1
|
Gao Y, Zhao Y, Li P, Qi X. Responses of the maize rhizosphere soil environment to drought-flood abrupt alternation stress. Front Microbiol 2023; 14:1295376. [PMID: 38170081 PMCID: PMC10760638 DOI: 10.3389/fmicb.2023.1295376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Accepted: 11/22/2023] [Indexed: 01/05/2024] Open
Abstract
Changes in the soil environment in the root zone will affect the growth, development and resistance of plants. The mechanism underlying the effect of drought and flood stress on rhizosphere bacterial diversity, soil metabolites and soil enzyme activity is not clear and needs further study. To analyze the dynamic changes in bacteria, metabolites and enzyme activities in the rhizosphere soil of maize under different drought-flood abrupt alternation (DFAA) stresses, the barrel test method was used to set up the 'sporadic light rain' to flooding (referring to trace rainfall to heavy rain) (DFAA1) group, 'continuous drought' to flooding (DFAA2) group and normal irrigation (CK) group from the jointing to the tassel flowering stage of maize. The results showed that Actinobacteria was the most dominant phylum in the two DFAA groups during the drought period and the rewatering period, and Proteobacteria was the most dominant phylum during the flooding period and the harvest period. The alpha diversity index of rhizosphere bacteria in the DFAA2 group during the flooding period was significantly lower than that in other stages, and the relative abundance of Chloroflexi was higher. The correlation analysis between the differential genera and soil metabolites of the two DFAA groups showed that the relative abundance of Paenibacillus in the DFAA1 group was higher during the drought period, and it was significantly positively correlated with the bioactive lipid metabolites. The differential SJA-15 bacterium was enriched in the DFAA2 group during the flooding period and were strongly correlated with biogenic amine metabolites. The relative abundances of Arthrobacter, Alphaproteobacteria and Brevibacillus in the DFAA2 group were higher compared with DFAA1 group from rewatering to harvest and were significantly positively correlated with hydrocarbon compounds and steroid hormone metabolites. The acid phosphatase activity of the DFAA1 group was significantly higher than that of the DFAA2 group during the flooding period. The study suggests that there is a yield compensation phenomenon in the conversion of 'continuous drought' to flooding compared with 'sporadic light rain', which is related to the improvement in the flooding tolerance of maize by the dominant bacteria Chloroflexi, bacterium SJA-15 and biogenic amine metabolites. These rhizosphere bacteria and soil metabolites may have the potential function of helping plants adapt to the DFAA environment. The study revealed the response of the maize rhizosphere soil environment to DFAA stress and provided new ideas for exploring the potential mechanism of crop yield compensation under DFAA.
Collapse
Affiliation(s)
| | - Yulong Zhao
- Farmland Irrigation Research Institute of CAAS, Xinxiang, China
| | | | - Xuebin Qi
- Farmland Irrigation Research Institute of CAAS, Xinxiang, China
| |
Collapse
|
2
|
Zhang C, Zhang Q, Luo M, Wang Q, Wu X. Bacillus cereus WL08 immobilized on tobacco stem charcoal eliminates butylated hydroxytoluene in soils and alleviates the continuous cropping obstacle of Pinellia ternata. JOURNAL OF HAZARDOUS MATERIALS 2023; 450:131091. [PMID: 36870095 DOI: 10.1016/j.jhazmat.2023.131091] [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: 12/29/2022] [Revised: 01/31/2023] [Accepted: 02/24/2023] [Indexed: 06/18/2023]
Abstract
Butylated hydroxytoluene (BHT), as an emerging contaminant in ecosystems, has potential influences on animals, aquatic organisms, and public health, and has been proven to be a major allelochemical of Pinellia ternata. In this study, Bacillus cereus WL08 was used to rapidly degrade BHT in liquid culture. Strain WL08 immobilized on tobacco stem charcoal (TSC) particles notably accelerated BHT removal in contract to its free cells, and exhibited excellent reutilization and storage capacities. The optimal removal parameters of TSC WL08 were ascertained to be pH 7.0, 30 °C, 50 mg L-1 BHT and 0.14 mg L-1 TSC WL08. Moreover, TSC WL08 significantly accelerated the degradation of 50 mg L-1 BHT in sterile and non-sterile soils compared to that of free WL08 or natural dissipation, and notably shortened their half-lives by 2.47- or 362.14- fold, and 2.20- or 14.99- fold, respectively. Simultaneously, TSC WL08 was introduced into the continuous cropping soils of P. ternata, which accelerated the elimination of allelochemical BHT, and notably enhanced the photosynthesis, growth, yield, and quality of P. ternata. This study provides new insights and strategies for the rapid in situ remediation of BHT-polluted soils and effective alleviation of P. ternata cropping obstacles.
