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León Ninin JM, Higa Mori A, Pausch J, Planer-Friedrich B. Long-term paddy use influences response of methane production, arsenic mobility and speciation to future higher temperatures. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 943:173793. [PMID: 38851333 DOI: 10.1016/j.scitotenv.2024.173793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 05/14/2024] [Accepted: 06/03/2024] [Indexed: 06/10/2024]
Abstract
Anaerobic microbial metabolisms make flooded paddy soils a major source of the greenhouse gas methane (CH4) and mobilize toxic arsenic (As), threatening rice production and consumption. Increasing temperatures due to climate change enhance these microbially mediated processes, increasing their related threats. Chronosequence studies show that long-term paddy use ("age") changes soil properties and redox biogeochemistry through soil organic carbon (SOC) accumulation, its association to amorphous iron (Fe) phases, and increased microbial activity. Using paddy and non-paddy soils from a chronosequence as proxies of soil development and incubating them at different temperatures, we show that paddy soil age influences the response of paddies to changes in temperature. Older paddies showed up to a 6-fold higher CH4 production with increasing temperature, compared to a 2-fold increase in young ones. Contrarily, changes in As mobility were higher in non-paddies and young paddies due to a lack of Fe-SOC-sorption sites. Temperature increased the formation of phytotoxic methylated As in all paddies, posing a risk for rice production. Mitigation strategies for future maintenance, abandonment, or management of paddy soils should include the consideration that history of use shapes the soils' biogeochemistry and microbiology and can influence the response of paddy soils to future temperature increases.
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Affiliation(s)
- José M León Ninin
- Environmental Geochemistry, Bayreuth Center for Ecology and Environmental Research (BayCEER), University of Bayreuth, 95440 Bayreuth, Germany
| | - Alejandra Higa Mori
- Environmental Geochemistry, Bayreuth Center for Ecology and Environmental Research (BayCEER), University of Bayreuth, 95440 Bayreuth, Germany
| | - Johanna Pausch
- Agroecology, Bayreuth Center for Ecology and Environmental Research (BayCEER), University of Bayreuth, 95440 Bayreuth, Germany
| | - Britta Planer-Friedrich
- Environmental Geochemistry, Bayreuth Center for Ecology and Environmental Research (BayCEER), University of Bayreuth, 95440 Bayreuth, Germany.
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León Ninin JM, Muehe EM, Kölbl A, Higa Mori A, Nicol A, Gilfedder B, Pausch J, Urbanski L, Lueders T, Planer-Friedrich B. Changes in arsenic mobility and speciation across a 2000-year-old paddy soil chronosequence. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:168351. [PMID: 37939938 DOI: 10.1016/j.scitotenv.2023.168351] [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: 09/13/2023] [Revised: 11/03/2023] [Accepted: 11/03/2023] [Indexed: 11/10/2023]
Abstract
Rice accumulates arsenic (As) when cultivated under flooded conditions in paddy soils threatening rice yield or its safety for human consumption, depending on As speciation. During long-term paddy use, repeated redox cycles systematically alter soil biogeochemistry and microbiology. In the present study, incubation experiments from a 2000-year-old paddy soil chronosequence revealed that As mobilization and speciation also change with paddy soil age. Younger paddies (≤100 years) showed the highest total As mobilization, with speciation dominated by carcinogenic inorganic oxyarsenic species and highly mobile inorganic thioarsenates. Inorganic thioarsenates formed by a high availability of reduced sulfur (S) due to low concentrations of reducible iron (Fe) and soil organic carbon (SOC). Long-term paddy use (>100 years) resulted in higher microbial activity and SOC, increasing the share of phytotoxic methylated As. Methylated oxyarsenic species are precursors for cytotoxic methylated thioarsenates. Methylated thioarsenates formed in soils of all ages being limited either by the availability of methylated As in young soils or that of reduced-S in older ones. The present study shows that via a linkage of As to the biogeochemistry of Fe, S, and C, paddy soil age can influence the kind and the extent of threat that As poses for rice cultivation.
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Affiliation(s)
- José M León Ninin
- Environmental Geochemistry, Bayreuth Center for Ecology and Environmental Research (BayCEER), University of Bayreuth, 95440 Bayreuth, Germany
| | - E Marie Muehe
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research (UFZ), 04318 Leipzig, Germany; Department of Geosciences, University of Tübingen, 72076 Tübingen, Germany
| | - Angelika Kölbl
- Soil Science and Soil Protection, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Alejandra Higa Mori
- Environmental Geochemistry, Bayreuth Center for Ecology and Environmental Research (BayCEER), University of Bayreuth, 95440 Bayreuth, Germany
| | - Alan Nicol
- Environmental Geochemistry, Bayreuth Center for Ecology and Environmental Research (BayCEER), University of Bayreuth, 95440 Bayreuth, Germany
| | - Ben Gilfedder
- Limnological Research Station, Bayreuth Center for Ecology and Environmental Research (BayCEER), University of Bayreuth, 95440 Bayreuth, Germany
| | - Johanna Pausch
- Agroecology, Bayreuth Center for Ecology and Environmental Research (BayCEER), University of Bayreuth, 95440 Bayreuth, Germany
| | - Livia Urbanski
- Chair of Soil Science, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Emil-Ramann-Str. 2, 85354 Freising, Germany
| | - Tillmann Lueders
- Ecological Microbiology, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, 95448 Bayreuth, Germany
| | - Britta Planer-Friedrich
- Environmental Geochemistry, Bayreuth Center for Ecology and Environmental Research (BayCEER), University of Bayreuth, 95440 Bayreuth, Germany.
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Guo X, Wang S, Wang C, Lan M, Yang S, Luo S, Li R, Xia J, Xiao B, Xie L, Wang Z, Guo Z. The Changes, Aggregation Processes, and Driving Factors for Soil Fungal Communities during Tropical Forest Restoration. J Fungi (Basel) 2023; 10:27. [PMID: 38248937 PMCID: PMC10817487 DOI: 10.3390/jof10010027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 12/10/2023] [Accepted: 12/29/2023] [Indexed: 01/23/2024] Open
Abstract
Soil fungal communities play crucial roles in mediating the functional associations between above- and belowground components during forest restoration. Forest restoration shapes the alterations in plant and soil environments, which exerts a crucial effect on soil fungal assemblages. However, the changes, assembly processes, and driving factors of soil fungi communities during tropical forest restoration are still uncertain. We used Illumina high-throughput sequencing to identify the changes of soil fungal communities across a tropical secondary forest succession chronosequence (i.e., 12-, 42-, and 53-yr stages) in Xishuangbanna. During forest restoration, the dominant taxa of soil fungi communities shifted from r- to K-strategists. The relative abundance of Ascomycota (r-strategists) decreased by 10.0% and that of Basidiomycota (K-strategists) increased by 4.9% at the 53-yr restoration stage compared with the 12-yr stage. From the 12-yr to 53-yr stage, the operational taxonomic unit (OTU), abundance-based coverage estimator (ACE), Chao1, and Shannon index of fungal communities declined by 14.5-57.4%. Although the stochastic processes were relatively important in determining fungal assemblages at the late stage, the fungal community assembly was dominated by deterministic processes rather than stochastic processes. The shifts in soil properties resulting from tropical forest restoration exerted significant effects on fungal composition and diversity. The positive effects of microbial biomass carbon, readily oxidizable carbon, and soil water content explained 11.5%, 9.6%, and 9.1% of the variations in fungal community composition, respectively. In contrast, microbial biomass carbon (40.0%), readily oxidizable carbon (14.0%), and total nitrogen (13.6%) negatively contributed to the variations in fungal community diversity. Our data suggested that the changes in fungal composition and diversity during tropical forest restoration were primarily mediated by the positive or negative impacts of soil carbon and nitrogen pools.
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Affiliation(s)
- Xiaofei Guo
- College of Ecology and Environment, Southwest Forestry University, Kunming 650224, China; (X.G.)
- College of Water Conservancy, Yunnan Agricultural University, Kunming 650201, China
| | - Shaojun Wang
- College of Ecology and Environment, Southwest Forestry University, Kunming 650224, China; (X.G.)
| | - Chen Wang
- College of Ecology and Environment, Southwest Forestry University, Kunming 650224, China; (X.G.)
| | - Mengjie Lan
- College of Ecology and Environment, Southwest Forestry University, Kunming 650224, China; (X.G.)
| | - Shengqiu Yang
- College of Ecology and Environment, Southwest Forestry University, Kunming 650224, China; (X.G.)
| | - Shuang Luo
- College of Ecology and Environment, Southwest Forestry University, Kunming 650224, China; (X.G.)
| | - Rui Li
- College of Ecology and Environment, Southwest Forestry University, Kunming 650224, China; (X.G.)
| | - Jiahui Xia
- College of Ecology and Environment, Southwest Forestry University, Kunming 650224, China; (X.G.)
| | - Bo Xiao
- College of Ecology and Environment, Southwest Forestry University, Kunming 650224, China; (X.G.)
| | - Lingling Xie
- College of Ecology and Environment, Southwest Forestry University, Kunming 650224, China; (X.G.)
| | - Zhengjun Wang
- College of Ecology and Environment, Southwest Forestry University, Kunming 650224, China; (X.G.)
| | - Zhipeng Guo
- College of Ecology and Environment, Southwest Forestry University, Kunming 650224, China; (X.G.)
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Yu Y, Li X, Fan H, Li Y, Yao H. Dose effect of polyethylene microplastics on nitrous oxide emissions from paddy soils cultivated for different periods. JOURNAL OF HAZARDOUS MATERIALS 2023; 453:131445. [PMID: 37088019 DOI: 10.1016/j.jhazmat.2023.131445] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/04/2023] [Accepted: 04/17/2023] [Indexed: 05/03/2023]
Abstract
The presence of microplastics (MPs) under flooded conditions is beneficial for nitrifiers and denitrifiers to produce nitrous oxide (N2O), but their dose effect remains unclear. This study evaluated the impact of different doses of polyethylene (PE) MPs on the release of N2O from paddy soils cultivated for different years. Compared with unpolluted soils, low doses of MPs (≤ 0.1%) had a negligible influence on N2O emissions, and high amounts of MPs (≥ 0.5%) significantly (p < 0.05) increased N2O emissions from the paddy soils cultivated for 3, 15 and 40 years by 2.5-4.3, 3.9-8.5 and 8.9-27.7 times, respectively. Moreover, an exponential model indicated that a 0.2% concentration of PE MPs appeared to be the dose threshold that accelerated the release of N2O from the all soils. Increased MP concentrations accelerated N2O emissions by affecting microbial functional genes involved in N2O production and reduction, but microbial taxonomic attributes involved in nitrogen cycling played an insignificant role in controlling N2O emissions. Overall, our results indicated that high doses (≥ 0.5%) of PE MPs essentially accelerated the emission of N2O from rice soils, and a longer cultivation period (40 years) enhanced the positive effect of MPs on N2O emissions.
