur, India
| | - Ali Asger Bhojiya
- Department of Agriculture and Veterinary Sciences, Mewar University, Chittorgarh, India
| | - Devendra Jain
- Department of Molecular Biology and Biotechnology, Maharana Pratap University of Agriculture and Technology, Udaipur, India
| | - Gyaneshwer Chaubey
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, India
| | - Padmanabh Dwivedi
- Department of Plant Physiology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, India
| | - Bechan Sharma
- Department of Biochemistry, Faculty of Science, University of Allahabad, Allahabad, India
| | - Tatiana Minkina
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, Russia
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24
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Redman RS, Anderson JA, Biaggi TM, Malmberg KEL, Rienstra MN, Weaver JL, Rodriguez RJ. Symbiotic Modulation as a Driver of Niche Expansion of Coastal Plants in the San Juan Archipelago of Washington State. Front Microbiol 2022; 13:868081. [PMID: 35814642 PMCID: PMC9260653 DOI: 10.3389/fmicb.2022.868081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 04/27/2022] [Indexed: 11/25/2022] Open
Abstract
Modern evolutionary theory and population genetics posit that adaptation and habitat expansion of plants result from processes exclusive to their genomes. Here, we present studies showing that plants can grow across complex habitat gradients by modulating symbiotic associations with Class 2 fungal endophytes. Endophyte analysis of three native (Leymus mollis, Distichlis spicata, and Salicornia pacifica) and one invasive (Spartina anglica) plant growing across adjacent microhabitats in the San Juan Archipelago altered associations with Class 2 fungal endophytes in response to soil salinity levels. At the microhabitat interfaces where the gradation of salinity varied, the plants were colonized by endophytes from both microhabitats. A reciprocal transplant study along a salt gradient demonstrated that Leymus mollis (dunegrass) required endophytes indigenous to each microhabitat for optimal fitness and/or survival. In contrast, when dunegrass and Grindelia integrifolia (gumweed) were found growing in low salinity, but high drought habitats, these plant species had their own unique dominant endophyte association regardless of geographic proximity and conferred drought but not high salt stress tolerance. Modulation of endophyte abundance occurred in planta based on the ability of the symbiont to confer tolerance to the stress imposed on plants. The ability of an endophyte to confer appropriate stress tolerance resulted in a significant increase of in planta fungal abundance. Conversely, the inability of an endophyte to confer stress tolerance resulted in a decrease of in planta fungal abundance. Our studies indicate that Class 2 fungal endophytes can provide a symbiotic mechanism for niche expansion and phenotypic plasticity across environmental gradients.
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25
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The Role of Serendipita indica (Piriformospora indica) in Improving Plant Resistance to Drought and Salinity Stresses. BIOLOGY 2022; 11:biology11070952. [PMID: 36101333 PMCID: PMC9312039 DOI: 10.3390/biology11070952] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/14/2022] [Accepted: 06/21/2022] [Indexed: 11/23/2022]
Abstract
Simple Summary Environmental stresses are one of the biggest threats to modern agriculture, and climate change has heightened the risks of these stresses in different parts of the world. Among all the environmental stresses, salinity and drought are a severe threat to arid and semi-arid regions of the world, and for a long time, scientists have been searching for ways to reduce the risk of these stresses. In recent decades, solutions have been developed to reduce the risk of environmental stress on plants by identifying beneficial soil microorganisms. This study was conducted to identify morphophysiological and molecular changes of plants in coexistence with Serendipita indica and their impact on drought and salinity stress reduction. The study also has investigated the stressors’ impact on plants and the plants’ mechanisms to cope with them; Furthermore, sharing results with researchers provides a clear path for future research. Abstract Plant stress is one of the biggest threats to crops, causing irreparable damage to farmers’ incomes; Therefore, finding suitable, affordable, and practical solutions will help the agricultural economy and prevent the loss of millions of tons of agricultural products. Scientists have taken significant steps toward improving farm productivity in the last few decades by discovering how beneficial soil microorganisms enhance plant resistance to environmental stresses. Among these microorganisms is Serendipita indica, which the benefits of coexisting this fungus with plant roots have been extensively explored in recent years. By investigating fungus specification and its effects on plants’ morphological, physiological, and molecular traits, the present study seeks to understand how Serendipita indica affects plant resistance to salinity and drought conditions. Furthermore, this study attempts to identify the unknown mechanisms of action of the coexistence of Serendipita indica with plants in the face of stress using information from previous studies. Thus, it provides a way for future research to assess the impact of this fungus on tackling environmental stresses and enhancing agricultural productivity.
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26
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Ma Y, Ankit, Tiwari J, Bauddh K. Plant-Mycorrhizal Fungi Interactions in Phytoremediation of Geogenic Contaminated Soils. Front Microbiol 2022; 13:843415. [PMID: 35283821 PMCID: PMC8908265 DOI: 10.3389/fmicb.2022.843415] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Accepted: 01/25/2022] [Indexed: 11/26/2022] Open
Abstract
Soil contamination by geogenic contaminants (GCs) represents an imperative environmental problem. Various soil remediation methods have been successfully employed to ameliorate the health risks associated with GCs. Phytoremediation is considered as an eco-friendly and economical approach to revegetate GC-contaminated soils. However, it is a very slow process, as plants take a considerable amount of time to gain biomass. Also, the process is limited only to the depth and surface area of the root. Inoculation of arbuscular mycorrhizal fungi (AMF) with remediating plants has been found to accelerate the phytoremediation process by enhancing plant biomass and their metal accumulation potential while improving the soil physicochemical and biological characteristics. Progress in the field application is hindered by a lack of understanding of complex interactions between host plant and AMF that contribute to metal detoxification/(im)mobilization/accumulation/translocation. Thus, this review is an attempt to reveal the underlying mechanisms of plant-AMF interactions in phytoremediation.
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Affiliation(s)
- Ying Ma
- College of Resources and Environment, Southwest University, Chongqing, China
| | - Ankit
- Department of Environmental Sciences, Central University of Jharkhand, Ranchi, India
| | - Jaya Tiwari
- Department of Community Medicine and School of Public Health, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Kuldeep Bauddh
- Department of Environmental Sciences, Central University of Jharkhand, Ranchi, India
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27
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Dastogeer KMG, Zahan MI, Rhaman MS, Sarker MSA, Chakraborty A. Microbe-Mediated Thermotolerance in Plants and Pertinent Mechanisms- A Meta-Analysis and Review. Front Microbiol 2022; 13:833566. [PMID: 35330772 PMCID: PMC8940538 DOI: 10.3389/fmicb.2022.833566] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Accepted: 02/04/2022] [Indexed: 01/10/2023] Open
Abstract
Microbial symbionts can mediate plant stress responses by enhancing thermal tolerance, but less attention has been paid to measuring these effects across plant-microbe studies. We performed a meta-analysis of published studies as well as discussed with relevant literature to determine how the symbionts influence plant responses under non-stressed versus thermal-stressed conditions. As compared to non-inoculated plants, inoculated plants had significantly higher biomass and photosynthesis under heat stress conditions. A significantly decreased accumulation of malondialdehyde (MDA) and hydrogen peroxide (H2O2) indicated a lower oxidation level in the colonized plants, which was also correlated with the higher activity of catalase, peroxidase, glutathione reductase enzymes due to microbial colonization under heat stress. However, the activity of superoxide dismutase, ascorbate oxidase, ascorbate peroxidase, and proline were variable. Our meta-analysis revealed that microbial colonization influenced plant growth and physiology, but their effects were more noticeable when their host plants were exposed to high-temperature stress than when they grew under ambient temperature conditions. We discussed the mechanisms of microbial conferred plant thermotolerance, including at the molecular level based on the available literature. Further, we highlighted and proposed future directions toward exploring the effects of symbionts on the heat tolerances of plants for their implications in sustainable agricultural production.
