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Ouyang Y, Cheng Q, Cheng C, Tang Z, Huang Y, Tan E, Ma S, Lin X, Xie Y, Zhou H. Effects of plants-associated microbiota on cultivation and quality of Chinese herbal medicines. CHINESE HERBAL MEDICINES 2024; 16:190-203. [PMID: 38706825 PMCID: PMC11064599 DOI: 10.1016/j.chmed.2022.12.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 10/24/2022] [Accepted: 12/29/2022] [Indexed: 02/05/2023] Open
Abstract
Microbial resource influences the life activities of medicinal plants from several perspectives. Endophytes, rhizosphere microorganisms, and other environmental microorganisms play essential roles in medicinal plant growth and development, plant yield, and clinical efficacy. The microbiota can influence the biosynthesis of active compounds in medicinal plants by stimulating specific metabolic pathways. They induce host plants to improve their resistance to environmental stresses by accumulating secondary metabolites. Microorganisms can interact with their host plants to produce long-term, targeted selection results and improve their ability to adapt to the environment. Due to the interdependence and interaction between microorganisms and medicinal plants, Chinese herbal medicines (CHMs) quality is closely related to the associated microorganisms. This review summarizes the relationship between medicinal plants and their associated microorganisms, including their species, distribution, life activities, and metabolites. Microorganisms can aid in quality control, improve the efficacy of medicinal plants, and provide markers for identifying the origin and storage time of CHMs. Therefore, a comprehensive understanding of the relationship between microorganisms and medicinal plants will help to control the quality of CHMs from different perspectives.
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Affiliation(s)
- Yue Ouyang
- Faculty of Chinese Medicine, Macau University of Science and Technology, Macao 999078, China
| | - Qiqing Cheng
- Faculty of Chinese Medicine, Macau University of Science and Technology, Macao 999078, China
- School of Pharmacy, Hubei University of Science and Technology, Xianning 437100, China
| | - Chunsong Cheng
- Key Laboratory of Plant Ex-situ Conservation and Research Center of Resource Plant, Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang 332900, China
| | - Ziyu Tang
- Faculty of Chinese Medicine, Macau University of Science and Technology, Macao 999078, China
| | - Yufeng Huang
- Guangdong Provincial Hospital of Chinese Medicine, Guangdong Provincial Academy of Chinese Medical Sciences, State Key Laboratory of Dampness Syndrome of Chinese Medicine, Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, Guangzhou 510006, China
| | - Eyu Tan
- Guangdong Provincial Hospital of Chinese Medicine, Guangdong Provincial Academy of Chinese Medical Sciences, State Key Laboratory of Dampness Syndrome of Chinese Medicine, Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, Guangzhou 510006, China
- Jiangmen Wuyi Hospital of Traditional Chinese Medicine, Jiangmen 529020, China
- Joint Laboratory for Translational Cancer Research of Chinese Medicine, Ministry of Education, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Shaofeng Ma
- Jiangmen Wuyi Hospital of Traditional Chinese Medicine, Jiangmen 529020, China
| | - Xinheng Lin
- Jiangmen Wuyi Hospital of Traditional Chinese Medicine, Jiangmen 529020, China
| | - Ying Xie
- Guangdong Provincial Hospital of Chinese Medicine, Guangdong Provincial Academy of Chinese Medical Sciences, State Key Laboratory of Dampness Syndrome of Chinese Medicine, Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, Guangzhou 510006, China
- Faculty of Chinese Medicine, Macau University of Science and Technology, Macao 999078, China
| | - Hua Zhou
- Guangdong Provincial Hospital of Chinese Medicine, Guangdong Provincial Academy of Chinese Medical Sciences, State Key Laboratory of Dampness Syndrome of Chinese Medicine, Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, Guangzhou 510006, China
- Faculty of Chinese Medicine, Macau University of Science and Technology, Macao 999078, China
- Joint Laboratory for Translational Cancer Research of Chinese Medicine, Ministry of Education, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
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Wu L, Zhao B, Deng Z, Wang B, Yu Y. A biosynthetic network for protoberberine production in Coptis chinensis. HORTICULTURE RESEARCH 2024; 11:uhad259. [PMID: 38282690 PMCID: PMC10812381 DOI: 10.1093/hr/uhad259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 11/26/2023] [Indexed: 01/30/2024]
Abstract
Protoberberine alkaloids are a group of tetracyclic isoquinoline compounds known for their well-established antimicrobial and anti-inflammatory properties. The richness and diversity of protoberberine alkaloids accumulated in the Coptis genus necessitate a comprehensive examination of the biosynthetic machinery to understand their ecological significance. Here, from Coptis chinensis we identified CcCYP719A1, which could install a methylenedioxy bridge on either ring A or ring D of the protoberberine backbone, thus diverging metabolite flux towards the biosynthesis of various protoberberine components. We also obtained CcCYP719A2 and CcCYP719A3, which underwent positive selection after diverging from CcCYP719A1 and maintained specific catalytic activity on ring D. Further, we resolved the biosynthetic pathway of jatrorrhizine by identifying two demethylases, which could also modulate protoberberine composition by removing the C-3 methyl group and methylenedioxy bridge of ring D, allowing demethylated metabolites to be redirected into different routes. Moreover, we characterized 2-O-methyltransferase CcOMT1 and flavin-dependent oxidase CcTHBO, respectively responsible for the commonly observed 2-O-methylation and aromatic ring-C assembly in protoberberine alkaloids. Overall, this study reveals an interconnected metabolite network from which diverse protoberberine alkaloids originate. It provides valuable insights into the existence of undiscovered protoberberine components, and paves the way for the targeted production of desired protoberberine components for potential therapeutic development.