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Affiliation(s)
- Yongxiang Yu
- Research Center for Environmental Ecology and Engineering, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, 206 Guanggu 1st Road, Wuhan 430205, PR China
| | - Xing Li
- Research Center for Environmental Ecology and Engineering, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, 206 Guanggu 1st Road, Wuhan 430205, PR China
| | - Haoxin Fan
- Research Center for Environmental Ecology and Engineering, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, 206 Guanggu 1st Road, Wuhan 430205, PR China
| | - Yaying Li
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, PR China
| | - Huaiying Yao
- Research Center for Environmental Ecology and Engineering, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, 206 Guanggu 1st Road, Wuhan 430205, PR China; Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, PR China.
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Qu ZL, Braima A, Liu B, Ma Y, Sun H. Soil Fungal Community Structure and Function Shift during a Disease-Driven Forest Succession. Microbiol Spectr 2022; 10:e0079522. [PMID: 36073819 PMCID: PMC9602832 DOI: 10.1128/spectrum.00795-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 08/05/2022] [Indexed: 12/30/2022] Open
Abstract
Forest succession is important for sustainable forest management in terrestrial ecosystems. However, knowledge about the response of soil microbes to forest disease-driven succession is limited. In this study, we investigated the soil fungal biomass, soil enzyme activity, and fungal community structure and function in forests suffering succession processes produced by pine wilt disease from conifer to broadleaved forests using Illumina Miseq sequencing coupled with FUNGuild analysis. The results showed that the broadleaved forest had the highest fungal biomass and soil enzyme activities in C, N, and S cycles, whereas the conifer forest had the highest enzyme activity in the P cycle. Along the succession, the fungal diversity and richness significantly increased (P < 0.05). The fungal communities were dominated by Ascomycota (42.0%), Basidiomycota (38.0%), and Mortierellomycota (9.5%), among which the abundance of Ascomycota significantly increased (P < 0.05), whereas that of Basidiomycota and Mortierellomycota decreased (P < 0.05). The abundance of species Mortierella humilis, Lactarius salmonicolor, and Russula sanguinea decreased, whereas that of Mortierella minutissima increased (P < 0.05). The forests in different succession stages formed distinct fungal communities and functional structures (P < 0.05). Functionally, the saprotrophs, symbiotrophs, and pathotrophs were the dominant groups in the conifer, mixed, and broadleaved forests, respectively. Soil pH and soil organic carbon were the key factors influencing the fungal community and functional structures during the succession. These findings provide useful information for better understanding the plant-microbe interaction during forest succession caused by forest disease. IMPORTANCE The studies on soil fungal communities in disease-driven forest succession are rare. This study showed that during the disease-driven forest succession, the soil enzyme activity, soil fungal diversity, and biomass increased along succession. The disease-driven forest succession changed the soil fungal community structure and function, in which the symbiotrophs were the most dominant group along the succession. These findings provide useful information for better understanding the plant-microbe interaction during forest succession caused by forest disease.
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Affiliation(s)
- Zhao-lei Qu
- Collaborative Innovation Center of Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Ahmed Braima
- Collaborative Innovation Center of Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Bing Liu
- Collaborative Innovation Center of Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
- Yangzhou Polytechnic College, Yangzhou, China
| | - Yang Ma
- Collaborative Innovation Center of Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Hui Sun
- Collaborative Innovation Center of Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
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Kang Z, Li X, Li Y, Ye L, Zhang B, Zhang X, Penttinen P, Gu Y. Black Truffles Affect Quercus aliena Physiology and Root-Associated nirK- and nirS-Type Denitrifying Bacterial Communities in the Initial Stage of Inoculation. Front Microbiol 2022; 13:792568. [PMID: 35572648 PMCID: PMC9096950 DOI: 10.3389/fmicb.2022.792568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 03/22/2022] [Indexed: 11/29/2022] Open
Abstract
Truffles (Tuber spp.) are edible ectomycorrhizal fungi with high economic value. Bacteria in ectomycorrhizosphere soils are considered to be associated with the nutrient uptake of truffles and hosts. Whether Tuber spp. inoculation can affect the growth of Quercus aliena, the ectomycorrhizosphere soil, and the rhizosphere nirK and nirS-denitrifier communities at the ectomycorrhizae formation stage is still unclear. Therefore, we inoculated Q. aliena with the black truffles Tuber melanosporum and Tuber indicum, determined the physiological activity and morphological indices of Q. aliena seedlings, analyzed the physicochemical properties of ectomycorrhizosphere soils, and applied DNA sequencing to assess the nirK and nirS- denitrifier community structure in ectomycorrhizosphere soils. Peroxidase activity was higher in the seedlings inoculated with T. melanosporum than in the T. indicum inoculation and uninoculated control treatments. The available phosphorus contents were lower and nitrate contents were higher in those with truffle inoculation, and T. melanosporum treatment differed more from the control than the T. indicum treatment. The richness of the nirK-community was highest in the T. indicum treatment and lowest in the uninoculated treatment. The differences in nirK-community composition across treatments were not statistically significant, but the nirS communities were different. The nirS-type bacteria correlated with three environmental factors (pH, available phosphorus, and nitrate contents), whereas the nirK-type bacteria were only associated with the nitrate contents. Generally, this work revealed that inoculation with Tuber spp. would change a few nutrient contents and richness of nirK-type bacteria and had little effects on growth of Q. aliena seedlings in the initial stage of inoculation. The results of this study may provide in-depth insights into the relationships between Tuber spp. and hosts, which should be taken into account when developing truffle production methods.
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Affiliation(s)
- Zongjing Kang
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
- Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Xiaolin Li
- Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Yan Li
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Lei Ye
- Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Bo Zhang
- Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Xiaoping Zhang
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
- Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Petri Penttinen
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
- Ecosystems and Environment Research Programme, University of Helsinki, Helsinki, Finland
| | - Yunfu Gu
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
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Zhang C, Zhou X, Wang X, Ge J, Cai B. Elaeagnus angustifolia can improve salt-alkali soil and the health level of soil: Emphasizing the driving role of core microbial communities. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 305:114401. [PMID: 34974219 DOI: 10.1016/j.jenvman.2021.114401] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 12/23/2021] [Accepted: 12/26/2021] [Indexed: 06/14/2023]
Abstract
Saline-alkali environments are widely distributed in China and significantly hinder the development of agriculture. This study characterizes the long-term effects of planting Elaeagnus angustifolia (E. angustifolia) on the physical and chemical properties, enzyme activities and microbial community characteristics of saline-alkali soil in the Songnen Plain (1, 2 and 3 years). The results showed that planting E. angustifolia reduced soil pH and electrical conductivity (EC) and increased soil total phosphorus (TP), total nitrogen (TN), nitrate nitrogen (Nni), total potassium (TK), dissolved organic C (DOC), dissolved organic matter (DOM) and available potassium (AK) content and catalase, urease, polyphenol oxidase, phosphatase, sucrase and cellulase enzyme activities, and the results peaked in the 3 year. High-throughput sequencing showed that the bacterial abundance and diversity were as follows (from high to low) y3 > y2 > y1 > CK. E. angustifolia resulted in an increase in the relative abundance of the dominant bacteria. Proteobacteria and Pseudomonas were the major phylum and genus, respectively. Redundancy analysis showed that changes in the soil microbial community significantly affect the physical and chemical properties of the soil, with Proteobacteria members being the key microorganisms that reduce soil salinity. Network analysis showed that Pseudomonas (Proteobacteria) participated in the synthesis of key soil enzymes. 16S rRNA sequencing predicted that the expression of genes related to carbon (rbcL, acsA, acsB, Pcc and accA) and nitrogen (amoA/B, nxrA, hao, gdh, ureC and nosZ) transformation increased, and Pseudomonas members were key regulators of carbon and nitrogen dynamics. In conclusion, the planting of E. angustifolia could improve the physical and chemical properties of the soil by releasing root exudates into the soil and increasing the diversity and richness of soil microbial communities to improve saline-alkali soil, providing a theoretical basis for improving saline-alkali soil and promoting the sustainable development of modern agriculture.
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Affiliation(s)
- Chi Zhang
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin, 150500, China; Key Laboratory of Microbiology, College of Heilongjiang Province, School of Life Sciences, Heilongjiang University, Harbin, 150080, China
| | - Xiaohang Zhou
- College of Basic Medicine, Mudanjiang Medical University, Mudanjiang, 157000, China
| | - Xiaoyu Wang
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin, 150500, China; Key Laboratory of Microbiology, College of Heilongjiang Province, School of Life Sciences, Heilongjiang University, Harbin, 150080, China
| | - Jingping Ge
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin, 150500, China; Key Laboratory of Microbiology, College of Heilongjiang Province, School of Life Sciences, Heilongjiang University, Harbin, 150080, China.
| | - Baiyan Cai
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin, 150500, China; Key Laboratory of Microbiology, College of Heilongjiang Province, School of Life Sciences, Heilongjiang University, Harbin, 150080, China.
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Enhancement of nitrous oxide emissions in soil microbial consortia via copper competition between proteobacterial methanotrophs and denitrifiers. Appl Environ Microbiol 2020; 87:e0230120. [PMID: 33355098 DOI: 10.1128/aem.02301-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Unique means of copper scavenging have been identified in proteobacterial methanotrophs, particularly the use of methanobactin, a novel ribosomally synthesized post-translationally modified polypeptide that binds copper with very high affinity. The possibility that copper sequestration strategies of methanotrophs may interfere with copper uptake of denitrifiers in situ and thereby enhance N2O emissions was examined using a suite of laboratory experiments performed with rice paddy microbial consortia. Addition of purified methanobactin from Methylosinus trichosporium OB3b to denitrifying rice paddy soil microbial consortia resulted in substantially increased N2O production, with more pronounced responses observed for soils with lower copper content. The N2O emission-enhancing effect of the soil's native mbnA-expressing Methylocystaceae methanotrophs on the native denitrifiers was then experimentally verified with a Methylocystaceae-dominant chemostat culture prepared from a rice paddy microbial consortium as the inoculum. Lastly, with microcosms amended with varying cell numbers of methanobactin-producing Methylosinus trichosporium OB3b before CH4 enrichment, microbiomes with different ratios of methanobactin-producing Methylocystaceae to gammaproteobacterial methanotrophs incapable of methanobactin production were simulated. Significant enhancement of N2O production from denitrification was evident in both Methylocystaceae-dominant and Methylococcaceae-dominant enrichments, albeit to a greater extent in the former, signifying the comparative potency of methanobactin-mediated copper sequestration while implying the presence of alternative copper abstraction mechanisms for Methylococcaceae These observations support that copper-mediated methanotrophic enhancement of N2O production from denitrification is plausible where methanotrophs and denitrifiers cohabit.IMPORTANCE Proteobacterial methanotrophs, groups of microorganisms that utilize methane as source of energy and carbon, have been known to utilize unique mechanisms to scavenge copper, namely utilization of methanobactin, a polypeptide that binds copper with high affinity and specificity. Previously the possibility that copper sequestration by methanotrophs may lead to alteration of cuproenzyme-mediated reactions in denitrifiers and consequently increase emission of potent greenhouse gas N2O has been suggested in axenic and co-culture experiments. Here, a suite of experiments with rice paddy soil slurry cultures with complex microbial compositions were performed to corroborate that such copper-mediated interplay may actually take place in environments co-habited by diverse methanotrophs and denitrifiers. As spatial and temporal heterogeneity allow for spatial coexistence of methanotrophy (aerobic) and denitrification (anaerobic) in soils, the results from this study suggest that this previously unidentified mechanism of N2O production may account for significant proportion of N2O efflux from agricultural soils.
