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Liu M, Xue R, Yang C, Han N, Hu Y, Gu K, Zhao J, Guan S, Su J, Jiang Y. Rotation with other crops slow down the fungal process in tobacco-growing soil. Sci Rep 2024; 14:14160. [PMID: 38898096 PMCID: PMC11187129 DOI: 10.1038/s41598-024-64735-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 06/12/2024] [Indexed: 06/21/2024] Open
Abstract
Continuous cultivation of tobacco could cause serious soil health problems, which could cause bacterial soil to change to fungal soil. In order to study the diversity and richness of fungal community in tobacco-growing soil under different crop rotation, three treatments were set up in this study: CK (tobacco continuous cropping); B (barley-tobacco rotation cropping) and R (oilseed rape-tobacco rotation cropping). The results of this study showed that rotation with other crops significantly decreased the soil fungal OTUs, and also decreased the community richness, evenness, diversity and coverage of fungal communities. Among them, B decreased the most. In the analysis of the composition and structure of the fungal community, it was found that the proportion of plant pathogens Nectriaceae decreased from 19.67% in CK to 5.63% in B, which greatly reduced the possibility of soil-borne diseases. In the analysis of the correlation between soil environmental factors and fungal communities, it was found that Filobasidiaceae had a strong correlation with TP and AP, and Erysiphaceae had a strong correlation with TK and AK. NO3--N and NH4+-N were the two environmental factors with the strongest correlation with fungal communities. The results of this study showed that rotation with other crops slowed down the process of soil fungi in tobacco-growing soil and changed the dominant species of soil fungi community. At the same time, crop rotation changed the diversity and richness of soil fungal community by changing the physical and chemical properties of soil.
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Affiliation(s)
- Ming Liu
- Dali Prefecture Branch of Yunnan Tobacco Company, Dali, 671000, Yunnan, China
- SouthWest University, Chongqing, 400715, China
| | - Rujun Xue
- Weishan City Branch of Yunnan Tobacco Company, Weishan, 672400, Yunnan, China
| | - Chengwei Yang
- Dali Prefecture Branch of Yunnan Tobacco Company, Dali, 671000, Yunnan, China
| | - Ningbo Han
- Weishan City Branch of Yunnan Tobacco Company, Weishan, 672400, Yunnan, China
| | - Yanxia Hu
- Dali Prefecture Branch of Yunnan Tobacco Company, Dali, 671000, Yunnan, China
| | - Kaiyuan Gu
- SouthWest University, Chongqing, 400715, China
| | - Jie Zhao
- SouthWest University, Chongqing, 400715, China
| | - Shuyue Guan
- SouthWest University, Chongqing, 400715, China
| | - Jiaen Su
- Dali Prefecture Branch of Yunnan Tobacco Company, Dali, 671000, Yunnan, China.
| | - Yonglei Jiang
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, China.
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Wang R, Ma W, Wu D, Zhang Y, Ma X, Lv G, Ding J, Fu Z, Chen C, Huang H. Soil bacterial community composition in rice-turtle coculture systems with different planting years. Sci Rep 2023; 13:22708. [PMID: 38123614 PMCID: PMC10733315 DOI: 10.1038/s41598-023-49701-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 12/11/2023] [Indexed: 12/23/2023] Open
Abstract
The rice-turtle coculture system is the most special rice-fish integrated farming system. In this study, we selected four paddy fields, including a rice monoculture paddy and three rice-turtle paddies with different planting years, to investigate the soil bacterial community composition with Illumina MiSeq sequencing technology. The results indicated that the contents of soil available nitrogen (AN), soil available phosphorus (AP) and soil organic matter (OM) in 9th year of rice-turtle paddy (RT9) were increased by 5.40%, 51.11% and 23.33% compared with rice monoculture paddy (CK), respectively. Significant differences of Acidobacteria, Desulfobacteria, Crenarchaeota were observed among the different rice farming systems. The relative abundance of Methylomonadaceae, Methylococcaceae and Methylophilaceae in RT9 was significantly higher than that in other treatments. RT9 had significantly lower relative abundance of Acidobacteria, but significantly higher relative abundance of Proteobacteria than other treatments. Redundancy analysis showed that soil AN and AP contents were the major factors influencing the abundance of the dominant microbes, wherein Methylomonadaceae, Methylococcaceae and Methylophilaceae were positively correlated with OM. The findings revealed the rice-turtle coculture system in the 9th year had higher soil nutrients and soil bacterial diversity, but there was also a risk of increasing methane emissions.