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Affiliation(s)
- Linrui Wu
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Disease, School of Pharmaceutical Sciences, Wuhan University, 185 East Lake Road, Wuhan 430071, China
| | - Binxin Zhao
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Disease, School of Pharmaceutical Sciences, Wuhan University, 185 East Lake Road, Wuhan 430071, China
| | - Zixin Deng
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Disease, School of Pharmaceutical Sciences, Wuhan University, 185 East Lake Road, Wuhan 430071, China
| | - Bin Wang
- State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Academy of Sciences, Nanning 530007, China
| | - Yi Yu
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Disease, School of Pharmaceutical Sciences, Wuhan University, 185 East Lake Road, Wuhan 430071, China
- State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Academy of Sciences, Nanning 530007, China
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Amon CER, Fossou RK, Ebou AET, Koua DK, Kouadjo CG, Brou YC, Voko Bi DRR, Cowan DA, Zézé A. The core bacteriobiome of Côte d'Ivoire soils across three vegetation zones. Front Microbiol 2023; 14:1220655. [PMID: 37692382 PMCID: PMC10483230 DOI: 10.3389/fmicb.2023.1220655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 08/08/2023] [Indexed: 09/12/2023] Open
Abstract
The growing understanding that soil bacteria play a critical role in ecosystem servicing has led to a number of large-scale biogeographical surveys of soil microbial diversity. However, most of such studies have focused on northern hemisphere regions and little is known of either the detailed structure or function of soil microbiomes of sub-Saharan African countries. In this paper, we report the use of high-throughput amplicon sequencing analyses to investigate the biogeography of soil bacteria in soils of Côte d'Ivoire. 45 surface soil samples were collected from Côte d'Ivoire, representing all major biomes, and bacterial community composition was assessed by targeting the V4-V5 hypervariable region of the 16S ribosomal RNA gene. Causative relationships of both soil physicochemical properties and climatic data on bacterial community structure were infered. 48 phyla, 92 classes, 152 orders, 356 families, and 1,234 genera of bacteria were identified. The core bacteriobiome consisted of 10 genera ranked in the following order of total abundance: Gp6, Gaiella, Spartobacteria_genera_incertae_sedis, WPS-1_genera_incertae_sedis, Gp4, Rhodoplanes, Pseudorhodoplanes, Bradyrhizobium, Subdivision3_genera_incertae_sedis, and Gp3. Some of these genera, including Gp4 and WPS-1_genera_incertae_sedis, were unequally distributed between forest and savannah areas while other taxa (Bradyrhizobium and Rhodoplanes) were consistently found in all biomes. The distribution of the core genera, together with the 10 major phyla, was influenced by several environmental factors, including latitude, pH, Al and K. The main pattern of distribution that was observed for the core bacteriobiome was the vegetation-independent distribution scheme. In terms of predicted functions, all core bacterial taxa were involved in assimilatory sulfate reduction, while atmospheric dinitrogen (N2) reduction was only associated with the genus Bradyrhizobium. This work, which is one of the first such study to be undertaken at this scale in Côte d'Ivoire, provides insights into the distribution of bacterial taxa in Côte d'Ivoire soils, and the findings may serve as biological indicator for land management in Côte d'Ivoire.
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Affiliation(s)
- Chiguié Estelle Raïssa Amon
- Laboratoire de Biotechnologies Végétale et Microbienne, UMRI Sciences Agronomiques et Génie rural, Institut National Polytechnique Félix Houphouët-Boigny, Yamoussoukro, Côte d'Ivoire
| | - Romain Kouakou Fossou
- Laboratoire de Biotechnologies Végétale et Microbienne, UMRI Sciences Agronomiques et Génie rural, Institut National Polytechnique Félix Houphouët-Boigny, Yamoussoukro, Côte d'Ivoire
| | - Anicet E. T. Ebou
- Laboratoire de Biotechnologies Végétale et Microbienne, UMRI Sciences Agronomiques et Génie rural, Institut National Polytechnique Félix Houphouët-Boigny, Yamoussoukro, Côte d'Ivoire
| | - Dominiqueua K. Koua
- Laboratoire de Biotechnologies Végétale et Microbienne, UMRI Sciences Agronomiques et Génie rural, Institut National Polytechnique Félix Houphouët-Boigny, Yamoussoukro, Côte d'Ivoire
| | - Claude Ghislaine Kouadjo
- Laboratoire Central de Biotechnologies, Centre National de la Recherche Agronomique, Abidjan, Côte d’Ivoire
| | - Yao Casimir Brou
- Laboratoire de Biotechnologies Végétale et Microbienne, UMRI Sciences Agronomiques et Génie rural, Institut National Polytechnique Félix Houphouët-Boigny, Yamoussoukro, Côte d'Ivoire
| | - Don Rodrigue Rosin Voko Bi
- Unité de Formation et de Recherche en Agroforesterie, Université Jean Lorougnon Guédé, Daloa, Côte d’Ivoire
| | - Don A. Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Adolphe Zézé
- Laboratoire de Biotechnologies Végétale et Microbienne, UMRI Sciences Agronomiques et Génie rural, Institut National Polytechnique Félix Houphouët-Boigny, Yamoussoukro, Côte d'Ivoire
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Ghouili E, Abid G, Hogue R, Jeanne T, D'Astous-Pagé J, Sassi K, Hidri Y, M'Hamed HC, Somenahally A, Xue Q, Jebara M, Nefissi Ouertani R, Riahi J, de Oliveira AC, Muhovski Y. Date Palm Waste Compost Application Increases Soil Microbial Community Diversity in a Cropping Barley ( Hordeum vulgare L.) Field. BIOLOGY 2023; 12:biology12040546. [PMID: 37106747 PMCID: PMC10135526 DOI: 10.3390/biology12040546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/29/2023] [Accepted: 04/01/2023] [Indexed: 04/29/2023]
Abstract
