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Liu M, Ke X, Liu X, Fan X, Xu Y, Li L, Solaiman ZM, Pan G. The effects of biochar soil amendment on rice growth may vary greatly with rice genotypes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 810:152223. [PMID: 34896147 DOI: 10.1016/j.scitotenv.2021.152223] [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: 08/17/2021] [Revised: 12/02/2021] [Accepted: 12/02/2021] [Indexed: 06/14/2023]
Abstract
While plant growth promotion with increased nutrient uptake had been well addressed for biochar soil amendment in agriculture, there was limited knowledge on the variation of such effects with crop genotypes. In a rice field experiment without and with biochar soil amendment at 20 t ha-1, 19 mutants of a rice cultivar Wuyunjing 7 (Oryza sativa L.) were tested for plant growth in split plots respectively. At harvest, the biomass of grain, stem and leaves were measured and soil and plant samples were collected for measuring N, P and K nutrients. Across the 19 mutants, relative change with biochar soil amendment varied in a range of -41.6% to +35.6% for biomass production and agronomic traits, and -87.0% to +117% for nutrient accumulation. For the nutrients content, the relative change for N was seen in a narrow range of -29.4% to +16.6%, being similar among grain, leaf and shoot samples while that for P in a wide range of -109% to +105%. With factor analysis, variation of biomass and nutrient uptake was least explained with biochar effect (up to 7.0%) but largely by genotype effect (mostly by 40-70%). However, the genotype × biochar interaction effect could also explain 10-40% of the total variations though the interaction explained 40-70% of leaf P variation. Therefore, mutant and mutant × biochar interactions dominated the agronomic variation of rice production of the Wuyunjing 7 cultivar. Furthermore, across the traits analyzed, genotype effects were shown very significantly but negatively correlated to biochar effects. In other words, biochar soil amendment provided little growth or nutrient enhancement for those mutants bred for high efficiency. Hence, genotype selection should be considered in optimizing prioritizing biochar application in crop production. Of course, variation of biochar effect with crop genotypes deserved further plant physio-ecological studies.
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Affiliation(s)
- Minglong Liu
- Institute of Resource, Ecosystem and Environment of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; UWA School of Agriculture and Environment, and the UWA Institute of Agriculture, University of Western Australia, Perth, WA 6009, Australia
| | - Xianlin Ke
- Institute of Resource, Ecosystem and Environment of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaoyu Liu
- Institute of Resource, Ecosystem and Environment of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaorong Fan
- Institute of Resource, Ecosystem and Environment of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Youzun Xu
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Lianqing Li
- Institute of Resource, Ecosystem and Environment of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Zakaria M Solaiman
- UWA School of Agriculture and Environment, and the UWA Institute of Agriculture, University of Western Australia, Perth, WA 6009, Australia
| | - Genxing Pan
- Institute of Resource, Ecosystem and Environment of Agriculture, Nanjing Agricultural University, Nanjing 210095, China.
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202
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Tayyab M, Fallah N, Zhang C, Pang Z, Islam W, Lin S, Lin W, Zhang H. Sugarcane cultivar-dependent changes in assemblage of soil rhizosphere fungal communities in subtropical ecosystem. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:20795-20807. [PMID: 34741271 DOI: 10.1007/s11356-021-17229-4] [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] [Received: 08/03/2021] [Accepted: 10/22/2021] [Indexed: 06/13/2023]
Abstract
Sugarcane cultivars (Saccharum officinarum L.) are widely cultivated for both sugar and renewable energy in China. The response of rhizosphere fungal composition and diversity to different emerging sugarcane cultivars is limited. Therefore, utilizing high-throughput sequencing, we explored fungal communities' structure in soils adhering to six sugarcane cultivars' roots (Guitang 08-120, Regan14-62, Guitang 08-1180, Haizhe 22, Liucheng 05-136, Taitang 22) in Guangxi Province, China. Our results suggested that sugarcane varieties significantly altered rhizosphere soil attributes, with Haizhe 22 having substantially lower soil pH, organic matter (OM), available phosphorus (AP), and soil water contents (SWC) than others cultivars. Different sugarcane varieties did not substantially affected the Shannon fungal diversity index, but the apparent effect on fungal richness was significant. Beta diversity analysis revealed that "Haizhe 22" distinguished the fungal community from the other five cultivars. Soil pH, OM, cultivars, and soil moisture were crucial determinants in shaping soil fungal composition. The Haizhe 22 rhizosphere significantly enriched the operational taxonomic units (OTUs) assigned to two fungal genera (Cephalotheca and Sagenomella), while rhizosphere of other verities significantly enriched the OTUs assigned to four fungal genera (Chaetomium, Chaetosphaeria, Mortierella, and Talaromyces), suggesting their essential role in plant development, disease tolerance, and bioremediation. These findings may help in selecting or breeding innovative genotypes capable of supporting abundant rhizosphere fungi beneficial to plants that would likely improve crops' agronomic potential and maintain soil ecosystem sustainability.
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Affiliation(s)
- Muhammad Tayyab
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian Provincial Key Laboratory of Agro-Ecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Nyumah Fallah
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Caifang Zhang
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin, 150040, China
- College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin, 150040, China
| | - Ziqin Pang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Waqar Islam
- Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Sheng Lin
- Fujian Provincial Key Laboratory of Agro-Ecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin, 150040, China
- College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin, 150040, China
| | - Wenxiong Lin
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin, 150040, China.
- College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin, 150040, China.
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, 35002, China.
| | - Hua Zhang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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203
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Ponsford JCB, Hubbard CJ, Harrison JG, Maignien L, Buerkle CA, Weinig C. Whole-Genome Duplication and Host Genotype Affect Rhizosphere Microbial Communities. mSystems 2022; 7:e0097321. [PMID: 35014873 PMCID: PMC8751390 DOI: 10.1128/msystems.00973-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 12/15/2021] [Indexed: 01/04/2023] Open
Abstract
The composition of microbial communities found in association with plants is influenced by host phenotype and genotype. However, the ways in which specific genetic architectures of host plants shape microbiomes are unknown. Genome duplication events are common in the evolutionary history of plants and influence many important plant traits, and thus, they may affect associated microbial communities. Using experimentally induced whole-genome duplication (WGD), we tested the effect of WGD on rhizosphere bacterial communities in Arabidopsis thaliana. We performed 16S rRNA amplicon sequencing to characterize differences between microbiomes associated with specific host genetic backgrounds (Columbia versus Landsberg) and ploidy levels (diploid versus tetraploid). We modeled relative abundances of bacterial taxa using a hierarchical Bayesian approach. We found that host genetic background and ploidy level affected rhizosphere community composition. We then tested to what extent microbiomes derived from a specific genetic background or ploidy level affected plant performance by inoculating sterile seedlings with microbial communities harvested from a prior generation. We found a negative effect of the tetraploid Columbia microbiome on growth of all four plant genetic backgrounds. These findings suggest an interplay between host genetic background and ploidy level and bacterial community assembly with potential ramifications for host fitness. Given the prevalence of ploidy-level variation in both wild and managed plant populations, the effects on microbiomes of this aspect of host genetic architecture could be a widespread driver of differences in plant microbiomes. IMPORTANCE Plants influence the composition of their associated microbial communities, yet the underlying host-associated genetic determinants are typically unknown. Genome duplication events are common in the evolutionary history of plants and affect many plant traits. Using Arabidopsis thaliana, we characterized how whole-genome duplication affected the composition of rhizosphere bacterial communities and how bacterial communities associated with two host plant genetic backgrounds and ploidy levels affected subsequent plant growth. We observed an interaction between ploidy level and genetic background that affected both bacterial community composition and function. This research reveals how genome duplication, a widespread genetic feature of both wild and crop plant species, influences bacterial assemblages and affects plant growth.
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Affiliation(s)
| | - Charley J. Hubbard
- Department of Botany, University of Wyoming, Laramie, Wyoming, USA
- Program in Ecology, University of Wyoming, Laramie, Wyoming, USA
| | | | - Lois Maignien
- Marine Biological Laboratory, Josephine Bay Paul Center, Woods Hole, Massachusetts, USA
- Laboratory of Microbiology of Extreme Environments, UMR 6197, Institut Européen de la Mer, Université de Bretagne Occidentale, Plouzane, France
| | - C. Alex Buerkle
- Department of Botany, University of Wyoming, Laramie, Wyoming, USA
- Program in Ecology, University of Wyoming, Laramie, Wyoming, USA
| | - Cynthia Weinig
- Department of Botany, University of Wyoming, Laramie, Wyoming, USA
- Program in Ecology, University of Wyoming, Laramie, Wyoming, USA
- Department of Molecular Biology, University of Wyoming, Laramie, Wyoming, USA
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204
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Defining the
Sphagnum
Core Microbiome across the North American Continent Reveals a Central Role for Diazotrophic Methanotrophs in the Nitrogen and Carbon Cycles of Boreal Peatland Ecosystems. mBio 2022. [PMCID: PMC8863050 DOI: 10.1128/mbio.03714-21] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Peat mosses of the genus Sphagnum are ecosystem engineers that frequently predominate over photosynthetic production in boreal peatlands. Sphagnum spp. host diverse microbial communities capable of nitrogen fixation (diazotrophy) and methane oxidation (methanotrophy), thereby potentially supporting plant growth under severely nutrient-limited conditions. Moreover, diazotrophic methanotrophs represent a possible “missing link” between the carbon and nitrogen cycles, but the functional contributions of the Sphagnum-associated microbiome remain in question. A combination of metagenomics, metatranscriptomics, and dual-isotope incorporation assays was applied to investigate Sphagnum microbiome community composition across the North American continent and provide empirical evidence for diazotrophic methanotrophy in Sphagnum-dominated ecosystems. Remarkably consistent prokaryotic communities were detected in over 250 Sphagnum SSU rRNA libraries from peatlands across the United States (5 states, 17 bog/fen sites, 18 Sphagnum species), with 12 genera of the core microbiome comprising 60% of the relative microbial abundance. Additionally, nitrogenase (nifH) and SSU rRNA gene amplicon analysis revealed that nitrogen-fixing populations made up nearly 15% of the prokaryotic communities, predominated by Nostocales cyanobacteria and Rhizobiales methanotrophs. While cyanobacteria comprised the vast majority (>95%) of diazotrophs detected in amplicon and metagenome analyses, obligate methanotrophs of the genus Methyloferula (order Rhizobiales) accounted for one-quarter of transcribed nifH genes. Furthermore, in dual-isotope tracer experiments, members of the Rhizobiales showed substantial incorporation of 13CH4 and 15N2 isotopes into their rRNA. Our study characterizes the core Sphagnum microbiome across large spatial scales and indicates that diazotrophic methanotrophs, here defined as obligate methanotrophs of the rare biosphere (Methyloferula spp. of the Rhizobiales) that also carry out diazotrophy, play a keystone role in coupling of the carbon and nitrogen cycles in nutrient-poor peatlands.
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205
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Soil Type Influences Rhizosphere Bacterial Community Assemblies of Pecan Plantations, a Case Study of Eastern China. FORESTS 2022. [DOI: 10.3390/f13030363] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The rhizosphere microbiome is closely related to forest health and productivity. However, whether soil type affects pecan (Carya illinoinensis) rhizosphere microbiomes is unclear. We aimed to explore the diversity and structural characteristics of rhizosphere bacteria associated with pecan plantations grown in three soil types (Luvisols, Cambisols, Solonchaks) in Eastern China and analyze their potential functions through high-throughput sequencing. The results showed that the diversity and community structure of rhizosphere bacteria in pecan plantations were significantly affected by soil type and the pH, available phosphorus content, electrical conductivity, soil moisture, and ammonium nitrogen contents were the main factors. At the phylum level, the rhizosphere bacterial community composition was consistent, mainly included Actinobacteria, Proteobacteria, Acidobacteria, and Chloroflexi. At the family level, the pecan plantations formed different rhizosphere enriched biomarkers due to the influence of soil type, with functional characteristics such as plant growth promotion and soil nutrient cycling. In addition, there existed low abundance core species such as Haliangiaceae, Bryobacteraceae, and Steroidobacteraceae. They played important roles in the rhizosphere environments through their functional characteristics and community linkages. Overall, this study provides a basis for the study of the rhizosphere microbiome in different soil types of pecan plantations, and plays an important role in the sustainable management of forest soil.
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206
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Qian Z, Wu C, Pan W, Xiong X, Xia L, Li W. Arsenic Transformation in Soil-Rice System Affected by Iron-Oxidizing Strain ( Ochrobactrum sp.) and Related Soil Metabolomics Analysis. Front Microbiol 2022; 13:794950. [PMID: 35256871 PMCID: PMC8897285 DOI: 10.3389/fmicb.2022.794950] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 01/14/2022] [Indexed: 11/29/2022] Open
Abstract
Iron-oxidizing bacteria (FeOB) could oxidize Fe(II) and mediate biomineralization, which provides the possibility for its potential application in arsenic (As) remediation. In the present study, a strain named Ochrobactrum EEELCW01 isolated previously, was inoculated into paddy soils to investigate the effect of FeOB inoculation on the As migration and transformation in paddy soils. The results showed that inoculation of Ochrobactrum sp. increased the proportion of As in iron-aluminum oxide binding fraction, which reduced the As bioavailability in paddy soils and effectively reduced the As accumulation in rice tissues. Moreover, the inoculation of iron oxidizing bacteria increased the abundance of KD4-96, Pedosphaeraceae and other bacteria in the soils, which could reduce the As toxicity in the soil through biotransformation. The abundance of metabolites such as carnosine, MG (0:0/14:0/0:0) and pantetheine 4'-phosphate increased in rhizosphere soils inoculated with FeOB, which indicated that the defense ability of soil-microorganism-plant system against peroxidation caused by As was enhanced. This study proved that FeOB have the potential application in remediation of As pollution in paddy soil, FeOB promotes the formation of iron oxide in paddy soil, and then adsorbed and coprecipitated with arsenic. On the other hand, the inoculation of Ochrobactrum sp. change soil microbial community structure and soil metabolism, increase the abundance of FeOB in soil, promote the biotransformation process of As in soil, and enhance the resistance of soil to peroxide pollution (As pollution).
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Affiliation(s)
- Ziyan Qian
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
- School of Metallurgy and Environment, Central South University, Changsha, China
| | - Chuan Wu
- School of Metallurgy and Environment, Central South University, Changsha, China
- Department of Science and Environmental Studies, The Education University of Hong Kong, Tai Po, Hong Kong SAR, China
| | - Weisong Pan
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Xiaoran Xiong
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Libing Xia
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Waichin Li
- Department of Science and Environmental Studies, The Education University of Hong Kong, Tai Po, Hong Kong SAR, China
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207
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Ajilogba CF, Olanrewaju OS, Babalola OO. Plant Growth Stage Drives the Temporal and Spatial Dynamics of the Bacterial Microbiome in the Rhizosphere of Vigna subterranea. Front Microbiol 2022; 13:825377. [PMID: 35250941 PMCID: PMC8891599 DOI: 10.3389/fmicb.2022.825377] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 01/10/2022] [Indexed: 11/23/2022] Open
Abstract
Bambara groundnut (BGN) is an underutilized legume commonly found in sub-Saharan Africa. It thrives in marginal soils and is resistant to drought stress. Several studies have been carried out on the nutritional properties of BGN, but very little is known about the effects of plant growth changes and development on rhizosphere bacterial dynamics and function. This study reports on the bacterial dynamics and function in the bulk and rhizosphere soils of BGN at different growth stages (vegetative, flowering, pod-filling, and maturation stages). Aside from the maturation stage that shows distinct community structure from the other growth stages, results obtained showed no significant differences in bacterial community structure among the other growth stages. At a closer level, Actinobacteria, Proteobacteria, and Acidobacteria were dominant in rhizosphere soils at all growth stages. The bulk soil had the least average phyla abundance, while the maturity stage was characterized by the highest average phyla abundance. Rubrobacter, Acidobacterium, and Skermanella were the most predominant genus. It was observed from the analysis of operational taxonomic units that there was significant change in the bacterial structure of the rhizosphere with a higher abundance of potential plant growth-promoting rhizobacteria, at the different growth stages, which include the genera Bacillus and Acidobacterium. Biomarker analysis revealed 7 and 4 highly significant bacterial biomarkers by linear discriminant analysis effect size and random forest analysis at the maturation stage, respectively. The results obtained in this study demonstrated that the bacterial communities of BGN rhizosphere microbiome dynamics and function are influenced by the plant’s growth stages.
