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Liu C, Han D, Yang H, Liu Z, Gao C, Liu Y. Effects of peach branch organic fertilizer on the soil microbial community in peach orachards. Front Microbiol 2023; 14:1223420. [PMID: 37485500 PMCID: PMC10361838 DOI: 10.3389/fmicb.2023.1223420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 06/22/2023] [Indexed: 07/25/2023] Open
Abstract
Peach branches is a by-product of peach industry. Making peach branch waste into peach branch organic fertilizer (PBOF) is a promising strategy of ecological utilization. In this study, the effects of PBOF on the yield and quality of peach fruit, chemical properties of bulk soil, and soil bacterial communities were investigated in a peach orchard. The results showed that the yield and sugar/acid ratio of two high-level PBOF treatments (SDH.4 and SKR.4) was higher than no fertilization treatment (CK), but there was no significant difference compared to the commercial organic fertilizer treatment (SYT.4). Moreover, the three fertilizer treatments increased soil nutrients such as soil organic matter (SOM) and available potassium (AK), compared to CK. Furthermore, PBOF increased the relative abundance of beneficial bacteria, and enhanced the soil bacterial co-occurrence pattern and the potential function of bacterial communities to degrade exogenous compounds. In addition, thanks to the local policy of encouraging the use of PBOF, the use cost of PBOF is lower than commercial organic fertilizer, which is conducive to the development of ecological agriculture.
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Affiliation(s)
- Chenyu Liu
- College of Bioscience and Resources Environment, Beijing University of Agriculture, Beijing, China
| | - Defeng Han
- College of Bioscience and Resources Environment, Beijing University of Agriculture, Beijing, China
| | | | - Zhiling Liu
- College of Bioscience and Resources Environment, Beijing University of Agriculture, Beijing, China
| | - Chengda Gao
- College of Humanities and Urban-Rural Development, Beijing University of Agriculture, Beijing, China
| | - Yueping Liu
- College of Bioscience and Resources Environment, Beijing University of Agriculture, Beijing, China
- Key Laboratory for Northern Urban Agriculture Ministry of Agriculture and Rural Affairs, Beijing University of Agriculture, Beijing, China
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2
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Variation of soil bacterial communities in a chronosequence of citrus orchard. ANN MICROBIOL 2022. [DOI: 10.1186/s13213-022-01681-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Purpose
Soil microorganisms are vital for soil ecosystems through bioconversion of soil nutrients and maintenance of soil fertility to promoting the growth and development of citrus. However, understanding of how different planting years affect the soil bacterial community structures as related to nutrient availability in citrus orchards is limited.
Methods
Here, Illumina MiSeq technology was used to investigate changes in bacterial community structures with different ages of citrus orchards that were 2, 5, 10, 15, and 18 years old.
Results
The data showed that (1) soil bacterial community structures changed over the different growth stages of citrus orchards. With the extension of plantation age, the microbial diversity of citrus orchards increased gradually so that it was highest in 10-year-old citrus plantations but then decreased where the diversity of 18-year-old citrus ages was significantly lower than that of 10 and 15-year-old ones. Proteobacteria, Actinobacteria, Acidobacteria, and Chloroflexi were the four dominant phyla in soil of citrus orchards, accounting for 30.85%, 24.89%, 14.27%, and 14.05% of the total soil bacterial communities, respectively. (2) Soil bacterial community structures in different succession stages were affected by soil pH and nutrients, in particular available potassium (AK).
Conclusion
This study advances the understanding of soil microbiota of orchards and their interactions related to environmental factors in citrus orchard, which will improve our ability to promote the function of soil bacteria, so as to improve soil pH and reduce potassium (K) fertilizer input and improve the fruit quality.