Collapse
Affiliation(s)
- Cheng Zhang
- Key Laboratory of Environmental Pollution Monitoring and Disease of Ministry of Education, School of Public Health, Guizhou Medical University, Guiyang 550025, China; Institute of Crop Protection, College of Agriculture, Guizhou University, Guiyang, Guizhou 550025, China
| | - Qinghai Zhang
- Key Laboratory of Environmental Pollution Monitoring and Disease of Ministry of Education, School of Public Health, Guizhou Medical University, Guiyang 550025, China
| | - Ming Luo
- Institute of Modern Chinese Herbal Medicines, Institute of Crop Germplasm Resources, Guizhou Academy of Agricultural Sciences, Guiyang 550025, China
| | - Qiuping Wang
- Institute of Crop Protection, College of Agriculture, Guizhou University, Guiyang, Guizhou 550025, China; Department of Food and Medicine, Guizhou Vocational College of Agriculture, Qingzhen, Guizhou 551400, China
| | - Xiaomao Wu
- Institute of Crop Protection, College of Agriculture, Guizhou University, Guiyang, Guizhou 550025, China.
| |
Collapse
|
3
|
Wang Y, Liu K, Zhou Y, Chen Y, Jin C, Hu Y. Integrated Analysis of microRNA and RNA-Seq Reveals Phenolic Acid Secretion Metabolism in Continuous Cropping of Polygonatum odoratum. PLANTS (BASEL, SWITZERLAND) 2023; 12:943. [PMID: 36840290 PMCID: PMC9962977 DOI: 10.3390/plants12040943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 02/08/2023] [Accepted: 02/16/2023] [Indexed: 06/18/2023]
Abstract
Polygonatum odoratum (Mill.) Druce is an essential Chinese herb, but continuous cropping (CC) often results in a serious root rot disease, reducing the yield and quality. Phenolic acids, released through plant root exudation, are typical autotoxic substances that easily cause root rot in CC. To better understand the phenolic acid biosynthesis of P. odoratum roots in response to CC, this study performed a combined microRNA (miRNA)-seq and RNA-seq analysis. The phenolic acid contents of the first cropping (FC) soil and CC soil were determined by HPLC analysis. The results showed that CC soils contained significantly higher levels of p-coumaric acid, phenylacetate, and caffeic acid than FC soil, except for cinnamic acid and sinapic acid. Transcriptome identification and miRNA sequencing revealed 15,788 differentially expressed genes (DEGs) and 142 differentially expressed miRNAs (DEMs) in roots from FC and CC plants. Among them, 28 DEGs and eight DEMs were involved in phenolic acid biosynthesis. Meanwhile, comparative transcriptome and microRNA-seq analysis demonstrated that eight miRNAs corresponding to five target DEGs related to phenolic acid synthesis were screened. Among them, ath-miR172a, ath-miR172c, novel_130, sbi-miR172f, and tcc-miR172d contributed to phenylalanine synthesis. Osa-miR528-5p and mtr-miR2673a were key miRNAs that regulate syringyl lignin biosynthesis. Nta-miR156f was closely related to the shikimate pathway. These results indicated that the key DEGs and DEMs involved in phenolic acid anabolism might play vital roles in phenolic acid secretion from roots of P. odoratum under the CC system. As a result of the study, we may have a better understanding of phenolic acid biosynthesis during CC of roots of P. odoratum.