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Affiliation(s)
- Caroline Fadeke Ajilogba
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, South Africa
- Agricultural Research Council, Natural Resources and Engineering, Division of Agrometeorology, Pretoria, South Africa
| | - Oluwaseyi Samuel Olanrewaju
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, South Africa
| | - Olubukola Oluranti Babalola
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, South Africa
- *Correspondence: Olubukola Oluranti Babalola,
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208
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Plant-Microbe Interaction in Sustainable Agriculture: The Factors That May Influence the Efficacy of PGPM Application. SUSTAINABILITY 2022. [DOI: 10.3390/su14042253] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The indiscriminate use of chemical fertilizers and pesticides has caused considerable environmental damage over the years. However, the growing demand for food in the coming years and decades requires the use of increasingly productive and efficient agriculture. Several studies carried out in recent years have shown how the application of plant growth-promoting microbes (PGPMs) can be a valid substitute for chemical industry products and represent a valid eco-friendly alternative. However, because of the complexity of interactions created with the numerous biotic and abiotic factors (i.e., environment, soil, interactions between microorganisms, etc.), the different formulates often show variable effects. In this review, we analyze the main factors that influence the effectiveness of PGPM applications and some of the applications that make them a useful tool for agroecological transition.
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209
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Abstract
Microbial composition and functions in the rhizosphere—an important microbial hotspot—are among the most fascinating yet elusive topics in microbial ecology. We used 557 pairs of published 16S rDNA amplicon sequences from the bulk soils and rhizosphere in different ecosystems around the world to generalize bacterial characteristics with respect to community diversity, composition, and functions. The rhizosphere selects microorganisms from bulk soil to function as a seed bank, reducing microbial diversity. The rhizosphere is enriched in Bacteroidetes, Proteobacteria, and other copiotrophs. Highly modular but unstable bacterial networks in the rhizosphere (common for r-strategists) reflect the interactions and adaptations of microorganisms to dynamic conditions. Dormancy strategies in the rhizosphere are dominated by toxin–antitoxin systems, while sporulation is common in bulk soils. Functional predictions showed that genes involved in organic compound conversion, nitrogen fixation, and denitrification were strongly enriched in the rhizosphere (11–182%), while genes involved in nitrification were strongly depleted. Understanding soil microbiota dynamics is key the development of soil-based sustainable agriculture and conservation strategies. This meta-analysis shows that bulk soil functions as a seed bank for the rhizosphere, which encompasses a rich microbiota adapted to dynamic conditions in hotpots.
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210
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Ao L, Zhao M, Li X, Sun G. Different Urban Forest Tree Species Affect the Assembly of the Soil Bacterial and Fungal Community. MICROBIAL ECOLOGY 2022; 83:447-458. [PMID: 34031701 DOI: 10.1007/s00248-021-01754-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 04/11/2021] [Indexed: 06/12/2023]
Abstract
The selection of tree species used for the afforestation of urban forests is very important for maintaining the urban ecosystem, while soil microbe is one of the driving factors of material cycling in the urban forest ecosystem and for health of forests. In this study, the characteristics of surface soil bacterial and fungal community structure in four urban forests (primarily composed of Fraxinus mandshurica (Fm), Quercus mongolica (Qm), Pinus sylvestris var. mongolica (Ps), and Pinus tabulaeformis var. Mukdensis (Pt) as the main dominant tree species, respectively) were investigated by high-throughput sequencing. Our results showed that the alpha diversity of the soil microbial community in the Fm urban forest was the highest, while the lowest was in the Ps urban forest. In the bacterial community, Proteobacteria was the most predominant phylum in soils from Fm, Ps, and Pt urban forests. The most relatively abundant phylum of the Qm urban forest soil was Acidobacteria. The relative abundances of the bacterial communities at the genus level in the soil of four urban forests were significantly different. The soil bacterial communities in Ps and Pt urban forests were more similar, and Qm and Fm were also more similar. In the fungal community, Basidiomycota was the most predominant phylum in soils from Qm, Ps, and Pt urban forests. The phylum with the greatest relative abundance in the Fm urban forest soil was Ascomycota. There were differences in the fungal community between Qm, Fm, Ps, and Pt urban forests. Soil microbial community composition was affected by environmental factors: soil bacterial and fungal community compositions were significantly related to soil electrical conductivity (EC), alkali hydrolysable nitrogen (AHN), total nitrogen (TN), and total phosphorus (TP). In conclusion, the soil microbial community structure was related to both forest's tree species and soil properties.
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Affiliation(s)
- Lun Ao
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, Heilongjiang, 150040, China
| | - Meichun Zhao
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, Heilongjiang, 150040, China
| | - Xin Li
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China.
- School of Forestry, Northeast Forestry University, Harbin, Heilongjiang, 150040, China.
| | - Guangyu Sun
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, Heilongjiang, 150040, China.
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211
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Zhou Q, He R, Zhao D, Zeng J, Yu Z, Wu QL. Contrasting Patterns of the Resident and Active Rhizosphere Bacterial Communities of Phragmites Australis. MICROBIAL ECOLOGY 2022; 83:314-327. [PMID: 33956174 DOI: 10.1007/s00248-021-01767-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 04/26/2021] [Indexed: 06/12/2023]
Abstract
Rhizosphere microbes play a key role in maintaining plant health and regulating biogeochemical cycles. The active bacterial community (ABC) in rhizosphere, as a small fraction of the rhizosphere resident bacterial community (RBC), has the potential to actively participate in nutrient cycling processes at the root-sediment interface. Here, we investigated the ABC and RBC within the rhizosphere of Phragmites australis (P. australis) subjected to different environmental conditions (i.e., seasons and flooding conditions) in Lake Taihu, China. Our results indicated that RBC exhibited significantly higher alpha diversity as well as lower beta diversity than ABC. The active ratios of 16S rRNA to 16S rDNA (also RNA/DNA) of the bacterial communities in summer and winter suggested a lower proportion of potential active taxa in the rhizosphere bacterial community during summer. Network analysis showed that negative correlations in each network were observed to dominate the species correlations between the rhizosphere and bulk sediment bacterial communities. Our results revealed that niche differentiation and seasonal variation played crucial roles in driving the assembly of ABC and RBC associated with the rhizospheres of P. australis. These findings broaden our knowledge about how rhizosphere bacterial communities respond to environmental variations through changing their diversity and composition.
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Affiliation(s)
- Qi Zhou
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, China
| | - Rujia He
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, China
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, 73 East Beijing Road, Nanjing, 210008, China
| | - Dayong Zhao
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, China
| | - Jin Zeng
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, 73 East Beijing Road, Nanjing, 210008, China.
| | - Zhongbo Yu
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, China
| | - Qinglong L Wu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, 73 East Beijing Road, Nanjing, 210008, China
- Sino-Danish Centre for Education and Research, University of Chinese Academy of Sciences, Beijing, 100039, China
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212
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Jiao N, Song X, Song R, Yin D, Deng X. Diversity and structure of the microbial community in rhizosphere soil of Fritillaria ussuriensis at different health levels. PeerJ 2022; 10:e12778. [PMID: 35127284 PMCID: PMC8796711 DOI: 10.7717/peerj.12778] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 12/21/2021] [Indexed: 01/10/2023] Open
Abstract
Fritillaria wilt is a kind of soil-borne disease that causes a large reduction in the yield of Fritillaria ussuriensis. The diversity and structure of the soil microbial community are important factors affecting the health of Fritillaria ussuriensis. The analysis of the microbial community in the diseased and healthy soils provided a theoretical basis for revealing the pathological mechanism and prevention of Fritillaria wilt disease. In the present study, we sequenced the soil microorganisms from healthy (H), pathology (P) and blank (B) soil samples by Illumina MiSeq. Determined the soil physicochemical properties respectively, analyzed the soil microbial diversity and structure, and constructed single factor co-correlation networks among microbial genera. The results showed that Ascomycota (48.36%), Mortierellomycota (23.06%), Basidiomycota (19.00%), Proteobacteria (31.74%), and Acidobacteria (20.95%) were dominant in the soil. The diversity of healthy soil was significantly greater than that of diseased soil samples (P and B) (P < 0.05). The populations of Fusarium and Humicola significantly increased in the diseased soil sample (P and B) (P < 0.05). RB41 (4.74%) and Arthrobacter (3.30%) were the most abundant genera in the healthy soil. Total nitrogen (TN), available nitrogen (AN), total potassium (TK), available potassium (AK), and inorganic salt (salt) were significantly correlated with soil microbial communities (P < 0.05). The relationship between fungi and the plant was mostly positive, whereas bacteria showed the opposite trend. In conclusion, the diversity and structure of the soil microbial community were closely related to the health level of Fritillaria ussuriensis. Fusarium and Humicola affect the severity of Fritillaria wilt disease, while RB41 and Arthrobacter are the important indicators for maintaining the health of Fritillaria ussuriensis. Moreover, environmental factors greatly affect the abundance and formation of soil microbial community. The interactions in microbial communities also influence the healthy growth of Fritillaria ussuriensis.
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Affiliation(s)
- Ning Jiao
- College of Forestry, Northeast Forestry University, Harbin, China
| | - Xiaoshuang Song
- Institute of Forestry Protection, Heilongjiang Forestry Academy, Harbin, China
| | - Ruiqing Song
- College of Forestry, Northeast Forestry University, Harbin, China
| | - Dachuan Yin
- College of Forestry, Shenyang Agricultural University, Shenyang, China
| | - Xun Deng
- Institute of Forestry Protection, Heilongjiang Forestry Academy, Harbin, China
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213
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The impact of different rotation regime on the soil bacterial and fungal communities in an intensively managed agricultural region. Arch Microbiol 2022; 204:142. [PMID: 35043270 DOI: 10.1007/s00203-021-02615-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 11/26/2021] [Accepted: 11/29/2021] [Indexed: 12/12/2022]
Abstract
The continuous wheat-maize planting has led to the increase in epidemic frequency of wheat diseases under climate change. Analyzation of the soil microbial composition in different rotation crops is essential to select alternative rotation regime. This study investigated the bacterial and fungal community abundance and composition, and potential microbe-microbe interactions in three rotations, including wheat-maize → spring maize (WMFS), wheat-soybean (WS) and continuous wheat-maize (WM) planting. The results revealed that there were 110, 156, and 195 bacterial, and 17, 8, and 15 fungal operational taxonomic units respectively enriched by WMFS, WS, and WM. WM increased the relative abundance of Actinobacteria and α-Proteobacteria in wheat, and the relative abundance and copy number of genus Fusarium in maize. WMFS and WS could decrease the abundance of Fusarium in summer-crop across the growth stages and in wheat at elongation. WS also increased the copy number of ammonia-oxidizing bacteria in wheat at flowering and harvest. Network analysis revealed that WM resulted in simple and isolated wheat network with small modules dominating and none Nitrospirae and β-Proteobacteria in the main modules. WS formed interconnected and intricate wheat network with the maximum number of large modules and module connectors. Under WS, positive correlation between antagonistic Streptomyces (Actinobacteria) and genus Fusarium was found in wheat. Soil physicochemical properties explained the majority of the variation in bacterial and fungal β-diversity in wheat (P < 0.01). Rotation regime switching from WM to WMFS and WS may effectively damp the risk of wheat disease and maintain the wheat yield in intensive cereal production.
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214
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Harnessing phytomicrobiome signals for phytopathogenic stress management. J Biosci 2022. [DOI: 10.1007/s12038-021-00240-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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215
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Jia B, Chang X, Fu Y, Heng W, Ye Z, Liu P, Liu L, Al Shoffe Y, Watkins CB, Zhu L. Metagenomic analysis of rhizosphere microbiome provides insights into occurrence of iron deficiency chlorosis in field of Asian pears. BMC Microbiol 2022; 22:18. [PMID: 34996363 PMCID: PMC8742312 DOI: 10.1186/s12866-021-02432-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 12/28/2021] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Fe-deficiency chlorosis (FDC) of Asian pear plants is widespread, but little is known about the association between the microbial communities in the rhizosphere soil and leaf chlorosis. The leaf mineral concentration, leaf subcellular structure, soil physiochemical properties, and bacterial species community and distribution had been analysed to gain insights into the FDC in Asian pear plant. RESULTS The total Fe in leaves with Fe-deficiency was positively correlated with total K, Mg, S, Cu, Zn, Mo and Cl contents, but no differences of available Fe (AFe) were detected between the rhizosphere soil of chlorotic and normal plants. Degraded ribosomes and degraded thylakloid stacks in chloroplast were observed in chlorotic leaves. The annotated microbiome indicated that there were 5 kingdoms, 52 phyla, 94 classes, 206 orders, 404 families, 1,161 genera, and 3,043 species in the rhizosphere soil of chlorotic plants; it was one phylum less and one order, 11 families, 59 genera, and 313 species more than in that of normal plant. Bacterial community and distribution patterns in the rhizosphere soil of chlorotic plants were distinct from those of normal plants and the relative abundance and microbiome diversity were more stable in the rhizosphere soils of normal than in chlorotic plants. Three (Nitrospira defluvii, Gemmatirosa kalamazoonesis, and Sulfuricella denitrificans) of the top five species (N. defluvii, G. kalamazoonesis, S. denitrificans, Candidatus Nitrosoarchaeum koreensis, and Candidatus Koribacter versatilis). were the identical and aerobic in both rhizosphere soils, but their relative abundance decreased by 48, 37, and 22%, respectively, and two of them (G. aurantiaca and Ca. S. usitatus) were substituted by an ammonia-oxidizing soil archaeon, Ca. N. koreensis and a nitrite and nitrate reduction related species, Ca. K. versatilis in that of chlorotic plants, which indicated the adverse soil aeration in the rhizosphere soil of chlorotic plants. A water-impermeable tables was found to reduce the soil aeration, inhibit root growth, and cause some absorption root death from infection by Fusarium solani. CONCLUSIONS It was waterlogging or/and poor drainage of the soil may inhibit Fe uptake not the amounts of AFe in the rhizosphere soil of chlorotic plants that caused FDC in this study.
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Affiliation(s)
- Bing Jia
- School of Horticulture, Anhui Agricultural University, Hefei, 230036, Anhui, P.R. China
| | - Xiao Chang
- School of Horticulture, Anhui Agricultural University, Hefei, 230036, Anhui, P.R. China
| | - Yuanyuan Fu
- School of Horticulture, Anhui Agricultural University, Hefei, 230036, Anhui, P.R. China
| | - Wei Heng
- School of Horticulture, Anhui Agricultural University, Hefei, 230036, Anhui, P.R. China
| | - Zhenfeng Ye
- School of Horticulture, Anhui Agricultural University, Hefei, 230036, Anhui, P.R. China
| | - Pu Liu
- School of Horticulture, Anhui Agricultural University, Hefei, 230036, Anhui, P.R. China
| | - Li Liu
- School of Horticulture, Anhui Agricultural University, Hefei, 230036, Anhui, P.R. China
| | - Yosef Al Shoffe
- College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, 14853, USA
| | | | - Liwu Zhu
- School of Horticulture, Anhui Agricultural University, Hefei, 230036, Anhui, P.R. China.