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Voegel TM, Larrabee MM, Nelson LM. Development of droplet digital PCR assays to quantify genes involved in nitrification and denitrification, comparison with quantitative real-time PCR and validation of assays in vineyard soil. Can J Microbiol 2020; 67:174-187. [PMID: 32910858 DOI: 10.1139/cjm-2020-0033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Quantifying genes in soil is important to relate the abundance of soil bacteria to biogeochemical cycles. Quantitative real-time PCR is widely used for quantification, but its use with environmental samples is limited by poor reaction efficiencies or by PCR inhibition through co-purified soil substances. Droplet digital PCR (ddPCR) is a technology for absolute, sensitive quantification of genes. This study optimized eight ddPCR assays to quantify total bacteria and archaea as well as the nitrification (bacterial and archaeal amoA) and denitrification (nirS, nirK, nosZI, nosZII) genes involved in the generation or reduction of the greenhouse gas nitrous oxide. Detection and quantification thresholds were compared with those of quantitative real-time PCR and were equal to, or improved, in ddPCR. To validate the assays using environmental samples, soil DNA was isolated from two vineyards in the Okanagan valley in British Columbia, Canada, over the 2017 growing season. Soil properties related to the observed gene abundances were determined. Total bacteria, nirK, and nosZII increased with time and the soil C/N ratio and NH4+-N concentration affected total archaea and archaeal amoA negatively. The results, compared with those of other studies, showed that ddPCR is a valid alternative to qPCR to quantify genes involved in nitrification or denitrification.
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Affiliation(s)
- Tanja M Voegel
- Irving K. Barber Faculty of Science, Department of Biology, University of British Columbia Okanagan, 1177 Research Road, Kelowna, BC V1V 1V7, Canada.,Irving K. Barber Faculty of Science, Department of Biology, University of British Columbia Okanagan, 1177 Research Road, Kelowna, BC V1V 1V7, Canada
| | - Melissa M Larrabee
- Irving K. Barber Faculty of Science, Department of Biology, University of British Columbia Okanagan, 1177 Research Road, Kelowna, BC V1V 1V7, Canada.,Irving K. Barber Faculty of Science, Department of Biology, University of British Columbia Okanagan, 1177 Research Road, Kelowna, BC V1V 1V7, Canada
| | - Louise M Nelson
- Irving K. Barber Faculty of Science, Department of Biology, University of British Columbia Okanagan, 1177 Research Road, Kelowna, BC V1V 1V7, Canada.,Irving K. Barber Faculty of Science, Department of Biology, University of British Columbia Okanagan, 1177 Research Road, Kelowna, BC V1V 1V7, Canada
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10
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Zhang H, Sun H, Zhou S, Bai N, Zheng X, Li S, Zhang J, Lv W. Effect of Straw and Straw Biochar on the Community Structure and Diversity of Ammonia-oxidizing Bacteria and Archaea in Rice-wheat Rotation Ecosystems. Sci Rep 2019; 9:9367. [PMID: 31249385 PMCID: PMC6597706 DOI: 10.1038/s41598-019-45877-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 06/11/2019] [Indexed: 01/27/2023] Open
Abstract
Ammonia oxidation is the first and rate-limiting step of nitrification, driven by ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA). Straw and straw biochar retention are the popular ways to utilize the agricultural by-products in China, but their long-term effects on AOB and AOA still remain poorly understood. Based on a 7-year plot experiment, which had 4 fertilization regimes: no fertilizer (CK), regular fertilization (RT), straw retention (SR) and straw biochar retention (SB), the abundance and the composition of AOB and AOA was investigated before both the harvest of rice and wheat season by quantitative PCR and 454 high-throughput pyrosequencing, respectively. (1) Compared to RT, straw and straw biochar increased AOB abundance and diversity significantly only in wheat season (P < 0.05), and they both ranked as SB > SR > RT. Among fertilized treatments, a significant difference between SR and RT was found in AOB community composition of the winter season (R value = 0.58, P value = 0.02); (2) In contrast, AOA was almost not responsive to organic addition, except the significant enhancement of abundance by biochar in wheat season; (3) After straw and straw biochar addition, soil potential nitrification rates (PNR) was positive correlated to AOB abundance in both rice and wheat season (P < 0.01), not to AOA abundance (P = 0.211 and 0.068, respectively). This study provides scientific support for the potential of straw utilization to improve nitrification in rice-wheat rotation system with respect to soil ammonia oxidation microorganism.
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Affiliation(s)
- Hanlin Zhang
- Eco-environmental Protection Institute, Shanghai Academy of Agricultural Science, Shanghai, 201403, China.,Agricultural Environment and Farmland Conservation Experiment Station of Ministry Agriculture, Shanghai, 201403, China.,Shanghai Key Laboratory of Horticultural Technology, Shanghai, 201403, China.,Shanghai Engineering Research Center of Low-carbon Agriculture, Shanghai, 201415, China
| | - Huifeng Sun
- Eco-environmental Protection Institute, Shanghai Academy of Agricultural Science, Shanghai, 201403, China.,Shanghai Engineering Research Center of Low-carbon Agriculture, Shanghai, 201415, China
| | - Sheng Zhou
- Eco-environmental Protection Institute, Shanghai Academy of Agricultural Science, Shanghai, 201403, China.,Shanghai Engineering Research Center of Low-carbon Agriculture, Shanghai, 201415, China
| | - Naling Bai
- Eco-environmental Protection Institute, Shanghai Academy of Agricultural Science, Shanghai, 201403, China.,Agricultural Environment and Farmland Conservation Experiment Station of Ministry Agriculture, Shanghai, 201403, China
| | - Xianqing Zheng
- Eco-environmental Protection Institute, Shanghai Academy of Agricultural Science, Shanghai, 201403, China.,Agricultural Environment and Farmland Conservation Experiment Station of Ministry Agriculture, Shanghai, 201403, China
| | - Shuangxi Li
- Eco-environmental Protection Institute, Shanghai Academy of Agricultural Science, Shanghai, 201403, China.,Agricultural Environment and Farmland Conservation Experiment Station of Ministry Agriculture, Shanghai, 201403, China
| | - Juanqin Zhang
- Eco-environmental Protection Institute, Shanghai Academy of Agricultural Science, Shanghai, 201403, China.,Agricultural Environment and Farmland Conservation Experiment Station of Ministry Agriculture, Shanghai, 201403, China
| | - Weiguang Lv
- Eco-environmental Protection Institute, Shanghai Academy of Agricultural Science, Shanghai, 201403, China. .,Agricultural Environment and Farmland Conservation Experiment Station of Ministry Agriculture, Shanghai, 201403, China. .,Shanghai Key Laboratory of Horticultural Technology, Shanghai, 201403, China. .,Shanghai Engineering Research Center of Low-carbon Agriculture, Shanghai, 201415, China.
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11
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Chai Y, Cao Y, Yue M, Tian T, Yin Q, Dang H, Quan J, Zhang R, Wang M. Soil Abiotic Properties and Plant Functional Traits Mediate Associations Between Soil Microbial and Plant Communities During a Secondary Forest Succession on the Loess Plateau. Front Microbiol 2019; 10:895. [PMID: 31105679 PMCID: PMC6499021 DOI: 10.3389/fmicb.2019.00895] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 04/08/2019] [Indexed: 11/13/2022] Open
Abstract
In the context of secondary forest succession, aboveground-belowground interactions are known to affect the dynamics and functional structure of plant communities. However, the links between soil microbial communities, soil abiotic properties, plant functional traits in the case of semi-arid and arid ecosystems, are unclear. In this study, we investigated the changes in soil microbial species diversity and community composition, and the corresponding effects of soil abiotic properties and plant functional traits, during a ≥150-year secondary forest succession on the Loess Plateau, which represents a typical semi-arid ecosystem in China. Plant community fragments were assigned to six successional stages: 1-4, 4-8, 8-15, 15-50, 50-100, and 100-150 years after abandonment. Bacterial and fungal communities were analyzed by high-throughput sequencing of the V4 hypervariable region of the 16S rRNA gene and the internal transcribed spacer (ITS2) region of the rRNA operon, respectively. A multivariate variation-partitioning approach was used to estimate the contributions of soil properties and plant traits to the observed microbial community composition. We found considerable differences in bacterial and fungal community compositions between the early (S1-S3) and later (S4-S6) successional stages. In total, 18 and 12 unique families were, respectively, obtained for bacteria and fungi, as indicators of microbial community succession across the six stages. Bacterial alpha diversity was positively correlated with plant species alpha diversity, while fungal diversity was negatively correlated with plant species diversity. Certain fungal and bacterial taxa appeared to be associated with the occurrence of dominant plant species at different successional stages. Soil properties (pH, total N, total C, NH4-N, NO3-N, and PO4-P concentrations) and plant traits explained 63.80% and 56.68% of total variance in bacterial and fungal community compositions, respectively. These results indicate that soil microbial communities are coupled with plant communities via the mediation of microbial species diversity and community composition over a long-term secondary forest succession in the semi-arid ecosystem. The bacterial and fungal communities show distinct patterns in response to plant community succession, according to both soil abiotic properties and plant functional traits.