Collapse
Affiliation(s)
- Yan Wang
- College of Agriculture and Biotechnology, Hunan University of Humanities, Science and Technology, Loudi 417000, China
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, National Center of Technology Innovation for Saline-Alkali Tolerant Rice, College of Biology, Hunan University, Changsha 410082, China
| | - Kaitai Liu
- College of Agriculture and Biotechnology, Hunan University of Humanities, Science and Technology, Loudi 417000, China
| | - Yunyun Zhou
- College of Agriculture and Biotechnology, Hunan University of Humanities, Science and Technology, Loudi 417000, China
| | - Yong Chen
- College of Agriculture and Biotechnology, Hunan University of Humanities, Science and Technology, Loudi 417000, China
| | - Chenzhong Jin
- College of Agriculture and Biotechnology, Hunan University of Humanities, Science and Technology, Loudi 417000, China
| | - Yihong Hu
- College of Agriculture and Biotechnology, Hunan University of Humanities, Science and Technology, Loudi 417000, China
| |
Collapse
|
4
|
Cheng H, Yuan M, Tang L, Shen Y, Yu Q, Li S. Integrated microbiology and metabolomics analysis reveal responses of soil microorganisms and metabolic functions to phosphorus fertilizer on semiarid farm. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 817:152878. [PMID: 34998744 DOI: 10.1016/j.scitotenv.2021.152878] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 12/24/2021] [Accepted: 12/30/2021] [Indexed: 05/13/2023]
Abstract
Localized fertilization of phosphorus has potential benefits in achieving higher crop productivity and nutrient use efficiency, but the underlying biological mechanisms of interactions between soil microorganisms and related metabolic cycle remain largely to be recognized. Here, we combined microbiology with non-target metabolomics to explore how P fertilizer levels and fertilization patterns affect wheat soil microbial communities and metabolic functions based on high-throughput sequencing and UPLC-MS/MS platforms. The results showed P fertilizer decreased the diversity of bacterial 16S rRNA genes and fungal ITS genes, and it did significantly change both soil bacterial and fungal overall community structures and compositions. The P levels and patterns also interfered with complexity of soil bacterial and fungal symbiosis networks. Moreover, metabolomics analysis showed that P fertilizer significantly changed soil metabolite spectrum, and the differential metabolites were significantly enriched to 7 main metabolic pathways, such as arginine and proline metabolism, biosynthesis of plant hormones, amino acids, plant secondary metabolites, and alkaloids derived from ornithine. Additionally, microbes also were closely related to the accumulation of metabolites through correlation analysis. Our results indicated that localized appropriate phosphorus fertilizer plays an important role in regulating soil microbial metabolism, and their interactions in soil providing valuable information for understanding how the changed phosphorus management practices affect the complex biological processes and the adaption capacity of plants to environments.
Collapse
Affiliation(s)
- Hongyan Cheng
- State Key Laboratory of Soil Erosion and Dry-land Farming on the Loess Plateau, Northwest A&F University, Yangling 712100, China; College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, China
| | - Minshu Yuan
- Center for Ecological Forecasting and Global Change, College of Forestry, Northwest A&F University, Yangling 712100, China
| | - Liang Tang
- State Key Laboratory of Soil Erosion and Dry-land Farming on the Loess Plateau, Northwest A&F University, Yangling 712100, China; College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, China
| | - Yufang Shen
- State Key Laboratory of Soil Erosion and Dry-land Farming on the Loess Plateau, Northwest A&F University, Yangling 712100, China; College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, China.
| | - Qiang Yu
- State Key Laboratory of Soil Erosion and Dry-land Farming on the Loess Plateau, Northwest A&F University, Yangling 712100, China
| | - Shiqing Li
- State Key Laboratory of Soil Erosion and Dry-land Farming on the Loess Plateau, Northwest A&F University, Yangling 712100, China
| |
Collapse
|
5
|
Nardi P, Laanbroek HJ, Nicol GW, Renella G, Cardinale M, Pietramellara G, Weckwerth W, Trinchera A, Ghatak A, Nannipieri P. Biological nitrification inhibition in the rhizosphere: determining interactions and impact on microbially mediated processes and potential applications. FEMS Microbiol Rev 2021; 44:874-908. [PMID: 32785584 DOI: 10.1093/femsre/fuaa037] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 08/10/2020] [Indexed: 12/11/2022] Open
Abstract
Nitrification is the microbial conversion of reduced forms of nitrogen (N) to nitrate (NO3-), and in fertilized soils it can lead to substantial N losses via NO3- leaching or nitrous oxide (N2O) production. To limit such problems, synthetic nitrification inhibitors have been applied but their performance differs between soils. In recent years, there has been an increasing interest in the occurrence of biological nitrification inhibition (BNI), a natural phenomenon according to which certain plants can inhibit nitrification through the release of active compounds in root exudates. Here, we synthesize the current state of research but also unravel knowledge gaps in the field. The nitrification process is discussed considering recent discoveries in genomics, biochemistry and ecology of nitrifiers. Secondly, we focus on the 'where' and 'how' of BNI. The N transformations and their interconnections as they occur in, and are affected by, the rhizosphere, are also discussed. The NH4+ and NO3- retention pathways alternative to BNI are reviewed as well. We also provide hypotheses on how plant compounds with putative BNI ability can reach their targets inside the cell and inhibit ammonia oxidation. Finally, we discuss a set of techniques that can be successfully applied to solve unresearched questions in BNI studies.