- College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, 14853, USA.
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216
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Li X, Wang S, Fan Y, Zhou Z, Xu S, Zhou P, Zhou J, Wang R. Peanut Rotation and Flooding Induce Rhizobacteriome Variation With Opposing Influences on the Growth and Medicinal Yield of Corydalis yanhusuo. FRONTIERS IN PLANT SCIENCE 2022; 12:779302. [PMID: 35069636 PMCID: PMC8782247 DOI: 10.3389/fpls.2021.779302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 12/16/2021] [Indexed: 06/14/2023]
Abstract
Corydalis yanhusuo, a precious herb of the Papaveraceae family, is widely used in multiple traditional Chinese medicines for the treatment of many painful conditions, and its medicinal part is the dried tuber. Yet how to improve this plant's medicinal yield as well as its economic efficiency remains a key problem in its cultivation. The planting of C. yanhusuo in rotation with peanut (Arachis hypogaea L.) aims to improve land utilization efficiency, but the total production of tubers is severely reduced relative to fields without rotation. However, an increased yield was observed in C. yanhusuo plants grown in previously flooded fields (HR field) compared to the ones grown in the fields that had been used to cultivate peanut (PL field) or in fields without rotation or flooding (N field). Based on these phenomena, in this study, we explored the potential factors responsible for the altered growth/yield of C. yanhusuo under different field conditions. Soil physicochemical properties and the diversity and community of rhizobacteriome of C. yanhusuo were both analyzed. By testing several soil physicochemical properties, we found that the cation exchange capacity (CEC), soil organic matter (SOM), total nitrogen (TN), and pH value differed significantly among these three types of fields. 16S rRNA amplicon sequencing revealed stark differences in the composition, diversity, and potential functions of the bacterial community in the rhizosphere of C. yanhusuo plants grown in field with the peanut rotation or flooding. Notably, the Acidobacteria were enriched in the HR field, while Actinobacteria were enriched in the PL field. More importantly, further analysis showed that changed soil physicochemical properties could be one reason for why the rhizospheric bacterial community has changed; hence, soil physicochemical properties might also be affecting plant performance indirectly by regulating the rhizospheric bacterial community. The RDA analysis distinguished CEC as the most important soil physicochemical property influencing the structure and composition of the C. yanhusuo rhizobacteriome. In summary, our results suggest peanut rotation- and flooding-induced soil physicochemical properties changes would further impact the rhizobacteriome of C. yanhusuo albeit differentially, culminating in opposite effects upon the plant growth and medicinal yield of C. yanhusuo.
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Affiliation(s)
- Xiaodan Li
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
- The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
| | - Songfeng Wang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
- The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
| | - Yating Fan
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
- The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
| | - Zhe Zhou
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
- The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
| | - Sheng Xu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
- The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
| | - Penglei Zhou
- Jiangsu Jiangtong Agricultural Science and Technology Development Co., Ltd., Huaian, China
| | - Jiayu Zhou
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
- The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
| | - Ren Wang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
- The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
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217
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Wang P, Yang L, Sun J, Yang Y, Qu Y, Wang C, Liu D, Huang L, Cui X, Liu Y. Structure and Function of Rhizosphere Soil and Root Endophytic Microbial Communities Associated With Root Rot of Panax notoginseng. FRONTIERS IN PLANT SCIENCE 2022; 12:752683. [PMID: 35069616 PMCID: PMC8766989 DOI: 10.3389/fpls.2021.752683] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 12/13/2021] [Indexed: 06/14/2023]
Abstract
Panax notoginseng (Burk.) F. H. Chen is a Chinese medicinal plant of the Araliaceae family used for the treatment of cardiovascular and cerebrovascular diseases in Asia. P. notoginseng is vulnerable to root rot disease, which reduces the yield of P. notoginseng. In this study, we analyzed the rhizosphere soil and root endophyte microbial communities of P. notoginseng from different geographical locations using high-throughput sequencing. Our results revealed that the P. notoginseng rhizosphere soil microbial community was more diverse than the root endophyte community. Rhodopseudomonas, Actinoplanes, Burkholderia, and Variovorax paradoxus can help P. notoginseng resist the invasion of root rot disease. Ilyonectria mors-panacis, Pseudomonas fluorescens, and Pseudopyrenochaeta lycopersici are pathogenic bacteria of P. notoginseng. The upregulation of amino acid transport and metabolism in the soil would help to resist pathogens and improve the resistance of P. notoginseng. The ABC transporter and gene modulating resistance genes can improve the disease resistance of P. notoginseng, and the increase in the number of GTs (glycosyltransferases) and GHs (glycoside hydrolases) families may be a molecular manifestation of P. notoginseng root rot. In addition, the complete genomes of two Flavobacteriaceae species and one Bacteroides species were obtained. This study demonstrated the microbial and functional diversity in the rhizosphere and root microbial community of P. notoginseng and provided useful information for a better understanding of the microbial community in P. notoginseng root rot. Our results provide insights into the molecular mechanism underlying P. notoginseng root rot and other plant rhizosphere microbial communities.
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Affiliation(s)
- Panpan Wang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Lifang Yang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Jialing Sun
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Ye Yang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
- Yunnan Provincial Key Laboratory of Panax notoginseng, Kunming, China
- Key Laboratory of Panax notoginseng Resources Sustainable Development and Utilization of State Administration of Traditional Chinese Medicine, Kunming, China
- Kunming Key Laboratory of Sustainable Development and Utilization of Famous-Region Drug, Kunming, China
| | - Yuan Qu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
- Yunnan Provincial Key Laboratory of Panax notoginseng, Kunming, China
- Key Laboratory of Panax notoginseng Resources Sustainable Development and Utilization of State Administration of Traditional Chinese Medicine, Kunming, China
- Kunming Key Laboratory of Sustainable Development and Utilization of Famous-Region Drug, Kunming, China
| | - Chengxiao Wang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
- Yunnan Provincial Key Laboratory of Panax notoginseng, Kunming, China
- Key Laboratory of Panax notoginseng Resources Sustainable Development and Utilization of State Administration of Traditional Chinese Medicine, Kunming, China
- Kunming Key Laboratory of Sustainable Development and Utilization of Famous-Region Drug, Kunming, China
| | - Diqiu Liu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
- Yunnan Provincial Key Laboratory of Panax notoginseng, Kunming, China
- Key Laboratory of Panax notoginseng Resources Sustainable Development and Utilization of State Administration of Traditional Chinese Medicine, Kunming, China
- Kunming Key Laboratory of Sustainable Development and Utilization of Famous-Region Drug, Kunming, China
| | - Luqi Huang
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Xiuming Cui
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
- Yunnan Provincial Key Laboratory of Panax notoginseng, Kunming, China
- Key Laboratory of Panax notoginseng Resources Sustainable Development and Utilization of State Administration of Traditional Chinese Medicine, Kunming, China
- Kunming Key Laboratory of Sustainable Development and Utilization of Famous-Region Drug, Kunming, China
| | - Yuan Liu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
- Yunnan Provincial Key Laboratory of Panax notoginseng, Kunming, China
- Key Laboratory of Panax notoginseng Resources Sustainable Development and Utilization of State Administration of Traditional Chinese Medicine, Kunming, China
- Kunming Key Laboratory of Sustainable Development and Utilization of Famous-Region Drug, Kunming, China
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218
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Chen J, Li N, Chang J, Ren K, Zhou J, Yang G. Taxonomic Structure of Rhizosphere Bacterial Communities and Its Association With the Accumulation of Alkaloidal Metabolites in Sophora flavescens. Front Microbiol 2022; 12:781316. [PMID: 34970241 PMCID: PMC8712762 DOI: 10.3389/fmicb.2021.781316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 11/15/2021] [Indexed: 11/13/2022] Open
Abstract
Plant secondary metabolites (SMs) play a crucial role in plant defense against pathogens and adaptation to environmental stresses, some of which are produced from medicinal plants and are the material basis of clinical efficacy and vital indicators for quality evaluation of corresponding medicinal materials. The influence of plant microbiota on plant nutrient uptake, production, and stress tolerance has been revealed, but the associations between plant microbiota and the accumulation of SMs in medicinal plants remain largely unknown. Plant SMs can vary among individuals, which could be partly ascribed to the shift in microbial community associated with the plant host. In the present study, we sampled fine roots and rhizosphere soils of Sophora flavescens grown in four well-separated cities/counties in China and determined the taxonomic composition of rhizosphere bacterial communities using Illumina 16S amplicon sequencing. In addition, the association of the rhizosphere bacterial microbiota with the accumulation of alkaloids in the roots of S. flavescens was analyzed. The results showed that S. flavescens hosted distinct bacterial communities in the rhizosphere across geographic locations and plant ages, also indicating that geographic location was a larger source of variation than plant age. Moreover, redundancy analysis revealed that spatial, climatic (mean annual temperature and precipitation), and edaphic factors (pH and available N and P) were the key drivers that shape the rhizosphere bacterial communities. Furthermore, the results of the Mantel test demonstrated that the rhizosphere bacterial microbiota was remarkably correlated with the contents of oxymatrine, sophoridine, and matrine + oxymatrine in roots. Specific taxa belonging to Actinobacteria and Chloroflexi were identified as potential beneficial bacteria associated with the total accumulation of matrine and oxymatrine by a random forest machine learning algorithm. Finally, the structural equation modeling indicated that the Actinobacteria phylum had a direct effect on the total accumulation of matrine and oxymatrine. The present study addresses the association between the rhizosphere bacterial communities and the accumulation of alkaloids in the medicinal plant S. flavescens. Our findings may provide a basis for the quality improvement and sustainable utilization of this medicinal plant thorough rhizosphere microbiota manipulation.
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Affiliation(s)
- Jie Chen
- School of Pharmaceutical Science, Shanxi Medical University, Taiyuan, China
| | - Na Li
- School of Pharmaceutical Science, Shanxi Medical University, Taiyuan, China
| | - Jiayu Chang
- School of Pharmaceutical Science, Shanxi Medical University, Taiyuan, China
| | - Kaida Ren
- School of Pharmaceutical Science, Shanxi Medical University, Taiyuan, China
| | - Jiangtao Zhou
- School of Pharmaceutical Science, Shanxi Medical University, Taiyuan, China
| | - Guan'e Yang
- School of Pharmaceutical Science, Shanxi Medical University, Taiyuan, China
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219
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Jiang H, Lv L, Ahmed T, Jin S, Shahid M, Noman M, Osman HEH, Wang Y, Sun G, Li X, Li B. Effect of the Nanoparticle Exposures on the Tomato Bacterial Wilt Disease Control by Modulating the Rhizosphere Bacterial Community. Int J Mol Sci 2021; 23:414. [PMID: 35008839 PMCID: PMC8745216 DOI: 10.3390/ijms23010414] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/27/2021] [Accepted: 12/29/2021] [Indexed: 01/04/2023] Open
Abstract
Ralstonia Solanacearum is one of the most infectious soil-borne bacterial plant pathogens, causing tomato bacterial wilt (TBW). Nanotechnology is an emerging area of research, particularly the application of nanoparticles (NPs) as nanopesticides to manage plant disease is gaining attention nowadays. However, the interaction between NPs and rhizosphere bacterial communities remains largely elusive. This study indicated that metal NPs (CuO, ZnO, and FeO) reduced the incidence of bacterial wilt to varying degrees and affected the composition and structure of the rhizosphere bacterial community. The results revealed that the application of metal oxide NPs can improve the morphological and physiological parameters of TBW infected tomato plants. Among all, CuONPs amendments significantly increase the Chao1 and Shannon index. In the early stage (the second week), it significantly reduces the relative abundance of pathogens. However, the relative abundance of beneficial Streptomyces bacteria increased significantly, negatively correlated with the relative abundance of pathogenic bacteria. In addition, the nano-treatment group will enrich some potential beneficial bacteria such as species from Sphingomonadaceae, Rhizobiaceae, etc. In general, our research provides evidence and strategies for preventing and controlling soil-borne disease tomato bacterial wilt with metal oxide NPs.
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Affiliation(s)
- Hubiao Jiang
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (H.J.); (L.L.); (T.A.); (S.J.); (M.N.)
| | - Luqiong Lv
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (H.J.); (L.L.); (T.A.); (S.J.); (M.N.)
| | - Temoor Ahmed
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (H.J.); (L.L.); (T.A.); (S.J.); (M.N.)
| | - Shaomin Jin
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (H.J.); (L.L.); (T.A.); (S.J.); (M.N.)
| | - Muhammad Shahid
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad 38000, Pakistan;
| | - Muhammad Noman
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (H.J.); (L.L.); (T.A.); (S.J.); (M.N.)
| | | | - Yanli Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Y.W.); (G.S.)
| | - Guochang Sun
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Y.W.); (G.S.)
| | - Xuqing Li
- Hangzhou Academy of Agricultural Science, Hangzhou 310024, China
| | - Bin Li
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (H.J.); (L.L.); (T.A.); (S.J.); (M.N.)
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220
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Smulders L, Ferrero V, de la Peña E, Pozo MJ, Díaz Pendón JA, Benítez E, López-García Á. Resistance and Not Plant Fruit Traits Determine Root-Associated Bacterial Community Composition along a Domestication Gradient in Tomato. PLANTS (BASEL, SWITZERLAND) 2021; 11:plants11010043. [PMID: 35009046 PMCID: PMC8747438 DOI: 10.3390/plants11010043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/20/2021] [Accepted: 12/20/2021] [Indexed: 05/12/2023]
Abstract
Soil bacterial communities are involved in multiple ecosystem services, key in determining plant productivity. Crop domestication and intensive agricultural practices often disrupt species interactions with unknown consequences for rhizosphere microbiomes. This study evaluates whether variation in plant traits along a domestication gradient determines the composition of root-associated bacterial communities; and whether these changes are related to targeted plant traits (e.g., fruit traits) or are side effects of less-often-targeted traits (e.g., resistance) during crop breeding. For this purpose, 18 tomato varieties (wild and modern species) differing in fruit and resistance traits were grown in a field experiment, and their root-associated bacterial communities were characterised. Root-associated bacterial community composition was influenced by plant resistance traits and genotype relatedness. When only considering domesticated tomatoes, the effect of resistance on bacterial OTU composition increases, while the effect due to phylogenetic relatedness decreases. Furthermore, bacterial diversity positively correlated with plant resistance traits. These results suggest that resistance traits not selected during domestication are related to the capacity of tomato varieties to associate with different bacterial groups. Taken together, these results evidence the relationship between plant traits and bacterial communities, pointing out the potential of breeding to affect plant microbiomes.