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Affiliation(s)
| | - Mst. I. Zahan
- Scientific Officer (Breeding Division), Bangladesh Sugarcrop Research Institute, Pabna, Bangladesh
| | - Mohammad S. Rhaman
- Department of Seed Science and Technology, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Mohammad S. A. Sarker
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute (BJRI), Dhaka, Bangladesh
| | - Anindita Chakraborty
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
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28
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Stock W, Willems A, Mangelinckx S, Vyverman W, Sabbe K. Selection constrains lottery assembly in the microbiomes of closely related diatom species. ISME COMMUNICATIONS 2022; 2:11. [PMID: 37938731 PMCID: PMC9723743 DOI: 10.1038/s43705-022-00091-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 01/13/2022] [Accepted: 01/18/2022] [Indexed: 04/25/2023]
Abstract
It is generally recognised that interactions between microalgae and bacteria play an important role in the functioning of marine ecosystems. In this context, increasing attention is paid to the processes that shape microalga-associated microbiomes. In recent years, conflicting evidence has been reported with respect to the relative importance of selective vs neutral processes in the assembly process. Whereas some studies report strong selection imposed by the host, others propose a more neutral, lottery-like assembly model according to which the chance of bacteria becoming part of the microbiome is proportional to their abundance in the environment and not driven by the selectional pressure created by the host. In the present study, we investigated to what degree selective vs neutral assembly processes constrain taxonomic, phylogenetic and functional variation within and between microbiomes associated with 69 isolates belonging to the Cylindrotheca closterium benthic marine diatom complex. The diatom cultures were initiated from non-axenic clonal isolates from different marine environments and geographic locations, and were then reared in a common garden (lab) environment. An important environmental imprint, likely due to in situ lottery dynamics, was apparent in the diatom microbiomes. However, microbiome assembly was also phylogenetically and functionally constrained through selective filtering related to the host microhabitat. Randomised microbiome assembly simulations revealed evidence for phylogenetic overdispersion in the observed microbiomes, reflecting an important role in the assembly process for competition between bacteria on the one hand and predominantly genetically driven differences between the hosts on the other hand. Our study thus shows that even between closely related diatom strains, host selection affects microbiome assembly, superimposing the predominantly stochastically driven recruitment process.
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Affiliation(s)
- Willem Stock
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, Krijgslaan 281 - S8, B-9000, Ghent, Belgium.
- Phycology Research Group, Department of Biology, Ghent University, Krijgslaan 281 - S8, B-9000, Ghent, Belgium.
| | - Anne Willems
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K.L. Ledeganckstraat 35, B-9000, Ghent, Belgium
| | - Sven Mangelinckx
- SynBioC, Department of Green Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| | - Wim Vyverman
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, Krijgslaan 281 - S8, B-9000, Ghent, Belgium
| | - Koen Sabbe
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, Krijgslaan 281 - S8, B-9000, Ghent, Belgium
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29
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Jiang M, Ye F, Liu F, Brestic M, Li X. Rhizosphere melatonin application reprograms nitrogen-cycling related microorganisms to modulate low temperature response in barley. FRONTIERS IN PLANT SCIENCE 2022; 13:998861. [PMID: 36275608 PMCID: PMC9583915 DOI: 10.3389/fpls.2022.998861] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 09/15/2022] [Indexed: 05/09/2023]
Abstract
Rhizospheric melatonin application has a positive effect on the tolerance of plants to low temperature; however, it remains unknown whether the rhizosphere microorganisms are involved in this process. The aim of this study was to investigate the effect of exogenous melatonin on the diversity and functioning of fungi and bacteria in rhizosphere of barley under low temperature. The results showed that rhizospheric melatonin application positively regulated the photosynthetic carbon assimilation and redox homeostasis in barley in response to low temperature. These effects might be associated with an altered diversity of microbial community in rhizosphere, especially the species and relative abundance of nitrogen cycling related microorganisms, as exemplified by the changes in rhizosphere metabolites in the pathways of amino acid synthesis and metabolism. Collectively, it was suggested that the altered rhizospheric microbial status upon melatonin application was associated with the response of barley to low temperature. This suggested that the melatonin induced microbial changes should be considered for its application in the crop cold-resistant cultivation.
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Affiliation(s)
- Miao Jiang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Science, Changchun, China
- Key Laboratory of Agricultural Soil and Water Engineering in Arid and Semiarid Areas, Ministry of Education of China, Northwest A & F University, Yangling, China
| | - Fan Ye
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Science, Changchun, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Fulai Liu
- Faculty of Science, Department of Plant and Environmental Sciences, University of Copenhagen, Tåstrup, Denmark
| | - Marian Brestic
- Department of Plant Physiology, Slovak Agricultural University, Nitra, Slovakia
- Department of Botany and Plant Physiology, Czech University of Life Sciences Prague, Prague, Czechia
| | - Xiangnan Li
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Science, Changchun, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
- Chinese Academy of Science (CAS) Engineering Laboratory for Eco-agriculture in Water Source of Liaoheyuan, Chinese Academy of Science, Changchun, China
- *Correspondence: Xiangnan Li,
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30
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Vandermeulen MD, Cullen PJ. Gene by Environment Interactions reveal new regulatory aspects of signaling network plasticity. PLoS Genet 2022; 18:e1009988. [PMID: 34982769 PMCID: PMC8759647 DOI: 10.1371/journal.pgen.1009988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 01/14/2022] [Accepted: 12/09/2021] [Indexed: 11/18/2022] Open
Abstract
Phenotypes can change during exposure to different environments through the regulation of signaling pathways that operate in integrated networks. How signaling networks produce different phenotypes in different settings is not fully understood. Here, Gene by Environment Interactions (GEIs) were used to explore the regulatory network that controls filamentous/invasive growth in the yeast Saccharomyces cerevisiae. GEI analysis revealed that the regulation of invasive growth is decentralized and varies extensively across environments. Different regulatory pathways were critical or dispensable depending on the environment, microenvironment, or time point tested, and the pathway that made the strongest contribution changed depending on the environment. Some regulators even showed conditional role reversals. Ranking pathways' roles across environments revealed an under-appreciated pathway (OPI1) as the single strongest regulator among the major pathways tested (RAS, RIM101, and MAPK). One mechanism that may explain the high degree of regulatory plasticity observed was conditional pathway interactions, such as conditional redundancy and conditional cross-pathway regulation. Another mechanism was that different pathways conditionally and differentially regulated gene expression, such as target genes that control separate cell adhesion mechanisms (FLO11 and SFG1). An exception to decentralized regulation of invasive growth was that morphogenetic changes (cell elongation and budding pattern) were primarily regulated by one pathway (MAPK). GEI analysis also uncovered a round-cell invasion phenotype. Our work suggests that GEI analysis is a simple and powerful approach to define the regulatory basis of complex phenotypes and may be applicable to many systems.