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Affiliation(s)
- Ren Wang
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
- Hunan Engineering Research Center of Rice Field Ecological Planting and Breeding, Changsha, 410128, China
| | - Weiwei Ma
- Yueyang Agricultural and Rural Affairs Center, Yueyang, 414004, China
| | - Dan Wu
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
- Hunan Engineering Research Center of Rice Field Ecological Planting and Breeding, Changsha, 410128, China
| | - Yin Zhang
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
- Hunan Engineering Research Center of Rice Field Ecological Planting and Breeding, Changsha, 410128, China
| | - Xuehu Ma
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
- Hunan Engineering Research Center of Rice Field Ecological Planting and Breeding, Changsha, 410128, China
| | - Guangdong Lv
- Hengyang Academy of Agricultural Sciences, Hengyang, 421100, China
| | - Jiaolong Ding
- Hunan Engineering Research Center of Rice Field Ecological Planting and Breeding, Changsha, 410128, China
| | - Zhiqiang Fu
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
- Hunan Engineering Research Center of Rice Field Ecological Planting and Breeding, Changsha, 410128, China
| | - Can Chen
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China.
- Hunan Engineering Research Center of Rice Field Ecological Planting and Breeding, Changsha, 410128, China.
| | - Huang Huang
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China.
- Hunan Engineering Research Center of Rice Field Ecological Planting and Breeding, Changsha, 410128, China.
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Feng C, Yi Z, Qian W, Liu H, Jiang X. Rotations improve the diversity of rhizosphere soil bacterial communities, enzyme activities and tomato yield. PLoS One 2023; 18:e0270944. [PMID: 36634092 PMCID: PMC9836298 DOI: 10.1371/journal.pone.0270944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 12/24/2022] [Indexed: 01/13/2023] Open
Abstract
The use of rotations is an effective strategy to control crop diseases and improve plant health. The soil bacterial communities in the rhizosphere are highly important for maintaining soil productivity. However, the composition and structure of soil bacterial communities in the rotations of vegetable crops remain unclear. In this study, we explored the bacterial diversity and community structure of the tomato rhizosphere, including enzyme activities, yield, and fruit quality, under three different cropping systems: tomato-tomato (Solanum lycopersicum) continuous cropping (TY1), eggplant (Solanum melongena)-tomato rotation (TY2) and arrowhead (Sagittaria trifolia)-tomato rotation (TY3). The composition and diversity of the rhizosphere bacterial communities differed significantly. The diversity was more in the TY2 and TY3 treatments than those in the TY1 treatment. Chujaibacter and Rhodanobacter were two predominant and unique strains detected only in TY1, while the relative abundances of Curvibacter and Luteimonas were the highest in TY2 and TY3, respectively. Moreover, Lysobacter was a relatively abundant type of biocontrol bacterium found only in the TY3 treatment, which could contribute to alleviating the obstacle of tomato continuous cropping. Compared with the TY1 treatment, the activities of catalase were significantly higher in the TY2 and TY3 treatments. In addition, compared with TY1, the TY2 and TY3 plots increased the following parameters: tomato yields by 24-46%, total soluble solids by 37-93%, total organic acid by 10-15.7% and soluble protein by 10-21%, while the content of nitrate was significantly reduced by 23%. Altogether, compared with the tomato monoculture, the rotations of tomato with eggplant and arrowhead shifted the rhizosphere bacterial communities and improved the yield and quality of the tomato. Moreover, a tomato rotation, particularly with arrowhead, was an effective way to alleviate the obstacles of continuous cropping.
