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Cao C, Zhang Y, Cui Z. Response of Soil Fungal Community to Reforestation on Shifting Sand Dune in the Horqin Sandy Land, Northeast China. Microorganisms 2024; 12:1545. [PMID: 39203387 PMCID: PMC11356087 DOI: 10.3390/microorganisms12081545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Revised: 07/26/2024] [Accepted: 07/26/2024] [Indexed: 09/03/2024] Open
Abstract
Reforestation of native shrub on shifting sand dunes has been widely used for desertification control in semi-arid grassland in Northeast China. Previous studies have confirmed that plantation establishment facilitates fixing sand dunes, restoring vegetation, and improving soil properties, but very few have focused on the response of the soil fungal community. In this study, a chronosequence of Caragana microphylla (CM) shrub sand-fixation plantations (8-, 19-, and 33-year-old), non-vegetated shifting sand dunes (0 years), and adjacent natural CM forests (NCFs; 50-year-old) in the Horqin sandy land were selected as experimental sites. Soil properties including enzymatic activities were determined, and the composition and structure of the soil fungal community were investigated using the Illumina MiSeq sequencing technique based on the internal transcribed spacer (ITS) rDNA. This study aimed to (1) describe the response of the soil fungal community to revegetation onto a moving sand dune by planting a native shrub plantation; (2) determine the main soil factors driving the succession of the fungal community; and (3) discuss whether the soil fungal community can be restored to its original state by reforestation. The reforestation of CM significantly ameliorated soil properties, increased soil fungal diversity, and altered the composition and structure of the soil fungal community. Ascomycota, Basidiomycota, and Zoopagomycota were the dominant phyla in all sites. Ascomycota did not respond to plantation development, whereas the other two dominant phyla linearly increased or decreased with the plantation age. The relative abundance of dominant genera varied with sites and showed a waning and waxing characteristic. The composition and structure of the soil fungal community in the 33-year CM plantation were very close to that of the NCF, indicating the restorability of the soil fungal community. The succession of the soil fungal community was directly driven by soil properties, of which soil moisture, organic matter, total N, urease, and protease were the main affecting factors.
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Affiliation(s)
- Chengyou Cao
- College of Life and Health Sciences, Northeastern University, Shenyang 110169, China; (Y.Z.); (Z.C.)
- Liaoning Province Key Laboratory of Bioresource Research and Development, Northeastern University, Shenyang 110169, China
| | - Ying Zhang
- College of Life and Health Sciences, Northeastern University, Shenyang 110169, China; (Y.Z.); (Z.C.)
- Liaoning Province Key Laboratory of Bioresource Research and Development, Northeastern University, Shenyang 110169, China
| | - Zhenbo Cui
- College of Life and Health Sciences, Northeastern University, Shenyang 110169, China; (Y.Z.); (Z.C.)
- Liaoning Province Key Laboratory of Bioresource Research and Development, Northeastern University, Shenyang 110169, China
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Lu B, Lou Y, Wang J, Liu Q, Yang SS, Ren N, Wu WM, Xing D. Understanding the Ecological Robustness and Adaptability of the Gut Microbiome in Plastic-Degrading Superworms ( Zophobas atratus) in Response to Microplastics and Antibiotics. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:12028-12041. [PMID: 38838251 DOI: 10.1021/acs.est.4c01692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2024]
Abstract
Recent discoveries indicate that several insect larvae are capable of ingesting and biodegrading plastics rapidly and symbiotically, but the ecological adaptability of the larval gut microbiome to microplastics (MPs) remains unclear. Here, we described the gut microbiome assemblage and MP biodegradation of superworms (Zophobas atratus larvae) fed MPs of five major petroleum-based polymers (polyethylene, polypropylene, polystyrene, polyvinyl chloride, and polyethylene terephthalate) and antibiotics. The shift of molecular weight distribution, characteristic peaks of C═O, and metabolic intermediates of residual polymers in egested frass proved depolymerization and biodegradation of all MPs tested in the larval intestines, even under antibiotic suppression. Superworms showed a wide adaptation to the digestion of the five polymer MPs. Antibiotic suppression negatively influenced the survival rate and plastic depolymerization patterns. The larval gut microbiomes differed from those fed MPs and antibiotics, indicating that antibiotic supplementation substantially shaped the gut microbiome composition. The larval gut microbiomes fed MPs had higher network complexity and stability than those fed MPs and antibiotics, suggesting that the ecological robustness of the gut microbiomes ensured the functional adaptability of larvae to different MPs. In addition, Mantel's test indicated that the gut microbiome assemblage was obviously related to the polymer type, the plastic degradability, antibiotic stress, and larval survival rate. This finding provided novel insights into the self-adaptation of the gut microbiome of superworms in response to different MPs.
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Affiliation(s)
- Baiyun Lu
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, P. R. China
| | - Yu Lou
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, P. R. China
| | - Jing Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, P. R. China
| | - Qiang Liu
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, P. R. China
| | - Shan-Shan Yang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, P. R. China
| | - Nanqi Ren
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, P. R. China
| | - Wei-Min Wu
- Department of Civil and Environmental Engineering, Department of Chemistry, William & Cloy Codiga Resource Recovery Center, Center for Sustainable Development & Global Competitiveness, Stanford University, Stanford, California 94305, United States
| | - Defeng Xing
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, P. R. China
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Li DD, Wang J, Jiang Y, Zhang P, Liu Y, Li YZ, Zhang Z. Quantifying functional redundancy in polysaccharide-degrading prokaryotic communities. MICROBIOME 2024; 12:120. [PMID: 38956705 PMCID: PMC11218364 DOI: 10.1186/s40168-024-01838-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 05/14/2024] [Indexed: 07/04/2024]
Abstract
BACKGROUND Functional redundancy (FR) is widely present, but there is no consensus on its formation process and influencing factors. Taxonomically distinct microorganisms possessing genes for the same function in a community lead to within-community FR, and distinct assemblies of microorganisms in different communities playing the same functional roles are termed between-community FR. We proposed two formulas to respectively quantify the degree of functional redundancy within and between communities and analyzed the FR degrees of carbohydrate degradation functions in global environment samples using the genetic information of glycoside hydrolases (GHs) encoded by prokaryotes. RESULTS Our results revealed that GHs are each encoded by multiple taxonomically distinct prokaryotes within a community, and the enzyme-encoding prokaryotes are further distinct between almost any community pairs. The within- and between-FR degrees are primarily affected by the alpha and beta community diversities, respectively, and are also affected by environmental factors (e.g., pH, temperature, and salinity). The FR degree of the prokaryotic community is determined by deterministic factors. CONCLUSIONS We conclude that the functional redundancy of GHs is a stabilized community characteristic. This study helps to determine the FR formation process and influencing factors and provides new insights into the relationships between prokaryotic community biodiversity and ecosystem functions. Video Abstract.
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Affiliation(s)
- Dan-Dan Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, China
| | - Jianing Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Yiru Jiang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Peng Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Ya Liu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Yue-Zhong Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China.
| | - Zheng Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China.
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Yang J, Wang C, Wang Z, Li Y, Yu H, Feng J, Xie S, Li X. Distribution patterns and co-occurrence network of eukaryotic algae in different salinity waters of Yuncheng Salt Lake, China. Sci Rep 2024; 14:8340. [PMID: 38594439 PMCID: PMC11003963 DOI: 10.1038/s41598-024-58636-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 04/01/2024] [Indexed: 04/11/2024] Open
Abstract
The community structure and co-occurrence pattern of eukaryotic algae in Yuncheng Salt Lake were analyzed based on marker gene analysis of the 18S rRNA V4 region to understand the species composition and their synergistic adaptations to the environmental factors in different salinity waters. The results showed indicated that the overall algal composition of Yuncheng Salt Lake showed a Chlorophyta-Pyrrophyta-Bacillariophyta type structure. Chlorophyta showed an absolute advantage in all salinity waters. In addition, Cryptophyta dominated in the least saline waters; Pyrrophyta and Bacillariophyta were the dominant phyla in the waters with salinity ranging from 13.2 to 18%. Picochlorum, Nannochloris, Ulva, and Tetraselmis of Chlorophyta, Biecheleria and Oxyrrhis of Pyrrophyta, Halamphora, Psammothidium, and Navicula of Bacillariophyta, Guillardia and Rhodomonas of Cryptophyta were not observed in previous surveys of the Yuncheng Salt Lake, suggesting that the algae are undergoing a constant turnover as the water environment of the Salt Lake continues to change. The network diagram demonstrated that the algae were strongly influenced by salinity, NO3-, and pH, changes in these environmental factors would lead to changes in the algal community structure, thus affecting the stability of the network structure.
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Affiliation(s)
- Jing Yang
- Shanxi Key Laboratory of Yuncheng Salt Lake Ecological Protection and Resource Utilization, College of Life Sciences, Yuncheng University, Yuncheng, 044000, China
| | - Chuanxu Wang
- Shanxi Key Laboratory of Yuncheng Salt Lake Ecological Protection and Resource Utilization, College of Life Sciences, Yuncheng University, Yuncheng, 044000, China
| | - Zhuo Wang
- Shanxi Key Laboratory of Yuncheng Salt Lake Ecological Protection and Resource Utilization, College of Life Sciences, Yuncheng University, Yuncheng, 044000, China
| | - Yunjie Li
- Shanxi Key Laboratory of Yuncheng Salt Lake Ecological Protection and Resource Utilization, College of Life Sciences, Yuncheng University, Yuncheng, 044000, China
| | - Huiying Yu
- Shanxi Key Laboratory of Yuncheng Salt Lake Ecological Protection and Resource Utilization, College of Life Sciences, Yuncheng University, Yuncheng, 044000, China
| | - Jia Feng
- School of Life Science, Shanxi University, Taiyuan, 030006, China
| | - Shulian Xie
- School of Life Science, Shanxi University, Taiyuan, 030006, China
| | - Xin Li
- Shanxi Key Laboratory of Yuncheng Salt Lake Ecological Protection and Resource Utilization, College of Life Sciences, Yuncheng University, Yuncheng, 044000, China.
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Bai X, Liu K, Ning T, Deng C, Wang L, Li D, Wang T, Li J. Effects of multiple N, P, and K fertilizer combinations on strawberry growth and the microbial community. PLoS One 2023; 18:e0293088. [PMID: 38011252 PMCID: PMC10681299 DOI: 10.1371/journal.pone.0293088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 10/05/2023] [Indexed: 11/29/2023] Open
Abstract
Nitrogen (N), phosphorus (P), and potassium (K) exert various effects on strawberry (Fragaria ananassa Duchesne) yields. In this study, we employed an orthogonal experimental design (T1-T9) with three fertilization treatments (N, P, and K) at three levels to identify an optimal fertilization scheme for strawberry cultivation. The effects of fertilizer combinations the rhizosphere soil microbial community were also explored by using bacterial full-length 16S rRNA and fungal ITS (internal transcribed spacer) sequencing (30 samples for each analysis). The results showed that the average plant height and leaf area of the fertilized groups were 24.6% and 41.6% higher than those of the non-fertilized group (T0). After 60 d of planting, the sucrase activity in the T6 group increased by 76.67% compared to the T0 group, with phosphate fertilizer exerting a more significant impact on sucrase activity. The T6 treatment group had the highest alpha diversity index among bacterial and fungal microorganisms, and had a different microbial community structure compared with the control group. The most abundant bacterial taxa in the strawberry rhizosphere soil were Proteobacteria, Bacteroidota, and Acidobacteriota, and the most abundant fungal phyla were Monoblepharomycota, Glomeromycota, and Mucoromycota. Application of the optimal combined fertilizer treatment (T6) significantly increased the abundance of Proteobacteria and altered the abundance of Gemmatimonas compared to other treatment groups. Notably, Gemmatimonas abundance positively correlated with strawberry plant height and soil N, P, and K levels. These findings indicated that the relative abundance of beneficial bacteria could be enhanced by the application of an optimal fertilizer ratio, ultimately improving strawberry agronomic traits.
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Affiliation(s)
- Xue Bai
- Engineering Research Center for Urban Modern Agriculture of Higher Education in Yunnan Province, School of Agriculture and Life Sciences, Kunming University, Kunming, China
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, China
| | - Kaili Liu
- Engineering Research Center for Urban Modern Agriculture of Higher Education in Yunnan Province, School of Agriculture and Life Sciences, Kunming University, Kunming, China
| | - Tiao Ning
- Engineering Research Center for Urban Modern Agriculture of Higher Education in Yunnan Province, School of Agriculture and Life Sciences, Kunming University, Kunming, China
| | | | - Li Wang
- Xinhui Forestry Science Institute, Jiangmen, China
| | - Diyan Li
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, China
| | - Tao Wang
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, China
| | - Jing Li
- Engineering Research Center for Urban Modern Agriculture of Higher Education in Yunnan Province, School of Agriculture and Life Sciences, Kunming University, Kunming, China
- Shangri-La Zangmei Agricultural Technology Co., Ltd., Diqing, China
- Shangri-La City Small Berry Research and Development Center, Diqing, China
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6
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Wang X, Huang T, Li Y, Zhao G, Zhao J. Elevational characteristics of soil bacterial community and their responses to soil translocation at a mountainside in northwest Sichuan, China. Sci Rep 2023; 13:17906. [PMID: 37863997 PMCID: PMC10589279 DOI: 10.1038/s41598-023-44811-2] [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: 05/17/2023] [Accepted: 10/12/2023] [Indexed: 10/22/2023] Open
Abstract
How the soil bacterial communities vary with elevation is context-dependent, and the effect of soil translocation between elevations on bacterial community structure and metabolic function was not fully understood yet. Here, the bacterial community composition and diversity at five elevations along a 1600-3000 m elevation gradient on a mountainside in northwest Sichuan were characterized, and the responses of soil bacterial community to simulated climate changes were further studied by soil translocation reciprocally at three elevations for 12 months. Significant differences were found in soil temperature and moisture at different elevations, but there was no observed change in bacterial alpha diversity. The relative abundance of bacterial phyla was significantly different among the five elevations except for Proteobacteria (the dominant bacterial phyla in five elevation), and most bacterial phyla correlated with soil temperature, moisture, pH and soil bulk density. The direct effect of soil properties (pH, soil nutrients and soil bulk density) on soil bacterial community was stronger than the direct effect of temperature and moisture. Soil translocation changed the relative abundance of some bacterial phyla, and taxonomic groups with significant changes were mainly non-dominant phyla rather than the dominant phyla. Metabolism was the primary function of bacterial community at all elevations, which accounted for ~ 80% of relative abundance, and soil translocation had little effect on metabolic function. These findings indicated that soil bacterial dominant taxa and soil bacterial metabolic functions are relatively stable, which contribute to the stability of the ecosystem when response to the climate change in the future.