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Affiliation(s)
- Yongfu Chai
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi’an, China
- School of Life Sciences, Northwest University, Xi’an, China
| | - Ying Cao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi’an, China
- School of Life Sciences, Northwest University, Xi’an, China
| | - Ming Yue
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi’an, China
- School of Life Sciences, Northwest University, Xi’an, China
| | - Tingting Tian
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi’an, China
- School of Life Sciences, Northwest University, Xi’an, China
| | - Qiulong Yin
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi’an, China
- School of Life Sciences, Northwest University, Xi’an, China
| | - Han Dang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi’an, China
- School of Life Sciences, Northwest University, Xi’an, China
| | - Jiaxin Quan
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi’an, China
| | - Ruichang Zhang
- Department of Plant Ecology, University of Tübingen, Tübingen, Germany
| | - Mao Wang
- College of Grassland and Environment Sciences, Xinjiang Agricultural University, Ürümqi, China
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12
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Zhang Y, Li Q, Chen Y, Dai Q, Hu J. Mudflat reclamation causes changes of gene abundance in nitrogen cycle under long-term rice cultivation. J Basic Microbiol 2019; 59:496-503. [PMID: 30900740 DOI: 10.1002/jobm.201800660] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 02/14/2019] [Accepted: 03/04/2019] [Indexed: 11/09/2022]
Abstract
Rice cultivation is the main method for mudflat reclamation. However, changes in the community structure of microbes involved in nitrogen (N) cycling in response to mudflat reclamation via rice cultivation remain poorly understood. This study used quantitative polymerase chain reaction to characterize the distribution of various inorganic N-cycling pathways in response to mudflat reclamation via rice cultivation. The results show that the abundance of functional genes followed an increasing trend, while the relative abundance showed a decreasing trend. The relative richness of functional genes in the inorganic N-cycling network showed different fluctuation trends and indicated that the nifH, archaea amoA, narG, nirS, nirK, norB, and nosZ genes greatly contribute to inorganic N-cycling. Redundancy analysis showed that soil properties, in particular, organic matter increased, while electrical conductivity decreased, driving the changes of gene distribution in the inorganic N-cycling network over the course of reclamation. Mudflat reclamation under long-term rice cultivation promoted the reproduction of microbes related to the N cycle, and also changed the distribution of functional genes that are involved in the inorganic N cycle due to changes of soil properties.
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Affiliation(s)
- Yang Zhang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops/Research Institute of Rice Industry Engineering Technology, Yangzhou University, Yangzhou, PR China
| | - Qing Li
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops/Research Institute of Rice Industry Engineering Technology, Yangzhou University, Yangzhou, PR China
| | - Yinglong Chen
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops/Research Institute of Rice Industry Engineering Technology, Yangzhou University, Yangzhou, PR China
| | - Qigen Dai
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops/Research Institute of Rice Industry Engineering Technology, Yangzhou University, Yangzhou, PR China
| | - Jian Hu
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, PR China
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13
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Hammerl V, Kastl EM, Schloter M, Kublik S, Schmidt H, Welzl G, Jentsch A, Beierkuhnlein C, Gschwendtner S. Influence of rewetting on microbial communities involved in nitrification and denitrification in a grassland soil after a prolonged drought period. Sci Rep 2019; 9:2280. [PMID: 30783152 PMCID: PMC6381133 DOI: 10.1038/s41598-018-38147-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 12/18/2018] [Indexed: 11/11/2022] Open
Abstract
The frequency of extreme drought and heavy rain events during the vegetation period will increase in Central Europe according to future climate change scenarios, which will affect the functioning of terrestrial ecosystems in multiple ways. In this study, we simulated an extreme drought event (40 days) at two different vegetation periods (spring and summer) to investigate season-related effects of drought and subsequent rewetting on nitrifiers and denitrifiers in a grassland soil. Abundance of the microbial groups of interest was assessed by quantification of functional genes (amoA, nirS/nirK and nosZ) via quantitative real-time PCR. Additionally, the diversity of ammonia-oxidizing archaea was determined based on fingerprinting of the archaeal amoA gene. Overall, the different time points of simulated drought and rewetting strongly influenced the obtained response pattern of microbial communities involved in N turnover as well as soil ammonium and nitrate dynamics. In spring, gene abundance of nirS was irreversible reduced after drought whereas nirK and nosZ remained unaffected. Furthermore, community composition of ammonia-oxidizing archaea was altered by subsequent rewetting although amoA gene abundance remained constant. In contrast, no drought/rewetting effects on functional gene abundance or diversity pattern of nitrifying archaea were observed in summer. Our results showed (I) high seasonal dependency of microbial community responses to extreme events, indicating a strong influence of plant-derived factors like vegetation stage and plant community composition and consequently close plant-microbe interactions and (II) remarkable resistance and/or resilience of functional microbial groups involved in nitrogen cycling to extreme weather events what might indicate that microbes in a silty soil are better adapted to stress situations as expected.
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Affiliation(s)
- Verena Hammerl
- Research Unit Comparative Microbiome Analysis - Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
- Chair for Soil Ecology - Technische Universität München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Eva-Maria Kastl
- Research Unit Comparative Microbiome Analysis - Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Michael Schloter
- Research Unit Comparative Microbiome Analysis - Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Susanne Kublik
- Research Unit Comparative Microbiome Analysis - Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Holger Schmidt
- Institute of Natural Sciences - Universität Koblenz Landau, Campus Koblenz, Universitätsstraße 1, 56070, Koblenz, Germany
| | - Gerhard Welzl
- Research Unit Comparative Microbiome Analysis - Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Anke Jentsch
- Disturbance Ecology - University of Bayreuth, Universitätsstr. 30, 95447, Bayreuth, Germany
| | - Carl Beierkuhnlein
- Chair of Biogeography - University of Bayreuth, Universitätsstr. 30, 95447, Bayreuth, Germany
| | - Silvia Gschwendtner
- Research Unit Comparative Microbiome Analysis - Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.
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14
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Wells NS, Clough TJ, Johnson-Beebout SE, Elberling B, Baisden WT. Effects of denitrification and transport on the isotopic composition of nitrate (δ 18O, δ 15N) in freshwater systems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 651:2228-2234. [PMID: 30326455 DOI: 10.1016/j.scitotenv.2018.10.065] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 10/05/2018] [Accepted: 10/05/2018] [Indexed: 06/08/2023]
Abstract
Nitrate isotopes (δ15N-NO3- and δ18O-NO3-) are a potentially powerful tool for tracking the biological removal of reactive nitrogen (N) as it is transported from land to sea. However, uncertainties about, 1) the variability of the strength of biological isotopic fractionation during anaerobic benthic NO3- reduction (the kinetic enrichment factor: εdenit), and, 2) how accurately these εdenit values are expressed in overlying aerobic surface waters (the effective enrichment factor: εeff), currently limit their use in freshwater systems. Here we used a combination of incubation experiments and numerical modelling to construct a simple framework for defining freshwater εdenit based on interactions between benthic denitrification and diffusive transport to surface waters. Under non-limited, anaerobic conditions the εdenit values produced in submerged soils (n = 3) and sediments (n = 4) with denitrification rates between 10 and 600 mg N m-2 d-1 ranged from -3‰ to -28‰. Critically, model results indicated that diffusive transport would homogenise this to an effective fractionation range of -6 ± 4‰. Evidence for biological and hydrological variability of NO3- isotope fractionation means that values measured in aerobic surface water environments are most appropriately evaluated by a range of fractionation values, rather than commonly used single 'site specific' εdenit values.
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Affiliation(s)
- Naomi S Wells
- Department of Soil & Physical Sciences, Faculty of Agriculture & Life Sciences, P.O. Box 85084, Lincoln University, Lincoln 7647, New Zealand; Centre for Coastal Biogeochemistry, School of Environment, Science & Engineering, Southern Cross University, PO Box 157, Lismore 2480, NSW, Australia.
| | - Tim J Clough
- Department of Soil & Physical Sciences, Faculty of Agriculture & Life Sciences, P.O. Box 85084, Lincoln University, Lincoln 7647, New Zealand
| | - Sarah E Johnson-Beebout
- Crop and Environmental Science Division, International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Bo Elberling
- Department of Geosciences and Natural Resource Management, University of Copenhagen, DK-1350 Copenhagen, Denmark
| | - W Troy Baisden
- National Isotope Centre, GNS Science, 30 Gracefield Road, Gracefield, Lower Hutt 5010, New Zealand; Faculty of Science and Engineering, University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
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15
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Baker BH, Brooks JP, Deng DD, Smith RK, Kröger R, Prince Czarnecki JM. Effects of Low-Grade Weirs on Soil Microbial Communities in Agricultural Drainage Ditches. JOURNAL OF ENVIRONMENTAL QUALITY 2018; 47:1155-1162. [PMID: 30272767 DOI: 10.2134/jeq2017.12.0489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Agricultural fertilizer application throughout the Mississippi River basin has been identified as a major source of N pollution to the Gulf of Mexico. Using best management practices, such as low-grade weirs, has been identified as a potential solution to mitigate nutrient loads in agricultural runoff. This study assessed impacts of weir implementation in four agricultural drainage ditches (three with weirs and one control site) in the Mississippi Delta. Soil samples collected from field locations in spring 2013 were analyzed for denitrifier abundance using genes (16s ribosomal RNA [rRNA] genes, , , and ) via quantitative polymerase chain reaction (qPCR), microbial community profiles via terminal-restriction fragment length polymorphism (T-RFLP) of 16s rRNA genes, soil parameters (C, N, and moisture), and vegetation presence at sample locations. Gene quantification was successful, except for , which was found below detection limits (5000 gene copies g soil). Distance from weirs was negatively correlated with 16S rRNA genes and soil moisture, and soil moisture was positively correlated with 16s rRNA and S gene abundance. Results of empirical Bayesian kriging did not exhibit obvious patterns of microbial diversity in relation to weir proximity. Preliminary assessment of seasonal trends showed genes 16s rRNA and , soil N, and mean T-RF values to be greater in fall than in spring. Results highlight that weirs had no direct impact on microbial diversity or denitrification functional gene abundance. Correlations between microbial measures and environmental parameters suggest that adequate management of N runoff from agricultural landscapes will require ecological engineering beyond weirs to optimize N mitigation.
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16
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Cui J, Li Y, Wang C, Kim KS, Wang T, Liu S. Characteristics of the rhizosphere bacterial community across different cultivation years in saline-alkaline paddy soils of Songnen Plain of China. Can J Microbiol 2018; 64:925-936. [PMID: 30114373 DOI: 10.1139/cjm-2017-0752] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The characteristics of the rhizosphere microbial community across different cultivation years (from 1, 3, 5, 15, 20, and 50 years) in saline-alkaline paddy soils in Songnen Plain of China were investigated based on sequence variation of 16S rDNA using Illumina MiSeq sequencing. The results showed that the microbial community diversity varied across cultivation years, showing higher diversity in cultivation years >15 than in cultivation years <15. The dominant microbial community of the rhizosphere was mainly composed of Proteobacteria, Acidobacteria, Firmicutes, and Bacteroidetes. Furthermore, soil microbial diversity appeared to be affected directly by changes in soil properties corresponding to cultivated years. Diversity of Proteobacteria decreased as cultivated years increased; however, that of Acidobacteria showed the opposite direction. In addition, the soil microbial communities were clustered into two main groups: one from the sites cultivated for fewer than 15 years, and the other from the sites cultivated for more than 15 years. The abundance of nitrogen-fixing microorganisms in the soil sample was significantly higher in soils cultivated for under 15 years than in those cultivated for over 15 years (P < 0.05). Moreover, there was an obvious negative correlation between the cultivated years and Methanosarcina. Our findings on the dynamics of microbial community and its specific function in response to variable soil conditions are important for understanding and improving physical and chemical characteristics of saline-alkaline soil in Songnen Plain of China.