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Affiliation(s)
- Cui Feng
- Taizhou Institute of Agricultural Sciences, Jiangsu Academy of Agricultural Sciences, Taizhou, China
| | - Zhengwei Yi
- Taizhou Institute of Agricultural Sciences, Jiangsu Academy of Agricultural Sciences, Taizhou, China
| | - Wei Qian
- Taizhou Institute of Agricultural Sciences, Jiangsu Academy of Agricultural Sciences, Taizhou, China
| | - Huiying Liu
- Taizhou Institute of Agricultural Sciences, Jiangsu Academy of Agricultural Sciences, Taizhou, China
| | - Xiaosan Jiang
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
- * E-mail:
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Effects of Different Land Use Types and Soil Depth on Soil Nutrients and Soil Bacterial Communities in a Karst Area, Southwest China. SOIL SYSTEMS 2022. [DOI: 10.3390/soilsystems6010020] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
To reveal the effect of the interactions between soil depth and different land use types on soil nutrients and soil bacterial communities in a karst area, fifty soil samples from five different karst land use types in Huajiang town, Guizhou province, Southwest China were collected, and the soil bacteria were analyzed using high-throughput absolute quantification sequencing. Our results showed that land use types (LUT) and soil depth (SD) significantly influenced the content of soil organic carbon (SOC), total nitrogen (TN), total phosphorus (TP), nitrate nitrogen (NN), ammonium nitrogen (AN) and available soil phosphorus (AP), and pH; further, the interaction of LUT and SD also significantly influenced SOC, NN, NA, AP, and pH. In addition, LUT clearly impacted the Chao1 and Shannon indexes, but, SD and LUT * SD markedly affect Chao1 and Shannon index, respectively. All the soil bacterial communities were significantly different in the five different five land use types according to PERMANOVA. Importantly, Acidobacteria and Proteobacteria were the predominant phyla at soil depths of 0–20 cm and 20–40 cm among all the LUTs. At 0–20 cm, TN, AN, and SOC exerted a strong positive influence on Acidobacteria, but NN exerted a strong negative influence on Acidobacteria; at 20–40 cm soil, TN and AN exerted a strong positive influence on Acidobacteria; TP exerted no marked influence on any of the phyla at these two soil depths. At 0–20 cm of soil depth, we also found that Chao1 index changes were closely related to the TN, SOC, AN, and NN; similarly, Shannon index changes were significantly correlated to the AN, TN, and SOC; the PCoA was clearly related to the TN, SOC, and AN. Interestingly, at soil depth of 20–40 cm, Chao 1 was markedly related to the TN and pH; Shannon was markedly correlated with the SOC, TP, AN, and AP; and the PCoA was significantly correlated with the TN and pH. Our findings imply that soil nutrients and soil bacteria communities are strongly influenced by land use types and soil depth in karst areas.
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Peeters J, Thas O, Shkedy Z, Kodalci L, Musisi C, Owokotomo OE, Dyczko A, Hamad I, Vangronsveld J, Kleinewietfeld M, Thijs S, Aerts J. Exploring the Microbiome Analysis and Visualization Landscape. FRONTIERS IN BIOINFORMATICS 2021; 1:774631. [PMID: 36303773 PMCID: PMC9580862 DOI: 10.3389/fbinf.2021.774631] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 10/29/2021] [Indexed: 02/02/2023] Open
Abstract
Research on the microbiome has boomed recently, which resulted in a wide range of tools, packages, and algorithms to analyze microbiome data. Here we investigate and map currently existing tools that can be used to perform visual analysis on the microbiome, and associate the including methods, visual representations and data features to the research objectives currently of interest in microbiome research. The analysis is based on a combination of a literature review and workshops including a group of domain experts. Both the reviewing process and workshops are based on domain characterization methods to facilitate communication and collaboration between researchers from different disciplines. We identify several research questions related to microbiomes, and describe how different analysis methods and visualizations help in tackling them.