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Affiliation(s)
- Matthew D. Vandermeulen
- Department of Biological Sciences, University at Buffalo, Buffalo, New York, United States of America
| | - Paul J. Cullen
- Department of Biological Sciences, University at Buffalo, Buffalo, New York, United States of America
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Goyal D, Kumar S, Meena D, Solanki SS, Swaroop S, Pandey J. Selection of ACC deaminase positive, thermohalotolerant and drought tolerance enhancing plant growth-promoting bacteria from rhizospheres of Cyamopsis tetragonoloba grown in arid regions. Lett Appl Microbiol 2021; 74:519-535. [PMID: 34919753 DOI: 10.1111/lam.13633] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 10/29/2021] [Accepted: 12/07/2021] [Indexed: 11/29/2022]
Abstract
Plant growth-promoting bacteria (PGPB) expressing 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase activity are widely acknowledged to have a role in mitigation of abiotic stress caused by extreme environmental conditions. Consequently, several studies have focused on the isolation of ACC deaminase positive PGPBs. However, the application of such strains in drought-prone arid regions has remained grossly under-exploited. In order to be used in arid agroecosystems, PGPBs need to have the dual capability: to express ACC deaminase and to have the ability to tolerate increased temperature and salt concentration. Conspicuously, to date, very few studies have reported about isolation and characterization of PGPBs with this kind of dual capability. Here we report the isolation of bacterial strains from rhizosphere(s) of Cyamopsis tetragonoloba, a commercial crop from arid regions of Rajasthan, India, and their characterization for ACC deaminase activity and thermohalotolerance. Isolates found positive for desired traits were subsequently assessed for plant growth promotion under simulated drought conditions. Our finding showed that although the bacterial diversity within the rhizosphere of C. tetragonoloba grown in the arid region is quite poor, multiple isolates are ACC deaminase positive. Four isolates were found to be ACC deaminase positive, thermohalotolerant, and successfully enhanced drought tolerance. These isolates were identified as strains belonging to genera Pseudomonas, Enterobacter, and Stenotrophomonas based on 16S rRNA sequence homology.
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Affiliation(s)
- D Goyal
- Department of Biotechnology, School of Life Sciences, Central University of Rajasthan, Ajmer, Rajasthan, India
| | - S Kumar
- Department of Biotechnology, School of Life Sciences, Central University of Rajasthan, Ajmer, Rajasthan, India
| | - D Meena
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Ajmer, Rajasthan, India
| | - S S Solanki
- Department of Biotechnology, School of Life Sciences, Central University of Rajasthan, Ajmer, Rajasthan, India
| | - S Swaroop
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Ajmer, Rajasthan, India
| | - J Pandey
- Department of Biotechnology, School of Life Sciences, Central University of Rajasthan, Ajmer, Rajasthan, India
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The Mycorrizal Status in Vineyards Affected by Esca. J Fungi (Basel) 2021; 7:jof7100869. [PMID: 34682291 PMCID: PMC8540504 DOI: 10.3390/jof7100869] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 10/11/2021] [Accepted: 10/12/2021] [Indexed: 12/16/2022] Open
Abstract
In this work we analyzed the relationship among native arbuscular mycorrhizal fungi (AMF) and vine roots affected by esca, a serious grapevine trunk disease. The AMF symbiosis was analyzed on the roots of neighboring plants (symptomatic and asymptomatic to esca) in 14 sites of three vineyards in Marche region (central–eastern Italy). The AMF colonization intensity, identified by non-vital staining, showed higher value in all esca symptomatic plants (ranging from 24.6% to 61.3%) than neighboring asymptomatic plants (from 17.4% to 57.6%). The same trend of Glomeromycota phylum abundance was detected by analyzing fungal operational taxonomic units (OTUs) linked to the AMF community, obtained by amplicon high throughput analysis of ITS 1 region. Overall, the highest amount of OTUs was detected on roots from symptomatic plants (0.42%), compared to asymptomatic roots (0.29%). Specific primer pairs for native Rhizophagus irregularis and Funneliformis mosseae AMF species, were designed in 28S rRNA and large subunit (LSU) ribosomal RNA, respectively, and droplet digital PCR protocol for absolute quantification was set up. A higher number of DNA copies of both fungal species were detected more frequently in symptomatic than asymptomatic vines. Our study suggests a relationship between esca and native AMF in grapevine. These results underline the importance of native rhizosphere microbial communities for a better knowledge of grapevine esca disease.
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Marasco R, Fusi M, Rolli E, Ettoumi B, Tambone F, Borin S, Ouzari H, Boudabous A, Sorlini C, Cherif A, Adani F, Daffonchio D. Aridity modulates belowground bacterial community dynamics in olive tree. Environ Microbiol 2021; 23:6275-6291. [PMID: 34490977 PMCID: PMC9290347 DOI: 10.1111/1462-2920.15764] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/24/2021] [Accepted: 09/04/2021] [Indexed: 11/30/2022]
Abstract
Aridity negatively affects the diversity and abundance of edaphic microbial communities and their multiple ecosystem services, ultimately impacting vegetation productivity and biotic interactions. Investigation about how plant-associated microbial communities respond to increasing aridity is of particular importance, especially in light of the global climate change predictions. To assess the effect of aridity on plant associated bacterial communities, we investigated the diversity and co-occurrence of bacteria associated with the bulk soil and the root system of olive trees cultivated in orchards located in higher, middle and lower arid regions of Tunisia. The results indicated that the selective process mediated by the plant root system is amplified with the increment of aridity, defining distinct bacterial communities, dominated by aridity-winner and aridity-loser bacteria negatively and positively correlated with increasing annual rainfall, respectively. Aridity regulated also the co-occurrence interactions among bacteria by determining specific modules enriched with one of the two categories (aridity-winners or aridity-losers), which included bacteria with multiple PGP functions against aridity. Our findings provide new insights into the process of bacterial assembly and interactions with the host plant in response to aridity, contributing to understand how the increasing aridity predicted by climate changes may affect the resilience of the plant holobiont.