Application of date palm waste compost is quite beneficial in improving soil properties and crop growth. However, the effect of its application on soil microbial communities is less understood. High-throughput sequencing and quantitative real-time PCR (qPCR) were used to evaluate the effect of compost application on the soil microbial composition in a barley field during the tillering, booting and ripening stages. The results showed that compost treatment had the highest bacterial and fungal abundance, and its application significantly altered the richness (Chao1 index) and α-diversity (Shannon index) of fungal and bacterial communities. The dominant bacterial phyla found in the samples were Proteobacteria and Actinobacteria while the dominant fungal orders were Ascomycota and Mortierellomycota. Interestingly, compost enriched the relative abundance of beneficial microorganisms such as Chaetomium, Actinobacteriota, Talaromyces and Mortierella and reduced those of harmful microorganisms such as Alternaria, Aspergillus and Neocosmospora. Functional prediction based on Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) showed that amplicon sequence variant (ASV) sequences related to energy metabolism, amino acid metabolism and carbohydrate metabolism were associated with compost-treated soil. Based on Fungi Functional Guild (FUNGuild), identified fungi community metabolic functions such as wood saprotroph, pathotroph, symbiotroph and endophyte were associated with compost-treated soil. Overall, compost addition could be considered as a sustainable practice for establishing a healthy soil microbiome and subsequently improving the soil quality and barley crop production.
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Affiliation(s)
- Emna Ghouili
- Laboratory of Legumes and Sustainable Agrosystems, Centre of Biotechnology of Borj-Cedria, (L2AD, CBBC), Hammam-Lif 2050, PB 901, Tunisia
| | - Ghassen Abid
- Laboratory of Legumes and Sustainable Agrosystems, Centre of Biotechnology of Borj-Cedria, (L2AD, CBBC), Hammam-Lif 2050, PB 901, Tunisia
| | - Richard Hogue
- Microbial Ecology Laboratory, Research and Development Institute for the Agri-Environment (IRDA), Einstein Street 2700, Québec City, QC G1P 3W8, Canada
| | - Thomas Jeanne
- Microbial Ecology Laboratory, Research and Development Institute for the Agri-Environment (IRDA), Einstein Street 2700, Québec City, QC G1P 3W8, Canada
| | - Joël D'Astous-Pagé
- Microbial Ecology Laboratory, Research and Development Institute for the Agri-Environment (IRDA), Einstein Street 2700, Québec City, QC G1P 3W8, Canada
| | - Khaled Sassi
- Laboratory of Agronomy, National Agronomy Institute of Tunisia (INAT), University of Carthage, Avenue Charles Nicolle, Tunis-Mahrajène 1082, BP 43, Tunisia
| | - Yassine Hidri
- Olive Tree Institute, Laboratory of Integrated Olive Production in the Humid, Sub-humid and Semi-arid Region (LR16IO3), Cité Mahragène 1082, BP 208, Tunisia
| | - Hatem Cheikh M'Hamed
- Agronomy Laboratory, National Institute of Agronomic Research of Tunis (INRAT), University of Carthage, Hedi Karray Street, Ariana 2049, Tunisia
| | - Anil Somenahally
- Department of Soil and Crop Sciences, Texas A&M University, 370 Olsen Blvd., College Station, TX 77843-2474, USA
| | - Qingwu Xue
- Texas A&M AgriLife Research and Extension Center, Amarillo, TX 79106, USA
| | - Moez Jebara
- Laboratory of Legumes and Sustainable Agrosystems, Centre of Biotechnology of Borj-Cedria, (L2AD, CBBC), Hammam-Lif 2050, PB 901, Tunisia
| | - Rim Nefissi Ouertani
- Laboratory of Plant Molecular Physiology, Centre of Biotechnology of Borj Cedria, Hammam-Lif 2050, BP 901, Tunisia
| | - Jouhaina Riahi
- Technical Center for Organic Agriculture, Chott Mariem, Sousse 4042, BP 54, Tunisia
| | - Ana Caroline de Oliveira
- Biological Engineering Unit, Department of Life Sciences, Walloon Agricultural Research Centre, Chaussée de Charleroi, 5030 Gembloux, 234 BP, Belgium
| | - Yordan Muhovski
- Biological Engineering Unit, Department of Life Sciences, Walloon Agricultural Research Centre, Chaussée de Charleroi, 5030 Gembloux, 234 BP, Belgium
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Song X, Mei P, Dou T, Liu Q, Li L. Multi-Omics Analysis Reveals the Resistance Mechanism and the Pathogens Causing Root Rot of Coptis chinensis. Microbiol Spectr 2023; 11:e0480322. [PMID: 36809123 PMCID: PMC10101010 DOI: 10.1128/spectrum.04803-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 01/31/2023] [Indexed: 02/23/2023] Open
Abstract
Coptis chinensis is a traditional Chinese medicinal herb used for more than 2,000 years. Root rot in C. chinensis can cause brown discoloration (necrosis) in the fibrous roots and rhizomes, leading to plants wilting and dying. However, little information exists about the resistance mechanism and the potential pathogens of the root rot of C. chinensis plants. As a result, in order to investigate the relationship between the underlying molecular processes and the pathogenesis of root rot, transcriptome and microbiome analyses were performed on healthy and diseased C. chinensis rhizomes. This study found that root rot can lead to the significant reduction of medicinal components of Coptis, including thaliotrine, columbamine, epiberberin, coptisine, palmatine chloride, and berberine, affecting its efficacy quality. In the present study, Diaporthe eres, Fusarium avenaceum, and Fusarium solani were identified as the main pathogens causing root rot in C. chinensis. At the same time, the genes in phenylpropanoid biosynthesis, plant hormone signal transduction, plant-pathogen interaction, and alkaloid synthesis pathways were involved in the regulation of root rot resistance and medicinal component synthesis. In addition, harmful pathogens (D. eres, F. avenaceum and F. solani) also induce the expression of related genes in C. chinensis root tissues to reduce active medicinal ingredients. These results provide insights into the root rot tolerance study and pave the way for process disease resistance breeding and quality production of C. chinensis. IMPORTANCE Root rot disease significantly reduces the medicinal quality of Coptis chinensis. In the present study, results found that the C. chinensis fibrous and taproot have different tactics in response to rot pathogen infection. Diaporthe eres, Fusarium avenaceum, and Fusarium solani were isolated and identified to cause different degrees of C. chinensis root rot. These results are helpful for researchers to further explore the mechanism of resistance to rhizoma Coptis root rot.