Collapse
Affiliation(s)
- Pierfrancesco Nardi
- Consiglio per la ricerca e l'analisi dell'economia agraria - Research Centre for Agriculture and Environment (CREA-AA), Via della Navicella 2-4, Rome 00184, Italy
| | - Hendrikus J Laanbroek
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands; Ecology and Biodiversity Group, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Graeme W Nicol
- Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, Ecully, 69134, France
| | - Giancarlo Renella
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padua, Viale dell'Università 16, 35020 Legnaro, Italy
| | - Massimiliano Cardinale
- Department of Biological and Environmental Sciences and Technologies - DiSTeBA, University of Salento, Centro Ecotekne - via Provinciale Lecce-Monteroni, I-73100, Lecce, Italy
| | - Giacomo Pietramellara
- Department of Agriculture, Food, Environment and Forestry, University of Firenze, P.le delle Cascine 28, Firenze 50144, Italy
| | - Wolfram Weckwerth
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, University of Vienna, Althanstrasse 14, Vienna, 1090, Austria; Vienna Metabolomics Center (VIME), University of Vienna, Althanstrasse 14, Vienna, 1090, Austria
| | - Alessandra Trinchera
- Consiglio per la ricerca e l'analisi dell'economia agraria - Research Centre for Agriculture and Environment (CREA-AA), Via della Navicella 2-4, Rome 00184, Italy
| | - Arindam Ghatak
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, University of Vienna, Althanstrasse 14, Vienna, 1090, Austria
| | - Paolo Nannipieri
- Department of Agriculture, Food, Environment and Forestry, University of Firenze, P.le delle Cascine 28, Firenze 50144, Italy
| |
Collapse
|
6
|
Jakl M, Kovač I, Ćavar Zeljković S, Jaklová Dytrtová J. Triazole fungicides in soil affect the yield of fruit, green biomass, and phenolics production of Solanum lycopersicum L. Food Chem 2021; 351:129328. [PMID: 33647697 DOI: 10.1016/j.foodchem.2021.129328] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 02/05/2021] [Accepted: 02/06/2021] [Indexed: 12/14/2022]
Abstract
A part of the fungicides used in foliar treatment penetrates into the soil. This study describes changes in the bioavailability of (essential) elements in soil, fructification, the amount of green biomass and the production of phenolic compounds related solely to the presence of triazoles (penconazole and cyproconazole) in soil, injected as a single compound or their mixture. The triazoles presence has substantially affected the bioavailability of Fe, Cu and Zn in soil. The amount of green biomass has significantly decreased, whereas the chlorophylls a and b have not been affected. As a potential mark of plant stress, the fruits of the treated variants are significantly bigger. The content of phenolics in tomato peel (e.g. quercetin, quercitrin, hesperidin, naringin, and chlorogenic, salicylic and p-coumaric acid) has been quantified. The biggest changes (increase/decrease) have been observed in the contents of p-coumaric and chlorogenic acid, quercetin and quercitrin.