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Affiliation(s)
- Xuemei Wang
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, 621000, Sichuan, China
- School of Resource and Environmental Engineering, Mianyang Normal University, Mianyang, 621000, Sichuan, China
| | - Tianzhi Huang
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, 621000, Sichuan, China
- School of Resource and Environmental Engineering, Mianyang Normal University, Mianyang, 621000, Sichuan, China
| | - Yunyun Li
- School of Resource and Environmental Engineering, Mianyang Normal University, Mianyang, 621000, Sichuan, China
| | - Guang Zhao
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jixia Zhao
- College of Resources and Environment, Yunnan Agricultural University, No. 95, Heijin Road, Panlong District, Kunming, 650201, China.
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Liu R, Liang B, Zhao H, Zhao Y. Impacts of various amendments on the microbial communities and soil organic carbon of coastal saline-alkali soil in the Yellow River Delta. Front Microbiol 2023; 14:1239855. [PMID: 37779720 PMCID: PMC10539599 DOI: 10.3389/fmicb.2023.1239855] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 08/16/2023] [Indexed: 10/03/2023] Open
Abstract
The utilization of industrial and agricultural resources, such as desulfurization gypsum and straw, is increasingly favored to improve saline alkali land. However, there is still a lack of comprehensive study on the mechanism of organic carbon turnover under the conditions of desulfurization gypsum and straw application. We studied the changes in soil chemical performance, microbial diversity, and microbial community structure in soils with the addition of various levels of straw (no straw, S0; low straw, Sl; medium straw, Sm; and high straw, Sh) and gypsum (no gypsum, DG0; low gypsum, DGl; and high gypsum, DGh) in a 120-day incubation experiment. The bacterial and fungal community richness was higher in the SmDGl treatment than in the SmDG0 treatment. The microbial community evenness showed a similar pattern between the SmDGl and SmDG0 treatments. The combination of the straw and desulfurization gypsum treatments altered the relative abundance of the main bacterial phyla Bacteroidetes and Firmicutes and the dominant fungal class Sordariomycetes, which increased with the enhancement of the SOC ratio. The combination of the straw and desulfurization gypsum treatments, particularly SmDGl, significantly decreased the soil pH and exchangeable sodium percentage (ESP), while it increased the soil organic carbon, microbial biomass carbon, and activities of soil enzymes. Improvement in the soil salinization environment clearly drove the changes in bacterial α-diversity and community, particularly those in the soil carbon fractions and ESP. In conclusion, these findings provide a strong framework to determine the impact of application practices on soil restoration, and the information gained in this study will help to develop more sustainable and effective integrated strategies for the restoration of saline-alkali soil.
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Affiliation(s)
| | | | - Huili Zhao
- College of Resources and Environmental Engineering, Ludong University, Yantai, China
| | - Ying Zhao
- College of Resources and Environmental Engineering, Ludong University, Yantai, China
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Wei Z, Xu Y, Shi Y, Zhou X, Lin J, Ruan A. The response mechanism of microorganisms to the organic carbon-driven formation of black and odorous water. ENVIRONMENTAL RESEARCH 2023; 231:116255. [PMID: 37245578 DOI: 10.1016/j.envres.2023.116255] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 05/15/2023] [Accepted: 05/26/2023] [Indexed: 05/30/2023]
Abstract
The formation of black and odorous water is a complex process influenced by various factors such as organic matter and environmental conditions. However, there are limited studies on the role of microorganisms in water and sediment during the blackening and odorization process. In this study, we investigated the characteristics of black and odorous water formation by simulating organic carbon-driven black and odorous water through indoor experiments. The study revealed that the water turned black and odorous when DOC reached 50 mg/L and the microbial community structure in the water changed significantly during this process, with the relative abundance of Desulfobacterota increasing significantly and Desulfovibrio being the main dominant genus in Desulfobacterota. Additionally, we observed a notable decrease in the α-diversity of the microbial community in water and a considerable increase in microbial function of sulfur compounds respiration in water. In contrast, the sediment microbial community changed slightly, and the main functions of the sediment microbial community remained unchanged. The partial least squares path model (PLS-PM) suggested that organic carbon will drive the blackening and odorization process by affecting DO levels and microbial community structure and that the contribution of Desulfobacterota in water to the formation of black and odorous water was higher than that in sediment. Overall, our study provides insights into the characteristics of black and odorous water formation and suggests potential ways to prevent its formation by controlling DOC and inhibiting the growth of Desulfobacterota in water bodies.
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Affiliation(s)
- Zhipeng Wei
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing 210098, China; College of Hydrology and Water Resources, Hohai University, Nanjing 210098, China
| | - Yaofei Xu
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing 210098, China; College of Hydrology and Water Resources, Hohai University, Nanjing 210098, China
| | - Yingying Shi
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing 210098, China; College of Hydrology and Water Resources, Hohai University, Nanjing 210098, China
| | - Xiaotian Zhou
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing 210098, China; College of Hydrology and Water Resources, Hohai University, Nanjing 210098, China
| | - Jie Lin
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing 210098, China; College of Hydrology and Water Resources, Hohai University, Nanjing 210098, China
| | - Aidong Ruan
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing 210098, China; College of Hydrology and Water Resources, Hohai University, Nanjing 210098, China.
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Liu YH, Mohamad OAA, Gao L, Xie YG, Abdugheni R, Huang Y, Li L, Fang BZ, Li WJ. Sediment prokaryotic microbial community and potential biogeochemical cycle from saline lakes shaped by habitat. Microbiol Res 2023; 270:127342. [PMID: 36848700 DOI: 10.1016/j.micres.2023.127342] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 02/19/2023] [Accepted: 02/20/2023] [Indexed: 02/23/2023]
Abstract
The microbial diversity and ecological function in different saline lakes was reduced or disappeared as the influence of climate change and human activities even before they were known. However, reports about prokaryotic microbial of saline lakes from Xinjiang are very limited especially in large-scale investigations. In this study, a total of 6 saline lakes represented three different habitats, including hypersaline lake (HSL), arid saline lake (ASL), and light saltwater lake (LSL) were involved. The distribution pattern and potential functions of prokaryotes were investigated by using the cultivation-independent method of amplicon sequencing. The results showed that Proteobacteria was the predominant community and was widely distributed in all kinds of saline lakes, Desulfobacterota was the representative community in hypersaline lakes, Firmicutes and Acidobacteriota were mainly distributed in arid saline lake samples, and Chloroflexi was more abundant in light saltwater lakes. Specifically, the archaeal community was mainly distributed in the HSL and ASL samples, whereas it was very rare in the LSL lakes. The functional group showed that fermentation was the main metabolic process of microbes in all saline lakes and covered 8 phyla, including Actinobacteriota, Bacteroidota, Desulfobacterota, Firmicutes, Halanaerobiaeota, Proteobacteria, Spirochaetota, and Verrucomicrobiota. Among the 15 functional phyla, Proteobacteria was a distinctly important community in saline lakes, as it exhibited wide functions in the biogeochemical cycle. According to the correlation of environmental factors, SO42-, Na+, CO32-, and TN were significantly affected in the microbial community from saline lakes in this study. Overall, our study provided more detailed information about microbial community composition and distribution from three different habitats of saline lakes, especially the potential functions of carbon, nitrogen, and sulfur cycles, which provided new insight for understanding the complex microbiota adapt to the extreme environment and new perspectives on evaluating microbial contributions to degraded saline lakes under environmental change.
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Affiliation(s)
- Yong-Hong Liu
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, PR China; Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, 830000 Urumqi, PR China
| | - Osama Abdalla Abdelshafy Mohamad
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, PR China; Department of Environmental Protection, Faculty of Environmental Agricultural Sciences, Arish University, Al-Arish 45511, Egypt
| | - Lei Gao
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, PR China
| | - Yuan-Guo Xie
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, PR China
| | - Rashidin Abdugheni
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, PR China
| | - Yin Huang
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, PR China
| | - Li Li
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, PR China
| | - Bao-Zhu Fang
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, PR China.
| | - Wen-Jun Li
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, PR China; State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China.
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Shinde R, Shahi DK, Mahapatra P, Naik SK, Thombare N, Singh AK. Potential of lignocellulose degrading microorganisms for agricultural residue decomposition in soil: A review. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 320:115843. [PMID: 36056484 DOI: 10.1016/j.jenvman.2022.115843] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 07/16/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
Lignocellulosic crop residues (LCCRs) hold a significant share of the terrestrial biomass, estimated at 5 billion Mg per annum globally. A massive amount of these LCCRs are burnt in many countries resulting in immense environmental pollution; hence, its proper disposal in a cost-effective and eco-friendly manner is a significant challenge. Among the different options for management of LCCRs, the use of lignocellulose degrading microorganisms (LCDMOs), like fungi and bacteria, has emerged as an eco-friendly and effective way for its on-site disposal. LCDMOs achieve degradation through various mechanisms, including multiple supportive enzymes, causing oxidative attacks by which recalcitrance of lignocellulose material is reduced, paving the way to further activity by depolymerizing enzymes. This improves the physical properties of soil, recycles plant nutrients, promotes plant growth and thus helps improve productivity. Rapid and proper microbial degradation may be achieved through the correct combination of the LCDMOs, supplementing nutrients and controlling different factors affecting microbial activity in the field. The review is a critical discussion of previous studies revealing the potential of individuals or a set of LCDMOs, factors controlling the rate of degradation and the key researchable areas for better understanding of the role of these decomposers for future use.
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Affiliation(s)
- Reshma Shinde
- ICAR- Research Complex for Eastern Region, Farming System Research Centre for Hill and Plateau Region, Ranchi, 834010, Jharkhand, India.
| | | | | | - Sushanta Kumar Naik
- ICAR- Research Complex for Eastern Region, Farming System Research Centre for Hill and Plateau Region, Ranchi, 834010, Jharkhand, India
| | - Nandkishore Thombare
- ICAR- Indian Institute of Natural Resin and Gums, Ranchi, 834010, Jharkhand, India
| | - Arun Kumar Singh
- ICAR- Research Complex for Eastern Region, Farming System Research Centre for Hill and Plateau Region, Ranchi, 834010, Jharkhand, India
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11
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He M, Hua Z, Chen H, Liu Y, Li Y, Zhang Z. Effects of simulated acid rain on rhizosphere microorganisms of invasive Alternanthera philoxeroides and native Alternanthera sessilis. Front Microbiol 2022; 13:993147. [PMID: 36160265 PMCID: PMC9500542 DOI: 10.3389/fmicb.2022.993147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 08/15/2022] [Indexed: 11/23/2022] Open
Abstract
Acid rain not only has serious harm to the environment, but also has the same threat to plants, but the invasive plant Alternanthera philoxeroides still grows well compared to the native plant Alternanthera sessilis under acid rain stress. However, the underlying mechanism of resistance to the acid rain environment in invasive Alternanthera philoxeroides remains unclear. In the current study, we comparatively analyzed the plant physiological characteristics, soil physicochemical properties, and rhizosphere microbial communities of invasive A. philoxeroides and native A. sessilis under different pH condition. The simulated acid rain had a significant inhibitory effect on the morphological and physiological traits of A. philoxeroides and A. sessilis and reduced the soil nutrient content. However, A. philoxeroides was more tolerant of acid rain. Compared with CK, simulated acid rain treatment at pH 2.5 significantly increased the Chao1, ACE, and Shannon indexes of A. philoxeroides microorganisms. Under simulated acid rain treatment at pH 2.5, the fungal flora Chao1, ACE and Shannon index were significantly higher than those of CK by 14.5%, 12.4%, and 30.4%, respectively. The dominant bacterial phyla of soil bacteria were Proteobacteria, Actinobacteria, Bacteroidota, Actinobacteria, Firmicutes, Myxococcota, Chloroflexi, Patescibacteria, Gemmatimonadota, Verrucomicrobiota, and Armatimonadota. The dominant fungi were Ascomycota, Basidiomycota, Rozellomycota, and Olpidiomycota. The bacterial and fungal diversity and structure of A. philoxeroides and A. sessilis showed the greatest difference between the pH 2.5 treatment and CK. Redundancy analysis showed that electrical conductivity (EC) and total phosphorus (TP) were the main factors changing the bacterial communities, and available phosphorus (AP), organic matter (OM), EC, and pH were the main factors changing the fungal communities. This study contributes to the microbial community structure of the invasive plant A. philoxeroides and provides a theoretical basis for studying the invasion mechanism of invasive plants under acid rain.
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Affiliation(s)
- Mengying He
- College of Resources and Environment, Anhui Agricultural University, Hefei, Anhui, China
| | - Zexun Hua
- College of Resources and Environment, Anhui Agricultural University, Hefei, Anhui, China
| | - Hanying Chen
- College of Resources and Environment, Anhui Agricultural University, Hefei, Anhui, China
| | - Yao Liu
- College of Resources and Environment, Anhui Agricultural University, Hefei, Anhui, China
| | - Yue Li
- College of Resources and Environment, Anhui Agricultural University, Hefei, Anhui, China
| | - Zhen Zhang
- College of Resources and Environment, Anhui Agricultural University, Hefei, Anhui, China
- Institute of Botany, Chinese Academy of Sciences, Beijing, China
- *Correspondence: Zhen Zhang,
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12
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Wang M, Xu S, Wang S, Chen C, Wang Y, Liu L. Responses of soil enzyme activities and bacterial community structure to different hydrological regimes during peatland restoration in the Changbai Mountain, northeast China. Front Microbiol 2022; 13:1005657. [PMID: 36118204 PMCID: PMC9478802 DOI: 10.3389/fmicb.2022.1005657] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 08/15/2022] [Indexed: 11/23/2022] Open
Abstract
Appropriate hydrological management is critical for peatland restoration. An important prerequisite for peatland restoration is a recovery of soil biological processes. However, little is known about the effects of different hydrological management practices on soil biological processes during peatland restoration. In this study, the variations in soil properties, enzyme activities, and bacterial communities across different peatlands, namely natural peatland (NP), peatland restored under high water level (HR), peatland restored under alternating high-low water level (HLR), peatland restored under low water level (LR), and degraded peatland (DP), in the Changbai Mountains were investigated. Results showed that soil organic carbon, soil water content, and total nitrogen in NP were significantly higher than those in restored and degraded peatlands, and these soil properties in restored peatlands increased with the water level. The activities of soil hydrolases including β-1, 4-glucosidase, β-1, 4-n-acetylglucosidase, and acid phosphatase in NP were higher than in restored and degraded peatlands, while the activity of polyphenol oxidase in NP was the lowest. In restored peatlands, all measured enzyme activities decreased with the decline in water level. Both bacterial diversity and richness in NP were the lowest, while the highest diversity and richness were observed in HR. Redundancy analysis indicated that soil organic carbon, water level, soil water content, total nitrogen, and pH were the most important factors that affected the soil enzyme activities and bacterial community. Our findings give insight into the effects of different hydrological regimes on soil biological processes during peatland restoration. Maintaining a high water level early in the restoration process is more beneficial to restoring the ecological functions of peatlands than other hydrological regimes.