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Affiliation(s)
- Jannes Peeters
- CENSTAT, Data Science Institute (DSI), Hasselt University, Diepenbeek, Belgium
- *Correspondence: Jannes Peeters ,
| | - Olivier Thas
- CENSTAT, Data Science Institute (DSI), Hasselt University, Diepenbeek, Belgium
| | - Ziv Shkedy
- CENSTAT, Data Science Institute (DSI), Hasselt University, Diepenbeek, Belgium
| | - Leyla Kodalci
- CENSTAT, Data Science Institute (DSI), Hasselt University, Diepenbeek, Belgium
| | - Connie Musisi
- CENSTAT, Data Science Institute (DSI), Hasselt University, Diepenbeek, Belgium
| | | | - Aleksandra Dyczko
- VIB Laboratory of Translational Immunomodulation, VIB Center for Inflammation Research (IRC), Hasselt University, Diepenbeek, Belgium
- Department of Immunology and Infection, Biomedical Research Institute (BIOMED), Hasselt University, Diepenbeek, Belgium
| | - Ibrahim Hamad
- VIB Laboratory of Translational Immunomodulation, VIB Center for Inflammation Research (IRC), Hasselt University, Diepenbeek, Belgium
- Department of Immunology and Infection, Biomedical Research Institute (BIOMED), Hasselt University, Diepenbeek, Belgium
| | - Jaco Vangronsveld
- Center for Environmental Sciences, Environmental Biology, Hasselt University, Diepenbeek, Belgium
- Department of Plant Physiology and Biophysics, Faculty of Biology and Biotechnology, Maria Curie–Skłodowska University, Lublin, Poland
| | - Markus Kleinewietfeld
- VIB Laboratory of Translational Immunomodulation, VIB Center for Inflammation Research (IRC), Hasselt University, Diepenbeek, Belgium
- Department of Immunology and Infection, Biomedical Research Institute (BIOMED), Hasselt University, Diepenbeek, Belgium
| | - Sofie Thijs
- Center for Environmental Sciences, Environmental Biology, Hasselt University, Diepenbeek, Belgium
| | - Jan Aerts
- CENSTAT, Data Science Institute (DSI), Hasselt University, Diepenbeek, Belgium
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Nyamwange MM, Njeru EM, Mucheru-Muna M. Tillage, Mulching and Nitrogen Fertilization Differentially Affects Soil Microbial Biomass, Microbial Populations and Bacterial Diversity in a Maize Cropping System. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2021. [DOI: 10.3389/fsufs.2021.614527] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Determination of biologically active components of the soil organic matter, such as soil microbial biomass carbon (C) and nitrogen (N) can be used as indicators for variations in soil productivity due to changes in soil management. Soil agronomic management practices bring about changes in the physical and chemical properties of the soil, resulting in variations in soil microbial biomass and microbial diversity. The effects of tillage, mulch and inorganic fertilizers on soil microbial biomass C and N, microbial populations and bacterial diversity were determined from the treatment combinations which had been applied for 5 years in Central Kenyan Highlands. The test crop used was maize (Zea mays L.). The study involved conventional and minimum tillage systems, mulching and inorganic fertilizers (120 kg N/ha). Tillage (P < 0.001), mulch (P < 0.001), and fertilizer (P = 0.009) significantly affected soil microbial biomass C and N whereby minimum tillage and mulch increased soil microbial biomass C and N. Interestingly, minimum tillage and mulch recorded the highest bacteria and fungi CFUs compared to conventional tillage and inorganic fertilizers. Only fertilizer and mulch (P < 0.001) had significant effect on actinobacteria CFUs. Amplified ribosomal DNA analysis (ARDRA) showed that the highest genetic distance of 0.611 was recorded between treatments conventional tillage + no mulch + no NPK fertilizer and conventional tillage + no mulch + NPK fertilizer. The results demonstrate that minimum tillage and mulching are attractive soil agronomic management practices since they increase soil microbial biomass and bacterial diversity in agricultural soils.
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Palma-Cano LE, Piñon-Castillo HA, Tarango-Rivero SH, Carbon A, Salas-Leiva J, Muñoz-Castellanos LN, Cravo-Laureau C, Duran R, Orrantia-Borunda E. Effect of organic and conventional farming on soil bacterial diversity of pecan tree (Carya illinoensis K. Kosh) orchard across two phenological stages. Lett Appl Microbiol 2021; 72:556-569. [PMID: 33453128 DOI: 10.1111/lam.13452] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 12/29/2020] [Accepted: 01/11/2021] [Indexed: 12/19/2022]
Abstract
We described the bacterial diversity of walnut grove soils under organic and conventional farming. The bacterial communities of rhizospheric and nonrhizospheric soils of pecan tree (Carya illinoensis K. Koch) were compared considering two phenological stages (sprouting and ripening). Sixteen operational taxonomic units (OTUs) were identified significantly more abundant according to the plant development, only one according to the farming condition, and none according to the soil origin. The OTUs specificaly abundant according to plant development included Actinobateria (2) and Betaproteobacteria (1) related OTUs more abundant at the sprouting stage, while at the fruit ripening (FR) stage the more abundant OTUs were related to Actinobacteria (6), Alphaproteobacteria (6), and unclassified Bacteria (1). The Gaiellaceae OTU18 (Actinobacteria) was more abundant under conventional farming. Thus, our study revealed that the plant development stage was the main factor shaping the bacterial community structure, while less influence was noticed for the farming condition. The bacterial communities exhibited specific metabolic capacities, a large range of carbon sources being used at the FR stage. The identified OTUs specifically more abundant represent indicators providing useful information on soil condition, potential tools for the management of soil bacterial communities.