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Affiliation(s)
- Ramona Marasco
- Biological and Environmental Sciences and Engineering Division (BESE)King Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia
| | - Marco Fusi
- School of Applied SciencesEdinburgh Napier UniversityEdinburghUK
| | - Eleonora Rolli
- Department of Food, Environmental and Nutritional Sciences (DeFENS)University of MilanoMilanItaly
| | - Besma Ettoumi
- Department of Food, Environmental and Nutritional Sciences (DeFENS)University of MilanoMilanItaly
| | - Fulvia Tambone
- Department of Agricultural and Environmental Sciences (DiSAA), Gruppo Ricicla LabUniversity of MilanoMilanItaly
| | - Sara Borin
- Department of Food, Environmental and Nutritional Sciences (DeFENS)University of MilanoMilanItaly
| | - Hadda‐Imene Ouzari
- Laboratoire Microorganismes et Biomolécules Actives (LR03ES03), Faculté des Sciences de TunisUniversité Tunis El ManarTunisTunisia
| | - Abdellatif Boudabous
- Laboratoire Microorganismes et Biomolécules Actives (LR03ES03), Faculté des Sciences de TunisUniversité Tunis El ManarTunisTunisia
| | - Claudia Sorlini
- Department of Food, Environmental and Nutritional Sciences (DeFENS)University of MilanoMilanItaly
| | - Ameur Cherif
- Institut Supérieur de Biotechnologie Sidi Thabet (ISBST)BVBGR‐LR11ES31, Biotechpole Sidi Thabet, University ManoubaArianaTunisia
| | - Fabrizio Adani
- Department of Agricultural and Environmental Sciences (DiSAA), Gruppo Ricicla LabUniversity of MilanoMilanItaly
| | - Daniele Daffonchio
- Biological and Environmental Sciences and Engineering Division (BESE)King Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia
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Sweet Sorghum Genotypes Tolerant and Sensitive to Nitrogen Stress Select Distinct Root Endosphere and Rhizosphere Bacterial Communities. Microorganisms 2021; 9:microorganisms9061329. [PMID: 34207412 PMCID: PMC8234256 DOI: 10.3390/microorganisms9061329] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 06/14/2021] [Accepted: 06/15/2021] [Indexed: 12/17/2022] Open
Abstract
The belowground microbiomes have many beneficial functions that assist plant growth, including nutrient cycling, acquisition and transport, as well as alleviation of stresses caused by nutrient limitations such as nitrogen (N). Here we analyzed the root endosphere, rhizosphere and soil bacterial communities of seven sweet sorghum genotypes differing in sensitivity to N-stress. Sorghum genotypes were grown in fields with no (low-N) or sufficient (high-N) N. The dry shoot weight ratio (low-N/high-N) was used to determine N-stress sensitivity. Our hypothesis was that genotypes tolerant and sensitive to N-stress select distinct bacterial communities. The endosphere and rhizosphere bacterial community structure were significantly different between the N-stress sensitive and tolerant genotypes in the high-N field, but not in the low-N field. However, significant changes in the relative abundance of specific bacterial taxa were observed in both fields. Streptomyces, a bacterial genus known to alleviate plant abiotic stresses, was enriched in the endosphere and rhizosphere of the tolerant genotypes in the low-N field. Our study indicates that sweet sorghum genotypes tolerant to N-stress select taxa that can potentially mitigate the N-stress, suggesting that the interactions between N-stress tolerant lines and the root-associated microbiome might be vital for coping with N-stress.
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Shahrtash M, Brown SP. A Path Forward: Promoting Microbial-Based Methods in the Control of Invasive Plant Species. PLANTS (BASEL, SWITZERLAND) 2021; 10:943. [PMID: 34065068 PMCID: PMC8151036 DOI: 10.3390/plants10050943] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 04/29/2021] [Accepted: 05/06/2021] [Indexed: 01/18/2023]
Abstract
In this review, we discuss the unrealized potential of incorporating plant-microbe and microbe-microbe interactions into invasive plant management strategies. While the development of this as a viable strategy is in its infancy, we argue that incorporation of microbial components into management plans should be a priority and has great potential for diversifying sustainable control options. We advocate for increased research into microbial-mediated phytochemical production, microbial controls to reduce the competitiveness of invasive plants, microbial-mediated increases of herbicidal tolerance of native plants, and to facilitate increased pathogenicity of plant pathogens of invasive plants.
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Affiliation(s)
| | - Shawn P. Brown
- Department of Biological Sciences, The University of Memphis, Memphis, TN 38152, USA;
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Petipas RH, Geber MA, Lau JA. Microbe-mediated adaptation in plants. Ecol Lett 2021; 24:1302-1317. [PMID: 33913572 DOI: 10.1111/ele.13755] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 10/07/2021] [Accepted: 03/17/2021] [Indexed: 12/30/2022]
Abstract
Interactions with microbial symbionts have yielded great macroevolutionary innovations across the tree of life, like the origins of chloroplasts and the mitochondrial powerhouses of eukaryotic cells. There is also increasing evidence that host-associated microbiomes influence patterns of microevolutionary adaptation in plants and animals. Here we describe how microbes can facilitate adaptation in plants and how to test for and differentiate between the two main mechanisms by which microbes can produce adaptive responses in higher organisms: microbe-mediated local adaptation and microbe-mediated adaptive plasticity. Microbe-mediated local adaptation is when local plant genotypes have higher fitness than foreign genotypes because of a genotype-specific affiliation with locally beneficial microbes. Microbe-mediated adaptive plasticity occurs when local plant phenotypes, elicited by either the microbial community or the non-microbial environment, have higher fitness than foreign phenotypes as a result of interactions with locally beneficial microbes. These microbial effects on adaptation can be difficult to differentiate from traditional modes of adaptation but may be prevalent. Ignoring microbial effects may lead to erroneous conclusions about the traits and mechanisms underlying adaptation, hindering management decisions in conservation, restoration, and agriculture.
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Affiliation(s)
- Renee H Petipas
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA.,Department of Plant Pathology, Washington State University, Pullman, WA, USA
| | - Monica A Geber
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Jennifer A Lau
- Department of Biology, Indiana University, Bloomington, IN, USA.,The Environmental Resilience Institute, Indiana University, Bloomington, IN, USA
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Jiao X, Takishita Y, Zhou G, Smith DL. Plant Associated Rhizobacteria for Biocontrol and Plant Growth Enhancement. FRONTIERS IN PLANT SCIENCE 2021; 12:634796. [PMID: 33815442 PMCID: PMC8009966 DOI: 10.3389/fpls.2021.634796] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 02/23/2021] [Indexed: 05/20/2023]
Abstract
Crop disease remains a major problem to global food production. Excess use of pesticides through chemical disease control measures is a serious problem for sustainable agriculture as we struggle for higher crop productivity. The use of plant growth promoting rhizobacteria (PGPR) is a proven environment friendly way of controlling plant disease and increasing crop yield. PGPR suppress diseases by directly synthesizing pathogen-antagonizing compounds, as well as by triggering plant immune responses. It is possible to identify and develop PGPR that both suppress plant disease and more directly stimulate plant growth, bringing dual benefit. A number of PGPR have been registered for commercial use under greenhouse and field conditions and a large number of strains have been identified and proved as effective biocontrol agents (BCAs) under environmentally controlled conditions. However, there are still a number of challenges before registration, large-scale application, and adoption of PGPR for the pest and disease management. Successful BCAs provide strong theoretical and practical support for application of PGPR in greenhouse production, which ensures the feasibility and efficacy of PGPR for commercial horticulture production. This could be pave the way for widespread use of BCAs in agriculture, including under field conditions, to assist with both disease management and climate change conditions.