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Wang Q, Wang C, Wei Y, Yao W, Lei Y, Sun Y. Soil Microbes Drive the Flourishing Growth of Plants From Leucocalocybe mongolica Fairy Ring. Front Microbiol 2022; 13:893370. [PMID: 35668763 PMCID: PMC9164162 DOI: 10.3389/fmicb.2022.893370] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 05/04/2022] [Indexed: 11/13/2022] Open
Abstract
Fairy ring is a natural phenomenon in which fungal fruiting bodies occur as a ring on a spot. This ring is produced due to spore ejection by Basidiomycetous fungi and forms a lush growing plant belt. However, the drivers for such formations and the potential plant growth-promoting rhizobacteria in fairy ring soils remain unknown. Fairy rings formed by Leucocalocybe mongolica were selected in this study. Soil characteristics and microbial (bacteria and fungi) community structures between beneath and outside the fairy rings were compared through high-throughput sequencing. Beneficial bacterial resources were excavated using dependent culturable methods. Soil electrical conductivity and available potassium were higher in the soil beneath the ring than outside it. These parameters were positively correlated with the dominant microbial community, but microbial diversity was lower. In the soil beneath the fairy ring, Bacteroidetes and Basidiomycota were more abundant, whereas Verrucomicrobia was less prevalent. Bacillus pumilus (strain BG-5) was isolated from the soil beneath the ring. Strain BG-5 can solubilize phosphorus and produce indole-3-acetic acid, NH4 +, and siderophores. Furthermore, strain BG-5 enhanced salt tolerance and promoted the growth of Arabidopsis thaliana, wheat (Triticum aestivum), and cotton (Gossypium hirsutum) seedlings. This study indicated the presence of abundant beneficial microbes driving the flourishing growth of plants in the fairy ring soil and provided bio-resources for agricultural growth-promoting agents.
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Affiliation(s)
- Qiqi Wang
- College of Life Sciences/Xinjiang Production and Construction Corps Key Laboratory of Oasis Town and Mountain-Basin System Ecology, Shihezi University, Shihezi, China
| | - Chong Wang
- Ürümqi Customs Technique Center, Ürümqi, China
| | - Yumei Wei
- College of Life Sciences/Xinjiang Production and Construction Corps Key Laboratory of Oasis Town and Mountain-Basin System Ecology, Shihezi University, Shihezi, China
| | - Weiqin Yao
- Ürümqi Customs Technique Center, Ürümqi, China
| | - Yonghui Lei
- Department of Plant protection, College of Agriculture, Shihezi University, Shihezi, China
| | - Yanfei Sun
- College of Life Sciences/Xinjiang Production and Construction Corps Key Laboratory of Oasis Town and Mountain-Basin System Ecology, Shihezi University, Shihezi, China
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Zhang H, Phillip FO, Wu L, Zhao F, Yu S, Yu K. Effects of Temperature and Nitrogen Application on Carbon and Nitrogen Accumulation and Bacterial Community Composition in Apple Rhizosphere Soil. FRONTIERS IN PLANT SCIENCE 2022; 13:859395. [PMID: 35444679 PMCID: PMC9014127 DOI: 10.3389/fpls.2022.859395] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 02/28/2022] [Indexed: 05/03/2023]
Abstract
Malus sieversii grows on the slopes of the Tianshan Mountains in Xinjiang where the difference in daily temperature is significant. In recent years, the rhizosphere soil health of Malus sieversii has been severely impacted by anthropogenic disturbance and pathogenic infestation. The soil nutrient content and soil microorganism diversity are the main components of soil health. Low temperature has negative effects on soil bacterial community structure by inhibiting the accumulation of carbon and nitrogen. However, the effects of temperature and nitrogen application on soil carbon and nitrogen accumulation and the bacterial community composition in the rhizosphere soil of Malus sieversii are unclear. We set two temperature levels, i.e., low temperature (L) and room temperature (R), combined with no nitrogen (N0) and nitrogen application (N1) to explore the response of plant carbon and nitrogen uptake, rhizosphere soil carbon and nitrogen accumulation and bacterial community composition to temperature and nitrogen fertilization. At the same temperature level, plant 13C abundance (P-Atom13C), plant 15N absolute abundance (P-Con15N), soil 15N abundance (S-Atom15N) and soil urease, protease and glutaminase activities were significantly higher under nitrogen application compared with the no-nitrogen application treatment. The bacterial community diversity and richness indices of the apple rhizosphere soil in the N1 treatment were higher than those in the N0 treatment. The relative abundances of Actinobacteria, Rhodopseudomonas, and Bradyrhizobium were higher in the LN1 treatment than in the LN0 treatment. Redundancy analysis (RDA) showed that plant 13C absolute abundance (P-Con13C) and plant 15N absolute abundance (P-Con15N) were the main factors affecting the soil bacterial community composition. In summary, Nitrogen application can alleviate the effects of low temperature stress on the soil bacterial community and is of benefit for the uptakes of carbon and nitrogen in Malus sieversii plants.