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Affiliation(s)
- Xuhong Song
- Chongqing Academy of Chinese Materia Medica, Chongqing, People’s Republic of China
| | - Pengying Mei
- Chongqing Academy of Chinese Materia Medica, Chongqing, People’s Republic of China
| | - Tao Dou
- Chongqing Academy of Chinese Materia Medica, Chongqing, People’s Republic of China
| | - Qundong Liu
- Chongqing Academy of Chinese Materia Medica, Chongqing, People’s Republic of China
| | - Longyun Li
- Chongqing Academy of Chinese Materia Medica, Chongqing, People’s Republic of China
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Effect of Different Types of Continuous Cropping on Microbial Communities and Physicochemical Properties of Black Soils. DIVERSITY 2022. [DOI: 10.3390/d14110954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The barriers caused by continuous tillage have had a negative impact on the crop and soil environment. Black soils are economically important as a valuable natural resource in Northeast China, but limited soil resources have led to continuous planting of major food crops and medicinal plants. At present, the extent to which two different types of plants—grains and medicinal plants that are successively grown on the same soil—have an impact on soil quality and microbiology is not known. In this study, we investigated the effects of different types of long-term continuous cropping on soil and soil microbial communities by determining the physicochemical properties, the soil community composition and function of grain crops and medicinal-plant soils with more than five years of continuous cropping, as well as fallow soils. The results showed that long-term continuous cropping reduced the pH of different types of soils, but there was no significant difference in the content of AK. The relative abundance of beneficial dominant phyla, such as Actinomycetes, Acidobacteria, and Green Campylobacter decreased and the relative abundance of pathogenic genera such as Alternaria and Didymellaceae, increased after the long-term continuous cropping of DM (grain crops) and DG (medicinal plants). Specifically, continuous cropping increased the relative abundance of fungi with pathogenic potential, such as Sordariomycetes, Dothideomycetes, Saccharomycetes, and Mucoromycetes in grain soils and Agaricostilbomycetes in herb soils. Among the soil physicochemical properties, NH4+-N and pH were the most important factors contributing to changes in the composition of bacterial and fungal communities, respectively. Continuous cropping of different types of plants altered the diversity of the microbial communities, with the most significant effect from the continuous cropping of food crops. Our findings provide a scientific and theoretical basis for future agricultural research to improve soil microbial activity, mitigate continuous-cropping barriers, and increase productivity.
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Liu W, Qiu K, Xie Y, Wang R, Li H, Meng W, Yang Y, Huang Y, Li Y, He Y. Years of sand fixation with Caragana korshinskii drive the enrichment of its rhizosphere functional microbes by accumulating soil N. PeerJ 2022; 10:e14271. [PMID: 36340191 PMCID: PMC9635361 DOI: 10.7717/peerj.14271] [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: 06/06/2022] [Accepted: 09/28/2022] [Indexed: 11/05/2022] Open
Abstract
C. korshinskii is one of the most widely-planted sand-fixing legumes in northwest China and exploring its rhizosphere microbiome is of great ecological importance. However, the effect of long-term sand fixation on the composition, diversity, and underlying functions of microbes in the C. korshinskii rhizosphere in dryland ecosystems remain unclear. Here, we performed high-throughput sequencing using a 16S rRNA (absolute quantification) and bacterial functional annotation of prokaryotic taxa (FAPROTAX) analysis and an ITS (relative quantification) and fungal functional guild (FUNGuild) analysis to investigate the C. korshinskii rhizosphere microbiome and metabolic functional groups at different sand-fixing ages (six years, CK6; twelve years, CK12; and eighteen years, CK18) and determined the physicochemical properties of the rhizosphere soil. Results showed that the key bacterial taxa of the rhizosphere were significantly more abundant in CK18 than in CK12 and CK6 at the phylum-class-genus level, and that fungal Glomeromycota was also significantly more abundant in the CK18 rhizosphere compared to CK12 and CK6. Among these bacterial taxa, the enrichment effect of key, functional, genus-level species of bacteria was the most obvious, including Rhizobium, Ensifer, Neorhizobium, Mesorhizobium, Streptomyces, Sphingomonas, and Flavobacterium, which are N-fixing and/or phosphate-solubilizing groups. The significant improvement seen in the physicochemical properties of the CK18 rhizosphere soil, including the higher total nitrogen (TN), available nitrogen (AN), pH, electrical conductivity (EC), higher N:P ratio, and lower C:N ratio, all demonstrated the relationship between the rhizosphere microbes and soil carbon (C) and nitrogen (N) cycling. A redundancy analysis (RDA) of different taxonomic levels indicated a close positive relationship between rhizosphere microbes and AN. In addition, the functional groups of the C. korshinskii rhizosphere bacteria were closely related to soil AN and were mainly composed of chemoheterotrophy and aerobic chemoheterotrophy. A Spearman correlation analysis revealed that these functional groups were mainly identified from bacterial Actinobacteria, Proteobacteria, Verrucomicrobia, Bacteroidetes, and fungal Glomeromycota. Our study provides evidence that the rhizosphere microbes of C. korshinskii are closely related to the accumulation of N in the restoration of desert ecosystems, and that the ecological functional processes they are involved in mainly involve C and N cycles, which play an important role in desertification reversal.