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Affiliation(s)
- Xiurong Jiao
- Institute of Agricultural Science and Technology Development of Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China
- Department of Plant Science, Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, QC, Canada
| | - Yoko Takishita
- Department of Plant Science, Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, QC, Canada
| | - Guisheng Zhou
- Institute of Agricultural Science and Technology Development of Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Donald L. Smith
- Department of Plant Science, Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, QC, Canada
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Interactive Effects of Scion and Rootstock Genotypes on the Root Microbiome of Grapevines (Vitis spp. L.). APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11041615] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Diversity and community structure of soil microorganisms are increasingly recognized as important contributors to sustainable agriculture and plant health. In viticulture, grapevine scion cultivars are grafted onto rootstocks to reduce the incidence of the grapevine pest phylloxera. However, it is unknown to what extent this practice influences root-associated microbial communities. A field survey of bacteria in soil surrounding the roots (rhizosphere) of 4 cultivars × 4 rootstock combinations was conducted to determine whether rootstock and cultivar genotypes are important drivers of rhizosphere community diversity and composition. Differences in α-diversity was highly dependent on rootstock–cultivar combinations, while bacterial community structure primarily clustered according to cultivar differences, followed by differences in rootstocks. Twenty-four bacterial indicator genera were significantly more abundant in one or more cultivars, while only thirteen were found to be specifically associated with one or more rootstock genotypes, but there was little overlap between cultivar and rootstock indicator genera. Bacterial diversity in grafted grapevines was affected by both cultivar and rootstock identity, but this effect was dependent on which diversity measure was being examined (i.e., α- or β-diversity) and specific rootstock–cultivar combinations. These findings could have functional implications, for instance, if specific combinations varied in their ability to attract beneficial microbial taxa which can control pathogens and/or assist plant performance.
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Mellidou I, Ainalidou A, Papadopoulou A, Leontidou K, Genitsaris S, Karagiannis E, Van de Poel B, Karamanoli K. Comparative Transcriptomics and Metabolomics Reveal an Intricate Priming Mechanism Involved in PGPR-Mediated Salt Tolerance in Tomato. FRONTIERS IN PLANT SCIENCE 2021; 12:713984. [PMID: 34484277 PMCID: PMC8416046 DOI: 10.3389/fpls.2021.713984] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 07/01/2021] [Indexed: 05/21/2023]
Abstract
Plant-associated beneficial strains inhabiting plants grown under harsh ecosystems can help them cope with abiotic stress factors by positively influencing plant physiology, development, and environmental adaptation. Previously, we isolated a potential plant growth promoting strain (AXSa06) identified as Pseudomonas oryzihabitans, possessing 1-aminocyclopropane-1-carboxylate deaminase activity, producing indole-3-acetic acid and siderophores, as well as solubilizing inorganic phosphorus. In this study, we aimed to further evaluate the effects of AXSa06 seed inoculation on the growth of tomato seedlings under excess salt (200 mM NaCl) by deciphering their transcriptomic and metabolomic profiles. Differences in transcript levels and metabolites following AXSa06 inoculation seem likely to have contributed to the observed difference in salt adaptation of inoculated plants. In particular, inoculations exerted a positive effect on plant growth and photosynthetic parameters, imposing plants to a primed state, at which they were able to respond more robustly to salt stress probably by efficiently activating antioxidant metabolism, by dampening stress signals, by detoxifying Na+, as well as by effectively assimilating carbon and nitrogen. The primed state of AXSa06-inoculated plants is supported by the increased leaf lipid peroxidation, ascorbate content, as well as the enhanced activities of antioxidant enzymes, prior to stress treatment. The identified signatory molecules of AXSa06-mediated salt tolerance included the amino acids aspartate, threonine, serine, and glutamate, as well as key genes related to ethylene or abscisic acid homeostasis and perception, and ion antiporters. Our findings represent a promising sustainable solution to improve agricultural production under the forthcoming climate change conditions.
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Affiliation(s)
- Ifigeneia Mellidou
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization DEMETER (ex NAGREF), Thermi, Greece
- *Correspondence: Ifigeneia Mellidou
| | - Aggeliki Ainalidou
- Laboratory of Agricultural Chemistry, School of Agriculture, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Anastasia Papadopoulou
- Laboratory of Agricultural Chemistry, School of Agriculture, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Kleopatra Leontidou
- Laboratory of Agricultural Chemistry, School of Agriculture, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Savvas Genitsaris
- Section of Ecology and Taxonomy, School of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Evangelos Karagiannis
- Laboratory of Pomology, Department of Horticulture, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Bram Van de Poel
- Division of Crop Biotechnics, Department of Biosystems, University of Leuven, Leuven, Belgium
| | - Katerina Karamanoli
- Laboratory of Agricultural Chemistry, School of Agriculture, Aristotle University of Thessaloniki, Thessaloniki, Greece
- Katerina Karamanoli
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40
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Baudson C, Delory BM, Spaepen S, du Jardin P, Delaplace P. Developmental plasticity of Brachypodium distachyon in response to P deficiency: Modulation by inoculation with phosphate-solubilizing bacteria. PLANT DIRECT 2021; 5:e00296. [PMID: 33532689 PMCID: PMC7833465 DOI: 10.1002/pld3.296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 06/17/2020] [Accepted: 11/14/2020] [Indexed: 06/12/2023]
Abstract
BACKGROUND Mineral phosphorus (P) fertilizers must be used wisely in order to preserve rock phosphate, a limited and non-renewable resource. The use of bio-inoculants to improve soil nutrient availability and trigger an efficient plant response to nutrient deficiency is one potential strategy in the attempt to decrease P inputs in agriculture. METHOD An in vitro co-cultivation system was used to study the response of Brachypodium distachyon to contrasted P supplies (soluble and poorly soluble forms of P) and inoculation with P solubilizing bacteria. Brachypodium's responses to P conditions and inoculation with bacteria were studied in terms of developmental plasticity and P use efficiency. RESULTS Brachypodium showed plasticity in its biomass allocation pattern in response to variable P conditions, specifically by prioritizing root development over shoot productivity under poorly soluble P conditions. Despite the ability of the bacteria to solubilize P, shoot productivity was depressed in plants inoculated with bacteria, although the root system development was maintained. The negative impact of bacteria on biomass production in Brachypodium might be attributed to inadequate C supply to bacteria, an increased competition for P between both organisms under P-limiting conditions, or an accumulation of toxic bacterial metabolites in our cultivation system. Both P and inoculation treatments impacted root system morphology. The modulation of Brachypodium's developmental response to P supplies by P solubilizing bacteria did not lead to improved P use efficiency. CONCLUSION Our results support the hypothesis that plastic responses of Brachypodium cultivated under P-limited conditions are modulated by P solubilizing bacteria. The considered experimental context impacts plant-bacteria interactions. Choosing experimental conditions as close as possible to real ones is important in the selection of P solubilizing bacteria. Both persistent homology and allometric analyses proved to be useful tools that should be considered when studying the impact of bio-inoculants on plant development in response to varying nutritional context.
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Affiliation(s)
- Caroline Baudson
- Plant SciencesGembloux Agro‐Bio TechUniversity of LiègeLiègeBelgium
| | | | - Stijn Spaepen
- Leuven Institute for Beer ResearchUniversity of LeuvenLeuvenBelgium
| | | | - Pierre Delaplace
- Plant SciencesGembloux Agro‐Bio TechUniversity of LiègeLiègeBelgium
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Alberton D, Valdameri G, Moure VR, Monteiro RA, Pedrosa FDO, Müller-Santos M, de Souza EM. What Did We Learn From Plant Growth-Promoting Rhizobacteria (PGPR)-Grass Associations Studies Through Proteomic and Metabolomic Approaches? FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2020. [DOI: 10.3389/fsufs.2020.607343] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Plant growth stimulation by microorganisms that interact in a mutually beneficial manner remains poorly understood. Understanding the nature of plant-bacteria interactions may open new routes for plant productivity enhancement, especially cereal crops consumed by humans. Proteomic and metabolomic analyses are particularly useful for elucidating these mechanisms. A complete depiction of these mechanisms will prompt researchers to develop more efficient plant-bacteria associations. The success of microorganisms as biofertilizers may replace the current massive use of chemical fertilizers, mitigating many environmental and economic issues. In this review, we discuss the recent advances and current state of the art in proteomics and metabolomics studies involving grass-bacteria associations. We also discuss essential subjects involved in the bacterial plant-growth promotion, such, nitrogen fixation, plant stress, defense responses, and siderophore production.