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Affiliation(s)
| | | | | | | | | | - Kun Yu
- The Key Laboratory of Characteristics of Fruit and Vegetable Cultivation and Utilization of Germplasm Resources of the Xinjiang Production and Construction Corps, Shihezi University, Xinjiang, China
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Wang L, Huang D. Nitrogen and phosphorus losses by surface runoff and soil microbial communities in a paddy field with different irrigation and fertilization managements. PLoS One 2021; 16:e0254227. [PMID: 34242302 PMCID: PMC8274659 DOI: 10.1371/journal.pone.0254227] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 06/22/2021] [Indexed: 11/24/2022] Open
Abstract
Rice cultivation usually involves high water and fertilizer application rates leading to the nonpoint pollution of surface waters with phosphorus (P) and nitrogen (N). Here, a 10-year field experiment was conducted to investigate N and P losses and their impact factors under different irrigation and fertilization regimes. Results indicated that T2 (Chemical fertilizer of 240 kg N ha-1, 52 kg P ha-1, and 198 kg K ha-1 combined with shallow intermittent irrigation) decreased N loss by 48.9% compared with T1 (Chemical fertilizer of 273 kg N ha-1, 59 kg P ha-1, and 112 kg K ha-1 combined with traditional flooding irrigation). The loss ratio (total N loss loading/amount of applied N) of N was 9.24-15.90%, whereas that of P was 1.13-1.31% in all treatments. Nitrate N (NO3--N) loss was the major proportion accounting for 88.30-90.65% of dissolved inorganic N loss through surface runoff. Moreover, the N runoff loss was mainly due to high fertilizer input, soil NO3--N, and ammonium N (NH4+-N) contents. In addition, the N loss was accelerated by Bacteroidetes, Proteobacteria, Planotomycetes, Nitrospirae, Firmicutes bacteria and Ascomycota fungi, but decreased by Chytridiomycota fungi whose contribution to the N transformation process. Furthermore, T2 increased agronomic N use efficiency (AEN) and rice yield by 32.81% and 7.36%, respectively, in comparison with T1. These findings demonstrated that T2 might be an effective approach to ameliorate soil chemical properties, regulate microbial community structure, increase AEN and consequently reduce N losses as well as maintaining rice yields in the present study.
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Affiliation(s)
- Limin Wang
- Soil and Fertilizer Institute, Fujian Academy of Agricultural Sciences,
Fuzhou, P. R. China
- Fujian Key Laboratory of Agro—products Quality & Safety, Fujian
Academy of Agricultural Sciences, Fuzhou, P. R. China
| | - Dongfeng Huang
- Soil and Fertilizer Institute, Fujian Academy of Agricultural Sciences,
Fuzhou, P. R. China
- Fujian Key Laboratory of Agro—products Quality & Safety, Fujian
Academy of Agricultural Sciences, Fuzhou, P. R. China
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Cao L, Yu X, Liu C, Liu M, Chen J, Qin H, Liang C, Xu Q, Penttinen P. Alteration of soil nitrifiers and denitrifiers and their driving factors during intensive management of Moso bamboo (Phyllostachys pubescens). THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 705:135236. [PMID: 31841899 DOI: 10.1016/j.scitotenv.2019.135236] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 10/24/2019] [Accepted: 10/25/2019] [Indexed: 06/10/2023]
Abstract
Long-term intensive management, such as inorganic fertilization and soil tillage, have been reported to decrease soil organic carbon content (SOC) and diversity of soil bacterial communities, as well as increase N2O emissions in moso bamboo forests. However, the response of the N-cycling soil microbial community to intensive management remains unclear. To address this, we examined the effects of intensive moso bamboo management on nitrifying and denitrifying microorganisms. Soils receiving non-management (NM) and 10, 15, 20, and 25 years of intensive management (IM10, IM15, IM20, IM25) were characterized using quantitative real-time PCR (qPCR) and high-through sequencing methods. Our results showed that abundances of ammonia monooxygenase (amoA) from ammonia-oxidizing archaea (AOA) significantly increased (P < 0.05) and were greatest in IM15 (8.37 × 107 copies/g dry soils) and IM25 (5.42 × 107 copies/g dry soils) in top- and subsoils, respectively, while nitrous oxide reductase (nosZ) abundance significantly decreased by 59.1% (topsoil) and 36.4% (subsoil) in IM20 (P < 0.05). GroupI.1a-associated affiliating to AOA, and Bradyrhizobium affiliating to nosZ, were keys groups for nitrifiers and denitrifiers, respectively, and showed the greatest variations in response to long-term intensive management. Abundances of ammonia-oxidizing bacteria (AOB) and the nitrite reductase gene nirS were less affected, as were the dominant Nitrosospira species belonging to the AOB community. Except the AOB amoA abundance, soil nitrogen was found to be the main factor influencing the abundance, diversity, and composition of nitrifying genes, while denitrifying genes were mainly affected by SOC and available potassium, indicating that different factors control populations of nitrifiers and denitrifiers. Collectively, our study revealed that groupings of nitrifying and denitrifying microorganisms responded differently to intensive management. This information is of potential value towards identifying strategies to minimize nitrogen loss in moso bamboo plantations.