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Affiliation(s)
- Juntao Cui
- a College of Resources and Environment, Jilin Agricultural University, Changchun 130118, People's Republic of China
| | - Yanan Li
- a College of Resources and Environment, Jilin Agricultural University, Changchun 130118, People's Republic of China.,b Jilin Provincial Academy of Forestry Science, Changchun 130118, People's Republic of China
| | - Chengyu Wang
- a College of Resources and Environment, Jilin Agricultural University, Changchun 130118, People's Republic of China
| | - Kyung Seok Kim
- c Department of Natural Resource Ecology and Management, Iowa State University, Ames, IA 500011, USA
| | - Tianye Wang
- a College of Resources and Environment, Jilin Agricultural University, Changchun 130118, People's Republic of China
| | - Shuxia Liu
- a College of Resources and Environment, Jilin Agricultural University, Changchun 130118, People's Republic of China
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17
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Compositional and abundance changes of nitrogen-cycling genes in plant-root microbiomes along a salt marsh chronosequence. Antonie Van Leeuwenhoek 2018; 111:2061-2078. [PMID: 29846874 DOI: 10.1007/s10482-018-1098-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 05/14/2018] [Indexed: 10/14/2022]
Abstract
Disentangling the relative influences of soil properties and plant-host on root-associated microbiomes in natural systems is challenging, given that spatially segregated soil types display distinct historical legacies. In addition, distant locations may also lead to biogeographical patterns of microbial communities. Here, we used an undisturbed salt marsh chronosequence spanning over a century of ecosystem development to investigate changes in the community composition and abundance of a set of nitrogen-cycling genes. Specifically, we targeted genes of diazotrophs and ammonia oxidizers associated with the bulk and rhizosphere soil of the plant species Limonium vulgare. Samples were collected across five distinct successional stages of the chronosequence (ranging from 5 to 105 years) at two time-points. Our results indicate that soil variables such as sand:silt:clay % content and pH strongly relates to the abundance of N-cycling genes in the bulk soil. However, in the rhizosphere samples, the abundance of ammonia-oxidizing organisms (both bacteria and archaea, AOB and AOA, respectively) was relatively constant across most of the successional stages, albeit displaying seasonal variation. This result indicates a potentially stronger control of plant host (rather than soil) on the abundance of these organisms. Interestingly, the plant host did not have a significant effect on the composition of AOA and AOB communities, being mostly divergent according to soil successional stages. The abundance of diazotrophic communities in rhizosphere samples was more affected by seasonality than those of bulk soil. Moreover, the abundance pattern of diazotrophs in the rhizosphere related to the systematic increase of plant biomass and soil organic matter along the successional gradient. These results suggest a potential season-dependent regulation of diazotrophs exerted by the plant host. Overall, this study contributes to a better understanding of how the natural formation of a soil and host plants influence the compositional and abundance changes of nitrogen-cycling genes in bulk and rhizosphere soil microhabitats.
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18
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Abstract
Ammonia oxidation is crucial in nitrogen removal and global nitrogen dynamics since it is the first step of the nitrification process. In this review, we focus on the distribution and community structure of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in East Asian paddy soils with variable soil properties. The available East Asian paddy soil data shows that the ammonium concentration and pH ranges from 0.4 to 370 mg/kg and 5.1 to 8.2, respectively. Our meta-analysis suggest that AOA specific gene sequences are generally more abundant than those of AOB in both acidic and alkaline paddy soils, where Nitrosophaera and Nitrosospira amoA clusters mainly dominate the microbial community, respectively. In addition, the contribution of ammonia oxidizers to the nitrification process has been demonstrated using DNA-SIP (DNA-based stable-isotope probing); the results of these studies indicate that pH is the most important factor in niche separation of AOA and AOB under a variety of edaphic conditions. Finally, we discuss a number of other environmental variables that affect the abundance, distribution, and activity of AOA and AOB in East Asian paddy soils.
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Yasuda T, Waki M, Fukumoto Y, Hanajima D, Kuroda K, Suzuki K. Characterization of the denitrifying bacterial community in a full-scale rockwool biofilter for compost waste-gas treatment. Appl Microbiol Biotechnol 2017; 101:6779-6792. [DOI: 10.1007/s00253-017-8398-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 05/22/2017] [Accepted: 06/16/2017] [Indexed: 11/29/2022]
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20
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A buried Neolithic paddy soil reveals loss of microbial functional diversity after modern rice cultivation. Sci Bull (Beijing) 2016. [DOI: 10.1007/s11434-016-1112-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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21
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Cultivable endophytic bacteria from heavy metal(loid)-tolerant plants. Arch Microbiol 2016; 198:941-956. [PMID: 27290648 DOI: 10.1007/s00203-016-1252-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 05/22/2016] [Accepted: 06/01/2016] [Indexed: 01/28/2023]
Abstract
To evaluate the interactions among endophytes, plants and heavy metal/arsenic contamination, root endophytic bacteria of Prosopis laevigata (Humb and Bonpl. ex Willd) and Sphaeralcea angustifolia grown in a heavy metal(loid)-contaminated zone in San Luis Potosi, Mexico, were isolated and characterized. Greater abundance and species richness were found in Prosopis than in Sphaeralcea and in the nutrient Pb-Zn-rich hill than in the poor nutrient and As-Cu-rich mine tailing. The 25 species identified among the 60 isolates formed three groups in the correspondence analysis, relating to Prosopis/hill (11 species), Prosopis/mine tailing (4 species) and Sphaeralcea/hill (4 species), with six species ungrouped. Most of the isolates showed high or extremely high resistance to arsenic, such as ≥100 mM for As(V) and ≥20 mM for As(III), in mineral medium. These results demonstrated that the abundance and community composition of root endophytic bacteria were strongly affected by the concentration and type of the heavy metals and metalloids (arsenic), as well as the plant species.
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22
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Microbial Nitrogen-Cycle Gene Abundance in Soil of Cropland Abandoned for Different Periods. PLoS One 2016; 11:e0154697. [PMID: 27140199 PMCID: PMC4854452 DOI: 10.1371/journal.pone.0154697] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 04/18/2016] [Indexed: 11/22/2022] Open
Abstract
In Inner Mongolia, steppe grasslands face desertification or degradation because of human overuse and abandonment after inappropriate agricultural management. The soils in these abandoned croplands exist in heterogeneous environments characterized by widely fluctuating microbial growth. Quantitative polymerase chain reaction analysis of microbial genes encoding proteins involved in the nitrogen cycle was used to study Azotobacter species, nitrifiers, and denitrifiers in the soils from steppe grasslands and croplands abandoned for 2, 6, and 26 years. Except for nitrifying archaea and nitrous oxide-reducing bacteria, the relative genotypic abundance of microbial communities involved in nitrogen metabolism differed by approximately 2- to 10-fold between abandoned cropland and steppe grassland soils. Although nitrogen-cycle gene abundances varied with abandonment time, the abundance patterns of nitrogen-cycle genes separated distinctly into abandoned cropland versus light-grazing steppe grassland, despite the lack of any cultivation for over a quarter-century. Plant biomass and plant diversity exerted a significant effect on the abundance of microbial communities that mediate the nitrogen cycle (P < 0.002 and P < 0.03, respectively). The present study elucidates the ecology of bacteria that mediate the nitrogen cycle in recently abandoned croplands.
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Is plant evolutionary history impacting recruitment of diazotrophs and nifH expression in the rhizosphere? Sci Rep 2016; 6:21690. [PMID: 26902960 PMCID: PMC4763242 DOI: 10.1038/srep21690] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 01/26/2016] [Indexed: 11/23/2022] Open
Abstract
Plant evolutionary history influences the taxonomic composition of the root-associated bacterial community, but whether it can also modulate its functioning is unknown. Here, we tested the hypothesis that crop diversification is a significant factor determining the ecology of the functional group of nitrogen-fixing bacteria the rhizosphere of Poaceae. A greenhouse experiment was carried out using a range of Poaceae, i.e. four Zea mays varieties (from two genetic groups) and teosinte (representing maize’s ancestor), sorghum (from the same Panicoideae subfamily), and wheat (from neighboring Pooideae subfamily), as well as the dicot tomato as external reference. Diazotroph rhizosphere community was characterized at 21 days in terms of size (quantitative PCR of nifH genes), composition (T-RFLP and partial sequencing of nifH alleles) and functioning (quantitative RT-PCR, T-RFLP and partial sequencing of nifH transcripts). Plant species and varieties had a significant effect on diazotroph community size and the number of nifH transcripts per root system. Contrarily to expectations, however, there was no relation between Poaceae evolutionary history and the size, diversity or expression of the rhizosphere diazotroph community. These results suggest a constant selection of this functional group through evolution for optimization of nitrogen fixation in the rhizosphere.
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Wang H, Liao G, D'Souza M, Yu X, Yang J, Yang X, Zheng T. Temporal and spatial variations of greenhouse gas fluxes from a tidal mangrove wetland in Southeast China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:1873-1885. [PMID: 26408111 DOI: 10.1007/s11356-015-5440-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 09/15/2015] [Indexed: 06/05/2023]
Abstract
Tidal mangrove wetlands are a source of methane (CH4) and nitrous oxide (N2O); but considering the high productivity of mangroves, they represent a significant sink for carbon dioxide (CO2). An exotic plant Spartina alterniflora has invaded east China over the last few decades, threatening these coastal mangrove ecosystems. However, the atmospheric gas fluxes in mangroves are poorly characterized and the impact of biological invasion on greenhouse gas (GHG) fluxes in the wetland remains unclear. In this study, the temporal and spatial dynamics of key GHG fluxes (CO2, CH4, and N2O) at an unvegetated mudflat, cordgrass (S. alterniflora), and mangrove (Kandelia obovata) sites along an estuary of the Jiulong River in Southeast China were investigated over a 2-year period. The CO2 and CH4 fluxes demonstrated a seasonal and vegetation-dependent variation while N2O fluxes showed no such dependent pattern. Air temperature was the main factor influencing CO2 and CH4 fluxes. Cumulative global warming potential (GWP) ranked in the order of mangrove > cordgrass > mudflat and summer > spring > autumn > winter. Moreover, CH4 accounted for the largest proportion (68%) of GWP, indicating its dominant contribution to the warming potential in mangroves. Notwithstanding the lack of information on plant coverage, cordgrass invasion exhibited a minor influence on GHG emissions. These findings support the notion that mangrove forests are net accumulation sites for GHGs. As vegetation showed considerable effects on fluxes, more information about the significance of vegetation type with a special emphasis on the effects of invasive plants is crucial.