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Mechri B, Tekaya M, Attia F, Hammami M, Chehab H. Drought stress improved the capacity of Rhizophagus irregularis for inducing the accumulation of oleuropein and mannitol in olive (Olea europaea) roots. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 156:178-191. [PMID: 32961433 DOI: 10.1016/j.plaphy.2020.09.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 09/04/2020] [Indexed: 06/11/2023]
Abstract
Olive trees are often subjected to a prolonged dry season with low water availability, which induces oxidative stress. Arbuscular mycorrhizal (AM) symbioses can improve olive plant tolerance to water deficit. This study investigated several aspects related to drought tolerance in AM fungi olive plants. Non-AM and AM plants were grown under well-watered or drought-stressed conditions, and mycorrhizal growth response, neutral lipid fatty acid (NLFA)16:1ω5 and phospholipid fatty acid (PLFA) 16:1ω5 in roots (intraradical mycelium) and in soil (extraradical mycelium), carbohydrates (monosaccharides, disaccharides and polyols) and phenolic compounds (phenolic alcohols, flavonoids, lignans, secoiridoids and hydroxycinnamic acid derivatives) were determined. Results showed that the amounts of PLFA 16:1ω5 and NLFA 16:1ω5 were significantly influenced by drought stress conditions. The NLFA 16:1ω5/PLFA 16:1ω5 ratio showed a dramatic decrease (-62%) with the application of water deficit stress, indicating that AM fungi allocated low carbon to storage structures under stress conditions. Mannitol and verbascoside are the main compounds detected in the roots of well-watered plants, whereas oleuropein and mannitol are the main compounds differentially accumulated in the roots of water-stressed plants. The oleuropein/verbascoside ratio increased in the case of drought-stressed AM plants by 30%, while the mannitol/oleuropein ratio was decreased by 46%, when compared to the non-AM stressed plants. Mycorrhization therefore oriented the flux toward the biosynthetic pathway of oleuropein and the data suggest that sugar and phenolic compound metabolism may have been redirected to the formation of oleuropein in roots of AM stressed plants, that may underlie their enhanced tolerance to drought stress.
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Affiliation(s)
- Beligh Mechri
- Laboratory of Biochemistry, USCR Mass Spectrometry, LR-NAFS/LR12ES05 Nutrition Functional Foods and Vascular Health, Faculty of Medicine, University of Monastir, 5019, Monastir, Tunisia.
| | - Meriem Tekaya
- Laboratory of Biochemistry, USCR Mass Spectrometry, LR-NAFS/LR12ES05 Nutrition Functional Foods and Vascular Health, Faculty of Medicine, University of Monastir, 5019, Monastir, Tunisia
| | - Faouzi Attia
- The Olive Tree Institute, Unit Specializing in Sousse, Ibn Khaldoun Street B.P. 14, 4061, Sousse, Tunisia
| | - Mohamed Hammami
- Laboratory of Biochemistry, USCR Mass Spectrometry, LR-NAFS/LR12ES05 Nutrition Functional Foods and Vascular Health, Faculty of Medicine, University of Monastir, 5019, Monastir, Tunisia
| | - Hechmi Chehab
- The Olive Tree Institute, Unit Specializing in Sousse, Ibn Khaldoun Street B.P. 14, 4061, Sousse, Tunisia
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43
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Hernández EG, Baraza E, Smit C, Berg MP, Falcão Salles J. Salt Marsh Elevation Drives Root Microbial Composition of the Native Invasive Grass Elytrigia atherica. Microorganisms 2020; 8:microorganisms8101619. [PMID: 33096699 PMCID: PMC7589393 DOI: 10.3390/microorganisms8101619] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 10/13/2020] [Accepted: 10/19/2020] [Indexed: 02/07/2023] Open
Abstract
Elytrigia atherica is a native invasive plant species whose expansion on salt marshes is attributed to genotypic and phenotypic adaptations to non-ideal environmental conditions, forming two ecotypes. It is unknown how E. atherica–microbiome interactions are contributing to its adaptation. Here we investigated the effect of sea-water flooding frequency and associated soil (a)biotic conditions on plant traits and root-associated microbial community composition and potential functions of two E. atherica ecotypes. We observed higher endomycorrhizal colonization in high-elevation ecotypes (HE, low inundation frequency), whereas low-elevation ecotypes (LE, high inundation frequency) had higher specific leaf area. Similarly, rhizosphere and endosphere bacterial communities grouped according to ecotypes. Soil ammonium content and elevation explained rhizosphere bacterial composition. Around 60% the endosphere amplicon sequence variants (ASVs) were also found in soil and around 30% of the ASVs were ecotype-specific. The endosphere of HE-ecotype harbored more unique sequences than the LE-ecotype, the latter being abundant in halophylic bacterial species. The composition of the endosphere may explain salinity and drought tolerance in relation to the local environmental needs of each ecotype. Overall, these results suggest that E. atherica is flexible in its association with soil bacteria and ecotype-specific dissimilar, which may enhance its competitive strength in salt marshes.
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Affiliation(s)
- Edisa García Hernández
- Microbial Community Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, 9747 AG Groningen, The Netherlands
- Correspondence: (E.G.H.); (J.F.S.); Tel.: +31-50-3632236 (E.G.H.); +31-50-36-32162 (J.F.S.)
| | - Elena Baraza
- Departamento de Biologia, Universitat de les Illes Balears-INAGEA, 07122 Mallorca, Spain;
| | - Christian Smit
- Community and Conservation Ecology Group, Groningen Institute for Evolutionary Life Sciences, University of Groningen, 9747 AG Groningen, The Netherlands; (C.S.); (M.P.B.)
| | - Matty P. Berg
- Community and Conservation Ecology Group, Groningen Institute for Evolutionary Life Sciences, University of Groningen, 9747 AG Groningen, The Netherlands; (C.S.); (M.P.B.)
- Department of Ecological Science, Section Animal Ecology, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Joana Falcão Salles
- Microbial Community Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, 9747 AG Groningen, The Netherlands
- Correspondence: (E.G.H.); (J.F.S.); Tel.: +31-50-3632236 (E.G.H.); +31-50-36-32162 (J.F.S.)