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Affiliation(s)
- Linhua Cao
- The State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, China; Zhejiang Provincial Collaborative Innovation Center for Bamboo Resources and High-Efficiency Utilization, Lin'an, Hangzhou 311300, China; College of Environmental and Resource Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, China
| | - Xiao Yu
- The State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, China; College of Environmental and Resource Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, China
| | - Caixia Liu
- The State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, China; College of Environmental and Resource Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, China
| | - Ming Liu
- The State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, China; College of Environmental and Resource Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, China
| | - Junhui Chen
- The State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, China; Zhejiang Provincial Collaborative Innovation Center for Bamboo Resources and High-Efficiency Utilization, Lin'an, Hangzhou 311300, China; College of Environmental and Resource Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, China
| | - Hua Qin
- The State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, China; Zhejiang Provincial Collaborative Innovation Center for Bamboo Resources and High-Efficiency Utilization, Lin'an, Hangzhou 311300, China; College of Environmental and Resource Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, China
| | - Chenfei Liang
- The State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, China; Zhejiang Provincial Collaborative Innovation Center for Bamboo Resources and High-Efficiency Utilization, Lin'an, Hangzhou 311300, China; College of Environmental and Resource Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, China
| | - Qiufang Xu
- The State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, China; Zhejiang Provincial Collaborative Innovation Center for Bamboo Resources and High-Efficiency Utilization, Lin'an, Hangzhou 311300, China; College of Environmental and Resource Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, China.
| | - Petri Penttinen
- College of Environmental and Resource Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, China
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Luo X, Wang MK, Hu G, Weng B. Seasonal Change in Microbial Diversity and Its Relationship with Soil Chemical Properties in an Orchard. PLoS One 2019; 14:e0215556. [PMID: 31891580 PMCID: PMC6938340 DOI: 10.1371/journal.pone.0215556] [Citation(s) in RCA: 11] [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: 04/13/2019] [Accepted: 12/06/2019] [Indexed: 11/19/2022] Open
Abstract
This study aimed to determine the microbial diversity at different soil depths (0–5 and 5–20 cm) in a subtropical orchard during different seasons (i.e., spring, summer and autumn) to advance knowledge of the roles of microbes in orchard ecosystem balance. In tracking experiments conducted in an orchard (established in 1996), the phospholipid fatty acid (PLFA) biomarker method was employed to determine the soil microbial system. The total PLFA concentration did not vary significantly between soil depths but changed between seasons. It peaked in the summer at 258.97 ± 23.48 μg g soil-1 from 0–5 cm and at 270.99 ± 58.94 μg g soil-1 from 5–20 cm. A total of 33 microbial fatty acid biomarkers were observed and identified in the sampled soil. The quantities of PLFAs for 29 microbial groups varied significantly between seasons, except for 15:0 iso 3OH, 15:1 iso G, 16:0 2OH, and 17:0 iso 3OH. The bacterial PLFAs and fungal and actinomycetic PLFAs in the orchard soil collected in summer were significantly more abundant than those collected in the spring or autumn (P < 0.01). The number of soil microorganism species (richness) and the Simpson and Shannon-Wiener indexes were all highest in summer. The total PLFAs, bacterial PLFAs, fungal PLFAs, actinomycetic PLFAs, richness, and Simpson and Shannon-Wiener indexes were all significantly negatively correlated with soil pH, total organic carbon (TOC), total nitrogen (TN) and the cation exchange capacity (CEC) (P < 0.05).