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Affiliation(s)
- L E Palma-Cano
- Centro de Investigación en Materiales Avanzados, Chihuahua, México
| | - H A Piñon-Castillo
- Facultad de Ciencias Químicas de la Universidad Autónoma de Chihuahua, Chihuahua, México
| | | | - A Carbon
- Université de Pau et des Pays de l'Adour, UPPA/E2S, IPREM, UMR CNRS 5254, Bat. IBEAS, Pau, France
| | - J Salas-Leiva
- Centro de Investigación en Materiales Avanzados, Chihuahua, México.,Cátedra-CONACyT, Centro de Investigación en Materiales Avanzados, Chihuahua, México
| | - L N Muñoz-Castellanos
- Facultad de Ciencias Químicas de la Universidad Autónoma de Chihuahua, Chihuahua, México
| | - C Cravo-Laureau
- Université de Pau et des Pays de l'Adour, UPPA/E2S, IPREM, UMR CNRS 5254, Bat. IBEAS, Pau, France
| | - R Duran
- Université de Pau et des Pays de l'Adour, UPPA/E2S, IPREM, UMR CNRS 5254, Bat. IBEAS, Pau, France
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Ma X, Du M, Liu P, Tang Y, Li H, Yuan Q, Ruan Y, Meng L, Zhang J, Lin M, Liu Z. Alternation of soil bacterial and fungal communities by tomato-rice rotation in Hainan Island in Southeast of China. Arch Microbiol 2020; 203:913-925. [PMID: 33078269 DOI: 10.1007/s00203-020-02086-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 09/18/2020] [Accepted: 10/06/2020] [Indexed: 11/29/2022]
Abstract
Tomato-rice rotation is prevalent in subtropical and tropical regions in China. This practice enhances crop productivity and the disease suppression property of soils against soil-borne plant pathogens. To explore the variations and dynamics of bacterial and fungal communities, bulk soil samples were collected during two consecutive years under a rotation system between tomato and rice originated from the year of 2010 in Hainan Island, and 16S rDNA and ITS amplicons were sequenced by Illumina MiSeq. The results demonstrated that potentially beneficial bacterial phyla Acidobacteria, Chloroflexi and genus Paenibacillus, as well as the fungal genus Mortierella were significantly enriched, while the potentially pathogenic fungal genus Fusarium was significantly decreased during the crop rotation. Measurements of soil physicochemical properties indicated that the soil acidification was improved. Redundancy analysis (RDA) revealed the correlation of the microbial community with soil pH and identified soil total phosphorus (TP) level as the highest determinant factor for both bacterial and fungal communities. This work provides a preliminary description of changes of the bacterial and fungal communities related to tomato-rice rotation in China and offered experimental evidences for exploring the effects of this agricultural practice on soil ecology.
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Affiliation(s)
- Xiang Ma
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, Haikou, 570228, China
| | - Minglun Du
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, Haikou, 570228, China
| | - Peng Liu
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, Haikou, 570228, China
| | - Yanqiong Tang
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, Haikou, 570228, China
| | - Hong Li
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, Haikou, 570228, China
| | - Qianhua Yuan
- School of Tropical Crops, Hainan University, Haikou, 570228, China
| | - Yunze Ruan
- School of Tropical Crops, Hainan University, Haikou, 570228, China
| | - Lei Meng
- School of Tropical Crops, Hainan University, Haikou, 570228, China
| | - Jiachao Zhang
- School of Tropical Crops, Hainan University, Haikou, 570228, China
| | - Min Lin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhu Liu
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, Haikou, 570228, China.