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Affiliation(s)
- Lisanne Smulders
- Department Enviromental Protection, Estación Experimental del Zaidín (EEZ), CSIC, 18008 Granada, Spain;
- Correspondence:
| | - Victoria Ferrero
- Department of Biodiversity and Environmental Management, Campus de Vegazana s/n, University of León, 24071 León, Spain;
| | - Eduardo de la Peña
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium;
- Department Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín (EEZ), CSIC, 18008 Granada, Spain; (M.J.P.); (Á.L.-G.)
| | - María J. Pozo
- Department Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín (EEZ), CSIC, 18008 Granada, Spain; (M.J.P.); (Á.L.-G.)
| | - Juan Antonio Díaz Pendón
- Finca Experimental “La Mayora” CSIC, Instituto de Hortofruticultura Subtropical y Mediterránea (IHSM-UMA-CSIC), 29750 Málaga, Spain;
| | - Emilio Benítez
- Department Enviromental Protection, Estación Experimental del Zaidín (EEZ), CSIC, 18008 Granada, Spain;
| | - Álvaro López-García
- Department Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín (EEZ), CSIC, 18008 Granada, Spain; (M.J.P.); (Á.L.-G.)
- Department Animal Biology, Plant Biology and Ecology, Universidad de Jaén, 23071 Jaén, Spain
- Instituto Interuniversitario de Investigación del Sistema Tierra en Andalucía (IISTA), 18006 Granada, Spain
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Zhang J, Ling J, Zhou W, Zhang W, Yang F, Wei Z, Yang Q, Zhang Y, Dong J. Biochar Addition Altered Bacterial Community and Improved Photosynthetic Rate of Seagrass: A Mesocosm Study of Seagrass Thalassia hemprichii. Front Microbiol 2021; 12:783334. [PMID: 34925287 PMCID: PMC8678274 DOI: 10.3389/fmicb.2021.783334] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 11/08/2021] [Indexed: 11/13/2022] Open
Abstract
Seagrass meadows, as typical “blue carbon” ecosystems, play critical ecological roles in the marine ecosystem and decline every year. The application of biochar in soil has been proposed as a potential soil amendment to improve soil quality and mitigate global climate change. The effects of biochar on soil bacterial activities are integrally linked to the potential of biochar in achieving these benefits. However, biochar has been rarely applied in marine ecosystems. Whether the application of biochar could work on the seagrass ecosystem remained unknown. In this study, we investigated the responses of sediment and rhizosphere bacterial communities of seagrass Thalassia hemprichii to the biochar addition derived from maize at ratios of 5% by dry weight in the soil during a one-month incubation. Results indicated that the biochar addition significantly changed the sedimental environment with increasing pH, total phosphorus, and total kalium while total nitrogen decreased. Biochar addition significantly altered both the rhizosphere and sediment bacterial community compositions. The significant changes in rhizosphere bacterial community composition occurred after 30days of incubation, while the significant variations in sediment bacterial community composition distinctly delayed than in sediment occurred on the 14th day. Biochar application improved nitrification and denitrification, which may accelerate nitrogen cycling. As a stabilizer to communities, biochar addition decreased the importance of deterministic selection in sediment and changed the bacterial co-occurrence pattern. The biochar addition may promote seagrass photosynthesis and growth by altering the bacterial community compositions and improving nutrient circulation in the seagrass ecosystem, contributing to the seagrass health improvement. This study provided a theoretical basis for applying biochar to the seagrass ecosystem and shed light on the feasible application of biochar in the marine ecosystem. ![]()
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Affiliation(s)
- Jian Zhang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.,Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Oceanology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Sanya, China.,Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China.,College of Marine Science, University of Chinese Academy of Sciences, Beijing, China
| | - Juan Ling
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.,Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Oceanology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Sanya, China.,Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China.,Sanya National Marine Ecosystem Research Station, Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya, China
| | - Weiguo Zhou
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.,Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Oceanology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Sanya, China.,Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
| | - Wenqian Zhang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.,Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Oceanology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Sanya, China.,Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China.,College of Marine Science, University of Chinese Academy of Sciences, Beijing, China
| | - Fangfang Yang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.,Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Oceanology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Sanya, China.,Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
| | - Zhangliang Wei
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.,Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Oceanology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Sanya, China.,Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
| | - Qingsong Yang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.,Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Oceanology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Sanya, China.,Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China.,Sanya National Marine Ecosystem Research Station, Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya, China
| | - Ying Zhang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.,Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Oceanology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Sanya, China.,Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
| | - Junde Dong
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.,Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Oceanology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Sanya, China.,Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China.,Sanya National Marine Ecosystem Research Station, Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya, China
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Abstract
We develop a method to artificially select for rhizosphere microbiomes that confer salt tolerance to the model grass Brachypodium distachyon grown under sodium salt stress or aluminum salt stress. In a controlled greenhouse environment, we differentially propagated rhizosphere microbiomes between plants of a nonevolving, highly inbred plant population; therefore, only microbiomes evolved in our experiment, but the plants did not evolve in parallel. To maximize microbiome perpetuation when transplanting microbiomes between plants and, thus, maximize response to microbiome selection, we improved earlier methods by (i) controlling microbiome assembly when inoculating seeds at the beginning of each selection cycle; (ii) fractionating microbiomes before transfer between plants to harvest, perpetuate, and select on only bacterial and viral microbiome components; (iii) ramping of salt stress gradually from minor to extreme salt stress with each selection cycle to minimize the chance of overstressing plants; (iv) using two nonselection control treatments (e.g., nonselection microbial enrichment and null inoculation) that permit comparison to the improving fitness benefits that selected microbiomes impart on plants. Unlike previous methods, our selection protocol generated microbiomes that enhance plant fitness after only 1 to 3 rounds of microbiome selection. After nine rounds of microbiome selection, the effect of microbiomes selected to confer tolerance to aluminum salt stress was nonspecific (these artificially selected microbiomes equally ameliorate sodium and aluminum salt stresses), but the effect of microbiomes selected to confer tolerance to sodium salt stress was specific (these artificially selected microbiomes do not confer tolerance to aluminum salt stress). Plants with artificially selected microbiomes had 55 to 205% greater seed production than plants with unselected control microbiomes. IMPORTANCE We developed an experimental protocol that improves earlier methods of artificial selection on microbiomes and then tested the efficacy of our protocol to breed root-associated bacterial microbiomes that confer salt tolerance to a plant. Salt stress limits growth and seed production of crop plants, and artificially selected microbiomes conferring salt tolerance may ultimately help improve agricultural productivity. Unlike previous experiments of microbiome selection, our selection protocol generated microbiomes that enhance plant productivity after only 1 to 3 rounds of artificial selection on root-associated microbiomes, increasing seed production under extreme salt stress by 55 to 205% after nine rounds of microbiome selection. Although we artificially selected microbiomes under controlled greenhouse conditions that differ from outdoor conditions, increasing seed production by 55 to 205% under extreme salt stress is a remarkable enhancement of plant productivity compared to traditional plant breeding. We describe a series of additional experimental protocols that will advance insights into key parameters that determine efficacy and response to microbiome selection.
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223
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Nwachukwu BC, Ayangbenro AS, Babalola OO. Comparative study of microbial structure and functional profile of sunflower rhizosphere grown in two fields. BMC Microbiol 2021; 21:337. [PMID: 34886803 PMCID: PMC8656072 DOI: 10.1186/s12866-021-02397-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 11/24/2021] [Indexed: 12/28/2022] Open
Abstract
Background Microbial communities inhabiting the rhizosphere play pivotal roles in determining plant health and yield. Manipulation of the rhizosphere microbial community is a promising means to enhance the productivity of economically viable and important agricultural crops such as sunflower (Helianthus annuus). This study was designed to gain insights into the taxonomic and functional structures of sunflower rhizosphere and bulk soil microbiome at two different locations (Sheila and Itsoseng) in South Africa. Results Microbial DNA extracted from the sunflower rhizosphere and bulk soils was subjected to next-generation sequencing using 16S amplicon sequencing technique. Firmicutes, Actnobacteria and Proteobacteria predominated sunflower rhizosphere soils. Firmicutes, Cyanobacteria, Deinococcus-Thermus and Fibrobacteres were positively influenced by Na+ and clay content, while Actinobacteria, Thaumarchaeota, Bacteroidetes, Planctomycetes, Aquificae and Chloroflexi were positively influenced by soil resistivity (Res) and Mg2+. The community-level physiological profiling (CLPP) analysis showed that the microbial communities in SHR and ITR used the amino acids tryptophan and malic acid efficiently. The metabolisms of these carbon substrates may be due to the dominant nature of some of the organisms, such as Actinobacteria in the soils. Conclusion The CLPP measurements of soil from sunflower rhizosphere were different from those of the bulk soil and the degree of the variations were based on the type of carbon substrates and the soil microbial composition. This study has shown the presence of certain taxa of rhizobacteria in sunflower rhizosphere which were positively influenced by Na+ and Mg2+, and taxa obtained from SHR and ITR were able to effectively utilized tryptophan and malic acid. Many unclassified microbial groups were also discovered and it is therefore recommended that efforts should further be made to isolate, characterize and identify these unclassified microbial species, as it might be plausible to discover new microbial candidates that can further be harnessed for biotechnological purpose.
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Affiliation(s)
- Blessing Chidinma Nwachukwu
- Food Security and Safety Niche, Faculty of Natural and Agricultural Science, Private Mail Bag X2046, North-West University, Mmabatho, 2735, South Africa
| | - Ayansina Segun Ayangbenro
- Food Security and Safety Niche, Faculty of Natural and Agricultural Science, Private Mail Bag X2046, North-West University, Mmabatho, 2735, South Africa
| | - Olubukola Oluranti Babalola
- Food Security and Safety Niche, Faculty of Natural and Agricultural Science, Private Mail Bag X2046, North-West University, Mmabatho, 2735, South Africa.
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224
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Soil bacterial community composition and diversity response to land conversion is depth-dependent. Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2021.e01923] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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225
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Liu Y, Wang H, Peng Z, Li D, Chen W, Jiao S, Wei G. Regulation of root secondary metabolites by partial root-associated microbiotas under the shaping of licorice ecotypic differentiation in northwest China. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:2093-2109. [PMID: 34655272 DOI: 10.1111/jipb.13179] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 10/08/2021] [Indexed: 06/13/2023]
Abstract
Interactions between plant hosts and their microbiotas are becoming increasingly evident, while the effects of plant communities on microbial communities in different geographic environments are poorly understood. Here, the differentiation of licorice plant ecotypes and the distribution of root-associated microbiotas were investigated across five sampling sites in northwest China. The interactions between the environment, plant and microbial communities, and their effects on licorice root secondary metabolites, were elucidated. The plant community was clearly differentiated into distinct ecotypes based on genotyping-by-sequencing and was primarily driven by geographic distance and available soil nitrogen. The bulk soil and root-associated microbiotas (rhizosphere soil and root endosphere) partially correlated with plant community, but all were significantly discriminated by plant clade. Moreover, these microbiotas were explained to different extents by distinct combinations of environment, geography, and plant community. Similarly, three structural equation models showed that licorice root secondary metabolites were complicatedly modulated by multiple abiotic and biotic factors, and were mostly explained by these factors in the rhizosphere model. Collectively, the results provide novel insights into the role of environment-plant-microbiota interactions in regulating root secondary metabolites. That should be accounted for when selecting appropriate licorice planting sites and management measures.
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Affiliation(s)
- Yang Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, Yangling, 712100, China
| | - Hao Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, Yangling, 712100, China
| | - Ziheng Peng
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, Yangling, 712100, China
| | - Da Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, Yangling, 712100, China
| | - Weimin Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, Yangling, 712100, China
| | - Shuo Jiao
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, Yangling, 712100, China
| | - Gehong Wei
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, Yangling, 712100, China
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226
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Dilla-Ermita CJ, Lewis RW, Sullivan TS, Hulbert SH. Wheat Genotype-Specific Recruitment of Rhizosphere Bacterial Microbiota Under Controlled Environments. FRONTIERS IN PLANT SCIENCE 2021; 12:718264. [PMID: 34925393 PMCID: PMC8671755 DOI: 10.3389/fpls.2021.718264] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 10/26/2021] [Indexed: 06/14/2023]
Abstract
Plants recruit beneficial microbial communities in the rhizosphere that are involved in a myriad of ecological services, such as improved soil quality, nutrient uptake, abiotic stress tolerance, and soil-borne disease suppression. Disease suppression caused by rhizosphere microbiomes has been important in managing soil-borne diseases in wheat. The low heritability of resistance in wheat to soil-borne diseases like Rhizoctonia root rot has made management of these diseases challenging, particularly in direct-seeded systems. Identification of wheat genotypes that recruit rhizosphere microbiomes that promote improved plant fitness and suppression of the pathogen could be an alternative approach to disease management through genetic improvement. Several growth chamber cycling experiments were conducted using six winter wheat genotypes (PI561725, PI561727, Eltan, Lewjain, Hill81, Madsen) to determine wheat genotypes that recruit suppressive microbiomes. At the end of the third cycle, suppression assays were done by inoculating R. solani into soils previously cultivated with specific wheat genotypes to test suppression of the pathogen by the microbiome. Microbiome composition was characterized by sequencing of 16S rDNA (V1-V3 region). Among the growth cycling lengths, 160-day growth cycles exhibited the most distinct rhizosphere microbiomes among the wheat genotypes. Suppression assays showed that rhizosphere microbiomes of different wheat genotypes resulted in significant differences in shoot length (value of p=0.018) and had an impact on the pathogenicity of R. solani, as observed in the reduced root disease scores (value of p=0.051). Furthermore, soils previously cultivated with the ALMT1 isogenic lines PI561725 and PI561727 exhibited better seedling vigor and reduced root disease. Microbiome analysis showed that Burkholderiales taxa, specifically Janthinobacterium, are differentially abundant in PI561727 and PI561725 cultivated soils and are associated with reduced root disease and better growth. This study demonstrates that specific wheat genotypes recruit different microbiomes in growth chamber conditions but the microbial community alterations were quite different from those previously observed in field plots, even though the same soils were used. Genotype selection or development appears to be a viable approach to controlling soil-borne diseases in a sustainable manner, and controlled environment assays can be used to see genetic differences but further work is needed to explain differences seen between growth chamber and field conditions.
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Affiliation(s)
| | - Ricky W Lewis
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States
| | - Tarah S Sullivan
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States
| | - Scot H Hulbert
- Department of Plant Pathology, Washington State University, Pullman, WA, United States
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States
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227
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Kumar A, Dubey A, Malla MA, Dames J. Pyrosequencing and phenotypic microarray to decipher bacterial community variation in Sorghum bicolor (L.) Moench rhizosphere. CURRENT RESEARCH IN MICROBIAL SCIENCES 2021; 2:100025. [PMID: 34841316 PMCID: PMC8610313 DOI: 10.1016/j.crmicr.2021.100025] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 02/18/2021] [Accepted: 02/21/2021] [Indexed: 11/17/2022] Open
Abstract
Different cultivation practices and climatic conditions play an important role in governing and modulating soil microbial communities. This work, investigated the changes in bacterial community composition at taxonomic and functional level in rhizosphere soil of sweet sorghum under extensive cultivation practices at three different field sites of South Africa. 16S rRNA amplicon sequencing data revealed that at the phylum level, the dominant group was Cyanobacteria with a relative abundance of 63.3%, 71.8% and 81.6% from ASHSOIL1, ASHSOIL2, and ASHSOIL3, respectively. Community-level physiological profiling (CLPP) analysis revealed that the metabolic activity of the bacterial community in ASHSOIL3 was the highest, followed by ASHSOIL1 and ASHSOIL2. Overall, this study showed that soil pH, nutrient availability and cultivation practices played significant roles in governing the bacterial community composition in sorghum rhizosphere.