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Affiliation(s)
- Ming Wang
- Key Laboratory of Geographical Processes and Ecological Security in Changbai Mountains, Ministry of Education, School of Geographical Sciences, Northeast Normal University, Changchun, China
| | - Shangqi Xu
- School of Ecology and Environment, Anhui Normal University, Wuhu, China
| | - Shengzhong Wang
- Key Laboratory of Geographical Processes and Ecological Security in Changbai Mountains, Ministry of Education, School of Geographical Sciences, Northeast Normal University, Changchun, China
- State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, Institute for Peat and Mire Research, Northeast Normal University, Changchun, China
| | - Cong Chen
- Key Laboratory of Geographical Processes and Ecological Security in Changbai Mountains, Ministry of Education, School of Geographical Sciences, Northeast Normal University, Changchun, China
| | - Yuting Wang
- Key Laboratory of Geographical Processes and Ecological Security in Changbai Mountains, Ministry of Education, School of Geographical Sciences, Northeast Normal University, Changchun, China
| | - Lei Liu
- Institute of Scientific and Technical Information of Jilin, Changchun, China
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13
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Yang T, Tang G, Li L, Ma L, Zhao Y, Guo Z. Interactions between bacteria and eukaryotic microorganisms and their response to soil properties and heavy metal exchangeability nearby a coal-fired power plant. CHEMOSPHERE 2022; 302:134829. [PMID: 35523290 DOI: 10.1016/j.chemosphere.2022.134829] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/27/2022] [Accepted: 04/29/2022] [Indexed: 06/14/2023]
Abstract
Persistent heavy metal (HM) contaminated soil provides special habitat for microorganisms, HM stress and complex abiotic factors bring great uncertainty for the development of bacteria and eukaryotic microbes. Despite numerous studies about HMs' effect on soil microorganisms, the key factors affecting microbial communities in severe HM contaminated soil and their interactions are still not definite. In this study, the effect of HM fractions and soil properties on the interaction between bacterial communities and eukaryotic microorganisms was studied by high-throughput Illumina sequencing and simplified continuous extraction of HM in severe HM contaminated soil. Based on amplification and sequencing of the 18S rRNA gene, this study revealed that protists and algae were the most predominant eukaryotic microorganisms, and the dominant phyla were SAR, Opisthokonta and Archaeplastida in HM seriously polluted soil. These results also showed that exchangeable As was negatively correlated with bacterial Shannon and Simpson indexes, while exchangeable Zn was positively correlated with Shannon and Simpson indexes of eukaryotic microbes. Moreover, the structural equation model illustrated that pH, moisture content, available potassium and phosphorus, and exchangeable Cd, As and Zn were the dominant factors shaping bacterial communities, while total organic carbon and exchangeable Zn made the predominant contributions to variations in eukaryotic microbes. In addition, eukaryotic microbes were intensely affected by the bacterial communities, with a standardized regression weight of 0.53, which exceeded the influence of other abiotic factors. It was suggested that community-level adaptions through cooperative interactions under serious HM stress in soil.
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Affiliation(s)
- Tongyi Yang
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212003, PR China.
| | - Guoteng Tang
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212003, PR China
| | - Ling Li
- Zhenjiang Customs District, Integrated Technology Center, Zhenjiang 212000, PR China
| | - Liuchang Ma
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212003, PR China
| | - Yuyuan Zhao
- Zhenjiang Key Laboratory of Functional Chemistry, Institute of Medicine & Chemical Engineering, Zhenjiang College, Zhenjiang 212000, China
| | - Zechong Guo
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212003, PR China
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14
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Changes in Soil Organic Carbon Fractions and Fungal Communities, Subsequent to Different Management Practices in Moso Bamboo Plantations. J Fungi (Basel) 2022; 8:jof8060640. [PMID: 35736123 PMCID: PMC9225535 DOI: 10.3390/jof8060640] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 06/11/2022] [Accepted: 06/15/2022] [Indexed: 12/03/2022] Open
Abstract
Moso bamboo (Phyllostachys pubescens) has an extremely fast growth rate and major carbon sequestration potential. However, little information is available on the dynamics of soil C accumulation and fungi communities related to different management practices. Here, we investigated changes in the soil organic carbon (SOC) fractions and fungal communities of a Moso bamboo plantation under three different management practices (M0: undisturbed; M1: extensively managed; and M2: intensively managed). Compared with M0, SOC levels were reduced by 41.2% and 71.5% in M1 and M2, respectively; furthermore, four SOC fractions (C1: very labile; C2: labile; C3: less labile; and C4: nonlabile) and the carbon management index (CMI) were also significantly reduced by plantation management. These practices further altered fungal communities, for example, by increasing Basidiomycota and Mortierellomycota, and by decreasing Ascomycota and Rozellomycota. Pyrenochaeta, Mortierella, Saitozyma, and Cladophialophora were identified as keystone taxa. Soil fungal communities were significantly related to the pH, NH4-N, AP, C3, and the C4 fractions of SOC. Random forest modeling identified soil C3 and Mortierella as the most important predictors of the CMI. Our results suggest that reducing human interference would be beneficial for fungal community improvement and C sequestration in Moso bamboo plantations.
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15
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Perron T, Kouakou A, Simon C, Mareschal L, Frédéric G, Soumahoro M, Kouassi D, Rakotondrazafy N, Rapidel B, Laclau JP, Brauman A. Logging residues promote rapid restoration of soil health after clear-cutting of rubber plantations at two sites with contrasting soils in Africa. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 816:151526. [PMID: 34752871 DOI: 10.1016/j.scitotenv.2021.151526] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 11/04/2021] [Accepted: 11/04/2021] [Indexed: 06/13/2023]
Abstract
Soil health is defined as the soil's capacity to deliver ecosystem functions within environmental constraints. On tree plantations, clear-cutting and land preparation between two crop cycles cause severe physical disturbances to the soil and seriously deplete soil organic carbon and biodiversity. Rubber, one of the main tropical perennial crops worldwide, has a plantation life cycle of 25 to 40 years, with successive replanting cycles on the same plot. The aim of this study was to assess the effects of clear-cutting disturbance on three soil functions (carbon transformation, nutrient cycling and structure maintenance) and their restoration after the planting of the new rubber crop, in two contrasting soil situations (Arenosol and Ferralsol) in Côte d'Ivoire. In this 18-month diachronic study, we intensively measured soil functions under different scenarios as regards the management of logging residues and the use or not of a legume cover crop. We investigated the relationship between soil macrofauna diversity and soil heath. At both sites, clear-cutting and land preparation disturbed carbon transformation and nutrient cycling significantly and, to a lesser extent, structure maintenance function. When logging residues were applied, carbon transformation and structure maintenance functions were fully restored within 12 to 18 months after disturbance. By contrast, no restoration of nutrient cycling was observed over the study period. A legume cover crop mainly improved the restoration of carbon transformation. We found a strong relationship (P ≤ 0.001; R2 = 0.62-0.66) between soil macrofauna diversity and soil health. Our overall results were very similar at the two sites, despite their contrasting soil conditions. Keeping logging residues in the plots and sowing a legume in the inter-row at replanting accelerated the restoration of soil functions after major disturbance caused by clear-cutting and land preparation. Our results confirm the necessity of taking soil macrofauna diversity into account in the management of tropical perennial crops.
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Affiliation(s)
- Thibaut Perron
- CIRAD, UMR ABSys, F-34398 Montpellier, France; ABSys, Univ Montpellier, CIHEAM-IAMM, CIRAD, INRAE, Institut Agro, Montpellier, France; CIRAD, UMR Eco&Sols, F-34398 Montpellier, France; SAPH, Direction of Industrial Plantations (DPI), Côte d'Ivoire.
| | - Aymard Kouakou
- Eco&Sols, Univ. Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France; Nangui Abrogoua University, Ecology and Sustainable Development Laboratory, Abidjan, Côte d'Ivoire
| | - Charlotte Simon
- Eco&Sols, Univ. Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Louis Mareschal
- CIRAD, UMR Eco&Sols, F-34398 Montpellier, France; Eco&Sols, Univ. Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Gay Frédéric
- CIRAD, UMR ABSys, F-34398 Montpellier, France; ABSys, Univ Montpellier, CIHEAM-IAMM, CIRAD, INRAE, Institut Agro, Montpellier, France
| | | | - Daouda Kouassi
- SOGB, Agricultural Technique, Auditing and Organisation Department (DTAO), SOCFIN, Côte d'Ivoire
| | - Nancy Rakotondrazafy
- Eco&Sols, Univ. Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Bruno Rapidel
- CIRAD, UMR ABSys, F-34398 Montpellier, France; ABSys, Univ Montpellier, CIHEAM-IAMM, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Jean-Paul Laclau
- CIRAD, UMR Eco&Sols, F-34398 Montpellier, France; Eco&Sols, Univ. Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Alain Brauman
- Eco&Sols, Univ. Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
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16
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Wolińska A, Podlewski J, Słomczewski A, Grządziel J, Gałązka A, Kuźniar A. Fungal Indicators of Sensitivity and Resistance to Long-Term Maize Monoculture: A Culture-Independent Approach. Front Microbiol 2022; 12:799378. [PMID: 35046921 PMCID: PMC8761758 DOI: 10.3389/fmicb.2021.799378] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 12/07/2021] [Indexed: 01/04/2023] Open
Abstract
Although fungi are regarded as very important components of soils, the knowledge of their community in agricultural (monocultural) soils is still limited. This indicates that soil fungal communities are investigated less intensively than bacteria. Therefore, the main goal of this paper was to evaluate the fungal mycobiome structure in monoculture soils in a culture-independent approach. Firstly, the study was conducted to identify the core mycobiome composition and its variability at different stages of the maize growing season (spring, summer, and autumn). Secondly, we identified and recommended fungal indicators of both sensitivity and resistance to long-term maize monoculture. Two neighboring fields from the Potulicka Foundation area were selected for the study: K20 sown with a Gorzow mixture (intercropping mixture) to improve soil quality after a maize monoculture in 2020 and K21, where long-term (over 30 years) monoculture cultivation was continued. The basic chemical features [acidity, redox potential, total organic carbon (TOC), and moisture] of soils were determined, fungal genetic diversity was assessed by ITS next generation sequencing (NGS) analyses, and biodiversity indices were calculated. The results of the NGS technique facilitated recognition and classification of the fungal mycobiome to the taxonomic genus level and changes in the fungal structure in the three periods (spring, summer, and autumn) were assessed. It was evidenced that the mycobiome composition was dependent on both the seasons and the agricultural practices. It was also found that even a 1-year break in the monoculture in favor of an intercropping mixture improved soil properties thus contributing to higher biodiversity. Mortierella was recommended as a potential indicator of sensitivity to long-term maize cultivation, whereas Solicoccozyma and Exophiala were proposed as indicators of resistance to long-term maize cultivation. We proved that the precision farming principles applied on the Potulicka Foundation farm had a very positive effect on fungal biodiversity, which was high even in the long-term maize monoculture field. Therefore, the monoculture cultivation carried out in this way does not induce biological degradation of monoculture soils but preserves their good biological quality.
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Affiliation(s)
- Agnieszka Wolińska
- Department of Biology and Biotechnology of Microorganisms, Institute of Biological Sciences, The John Paul II Catholic University of Lublin, Lublin, Poland
| | | | | | - Jarosław Grządziel
- Department of Agriculture Microbiology, Institute of Soil Science and Plant Cultivation in Pulawy, Puławy, Poland
| | - Anna Gałązka
- Department of Agriculture Microbiology, Institute of Soil Science and Plant Cultivation in Pulawy, Puławy, Poland
| | - Agnieszka Kuźniar
- Department of Biology and Biotechnology of Microorganisms, Institute of Biological Sciences, The John Paul II Catholic University of Lublin, Lublin, Poland
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Yang S, Xiao J, Liang T, He W, Tan H. Response of soil biological properties and bacterial diversity to different levels of nitrogen application in sugarcane fields. AMB Express 2021; 11:172. [PMID: 34919198 PMCID: PMC8683519 DOI: 10.1186/s13568-021-01331-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 12/10/2021] [Indexed: 11/22/2022] Open
Abstract
To select an eco-friendly nitrogen (N) application level for sugarcane production, soil fertility and soil bacterial diversity under different nitrogen application levels were analyzed. Four levels of urea applications were high Nitrogen (H, 964 kg ha−1), medium Nitrogen (M, 482 kg ha−1), low Nitrogen (L, 96 kg ha−1) and no Nitrogen (CK, 0 kg ha−1) treatments, respectively. The results showed that the soil microbial biomass carbon and phosphorus were altered significantly by CK and L treatments. Moreover, the indexes of soil bacterial richness and diversity in the sugarcane field could be significantly improved by L. At the genus level, SC-I-84, Mycobacterium, Micropepsaceae, Saccharimonadales, Subgroup_2 and Acetobacteraceae were the unique dominant bacteria in the soil with the H treatment. JG30-KF-CM45 and Jatrophihabitans were the unique dominant genera in the M treatment. Subgroup_6, HSB_OF53-F07, Streptomyces, 67–14, SBR1031 and KD4-96 were the unique dominant genera in the L treatment. In contrast, FCPS473, Actinospica, 1921–2, Sinomonas, and Ktedonobacteraceae were the unique dominant genera in the CK treatment. The findings suggest that soil fertility all could be changed by different N application levels, but the most increasing integral effect only could be found in L. Moreover, even though soil bacterial richness could be significantly promoted by the M and H treatments, but soil bacterial diversity could not be significantly improved. On the contrary, soil bacterial diversity and richness all could be improved by L treatment. In addition, higher abundance of unique soil dominant bacteria could be only found in L treatment which compared to the CK, M and H treatments. These findings suggest that the rate of 96 kg ha−1 N application is ecofriendly for sugarcane production in Guangxi.
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Tan H, Liu T, Yu Y, Tang J, Jiang L, Martin FM, Peng W. Morel Production Related to Soil Microbial Diversity and Evenness. Microbiol Spectr 2021; 9:e0022921. [PMID: 34643439 PMCID: PMC8515941 DOI: 10.1128/spectrum.00229-21] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 09/10/2021] [Indexed: 01/23/2023] Open
Abstract
Black morel is a widely prized ascomycetous mushroom with culinary value. It was once uncultivable but can now be cultivated routinely in ordinary farmland soils. Large-scale morel farming sometimes encounters nonfructification for unknown reasons. In spring 2020, many morel farms in the area of Chengdu-Plain, China, exhibited no fructification at all, causing disastrous economic loss to the farmers. To determine potential ecological factors associated with the different performance of morel production in these farms, 21 affected sites versus 11 sites with normal fructification performance were analyzed to compare soil microbiota and physiochemical characteristics during fructification. The results indicated that soil physiochemical characteristics were unlikely to be a major reason for the difference between successful fructification and nonfructification. The soils with successful fructification had significantly higher diversity in both the fungal and bacterial communities than those with nonfructification. Morel yield was positively correlated with the α-diversity of fungal communities. The higher diversity of the successfully fructified soils was contributed by community evenness rather than taxonomic richness. In contrast, most nonfructification soils were dominated by a high proportion of a certain fungal genus, typically Acremonium or Mortierella, in the fungal communities. Our findings demonstrate the importance of microbial ecology to the large-scale agroindustry of soil-cultivated mushrooms. IMPORTANCE Saprotrophic mushrooms cultivated in soils are subject to complex influences from soil microbial communities. Research on growing edible mushrooms has revealed connections between fungi and a few species of growth-promoting bacteria colonizing the mycosphere. The composition and diversity of the whole microbial community may also have an influence on the growth and production of soil-saprotrophic mushrooms. Morel mushrooms (Morchella spp.) are economically and culturally important and are widely prized throughout the world. This study used the large-scale farming of morels as an example of an agroecosystem for soil-saprotrophic mushroom cultivation. It demonstrated a typical pattern of how the microbial ecology in soil agroecosystems, especially the α-diversity level and community evenness among soil fungal taxa, could affect the production of high-value cash crops and the income of farmers.