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44
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Krey KL, Nabity PD, Blubaugh CK, Fu Z, Van Leuven JT, Reganold JP, Berim A, Gang DR, Jensen AS, Snyder WE. Organic Farming Sharpens Plant Defenses in the Field. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2020; 4. [PMID: 33073178 DOI: 10.3389/fsufs.2020.00097] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Plants deploy a variety of chemical and physical defenses to protect themselves against herbivores and pathogens. Organic farming seeks to enhance these responses by improving soil quality, ultimately altering bottom up regulation of plant defenses. While laboratory studies suggest this approach is effective, it remains unclear whether organic agriculture encourages more-active plant defenses under real-world conditions. Working on the farms of cooperating growers, we examined gene expression in the leaves of two potato (Solanum tuberosum) varieties, grown on organic vs. conventional farms. For one variety, Norkotah, we found significantly heightened initiation of genes associated with plant-defense pathways in plants grown in organic vs. conventional fields. Organic Norkotah fields exhibited lower levels of nitrate in soil and of nitrogen in plant foliage, alongside differences in communities of soil bacteria, suggesting possible links between soil management and observed differences in plant defenses. Additionally, numbers of predatory and phloem-feeding insects were higher in organic than conventional fields. A second potato variety, Alturas, which is generally grown using fewer inputs and in poorer-quality soils, exhibited lower overall herbivore and predator numbers, few differences in soil ecology, and no differences in gene-activity in organic and conventional farming systems. Altogether, our results suggest that organic farming has the potential to increase plants' resistance to herbivores, possibly facilitating reduced need for insecticide applications. These benefits appear to be mediated by plant variety and/or farming context.
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Affiliation(s)
- Karol L Krey
- Department of Entomology, Washington State University, Pullman, WA, United States
| | - Paul D Nabity
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, United States
| | - Carmen K Blubaugh
- Plant and Environmental Sciences Department, Clemson University, Clemson, SC, United States
| | - Zhen Fu
- Department of Entomology, Washington State University, Pullman, WA, United States.,Department of Entomology, Texas A&M University, College Station, TX, United States
| | - James T Van Leuven
- Department of Biological Sciences, University of Idaho, Moscow, ID, United States
| | - John P Reganold
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States
| | - Anna Berim
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
| | - David R Gang
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
| | - Andrew S Jensen
- Northwest Potato Research Consortium, Lakeview, OR, United States
| | - William E Snyder
- Department of Entomology, University of Georgia, Athens, GA, United States
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45
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Liu Y, Medeiros JS, Burns JH. The soil biotic community protects Rhododendron spp. across multiple clades from the oomycete Phytophthora cinnamomi at a cost to plant growth. Oecologia 2020; 195:1-12. [PMID: 33025264 DOI: 10.1007/s00442-020-04762-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 09/18/2020] [Indexed: 11/27/2022]
Abstract
The effects of whole soil biotic communities on plants is a result of positive and negative interactions from a complex suite of mutualists and pathogens. However, few experiments have evaluated the composite effects of whole soil biotic communities on plant growth and disease resistance. We conducted a factorial greenhouse experiment with 14 Rhododendron species grown with and without live conspecific soil biota and with and without the disease, Phytophthora cinnamomi. We tested the prediction that the presence of whole soil biotic communities influences survival in the presence of disease. We also explored functional trait correlations with disease susceptibility across the phylogeny. The presence of live soil biota led to higher survival in the presence of disease compared with sterilized soils, and the direction of this effect was consistent for seven species across four clades. The presence of live soil biota also significantly reduced plant growth rate and decreased shoot biomass, relative to plants grown in sterilized soil, indicating that live soil biota might influence plant allocation strategies. We found that Rhododendron species with higher Root Shoot Ratios were less susceptible to Phytophthora, suggesting that water relations influence disease susceptibility. Our findings that disease resistance and susceptibility occur independently across multiple clades and that whole soil biotic communities consistently enhance disease resistance across clades, suggest that soil biota may play an important role in disease resistance and can moderate disease-induced mortality.
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Affiliation(s)
- Yu Liu
- Department of Biology, Case Western Reserve University, Cleveland, OH, 44106-7080, USA.
| | | | - Jean H Burns
- Department of Biology, Case Western Reserve University, Cleveland, OH, 44106-7080, USA
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46
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Valencia JB, Mesa J, León JG, Madriñán S, Cortés AJ. Climate Vulnerability Assessment of the Espeletia Complex on Páramo Sky Islands in the Northern Andes. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.565708] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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47
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Singh DP, Singh V, Shukla R, Sahu P, Prabha R, Gupta A, Sarma BK, Gupta VK. Stage-dependent concomitant microbial fortification improves soil nutrient status, plant growth, antioxidative defense system and gene expression in rice. Microbiol Res 2020; 239:126538. [PMID: 32717536 DOI: 10.1016/j.micres.2020.126538] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 06/17/2020] [Accepted: 06/24/2020] [Indexed: 12/20/2022]
Abstract
Stage-dependent concomitant fortification of rice (Oryza sativa L.) varieties PB1612 and CO51 with microbial inoculants Trichoderma asperellum and Pseudomonas fluorescens as seed coating, seedling root inoculation and soil application enhanced growth, activated antioxidant enzymes and modulated defence-related genes in plants. Microbial inoculants improved shoot height, tiller numbers, fresh weight and dry biomass. Co-inoculation was more impactful in enhancing plant growth and development as compared to single inoculation. Single and co-inoculation improved organic carbon (OC) and N, P and K content in the soil substantially. Mean values between control and co-inoculation varied significantly for OC in PB1612 (p0.001) and CO51 (p0.019) and phosphorus content in PB1612 (p0.044) and CO51 (p0.021). Microbial inoculation enhanced soil nutrients and increased their bioavailability for the plants. Total polyphenolics, flavonoids and protein content increased in the leaves following microbial inoculation. Enhanced non-enzymatic antioxidant parameters (ABTS, DPPH, Fe-ion reducing power and Fe-ion chelation) was found in microbe inoculated rice reflecting high free radical scavenging activity in polyphenolics-rich leaf extracts. Increased enzyme activity of superoxide dismutase (SOD), glutathione reductase (GR), phenylalanine ammonia-lyase (PAL), peroxidase (PO), glutathione peroxidase (GPX), ascorbate peroxidase (APX) and catalase (CAT) showed improved ROS scavenging in rice plants having co-inoculation. Over-expression of PAL, cCuZn-SOD and CAT genes in microbial inoculated rice plants was recorded. The study concludes that plant stage-wise concomitant fortification by microbial inoculants could play multi-pronged manifestations at physiological, biochemical and molecular level in rice to positively influence growth, development and defense attributes in plants.
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Affiliation(s)
- Dhananjaya Pratap Singh
- ICAR-National Bureau of Agriculturally Important Microorganisms, Kushmaur, Maunath Bhanjan 275103, India; ICAR-Indian Institute of Vegetable Research, Jakhini, Varanasi 221305, India.