Different cultivation practices and climatic conditions play an important role in governing and modulating soil microbial communities as well as soil health. This study investigated, for the first time, keystone microbial taxa inhabiting the rhizosphere of sweet sorghum (Sorghum bicolor) under extensive cultivation practices at three different field sites of South Africa (North West-South (ASHSOIL1); Mpumalanga-West – (ASHSOIL2); and Free State-North West – (ASHSOIL3)). Soil analysis of these sites revealed differences in P, K, Mg, and pH. 16S rRNA amplicon sequencing data revealed that the rhizosphere bacterial microbiome differed significantly both in the structure and composition across the samples. The sequencing data revealed that at the phylum level, the dominant group was Cyanobacteria with a relative abundance of 63.3%, 71.8%, and 81.6% from ASHSOIL1, ASHSOIL2, and ASHSOIL3, respectively. Putative metabolic requirements analyzed by METAGENassist software revealed the ASHSOIL1 sample as the prominent ammonia degrader (21.1%), followed by ASHSOIL3 (17.3%) and ASHSOIL2 (11.1%). The majority of core-microbiome taxa were found to be from Cyanobacteria, Bacteroidetes, and Proteobacteria. Functionally, community-level physiological profiling (CLPP) analysis revealed that the metabolic activity of the bacterial community in ASHSOIL3 was the highest, followed by ASHSOIL1 and ASHSOIL2. This study showed that soil pH and nutrient availability and cultivation practices played significant roles in governing the bacterial community composition in the sorghum rhizosphere across the different sites.
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Affiliation(s)
- Ashwani Kumar
- Mycorrhizal Research Laboratory, Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa
- Metagenomics and Secretomics Research laboratory, Department of Botany, Dr. Harisingh Gour University (Central University), Sagar 470003, MP, India
- Corresponding author at: Metagenomics and Secretomics Research laboratory, Department of Botany, Dr. Harisingh Gour University (Central University), Sagar 470003, MP, India.
| | - Anamika Dubey
- Metagenomics and Secretomics Research laboratory, Department of Botany, Dr. Harisingh Gour University (Central University), Sagar 470003, MP, India
| | - Muneer Ahmad Malla
- Department of Zoology, Dr. Harisingh Gour University (Central University), Sagar 470003, MP, India
| | - Joanna Dames
- Mycorrhizal Research Laboratory, Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa
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228
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Host genotype structures the microbiome of a globally dispersed marine phytoplankton. Proc Natl Acad Sci U S A 2021; 118:2105207118. [PMID: 34810258 PMCID: PMC8640791 DOI: 10.1073/pnas.2105207118] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/08/2021] [Indexed: 11/18/2022] Open
Abstract
Microscale interactions between marine phytoplankton and their bacterial microbiomes can influence ecosystem functioning and global biogeochemical cycling through complex exchanges of metabolites and sophisticated ecological processes. Previous investigation of the phytoplankton microbiome has not focused on the role of a host’s underlying genetic background. Through examination of a single phytoplankton species’ microbiome across the global ocean, we found that host genotype strongly influenced microbiome community composition, with associations that potentially persist across generations and ocean basins but assemble rapidly (within days). The long-term association of microbiomes with host genetic background could explain the evolution and maintenance of intricate phytoplankton–bacteria interactions. Phytoplankton support complex bacterial microbiomes that rely on phytoplankton-derived extracellular compounds and perform functions necessary for algal growth. Recent work has revealed sophisticated interactions and exchanges of molecules between specific phytoplankton–bacteria pairs, but the role of host genotype in regulating those interactions is unknown. Here, we show how phytoplankton microbiomes are shaped by intraspecific genetic variation in the host using global environmental isolates of the model phytoplankton host Thalassiosira rotula and a laboratory common garden experiment. A set of 81 environmental T. rotula genotypes from three ocean basins and eight genetically distinct populations did not reveal a core microbiome. While no single bacterial phylotype was shared across all genotypes, we found strong genotypic influence of T. rotula, with microbiomes associating more strongly with host genetic population than with environmental factors. The microbiome association with host genetic population persisted across different ocean basins, suggesting that microbiomes may be associated with host populations for decades. To isolate the impact of host genotype on microbiomes, a common garden experiment using eight genotypes from three distinct host populations again found that host genotype influenced microbial community composition, suggesting that a process we describe as genotypic filtering, analogous to environmental filtering, shapes phytoplankton microbiomes. In both the environmental and laboratory studies, microbiome variation between genotypes suggests that other factors influenced microbiome composition but did not swamp the dominant signal of host genetic background. The long-term association of microbiomes with specific host genotypes reveals a possible mechanism explaining the evolution and maintenance of complex phytoplankton–bacteria chemical exchanges.
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229
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Yin F, Zhang F, Wang H. Rhizosphere bacteria community and functions under typical natural halophyte communities in North China salinized areas. PLoS One 2021; 16:e0259515. [PMID: 34762689 PMCID: PMC8584676 DOI: 10.1371/journal.pone.0259515] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 10/20/2021] [Indexed: 11/18/2022] Open
Abstract
Soil salinity is a serious environmental issue in arid China. Halophytes show extreme salt tolerance and are grow in saline-alkaline environments. There rhizosphere have complex bacterial communities, which mediate a variety of interactions between plants and soil. High-throughput sequencing was used to investigated rhizosphere bacterial community changes under the typical halophyte species in arid China. Three typical halophytes were Leymus chinensis (LC), Puccinellia tenuiflora (PT), Suaeda glauca (SG). The dominant phyla were Proteobacteria, Actinobacteria, Chloroflexi, Gemmatimonadetes, Acidobacteria and Bacteroidetes, Suaeda glauca rhizosphere has stronger enrichment of Nitrospirae and Cyanobacteria. The Ace, Chao and Shannon indices were significantly higher in soils under LC and SG (P<0.05). Functional predictions, based on 16S rRNA gene by PICRUSt, indicated that Energy metabolism, Amino acid metabolism, Carbohydrate metabolism and Fatty acid metabolism are dominant bacterial functions in three halophytes rhizosphere soil. Carbon metabolism, Oxidative phosphorylation, Methane metabolism, Sulfur metabolism and Nitrogen metabolism in SG were significantly higher than that in LC and PT. Regression analysis revealed that rhizosphere soil bacterial community structure is influenced by soil organic matter (SOM) and soil water content (SWC), while soil bacterial community diversity is affected by soil pH. This study contributes to our understanding of the distribution characteristics and metabolic functions under different halophyte rhizosphere bacterial communities, and will provide references for the use of rhizosphere bacteria to regulate the growth of halophytes and ecological restoration of saline soil.
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Affiliation(s)
- Fating Yin
- Agricultural College, Shihezi University, Shihezi City, China
- Key Laboratory of Oasis Eco-agriculture, Xinjiang Production and Construction Corps, Shihezi University, Shihezi, Xinjiang, China
| | - Fenghua Zhang
- Agricultural College, Shihezi University, Shihezi City, China
- Key Laboratory of Oasis Eco-agriculture, Xinjiang Production and Construction Corps, Shihezi University, Shihezi, Xinjiang, China
- * E-mail:
| | - Haoran Wang
- Agricultural College, Shihezi University, Shihezi City, China
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Liu Q, Xie S, Zhao X, Liu Y, Xing Y, Dao J, Wei B, Peng Y, Duan W, Wang Z. Drought Sensitivity of Sugarcane Cultivars Shapes Rhizosphere Bacterial Community Patterns in Response to Water Stress. Front Microbiol 2021; 12:732989. [PMID: 34745035 PMCID: PMC8568056 DOI: 10.3389/fmicb.2021.732989] [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: 06/29/2021] [Accepted: 09/16/2021] [Indexed: 12/13/2022] Open
Abstract
Rhizosphere bacteria, the main functional microorganisms inhabiting the roots of terrestrial plants, play important roles in regulating plant growth and environmental stress resistance. However, limited information is available regarding changes occurring within the structure of the root microbial community and the response mechanisms of host plants that improve adaptability to drought stress. In this study, we conducted an experiment on two sugarcane varieties with different drought tolerance levels under drought and control treatments and analyzed the rhizosphere bacterial communities using 16S rRNA high-throughput sequencing. Correlation analysis results clarified the influence of various factors on the rhizosphere bacterial community structure. Drought stress reduced the diversity of the bacterial community in the rhizosphere of sugarcane. Interestingly, the bacterial community of the drought-sensitive sugarcane cultivar GT39 changed more than that of the drought-tolerant cultivar ZZ9. In addition, ZZ9 had a high abundance of drought-resistant bacteria in the rhizosphere under optimal soil water conditions, whereas GT39 accumulated a large number of drought-resistant bacteria only under drought stress. GT39 mainly relied on Actinobacteria in its response to drought stress, and the abundance of this phylum was positively correlated with soil acid phosphatase and protease levels. In contrast, ZZ9 mainly relied on Bacilli in its response to drought stress, and the abundance of this class was positively correlated with only soil acid phosphatase levels. In conclusion, drought stress can significantly reduce the bacterial diversity and increase the abundance of drought-resistant bacteria in the sugarcane rhizosphere. The high abundance of drought-resistant bacteria in the rhizosphere of drought-tolerant cultivars under non-drought conditions is an important factor contributing to the high drought adaptability of these cultivars. Moreover, the core drought-resistant bacteria of the sugarcane rhizosphere and root exudates jointly affect the resistance of sugarcane to drought.
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Affiliation(s)
- Qi Liu
- Guangxi Key Laboratory of Sugarcane Biology, Nanning, China.,State Key Laboratory for Conservation & Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China.,College of Agronomy, Guangxi University, Nanning, China
| | - Sasa Xie
- Guangxi Key Laboratory of Sugarcane Biology, Nanning, China.,State Key Laboratory for Conservation & Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China.,College of Agronomy, Guangxi University, Nanning, China
| | - Xiaowen Zhao
- Guangxi Key Laboratory of Sugarcane Biology, Nanning, China.,State Key Laboratory for Conservation & Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China.,College of Agronomy, Guangxi University, Nanning, China
| | - Yue Liu
- Guangxi Key Laboratory of Sugarcane Biology, Nanning, China.,State Key Laboratory for Conservation & Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China.,College of Agronomy, Guangxi University, Nanning, China
| | - Yuanjun Xing
- Guangxi Key Laboratory of Sugarcane Biology, Nanning, China.,State Key Laboratory for Conservation & Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China.,College of Agronomy, Guangxi University, Nanning, China
| | - Jicao Dao
- Guangxi Key Laboratory of Sugarcane Biology, Nanning, China.,State Key Laboratory for Conservation & Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China.,College of Agronomy, Guangxi University, Nanning, China
| | - Beilei Wei
- Guangxi Key Laboratory of Sugarcane Biology, Nanning, China.,State Key Laboratory for Conservation & Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China.,College of Agronomy, Guangxi University, Nanning, China
| | - Yunchang Peng
- Guangxi Key Laboratory of Sugarcane Biology, Nanning, China.,State Key Laboratory for Conservation & Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China.,College of Agronomy, Guangxi University, Nanning, China
| | - Weixing Duan
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Ziting Wang
- Guangxi Key Laboratory of Sugarcane Biology, Nanning, China.,State Key Laboratory for Conservation & Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China.,College of Agronomy, Guangxi University, Nanning, China
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231
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Johnston-Monje D, Gutiérrez JP, Lopez-Lavalle LAB. Seed-Transmitted Bacteria and Fungi Dominate Juvenile Plant Microbiomes. Front Microbiol 2021; 12:737616. [PMID: 34745040 PMCID: PMC8569520 DOI: 10.3389/fmicb.2021.737616] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 09/13/2021] [Indexed: 11/13/2022] Open
Abstract
Plant microbiomes play an important role in agricultural productivity, but there is still much to learn about their provenance, diversity, and organization. In order to study the role of vertical transmission in establishing the bacterial and fungal populations of juvenile plants, we used high-throughput sequencing to survey the microbiomes of seeds, spermospheres, rhizospheres, roots, and shoots of the monocot crops maize (B73), rice (Nipponbare), switchgrass (Alamo), Brachiaria decumbens, wheat, sugarcane, barley, and sorghum; the dicot crops tomato (Heinz 1706), coffee (Geisha), common bean (G19833), cassava, soybean, pea, and sunflower; and the model plants Arabidopsis thaliana (Columbia-0) and Brachypodium distachyon (Bd21). Unsterilized seeds were planted in either sterile sand or farm soil inside hermetically sealed jars, and after as much as 60 days of growth, DNA was extracted to allow for amplicon sequence-based profiling of the bacterial and fungal populations that developed. Seeds of most plants were dominated by Proteobacteria and Ascomycetes, with all containing operational taxonomic units (OTUs) belonging to Pantoea and Enterobacter. All spermospheres also contained DNA belonging to Pseudomonas, Bacillus, and Fusarium. Despite having only seeds as a source of inoculum, all plants grown on sterile sand in sealed jars nevertheless developed rhizospheres, endospheres, and phyllospheres dominated by shared Proteobacteria and diverse fungi. Compared to sterile sand-grown seedlings, growth on soil added new microbial diversity to the plant, especially to rhizospheres; however, all 63 seed-transmitted bacterial OTUs were still present, and the most abundant bacteria (Pantoea, Enterobacter, Pseudomonas, Klebsiella, and Massilia) were the same dominant seed-transmitted microbes observed in sterile sand-grown plants. While most plant mycobiome diversity was observed to come from soil, judging by read abundance, the dominant fungi (Fusarium and Alternaria) were also vertically transmitted. Seed-transmitted fungi and bacteria appear to make up the majority of juvenile crop plant microbial populations by abundance, and based on occupancy, there seems to be a pan-angiosperm seed-transmitted core bacterial microbiome. Further study of these seed-transmitted microbes will be important to understand their role in plant growth and health, as well as their fate during the plant life cycle and may lead to innovations for agricultural inoculant development.
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Affiliation(s)
- David Johnston-Monje
- MaxPlanck Tandem Group in Plant Microbial Ecology, Universidad del Valle, Cali, Colombia.,International Center for Tropical Agriculture, Palmira, Colombia.,Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
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232
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Gao P, Song B, Xu R, Sun X, Lin H, Xu F, Li B, Sun W. Structure and variation of root-associated bacterial communities of Cyperus rotundus L. in the contaminated soils around Pb/Zn mine sites. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:58523-58535. [PMID: 34115291 DOI: 10.1007/s11356-021-14595-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 05/24/2021] [Indexed: 06/12/2023]
Abstract
Soil contamination due to mining activities is a great concern in China. Although the effects of mining pollution resulting in changes of soil characteristics and the microbiome have been documented, studies on the responses of plant root-associated microbial assemblages remain scarce. In this work, we collected bulk soil, rhizosphere soil, and root endosphere samples of Cyperus rotundus L (Cyp) plants from two Pb/Zn mines, of which, one was abandoned (SL) and the other was active (GD), to investigate the bacterial community responses across different site contamination levels and Cyp plant compartments. For comparison, one unpolluted site (SD) was included. Results revealed that soils from the SL and GD sites were seriously contaminated by metal(loid)s, including Pb, Zn, As, and Sb. Bacterial richness and diversity depended on the sampling site and plant compartment. All sample types from the SL site had the lowest bacterial diversities and their bacterial communities also exhibited distinct patterns compared to GD and SD samples. As for the specific sampling site, bacterial communities from the root endosphere exhibited different patterns from those in bulk and rhizosphere soil. Compared to the GD and SD sites, the root endosphere and the rhizosphere soil from the SL site shared core microbes, including Halomonas, Pelagibacterium, and Chelativorans, suggesting that they play key roles in Cyp plant survival in such harsh environments.