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Affiliation(s)
- Hao Tan
- Institute of Agricultural Resources and Environments, Sichuan Academy of Agricultural Sciences, Chengdu, China
- School of Bioengineering, Jiangnan University, Wuxi, China
- Scientific Observation and Experimental Station of Agro-microbial Resource and Utilization in Southwest China, Ministry of Agriculture and Rural Affairs, Chengdu, China
| | - Tianhai Liu
- Institute of Agricultural Resources and Environments, Sichuan Academy of Agricultural Sciences, Chengdu, China
- Scientific Observation and Experimental Station of Agro-microbial Resource and Utilization in Southwest China, Ministry of Agriculture and Rural Affairs, Chengdu, China
| | - Yang Yu
- Institute of Agricultural Resources and Environments, Sichuan Academy of Agricultural Sciences, Chengdu, China
- Scientific Observation and Experimental Station of Agro-microbial Resource and Utilization in Southwest China, Ministry of Agriculture and Rural Affairs, Chengdu, China
| | - Jie Tang
- Institute of Agricultural Resources and Environments, Sichuan Academy of Agricultural Sciences, Chengdu, China
- Scientific Observation and Experimental Station of Agro-microbial Resource and Utilization in Southwest China, Ministry of Agriculture and Rural Affairs, Chengdu, China
| | - Lin Jiang
- Institute of Agricultural Resources and Environments, Sichuan Academy of Agricultural Sciences, Chengdu, China
- Scientific Observation and Experimental Station of Agro-microbial Resource and Utilization in Southwest China, Ministry of Agriculture and Rural Affairs, Chengdu, China
| | - Francis M. Martin
- Université de Lorraine, Institut National de la Recherche Agronomique, UMR Interactions Arbres/Microorganismes, Centre INRA-GrandEst-Lorraine, Champenoux, France
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
| | - Weihong Peng
- Institute of Agricultural Resources and Environments, Sichuan Academy of Agricultural Sciences, Chengdu, China
- Scientific Observation and Experimental Station of Agro-microbial Resource and Utilization in Southwest China, Ministry of Agriculture and Rural Affairs, Chengdu, China
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19
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Gu Y, Wang J, Cai W, Li G, Mei Y, Yang S. Different Amounts of Nitrogen Fertilizer Applications Alter the Bacterial Diversity and Community Structure in the Rhizosphere Soil of Sugarcane. Front Microbiol 2021; 12:721441. [PMID: 34616383 PMCID: PMC8489880 DOI: 10.3389/fmicb.2021.721441] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 08/06/2021] [Indexed: 11/25/2022] Open
Abstract
Sugarcane cropping systems receive elevated application of nitrogen (N) fertilizer for higher production, which may affect production costs and cause environmental pollution. Therefore, it is critical to elucidate the response of soil microbial to N fertilizer inputs in sugarcane soil. A field experiment was carried out to investigate the effects of optimum (N375, 375 kg N/ha) and excessive (N563, 563 kg N/ha) amounts of N fertilizer on soil bacterial diversity and community structure in a sugarcane cropping system by MiSeq high-throughput sequencing; 50,007 operational taxonomic units (OTUs) were obtained by sequencing the 16S rRNA gene amplicons. Results showed that the most abundant phyla in the sugarcane rhizosphere soil were Proteobacteria, Actinobacteria, Acidobacteria, and Planctomycetes, whose ensemble mean accounted for 74.29%. Different amounts of N application indeed change the bacterial diversity and community structures. Excessive application of N fertilizers significantly decreased the pH and increased the available N in soils and unexpectedly obtained a lower yield. Excessive N resulted in a relatively lower bacterial species richness and significantly increased the relative abundance of phyla Proteobacteria, Acidobacteria, and Bacteroidetes and the genera Sphingomonas and Gemmatimonas, while optimum N treatment significantly increased the phylum Actinobacteria and the genera Bacillus and Nitrospira (P < 0.05). N application shifted the N cycle in nitrification, mainly on the Nitrospira, but showed no significant effect on the genera related to nitrogen fixation, methane oxidation, sulfate reduction, and sulfur oxidation (P > 0.05). Overall, the optimum amount of N application might be conducive to beneficial microorganisms, such as Actinobacteria, Nitrospira, and Bacillus and, thus, result in a healthier ecosystem and higher sustainable crop production.
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Affiliation(s)
- Yan Gu
- Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Crop Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Jihua Wang
- Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Crop Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Weijun Cai
- Zhanjiang Academy of Agricultural Sciences, Zhanjiang, China
| | - Guoliang Li
- Institute of Agricultural Resources and Environment, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Yu Mei
- Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Crop Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Shaohai Yang
- Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Crop Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
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Tandon K, Wan MT, Yang CC, Yang SH, Baatar B, Chiu CY, Tsai JW, Liu WC, Ng CS, Tang SL. Aquatic microbial community is partially functionally redundant: Insights from an in situ reciprocal transplant experiment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 786:147433. [PMID: 33971597 DOI: 10.1016/j.scitotenv.2021.147433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/06/2021] [Accepted: 04/25/2021] [Indexed: 06/12/2023]
Abstract
Microbial communities are considered to be functionally redundant, but few studies have tested this hypothesis empirically. In this study, we performed an in situ reciprocal transplant experiment on the surface and bottom waters of two lakes (Tsuei-Feng (T) and Yuan-Yang (Y)) with disparate trophic states and tracked changes in their microbial community composition and functions for 6 weeks using high-throughput sequencing and functional approaches. T lake's surface (Ts) and bottom (Tb) water active bacterial community (16S rRNA gene-transcript) was dominated by Actinobacteria, Bacteroidia, and Cyanobacteria, whereas Y lake's surface (Ys) and bottom (Yb) water had Gammaproteobacteria, Alphaproteobacteria, and Bacteroidia as the dominant classes. The community composition was resistant to changes in environmental conditions following the reciprocal transplant, but their functions tended to become similar to the incubating lakes' functional profiles. A significant linear positive relationship was observed between the microbial community and functional attributes (surface: R2 = 0.5065, p < 0.0001; bottom: R2 = 0.4592, p < 0.0001), though with varying scales of similarity (1-Bray Curtis distance), suggesting partial functional redundancy. Also, the entropy-based L-divergence measure identified high divergence in community composition (surface: 1.21 ± 0.54; bottom: 1.17 ± 0.51), and relatively low divergence in functional attributes (surface: 0.04 ± 0.01; bottom: 0.04 ± 0.01) in the two lakes' surface and bottom waters, providing further support for the presence of partial functional redundancy. This study enriches our understanding of community functional relationships and establishes the presence of partial functional redundancy in freshwater ecosystems.
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Affiliation(s)
- Kshitij Tandon
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan; Bioinformatics Program, Institute of Information Science, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan; Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Min-Tao Wan
- EcoHealth Microbiology Laboratory, WanYu Co., Ltd., Chiayi 600, Taiwan
| | - Chia-Chin Yang
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Shan-Hua Yang
- Institute of Fisheries Science, National Taiwan University, Taipei 10617, Taiwan
| | | | - Chih-Yu Chiu
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Jeng-Wei Tsai
- China Medical University, Department of Biological Science and Technology, Taichung 404, Taiwan
| | - Wen-Cheng Liu
- Department of Civil and Disaster Prevention Engineering, National United University, Miao-Li, Taiwan
| | - Chen Siang Ng
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Sen-Lin Tang
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan; Bioinformatics Program, Institute of Information Science, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan.
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21
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Silva-Olaya AM, Mora-Motta DA, Cherubin MR, Grados D, Somenahally A, Ortiz-Morea FA. Soil enzyme responses to land use change in the tropical rainforest of the Colombian Amazon region. PLoS One 2021; 16:e0255669. [PMID: 34407107 PMCID: PMC8372923 DOI: 10.1371/journal.pone.0255669] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 07/21/2021] [Indexed: 11/18/2022] Open
Abstract
Soil enzymes mediate key processes and functions of the soils, such as organic matter decomposition and nutrient cycling in both natural and agricultural ecosystems. Here, we studied the activity of five extracellular soil enzymes involved in the C, N, and P-mineralizing process in both litter and surface soil layer of rainforest in the northwest region of the Colombian Amazon and the response of those soil enzymes to land use change. The experimental study design included six study sites for comparing long-term pasture systems to native forest and regeneration practices after pasture, within the main landscapes of the region, mountain and hill landscapes separately. Results showed considerable enzymatic activity in the litter layer of the forest, highlighting the vital role of this compartment in the nutrient cycling of low fertility soils from tropical regions. With the land use transition to pastures, changes in soil enzymatic activities were driven by the management of pastures, with SOC and N losses and reduced absolute activity of soil enzymes in long-term pastures under continuous grazing (25 years). However, the enzyme activities expressed per unit of SOC did not show changes in C and N-acquiring enzymes, suggesting a higher mineralization potential in pastures. Enzymatic stoichiometry analysis indicated a microbial P limitation that could lead to a high catabolic activity with a potential increase in the use of SOC by microbial communities in the search for P, thus affecting soil C sequestration, soil quality and the provision of soil-related ecosystem services.
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Affiliation(s)
| | - Dúber A. Mora-Motta
- Amazonian Research Center CIMAZ-MACAGUAL, University of the Amazon, Florencia, Colombia
| | - Maurício R. Cherubin
- Department of Soil Science, ‘‘Luiz de Queiroz” College of Agriculture, University of Sao Paulo, Sao Paulo, Brazil
| | - Daniel Grados
- Instituto del Mar del Perú, Esquina Gamarra y General Valle s/n Chucuito, Callao, Perú
| | - Anil Somenahally
- Department of Soil and Crop Sciences, Texas A&M University, Overton, Texas, United States of America
| | - Fausto A. Ortiz-Morea
- Amazonian Research Center CIMAZ-MACAGUAL, University of the Amazon, Florencia, Colombia
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Saadouli I, Mosbah A, Ferjani R, Stathopoulou P, Galiatsatos I, Asimakis E, Marasco R, Daffonchio D, Tsiamis G, Ouzari HI. The Impact of the Inoculation of Phosphate-Solubilizing Bacteria Pantoea agglomerans on Phosphorus Availability and Bacterial Community Dynamics of a Semi-Arid Soil. Microorganisms 2021; 9:1661. [PMID: 34442740 PMCID: PMC8400695 DOI: 10.3390/microorganisms9081661] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 07/02/2021] [Accepted: 07/04/2021] [Indexed: 11/29/2022] Open
Abstract
The bacterial genus Pantoea has been widely evaluated as promising bacteria to increase phosphorus (P) availability in soil. The aim of this study was to characterize the phosphate solubilizing (PS) activity of a Pantoea agglomerans strain and to evaluate the impact of its application in a semi-arid soil on phosphate availability and structure of the bacterial communities as a whole. An incubation experiment under close-to-natural soil environmental conditions was conducted for 15 days at 30 °C. High-throughput sequencing of the bacterial 16S rRNA gene was used to characterize and to compare the bacterial community structure of P. agglomerans-inoculated soil with non-inoculated control. Furthermore, a qPCR-based method was developed for detection and quantification of the functional genes related to the expression of mineral phosphate solubilization (MPS) phenotype in P. agglomerans. The results showed that in vitro solubilization of Ca3(PO4)2 by P. agglomerans strain was very efficient (980 mg/L), and it was associated with a drop in pH due to the secretion of gluconic acid; these changes were concomitant with the detection of gdh and pqqC genes. Moreover, P. agglomerans inoculum application significantly increased the content of available P in semi-arid soil by 69%. Metagenomic analyses showed that P. agglomerans treatment modified the overall edaphic bacterial community, significantly impacting its structure and composition. In particular, during P. agglomerans inoculation the relative abundance of bacteria belonging to Firmicutes (mainly Bacilli class) significantly increased, whereas the abundance of Actinobacteria together with Acidobacteria and Chloroflexi phyla decreased. Furthermore, genera known for their phosphate solubilizing activity, such as Aneurinibacillus, Lysinibacillus, Enterococcus, and Pontibacter, were exclusively detected in P. agglomerans-treated soil. Pearson's correlation analysis revealed that changes in soil bacterial community composition were closely affected by soil characteristics, such as pH and available P. This study explores the effect of the inoculation of P. agglomerans on the bacterial community structure of a semi-arid soil. The effectiveness in improving the phosphate availability and modification in soil bacterial community suggested that P. agglomerans represent a promising environmental-friendly biofertilizer in arid and semi-arid ecosystems.
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Affiliation(s)
- Ilhem Saadouli
- Laboratoire de Microorganismes et Biomolécules Actives (LR03ES03), Facultédes Sciences de Tunis, Université Tunis El Manar, 2092 Tunis, Tunisia; (I.S.); (R.F.)
| | - Amor Mosbah
- Higher Institute for Biotechnology (ISBST), LR Biotechnology and Bio-Geo Resources Valorization, University of Manouba, BVBGR-LR11ES31, Biotechpole Sidi Thabet, 2020 Ariana, Tunisia;
| | - Raoudha Ferjani
- Laboratoire de Microorganismes et Biomolécules Actives (LR03ES03), Facultédes Sciences de Tunis, Université Tunis El Manar, 2092 Tunis, Tunisia; (I.S.); (R.F.)
| | - Panagiota Stathopoulou
- Laboratory of Systems Microbiology and Applied Genomics, Department of Environmental Engineering, University of Patras, 2 Seferi St., 30100 Agrinio, Greece; (P.S.); (I.G.); (E.A.)
| | - Ioannis Galiatsatos
- Laboratory of Systems Microbiology and Applied Genomics, Department of Environmental Engineering, University of Patras, 2 Seferi St., 30100 Agrinio, Greece; (P.S.); (I.G.); (E.A.)
| | - Elias Asimakis
- Laboratory of Systems Microbiology and Applied Genomics, Department of Environmental Engineering, University of Patras, 2 Seferi St., 30100 Agrinio, Greece; (P.S.); (I.G.); (E.A.)
| | - Ramona Marasco
- Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (R.M.); (D.D.)
| | - Daniele Daffonchio
- Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (R.M.); (D.D.)
| | - George Tsiamis
- Laboratory of Systems Microbiology and Applied Genomics, Department of Environmental Engineering, University of Patras, 2 Seferi St., 30100 Agrinio, Greece; (P.S.); (I.G.); (E.A.)
| | - Hadda-Imene Ouzari
- Laboratoire de Microorganismes et Biomolécules Actives (LR03ES03), Facultédes Sciences de Tunis, Université Tunis El Manar, 2092 Tunis, Tunisia; (I.S.); (R.F.)