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Affiliation(s)
- Haitao Wang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, 361102, China
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China
| | - Guanshun Liao
- Suntar Membrane Technology (Xiamen) Co., Ltd., Suntar Park Zhongyacheng Xinglin, Xiamen, 361022, China
| | - Melissa D'Souza
- Department of Ecology and Evolution, University of Chicago, 1101 E 57th Street, Chicago, IL, 60637, USA
| | - Xiaoqing Yu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China
| | - Jun Yang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China
| | - Xiaoru Yang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China.
| | - Tianling Zheng
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, 361102, China.
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Baker BH, Kröger R, Brooks JP, Smith RK, Czarnecki JMP. Investigation of denitrifying microbial communities within an agricultural drainage system fitted with low-grade weirs. WATER RESEARCH 2015; 87:193-201. [PMID: 26414296 DOI: 10.1016/j.watres.2015.09.028] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 09/14/2015] [Accepted: 09/15/2015] [Indexed: 06/05/2023]
Abstract
Enhancing wetland characteristics in agricultural drainage ditches with the use of low-grade weirs, has been identified as a best management practice (BMP) to mitigate nutrient runoff from agriculture landscapes. A major objective of utilizing low-grade weirs as a BMP includes fostering environments suitable for the biogeochemical removal of nitrogen via denitrification. This study examined the spatial resolution of microbial communities involved in denitrification in agricultural drainage systems fitted with low-grade weirs. Appropriate sampling scales of microbial communities were investigated using 16S rRNA and denitrification functional genes nosZ, nirS, and nirK via quantitative polymerase chain reaction (qPCR) and terminal-restriction fragment length polymorphism (T-RFLP) analysis. Genes 16S rRNA, nosZ, and nirS were all successfully detected in soil samples, while nirK was below the detection limit throughout the study. Utilizing a combination of three sampling regimes (management, reach, catchment) was found to be effective in capturing microbial community patterns, as ANOVA results revealed nosZ gene abundance was significantly greater at the management rather than reach scale (p = 0.045; F = 3.311), although, no significant differences were observed in 16S rRNA or nirS between sampling scales (p > 0.05). A Pearson correlation matrix confirmed that 16S rRNA and nosZ gene abundances were positively correlated with soil carbon (C), nitrogen (N), and moisture, while nirS abundance was only positively correlated with soil C and soil moisture. This highlights the potential for wetland-like characteristics to be recovered in agricultural drainage systems, as weir proximity is observed to enhance soil moisture and conditions for N remediation. This study provides the basis for additional investigations of these unique environments in the Mississippi Alluvial Valley and a starting point for adaptive management to enhance agricultural drainage systems for microbial communities towards nutrient remediation goals.
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Affiliation(s)
- Beth H Baker
- Department of Wildlife, Fisheries and Aquaculture, MS, USA.
| | - Robert Kröger
- Department of Wildlife, Fisheries and Aquaculture, MS, USA
| | - John P Brooks
- United States Department of Agriculture-Agricultural Research Service, MS, USA
| | - Renotta K Smith
- United States Department of Agriculture-Agricultural Research Service, MS, USA
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Wang P, Liu Y, Li L, Cheng K, Zheng J, Zhang X, Zheng J, Joseph S, Pan G. Long-term rice cultivation stabilizes soil organic carbon and promotes soil microbial activity in a salt marsh derived soil chronosequence. Sci Rep 2015; 5:15704. [PMID: 26503629 PMCID: PMC4622084 DOI: 10.1038/srep15704] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 09/29/2015] [Indexed: 11/09/2022] Open
Abstract
Soil organic carbon (SOC) sequestration with enhanced stable carbon storage has been widely accepted as a very important ecosystem property. Yet, the link between carbon stability and bio-activity for ecosystem functioning with OC accumulation in field soils has not been characterized. We assessed the changes in microbial activity versus carbon stability along a paddy soil chronosequence shifting from salt marsh in East China. We used mean weight diameter, normalized enzyme activity (NEA) and carbon gain from straw amendment for addressing soil aggregation, microbial biochemical activity and potential C sequestration, respectively. In addition, a response ratio was employed to infer the changes in all analyzed parameters with prolonged rice cultivation. While stable carbon pools varied with total SOC accumulation, soil respiration and both bacterial and fungal diversity were relatively constant in the rice soils. Bacterial abundance and NEA were positively but highly correlated to total SOC accumulation, indicating an enhanced bio-activity with carbon stabilization. This could be linked to an enhancement of particulate organic carbon pool due to physical protection with enhanced soil aggregation in the rice soils under long-term rice cultivation. However, the mechanism underpinning these changes should be explored in future studies in rice soils where dynamic redox conditions exist.
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Affiliation(s)
- Ping Wang
- Institute of Resource, Ecosystem and Environment of Agriculture, and Department of Soil Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Yalong Liu
- Institute of Resource, Ecosystem and Environment of Agriculture, and Department of Soil Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Lianqing Li
- Institute of Resource, Ecosystem and Environment of Agriculture, and Department of Soil Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Kun Cheng
- Institute of Resource, Ecosystem and Environment of Agriculture, and Department of Soil Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Jufeng Zheng
- Institute of Resource, Ecosystem and Environment of Agriculture, and Department of Soil Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Xuhui Zhang
- Institute of Resource, Ecosystem and Environment of Agriculture, and Department of Soil Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Jinwei Zheng
- Institute of Resource, Ecosystem and Environment of Agriculture, and Department of Soil Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Stephen Joseph
- Institute of Resource, Ecosystem and Environment of Agriculture, and Department of Soil Science, Nanjing Agricultural University, Nanjing 210095, China.,School of Materials Science and Engineering, University of New South Wales, Sydney, NSW 2052, Australia.,Discipline of Chemistry, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Genxing Pan
- Institute of Resource, Ecosystem and Environment of Agriculture, and Department of Soil Science, Nanjing Agricultural University, Nanjing 210095, China
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Lammel DR, Feigl BJ, Cerri CC, Nüsslein K. Specific microbial gene abundances and soil parameters contribute to C, N, and greenhouse gas process rates after land use change in Southern Amazonian Soils. Front Microbiol 2015; 6:1057. [PMID: 26500618 PMCID: PMC4594008 DOI: 10.3389/fmicb.2015.01057] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2015] [Accepted: 09/14/2015] [Indexed: 11/30/2022] Open
Abstract
Ecological processes regulating soil carbon (C) and nitrogen (N) cycles are still poorly understood, especially in the world’s largest agricultural frontier in Southern Amazonia. We analyzed soil parameters in samples from pristine rainforest and after land use change to pasture and crop fields, and correlated them with abundance of functional and phylogenetic marker genes (amoA, nirK, nirS, norB, nosZ, nifH, mcrA, pmoA, and 16S/18S rRNA). Additionally, we integrated these parameters using path analysis and multiple regressions. Following forest removal, concentrations of soil C and N declined, and pH and nutrient levels increased, which influenced microbial abundances and biogeochemical processes. A seasonal trend was observed, suggesting that abundances of microbial groups were restored to near native levels after the dry winter fallow. Integration of the marker gene abundances with soil parameters using path analysis and multiple regressions provided good predictions of biogeochemical processes, such as the fluxes of NO3, N2O, CO2, and CH4. In the wet season, agricultural soil showed the highest abundance of nitrifiers (amoA) and Archaea, however, forest soils showed the highest abundances of denitrifiers (nirK, nosZ) and high N, which correlated with increased N2O emissions. Methanogens (mcrA) and methanotrophs (pmoA) were more abundant in forest soil, but methane flux was highest in pasture sites, which was related to soil compaction. Rather than analyzing direct correlations, the data integration using multivariate tools provided a better overview of biogeochemical processes. Overall, in the wet season, land use change from forest to agriculture reduced the abundance of different functional microbial groups related to the soil C and N cycles; integrating the gene abundance data and soil parameters provided a comprehensive overview of these interactions. Path analysis and multiple regressions addressed the need for more comprehensive approaches to improve our mechanistic understanding of biogeochemical cycles.
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Affiliation(s)
- Daniel R Lammel
- Centro de Energia Nuclear na Agricultura, University of São Paulo Piracicaba, Brazil ; Department of Microbiology, University of Massachusetts Amherst, MA, USA
| | - Brigitte J Feigl
- Centro de Energia Nuclear na Agricultura, University of São Paulo Piracicaba, Brazil
| | - Carlos C Cerri
- Centro de Energia Nuclear na Agricultura, University of São Paulo Piracicaba, Brazil
| | - Klaus Nüsslein
- Department of Microbiology, University of Massachusetts Amherst, MA, USA
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Larsen PE, Collart FR, Dai Y. Predicting Ecological Roles in the Rhizosphere Using Metabolome and Transportome Modeling. PLoS One 2015; 10:e0132837. [PMID: 26332409 PMCID: PMC4557938 DOI: 10.1371/journal.pone.0132837] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 06/18/2015] [Indexed: 12/17/2022] Open
Abstract
The ability to obtain complete genome sequences from bacteria in environmental samples, such as soil samples from the rhizosphere, has highlighted the microbial diversity and complexity of environmental communities. However, new algorithms to analyze genome sequence information in the context of community structure are needed to enhance our understanding of the specific ecological roles of these organisms in soil environments. We present a machine learning approach using sequenced Pseudomonad genomes coupled with outputs of metabolic and transportomic computational models for identifying the most predictive molecular mechanisms indicative of a Pseudomonad's ecological role in the rhizosphere: a biofilm, biocontrol agent, promoter of plant growth, or plant pathogen. Computational predictions of ecological niche were highly accurate overall with models trained on transportomic model output being the most accurate (Leave One Out Validation F-scores between 0.82 and 0.89). The strongest predictive molecular mechanism features for rhizosphere ecological niche overlap with many previously reported analyses of Pseudomonad interactions in the rhizosphere, suggesting that this approach successfully informs a system-scale level understanding of how Pseudomonads sense and interact with their environments. The observation that an organism's transportome is highly predictive of its ecological niche is a novel discovery and may have implications in our understanding microbial ecology. The framework developed here can be generalized to the analysis of any bacteria across a wide range of environments and ecological niches making this approach a powerful tool for providing insights into functional predictions from bacterial genomic data.