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Affiliation(s)
- Xuhui Luo
- Agricultural Ecology Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian Province, China
- * E-mail:
| | - Ming Kuang Wang
- Department of Agricultural Chemistry, National Taiwan University, Taipei, Taiwan
| | - Guiping Hu
- Jiangxi Sericulture and Tea of Research Institute, Nanchang, Jiangxi Province, China
| | - Boqi Weng
- Fuzhou Scientific Observing and Experimental Station of Agro-Environment, Ministry of Agriculture and Rural Affairs of People’s Republic China, Fuzhou, Fujian Province, China
- Fujian Key Laboratory on Ecological Processes of Hilly Agriculture in Red Soil Region, Agency of Fujian Science and Technology, Fuzhou, Fujian Province, China
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Lee SA, Kim Y, Kim JM, Chu B, Joa JH, Sang MK, Song J, Weon HY. A preliminary examination of bacterial, archaeal, and fungal communities inhabiting different rhizocompartments of tomato plants under real-world environments. Sci Rep 2019; 9:9300. [PMID: 31243310 PMCID: PMC6594962 DOI: 10.1038/s41598-019-45660-8] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 06/10/2019] [Indexed: 01/21/2023] Open
Abstract
Plant microbiota is a key determinant of plant health and productivity. The composition and structure of plant microbiota varies according to plant tissue and compartment, which are specific habitats for microbial colonization. To investigate the structural composition of the microbiome associated with tomato roots under natural systems, we characterized the bacterial, archaeal, and fungal communities of three belowground compartments (rhizosphere, endosphere, and bulk soil) of tomato plants collected from 23 greenhouses in 7 geographic locations of South Korea. The microbial diversity and structure varied by rhizocompartment, with the most distinctive community features found in the endosphere. The bacterial and fungal communities in the bulk soil and rhizosphere were correlated with soil physicochemical properties, such as pH, electrical conductivity, and exchangeable cation levels, while this trend was not evident in the endosphere samples. A small number of core bacterial operational taxonomic units (OTUs) present in all samples from the rhizosphere and endosphere represented more than 60% of the total relative abundance. Among these core microbes, OTUs belonging to the genera Acidovorax, Enterobacter, Pseudomonas, Rhizobium, Streptomyces, and Variovorax, members of which are known to have beneficial effects on plant growth, were more relatively abundant in the endosphere samples. A co-occurrence network analysis indicated that the microbial community in the rhizosphere had a larger and more complex network than those in the bulk soil and endosphere. The analysis also identified keystone taxa that might play important roles in microbe-microbe interactions in the community. Additionally, profiling of predicted gene functions identified many genes associated with membrane transport in the endospheric and rhizospheric communities. Overall, the data presented here provide preliminary insight into bacterial, archaeal, and fungal phylogeny, functionality, and interactions in the rhizocompartments of tomato roots under real-world environments.
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Affiliation(s)
- Shin Ae Lee
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Wanju, 55365, South Korea
| | - Yiseul Kim
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Wanju, 55365, South Korea
| | - Jeong Myeong Kim
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Wanju, 55365, South Korea
| | - Bora Chu
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Wanju, 55365, South Korea
| | - Jae-Ho Joa
- Research Institute of Climate Change and Agriculture, National Institute of Horticultural & Herbal Science, RDA, Jeju, 63240, South Korea
| | - Mee Kyung Sang
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Wanju, 55365, South Korea
| | - Jaekyeong Song
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Wanju, 55365, South Korea
| | - Hang-Yeon Weon
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Wanju, 55365, South Korea.
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Wang B, Adachi Y, Sugiyama S. Soil productivity and structure of bacterial and fungal communities in unfertilized arable soil. PLoS One 2018; 13:e0204085. [PMID: 30248134 PMCID: PMC6152964 DOI: 10.1371/journal.pone.0204085] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 09/04/2018] [Indexed: 01/22/2023] Open
Abstract
Soil productivity is strongly influenced by the activities of microbial communities. However, it is not well understood how community structure, including its richness, mass, and composition, influences soil functions. We investigated the relationships between soil productivity and microbial communities in unfertilized arable soils extending over 1000 km in eastern Japan. Soil properties, including C turnover rate, N mineralization rate, microbial C, and various soil chemical properties, were measured. Soil bacterial and fungal communities were analyzed by Illumina's MiSeq using 16S rRNA and ITS regions. In addition, root microbial communities from maize grown in each soil were also investigated. Soil bacterial communities shared many operational taxonomic units (OTUs) among farms. An ordination plot based on correspondence analysis revealed convergent distribution of soil bacterial communities across the farms, which seemed to be a result of similar agricultural management practices. Although fungal communities showed lower richness and a lower proportion of shared OTUs than bacterial communities, community structure between the farms tended to be convergent. On the other hand, root communities had lower richness and a higher abundance of specific taxa than the soil communities. Two soil functions, decomposition activity and soil productivity, were extracted by principal component analysis (PCA) based on eight soil properties. Soil productivity correlated with N mineralization rate, P2O5, and maize growth, but not with decomposition activity, which is characterized by C turnover rate, soil organic C, and microbial mass. Soil productivity showed a significant association with community composition, but not with richness and mass of soil microbial communities. Soil productivity also correlated with the abundance of several specific taxa, both in bacteria and fungi. Root communities did not show any clear correlations with soil productivity. These results demonstrate that community composition and abundance of soil microbial communities play important roles in determining soil productivity.