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Affiliation(s)
- Wangsuo Liu
- School of Agriculture, Ningxia University, Yinchuan, China,Department of Desertification Prevention, Ningxia Grape Wine and Desertification Prevention Technical College, Yinchuan, Ningxia, China
| | - Kaiyang Qiu
- School of Agriculture, Ningxia University, Yinchuan, China,Breeding Base for State Key Laboratory of Land Degradation and Ecological Restoration of Northwest China, Yinchuan, China,Ningxia Grassland and Animal Husbandry Engineering Technology Research Center, Yinchuan, China
| | - Yingzhong Xie
- School of Agriculture, Ningxia University, Yinchuan, China,Breeding Base for State Key Laboratory of Land Degradation and Ecological Restoration of Northwest China, Yinchuan, China,Ningxia Grassland and Animal Husbandry Engineering Technology Research Center, Yinchuan, China
| | - Ruixia Wang
- Ningxia Administration of Baijitan National Nature Reserve, Yinchuan, China
| | - Haichao Li
- Ningxia Administration of Baijitan National Nature Reserve, Yinchuan, China
| | - Wenfen Meng
- School of Agriculture, Ningxia University, Yinchuan, China
| | - Yi Yang
- School of Agriculture, Ningxia University, Yinchuan, China
| | - Yeyun Huang
- School of Agriculture, Ningxia University, Yinchuan, China
| | - Yayuan Li
- School of Agriculture, Ningxia University, Yinchuan, China
| | - Yi He
- School of Agriculture, Ningxia University, Yinchuan, China
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8
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Yang GJ, Liu YJ, Ding LJ, Tao F, Zhu MH, Shi ZY, Wen JM, Niu MY, Li X, Xu ZS, Qin WJ, Fei CJ, Chen J. A state-of-the-art review on LSD1 and its inhibitors in breast cancer: Molecular mechanisms and therapeutic significance. Front Pharmacol 2022; 13:989575. [PMID: 36188536 PMCID: PMC9523086 DOI: 10.3389/fphar.2022.989575] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 08/15/2022] [Indexed: 11/13/2022] Open
Abstract
Breast cancer (BC) is a kind of malignant cancer in women, and it has become the most diagnosed cancer worldwide since 2020. Histone methylation is a common biological epigenetic modification mediating varieties of physiological and pathological processes. Lysine-specific demethylase 1 (LSD1), a first identified histone demethylase, mediates the removal of methyl groups from histones H3K4me1/2 and H3K9me1/2 and plays a crucial role in varieties of cancer progression. It is also specifically amplified in breast cancer and contributes to BC tumorigenesis and drug resistance via both demethylase and non-demethylase manners. This review will provide insight into the overview structure of LSD1, summarize its action mechanisms in BC, describe the therapeutic potential of LSD1 inhibitors in BC, and prospect the current opportunities and challenges of targeting LSD1 for BC therapy.
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Affiliation(s)
- Guan-Jun Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, Zhejiang, China
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo, China
| | - Yan-Jun Liu
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Li-Jian Ding
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Department of Marine Pharmacy, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, China
| | - Fan Tao
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Ming-Hui Zhu
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Zhen-Yuan Shi
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Juan-Ming Wen
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Meng-Yao Niu
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Xiang Li
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Zhan-Song Xu
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Wan-Jia Qin
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Chen-Jie Fei
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, Zhejiang, China
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo, China
| | - Jiong Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, Zhejiang, China
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo, China
- *Correspondence: Jiong Chen, ,
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9
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Liu X, Shi Y, Kong L, Tong L, Cao H, Zhou H, Lv Y. Long-Term Application of Bio-Compost Increased Soil Microbial Community Diversity and Altered Its Composition and Network. Microorganisms 2022; 10:microorganisms10020462. [PMID: 35208916 PMCID: PMC8878586 DOI: 10.3390/microorganisms10020462] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 02/08/2022] [Indexed: 01/10/2023] Open
Abstract
The influence of bio-compost on the diversity, composition and structure of soil microbial communities is less understood. Here, Illumina MiSeq sequencing and a network analysis were used to comprehensively characterize the effects of 25 years of bio-compost application on the microbial diversity of soil and community composition. High dosages of bio-compost significantly increased the bacterial and fungal richness. The compositions of bacterial and fungal communities were significantly altered by bio-compost addition. Bio-compost addition enriched the relative abundance of beneficial microorganisms (such as Sphingomonas, Acidibacter, Nocardioides, etc.) and reduced the relative abundance of harmful microorganisms (such as Stachybotrys and Aspergillus). Electrical conductivity, soil organic matter and total phosphorus were the key factors in shaping soil microbial community composition. The bacterial network was more complex than fungal network, and bacteria were more sensitive to changes in environmental factors than fungi. Positive interactions dominated both the bacterial and fungal networks, with stronger positive interactions found in the bacterial network. Functional prediction suggested that bio-composts altered the soil bacterial-community metabolic function with respect to carbon, nitrogen and phosphorus cycles and fungal community trophic modes. In conclusion, suitable bio-compost addition is beneficial to the improvement of soil health and crop quality and therefore the sustainability of agriculture.