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Affiliation(s)
- Peter E. Larsen
- Argonne National Laboratory, Biosciences Division, Argonne, IL, United States of America
- University of Illinois at Chicago, Department of Bioengineering, Chicago, IL, United States of America
| | - Frank R. Collart
- Argonne National Laboratory, Biosciences Division, Argonne, IL, United States of America
| | - Yang Dai
- University of Illinois at Chicago, Department of Bioengineering, Chicago, IL, United States of America
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Feld L, Hjelmsø MH, Nielsen MS, Jacobsen AD, Rønn R, Ekelund F, Krogh PH, Strobel BW, Jacobsen CS. Pesticide Side Effects in an Agricultural Soil Ecosystem as Measured by amoA Expression Quantification and Bacterial Diversity Changes. PLoS One 2015; 10:e0126080. [PMID: 25938467 PMCID: PMC4418756 DOI: 10.1371/journal.pone.0126080] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 03/29/2015] [Indexed: 11/26/2022] Open
Abstract
Background and Methods Assessing the effects of pesticide hazards on microbiological processes in the soil is currently based on analyses that provide limited insight into the ongoing processes. This study proposes a more comprehensive approach. The side effects of pesticides may appear as changes in the expression of specific microbial genes or as changes in diversity. To assess the impact of pesticides on gene expression, we focused on the amoA gene, which is involved in ammonia oxidation. We prepared soil microcosms and exposed them to dazomet, mancozeb or no pesticide. We hypothesized that the amount of amoA transcript decreases upon pesticide application, and to test this hypothesis, we used reverse-transcription qPCR. We also hypothesized that bacterial diversity is affected by pesticides. This hypothesis was investigated via 454 sequencing and diversity analysis of the 16S ribosomal RNA and RNA genes, representing the active and total soil bacterial communities, respectively. Results and Conclusion Treatment with dazomet reduced both the bacterial and archaeal amoA transcript numbers by more than two log units and produced long-term effects for more than 28 days. Mancozeb also inhibited the numbers of amoA transcripts, but only transiently. The bacterial and archaeal amoA transcripts were both sensitive bioindicators of pesticide side effects. Additionally, the numbers of bacterial amoA transcripts correlated with nitrate production in N-amended microcosms. Dazomet reduced the total bacterial numbers by one log unit, but the population size was restored after twelve days. The diversity of the active soil bacteria also seemed to be re-established after twelve days. However, the total bacterial diversity as reflected in the 16S ribosomal RNA gene sequences was largely dominated by Firmicutes and Proteobacteria at day twelve, likely reflecting a halt in the growth of early opportunists and the re-establishment of a more diverse population. We observed no effects of mancozeb on diversity.
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Affiliation(s)
- Louise Feld
- Geological Survey of Denmark and Greenland (GEUS), Department of Geochemistry, Copenhagen, Denmark
- * E-mail:
| | - Mathis Hjort Hjelmsø
- Geological Survey of Denmark and Greenland (GEUS), Department of Geochemistry, Copenhagen, Denmark
| | - Morten Schostag Nielsen
- Geological Survey of Denmark and Greenland (GEUS), Department of Geochemistry, Copenhagen, Denmark
| | - Anne Dorthe Jacobsen
- Geological Survey of Denmark and Greenland (GEUS), Department of Geochemistry, Copenhagen, Denmark
| | - Regin Rønn
- University of Copenhagen, Department of Biology, Section of Terrestrial Ecology, Copenhagen, Denmark
| | - Flemming Ekelund
- University of Copenhagen, Department of Biology, Section of Terrestrial Ecology, Copenhagen, Denmark
| | - Paul Henning Krogh
- University of Aarhus, Department of Bioscience, Section of Soil Fauna Ecology and Ecotoxicology, Silkeborg, Denmark
| | - Bjarne Westergaard Strobel
- University of Copenhagen, Department of Plant and Environmental Sciences, Section of Environmental Chemistry and Physics, Frederiksberg, Denmark
| | - Carsten Suhr Jacobsen
- Geological Survey of Denmark and Greenland (GEUS), Department of Geochemistry, Copenhagen, Denmark
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Site history and edaphic features override the influence of plant species on microbial communities in restored tidal freshwater wetlands. Appl Environ Microbiol 2015; 81:3482-91. [PMID: 25769832 DOI: 10.1128/aem.00038-15] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 03/07/2015] [Indexed: 11/20/2022] Open
Abstract
Restored wetland soils differ significantly in physical and chemical properties from their natural counterparts even when plant community compositions are similar, but effects of restoration on microbial community composition and function are not well understood. Here, we investigate plant-microbe relationships in restored and natural tidal freshwater wetlands from two subestuaries of the Chesapeake Bay. Soil samples were collected from the root zone of Typha latifolia, Phragmites australis, Peltandra virginica, and Lythrum salicaria. Soil microbial composition was assessed using 454 pyrosequencing, and genes representing bacteria, archaea, denitrification, methanogenesis, and methane oxidation were quantified. Our analysis revealed variation in some functional gene copy numbers between plant species within sites, but intersite comparisons did not reveal consistent plant-microbe trends. We observed more microbial variations between plant species in natural wetlands, where plants have been established for a long period of time. In the largest natural wetland site, sequences putatively matching methanogens accounted for ∼17% of all sequences, and the same wetland had the highest numbers of genes coding for methane coenzyme A reductase (mcrA). Sequences putatively matching aerobic methanotrophic bacteria and anaerobic methane-oxidizing archaea (ANME) were detected in all sites, suggesting that both aerobic and anaerobic methane oxidation are possible in these systems. Our data suggest that site history and edaphic features override the influence of plant species on microbial communities in restored wetlands.
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Su JQ, Ding LJ, Xue K, Yao HY, Quensen J, Bai SJ, Wei WX, Wu JS, Zhou J, Tiedje JM, Zhu YG. Long-term balanced fertilization increases the soil microbial functional diversity in a phosphorus-limited paddy soil. Mol Ecol 2014; 24:136-50. [DOI: 10.1111/mec.13010] [Citation(s) in RCA: 144] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 11/13/2014] [Accepted: 11/17/2014] [Indexed: 12/18/2022]
Affiliation(s)
- Jian-Qiang Su
- Key Lab of Urban Environment and Health; Institute of Urban Environment; Chinese Academy of Sciences; Xiamen 361021 China
| | - Long-Jun Ding
- State Key Lab of Urban and Regional Ecology; Research Center for Eco-environmental Sciences; Chinese Academy of Sciences; Beijing 100085 China
| | - Kai Xue
- Department of Microbiology and Plant Biology; Institute for Environmental Genomics; University of Oklahoma; 101 David L Boren Blvd Norman OK 73019 USA
| | - Huai-Ying Yao
- Key Lab of Urban Environment and Health; Institute of Urban Environment; Chinese Academy of Sciences; Xiamen 361021 China
| | - John Quensen
- Center for Microbial Ecology; Department of Plant, Soil and Microbial Sciences; Michigan State University; East Lansing MI 48824 USA
| | - Shi-Jie Bai
- Department of Microbiology and Plant Biology; Institute for Environmental Genomics; University of Oklahoma; 101 David L Boren Blvd Norman OK 73019 USA
| | - Wen-Xue Wei
- Key Laboratory of Agro-ecological Processes in Subtropical Regions and Taoyuan Station of Agro-ecology Research; Institute of Subtropical Agriculture; Chinese Academy of Sciences; Changsha 410125 China
| | - Jin-Shui Wu
- Key Laboratory of Agro-ecological Processes in Subtropical Regions and Taoyuan Station of Agro-ecology Research; Institute of Subtropical Agriculture; Chinese Academy of Sciences; Changsha 410125 China
| | - Jizhong Zhou
- Department of Microbiology and Plant Biology; Institute for Environmental Genomics; University of Oklahoma; 101 David L Boren Blvd Norman OK 73019 USA
- Earth Science Division; Lawrence Berkeley National Laboratory; Berkeley CA 94720 USA
- State Key Joint Laboratory of Environment Simulation and Pollution Control; School of Environment; Tsinghua University; Beijing 100084 China
| | - James M. Tiedje
- Center for Microbial Ecology; Department of Plant, Soil and Microbial Sciences; Michigan State University; East Lansing MI 48824 USA
| | - Yong-Guan Zhu
- Key Lab of Urban Environment and Health; Institute of Urban Environment; Chinese Academy of Sciences; Xiamen 361021 China
- State Key Lab of Urban and Regional Ecology; Research Center for Eco-environmental Sciences; Chinese Academy of Sciences; Beijing 100085 China
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Abed RMM, Al-Kharusi S, Prigent S, Headley T. Diversity, distribution and hydrocarbon biodegradation capabilities of microbial communities in oil-contaminated cyanobacterial mats from a constructed wetland. PLoS One 2014; 9:e114570. [PMID: 25514025 PMCID: PMC4267807 DOI: 10.1371/journal.pone.0114570] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 11/11/2014] [Indexed: 02/01/2023] Open
Abstract
Various types of cyanobacterial mats were predominant in a wetland, constructed for the remediation of oil-polluted residual waters from an oil field in the desert of the south-eastern Arabian Peninsula, although such mats were rarely found in other wetland systems. There is scarce information on the bacterial diversity, spatial distribution and oil-biodegradation capabilities of freshwater wetland oil-polluted mats. Microbial community analysis by Automated Ribosomal Spacer Analysis (ARISA) showed that the different mats hosted distinct microbial communities. Average numbers of operational taxonomic units (OTUsARISA) were relatively lower in the mats with higher oil levels and the number of shared OTUsARISA between the mats was <60% in most cases. Multivariate analyses of fingerprinting profiles indicated that the bacterial communities in the wetland mats were influenced by oil and ammonia levels, but to a lesser extent by plant density. In addition to oil and ammonia, redundancy analysis (RDA) showed also a significant contribution of temperature, dissolved oxygen and sulfate concentration to the variations of the mats' microbial communities. Pyrosequencing yielded 282,706 reads with >90% of the sequences affiliated to Proteobacteria (41% of total sequences), Cyanobacteria (31%), Bacteriodetes (11.5%), Planctomycetes (7%) and Chloroflexi (3%). Known autotrophic (e.g. Rivularia) and heterotrophic (e.g. Azospira) nitrogen-fixing bacteria as well as purple sulfur and non-sulfur bacteria were frequently encountered in all mats. On the other hand, sequences of known sulfate-reducing bacteria (SRBs) were rarely found, indicating that SRBs in the wetland mats probably belong to yet-undescribed novel species. The wetland mats were able to degrade 53-100% of C12-C30 alkanes after 6 weeks of incubation under aerobic conditions. We conclude that oil and ammonia concentrations are the major key players in determining the spatial distribution of the wetland mats' microbial communities and that these mats contribute directly to the removal of hydrocarbons from oil field wastewaters.