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23
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Alt LM, Iverson AN, Soupir ML, Moorman TB, Howe A. Antibiotic resistance gene dissipation in soil microcosms amended with antibiotics and swine manure. JOURNAL OF ENVIRONMENTAL QUALITY 2021; 50:911-922. [PMID: 33982299 DOI: 10.1002/jeq2.20240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 05/10/2021] [Indexed: 06/12/2023]
Abstract
The use of antibiotics in animal agriculture has exacerbated the presence of both antibiotic resistance genes (ARGs) and residual antibiotics excreted in animal manure. Field application of this manure is a common practice because its nutrient rich material can benefit crop growth. However, this practice can also introduce antibiotics and ARGs into nonagricultural settings. The integration of prairie buffer strips within and at the edge of crop fields is a potential management solution to reduce concentrations of ARGs commonly transported via water runoff and infiltration. An incubation experiment was conducted to investigate the fate of ARGs in directly manured crop field soils and the surrounding affected prairie strip soils. Row crop and prairie strip soils sampled from three sites received either an antibiotic spike and swine manure addition or a control water addition. The concentrations of select ARGs were then monitored over a 72-d period. Although soil vegetation and site location were not observed to influence ARG dissipation, the select genes did display different half-lives from one another. For example, tetM demonstrated the fastest dissipation of the genes quantified (average half-life, 5.18 d). Conversely, sul1 did not conform to the first-order linear regression kinetics used to describe the other investigated genes and was highly abundant in control prairie strip soils. The quantified half-lives of these select ARGs are comparable to previous studies and can inform monitoring and mitigative efforts aimed at reducing the spread of ARGs in the environment.
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Affiliation(s)
- Laura M Alt
- Dep. of Agricultural and Biosystems Engineering, IA State Univ., Elings Hall, 605 Bissell Rd., Ames, IA, 50011, USA
| | - Alyssa N Iverson
- Dep. of Agricultural and Biosystems Engineering, IA State Univ., Elings Hall, 605 Bissell Rd., Ames, IA, 50011, USA
| | - Michelle L Soupir
- Dep. of Agricultural and Biosystems Engineering, IA State Univ., Elings Hall, 605 Bissell Rd., Ames, IA, 50011, USA
| | - Thomas B Moorman
- National Lab. for Agriculture and the Environment, USDA-ARS, 1015 N University Blvd., Ames, IA, 50011, USA
| | - Adina Howe
- Dep. of Agricultural and Biosystems Engineering, IA State Univ., Elings Hall, 605 Bissell Rd., Ames, IA, 50011, USA
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Díaz‐Vallejo EJ, Seeley M, Smith AP, Marín‐Spiotta E. A meta‐analysis of tropical land‐use change effects on the soil microbiome: Emerging patterns and knowledge gaps. Biotropica 2021. [DOI: 10.1111/btp.12931] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Megan Seeley
- School of Geographical Studies and Urban Planning Arizona State University Tempe AZ USA
| | - A. Peyton Smith
- Department of Crops and Soil Science Texas A&M University Agriculture and Life Sciences College Station TX USA
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25
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Zhang C, Lin Z, Que Y, Fallah N, Tayyab M, Li S, Luo J, Zhang Z, Abubakar AY, Zhang H. Straw retention efficiently improves fungal communities and functions in the fallow ecosystem. BMC Microbiol 2021; 21:52. [PMID: 33596827 PMCID: PMC7890633 DOI: 10.1186/s12866-021-02115-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 02/04/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Straw retention is a substitute for chemical fertilizers, which effectively maintain organic matter and improve microbial communities on agricultural land. The purpose of this study was to provide sufficient information on soil fungal community networks and their functions in response to straw retention. Hence, we used quantitative real-time PCR (qRT-PCR), Illumina MiSeq (ITS rRNA) and FUNGuild to examine ITS rRNA gene populations, soil fungal succession and their functions under control (CK) and sugarcane straw retention (SR) treatments at different soil layers (0-10, 10-20, 20-30, and 30-40 cm) in fallow fields. RESULT The result showed that SR significantly enhanced ITS rRNA gene copy number and Shannon index at 0-10 cm soil depth. Fungi abundance, OTUs number and ACE index decreased with the increasing soil depth. The ANOSIM analysis revealed that the fungal community of SR significantly differed from that of CK. Similarly, significant difference was also observed between topsoil (0-20 cm) and subsoil (20-40 cm). Compared with CK, SR decreased the relative abundance of the pathogen, while increased the proportion of saprotroph. Regarding soil depth, pathogen relative abundance in topsoil was lower than that in subsoil. Besides, both sugarcane straw retention and soil depths (topsoil and subsoil) significantly altered the co-occurrence patterns and fungal keystone taxa closely related to straw decomposition. Furthermore, both SR and topsoil had higher average clustering coefficients (aveCC), negative edges and varied modularity. CONCLUSIONS Overall, straw retention improved α-diversity, network structure and fungal community, while reduced soil pathogenic microbes across the entire soil profile. Thus, retaining straw to improve fungal composition, community stability and their functions, in addition to reducing soil-borne pathogens, can be an essential agronomic practice in developing a sustainable agricultural system.
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Affiliation(s)
- Caifang Zhang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Zhaoli Lin
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Nyumah Fallah
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Muhammad Tayyab
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Shiyan Li
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Jun Luo
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Zichu Zhang
- Fuzhou No.8 High School, Fuzhou, 350000 China
| | - Ahmad Yusuf Abubakar
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Hua Zhang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
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26
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Osbiston K, Oxbrough A, Fernández-Martínez LT. Antibiotic resistance levels in soils from urban and rural land uses in Great Britain. Access Microbiol 2020; 3:acmi000181. [PMID: 33997612 PMCID: PMC8115975 DOI: 10.1099/acmi.0.000181] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 11/03/2020] [Indexed: 12/24/2022] Open
Abstract
Although soil is one of the largest microbial diversity reservoirs, the processes that define its microbial community dynamics are not fully understood. Improving our understanding of the levels of antibiotic resistance in soils with different land uses in Great Britain is not only important for the protection of animal health (including humans), but also for gaining an insight into gene transfer levels in microbial communities. This study looked at the levels of antibiotic-resistant bacteria (ARB) able to survive inhibitory concentrations of chloramphenicol, erythromycin and vancomycin, as well as subinhibitory (10 µg ml−1) erythromycin concentrations. Soils from nine different sites across Great Britain with three distinct land uses (agricultural, urban and semi-natural) were sampled and the percentage of ARB was calculated for each site. Statistical analyses confirmed a significant difference in the level of ARB found in agricultural land compared to urban or semi-natural sites. The results also showed that resistance levels to vancomycin and chloramphenicol in the agricultural and urban sites sampled were significantly higher than those for erythromycin, whilst in semi-natural sites all three antibiotics show similar resistance levels. Finally, although the levels of resistance to a subinhibitory (10 µg ml−1) erythromycin concentration were significantly higher across land use types when compared to the levels of resistance to an inhibitory (20 µg ml−1) concentration, these were much less marked in soil from agricultural land compared to that from urban or semi-natural land use soil.
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Affiliation(s)
- Kieran Osbiston
- Biology Department, Edge Hill University, Ormskirk, L39 4QP, UK
| | - Anne Oxbrough
- Biology Department, Edge Hill University, Ormskirk, L39 4QP, UK
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Liu YM, Cao WQ, Chen XX, Yu BG, Lang M, Chen XP, Zou CQ. The responses of soil enzyme activities, microbial biomass and microbial community structure to nine years of varied zinc application rates. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 737:140245. [PMID: 32783848 DOI: 10.1016/j.scitotenv.2020.140245] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 05/30/2020] [Accepted: 06/13/2020] [Indexed: 05/27/2023]
Abstract
Zinc (Zn) fertilizer application can certainly improve the production and nutritional quality of cereal crops. However, Zn accumulation in the soil may lead to some deleterious environmental impacts in agroecosystems. The effects of long-term Zn application on soil microbial properties remain unclear, but it is imperative to understand such effects. In this study, we collected soil samples from a nine-year field experiment in a wheat-maize system that continuously received Zn applied at various rates (0, 2.3, 5.7, 11.4, 22.7 and 34.1 kg ha-1) to evaluate the soil enzymes, microbial biomass and microbial community structure. The results showed that Zn application at the rate of 5.7 kg ha-1 significantly increased the activities of urease, invertase, alkaline phosphatase and catalase in the soil, while the rate of 34.1 kg ha-1 significantly decreased the evaluated enzyme activities. The microbial biomass carbon (C) and nitrogen (N) were not affected by Zn application rates, although an increase in the microbial biomass C was observed in the 11.4 kg ha-1 treatment. Moreover, the alpha diversity of the bacterial and fungal communities did not vary among the nil Zn, optimal Zn (5.7 kg ha-1) and excess Zn (34.1 kg ha-1) treatments. However, the bacterial communities in the soil receiving the optimal and excess Zn application rates were slightly changed. Compared to the nil Zn treatment, the other Zn application rates increased the relative abundances of the Rhodospirillales, Gaiellales and Frankiales orders and decreased the abundance of the Latescibacteria phylum. The redundancy analysis further indicated that the soil bacterial community composition significantly correlated with the concentrations of soil DTPA-Zn and total Zn. These results highlight the importance of optimal Zn application in achieving high production and high grain quality while concurrently promoting soil microbial activity, improving the bacterial community and further maintaining the sustainability of the agroecological environment.
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Affiliation(s)
- Yu-Min Liu
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing 100193, China
| | - Wen-Qing Cao
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing 100193, China
| | - Xiu-Xiu Chen
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing 100193, China
| | - Bao-Gang Yu
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing 100193, China
| | - Ming Lang
- College of Resources and Environment, Southwest University, Chongqing 400715, China
| | - Xin-Ping Chen
- College of Resources and Environment, Southwest University, Chongqing 400715, China
| | - Chun-Qin Zou
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing 100193, China.
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How Do Soil Bacterial Diversity and Community Composition Respond under Recommended and Conventional Nitrogen Fertilization Regimes? Microorganisms 2020; 8:microorganisms8081193. [PMID: 32764443 PMCID: PMC7466009 DOI: 10.3390/microorganisms8081193] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/30/2020] [Accepted: 08/03/2020] [Indexed: 11/17/2022] Open
Abstract
Shifts in soil bacterial diversity and community composition are suggested to be induced by elevated input of nitrogen (N) fertilization with implications for soil quality, and consequently production. In this study, we evaluated the impacts of recommended fertilization (RF) and conventional fertilization (CF) on soil chemical properties, crop yield, bacterial diversity, and community composition from two long-term experiments conducted in fluvo-aquic soil and black soil of China. Each site comprised of four treatments, i.e., RF N−, RF N+, CF N−, CF N+. No N fertilization was indicated by N− and N fertilization was indicated by N+. Across both sites, N fertilization significantly increased crop yield compared with no N fertilization and RF successfully enhanced crop yield over CF. Interestingly, the RF maintained bacterial diversity, while CF depressed bacterial diversity in the two soils. Microbial taxa performing important ecological roles such as order Rhodospirillales and Bacillales were significantly enhanced in the RF approach, while Rhizobiales declined under CF. Furthermore, the results of partial least square path modeling revealed that soil available phosphorus (AP) negatively affected bacterial diversity while it positively affected bacterial community structure in fluvo-aquic soils. In contrast, soil pH was positively linked with both bacterial diversity and community structure in black soil. Overall, our study demonstrated that RF is an environmentally friendly approach which not only maintained above ground plant productivity, but also preserved belowground microbial populations and important soil variables regulating bacterial communities varied in different soil types.
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29
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Zhao J, Meng Y, Drewer J, Skiba UM, Prosser JI, Gubry-Rangin C. Differential Ecosystem Function Stability of Ammonia-Oxidizing Archaea and Bacteria following Short-Term Environmental Perturbation. mSystems 2020; 5:e00309-20. [PMID: 32546672 PMCID: PMC7300361 DOI: 10.1128/msystems.00309-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 05/29/2020] [Indexed: 11/20/2022] Open
Abstract
Rapidly expanding conversion of tropical forests to oil palm plantations in Southeast Asia leads to soil acidification following intensive nitrogen fertilization. Changes in soil pH are predicted to have an impact on archaeal ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and complete (comammox) ammonia oxidizers and, consequently, on nitrification. It is therefore critical to determine whether the predicted effects of pH on ammonia oxidizers and nitrification activity apply in tropical soils subjected to various degrees of anthropogenic activity. This was investigated by experimental manipulation of pH in soil microcosms from a land-use gradient (forest, riparian, and oil palm soils). The nitrification rate was greater in forest soils with native neutral pH than in converted acidic oil palm soils. Ammonia oxidizer activity decreased following acidification of the forest soils but increased after liming of the oil palm soils, leading to a trend of a reversed net nitrification rate after pH modification. AOA and AOB nitrification activity was dependent on pH, but AOB were more sensitive to pH modification than AOA, which demonstrates a greater stability of AOA than AOB under conditions of short-term perturbation. In addition, these results predict AOB to be a good bioindicator of nitrification response following pH perturbation during land-use conversion. AOB and/or comammox species were active in all soils along the land-use gradient, even, unexpectedly, under acidic conditions, suggesting their adaptation to native acidic or acidified soils. The present study therefore provided evidence for limited stability of soil ammonia oxidizer activity following intensive anthropogenic activities, which likely aggravates the vulnerability of nitrogen cycle processes to environmental disturbance.IMPORTANCE Physiological and ecological studies have provided evidence for pH-driven niche specialization of ammonia oxidizers in terrestrial ecosystems. However, the functional stability of ammonia oxidizers following pH change has not been investigated, despite its importance in understanding the maintenance of ecosystem processes following environmental perturbation. This is particularly true after anthropogenic perturbation, such as the conversion of tropical forest to oil palm plantations. This study demonstrated a great impact of land-use conversion on nitrification, which is linked to changes in soil pH due to common agricultural practices (intensive fertilization). In addition, the different communities of ammonia oxidizers were differently affected by short-term pH perturbations, with implications for future land-use conversions but also for increased knowledge of associated global nitrous oxide emissions and current climate change concerns.