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Affiliation(s)
- Pin Gao
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, 808 Tianyuan Road, Guangzhou, 510650, Guangdong, China
| | - Benru Song
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, 808 Tianyuan Road, Guangzhou, 510650, Guangdong, China
| | - Rui Xu
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, 808 Tianyuan Road, Guangzhou, 510650, Guangdong, China
| | - Xiaoxu Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, 808 Tianyuan Road, Guangzhou, 510650, Guangdong, China
| | - Hanzhi Lin
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, 808 Tianyuan Road, Guangzhou, 510650, Guangdong, China
| | - Fuqing Xu
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, 808 Tianyuan Road, Guangzhou, 510650, Guangdong, China
| | - Baoqin Li
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, 808 Tianyuan Road, Guangzhou, 510650, Guangdong, China
| | - Weimin Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, 808 Tianyuan Road, Guangzhou, 510650, Guangdong, China.
- School of Environment, Henan Normal University, Xinxiang, Henan, China.
- Key Laboratory of Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, Henan Normal University, Xinxiang, Henan, China.
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233
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Deng S, Caddell DF, Xu G, Dahlen L, Washington L, Yang J, Coleman-Derr D. Genome wide association study reveals plant loci controlling heritability of the rhizosphere microbiome. THE ISME JOURNAL 2021; 15:3181-3194. [PMID: 33980999 PMCID: PMC8528814 DOI: 10.1038/s41396-021-00993-z] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 04/02/2021] [Accepted: 04/20/2021] [Indexed: 02/03/2023]
Abstract
Host genetics has recently been shown to be a driver of plant microbiome composition. However, identifying the underlying genetic loci controlling microbial selection remains challenging. Genome-wide association studies (GWAS) represent a potentially powerful, unbiased method to identify microbes sensitive to the host genotype and to connect them with the genetic loci that influence their colonization. Here, we conducted a population-level microbiome analysis of the rhizospheres of 200 sorghum genotypes. Using 16S rRNA amplicon sequencing, we identify rhizosphere-associated bacteria exhibiting heritable associations with plant genotype, and identify significant overlap between these lineages and heritable taxa recently identified in maize. Furthermore, we demonstrate that GWAS can identify host loci that correlate with the abundance of specific subsets of the rhizosphere microbiome. Finally, we demonstrate that these results can be used to predict rhizosphere microbiome structure for an independent panel of sorghum genotypes based solely on knowledge of host genotypic information.
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Affiliation(s)
- Siwen Deng
- grid.47840.3f0000 0001 2181 7878Department of Plant and Microbial Biology, University of California, Berkeley, CA USA ,grid.465232.4Plant Gene Expression Center, USDA-ARS, Albany, CA USA
| | | | - Gen Xu
- grid.24434.350000 0004 1937 0060Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE USA ,grid.24434.350000 0004 1937 0060Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE USA
| | - Lindsay Dahlen
- grid.47840.3f0000 0001 2181 7878Department of Plant and Microbial Biology, University of California, Berkeley, CA USA ,grid.27860.3b0000 0004 1936 9684Present Address: Department of Plant Sciences, University of California, Davis, CA USA
| | - Lorenzo Washington
- grid.47840.3f0000 0001 2181 7878Department of Plant and Microbial Biology, University of California, Berkeley, CA USA
| | - Jinliang Yang
- grid.24434.350000 0004 1937 0060Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE USA ,grid.24434.350000 0004 1937 0060Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE USA
| | - Devin Coleman-Derr
- grid.47840.3f0000 0001 2181 7878Department of Plant and Microbial Biology, University of California, Berkeley, CA USA ,grid.465232.4Plant Gene Expression Center, USDA-ARS, Albany, CA USA
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234
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Wang X, Wang J, Zhao YG, Maqbool F, Guo L, Gao M, Jin C, Ji J. Control of toxic sulfide in mariculture environment by iron-coated ceramsite and immobilized sulfur oxidizing bacteria. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 793:148658. [PMID: 34328974 DOI: 10.1016/j.scitotenv.2021.148658] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/18/2021] [Accepted: 06/21/2021] [Indexed: 06/13/2023]
Abstract
Hydrogen sulfide (H2S) is considered one of the serious toxic pollutants in mariculture environment. Consequently, it is necessary to develop an effective strategy to prevent the production of sulfide. In this study, we modified the ceramsite with iron (ICC) and prepared a microbial agent, i.e., the immobilized sulfur-oxidizing-bacterium on the ICC (SICC), the microbial agent was following dosed in the simulated mariculture systems to control the sulfide pollutant. Results showed that the sulfide removal capacity of the new material ICC reached to 3.42 mg S g-1 in 24 h. Comparably, the microbial agent SICC presented a stable capability in oxidizing sulfide and the sulfide removal was above 65% in test media feeding with 600 mg L-1 sulfide even after five times of recycling. The microcosm experiments conducted in the simulated mariculture systems showed that the application of the ICC together with the SICC was able to quickly remove the existing sulfide and persistently inhibit the production of sulfide, the immobilized sulfur-oxidizing-bacterium survived stably in the new environment accounting for 1.22% of total microbial community. Therefore, dosing the ICC and SICC simultaneously might be a preferable strategy and presented a promising perspective in remediating the deteriorated mariculture environment.
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Affiliation(s)
- Xiao Wang
- Shandong Provincial Key Laboratory of Marine Environment and Geological Engineering (MEGE), College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China
| | - Junpeng Wang
- Shandong Provincial Key Laboratory of Marine Environment and Geological Engineering (MEGE), College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China
| | - Yang-Guo Zhao
- Shandong Provincial Key Laboratory of Marine Environment and Geological Engineering (MEGE), College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China; Key Lab of Marine Environmental Science and Ecology (Ocean University of China), Ministry of Education, Qingdao 266100, China.
| | - Farhana Maqbool
- Department of Microbiology, Hazara University, Mansehra 21300, Pakistan
| | - Liang Guo
- Shandong Provincial Key Laboratory of Marine Environment and Geological Engineering (MEGE), College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China; Key Lab of Marine Environmental Science and Ecology (Ocean University of China), Ministry of Education, Qingdao 266100, China
| | - Mengchun Gao
- Shandong Provincial Key Laboratory of Marine Environment and Geological Engineering (MEGE), College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China; Key Lab of Marine Environmental Science and Ecology (Ocean University of China), Ministry of Education, Qingdao 266100, China
| | - Chunji Jin
- Shandong Provincial Key Laboratory of Marine Environment and Geological Engineering (MEGE), College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China; Key Lab of Marine Environmental Science and Ecology (Ocean University of China), Ministry of Education, Qingdao 266100, China
| | - Junyuan Ji
- Shandong Provincial Key Laboratory of Marine Environment and Geological Engineering (MEGE), College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China; Key Lab of Marine Environmental Science and Ecology (Ocean University of China), Ministry of Education, Qingdao 266100, China.
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235
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Liu Q, Zhao X, Liu Y, Xie S, Xing Y, Dao J, Wei B, Peng Y, Duan W, Wang Z. Response of Sugarcane Rhizosphere Bacterial Community to Drought Stress. Front Microbiol 2021; 12:716196. [PMID: 34690961 PMCID: PMC8527094 DOI: 10.3389/fmicb.2021.716196] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 09/13/2021] [Indexed: 12/02/2022] Open
Abstract
Sugarcane is an important sugar and energy crop, and its yield is greatly affected by drought. Although a large number of studies have shown that rhizosphere microorganisms can help improve the adaptability of plants to biotic or abiotic stresses, there is a lack of studies on the adaptability of sugarcane rhizosphere microbial communities to host plants. Therefore, we conducted drought stress treatment and normal irrigation treatment on three sugarcane varieties GT21, GT31, and GT42 widely cultivated in Guangxi. Using 16S rDNA sequencing technology to analyze the changes in abundance of the sugarcane rhizosphere bacterial community under different treatments, combined with the determination of soil enzyme activity, soil nutrient content, and sugarcane physiological characteristics, we explored the sugarcane rhizosphere bacterial community response to drought stress. In addition, we used the structural equation model to verify the response path of sugarcane rhizosphere bacteria. The results show that the bacterial community structure in the rhizosphere of sugarcane is stable under normal water conditions. The change in the bacterial community structure under drought stress has a 25.2% correlation with the drought adaptability of sugarcane, but the correlation with drought stress is as high as 42.17%. The changes in abundance of rhizosphere bacteria under drought stress are mainly concentrated in the phylum Rhizobiales and Streptomycetales. This change is directly related to the physiological state of the host plant under drought stress, soil available phosphorus, soil urease and soil acid protease. We investigated the response species of rhizosphere microorganisms and their response pathways under drought stress, providing a scientific basis for rhizosphere microorganisms to assist host plants to improve drought adaptability.
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Affiliation(s)
- Qi Liu
- Guangxi Key Laboratory of Sugarcane Biology, Nanning, China.,College of Agronomy, Guangxi University, Nanning, China.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| | - Xiaowen Zhao
- Guangxi Key Laboratory of Sugarcane Biology, Nanning, China.,College of Agronomy, Guangxi University, Nanning, China.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| | - Yue Liu
- Guangxi Key Laboratory of Sugarcane Biology, Nanning, China.,College of Agronomy, Guangxi University, Nanning, China.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| | - Sasa Xie
- Guangxi Key Laboratory of Sugarcane Biology, Nanning, China.,College of Agronomy, Guangxi University, Nanning, China.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| | - Yuanjun Xing
- College of Agriculture, Guangxi University, Nanning, China
| | - Jicao Dao
- College of Agriculture, Guangxi University, Nanning, China
| | - Beilei Wei
- College of Agriculture, Guangxi University, Nanning, China
| | - Yunchang Peng
- College of Agriculture, Guangxi University, Nanning, China
| | - Weixing Duan
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Ziting Wang
- Guangxi Key Laboratory of Sugarcane Biology, Nanning, China.,College of Agronomy, Guangxi University, Nanning, China.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
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236
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Lu T, Zhang Z, Li Y, Zhang Q, Cui H, Sun L, Peijnenburg WJGM, Peñuelas J, Zhu L, Zhu YG, Chen J, Qian H. Does biological rhythm transmit from plants to rhizosphere microbes? Environ Microbiol 2021; 23:6895-6906. [PMID: 34658124 DOI: 10.1111/1462-2920.15820] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 10/07/2021] [Indexed: 11/28/2022]
Abstract
Plant physiological and metabolic processes are modulated by rhythmic gene expression in a large part. Meanwhile, plants are also regulated by rhizosphere microorganisms, which are fed by root exudates and provide beneficial functions to their plant host. Whether the biorhythms in plants would transfer to the rhizosphere microbial community is still uncertain and their intricate connection remains poorly understood. Here, we investigated the role of the Arabidopsis circadian clock in shaping the rhizosphere microbial community using wild-type plants and clock mutants (cca1-1 and toc1-101) with transcriptomic, metabolomic and 16S rRNA gene sequencing analysis throughout a 24-h period. Deficiencies of the central circadian clock led to abnormal diurnal rhythms for thousands of expressed genes and dozens of root exudates. The bacterial community failed to follow obvious patterns in the 24-h period, and there was lack of coordination with plant growth in the clock mutants. Our results suggest that the robust rhythmicity of genes and root exudation due to circadian clock in plants is an important driving force for the positive succession of rhizosphere communities, which will feedback on plant development.
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Affiliation(s)
- Tao Lu
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, People's Republic of China
| | - Zhenyan Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, People's Republic of China
| | - Yan Li
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, People's Republic of China
| | - Qi Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, People's Republic of China
| | - Hengzheng Cui
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, People's Republic of China
| | - Liwei Sun
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, People's Republic of China
| | - W J G M Peijnenburg
- Institute of Environmental Sciences (CML), Leiden University, Leiden, 2300 RA, The Netherlands
| | - Josep Peñuelas
- CSIC, Global Ecology Unit, CREAF- CSIC-UAB, Barcelona, Catalonia, Spain.,CREAF, Cerdanyola del Vallès, Barcelona, Catalonia, Spain
| | - Lizhong Zhu
- Department of Environmental Science, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Yong-Guan Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, People's Republic of China
| | - Jianmeng Chen
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, People's Republic of China
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, People's Republic of China
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237
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Ha J, Gao Y, Zhang R, Li K, Zhang Y, Niu X, Chen X, Luo K, Chen Y. Diversity of the Bacterial Microbiome Associated With the Endosphere and Rhizosphere of Different Cassava ( Manihot esculenta Crantz) Genotypes. Front Microbiol 2021; 12:729022. [PMID: 34659156 PMCID: PMC8515189 DOI: 10.3389/fmicb.2021.729022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 09/01/2021] [Indexed: 11/13/2022] Open
Abstract
Root-associated microbial communities play important roles in plant growth and development. However, little attention has been paid to the microbial community structures associated with cassava, which is a staple food for approximately 800 million people worldwide. Here, we studied the diversity and structure of tuber endosphere and rhizosphere bacterial communities in fourteen cassava genotypes: SC5, SC8, SC9, SC205, KU50, R72, XL1, FX01, SC16, 4612, 587, 045, S0061, and 1110. The results of bacterial 16S rDNA sequencing showed that the richness and diversity of bacteria in the rhizosphere were higher than those in the tuber endosphere across the 14 cassava genotypes. After sequencing, 21 phyla and 310 genera were identified in the tuberous roots, and 36 phyla and 906 genera were identified in the rhizosphere soils. The dominant phylum across all tuber samples was Firmicutes, and the dominant phyla across all rhizosphere samples were Actinobacteria, Proteobacteria, and Acidobacteria. The numbers of core bacterial taxa within the tuber endospheres and the rhizospheres of all cassava genotypes were 11 and 236, respectively. Principal coordinate analysis and hierarchical cluster analysis demonstrated significant differences in the compositions of rhizosphere soil microbiota associated with the different cassava genotypes. Furthermore, we investigated the metabolic changes in tuber roots of three genotypes, KU50, SC205, and SC9. The result showed that the abundances of Firmicutes, Proteobacteria, and Actinobacteria in tuber samples were positively correlated with organic acids and lipids and negatively correlated with vitamins and cofactors. These results strongly indicate that there are clear differences in the structure and diversity of the bacterial communities associated with different cassava genotypes.
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Affiliation(s)
- Jingwen Ha
- Hainan Key Laboratory for the Sustainable Utilization of Tropical Bioresources, Hainan University, Haikou, China
| | - Yu Gao
- Hainan Key Laboratory for the Sustainable Utilization of Tropical Bioresources, Hainan University, Haikou, China
| | - Rui Zhang
- Hainan Key Laboratory for the Sustainable Utilization of Tropical Bioresources, Hainan University, Haikou, China
| | - Ke Li
- Hainan Key Laboratory for the Sustainable Utilization of Tropical Bioresources, Hainan University, Haikou, China
| | - Yijie Zhang
- Hainan Key Laboratory for the Sustainable Utilization of Tropical Bioresources, Hainan University, Haikou, China
| | - Xiaolei Niu
- Hainan Key Laboratory for the Sustainable Utilization of Tropical Bioresources, Hainan University, Haikou, China
| | - Xin Chen
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Kai Luo
- Hainan Key Laboratory for the Sustainable Utilization of Tropical Bioresources, Hainan University, Haikou, China
| | - Yinhua Chen
- Hainan Key Laboratory for the Sustainable Utilization of Tropical Bioresources, Hainan University, Haikou, China
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238
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Yu H, Wang F, Shao M, Huang L, Xie Y, Xu Y, Kong L. Effects of Rotations With Legume on Soil Functional Microbial Communities Involved in Phosphorus Transformation. Front Microbiol 2021; 12:661100. [PMID: 34659135 PMCID: PMC8519609 DOI: 10.3389/fmicb.2021.661100] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 08/19/2021] [Indexed: 11/13/2022] Open
Abstract
Including legumes in the cereal cropping could improve the crop yield and the uptake of nitrogen (N) and phosphorus (P) of subsequent cereals. The effects of legume-cereal crop rotations on the soil microbial community have been studied in recent years, the impact on soil functional genes especially involved in P cycling is raising great concerns. The metagenomic approach was used to investigate the impacts of crop rotation managements of soybean-wheat (SW) and maize-wheat (MW) lasting 2 and 7years on soil microbial communities and genes involved in P transformation in a field experiment. Results indicated that SW rotation increased the relative abundances of Firmicutes and Bacteroidetes, reduced Actinobacteria, Verrucomicrobia, and Chloroflexi compared to MW rotation. gcd, phoR, phoD, and ppx predominated in genes involved in P transformation in both rotations. Genes of gcd, ppa, and ugpABCE showed higher abundances in SW rotation than in MW rotation, whereas gadAC and pstS showed less abundances. Proteobacteria, Acidobacteria, and Gemmatimonadetes played predominant roles in microbial P cycling. Our study provides a novel insight into crop P, which requires strategy and help to understand the mechanism of improving crop nutrient uptake and productivity in different rotations.