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Affiliation(s)
- Boxi Wang
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori, Japan
- The United Graduate School of Agricultural Sciences, Iwate University, Morioka, Iwate, Japan
| | - Yoichi Adachi
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori, Japan
| | - Shuichi Sugiyama
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori, Japan
- * E-mail:
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Shah V, Subramaniam S. Bradyrhizobium japonicum USDA110: A representative model organism for studying the impact of pollutants on soil microbiota. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 624:963-967. [PMID: 29275259 DOI: 10.1016/j.scitotenv.2017.12.185] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 11/28/2017] [Accepted: 12/17/2017] [Indexed: 06/07/2023]
Abstract
Photobacteria phosoreum or Escherichia coli are widely used in the scientific, industrial, and regulatory industries for evaluating the toxicity of pollutants against the soil microbial community. The organisms, however, are not part of the soil microbiota and the toxicity data obtained using these organisms could be misleading. Analysis of microbiota present in the soil obtained from across the world indicates that organisms from the Bradyrhizobium genus are the most ubiquitous of all microorganisms. Playing a critical role in nitrogen fixation and soil fertility, organisms from this genus should be used for studying the toxicity of pollutants. Indeed, we propose that Bradyrhizobium japonicum USDA110 be used as a model organism for screening pollutants for toxicity against a soil microbial community.
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Affiliation(s)
- Vishal Shah
- College of the Sciences and Mathematics, West Chester University of Pennsylvania, West Chester, PA, United States.
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11
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Blaustein RA, Lorca GL, Teplitski M. Challenges for Managing Candidatus Liberibacter spp. (Huanglongbing Disease Pathogen): Current Control Measures and Future Directions. PHYTOPATHOLOGY 2018; 108:424-435. [PMID: 28990481 DOI: 10.1094/phyto-07-17-0260-rvw] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Huanglongbing (HLB; "citrus greening" disease) has caused significant damages to the global citrus industry as it has become well established in leading citrus-producing regions and continues to spread worldwide. Insecticidal control has been a critical component of HLB disease management, as there is a direct relationship between vector control and Candidatus Liberibacter spp. (i.e., the HLB pathogen) titer in HLB-infected citrus trees. In recent years, there have been substantial efforts to develop practical strategies for specifically managing Ca. Liberibacter spp.; however, a literature review on the outcomes of such attempts is still lacking. This work summarizes the greenhouse and field studies that have documented the effects and implications of chemical-based treatments (i.e., applications of broad-spectrum antibiotics, small molecule compounds) and nonchemical measures (i.e., applications of plant-beneficial compounds, applications of inorganic fertilizers, biological control, thermotherapy) for phytopathogen control. The ongoing challenges associated with mitigating Ca. Liberibacter spp. populations at the field-scale, such as the seasonality of the phytopathogen and associated HLB disease symptoms, limitations for therapeutics to contact the phytopathogen in planta, adverse impacts of broad-spectrum treatments on plant-beneficial microbiota, and potential implications on public and ecosystem health, are also discussed.