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Affiliation(s)
- Xiayan Liu
- Department of Soil and Water Sciences, College of Land Science and Technology, China Agricultural University, Beijing 100193, China; (X.L.); (L.K.); (H.C.)
| | - Yu Shi
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China;
| | - Lingyu Kong
- Department of Soil and Water Sciences, College of Land Science and Technology, China Agricultural University, Beijing 100193, China; (X.L.); (L.K.); (H.C.)
| | - Lihong Tong
- State Key Laboratory of Hydroscience and Engineering, Department of Hydraulic Engineering, Tsinghua University, Beijing 100084, China;
| | - Haoxuan Cao
- Department of Soil and Water Sciences, College of Land Science and Technology, China Agricultural University, Beijing 100193, China; (X.L.); (L.K.); (H.C.)
| | - Hu Zhou
- Department of Soil and Water Sciences, College of Land Science and Technology, China Agricultural University, Beijing 100193, China; (X.L.); (L.K.); (H.C.)
- Correspondence: (H.Z.); (Y.L.); Tel.: +86-010-62731890 (H.Z.); +86-010-62731431 (Y.L.)
| | - Yizhong Lv
- Department of Soil and Water Sciences, College of Land Science and Technology, China Agricultural University, Beijing 100193, China; (X.L.); (L.K.); (H.C.)
- Correspondence: (H.Z.); (Y.L.); Tel.: +86-010-62731890 (H.Z.); +86-010-62731431 (Y.L.)
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10
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Wang T. Analysis on the Structure and Function of the Bacterial Community in the Replanting Soil of Basswood Ganoderma lingzhi (Agaricomycetes). Int J Med Mushrooms 2022; 24:45-59. [DOI: 10.1615/intjmedmushrooms.2022044898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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11
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Metagenomic Analyses of Plant Growth-Promoting and Carbon-Cycling Genes in Maize Rhizosphere Soils with Distinct Land-Use and Management Histories. Genes (Basel) 2021; 12:genes12091431. [PMID: 34573413 PMCID: PMC8466292 DOI: 10.3390/genes12091431] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/04/2021] [Accepted: 09/13/2021] [Indexed: 11/16/2022] Open
Abstract
Many studies have shown that the maize rhizosphere comprises several plant growth-promoting microbes, but there is little or no study on the effects of land-use and management histories on microbial functional gene diversity in the maize rhizosphere soils in Africa. Analyzing microbial genes in the rhizosphere of plants, especially those associated with plant growth promotion and carbon cycling, is important for improving soil fertility and crop productivity. Here, we provide a comparative analysis of microbial genes present in the rhizosphere samples of two maize fields with different agricultural histories using shotgun metagenomics. Genes involved in the nutrient mobilization, including nifA, fixJ, norB, pstA, kefA and B, and ktrB were significantly more abundant (α = 0.05) in former grassland (F1) rhizosphere soils. Among the carbon-cycling genes, the abundance of 12 genes, including all those involved in the degradation of methane were more significant (α = 0.05) in the F1 soils, whereas only five genes were significantly more abundant in the F2 soils. α-diversity indices were different across the samples and significant differences were observed in the β diversity of plant growth-promoting and carbon-cycling genes between the fields (ANOSIM, p = 0.01 and R = 0.52). Nitrate-nitrogen (N-NO3) was the most influential physicochemical parameter (p = 0.05 and contribution = 31.3%) that affected the distribution of the functional genes across the samples. The results indicate that land-use and management histories impact the composition and diversity of plant growth-promoting and carbon-cycling genes in the plant rhizosphere. The study widens our understanding of the effects of anthropogenic activities on plant health and major biogeochemical processes in soils.
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12
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Pang Z, Dong F, Liu Q, Lin W, Hu C, Yuan Z. Soil Metagenomics Reveals Effects of Continuous Sugarcane Cropping on the Structure and Functional Pathway of Rhizospheric Microbial Community. Front Microbiol 2021; 12:627569. [PMID: 33746921 PMCID: PMC7973049 DOI: 10.3389/fmicb.2021.627569] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 02/08/2021] [Indexed: 12/25/2022] Open
Abstract
The continuous cropping of plants can result in the disruption of the soil microbial community and caused significant declines in yields. However, there are few reports on the effects of continuous cropping of sugarcane on the microbial community structure and functional pathway. In the current study, we analyzed the structural and functional changes of microbial community structure in the rhizospheric soil of sugarcane in different continuous cropping years using Illumina Miseq high-throughput sequencing and metagenomics analysis. We collected rhizosphere soils from fields of no continuous cropping history (NCC), 10 years of continuous cropping (CC10), and 30 years of continuous cropping (CC30) periods in the Fujian province. The results demonstrated that continuous sugarcane cropping resulted in significant changes in the physicochemical properties of soil and the composition of soil bacterial and fungal communities. With the continuous cropping, the crop yield dramatically declined from NCC to CC30. Besides, the redundancy analysis (RDA) of the dominant bacterial and fungal phyla and soil physicochemical properties revealed that the structures of the bacterial and fungal communities were mainly driven by pH and TS. Analysis of potential functional pathways during the continuous cropping suggests that different KEGG pathways were enriched in different continuous cropping periods. The significant reduction of bacteria associated with rhizospheric soil nitrogen and sulfur cycling functions and enrichment of pathogenic bacteria may be responsible for the reduction of effective nitrogen and total sulfur content in rhizospheric soil of continuous sugarcane as well as the reduction of sugarcane yield and sugar content. Additionally, genes related to nitrogen and sulfur cycling were identified in our study, and the decreased abundance of nitrogen translocation genes and AprAB and DsrAB in the dissimilatory sulfate reduction pathway could be the cause of declined biomass. The findings of this study may provide a theoretical basis for uncovering the mechanism of obstacles in continuous sugarcane cropping and provide better guidance for sustainable development of the sugarcane.