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Affiliation(s)
- Hui Yu
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and the Environment, Shandong Agricultural University, Taian, China
| | - Fenghua Wang
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and the Environment, Shandong Agricultural University, Taian, China.,State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian, China
| | - Minmin Shao
- Jining Academy of Agricultural Sciences, Jining, China
| | - Ling Huang
- Jining Academy of Agricultural Sciences, Jining, China
| | - Yangyang Xie
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and the Environment, Shandong Agricultural University, Taian, China
| | - Yuxin Xu
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and the Environment, Shandong Agricultural University, Taian, China
| | - Lingrang Kong
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian, China
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239
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Wu N, Shi W, Liu W, Gao Z, Han L, Wang X. Differential impact of Bt-transgenic rice plantings on bacterial community in three niches over consecutive years. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 223:112569. [PMID: 34352582 DOI: 10.1016/j.ecoenv.2021.112569] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 06/11/2021] [Accepted: 07/25/2021] [Indexed: 05/26/2023]
Abstract
Transgenic-Bacillus thuringiensis (Bt) crops express insecticidal proteins, which can accumulate in plants and soil where they may influence microbial populations. The impact of Bt crops on bacterial communities has only been assessed under short-term, and results have been contradictory. Here, we analyzed the bacterial communities in three niches, rhizosphere soil (RS), root endosphere (RE) and leaf endosphere (LE), of three Bt rice and their non-Bt parental lines for three consecutive years by high-throughput sequencing. In principal coordinate analysis (PCoA) and PERMANOVA (Adonis) analysis, operational taxonomic units (OTUs) were clustered primarily by niche type and differed significantly in the RE and LE but not in the RS between each of three Bt lines compared with the non-Bt rice line, and not in each respective niche among the three Bt rice lines. The bacterial communities in the RS of different rice lines over the 3 years were clustered mainly by year rather than by lines. The differential bacterial taxa among the lines did not overlap between years, presumably because Cry proteins are rapidly degraded in the soil. A network analysis of RS bacterial communities showed that the network complexity and density for the three Bt rice lines did not decrease compared with those for the non-Bt line. In conclusion, our results demonstrated that bacterial communities differed significantly in RE and LE between Bt and non-Bt rice lines, but the differences were mild and transient, and had no adverse impact on RS over the 3 years. This study provides favorable evidence in support of the commercialization of Bt rice.
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Affiliation(s)
- Nan Wu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Wencong Shi
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, China
| | - Wenwen Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Zheng Gao
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, China
| | - Lanzhi Han
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Xifeng Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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240
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Wille L, Kurmann M, Messmer MM, Studer B, Hohmann P. Untangling the Pea Root Rot Complex Reveals Microbial Markers for Plant Health. FRONTIERS IN PLANT SCIENCE 2021; 12:737820. [PMID: 34712258 PMCID: PMC8545811 DOI: 10.3389/fpls.2021.737820] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 09/15/2021] [Indexed: 06/13/2023]
Abstract
Plant health is recognised as a key element to ensure global food security. While plant breeding has substantially improved crop resistance against individual pathogens, it showed limited success for diseases caused by the interaction of multiple pathogens such as root rot in pea (Pisum sativum L.). To untangle the causal agents of the pea root rot complex and determine the role of the plant genotype in shaping its own detrimental or beneficial microbiome, fungal and oomycete root rot pathogens, as well as previously identified beneficials, i.e., arbuscular mycorrhizal fungi (AMF) and Clonostachys rosea, were qPCR quantified in diseased roots of eight differently resistant pea genotypes grown in four agricultural soils under controlled conditions. We found that soil and pea genotype significantly determined the microbial compositions in diseased pea roots. Despite significant genotype x soil interactions and distinct soil-dependent pathogen complexes, our data revealed key microbial taxa that were associated with plant fitness. Our study indicates the potential of fungal and oomycete markers for plant health and serves as a precedent for other complex plant pathosystems. Such microbial markers can be used to complement plant phenotype- and genotype-based selection strategies to improve disease resistance in one of the world's most important pulse crops of the world.
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Affiliation(s)
- Lukas Wille
- Department of Crop Sciences, Research Institute of Organic Agriculture (FiBL), Frick, Switzerland
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zürich, Zurich, Switzerland
| | - Mario Kurmann
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zürich, Zurich, Switzerland
| | - Monika M. Messmer
- Department of Crop Sciences, Research Institute of Organic Agriculture (FiBL), Frick, Switzerland
| | - Bruno Studer
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zürich, Zurich, Switzerland
| | - Pierre Hohmann
- Department of Crop Sciences, Research Institute of Organic Agriculture (FiBL), Frick, Switzerland
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241
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Dong H, Fan S, Sun H, Chen C, Wang A, Jiang L, Ma D. Rhizosphere-Associated Microbiomes of Rice ( Oryza sativa L.) Under the Effect of Increased Nitrogen Fertilization. Front Microbiol 2021; 12:730506. [PMID: 34621256 PMCID: PMC8490883 DOI: 10.3389/fmicb.2021.730506] [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: 06/25/2021] [Accepted: 09/01/2021] [Indexed: 11/13/2022] Open
Abstract
Crops assemble and rely on rhizosphere-associated microbiomes for plant nutrition, which is crucial to their productivity. Historically, excessive nitrogen fertilization did not result in continuously increasing yields but rather caused environmental issues. A comprehensive understanding should be developed regarding the ways in which crops shape rhizosphere-associated microbiomes under conditions of increased nitrogen fertilization. In this study, we applied 16S and 18S ribosomal RNA gene profiling to characterize bacterial and fungal communities in bulk and rhizosphere soil of rice subjected to three levels of nitrogen fertilization for 5 years. Soil biochemical properties were characterized, and carbon-, nitrogen-, and phosphorus-related soil enzyme activities were investigated, by assays. Increasing nitrogen fertilization led to a decreasing trend in the variation of microbial community structures and demonstrated a more definite influence on fungal rather than bacterial community compositions and functions. Changes in the level of nitrogen fertilization significantly affected chemical properties such as soil pH, nutrient content, and microbial biomass levels in both rhizosphere and bulk soil. Soil enzyme activity levels varied substantially across nitrogen fertilization intensities and correlated more with the fungal than with the bacterial community. Our results indicated that increased nitrogen input drives alterations in the structures and functions of microbial communities, properties of soil carbon, nitrogen, and phosphorus, as well as enzyme activities. These results provide novel insights into the associations among increased nitrogen input, changes in biochemical properties, and shifts in microbial communities in the rhizosphere of agriculturally intensive ecosystems.
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Affiliation(s)
- Hangyu Dong
- Key Laboratory of Northeast Rice Biology and Breeding, National Rice Regional Technology Innovation Center, Rice Research Institute, Shenyang Agricultural University, Shenyang, China.,College of Agronomy, Shenyang Agricultural University, Shenyang, China
| | - Shuxiu Fan
- College of Agronomy, Shenyang Agricultural University, Shenyang, China
| | - Haoyuan Sun
- Key Laboratory of Northeast Rice Biology and Breeding, National Rice Regional Technology Innovation Center, Rice Research Institute, Shenyang Agricultural University, Shenyang, China.,College of Agronomy, Shenyang Agricultural University, Shenyang, China
| | - Conglin Chen
- Key Laboratory of Northeast Rice Biology and Breeding, National Rice Regional Technology Innovation Center, Rice Research Institute, Shenyang Agricultural University, Shenyang, China.,College of Agronomy, Shenyang Agricultural University, Shenyang, China
| | - Aixin Wang
- Key Laboratory of Northeast Rice Biology and Breeding, National Rice Regional Technology Innovation Center, Rice Research Institute, Shenyang Agricultural University, Shenyang, China.,College of Agronomy, Shenyang Agricultural University, Shenyang, China
| | - Linlin Jiang
- Key Laboratory of Northeast Rice Biology and Breeding, National Rice Regional Technology Innovation Center, Rice Research Institute, Shenyang Agricultural University, Shenyang, China.,College of Agronomy, Shenyang Agricultural University, Shenyang, China
| | - Dianrong Ma
- Key Laboratory of Northeast Rice Biology and Breeding, National Rice Regional Technology Innovation Center, Rice Research Institute, Shenyang Agricultural University, Shenyang, China.,College of Agronomy, Shenyang Agricultural University, Shenyang, China
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242
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Li H, La S, Zhang X, Gao L, Tian Y. Salt-induced recruitment of specific root-associated bacterial consortium capable of enhancing plant adaptability to salt stress. THE ISME JOURNAL 2021; 15:2865-2882. [PMID: 33875820 PMCID: PMC8443564 DOI: 10.1038/s41396-021-00974-2] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 03/12/2021] [Accepted: 04/06/2021] [Indexed: 02/01/2023]
Abstract
Salinity is a major abiotic stress threatening crop production. Root-derived bacteria (RDB) are hypothesized to play a role in enhancing plant adaptability to various stresses. However, it is still unclear whether and how plants build up specific RDB when challenged by salinity. In this study, we measured the composition and variation in the rhizosphere and endophyte bacteria of salt-sensitive (SSs) and salt-resistant (SRs) plants under soil conditions with/without salinity. The salt-induced RDB (both rhizobiomes and endophytes) were isolated to examine their effects on the physiological responses of SSs and SRs to salinity challenge. Moreover, we examined whether functional redundancy exists among salt-induced RDB in enhancing plant adaptability to salt stress. We observed that although SSs and SRs recruited distinct RDB and relevant functions when challenged by salinity, salt-induced recruitment of specific RDB led to a consistent growth promotion in plants regardless of their salinity tolerance capacities. Plants employed a species-specific strategy to recruit beneficial soil bacteria in the rhizosphere rather than in the endosphere. Furthermore, we demonstrated that the consortium, but not individual members of the salt-induced RDB, provided enduring resistance against salt stress. This study confirms the critical role of salt-induced RDB in enhancing plant adaptability to salt stress.
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Affiliation(s)
- Hong Li
- grid.22935.3f0000 0004 0530 8290Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, P. R. China
| | - Shikai La
- grid.22935.3f0000 0004 0530 8290Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, P. R. China
| | - Xu Zhang
- grid.22935.3f0000 0004 0530 8290Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, P. R. China
| | - Lihong Gao
- grid.22935.3f0000 0004 0530 8290Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, P. R. China
| | - Yongqiang Tian
- grid.22935.3f0000 0004 0530 8290Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, P. R. China
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243
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Xun W, Shao J, Shen Q, Zhang R. Rhizosphere microbiome: Functional compensatory assembly for plant fitness. Comput Struct Biotechnol J 2021; 19:5487-5493. [PMID: 34712394 PMCID: PMC8515068 DOI: 10.1016/j.csbj.2021.09.035] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/29/2021] [Accepted: 09/29/2021] [Indexed: 01/13/2023] Open
Abstract
Environmental pressure to reduce our reliance on agrochemicals and the necessity to increase crop production in a sustainable way have made the rhizosphere microbiome an untapped resource for combating challenges to agricultural sustainability. In recent years, substantial efforts to characterize the structural and functional diversity of rhizosphere microbiomes of the model plant Arabidopsis thaliana and various crops have demonstrated their importance for plant fitness. However, the plant benefiting mechanisms of the rhizosphere microbiome as a whole community rather than as an individual rhizobacterium have only been revealed in recent years. The underlying principle dominating the assembly of the rhizosphere microbiome remains to be elucidated, and we are still struggling to harness the rhizosphere microbiome for agricultural sustainability. In this review, we summarize the recent progress of the driving factors shaping the rhizosphere microbiome and provide community-level mechanistic insights into the benefits that the rhizosphere microbiome has for plant fitness. We then propose the functional compensatory principle underlying rhizosphere microbiome assembly. Finally, we suggest future research efforts to explore the rhizosphere microbiome for agricultural sustainability.
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Affiliation(s)
- Weibing Xun
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China
| | - Jiahui Shao
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China
| | - Qirong Shen
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China
| | - Ruifu Zhang
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
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244
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Liu Y, Ma W, He H, Wang Z, Cao Y. Effects of Sugarcane and Soybean Intercropping on the Nitrogen-Fixing Bacterial Community in the Rhizosphere. Front Microbiol 2021; 12:713349. [PMID: 34659143 PMCID: PMC8515045 DOI: 10.3389/fmicb.2021.713349] [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: 05/22/2021] [Accepted: 09/06/2021] [Indexed: 11/24/2022] Open
Abstract
Intercropping between sugarcane and soybean is widely used to increase crop yield and promote the sustainable development of the sugarcane industry. However, our understanding of the soil microenvironment in intercropping systems, especially the effect of crop varieties on rhizosphere soil bacterial communities, remains poor. We selected two excellent sugarcane cultivars, Zhongzhe1 (ZZ1) and Zhongzhe9 (ZZ9), from Guangxi and the local soybean variety GUIZAO2 from Guangxi for field interplanting experiments. These two cultivars of sugarcane have good drought resistance. Rhizosphere soil samples were collected from the two intercropping systems to measure physicochemical properties and soil enzyme activities and to extract total soil DNA for high-throughput sequencing. We found that the diversity of the rhizosphere bacterial community was significantly different between the two intercropping systems. Compared with ZZ1, the ZZ9 intercropping system enriched the nitrogen-fixing bacteria, increasing the available nitrogen content by 18% compared with that with ZZ1. In addition, ZZ9 intercropping with soybean formed a more compact rhizosphere environment than ZZ1, thus providing favorable conditions for sugarcane growth. These results provide guidance for the sugarcane industry, especially for the management of sugarcane and soybean intercropping in Guangxi, China.