| | - Vivek Singh
- ICAR-National Bureau of Agriculturally Important Microorganisms, Kushmaur, Maunath Bhanjan 275103, India
| | - Renu Shukla
- ICAR-National Bureau of Agriculturally Important Microorganisms, Kushmaur, Maunath Bhanjan 275103, India
| | - Pramod Sahu
- ICAR-National Bureau of Agriculturally Important Microorganisms, Kushmaur, Maunath Bhanjan 275103, India
| | - Ratna Prabha
- ICAR-National Bureau of Agriculturally Important Microorganisms, Kushmaur, Maunath Bhanjan 275103, India; ICAR-Indian Agricultural Statistical Research Institute, New Delhi, 110012, India
| | - Amrita Gupta
- ICAR-National Bureau of Agriculturally Important Microorganisms, Kushmaur, Maunath Bhanjan 275103, India
| | - Birinchi K Sarma
- Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi 221005, India
| | - Vijai K Gupta
- AgroBioSciences and Chemical & Biochemical Sciences Department, University Mohammed VI Polytechnic (UM6P), Lot 660, Hay Moulay Rachid, Benguerir 43150, Morocco
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48
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Fang K, Park OJ, Hong SH. Controlling biofilms using synthetic biology approaches. Biotechnol Adv 2020; 40:107518. [PMID: 31953206 PMCID: PMC7125041 DOI: 10.1016/j.biotechadv.2020.107518] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 01/09/2020] [Accepted: 01/11/2020] [Indexed: 12/22/2022]
Abstract
Bacterial biofilms are formed by the complex but ordered regulation of intra- or inter-cellular communication, environmentally responsive gene expression, and secretion of extracellular polymeric substances. Given the robust nature of biofilms due to the non-growing nature of biofilm bacteria and the physical barrier provided by the extracellular matrix, eradicating biofilms is a very difficult task to accomplish with conventional antibiotic or disinfectant treatments. Synthetic biology holds substantial promise for controlling biofilms by improving and expanding existing biological tools, introducing novel functions to the system, and re-conceptualizing gene regulation. This review summarizes synthetic biology approaches used to eradicate biofilms via protein engineering of biofilm-related enzymes, utilization of synthetic genetic circuits, and the development of functional living agents. Synthetic biology also enables beneficial applications of biofilms through the production of biomaterials and patterning biofilms with specific temporal and spatial structures. Advances in synthetic biology will add novel biofilm functionalities for future therapeutic, biomanufacturing, and environmental applications.
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Affiliation(s)
- Kuili Fang
- Department of Chemical and Biological Engineering, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Oh-Jin Park
- Department of Chemical and Biological Engineering, Illinois Institute of Technology, Chicago, IL 60616, USA; Department of Biological and Chemical Engineering, Yanbian University of Science and Technology, Yanji, Jilin, People's Republic of China
| | - Seok Hoon Hong
- Department of Chemical and Biological Engineering, Illinois Institute of Technology, Chicago, IL 60616, USA.
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49
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Acuña-Rodríguez IS, Newsham KK, Gundel PE, Torres-Díaz C, Molina-Montenegro MA. Functional roles of microbial symbionts in plant cold tolerance. Ecol Lett 2020; 23:1034-1048. [PMID: 32281227 DOI: 10.1111/ele.13502] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/14/2020] [Accepted: 03/06/2020] [Indexed: 12/12/2022]
Abstract
In this review, we examine the functional roles of microbial symbionts in plant tolerance to cold and freezing stresses. The impacts of symbionts on antioxidant activity, hormonal signaling and host osmotic balance are described, including the effects of the bacterial endosymbionts Burkholderia, Pseudomonas and Azospirillum on photosynthesis and the accumulation of carbohydrates such as trehalose and raffinose that improve cell osmotic regulation and plasma membrane integrity. The influence of root fungal endophytes and arbuscular mycorrhizal fungi on plant physiology at low temperatures, for example their effects on nutrient acquisition and the accumulation of indole-3-acetic acid and antioxidants in tissues, are also reviewed. Meta-analyses are presented showing that aspects of plant performance (shoot biomass, relative water content, sugar and proline concentrations and Fv /Fm ) are enhanced in symbiotic plants at low (-1 to 15 °C), but not at high (20-26 °C), temperatures. We discuss the implications of microbial symbionts for plant performance at low and sub-zero temperatures in the natural environment and propose future directions for research into the effects of symbionts on the cold and freezing tolerances of plants, concluding that further studies should routinely incorporate symbiotic microbes in their experimental designs.
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Affiliation(s)
- Ian S Acuña-Rodríguez
- Laboratorio de Biología Vegetal, Instituto de Ciencias Biológicas, Universidad de Talca, Campus Lircay, Talca, Chile
| | | | - Pedro E Gundel
- IFEVA, CONICET, Universidad de Buenos Aires, Facultad de Agronomía, Buenos Aires, Argentina
| | - Cristian Torres-Díaz
- Grupo de Biodiversidad y Cambio Global (BCG), Departamento de Ciencias Básicas, Universidad del Bío-Bío, Campus Fernando May, Chillán, Chile
| | - Marco A Molina-Montenegro
- Laboratorio de Biología Vegetal, Instituto de Ciencias Biológicas, Universidad de Talca, Campus Lircay, Talca, Chile.,Centro de Estudios Avanzados en Zonas Áridas (CEAZA), Facultad de Ciencias del Mar, Universidad Católica del Norte, Coquimbo, Chile.,Centro de Investigación en Estudios Avanzados del Maule (CIEAM), Universidad Católica del Maule, Campus San Miguel, Talca, Chile
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50
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Ortiz Y, Restrepo C, Vilanova-Cuevas B, Santiago-Valentin E, Tringe SG, Godoy-Vitorino F. Geology and climate influence rhizobiome composition of the phenotypically diverse tropical tree Tabebuia heterophylla. PLoS One 2020; 15:e0231083. [PMID: 32255799 PMCID: PMC7138329 DOI: 10.1371/journal.pone.0231083] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 03/17/2020] [Indexed: 11/19/2022] Open
Abstract
Plant-associated microbial communities have diverse phenotypic effects on their hosts that are only beginning to be revealed. We hypothesized that morpho-physiological variations in the tropical tree Tabebuia heterophylla, observed on different geological substrates, arise in part due to microbial processes in the rhizosphere. We characterized the microbiota of the rhizosphere and soil communities associated with T. heterophylla trees in high and low altitude sites (with varying temperature and precipitation) of volcanic, karst and serpentine geologies across Puerto Rico. We sampled 6 areas across the island in three geological materials including volcanic, serpentine and karst soils. Collection was done in 2 elevations (>450m and 0-300m high), that included 3 trees for each site and 4 replicate soil samples per tree of both bulk and rhizosphere. Genomic DNA was extracted from 144 samples, and 16S rRNA V4 sequencing was performed on the Illumina MiSeq platform. Proteobacteria, Actinobacteria, and Verrucomicrobia were the most dominant phyla, and microbiomes clustered by geological substrate and elevation. Volcanic samples were enriched in Verrucomicrobia; karst was dominated by nitrogen-fixing Proteobacteria, and serpentine sites harbored the most diverse communities, with dominant Cyanobacteria. Sites with similar climates but differing geologies showed significant differences on rhizobiota diversity and composition demonstrating the importance of geology in shaping the rhizosphere microbiota, with implications for the plant's phenotype. Our study sheds light on the combined role of geology and climate in the rhizosphere microbial consortia, likely contributing to the phenotypic plasticity of the trees.
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Affiliation(s)
- Yakshi Ortiz
- Department of Biology, University of Puerto Rico, San Juan, Puerto Rico
| | - Carla Restrepo
- Department of Biology, University of Puerto Rico, San Juan, Puerto Rico
| | - Brayan Vilanova-Cuevas
- Department of Microbiology and Medical Zoology, University of Puerto Rico, School of Medicine, San Juan, Puerto Rico
| | | | - Susannah G. Tringe
- Department of Energy, Joint Genome Institute, Walnut Creek, California, United States of America
| | - Filipa Godoy-Vitorino
- Department of Microbiology and Medical Zoology, University of Puerto Rico, School of Medicine, San Juan, Puerto Rico
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