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Affiliation(s)
- Ziqin Pang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Agricultural, Fujian Agriculture and Forestry University, Fuzhou, China
- Province and Ministry Co-sponsored Collaborative Innovation Center of Sugar Industry, Nanning, China
| | - Fei Dong
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qiang Liu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Agricultural, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wenxiong Lin
- College of Agricultural, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Chaohua Hu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhaonian Yuan
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Agricultural, Fujian Agriculture and Forestry University, Fuzhou, China
- Province and Ministry Co-sponsored Collaborative Innovation Center of Sugar Industry, Nanning, China
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13
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Fu DJ, Li J, Yu B. Annual review of LSD1/KDM1A inhibitors in 2020. Eur J Med Chem 2021; 214:113254. [PMID: 33581557 DOI: 10.1016/j.ejmech.2021.113254] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 01/24/2021] [Accepted: 01/30/2021] [Indexed: 02/07/2023]
Abstract
Lysine-specific demethylase 1 (LSD1/KDM1A) has emerged as a promising target for the discovery of specific inhibitors as antitumor drugs. Based on the source of compounds, all LSD1 inhibitors in this review are divided into two categories: natural LSD1 inhibitors and synthetic LSD1 inhibitors. This review highlights the research progress of LSD1 inhibitors with the potential to treat cancer covering articles published in 2020. Design strategies, structure-activity relationships, co-crystal structure analysis and action mechanisms are also highlighted.
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Affiliation(s)
- Dong-Jun Fu
- Modern Research Center for Traditional Chinese Medicine, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Jun Li
- Modern Research Center for Traditional Chinese Medicine, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China.
| | - Bin Yu
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, 450001, China.
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14
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Colabella C, Casagrande Pierantoni D, Corte L, Roscini L, Conti A, Bassetti M, Tascini C, Robert V, Cardinali G. Single Strain High-Depth NGS Reveals High rDNA (ITS-LSU) Variability in the Four Prevalent Pathogenic Species of the Genus Candida. Microorganisms 2021; 9:microorganisms9020302. [PMID: 33540602 PMCID: PMC7912828 DOI: 10.3390/microorganisms9020302] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/27/2021] [Accepted: 01/29/2021] [Indexed: 01/08/2023] Open
Abstract
Ribosomal RNA in fungi is encoded by a series of genes and spacers included in a large operon present in 100 tandem repeats, normally in a single locus. The multigene nature of this locus was somehow masked by Sanger sequencing, which produces a single sequence reporting the prevalent nucleotide of each site. The introduction of next generation sequencing led to deeper knowledge of the individual sequences (reads) and therefore of the variants between the same DNA sequences located in different tandem repeats. In this framework, NGS sequencing of the rDNA region was used to elucidate the extent of intra- and inter-genomic variation at both the strain and species level. Specifically, the use of an innovative NGS technique allowed the high-throughput high-depth sequencing of the ITS1-LSU D1/D2 amplicons of 252 strains belonging to four opportunistic yeast species of the genus Candida. Results showed the presence of a large extent of variability among strains and species. These variants were differently distributed throughout the analyzed regions with a higher concentration within the Internally Transcribed Spacer (ITS) region, suggesting that concerted evolution was not able to totally homogenize these sequences. Both the internal variability and the SNPs between strain can be used for a deep typing of the strains and to study their ecology.
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Affiliation(s)
- Claudia Colabella
- Department of Pharmaceutical Sciences, University of Perugia, 06121 Perugia, Italy; (C.C.); (D.C.P.); (L.C.); (L.R.); (A.C.)
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “Togo Rosati”, 06126 Perugia, Italy
| | - Debora Casagrande Pierantoni
- Department of Pharmaceutical Sciences, University of Perugia, 06121 Perugia, Italy; (C.C.); (D.C.P.); (L.C.); (L.R.); (A.C.)
| | - Laura Corte
- Department of Pharmaceutical Sciences, University of Perugia, 06121 Perugia, Italy; (C.C.); (D.C.P.); (L.C.); (L.R.); (A.C.)
| | - Luca Roscini
- Department of Pharmaceutical Sciences, University of Perugia, 06121 Perugia, Italy; (C.C.); (D.C.P.); (L.C.); (L.R.); (A.C.)
| | - Angela Conti
- Department of Pharmaceutical Sciences, University of Perugia, 06121 Perugia, Italy; (C.C.); (D.C.P.); (L.C.); (L.R.); (A.C.)
| | - Matteo Bassetti
- Department Science and Health, University of Genoa and Genoa Hospital, 16100 Genova, Italy;
| | - Carlo Tascini
- Department of Medical Art, University of Udine and Udine Hospital, 33100 Udine, Italy;
| | - Vincent Robert
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands;
| | - Gianluigi Cardinali
- Department of Pharmaceutical Sciences, University of Perugia, 06121 Perugia, Italy; (C.C.); (D.C.P.); (L.C.); (L.R.); (A.C.)