Collapse
Affiliation(s)
- Michal Jakl
- Czech University of Life Sciences Prague, Faculty of Agrobiology, Food and Natural Resources, Department of Agro-Environmental Chemistry and Plant Nutrition, Kamýcká 129, 165 00 Prague - Suchdol, Czech Republic
| | - Ishak Kovač
- Czech Academy of Sciences, Institute of Organic Chemistry and Biochemistry, Flemingovo nám. 542/2, 166 10 Prague 6, Czech Republic; Charles University, Faculty of Science, Department of Analytical Chemistry, Hlavova 2030, 128 43 Prague 2, Czech Republic
| | - Sanja Ćavar Zeljković
- Centre of the Region Haná for Biotechnological and Agricultural Research, Department of Genetic Resources for Vegetables, Medicinal and Special Plants, Crop Research Institute, Šlechtitelů 892/29, 783 71 Olomouc, Czech Republic; Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University, Department of Phytochemistry, Šlechtitelů 241/27, 783 71 Olomouc, Czech Republic
| | - Jana Jaklová Dytrtová
- Czech Academy of Sciences, Institute of Organic Chemistry and Biochemistry, Flemingovo nám. 542/2, 166 10 Prague 6, Czech Republic; Charles University, Faculty of Physical Education and Sport, Department of Physiology and Biochemistry, José Martího 269/31, 162 52 Prague 6, Czech Republic.
| |
Collapse
|
7
|
Baune M, Kang K, Schenkeveld WDC, Kraemer SM, Hayen H, Weber G. Importance of oxidation products in coumarin-mediated Fe(hydr)oxide mineral dissolution. Biometals 2020; 33:305-321. [DOI: 10.1007/s10534-020-00248-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 09/12/2020] [Indexed: 12/18/2022]
|
8
|
Liu C, Lin H, Li B, Dong Y, Yin T. Responses of microbial communities and metabolic activities in the rhizosphere during phytoremediation of Cd-contaminated soil. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 202:110958. [PMID: 32800230 DOI: 10.1016/j.ecoenv.2020.110958] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/27/2020] [Accepted: 06/28/2020] [Indexed: 06/11/2023]
Abstract
Phytoremediation is an effective way to repair heavy metal contaminated soil and rhizosphere microorganisms play an important role in plant regulation. Nevertheless, little information is known about the variation of microbial metabolic activities and community structure in rhizosphere during phytoremediation. In this study, the rhizosphere soil microbial metabolic activities and community structure of Trifolium repensL. during Cd-contaminated soil phytoremediation, were analyzed by Biolog EcoPlate™ and high-throughput sequencing. The uptake in the roots of Trifolium repensL. grown in 5.68 and 24.23 mg/kg Cd contaminated soil was 33.51 and 84.69 mg/kg respectively, causing the acid-soluble Cd fractions decreased 7.3% and 5.4%. Phytoremediation significantly influenced microbial community and Trifolium repensL. planting significantly increased the rhizosphere microbial population, diversity, the relative abundance of plant growth promoting bacteria (Kaistobacter and Flavisolibacter), and the utilization of difficultly metabolized compounds. The correlation analysis among substrate utilization and microbial communities revealed that the relative abundance increased microorganisms possessed stronger carbon utilization capacity, which was beneficial to regulate the stability of plant-microbial system. Collectively, the results of this study provide fundamental insights into the microbial metabolic activities and community structure during heavy metal contaminated soil phytoremediation, which may aid in the bioregulation of phytoremediation.
Collapse
Affiliation(s)
- Chenjing Liu
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, 100083, China; Beijing Key Laboratory on Resource-Oriented Treatment of Industrial Pollutants, Beijing, 100083, China
| | - Hai Lin
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, 100083, China; Beijing Key Laboratory on Resource-Oriented Treatment of Industrial Pollutants, Beijing, 100083, China.
| | - Bing Li
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, 100083, China; Beijing Key Laboratory on Resource-Oriented Treatment of Industrial Pollutants, Beijing, 100083, China
| | - Yingbo Dong
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, 100083, China; Beijing Key Laboratory on Resource-Oriented Treatment of Industrial Pollutants, Beijing, 100083, China.