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Affiliation(s)
- Jun Zhao
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Yiyu Meng
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Julia Drewer
- Centre for Ecology and Hydrology, Penicuik, United Kingdom
| | - Ute M Skiba
- Centre for Ecology and Hydrology, Penicuik, United Kingdom
| | - James I Prosser
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Cécile Gubry-Rangin
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
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Nikinmaa L, Lindner M, Cantarello E, Jump AS, Seidl R, Winkel G, Muys B. Reviewing the Use of Resilience Concepts in Forest Sciences. CURRENT FORESTRY REPORTS 2020; 6:61-80. [PMID: 35747899 PMCID: PMC7612878 DOI: 10.1007/s40725-020-00110-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
PURPOSE OF REVIEW Resilience is a key concept to deal with an uncertain future in forestry. In recent years, it has received increasing attention from both research and practice. However, a common understanding of what resilience means in a forestry context and how to operationalise it is lacking. Here, we conducted a systematic review of the recent forest science literature on resilience in the forestry context, synthesizing how resilience is defined and assessed. RECENT FINDINGS Based on a detailed review of 255 studies, we analysed how the concepts of engineering resilience, ecological resilience and social-ecological resilience are used in forest sciences. A clear majority of the studies applied the concept of engineering resilience, quantifying resilience as the recovery time after a disturbance. The two most used indicators for engineering resilience were basal area increment and vegetation cover, whereas ecological resilience studies frequently focus on vegetation cover and tree density. In contrast, important social-ecological resilience indicators used in the literature are socioeconomic diversity and stock of natural resources. In the context of global change, we expected an increase in studies adopting the more holistic social-ecological resilience concept, but this was not the observed trend. SUMMARY Our analysis points to the nestedness of these three resilience concepts, suggesting that they are complementary rather than contradictory. It also means that the variety of resilience approaches does not need to be an obstacle for operationalisation of the concept. We provide guidance for choosing the most suitable resilience concept and indicators based on the management, disturbance and application context.
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Affiliation(s)
- L. Nikinmaa
- European Forest Institute, Platz der Vereinten Nationen 7, 53113 Bonn, Germany
- Division of Forest, Nature and Landscape, KU Leuven, Celestijnenlaan 200E, Box 2411, 3001 Leuven, Belgium
| | - M. Lindner
- European Forest Institute, Platz der Vereinten Nationen 7, 53113 Bonn, Germany
| | - E. Cantarello
- Department of Life and Environmental Sciences, Bournemouth University, Poole BH12 5BB, UK
| | - A. S. Jump
- Biological and Environmental Sciences, University of Stirling, Stirling FK9 4LA, UK
| | - R. Seidl
- Institute of Silviculture, Department of Forest- and Soil Sciences, University of Natural Resources and Life Sciences in Vienna, Peter Jordan Str. 82, 1190 Vienna, Austria
- Ecosystem Dynamics and Forest Management Group, School of Life Sciences, Technical University of Munich, Hans-Carl-von-Carlowitz-Platz 2, 85354 Freising, Germany
| | - G. Winkel
- European Forest Institute, Platz der Vereinten Nationen 7, 53113 Bonn, Germany
| | - B. Muys
- Division of Forest, Nature and Landscape, KU Leuven, Celestijnenlaan 200E, Box 2411, 3001 Leuven, Belgium
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Gu L, Wu JY, Hua ZL, Chu KJ. The response of nitrogen cycling and bacterial communities to E. coli invasion in aquatic environments with submerged vegetation. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2020; 261:110204. [PMID: 32148275 DOI: 10.1016/j.jenvman.2020.110204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Revised: 01/20/2020] [Accepted: 01/26/2020] [Indexed: 06/10/2023]
Abstract
The effects of exogenous Escherichia coli on nitrogen cycling (N-cycling) in freshwater remains unclear. Thus, seven ecosystems, six with submerged plants-Potamogeton crispus (PC) and Myriophyllum aquaticum (MA)-and one with no plants were set up. Habitats were assessed before and after E. coli addition (107 colony-forming units/mL). E. coli colonization of freshwater ecosystems had significant effects on bacterial community structure in plant surface biofilms and surface sediments (ANOVA, P < 0.05). It reduced the relative abundance of nitrosification bacteria (-70.94 ± 26.17%) and nitrifiers (-47.86 ± 23.68%) in biofilms which lead to significant reduction of ammoxidation in water (P < 0.05). The N-cycling intensity from PC systems was affected more strongly by E. coli than were MA systems. Furthermore, the coupling coefficient of exogenous E. coli to indigenous N-cycling bacteria in sediments (6.061, average connectivity degree) was significantly weaker than that in biofilms (9.852). Additionally, at the genus level, E. coli were most-closely associated with N-cycling bacteria such as Prosthecobacter, Hydrogenophaga, and Bacillus in sediments and biofilms according to co-occurrence bacterial network (Spearman). E. coli directly changed their abundance, so that the variability of species composition of N-cycling bacterial taxa was triggered, as well. Overall, exogenous E. coli repressed ammoxidation, but promoted ammonification and denitrification. Our results provided new insights into how pathogens influence the nitrogen cycle in freshwater ecosystems.
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Affiliation(s)
- Li Gu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China; National Engineering Research Center of Water Resources Efficient Utilization and Engineering Safety, Hohai University, Nanjing 210098, China
| | - Jian-Yi Wu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China; National Engineering Research Center of Water Resources Efficient Utilization and Engineering Safety, Hohai University, Nanjing 210098, China.
| | - Zu-Lin Hua
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China; National Engineering Research Center of Water Resources Efficient Utilization and Engineering Safety, Hohai University, Nanjing 210098, China.
| | - Ke-Jian Chu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
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Tang T, Sun X, Liu Q, Dong Y, Xiang Y. Different effects of soil bacterial communities affected by biocontrol agent YH-07 on tomato Fusarium wilt inhibition. RSC Adv 2020; 10:34977-34985. [PMID: 35515690 PMCID: PMC9056849 DOI: 10.1039/d0ra05452f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 09/14/2020] [Indexed: 11/21/2022] Open
Abstract
The model plant tomato was used to verify the effect and mechanism of a novel discovered strain YH-07 which is a potential agent for biological control of soil borne disease named tomato Fusarium wilt.
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Affiliation(s)
- Tongtong Tang
- School of Biological Science and Food Engineering
- Chuzhou University
- Chuzhou 239000
- China
| | - Xing Sun
- School of Biological Science and Food Engineering
- Chuzhou University
- Chuzhou 239000
- China
| | - Qin Liu
- Institute of Soil Science Chinese Academy of Sciences
- Nanjing 210008
- China
- University of Chinese Academy of Sciences
- Beijing 100049
| | - Yuanhua Dong
- Institute of Soil Science Chinese Academy of Sciences
- Nanjing 210008
- China
- University of Chinese Academy of Sciences
- Beijing 100049
| | - Yuyong Xiang
- School of Biological Science and Food Engineering
- Chuzhou University
- Chuzhou 239000
- China
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Evaluating the effects of canine urine on urban soil microbial communities. Urban Ecosyst 2019. [DOI: 10.1007/s11252-019-00842-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Wang Z, Tian H, Tan X, Wang F, Jia H, Megharaj M, He W. Long-term As contamination alters soil enzyme functional stability in response to additional heat disturbance. CHEMOSPHERE 2019; 229:471-480. [PMID: 31091488 DOI: 10.1016/j.chemosphere.2019.05.055] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Revised: 05/01/2019] [Accepted: 05/07/2019] [Indexed: 06/09/2023]
Abstract
The functional stability of soil enzymes is fundamental to the sustainability of soil biochemical processes and is affected by many environmental stressors. This study focused on the influences of long-term arsenic (As) contamination on soil enzyme functional stability: the resistance (ratio of the disturbed to control) and resilience (integrated recovery rate) of soil enzyme activities (β-glucosidase, urease, acid phosphatase, fluorescein diacetate (FDA) hydrolase) over 30 days incubation after an experimental heat disturbance (50 oC for 18 h). Results showed that the resistance of soil enzymes to heat disturbance differed among the enzyme types and followed the order: urease > β-glucosidase > acid phosphatase > FDA hydrolase. Urease activity was generally not affected and showed high stability against heat disturbance. The β-glucosidase activity recovered to the control level by 30 days, while 80% and 90% recovery on average occurred for acid phosphatase and FDA hydrolase, respectively. Long-term As contamination altered soil enzyme functional resistance and resilience to heat disturbance and resulted in three kinds of responses: (i) no apparent alteration (urease); (ii) moderate As contamination increased enzyme heat resistance (β-glucosidase); (iii) the resistance and resilience decreased with increasing As concentration (acid phosphatase and FDA hydrolase). The results demonstrated that different enzyme-catalytic biochemical processes have different functional stabilities under combined As and heat disturbance, and the negative changes in the soil enzyme activity led to losses in soil functions. Our study provides further evidence on the impacts of heavy metal/metalloid on soil enzyme functional stability in response to additional disturbance.
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Affiliation(s)
- Ziquan Wang
- College of Natural Resources and Environment, Northwest A&F University, Key Laboratory of Plant Nutrition and Agro-environment in Northwest China, Ministry of Agriculture, Yangling, 712100, Shaanxi, China; Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Haixia Tian
- College of Natural Resources and Environment, Northwest A&F University, Key Laboratory of Plant Nutrition and Agro-environment in Northwest China, Ministry of Agriculture, Yangling, 712100, Shaanxi, China
| | - Xiangping Tan
- College of Natural Resources and Environment, Northwest A&F University, Key Laboratory of Plant Nutrition and Agro-environment in Northwest China, Ministry of Agriculture, Yangling, 712100, Shaanxi, China; Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, 723 Xingke Rd., Tianhe District, Guangzhou, 510650, China
| | - Fang Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Hanzhong Jia
- College of Natural Resources and Environment, Northwest A&F University, Key Laboratory of Plant Nutrition and Agro-environment in Northwest China, Ministry of Agriculture, Yangling, 712100, Shaanxi, China
| | - Mallavarapu Megharaj
- Global Centre for Environmental Remediation, Faculty of Science, University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Wenxiang He
- College of Natural Resources and Environment, Northwest A&F University, Key Laboratory of Plant Nutrition and Agro-environment in Northwest China, Ministry of Agriculture, Yangling, 712100, Shaanxi, China.
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Wu X, Li J, Ji M, Wu Q, Wu X, Ma Y, Sui W, Zhao L, Zhang X. Non-synchronous Structural and Functional Dynamics During the Coalescence of Two Distinct Soil Bacterial Communities. Front Microbiol 2019; 10:1125. [PMID: 31191473 PMCID: PMC6548817 DOI: 10.3389/fmicb.2019.01125] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 05/03/2019] [Indexed: 01/13/2023] Open
Abstract
Soil is a unique environment in which the microbiota is frequently subjected to community coalescence. Additions of organic fertilizer and precipitation of dust induce coalescent events in soil. However, the fates of these communities after coalescence remain uncharted. Thus, to explore the effects of microbiota coalescence, we performed reciprocal inoculation and incubation experiments in microcosms using two distinct soils. The soils were, respectively, collected from a cropland and an industrial site, and the reciprocal inoculation was performed as models for the incursion of highly exotic microbiota into the soil. After incubation under either aerobic or anaerobic conditions for two months, the soils were assayed for their bacterial community structure and denitrification function. According to the 16S rRNA gene sequencing results, the inoculated soil showed a significant shift in bacterial community structure after incubation-particularly in the industrial soil. The structures of the bacterial communities changed following the coalescence but were predicted to have the same functional potential, e.g., nitrogen metabolism, as determined by the quantification of denitrifying genes and nitrogen gas production in the inoculated soil samples, which showed values equivalent those in the original recipient soil samples regardless of inoculum used. The functional prediction based on the known genomes of the taxa that shifted in the incubated sample communities indicates that the high functional overlap and redundancy across bacteria acted as a mechanism that preserved all the metabolic functions in the soil. These findings hint at the mechanisms underlying soil biodiversity maintenance and ecosystem function.
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Affiliation(s)
- Xiaogang Wu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Ji Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Mengmeng Ji
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Qiaoyu Wu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xinxin Wu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yiming Ma
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Weikang Sui
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Liping Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaojun Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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Luláková P, Perez-Mon C, Šantrůčková H, Ruethi J, Frey B. High-Alpine Permafrost and Active-Layer Soil Microbiomes Differ in Their Response to Elevated Temperatures. Front Microbiol 2019; 10:668. [PMID: 31001236 PMCID: PMC6456652 DOI: 10.3389/fmicb.2019.00668] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Accepted: 03/18/2019] [Indexed: 02/01/2023] Open
Abstract
The response of microbial communities to the predicted rising temperatures in alpine regions might be an important part of the ability of these ecosystems to deal with climate change. Soil microbial communities might be significantly affected by elevated temperatures, which influence the functioning of soils within high-alpine ecosystems. To evaluate the potential of the permafrost microbiome to adapt to short-term moderate and extreme warming, we set up an incubation experiment with permafrost and active soil layers from northern and southern slopes of a high-alpine mountain ridge on Muot da Barba Peider in the Swiss Alps. Soils were acclimated to increasing temperatures (4–40°C) for 26 days before being exposed to a heat shock treatment of 40°C for 4 days. Alpha-diversity in all soils increased slightly under gradual warming, from 4 to 25°C, but then dropped considerably at 40°C. Similarly, heat shock induced strong changes in microbial community structures and functioning in the active layer of soils from both northern and southern slope aspects. In contrast, permafrost soils showed only minor changes in their microbial community structures and no changes in their functioning, except regarding specific respiration activity. Shifts in microbial community structures with increasing temperature were significantly more pronounced for bacteria than for fungi, regardless of the soil origin, suggesting higher resistance of high-alpine fungi to short-term warming. Firmicutes, mainly represented by Tumebacillus and Alicyclobacillaceae OTUs, increased strongly at 40°C in active layer soils, reaching almost 50% of the total abundance. In contrast, Saccharibacteria decreased significantly with increasing temperature across all soil samples. Overall, our study highlights the divergent responses of fungal and bacterial communities to increased temperature. Fungi were highly resistant to increased temperatures compared to bacteria, and permafrost communities showed surprisingly low response to rising temperature. The unique responses were related to both site aspect and soil origin indicating that distinct differences within high-alpine soils may be driven by substrate limitation and legacy effects of soil temperatures at the field site.