- CEMIN Excellence Research Centre, University of Perugia, 06123 Perugia, Italy
- Correspondence: ; Tel.: +39-075-585-6484
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15
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Wang S, Cheng J, Li T, Liao Y. Response of soil fungal communities to continuous cropping of flue-cured tobacco. Sci Rep 2020; 10:19911. [PMID: 33199813 PMCID: PMC7669846 DOI: 10.1038/s41598-020-77044-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 11/05/2020] [Indexed: 12/23/2022] Open
Abstract
Fungal communities are considered to be critically important for crop health and soil fertility. However, our knowledge of the response of fungal community structure to the continuous cropping of flue-cured tobacco is limited, and the interaction of soil fungal communities under different cropping systems remains unclear. In this study, we comparatively investigated the fungal abundance, diversity, and community composition in the soils in which continuous cropping of flue-cured tobacco for 3 years (3ys), 5 years (5ys), and cropping for 1 year (CK) using quantitative polymerase chain reaction and high-throughput sequencing technology. The results revealed that continuous cropping of flue-cured tobacco changed the abundance of soil fungi, and caused a significant variation in fungal diversity. In particular, continuous cropping increased the relative abundance of Mortierellales, which can dissolve mineral phosphorus in soil. Unfortunately, continuous cropping also increased the risk of potential pathogens. Moreover, long-term continuous cropping had more complex and stabilize network. This study also indicated that available potassium and available phosphorous were the primary soil factors shifting the fungal community structure. These results suggested that several soil variables may affect fungal community structure. The continuous cropping of flue-cured tobacco significantly increased the abundance and diversity of soil fungal communities.
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Affiliation(s)
- Shengnan Wang
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
- School of Biological and Chemical Engineering, Panzhihua University, Panzhihua, 617000, Sichuan, China
| | - Jiangke Cheng
- School of Mathematics and Computer Science, Panzhihua University, Panzhihua, 617000, Sichuan, China
| | - Tong Li
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yuncheng Liao
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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16
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Liu C, Li L, Xie J, Coulter JA, Zhang R, Luo Z, Cai L, Wang L, Gopalakrishnan S. Soil Bacterial Diversity and Potential Functions Are Regulated by Long-Term Conservation Tillage and Straw Mulching. Microorganisms 2020; 8:microorganisms8060836. [PMID: 32498450 PMCID: PMC7355473 DOI: 10.3390/microorganisms8060836] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 05/25/2020] [Accepted: 05/30/2020] [Indexed: 12/23/2022] Open
Abstract
Soil physiochemical properties are regulated by cropping practices, but little is known about how tillage influences soil microbial community diversity and functions. Here, we assessed soil bacterial community assembly and functional profiles in relation to tillage. Soils, collected in 2018 from a 17-year field experiment in northwestern China, were analyzed using high-throughput sequencing and the PICRUSt approach. The taxonomic diversity of bacterial communities was dominated primarily by the phyla Proteobacteria (32–56%), Bacteroidetes (12–33%), and Actinobacteria (17–27%). Alpha diversity (Chao1, Shannon, Simpson, and operational taxonomic unit (OTU) richness) was highest under no-tillage with crop residue removed (NT). Crop residue retention on the soil surface (NTS) or incorporated into soil (TS) promoted the abundance of Proteobacteria by 16 to 74% as compared to conventional tillage (T). Tillage practices mainly affected the pathways of soil metabolism, genetic information processing, and environmental information processing. Soil organic C and NH4–N were the principal contributors to the diversity and composition of soil microbiota, whereas soil pH, total nitrogen, total P, and moisture had little effect. Our results suggest that long-term conservation practices with no-tillage and crop residue retention shape soil bacterial community composition through modifying soil physicochemical properties and promoting the metabolic function of soil microbiomes.
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Affiliation(s)
- Chang Liu
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (C.L.); (J.X.); (R.Z.); (Z.L.); (L.C.); (L.W.)
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Lingling Li
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (C.L.); (J.X.); (R.Z.); (Z.L.); (L.C.); (L.W.)
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
- Correspondence:
| | - Junhong Xie
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (C.L.); (J.X.); (R.Z.); (Z.L.); (L.C.); (L.W.)
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Jeffrey A. Coulter
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA;
| | - Renzhi Zhang
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (C.L.); (J.X.); (R.Z.); (Z.L.); (L.C.); (L.W.)
- College of Resource and Environment, Gansu Agricultural University, Lanzhou 730070, China
| | - Zhuzhu Luo
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (C.L.); (J.X.); (R.Z.); (Z.L.); (L.C.); (L.W.)
- College of Resource and Environment, Gansu Agricultural University, Lanzhou 730070, China
| | - Liqun Cai
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (C.L.); (J.X.); (R.Z.); (Z.L.); (L.C.); (L.W.)
- College of Resource and Environment, Gansu Agricultural University, Lanzhou 730070, China
| | - Linlin Wang
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (C.L.); (J.X.); (R.Z.); (Z.L.); (L.C.); (L.W.)
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Subramaniam Gopalakrishnan
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana 502324, India;
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