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Affiliation(s)
- Yue Liu
- College of Agronomy, Guangxi University, Nanning, China
| | - Wenqing Ma
- Guangxi South Subtropical Agricultural Science Research Institute, Chongzuo, China
| | - Hongliang He
- Guangxi South Subtropical Agricultural Science Research Institute, Chongzuo, China
| | - Ziting Wang
- College of Agronomy, Guangxi University, Nanning, China
| | - Yanhong Cao
- Guangxi Key Laboratory of Livestock Genetic Improvement, The Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region, Nanning, China
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245
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Saeed Q, Xiukang W, Haider FU, Kučerik J, Mumtaz MZ, Holatko J, Naseem M, Kintl A, Ejaz M, Naveed M, Brtnicky M, Mustafa A. Rhizosphere Bacteria in Plant Growth Promotion, Biocontrol, and Bioremediation of Contaminated Sites: A Comprehensive Review of Effects and Mechanisms. Int J Mol Sci 2021; 22:10529. [PMID: 34638870 PMCID: PMC8509026 DOI: 10.3390/ijms221910529] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 09/23/2021] [Accepted: 09/27/2021] [Indexed: 01/23/2023] Open
Abstract
Agriculture in the 21st century is facing multiple challenges, such as those related to soil fertility, climatic fluctuations, environmental degradation, urbanization, and the increase in food demand for the increasing world population. In the meanwhile, the scientific community is facing key challenges in increasing crop production from the existing land base. In this regard, traditional farming has witnessed enhanced per acre crop yields due to irregular and injudicious use of agrochemicals, including pesticides and synthetic fertilizers, but at a substantial environmental cost. Another major concern in modern agriculture is that crop pests are developing pesticide resistance. Therefore, the future of sustainable crop production requires the use of alternative strategies that can enhance crop yields in an environmentally sound manner. The application of rhizobacteria, specifically, plant growth-promoting rhizobacteria (PGPR), as an alternative to chemical pesticides has gained much attention from the scientific community. These rhizobacteria harbor a number of mechanisms through which they promote plant growth, control plant pests, and induce resistance to various abiotic stresses. This review presents a comprehensive overview of the mechanisms of rhizobacteria involved in plant growth promotion, biocontrol of pests, and bioremediation of contaminated soils. It also focuses on the effects of PGPR inoculation on plant growth survival under environmental stress. Furthermore, the pros and cons of rhizobacterial application along with future directions for the sustainable use of rhizobacteria in agriculture are discussed in depth.
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Affiliation(s)
- Qudsia Saeed
- College of Natural Resources and Environment, Northwest Agriculture and Forestry University, Yangling 712100, China;
| | - Wang Xiukang
- College of Life Sciences, Yan’an University, Yan’an 716000, China
| | - Fasih Ullah Haider
- College of Resources and Environmental Sciences, Gansu Agricultural University, Lanzhou 730070, China;
| | - Jiří Kučerik
- Institute of Chemistry and Technology of Environmental Protection, Faculty of Chemistry, Brno University of Technology, Purkynova 118, 612 00 Brno, Czech Republic; (J.K.); (M.B.)
| | - Muhammad Zahid Mumtaz
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Defense Road, Lahore 54000, Pakistan;
| | - Jiri Holatko
- Department of Agrochemistry, Soil Science, Microbiology and Plant Nutrition, Faculty of AgriSciences, Mendel University in Brno, Zemedelska 1, 613 00 Brno, Czech Republic; (J.H.); (A.K.)
| | - Munaza Naseem
- Institute of Soil and Environmental Science, University of Agriculture Faisalabad, Faisalabad 38040, Pakistan; (M.N.); (M.N.)
| | - Antonin Kintl
- Department of Agrochemistry, Soil Science, Microbiology and Plant Nutrition, Faculty of AgriSciences, Mendel University in Brno, Zemedelska 1, 613 00 Brno, Czech Republic; (J.H.); (A.K.)
- Agricultural Research, Ltd., Zahradni 400/1, 664 41 Troubsko, Czech Republic
| | - Mukkaram Ejaz
- School of Environmental and Municipal Engineering, Lanzhou Jiaotong University, Lanzhou 730070, China;
| | - Muhammad Naveed
- Institute of Soil and Environmental Science, University of Agriculture Faisalabad, Faisalabad 38040, Pakistan; (M.N.); (M.N.)
| | - Martin Brtnicky
- Institute of Chemistry and Technology of Environmental Protection, Faculty of Chemistry, Brno University of Technology, Purkynova 118, 612 00 Brno, Czech Republic; (J.K.); (M.B.)
- Department of Agrochemistry, Soil Science, Microbiology and Plant Nutrition, Faculty of AgriSciences, Mendel University in Brno, Zemedelska 1, 613 00 Brno, Czech Republic; (J.H.); (A.K.)
| | - Adnan Mustafa
- Biology Center CAS, SoWa RI, Na Sadkach 7, 370 05 České Budějovice, Czech Republic
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246
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Continuous Sugarcane Planting Negatively Impacts Soil Microbial Community Structure, Soil Fertility, and Sugarcane Agronomic Parameters. Microorganisms 2021; 9:microorganisms9102008. [PMID: 34683329 PMCID: PMC8537732 DOI: 10.3390/microorganisms9102008] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 09/19/2021] [Accepted: 09/20/2021] [Indexed: 01/28/2023] Open
Abstract
Continuous planting has a negative impact on sugarcane plant growth and reduces global sugarcane crop production, including in China. The response of soil bacteria, fungal, and arbuscular mycorrhizae (AM) fungal communities to continuous sugarcane cultivation has not been thoroughly documented. Using MiSeq sequencing technology, we analyzed soil samples from sugarcane fields with 1, 10, and 30 years of continuous cropping to see how monoculture time affected sugarcane yield, its rhizosphere soil characteristics and microbiota. The results showed that continuous sugarcane planting reduced sugarcane quality and yield. Continuous sugarcane planting for 30 years resulted in soil acidification, as well as C/N, alkali hydrolyzable nitrogen, organic matter, and total sulfur content significantly lower than in newly planted fields. Continuous sugarcane planting affected soil bacterial, fungal, and AM fungal communities, according to PCoA and ANOSIM analysis. Redundancy analysis (RDA) results showed that bacterial, fungal, and AM fungal community composition were strongly associated with soil properties and attributes, e.g., soil AN, OM, and TS were critical environmental factors in transforming the bacterial community. The LEfSe analysis revealed bacterial families (e.g., Gaiellaceae, Pseudomonadaceae, Micromonosporaceae, Nitrosomonadaceae, and Methyloligellaceae) were more prevalent in the newly planted field than in continuously cultivated fields (10 and 30 years), whereas Sphingomonadaceae, Coleofasciculaceae, and Oxyphotobacteria were depleted. Concerning fungal families, the newly planted field was more dominated than the continuously planted field (30 years) with Mrakiaceae and Ceratocystidaceae, whereas Piskurozymaceae, Trimorphomycetaceae, Lachnocladiaceae, and Stigmatodisc were significantly enriched in the continuously planted fields (10 and 30 years). Regarding AMF families, Diversisporaceae was considerably depleted in continuously planted fields (10 and 30 years) compared to the newly planted field. These changes in microbial composition may ultimately lead to a decrease in sugarcane yield and quality in the monoculture system, which provides a theoretical basis for the obstruction mechanism of the continuous sugarcane planting system. However, continuous planting obstacles remain uncertain and further need to be coupled with root exudates, soil metabolomics, proteomics, nematodes, and other exploratory methods.
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247
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Malviya MK, Solanki MK, Li CN, Wang Z, Zeng Y, Verma KK, Singh RK, Singh P, Huang HR, Yang LT, Song XP, Li YR. Sugarcane-Legume Intercropping Can Enrich the Soil Microbiome and Plant Growth. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2021. [DOI: 10.3389/fsufs.2021.606595] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Soil microbes have a direct impact on plant metabolism and health. The current study investigates the comparative rhizobiome between sugarcane monoculture and sugarcane–soybean intercropping. A greenhouse experiment was performed with two treatments: (1) sugarcane monoculture and (2) sugarcane–soybean intercropped. We used a high-throughput sequencing (HTS) platform to analyze the microbial community. We used the 16S rRNA gene and internal transcribed spacer region primers to identify the microbial diversity. HTS results revealed that a total of 2,979 and 124 bacterial and fungal operational taxonomic units (OTUs) were observed, respectively. Microbial diversity results concluded that the intercropping system has a beneficial impact on soil microbes. The highest numbers of bacterial and fungal OTUs were found in the intercropping system, and these results also collaborated with quantitative PCR results. Additionally, intercropped sugarcane plants showed a higher weight of above- and below-ground parts than the monoculture. Soil chemical analysis results also complemented that the intercropping system nourished organic carbon, total nitrogen, and soil enzyme activities. Correlation analysis of the diversity index and abundance concluded that soil nutrient content positively influenced the microbial abundance that improves plant growth. The present study frames out the profound insights of microbial community interaction under the sugarcane–soybean intercropping system. This information could help improve or increase the sugarcane crop production without causing any negative impact on sugarcane plant growth and development.
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248
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Zhang J, Xing P, Niu M, Wei G, Shi P. Taxonomic Compositions and Co-occurrence Relationships of Protists in Bulk Soil and Rhizosphere of Soybean Fields in Different Regions of China. Front Microbiol 2021; 12:738129. [PMID: 34603268 PMCID: PMC8485050 DOI: 10.3389/fmicb.2021.738129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 08/27/2021] [Indexed: 11/13/2022] Open
Abstract
As the main consumers of bacteria and fungi in farmed soils, protists remain poorly understood. The aim of this study was to explore protist community assembly and ecological roles in soybean fields. Here, we investigated differences in protist communities using high-throughput sequencing and their inferred potential interactions with bacteria and fungi between the bulk soil and rhizosphere compartments of three soybean cultivars collected from six ecological regions in China. Distinct protist community structures characterized the bulk soil and rhizosphere of soybean plants. A significantly higher relative abundance of phagotrophs was observed in the rhizosphere (25.1%) than in the bulk soil (11.3%). Spatial location (R 2 = 0.37-0.51) explained more of the variation in protist community structures of soybean fields than either the compartment (R 2 = 0.08-0.09) or cultivar type (R 2 = 0.02-0.03). The rhizosphere protist network (76 nodes and 414 edges) was smaller and less complex than the bulk soil network (147 nodes and 880 edges), indicating a smaller potential of niche overlap and interactions in the rhizosphere due to the increased resources in the rhizosphere. Furthermore, more inferred potential predator-prey interactions occur in the rhizosphere. We conclude that protists have a crucial ecological role to play as an integral part of microbial co-occurrence networks in soybean fields.
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Affiliation(s)
| | | | | | | | - Peng Shi
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, China
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Gao M, Xiong C, Gao C, Tsui CKM, Wang MM, Zhou X, Zhang AM, Cai L. Disease-induced changes in plant microbiome assembly and functional adaptation. MICROBIOME 2021; 9:187. [PMID: 34526096 PMCID: PMC8444440 DOI: 10.1186/s40168-021-01138-2] [Citation(s) in RCA: 117] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 07/27/2021] [Indexed: 05/20/2023]
Abstract
BACKGROUND The plant microbiome is an integral part of the host and increasingly recognized as playing fundamental roles in plant growth and health. Increasing evidence indicates that plant rhizosphere recruits beneficial microbes to the plant to suppress soil-borne pathogens. However, the ecological processes that govern plant microbiome assembly and functions in the below- and aboveground compartments under pathogen invasion are not fully understood. Here, we studied the bacterial and fungal communities associated with 12 compartments (e.g., soils, roots, stems, and fruits) of chili pepper (Capsicum annuum L.) using amplicons (16S and ITS) and metagenomics approaches at the main pepper production sites in China and investigated how Fusarium wilt disease (FWD) affects the assembly, co-occurrence patterns, and ecological functions of plant-associated microbiomes. RESULTS The amplicon data analyses revealed that FWD affected less on the microbiome of pepper reproductive organs (fruit) than vegetative organs (root and stem), with the strongest impact on the upper stem epidermis. Fungal intra-kingdom networks were less stable and their communities were more sensitive to FWD than the bacterial communities. The analysis of microbial interkingdom network further indicated that FWD destabilized the network and induced the ecological importance of fungal taxa. Although the diseased plants were more susceptible to colonization by other pathogenic fungi, their below- and aboveground compartments can also recruit potential beneficial bacteria. Some of the beneficial bacterial taxa enriched in the diseased plants were also identified as core taxa for plant microbiomes and hub taxa in networks. On the other hand, metagenomic analysis revealed significant enrichment of several functional genes involved in detoxification, biofilm formation, and plant-microbiome signaling pathways (i.e., chemotaxis) in the diseased plants. CONCLUSIONS Together, we demonstrate that a diseased plant could recruit beneficial bacteria and mitigate the changes in reproductive organ microbiome to facilitate host or its offspring survival. The host plants may attract the beneficial microbes through the modulation of plant-microbiome signaling pathways. These findings significantly advance our understanding on plant-microbiome interactions and could provide fundamental and important data for harnessing the plant microbiome in sustainable agriculture. Video abstract.
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Affiliation(s)
- Min Gao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chao Xiong
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 100085, Beijing, China
| | - Cheng Gao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Clement K M Tsui
- Department of Pathology, Sidra Medicine, Doha, Qatar
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine-Qatar, Doha, Qatar
- Division of Infectious Diseases, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Meng-Meng Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xin Zhou
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ai-Min Zhang
- Pepper Research Institute, Guizhou Provincial Academy of Agricultural Sciences, 550009, Guiyang, China
| | - Lei Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
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Tayyab M, Yang Z, Zhang C, Islam W, Lin W, Zhang H. Sugarcane monoculture drives microbial community composition, activity and abundance of agricultural-related microorganisms. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:48080-48096. [PMID: 33904129 DOI: 10.1007/s11356-021-14033-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 04/16/2021] [Indexed: 05/28/2023]
Abstract
Sugarcane monoculture (SM) often leads to soil problems, like soil acidification, degradation, and soil-borne diseases, which ultimately pose a negative impact on agricultural productivity and sustainability. Understanding the change in microbial communities' composition, activities, and functional microbial taxa associated with the plant and soil under SM is unclear. Using multidisciplinary approaches such as Illumina sequencing, measurements of soil properties, and enzyme activities, we analyzed soil samples from three sugarcane fields with different monoculture histories (1-, 2-, and 4-year cultivation times, respectively). We observed that SM induced soil acidity and had adverse effects on soil fertility, i.e., soil organic matter (OM), total nitrogen (TN), total carbon (TC), and available potassium (AK), as well as enzyme activities indicative for carbon, phosphorus, and nitrogen cycles. Non-metric multidimensional scaling (NMDS) analysis showed that SM time greatly affected soil attribute patterns. We observed strong correlation among soil enzymes activities and soil physiochemical properties (soil pH, OM, and TC). Alpha diversity analysis showed a varying response of the microbes to SM time. Bacterial diversity increased with increasing oligotrophs (e.g., Acidobacteria and Chloroflexi), while fungal diversity decreased with reducing copiotrophs (e.g., Ascomycota). β-Diversity analysis showed that SM time had a great influence on soil microbial structure and soil properties, which led to the changes in major components of microbial structure (soil pH, OM, TC, bacteria and soil pH; TC, fungi). Additionally, SM time significantly stimulated (four bacterial and ten fungal) and depleted (12 bacterial and three fungal) agriculturally and ecologically important microbial genera that were strongly and considerably correlated with soil characteristics (soil pH, OM, TC, and AK). In conclusion, SM induces soil acidity, reduces soil fertility, shifts microbial structure, and reduces its activity. Furthermore, most beneficial bacterial genera decreased significantly due to SM, while beneficial fungal genera showed a reverse trend. Therefore, mitigating soil acidity, improving soil fertility, and soil enzymatic activities, including improved microbial structure with beneficial service to plants and soil, can be an effective measure to develop a sustainable sugarcane cropping system.
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Affiliation(s)
- Muhammad Tayyab
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian Provincial Key Laboratory of Agro-ecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, 35002, China
| | - Ziqi Yang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Caifang Zhang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Waqar Islam
- College of Geography, Fujian Normal University, Fuzhou, 350007, China
| | - Wenxiong Lin
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- Fujian Provincial Key Laboratory of Agro-ecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, 35002, China.
| | - Hua Zhang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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