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Chen QL, Cai L, Wang HC, Cai LT, Goodwin P, Ma J, Wang F, Li Z. Fungal Composition and Diversity of the Tobacco Leaf Phyllosphere During Curing of Leaves. Front Microbiol 2020; 11:554051. [PMID: 33013785 PMCID: PMC7499341 DOI: 10.3389/fmicb.2020.554051] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 08/12/2020] [Indexed: 11/16/2022] Open
Abstract
Rhizopus oryzae causes tobacco pole rot in China during tobacco flue-curing. Flue-curing is a post-harvest process done to prepare tobacco leaves and involves three different stages: the yellowing stage has the lowest temperatures and highest humidity, then the color-fixing stage has higher temperatures and medium humidity, and finally the stem-drying stage has the highest temperatures and lowest humidity. In this study, fungal culturing and IonS5XL high-throughput sequencing techniques were used to reveal the fungal community of the petioles and lamina of tobacco leaves infected with pole rot during flue-curing. A total of 108 fungal isolates belonging to 6 genera were isolated on media. The most common fungal species isolated was the pathogen, R. oryzae, that was most often found equally on petioles and laminas in the color-fixing stage, followed by saprotrophs, mostly Aspergillus spp. High-throughput sequencing revealed saprotrophs with Alternaria being the most abundant genus, followed by Phoma, Cercospora, and Aspergillus, whereas Rhizopus was the tenth most abundant genus, which was mostly found on petioles at the yellowing stage. Both culturable fungal diversity and fungal sequence diversity was higher at stem-drying stage than the yellowing and color-fixing stages, and diversity was higher with leaf lamina than petioles revealing that the changes in fungal composition and diversity during the curing process were similar with both methods. This study demonstrates that the curing process affects the leaf microbiome of tobacco during the curing process, and future work could examine if any of these saprotrophic fungi detected during the curing of tobacco leaves may be potential biocontrol agents for with pole rot in curing chambers.
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Affiliation(s)
- Qian-Li Chen
- Key Laboratory of Molecular Genetics, Guizhou Academy of Tobacco Science, Guiyang, China
- College of Agriculture, Guizhou University, Guiyang, China
| | - Lin Cai
- College of Plant Protection, Southwest University, Chongqing, China
| | - Han-Cheng Wang
- Key Laboratory of Molecular Genetics, Guizhou Academy of Tobacco Science, Guiyang, China
| | - Liu-Ti Cai
- Key Laboratory of Molecular Genetics, Guizhou Academy of Tobacco Science, Guiyang, China
| | - Paul Goodwin
- School of Environmental Sciences, University of Guelph, Guelph, ON, Canada
| | - Jun Ma
- Qianxinan Branch of Guizhou Tobacco Company, Guiyang, China
| | - Feng Wang
- Key Laboratory of Molecular Genetics, Guizhou Academy of Tobacco Science, Guiyang, China
| | - Zhong Li
- College of Agriculture, Guizhou University, Guiyang, China
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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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11
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Xia X, Zhang P, He L, Gao X, Li W, Zhou Y, Li Z, Li H, Yang L. Effects of tillage managements and maize straw returning on soil microbiome using 16S rDNA sequencing. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2019; 61:765-777. [PMID: 30912294 DOI: 10.1111/jipb.12802] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Accepted: 03/12/2019] [Indexed: 05/07/2023]
Abstract
Agricultural practices could affect bacterial diversity and community structure by altering soil physical and chemical properties. Straw returning and tillage practices are widely used in agriculture, however, the effects of these agricultural practices on microbiomes are still unclear. In the present study, we compared the 18 bacterial communities of soil with different straw returning and tillage treatment combinations. The V3-V4 regions of the 16S ribosomal RNA were amplified and analyzed by high-throughput sequencing technology. The results showed that the bacterial communities were consistently dominated by Acidobacteria, Proteobacteria, Actinobacteria, and Chloroflexi. Short-term straw returning and tillage practices significantly altered the diversity, relative abundance and functions of the soil microbiome. Soil subjected to rotary tillage and straw returning (RTS) combination possessed the highest bacterial diversity and lowest ratio of G+/G- bacteria, indicating that RTS could be an efficient integrated management system to improve microbiome in the short term. Double verifications based on relative abundance and network analysis, revealed close relationships of Mycobacterium and Methylibium with RTS, indicating they could serve as biomarkers for RTS. Investigating microbial changes under different agricultural practices will provide valuable foundations for land sustainable utilization and increase crop yields.