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Affiliation(s)
- Ryan A Blaustein
- First and third authors: Department of Soil and Water Sciences, Genetics Institute, University of Florida, Gainesville; and second author: Department of Microbiology and Cell Science, Genetics Institute, University of Florida, Gainesville
| | - Graciela L Lorca
- First and third authors: Department of Soil and Water Sciences, Genetics Institute, University of Florida, Gainesville; and second author: Department of Microbiology and Cell Science, Genetics Institute, University of Florida, Gainesville
| | - Max Teplitski
- First and third authors: Department of Soil and Water Sciences, Genetics Institute, University of Florida, Gainesville; and second author: Department of Microbiology and Cell Science, Genetics Institute, University of Florida, Gainesville
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Xu L, Yi M, Yi H, Guo E, Zhang A. Manure and mineral fertilization change enzyme activity and bacterial community in millet rhizosphere soils. World J Microbiol Biotechnol 2017; 34:8. [PMID: 29236189 DOI: 10.1007/s11274-017-2394-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 12/05/2017] [Indexed: 11/27/2022]
Abstract
Fertilization is a key agricultural practice for increasing millet yields and influencing soil properties, enzyme activities and rhizosphere bacterial communities. High throughput Illumina sequencing of the 16S rDNA was applied to compare the bacterial community structures and diversities among six different soil samples. The experiments involved the following: no fertilizer (CK), phosphate (P) and potassium (K) plus organic manure (M) (PKM), nitrogen (N) and K plus M (NKM), NPM, NPK and NPKM fertilization. The results showed that the NPKM fertilization of the millet field had a maximal yield of 3617 kg ha-1 among the six different treatments. The abundances of the Actinobacteria and Bacteroidetes phyla, especially the Devosia, Mycobacterium, Opitutus and Chitinophaga genera, were higher in NPKM than those in the other samples. Redundancy analysis showed that the soil organic matter (SOM), available phosphorus (AP), and urease (UR) activity were significantly correlated with bacterial communities, while SOM and AP were strongly correlated with soil enzyme activities. Pearson's correlation showed that the available nitrogen was strongly correlated with Devosia and Mycobacterium, and SOM was strongly correlated with Opitutus and Chitinophaga. Besides, catalase was significantly related to Iamia, the UR was significantly related to Devosia, phosphatase was significantly related to Luteimonas and Chitinophaga. Based on the soil quality and millet yield, NPKM treatment was a better choice for the millet field fertilization practices. These findings provide a better understanding of the importance of fertilization in influencing millet yield, soil fertility and microbial diversity, and they lead to a choice of scientific fertilization practices for sustainable development of the agroecosystem.
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Affiliation(s)
- Lixia Xu
- School of Life Science, Shanxi University, Taiyuan, 030006, China.,Department of Traditional Chinese Pharmacy, Shanxi Pharmaceutical Vocational College, Taiyuan, 030031, China
| | - Min Yi
- School of Life Science, Shanxi University, Taiyuan, 030006, China
| | - Huilan Yi
- School of Life Science, Shanxi University, Taiyuan, 030006, China.
| | - Erhu Guo
- Institute of Millet Crops, Shanxi Academy of Agricultural Sciences, Changzhi, 046011, China.
| | - Aiying Zhang
- Institute of Millet Crops, Shanxi Academy of Agricultural Sciences, Changzhi, 046011, China
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Lee SA, Park J, Chu B, Kim JM, Joa JH, Sang MK, Song J, Weon HY. Comparative analysis of bacterial diversity in the rhizosphere of tomato by culture-dependent and -independent approaches. J Microbiol 2016; 54:823-831. [PMID: 27888459 DOI: 10.1007/s12275-016-6410-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 10/14/2016] [Accepted: 10/17/2016] [Indexed: 12/14/2022]
Abstract
The microbiome in the rhizosphere-the region surrounding plant roots-plays a key role in plant growth and health, enhancing nutrient availability and protecting plants from biotic and abiotic stresses. To assess bacterial diversity in the tomato rhizosphere, we performed two contrasting approaches: culture-dependent and -independent. In the culture-dependent approach, two culture media (Reasoner's 2A agar and soil extract agar) were supplemented with 12 antibiotics for isolating diverse bacteria from the tomato rhizosphere by inhibiting predominant bacteria. A total of 689 bacterial isolates were clustered into 164 operational taxonomic units (OTUs) at 97% sequence similarity, and these were found to belong to five bacterial phyla (Proteobacteria, Actinobacteria, Bacteroidetes, Acidobacteria, and Firmicutes). Of these, 122 OTUs were retrieved from the antibiotic-containing media, and 80 OTUs were recovered by one specific antibiotic-containing medium. In the culture-independent approach, we conducted Illumina MiSeq amplicon sequencing of the 16S rRNA gene and obtained 19,215 high-quality sequences, which clustered into 478 OTUs belonging to 16 phyla. Among the total OTUs from the MiSeq dataset, 22% were recovered in the culture collection, whereas 41% of OTUs in the culture collection were not captured by MiSeq sequencing. These results showed that antibiotics were effective in isolating various taxa that were not readily isolated on antibiotic-free media, and that both contrasting approaches provided complementary information to characterize bacterial diversity in the tomato rhizosphere.