| | - Tingting Yin
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, 100083, China; Beijing Key Laboratory on Resource-Oriented Treatment of Industrial Pollutants, Beijing, 100083, China
| |
Collapse
|
9
|
Nguyen TD, Lesani M, Forrest I, Lan Y, Dean DA, Gibaut QMR, Guo Y, Hossain E, Olvera M, Panlilio H, Parab AR, Wu C, Bernatchez JA, Cichewicz RH, McCall LI. Local Phenomena Shape Backyard Soil Metabolite Composition. Metabolites 2020; 10:E86. [PMID: 32121389 PMCID: PMC7143036 DOI: 10.3390/metabo10030086] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 02/26/2020] [Accepted: 02/27/2020] [Indexed: 01/10/2023] Open
Abstract
Soil covers most of Earth's continental surface and is fundamental to life-sustaining processes such as agriculture. Given its rich biodiversity, soil is also a major source for natural product drug discovery from soil microorganisms. However, the study of the soil small molecule profile has been challenging due to the complexity and heterogeneity of this matrix. In this study, we implemented high-resolution liquid chromatography-tandem mass spectrometry and large-scale data analysis tools such as molecular networking to characterize the relative contributions of city, state and regional processes on backyard soil metabolite composition, in 188 soil samples collected from 14 USA States, representing five USA climate regions. We observed that region, state and city of collection all influence the overall soil metabolite profile. However, many metabolites were only detected in unique sites, indicating that uniquely local phenomena also influence the backyard soil environment, with both human-derived and naturally-produced (plant-derived, microbially-derived) metabolites identified. Overall, these findings are helping to define the processes that shape the backyard soil metabolite composition, while also highlighting the need for expanded metabolomic studies of this complex environment.
Collapse
Affiliation(s)
- Tra D. Nguyen
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA
| | - Mahbobeh Lesani
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Ines Forrest
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA
| | - Yunpeng Lan
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA
| | - Danya A. Dean
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA
| | - Quentin M. R. Gibaut
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA
| | - Yanting Guo
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA
| | - Ekram Hossain
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA
| | - Marcela Olvera
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA
| | - Hannah Panlilio
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA
| | - Adwaita R. Parab
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Chaoyi Wu
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA
| | - Jean A. Bernatchez
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
- Center for Discovery and Innovation in Parasitic Diseases, University of California, San Diego, La Jolla, CA 92093, USA
| | - Robert H. Cichewicz
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA
| | - Laura-Isobel McCall
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
- Stephenson Cancer Center, University of Oklahoma, Oklahoma City, OK 73104, USA
- Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, OK 73019, USA
| |
Collapse
|
10
|
Song W, Tong X, Liu Y, Li W. Microbial Community, Newly Sequestered Soil Organic Carbon, and δ 15N Variations Driven by Tree Roots. Front Microbiol 2020; 11:314. [PMID: 32174905 PMCID: PMC7056912 DOI: 10.3389/fmicb.2020.00314] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 02/12/2020] [Indexed: 12/04/2022] Open
Abstract
Rhizosphere microbes in forests are key elements of the carbon sequestration of terrestrial ecosystems. To date, little is known about how the diversity and species interactions of the active rhizomicrobial community change during soil carbon sequestration and what interactions drive these changes. In this study, we used a combination of DNA and stable isotope method to explore correlations between the composition of microbial communities, N transformation, and the sequestration de novo of carbon in soils around Pinus tabuliformis and Quercus variabilis roots in North China. Rhizosphere soils from degraded lands, primary stage land (tree roots had colonized in degraded soil for 1 year), and nature forest were sampled for analyses. The results showed that microbial communities and newly sequestered soil organic carbon (SOC) contents changed with different tree species, environments, and successive stages. The fungal unweighted and weighted UniFrac distances could better show the different microbial species structures and differences in successive stages. Newly sequestered SOC was positively correlated with the bacterial order Rhizobiales (in P. tabuliformis forests), the fungal order Russulales (in Q. variabilis forests), and δ15N. Consequently, the bacterial order Rhizobiales acted as an important taxa for P. tabuliformis root-driven carbon sequestration, and the fungal order Russulales acted as an important taxa for Q. variabilis root-driven carbon sequestration. The two plant species allocated root exudates to different portion of their root systems, which in turn altered microbial community composition and function. The δ15N of soil organic matter could be an important indicator to estimate root-driven carbon sequestration.