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Affiliation(s)
- Petra Luláková
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland.,Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Carla Perez-Mon
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Hana Šantrůčková
- Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Joel Ruethi
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Beat Frey
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
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Zhang F, Xu X, Huo Y, Xiao Y. Trichoderma-Inoculation and Mowing Synergistically Altered Soil Available Nutrients, Rhizosphere Chemical Compounds and Soil Microbial Community, Potentially Driving Alfalfa Growth. Front Microbiol 2019; 9:3241. [PMID: 30666243 PMCID: PMC6330351 DOI: 10.3389/fmicb.2018.03241] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 12/13/2018] [Indexed: 01/15/2023] Open
Abstract
Trichoderma spp. are proposed as major plant growth-promoting fungi (PGPF) to increase plants growth and productivity. Mowing can stimulate aboveground regrowth to improve plant biomass and nutritional quality. However, the synergistic effects of Trichoderma and mowing on plants growth, particularly the underlying microbial mechanisms mediated by rhizosphere soil chemical compounds, have rarely been reported. In the present study, we employed Trichoderma harzianum T-63 and conducted a pot experiment to investigate the synergistic effect of Trichoderma-inoculation and mowing on alfalfa growth, and the potential soil microbial ecological mechanisms were also explored. Alfalfa treated with Trichoderma-inoculation and/or mowing (T, M, and TM) had significant (P < 0.05) increases in plant shoot and root dry weights and soil available nutrients (N, P, and K), compared with those of the control (CK). Non-metric multidimensional scaling (NMDS) demonstrated that the rhizosphere chemical compounds and soil bacterial and fungal communities were, respectively, separated according to different treatments. There was a clear significant (P < 0.05) positive correlation between alfalfa biomass and the relative abundance of Trichoderma (R2 = 0.3451, P = 0.045). However, Pseudomonas, Flavobacterium, Arthrobacter, Bacillus, Agrobacterium, and Actinoplanes were not significantly correlated with alfalfa biomass. According to structure equation modeling (SEM), Trichoderma abundance and available P served as primary contributors to alfalfa growth promotion. Additionally, Trichoderma-inoculation and mowing altered rhizosphere soil chemical compounds to drive the soil microbial community, indirectly influencing alfalfa growth. Our research provides a basis for promoting alfalfa growth from a soil microbial ecology perspective and may provide a scientific foundation for guiding the farming of alfalfa.
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Affiliation(s)
- Fengge Zhang
- College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Xixi Xu
- College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Yunqian Huo
- College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Yan Xiao
- College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing, China
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Liu Y, Feng C, Sheng Y, Dong S, Chen N, Hao C. Effect of Fe(II) on reactivity of heterotrophic denitrifiers in the remediation of nitrate- and Fe(II)-contaminated groundwater. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2018; 166:437-445. [PMID: 30292110 DOI: 10.1016/j.ecoenv.2018.09.104] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 09/07/2018] [Accepted: 09/24/2018] [Indexed: 06/08/2023]
Abstract
Heterotrophic denitrifiers, capable of simultaneous nitrate reduction and Fe(II) oxidation, can be applied for the remediation of nitrate and Fe(II) combined contamination in groundwater. Under strictly anaerobic condition, denitrifying microbial communities were enriched with the coexistence of soluble nitrate, Fe(II) and associated nutrient elements to monitor the denitrification process. Low abundance of Fe(II) (e.g., 10 mg L-1 in this study) tended to stimulate the activity of denitrifying microbial communities. However, elevated Fe(II) concentration (50 and 100 mg L-1 in this study), acted as a stress, strongly inhibited the activity and reproduction of denitrifiers. Besides, through thermodynamics calculations, methanol rather than Fe(II) was proved to be the preferable electron donors for both energy metabolism and anabolism. Betaproteobacteria was found to be the most predominant (sub)phylum in all enriched microbial assemblages. Methylovesartilis was the most predominant group mainly catalyzed for methanol based denitrification, and others denitrifiers included Methylophilaceae, Dechloromonas and Denitratisoma. Excessive Fe(II) in the solution greatly reduced the proportions of these denitrifying groups, while the influence seemed to be less apparent on functional genes composition. As such, a conceptional metabolism pathway of the most dominant genus (i.e., Methylovesartilis) for nitrate reducing as well as methanol and Fe(II) oxidation confirmed that biotic nitrate reducing and Fe(II) oxidizing were potentially proceeded in cytoplasm by enzymes such as NarGHI. The Fe(II) oxidation rate depended on the rate of Fe(II) entering into the cell. These findings provide a clear mechanistic understanding of heterotrophic denitrification coupling with Fe(II) oxidation, and environmental implication for the bioremediation of nitrate and Fe(II) contaminated groundwater.
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Affiliation(s)
- Ying Liu
- Key Laboratory of Groundwater Circulation and Environmental Evolution (China University of Geosciences (Beijing)), Ministry of Education, Beijing 100083, China; School of Water Resources and Environment, China University of Geosciences, Beijing 100083, China
| | - Chuanping Feng
- Key Laboratory of Groundwater Circulation and Environmental Evolution (China University of Geosciences (Beijing)), Ministry of Education, Beijing 100083, China; School of Water Resources and Environment, China University of Geosciences, Beijing 100083, China.
| | - Yizhi Sheng
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Shanshan Dong
- Key Laboratory of Groundwater Circulation and Environmental Evolution (China University of Geosciences (Beijing)), Ministry of Education, Beijing 100083, China; School of Water Resources and Environment, China University of Geosciences, Beijing 100083, China
| | - Nan Chen
- Key Laboratory of Groundwater Circulation and Environmental Evolution (China University of Geosciences (Beijing)), Ministry of Education, Beijing 100083, China; School of Water Resources and Environment, China University of Geosciences, Beijing 100083, China
| | - Chunbo Hao
- Key Laboratory of Groundwater Circulation and Environmental Evolution (China University of Geosciences (Beijing)), Ministry of Education, Beijing 100083, China; School of Water Resources and Environment, China University of Geosciences, Beijing 100083, China
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Webster AJ, Groffman PM, Cadenasso ML. Controls on denitrification potential in nitrate-rich waterways and riparian zones of an irrigated agricultural setting. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2018; 28:1055-1067. [PMID: 29465768 DOI: 10.1002/eap.1709] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 01/26/2018] [Accepted: 01/29/2018] [Indexed: 06/08/2023]
Abstract
Denitrification, the microbial conversion of NO3- to N gases, is an important process contributing to whether lotic and riparian ecosystems act as sinks for excess NO3- from agricultural activities. Though agricultural waterways and riparian zones have been a focus of denitrification research for decades, almost none of this research has occurred in the irrigated agricultural settings of arid and semiarid climates. In this study, we conducted a broad survey of denitrification potential in riparian soils and channel sediments from 79 waterway reaches in the irrigated agricultural landscape of California's Central Valley. With this approach, we sought to capture the wide range of variation that arose from diverse waterway management and fluctuating flow conditions, and use this variation to identify promising management interventions. We explored associations of denitrification potentials with surface water NO3- -N, organic matter, flow conditions, vegetation cover, near-channel riparian bank slope, and channel geomorphic features using generalized linear mixed models. We found strong associations of sediment denitrification potentials with reach flow conditions, which we hypothesize was the result of variation in microbial communities' tolerance to dry-wet cycles. Denitrification potentials in riparian soils, in contrast, did not appear affected by flow conditions, but instead were associated with organic matter, vegetation cover, and bank slope in the riparian zone. These results suggest a strong need for further work on how denitrification responds to varying flow conditions and dry-wet cycles in non-perennial lotic ecosystems. Our findings also demonstrate that denitrifier communities respond to key features of waterway management, which can therefore be leveraged to control denitrification through a variety of management actions.
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Affiliation(s)
- Alex J Webster
- Department of Plant Sciences, University of California Davis, Shields Avenue, Davis, California, 95616, USA
- Graduate Group in Ecology, University of California Davis, Shields Avenue, Davis, California, 95616, USA
| | - Peter M Groffman
- Cary Institute of Ecosystem Studies, Millbrook, New York, 12545, USA
- Advanced Research Center and Brooklyn College, City University of New York, New York, New York, 12210, USA
| | - Mary L Cadenasso
- Department of Plant Sciences, University of California Davis, Shields Avenue, Davis, California, 95616, USA
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40
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Frąc M, Hannula SE, Bełka M, Jędryczka M. Fungal Biodiversity and Their Role in Soil Health. Front Microbiol 2018; 9:707. [PMID: 29755421 PMCID: PMC5932366 DOI: 10.3389/fmicb.2018.00707] [Citation(s) in RCA: 179] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Accepted: 03/27/2018] [Indexed: 11/23/2022] Open
Abstract
Soil health, and the closely related terms of soil quality and fertility, is considered as one of the most important characteristics of soil ecosystems. The integrated approach to soil health assumes that soil is a living system and soil health results from the interaction between different processes and properties, with a strong effect on the activity of soil microbiota. All soils can be described using physical, chemical, and biological properties, but adaptation to environmental changes, driven by the processes of natural selection, are unique to the latter one. This mini review focuses on fungal biodiversity and its role in the health of managed soils as well as on the current methods used in soil mycobiome identification and utilization next generation sequencing (NGS) approaches. The authors separately focus on agriculture and horticulture as well as grassland and forest ecosystems. Moreover, this mini review describes the effect of land-use on the biodiversity and succession of fungi. In conclusion, the authors recommend a shift from cataloging fungal species in different soil ecosystems toward a more global analysis based on functions and interactions between organisms.
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Affiliation(s)
- Magdalena Frąc
- Institute of Agrophysics, Polish Academy of Sciences, Lublin, Poland
| | | | - Marta Bełka
- Department of Forest Pathology, Poznań University of Life Sciences, Poznań, Poland
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Ma M, Jiang X, Wang Q, Ongena M, Wei D, Ding J, Guan D, Cao F, Zhao B, Li J. Responses of fungal community composition to long-term chemical and organic fertilization strategies in Chinese Mollisols. Microbiologyopen 2018; 7:e00597. [PMID: 29573192 PMCID: PMC6182557 DOI: 10.1002/mbo3.597] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 01/02/2018] [Accepted: 01/09/2018] [Indexed: 11/07/2022] Open
Abstract
How fungi respond to long-term fertilization in Chinese Mollisols as sensitive indicators of soil fertility has received limited attention. To broaden our knowledge, we used high-throughput pyrosequencing and quantitative PCR to explore the response of soil fungal community to long-term chemical and organic fertilization strategies. Soils were collected in a 35-year field experiment with four treatments: no fertilizer, chemical phosphorus, and potassium fertilizer (PK), chemical phosphorus, potassium, and nitrogen fertilizer (NPK), and chemical phosphorus and potassium fertilizer plus manure (MPK). All fertilization differently changed soil properties and fungal community. The MPK application benefited soil acidification alleviation and organic matter accumulation, as well as soybean yield. Moreover, the community richness indices (Chao1 and ACE) were higher under the MPK regimes, indicating the resilience of microbial diversity and stability. With regards to fungal community composition, the phylum Ascomycota was dominant in all samples, followed by Zygomycota, Basidiomycota, Chytridiomycota, and Glomeromycota. At each taxonomic level, the community composition dramatically differed under different fertilization strategies, leading to different soil quality. The NPK application caused a loss of Leotiomycetes but an increase in Eurotiomycetes, which might reduce the plant-fungal symbioses and increase nitrogen losses and greenhouse gas emissions. According to the linear discriminant analysis (LDA) coupled with effect size (LDA score > 3.0), the NPK application significantly increased the abundances of fungal taxa with known pathogenic traits, such as order Chaetothyriales, family Chaetothyriaceae and Pleosporaceae, and genera Corynespora, Bipolaris, and Cyphellophora. In contrast, these fungi were detected at low levels under the MPK regime. Soil organic matter and pH were the two most important contributors to fungal community composition.
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Affiliation(s)
- Mingchao Ma
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China.,Microbial Processes and Interactions Research Unit, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Xin Jiang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China.,Laboratory of Quality & Safety Risk Assessment for Microbial Products, Ministry of Agriculture, Beijing, China
| | - Qingfeng Wang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Marc Ongena
- Microbial Processes and Interactions Research Unit, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Dan Wei
- The Institute of Soil Fertility and Environmental Sources, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Jianli Ding
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China.,Laboratory of Quality & Safety Risk Assessment for Microbial Products, Ministry of Agriculture, Beijing, China
| | - Dawei Guan
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China.,Laboratory of Quality & Safety Risk Assessment for Microbial Products, Ministry of Agriculture, Beijing, China
| | - Fengming Cao
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China.,Laboratory of Quality & Safety Risk Assessment for Microbial Products, Ministry of Agriculture, Beijing, China
| | - Baisuo Zhao
- Laboratory of Quality & Safety Risk Assessment for Microbial Products, Ministry of Agriculture, Beijing, China
| | - Jun Li
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China.,Laboratory of Quality & Safety Risk Assessment for Microbial Products, Ministry of Agriculture, Beijing, China
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Effect of long-term fertilization strategies on bacterial community composition in a 35-year field experiment of Chinese Mollisols. AMB Express 2018; 8:20. [PMID: 29442257 PMCID: PMC5811423 DOI: 10.1186/s13568-018-0549-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 02/05/2018] [Indexed: 11/10/2022] Open
Abstract
Bacteria play vital roles in soil biological fertility; however, it remains poorly understood about their response to long-term fertilization in Chinese Mollisols, especially when organic manure is substituted for inorganic nitrogen (N) fertilizer. To broaden our knowledge, high-throughput pyrosequencing and quantitative PCR were used to explore the impacts of inorganic fertilizer and manure on bacterial community composition in a 35-year field experiment of Chinese Mollisols. Soils were collected from four treatments: no fertilizer (CK), inorganic phosphorus (P) and potassium (K) fertilizer (PK), inorganic P, K, and N fertilizer (NPK), and inorganic P and K fertilizer plus manure (MPK). All fertilization differently changed soil properties. Compared with CK, the PK and NPK treatments acidified soil by significantly decreasing soil pH from 6.48 to 5.53 and 6.16, respectively, while MPK application showed no significant differences of soil pH, indicating alleviation of soil acidification. Moreover, all fertilization significantly increased soil organic matter (OM) and soybean yields, with the highest observed under MPK regime. In addition, the community composition at each taxonomic level varied considerably among the fertilization strategies. Bacterial taxa, associated with plant growth promotion, OM accumulation, disease suppression, and increased soil enzyme activity, were overrepresented in the MPK regime, while they were present at low abundant levels under NPK treatment, i.e. phyla Proteobacteria and Bacteroidetes, class Alphaproteobacteria, and genera Variovorax, Chthoniobacter, Massilia, Lysobacter, Catelliglobosispora and Steroidobacter. The application of MPK shifted soil bacterial community composition towards a better status, and such shifts were primarily derived from changes in soil pH and OM.