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Affiliation(s)
- Xinyao Xia
- Agricultural Big-Data Research Center, College of Plant Protection, Shandong Agricultural University, Taian, 271018, China
| | - Piaopiao Zhang
- Department of Clinical, Taishan Medical University, Taian, 271016, China
| | - Linlin He
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China
| | - Xingxing Gao
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China
| | - Weijun Li
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China
| | - Yuanyuan Zhou
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China
| | - Zongxin Li
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Hui Li
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China
| | - Long Yang
- Agricultural Big-Data Research Center, College of Plant Protection, Shandong Agricultural University, Taian, 271018, China
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12
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Yang Y, Zhang S, Li N, Chen H, Jia H, Song X, Liu G, Ni C, Wang Z, Shao H, Zhang S. Metagenomic insights into effects of wheat straw compost fertiliser application on microbial community composition and function in tobacco rhizosphere soil. Sci Rep 2019; 9:6168. [PMID: 30992508 PMCID: PMC6467887 DOI: 10.1038/s41598-019-42667-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 04/03/2019] [Indexed: 11/25/2022] Open
Abstract
The application of fertilisers incorporated with plant residues improves nutrient availability in soils, which shifts the microbial community structure and favours plant growth. To understand the impact of wheat straw compost fertiliser on soil properties and microbial community structure, tobacco planting soils were treated with four different fertilisers using varied amounts of straw compost fertiliser and a no fertiliser control (CK). Results showed that different fertilisers affected available soil nutrient contents differently. Treatment of tobacco soil with application of combined chemical fertiliser/wheat straw compost led to improved soil chemical properties, and increased soil organic matter and available phosphorus and potassium content. Treatment with FT1 200 kg/mu straw was found to be superior in improving soil fertility. Metagenomic DNA sequencing revealed that different fertiliser treatments resulted in changes in the microbial community composition. In soil treated with FT2 300 kg/mu straw for 60 days, the predominant bacterial phyla were Proteobacteria, Actinobacteria, and Verrucomicrobia, whereas Cyanobacteria, Basidiomycota, and Chlorophyta were found in high abundance in soil samples treated with FT1 200 kg/mu straw for 30 days. Functional annotation of metagenomic sequences revealed that genes involved in metabolic pathways were among the most abundant type. PCoA analysis clearly separated the samples containing straw compost fertiliser and chemical fertiliser. A significant correlation between soil properties and the dominant phyla was identified.
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Affiliation(s)
- Yongfeng Yang
- Henan Agricultural University, College of Tobacco Science, Tobacco Cultivation Key Laboratory of China Tobacco, Zhengzhou, 450002, China
| | - Songjie Zhang
- Henan Agricultural University, College of Tobacco Science, Tobacco Cultivation Key Laboratory of China Tobacco, Zhengzhou, 450002, China
| | - Ning Li
- Henan Agricultural University, College of Tobacco Science, Tobacco Cultivation Key Laboratory of China Tobacco, Zhengzhou, 450002, China
| | - Hongli Chen
- Henan Agricultural University, College of Tobacco Science, Tobacco Cultivation Key Laboratory of China Tobacco, Zhengzhou, 450002, China
| | - Hongfang Jia
- Henan Agricultural University, College of Tobacco Science, Tobacco Cultivation Key Laboratory of China Tobacco, Zhengzhou, 450002, China
| | - Xiaoning Song
- Henan Agricultural University, College of Tobacco Science, Tobacco Cultivation Key Laboratory of China Tobacco, Zhengzhou, 450002, China
| | - Guoshun Liu
- Henan Agricultural University, College of Tobacco Science, Tobacco Cultivation Key Laboratory of China Tobacco, Zhengzhou, 450002, China
| | - Chao Ni
- China Tobacco Chongqing Industrial Corporation, Chongqing, 400000, China
| | - Zhizhong Wang
- Wuyang County Tobacco Branch of Luohe Tobacco Company, Luohe, Henan Province, 462000, China
| | - Huifang Shao
- Henan Agricultural University, College of Tobacco Science, Tobacco Cultivation Key Laboratory of China Tobacco, Zhengzhou, 450002, China
| | - Songtao Zhang
- Henan Agricultural University, College of Tobacco Science, Tobacco Cultivation Key Laboratory of China Tobacco, Zhengzhou, 450002, China.