Collapse
Affiliation(s)
- Wenchen Song
- College of Forestry, Beijing Forestry University, Beijing, China
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xiaojuan Tong
- College of Forestry, Beijing Forestry University, Beijing, China
| | - Yanhong Liu
- Key Laboratory for Forest Resources and Ecosystem Processes of Beijing, Beijing Forestry University, Beijing, China
| | - Weike Li
- College of Forestry, Beijing Forestry University, Beijing, China
| |
Collapse
|
11
|
|
12
|
Mastronardi E, Monreal C, DeRosa MC. Personalized Medicine for Crops? Opportunities for the Application of Molecular Recognition in Agriculture. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:6457-6461. [PMID: 28985063 DOI: 10.1021/acs.jafc.7b03295] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
This perspective examines the detection of rhizosphere biomarkers, namely, root exudates and microbial metabolites, using molecular recognition elements, such as molecularly imprinted polymers, antibodies, and aptamers. Tracking these compounds in the rhizosphere could provide valuable insight into the status of the crop and soil in a highly localized way. The outlook and potential impact of the combination of molecular recognition and other innovations, such as nanotechnology and precision agriculture, and the comparison to advances in personalized medicine are considered.
Collapse
Affiliation(s)
- Emily Mastronardi
- Department of Chemistry , Carleton University , 1125 Colonel By Drive , Ottawa , Ontario K1S 5B6 , Canada
| | - Carlos Monreal
- Agriculture and Agrifood Canada , 960 Carling Avenue , Neatby Building, Ottawa , Ontario K1Y 4X2 , Canada
| | - Maria C DeRosa
- Department of Chemistry , Carleton University , 1125 Colonel By Drive , Ottawa , Ontario K1S 5B6 , Canada
| |
Collapse
|
13
|
Wu H, Xu J, Wang J, Qin X, Wu L, Li Z, Lin S, Lin W, Zhu Q, Khan MU, Lin W. Insights into the Mechanism of Proliferation on the Special Microbes Mediated by Phenolic Acids in the Radix pseudostellariae Rhizosphere under Continuous Monoculture Regimes. FRONTIERS IN PLANT SCIENCE 2017; 8:659. [PMID: 28512464 PMCID: PMC5411758 DOI: 10.3389/fpls.2017.00659] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 04/11/2017] [Indexed: 05/11/2023]
Abstract
As potent allelochemicals, phenolic acids are believed to be associated with replanting disease and cause microflora shift and structural disorder in the rhizosphere soil of continuously monocultured Radix pseudostellariae. The transcriptome sequencing was used to reveal the mechanisms underlying the differential response of pathogenic bacterium Kosakonia sacchari and beneficial bacterium Bacillus pumilus on their interactions with phenolic acids, the main allelochemicals in root exudates of R. pseudostellariae in the monoculture system. The microbes were inoculated in the pots containing soil and the medicinal plant in this study. The results showed that the addition of beneficial B. pumilus to the 2-year planted soil significantly decreased the activity of soil urease, catalase, sucrase, and cellulase and increased the activity of chitinase compared with those in the 2nd-year monocropping rhizosphere soil without any treatment. However, opposite results were obtained when K. sacchari was added. Transcriptome analysis showed that vanillin enhanced glycolysis/gluconeogenesis, fatty acid biosynthesis, pentose phosphate, bacterial chemotaxis, flagellar assembly, and phosphotransferase system pathway in K. sacchari. However, protocatechuic acid, a metabolite produced by K. sacchari from vanillin, had negative effects on the citrate cycle and biosynthesis of novobiocin, phenylalanine, tyrosine, and tryptophan in B. pumilus. Concurrently, the protocatechuic acid decreased the biofilm formation of B. pumilus. These results unveiled the mechanisms how phenolic acids differentially mediate the shifts of microbial flora in rhizosphere soil, leading to the proliferation of pathogenic bacteria (i.e., K. sacchari) and the attenuation of beneficial bacteria (i.e., B. pumilus) under the monocropping system of R. pseudostellariae.
Collapse
Affiliation(s)
- Hongmiao Wu
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry UniversityFuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Junjian Xu
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry UniversityFuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Juanying Wang
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry UniversityFuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Xianjin Qin
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry UniversityFuzhou, China
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops/College of Crop Science, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Linkun Wu
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry UniversityFuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Zhicheng Li
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry UniversityFuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Sheng Lin
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry UniversityFuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Weiwei Lin
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry UniversityFuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Quan Zhu
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry UniversityFuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Muhammad U. Khan
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry UniversityFuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Wenxiong Lin
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry UniversityFuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry UniversityFuzhou, China
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops/College of Crop Science, Fujian Agriculture and Forestry UniversityFuzhou, China
- *Correspondence: Wenxiong Lin,
| |
Collapse
|