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43
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Quality of Irrigation Water Affects Soil Functionality and Bacterial Community Stability in Response to Heat Disturbance. Appl Environ Microbiol 2018; 84:AEM.02087-17. [PMID: 29180372 DOI: 10.1128/aem.02087-17] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 11/20/2017] [Indexed: 11/20/2022] Open
Abstract
Anthropogenic activities alter the structure and function of a bacterial community. Furthermore, bacterial communities structured by the conditions the anthropogenic activities present may consequently reduce their stability in response to an unpredicted acute disturbance. The present mesocosm-scale study exposed soil bacterial communities to different irrigation water types, including freshwater, fertilized freshwater, treated wastewater, and artificial wastewater, and evaluated their response to a disturbance caused by heat. These effectors may be considered deterministic and stochastic forces common in agricultural operations of arid and semiarid regions. Bacterial communities under conditions of high mineral and organic carbon availability (artificial wastewater) differed from the native bacterial community and showed a proteobacterial dominance. These bacterial communities had a lower resistance to the heat treatment disturbance than soils under conditions of low resource availability (high-quality treated wastewater or freshwater). The latter soil bacterial communities showed a higher abundance of operational taxonomic units (OTUs) classified as Bacilli These results were elucidated by soil under conditions of high resource availability, which lost higher degrees of functional potential and had a greater bacterial community composition change. However, the functional resilience, after the disturbance ended, was higher under a condition of high resource availability despite the bacterial community composition shift and the decrease in species richness. The functional resilience was directly connected to the high growth rates of certain Bacteroidetes and proteobacterial groups. A high stability was found in samples that supported the coexistence of both resistant OTUs and fast-growing OTUs.IMPORTANCE This report presents the results of a study employing a hypothesis-based experimental approach to reveal the forces involved in determining the stability of a soil bacterial community to disturbance. The resultant postdisturbance bacterial community composition dynamics and functionality were analyzed. The paper demonstrates the relatedness of community structure and stability under cultivation conditions prevalent in an arid area under irrigation with water of different qualities. The use of common agricultural practices to demonstrate these features has not been described before. The combination of a fundamental theoretical issue in ecology with common and concerning disturbances caused by agricultural practice makes this study unique. Furthermore, the results of the present study have applicable importance regarding soil conservation, as it enables a better characterization and monitoring of stressed soil bacterial communities and possible intervention to reduce the stress. It will also be of valued interest in coming years, as fresh water scarcity and the use of alternative water sources are expected to rise globally.
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Dang YP, Balzer A, Crawford M, Rincon-Florez V, Liu H, Melland AR, Antille D, Kodur S, Bell MJ, Whish JPM, Lai Y, Seymour N, Carvalhais LC, Schenk P. Strategic tillage in conservation agricultural systems of north-eastern Australia: why, where, when and how? ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:1000-1015. [PMID: 28390024 DOI: 10.1007/s11356-017-8937-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 03/24/2017] [Indexed: 06/07/2023]
Abstract
Farmers often resort to an occasional tillage (strategic tillage (ST)) operation to combat constraints of no-tillage (NT) farming systems. There are conflicting reports regarding impacts of ST and a lack of knowledge around when, where and how ST is implemented to maximise its benefits without impacting negatively on soil and environment. We established 14 experiments during 2012-2015 on farms with long-term history of continuous NT to (i) quantify the associated risks and benefits to crop productivity, soil and environmental health and (ii) explore key factors that need to be considered in decisions to implement ST in an otherwise NT system. Results showed that introduction of ST reduced weed populations and improved crop productivity and profitability in the first year after tillage, with no impact in subsequent 4 years. Soil properties were not impacted in Vertosols; however, Sodosols and Dermosols suffered short-term negative soil health impacts (e.g. increased bulk density). A Sodosol and a Dermosol also posed higher risks of runoff and associated loss of nutrients and sediment during intense rainfall after ST. The ST reduced plant available water in the short term, which could result in unreliable sowing opportunities for the following crop especially in semi-arid climate that prevails in north-eastern Australia. The results show that generally, there were no significant differences in crop productivity and soil health between tillage implements and tillage frequencies between ST and NT. The study suggests that ST can be a viable strategy to manage constraints of NT systems, with few short-term soil and environmental costs and some benefits such as short-term farm productivity and profitability and reduced reliance on herbicides.
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Affiliation(s)
- Yash Pal Dang
- School of Agriculture and Food Sciences, The University of Queensland, St Lucia, Australia.
| | - Anna Balzer
- School of Agriculture and Food Sciences, The University of Queensland, St Lucia, Australia
| | - Mark Crawford
- Department of Natural Resources and Mines, Toowoomba, Australia
| | - Vivian Rincon-Florez
- School of Agriculture and Food Sciences, The University of Queensland, St Lucia, Australia
| | - Hongwei Liu
- School of Agriculture and Food Sciences, The University of Queensland, St Lucia, Australia
| | | | | | | | - Michael John Bell
- School of Agriculture and Food Sciences, The University of Queensland, St Lucia, Australia
| | | | - Yunru Lai
- School of Agriculture and Food Sciences, The University of Queensland, St Lucia, Australia
| | - Nikki Seymour
- Department of Agriculture and Forestry, Toowoomba, Australia
| | - Lilia Costa Carvalhais
- School of Agriculture and Food Sciences, The University of Queensland, St Lucia, Australia
| | - Peer Schenk
- School of Agriculture and Food Sciences, The University of Queensland, St Lucia, Australia
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Bononi L, Taketani RG, Souza DT, Moitinho MA, Kavamura VN, Melo IS. Higher phylogenetic diversity prevents loss of functional diversity caused by successive drying and rewetting cycles. Antonie van Leeuwenhoek 2017; 111:1033-1045. [DOI: 10.1007/s10482-017-1003-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 12/14/2017] [Indexed: 11/24/2022]
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46
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Bartkowiak A, Lemanowicz J, Breza-Boruta B. Evaluation of the content of Zn, Cu, Ni and Pb as well as the enzymatic activity of forest soils exposed to the effect of road traffic pollution. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:23893-23902. [PMID: 28871517 PMCID: PMC5641288 DOI: 10.1007/s11356-017-0013-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2017] [Accepted: 08/22/2017] [Indexed: 05/20/2023]
Abstract
The paper evaluates the contents of total forms of selected heavy metals (Zn, Cu, Ni and Pb) as well as the activity of catalase (CAT), dehydrogenases (DEH), alkaline phosphatase (AlP) and acid phosphatase (AcP) in mineral surface horizons of forest soils exposed to the effect of road traffic pollutions. The sampling locations (n = 24) were determined in the area covered by the Szubin Forest along the exit road from Bydgoszcz to Poznań (provincial road no. 223). Soil was sampled 25 m away from the traffic lane, from two depths, 5-20 cm (humus horizons) and 20-50 cm (eluvial horizons). The contents of the heavy metals analysed were in the order of Pb > Zn > Cu > Ni. Despite intensive road traffic, with the Integrated Pollution Index (IPI) calculated, there was found a low pollution with nickel, average with zinc and copper and high with lead only. However, under the Regulation of the Minister of Environment, heavy metal values recorded allow for classifying the soils analysed as soils unpolluted with those metals. In the soil samples analysed, there were found significant positive dependencies between the content of clay fraction and zinc (r = 0.455; P < 0.05) and copper (r = 0.430; P < 0.05). With the enzyme activity results, values of the soil resistance index (RS) were calculated. The enzymes analysed were classified in the following decreasing order in terms of their resistance to traffic pollution: catalase > acid phosphatase > alkaline phosphatase > dehydrogenases (humus horizons) and catalase > dehydrogenases > alkaline phosphatase > acid phosphatase (eluvial horizons). Organic carbon showed a significant positive correlation with the activities of alkaline (r = 0.668; P < 0.05) and acid phosphatase (r = 0.668; P < 0.05) however not with catalase and dehydrogenases.
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Affiliation(s)
- Agata Bartkowiak
- Department of Soil Science and Soil Protection, Faculty of Agriculture and Biotechnology, UTP University of Science and Technology, 6 Bernardyńska Street, 85-029, Bydgoszcz, Poland.
| | - Joanna Lemanowicz
- Sub-Department of Biochemistry, Faculty of Agriculture and Biotechnology, UTP University of Science and Technology, 6 Bernardyńska Street, 85-029, Bydgoszcz, Poland
| | - Barbara Breza-Boruta
- Department of Microbiology and Food Technology, Faculty of Agriculture and Biotechnology, UTP University of Science and Technology, 6 Bernardyńska Street, 85-029, Bydgoszcz, Poland
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47
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Dean SL, Billingsley Tobias T, Phippen WB, Clayton AW, Gruver J, Porras-Alfaro A. A study of Glycine max (soybean) fungal communities under different agricultural practices. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.plgene.2016.11.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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48
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Hua J, Feng Y, Jiang Q, Bao X, Yin Y. Shift of bacterial community structure along different coastal reclamation histories in Jiangsu, Eastern China. Sci Rep 2017; 7:10096. [PMID: 28855690 PMCID: PMC5577240 DOI: 10.1038/s41598-017-10608-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 08/11/2017] [Indexed: 11/09/2022] Open
Abstract
Tideland reclamation has drastic effects on coastal ecosystem involved in soil microorganisms. However, the knowledge regarding temporal variations of microbial community along reclamation chronosequence and their environmental variable predictor is still poorly known. Using Illumina sequencing, we qualified bacterial community composition in soils collected from one tideland and four reclamation stages, i.e. 2-year, 7-year, 19-year and 39-year in Jiangsu, Eastern China. Across all samples, the dominant groups were Proteobacteria, Bacteroidete, Acidobacteria, Planctomycetes and Chloroflexi. Reclamation activity and its histories greatly altered bacterial community structure, and only 0.28% of phylotypes were shared by five soils. Specially, some typical marine bacteria (Gaetulibacter, Alcanivorax …) disappeared in reclamation soils, while other groups (Niabella, Flavisolibacter…) were gradually eminent. Generally, bacterial diversity and richness increased with reclamation histories. Bacterial community was correlated with most of soil physico-chemical properties. Amongst, mean weight diameter of soil aggregates (MWD) was detected as a primary factor predicting bacterial community composition. Together, our results indicated that effects of reclamation on bacterial community varied with diked histories, and MWD was a major factor predicting bacterial community during progressive reclamation. These findings offer predicting case study for understanding the impact of reclamation and its histories on microbial community in a coastal ecosystem.
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Affiliation(s)
- Jianfeng Hua
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China.,State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Youzhi Feng
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Qian Jiang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Xuewen Bao
- Nanjing Forest Police College, Nanjing, China.
| | - Yunlong Yin
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
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Chen J, Nie Y, Liu W, Wang Z, Shen W. Ammonia-Oxidizing Archaea Are More Resistant Than Denitrifiers to Seasonal Precipitation Changes in an Acidic Subtropical Forest Soil. Front Microbiol 2017; 8:1384. [PMID: 28790990 PMCID: PMC5522861 DOI: 10.3389/fmicb.2017.01384] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 07/10/2017] [Indexed: 12/02/2022] Open
Abstract
Seasonal precipitation changes are increasingly severe in subtropical areas. However, the responses of soil nitrogen (N) cycle and its associated functional microorganisms to such precipitation changes remain unclear. In this study, two projected precipitation patterns were manipulated: intensifying the dry-season drought (DD) and extending the dry-season duration (ED) but increasing the wet-season storms following the DD and ED treatment period. The effects of these two contrasting precipitation patterns on soil net N transformation rates and functional gene abundances were quantitatively assessed through a resistance index. Results showed that the resistance index of functional microbial abundance (-0.03 ± 0.08) was much lower than that of the net N transformation rate (0.55 ± 0.02) throughout the experiment, indicating that microbial abundance was more responsive to precipitation changes compared with the N transformation rate. Spring drought under the ED treatment significantly increased the abundances of both nitrifying (amoA) and denitrifying genes (nirK, nirS, and nosZ), while changes in these gene abundances overlapped largely with control treatment during droughts in the dry season. Interestingly, the resistance index of the ammonia-oxidizing archaea (AOA) amoA abundance was significantly higher than that of the denitrifying gene abundances, suggesting that AOA were more resistant to the precipitation changes. This was attributed to the stronger environmental adaptability and higher resource utilization efficiency of the AOA community, as indicated by the lack of correlations between AOA gene abundance and environmental factors [i.e., soil water content, ammonium (NH4+) and dissolved organic carbon concentrations] during the experiment.
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Affiliation(s)
- Jie Chen
- Center for Ecological and Environmental Sciences, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China.,College of Life Science, University of Chinese Academy of SciencesBeijing, China.,Department of Soil Science of Temperate Ecosystems, University of GöttingenGöttingen, Germany
| | - Yanxia Nie
- Center for Ecological and Environmental Sciences, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
| | - Wei Liu
- Center for Ecological and Environmental Sciences, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
| | - Zhengfeng Wang
- Center for Ecological and Environmental Sciences, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
| | - Weijun Shen
- Center for Ecological and Environmental Sciences, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
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50
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Zhou J, Jiang X, Wei D, Zhao B, Ma M, Chen S, Cao F, Shen D, Guan D, Li J. Consistent effects of nitrogen fertilization on soil bacterial communities in black soils for two crop seasons in China. Sci Rep 2017; 7:3267. [PMID: 28607352 PMCID: PMC5468298 DOI: 10.1038/s41598-017-03539-6] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 05/01/2017] [Indexed: 01/08/2023] Open
Abstract
Long-term use of inorganic nitrogen (N) fertilization has greatly influenced the bacterial community in black soil of northeast China. It is unclear how N affects the bacterial community in two successive crop seasons in the same field for this soil type. We sampled soils from a long-term fertilizer experimental field in Harbin city with three N gradients. We applied sequencing and quantitative PCR targeting at the 16S rRNA gene to examine shifts in bacterial communities and test consistent shifts and driving-factors bacterial responses to elevated N additions. N addition decreased soil pH and bacterial 16S rDNA copy numbers, and increased soil N and crop yield. N addition consistently decreased bacterial diversity and altered bacterial community composition, by increasing the relative abundance of Proteobacteria, and decreasing that of Acidobacteria and Nitrospirae in both seasons. Consistent changes in the abundant classes and genera, and the structure of the bacterial communities across both seasons were observed. Our results suggest that increases in N inputs had consistent effects on the richness, diversity and composition of soil bacterial communities across the crop seasons in two continuous years, and the N addition and the subsequent edaphic changes were important factors in shaping bacterial community structures.
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Affiliation(s)
- Jing Zhou
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China.,College of Biological Sciences, China Agricultural University, Beijing, 100094, PR China
| | - Xin Jiang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China. .,Laboratory of Quality & Safety Risk Assessment for Microbial Products (Beijing), Ministry of Agriculture, Beijing, 100081, PR China.
| | - Dan Wei
- The Institute of Soil Fertility and Environmental Sources, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, PR China
| | - Baisuo Zhao
- Laboratory of Quality & Safety Risk Assessment for Microbial Products (Beijing), Ministry of Agriculture, Beijing, 100081, PR China
| | - Mingchao Ma
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China.,Laboratory of Quality & Safety Risk Assessment for Microbial Products (Beijing), Ministry of Agriculture, Beijing, 100081, PR China
| | - Sanfeng Chen
- College of Biological Sciences, China Agricultural University, Beijing, 100094, PR China
| | - Fengming Cao
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China.,Laboratory of Quality & Safety Risk Assessment for Microbial Products (Beijing), Ministry of Agriculture, Beijing, 100081, PR China
| | - Delong Shen
- Laboratory of Quality & Safety Risk Assessment for Microbial Products (Beijing), Ministry of Agriculture, Beijing, 100081, PR China
| | - Dawei Guan
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Jun Li
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China. .,Laboratory of Quality & Safety Risk Assessment for Microbial Products (Beijing), Ministry of Agriculture, Beijing, 100081, PR China.
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