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13
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Genome analysis of Rubritalea profundi SAORIC-165 T, the first deep-sea verrucomicrobial isolate, from the northwestern Pacific Ocean. J Microbiol 2019; 57:413-422. [PMID: 30806980 DOI: 10.1007/s12275-019-8712-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 01/04/2019] [Accepted: 01/04/2019] [Indexed: 12/13/2022]
Abstract
Although culture-independent studies have shown the presence of Verrucomicrobia in the deep sea, verrucomicrobial strains from deep-sea environments have been rarely cultured and characterized. Recently, Rubritalea profundi SAORIC-165T, a psychrophilic bacterium of the phylum Verrucomicrobia, was isolated from a depth of 2,000 m in the northwestern Pacific Ocean. In this study, the genome sequence of R. profundi SAORIC-165T, the first deep-sea verrucomicrobial isolate, is reported with description of the genome properties and comparison to surface-borne Rubritalea genomes. The draft genome consisted of four contigs with an entire size of 4,167,407 bp and G+C content of 47.5%. The SAORIC-165T genome was predicted to have 3,844 proteincoding genes and 45 non-coding RNA genes. The genome contained a repertoire of metabolic pathways, including the Embden-Meyerhof-Parnas pathway, pentose phosphate pathway, tricarboxylic acid cycle, assimilatory sulfate reduction, and biosynthesis of nicotinate/nicotinamide, pantothenate/coenzyme A, folate, and lycopene. The comparative genomic analyses with two surface-derived Rubritalea genomes showed that the SAORIC-165T genome was enriched in genes involved in transposition of mobile elements, signal transduction, and carbohydrate metabolism, some of which might be related to bacterial enhancement of ecological fitness in the deep-sea environment. Amplicon sequencing of 16S rRNA genes from the water column revealed that R. profundi-related phylotypes were relatively abundant at 2,000 m and preferred a particle-associated life style in the deep sea. These findings suggest that R. profundi represents a genetically unique and ecologically relevant verrucomicrobial group well adapted to the deep-sea environment.
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14
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Yu D, Wen Z, Li X, Song X, Wu H, Yang P. Effects of straw return on bacterial communities in a wheat-maize rotation system in the North China Plain. PLoS One 2018; 13:e0198087. [PMID: 29879153 PMCID: PMC5991650 DOI: 10.1371/journal.pone.0198087] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 05/14/2018] [Indexed: 11/18/2022] Open
Abstract
Straw return plays an important role in reducing the use of chemical fertilizer, promoting soil carbon sequestration, thus maintaining soil fertility and alleviating environmental pollution. To examine the effects of straw return on soil bacterial communities, quantitative PCR and high-throughput sequencing approaches were used to analyze the bacterial abundance and community structures at the depths of 5-25 cm and 25-45 cm in the soils under six-year continuous straw return and removal treatments in Langfang, Hebei, the North China Plain. As a result, straw return had no effects on soil chemical properties, bacterial abundance, richness or diversity at both soil depths. In contrast, vertical distributions of available nitrogen and available potassium were affected. Similarly, straw return also changed the vertical distributions of Proteobacteria and Chloroflexi. Principal coordinate analysis based on weighted UniFrac distance matrix indicated a moderate separation of the bacterial community in the soil treated with straw return from that with straw removal at 5-25 cm depth, but they were not distinctly distinguished at 25-45 cm depth. T-test identified increased abundance of Candidatus Latescibacteria in the soil under straw return treatment at 5-25 cm depth but no differentially abundant phyla at 25-45 cm depth was found. These results suggested a selection effect from the six-year continuous straw return treatment and the soil bacterial communities were moderately changed.
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Affiliation(s)
- Dali Yu
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
- School of Life Sciences, Qilu Normal University, Jinan, P. R. China
| | - Zhiguo Wen
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Xiumei Li
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Xiaojun Song
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Huijun Wu
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
- * E-mail: (HW); (PY)
| | - Peilong Yang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
- * E-mail: (HW); (PY)
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