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Affiliation(s)
- Shin Ae Lee
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Wanju, 55365, Republic of Korea
| | - Jiyoung Park
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Wanju, 55365, Republic of Korea
| | - Bora Chu
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Wanju, 55365, Republic of Korea
| | - Jeong Myeong Kim
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Wanju, 55365, Republic of Korea
| | - Jae-Ho Joa
- Research Institute of Climate Change and Agriculture, National Institute of Horticultural & Herbal Science, RDA, Jeju, 63240, Republic of Korea
| | - Mee Kyung Sang
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Wanju, 55365, Republic of Korea
| | - Jaekyeong Song
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Wanju, 55365, Republic of Korea
| | - Hang-Yeon Weon
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Wanju, 55365, Republic of Korea.
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Kim JM, Roh AS, Choi SC, Kim EJ, Choi MT, Ahn BK, Kim SK, Lee YH, Joa JH, Kang SS, Lee SA, Ahn JH, Song J, Weon HY. Soil pH and electrical conductivity are key edaphic factors shaping bacterial communities of greenhouse soils in Korea. J Microbiol 2016; 54:838-845. [DOI: 10.1007/s12275-016-6526-5] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 10/31/2016] [Indexed: 12/27/2022]
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Francioli D, Schulz E, Lentendu G, Wubet T, Buscot F, Reitz T. Mineral vs. Organic Amendments: Microbial Community Structure, Activity and Abundance of Agriculturally Relevant Microbes Are Driven by Long-Term Fertilization Strategies. Front Microbiol 2016; 7:1446. [PMID: 27683576 PMCID: PMC5022044 DOI: 10.3389/fmicb.2016.01446] [Citation(s) in RCA: 197] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 08/30/2016] [Indexed: 02/02/2023] Open
Abstract
Soil management is fundamental to all agricultural systems and fertilization practices have contributed substantially to the impressive increases in food production. Despite the pivotal role of soil microorganisms in agro-ecosystems, we still have a limited understanding of the complex response of the soil microbiota to organic and mineral fertilization in the very long-term. Here, we report the effects of different fertilization regimes (mineral, organic and combined mineral and organic fertilization), carried out for more than a century, on the structure and activity of the soil microbiome. Organic matter content, nutrient concentrations, and microbial biomass carbon were significantly increased by mineral, and even more strongly by organic fertilization. Pyrosequencing revealed significant differences between the structures of bacterial and fungal soil communities associated to each fertilization regime. Organic fertilization increased bacterial diversity, and stimulated microbial groups (Firmicutes, Proteobacteria, and Zygomycota) that are known to prefer nutrient-rich environments, and that are involved in the degradation of complex organic compounds. In contrast, soils not receiving manure harbored distinct microbial communities enriched in oligotrophic organisms adapted to nutrient-limited environments, as Acidobacteria. The fertilization regime also affected the relative abundances of plant beneficial and detrimental microbial taxa, which may influence productivity and stability of the agroecosystem. As expected, the activity of microbial exoenzymes involved in carbon, nitrogen, and phosphorous mineralization were enhanced by both types of fertilization. However, in contrast to comparable studies, the highest chitinase and phosphatase activities were observed in the solely mineral fertilized soil. Interestingly, these two enzymes showed also a particular high biomass-specific activities and a strong negative relation with soil pH. As many soil parameters are known to change slowly, the particularity of unchanged fertilization treatments since 1902 allows a profound assessment of linkages between management and abiotic as well as biotic soil parameters. Our study revealed that pH and TOC were the majors, while nitrogen and phosphorous pools were minors, drivers for structure and activity of the soil microbial community. Due to the long-term treatments studied, our findings likely represent permanent and stable, rather than transient, responses of soil microbial communities to fertilization.
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Affiliation(s)
- Davide Francioli
- Department of Soil Ecology, Helmholtz Centre for Environmental Research - UFZ Halle, Germany
| | - Elke Schulz
- Department of Soil Ecology, Helmholtz Centre for Environmental Research - UFZ Halle, Germany
| | - Guillaume Lentendu
- Department of Ecology, University of Kaiserslautern Kaiserslautern, Germany
| | - Tesfaye Wubet
- Department of Soil Ecology, Helmholtz Centre for Environmental Research - UFZHalle, Germany; German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-LeipzigLeipzig, Germany
| | - François Buscot
- Department of Soil Ecology, Helmholtz Centre for Environmental Research - UFZHalle, Germany; German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-LeipzigLeipzig, Germany
| | - Thomas Reitz
- Department of Soil Ecology, Helmholtz Centre for Environmental Research - UFZHalle, Germany; German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-LeipzigLeipzig, Germany
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