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Affiliation(s)
- Raeid M. M. Abed
- Sultan Qaboos University, College of Science, Biology Department, P.O. Box: 36, postal code 123, Al Khoud, Sultanate of Oman
- * E-mail:
| | - Samiha Al-Kharusi
- Sultan Qaboos University, College of Science, Biology Department, P.O. Box: 36, postal code 123, Al Khoud, Sultanate of Oman
| | - Stephane Prigent
- BAUER Resources, Constructed Wetland Competence Centre, P.O. Box 1186, P.C. 114, Al Mina, Muscat, Sultanate of Oman
| | - Tom Headley
- BAUER Resources, Constructed Wetland Competence Centre, P.O. Box 1186, P.C. 114, Al Mina, Muscat, Sultanate of Oman
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Long A, Song B, Fridey K, Silva A. Detection and diversity of copper containing nitrite reductase genes (nirK) in prokaryotic and fungal communities of agricultural soils. FEMS Microbiol Ecol 2014; 91:1-9. [PMID: 25764542 DOI: 10.1093/femsec/fiu004] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Microorganisms are capable of producing N2 and N2O gases as the end products of denitrification. Copper-containing nitrite reductase (NirK), a key enzyme in the microbial N-cycle, has been found in bacteria, archaea and fungi. This study seeks to assess the diversity of nirK genes in the prokaryotic and fungal communities of agricultural soils in the United States. New primers targeting the nirK genes in fungi were developed, while nirK genes in archaea and bacteria were detected using previously published methods. The new primers were able to detect fungal nirK genes as well as bacterial nirK genes from a group that could not be observed with previously published primers. Based on the sequence analyses from three different primer sets, five clades of nirK genes were identified, which were associated with soil archaea, ammonium-oxidizing bacteria, denitrifying bacteria and fungi. The diversity of nirK genes in the two denitrifying bacteria clades was higher than the diversity found in other clades. Using a newly designed primer set, this study showed the detection of fungal nirK genes from environmental samples. The newly designed PCR primers in this study enhance the ability to detect the diversity of nirK-encoding microorganisms in soils.
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Affiliation(s)
- Andrew Long
- Department of Biology and Marine Biology, University of North Carolina, Wilmington, NC 28403
| | - Bongkeun Song
- Department of Biology and Marine Biology, University of North Carolina, Wilmington, NC 28403 Department of Biological Sciences, Virginia Institute of Marine Sciences, Gloucester Point, VA 23062, USA Department of Life Science, Dongguk University-Seoul, Seoul 100-715, South Korea
| | - Kelly Fridey
- Department of Biology and Marine Biology, University of North Carolina, Wilmington, NC 28403
| | - Amy Silva
- Department of Biology and Marine Biology, University of North Carolina, Wilmington, NC 28403
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Legay N, Baxendale C, Grigulis K, Krainer U, Kastl E, Schloter M, Bardgett RD, Arnoldi C, Bahn M, Dumont M, Poly F, Pommier T, Clément JC, Lavorel S. Contribution of above- and below-ground plant traits to the structure and function of grassland soil microbial communities. ANNALS OF BOTANY 2014; 114:1011-21. [PMID: 25122656 PMCID: PMC4171078 DOI: 10.1093/aob/mcu169] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 07/03/2014] [Indexed: 05/04/2023]
Abstract
BACKGROUND AND AIMS Abiotic properties of soil are known to be major drivers of the microbial community within it. Our understanding of how soil microbial properties are related to the functional structure and diversity of plant communities, however, is limited and largely restricted to above-ground plant traits, with the role of below-ground traits being poorly understood. This study investigated the relative contributions of soil abiotic properties and plant traits, both above-ground and below-ground, to variations in microbial processes involved in grassland nitrogen turnover. METHODS In mountain grasslands distributed across three European sites, a correlative approach was used to examine the role of a large range of plant functional traits and soil abiotic factors on microbial variables, including gene abundance of nitrifiers and denitrifiers and their potential activities. KEY RESULTS Direct effects of soil abiotic parameters were found to have the most significant influence on the microbial groups investigated. Indirect pathways via plant functional traits contributed substantially to explaining the relative abundance of fungi and bacteria and gene abundances of the investigated microbial communities, while they explained little of the variance in microbial activities. Gene abundances of nitrifiers and denitrifiers were most strongly related to below-ground plant traits, suggesting that they were the most relevant traits for explaining variation in community structure and abundances of soil microbes involved in nitrification and denitrification. CONCLUSIONS The results suggest that consideration of plant traits, and especially below-ground traits, increases our ability to describe variation in the abundances and the functional characteristics of microbial communities in grassland soils.
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Affiliation(s)
- N Legay
- Laboratoire d'Ecologie Alpine, UMR CNRS 5553, Université Joseph Fourier, Grenoble, France
| | - C Baxendale
- Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, UK
| | - K Grigulis
- Laboratoire d'Ecologie Alpine, UMR CNRS 5553, Université Joseph Fourier, Grenoble, France Station Alpine Joseph Fourier, UMS 3370 CNRS - Université Joseph Fourier, BP 53, 2233 Rue de la Piscine, 38041 Grenoble Cedex 9, France
| | - U Krainer
- Institute of Ecology, University of Innsbruck, Sternwartestrasse 15, A-6020 Innsbruck, Austria
| | - E Kastl
- Research Unit for Environmental Genomics, Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
| | - M Schloter
- Research Unit for Environmental Genomics, Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
| | - R D Bardgett
- Faculty of Life Sciences, Michael Smith Building, The University of Manchester, Oxford Road, Manchester M13 9PT, UK and
| | - C Arnoldi
- Laboratoire d'Ecologie Alpine, UMR CNRS 5553, Université Joseph Fourier, Grenoble, France
| | - M Bahn
- Institute of Ecology, University of Innsbruck, Sternwartestrasse 15, A-6020 Innsbruck, Austria
| | - M Dumont
- Laboratoire d'Ecologie Microbienne, Université Lyon1, Université de Lyon, 15 USC INRA 1364, UMR CNRS 5557, Villeurbanne Cedex, France
| | - F Poly
- Laboratoire d'Ecologie Microbienne, Université Lyon1, Université de Lyon, 15 USC INRA 1364, UMR CNRS 5557, Villeurbanne Cedex, France
| | - T Pommier
- Laboratoire d'Ecologie Microbienne, Université Lyon1, Université de Lyon, 15 USC INRA 1364, UMR CNRS 5557, Villeurbanne Cedex, France
| | - J C Clément
- Laboratoire d'Ecologie Alpine, UMR CNRS 5553, Université Joseph Fourier, Grenoble, France
| | - S Lavorel
- Laboratoire d'Ecologie Alpine, UMR CNRS 5553, Université Joseph Fourier, Grenoble, France
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Park S, Kim HG, Kim S, Lee MK, Lee GM, Kim Y, Kim MS, Kim T. Evaluation of Natural Attenuation by Addition of Fumarate as Carbon Source and Gene Analysis in Groundwater Sample. ACTA ACUST UNITED AC 2014. [DOI: 10.7857/jsge.2014.19.4.062] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Sims A, Zhang Y, Gajaraj S, Brown PB, Hu Z. Toward the development of microbial indicators for wetland assessment. WATER RESEARCH 2013; 47:1711-1725. [PMID: 23384515 DOI: 10.1016/j.watres.2013.01.023] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Revised: 01/10/2013] [Accepted: 01/11/2013] [Indexed: 06/01/2023]
Abstract
Wetland assessment tools are being developed and employed in wetland monitoring and conservation based on physical, chemical and biological characterization. In wetland biological assessment, various ecological functions have been described by biological traits of an entire species pool that adapts to different types of wetland environments. Since microorganisms play a key role in wetland biogeochemical processes and respond quickly to environmental disturbances, this review paper describes the different macro indicators used in wetland biological monitoring and expands the potential use of microbial indicators in wetland assessment and management. Application of molecular microbial technologies paves the path to an integrated measure of wetland health conditions. For example, the ratio of ammonia-oxidizing archaeal and bacterial populations has been proposed to serve as a microbial indicator of wetland nutrient conditions. The microbial indicators coupled with physical, chemical and other biological parameters are vital to the development of multi-metric index for measuring wetland health conditions. Inclusion of microbial indicators will lead to a more comprehensive wetland assessment for wetland restoration and management practices.
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Affiliation(s)
- Atreyee Sims
- Department of Civil and Environmental Engineering, University of Missouri, E2509 Lafferre Hall, Columbia, MO 65211, USA
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Evidence for niche partitioning revealed by the distribution of sulfur oxidation genes collected from areas of a terrestrial sulfidic spring with differing geochemical conditions. Appl Environ Microbiol 2012; 79:1171-82. [PMID: 23220955 DOI: 10.1128/aem.02812-12] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The diversity and phylogenetic significance of bacterial genes in the environment has been well studied, but comparatively little attention has been devoted to understanding the functional significance of different variations of the same metabolic gene that occur in the same environment. We analyzed the geographic distribution of 16S rRNA pyrosequences and soxB genes along a geochemical gradient in a terrestrial sulfidic spring to identify how different taxonomic variations of the soxB gene were naturally distributed within the spring outflow channel and to identify possible evidence for altered SoxB enzyme function in nature. Distinct compositional differences between bacteria that utilize their SoxB enzyme in the Paracoccus sulfide oxidation pathway (e.g., Bradyrhizobium, Paracoccus, and Rhodovulum) and bacteria that utilize their SoxB enzyme in the branched pathway (e.g., Chlorobium, Thiothrix, Thiobacillus, Halothiobacillus, and Thiomonas) were identified. Different variations of the soxB genes were present at different locations within the spring outflow channel in a manner that significantly corresponded to geochemical conditions. The distribution of the different soxB gene sequence variations suggests that the enzymes encoded by these genes are functionally different and could be optimized to specific geochemical conditions that define niche space for bacteria capable of oxidizing reduced sulfur compounds.
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Ahn JH, Song J, Kim BY, Kim MS, Joa JH, Weon HY. Characterization of the bacterial and archaeal communities in rice field soils subjected to long-term fertilization practices. J Microbiol 2012; 50:754-65. [PMID: 23124742 DOI: 10.1007/s12275-012-2409-6] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Accepted: 09/26/2012] [Indexed: 12/23/2022]
Abstract
The bacterial and archaeal communities in rice field soils subjected to different fertilization regimes for 57 years were investigated in two different seasons, a non-planted, drained season (April) and a rice-growing, flooded season (August), by performing soil dehydrogenase assay, real-time PCR assay and pyrosequencing analysis. All fertilization regimes increased the soil dehydrogenase activity while the abundances of bacteria and archaea increased in the plots receiving inorganic fertilizers plus compost and not in those receiving inorganic fertilizers only. Rice-growing and flooding decreased the soil dehydrogenase activity while they increased the bacterial diversity in rice field soils. The bacterial communities were dominated by Chloroflexi, Proteobacteria, and Actinobacteria and the archaeal communities by Crenarchaeota at the phylum level. In principal coordinates analysis based on the weighted Fast UniFrac metric, the bacterial and archaeal communities were separated primarily by season, and generally distributed along with soil pH, the variation of which had been caused by long-term fertilization. Variations in the relative abundance according to the season or soil pH were observed for many bacterial and archaeal groups. In conclusion, the microbial activity, prokaryotic abundance and diversity, and prokaryotic community structure in the rice field soils were changed by season and long-term fertilization.
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Affiliation(s)
- Jae-Hyung Ahn
- Agricultural Microbiology Division, National Academy of Agricultural Science, Rural Development Administration, Suwon 441-707, Republic of Korea
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Jung J, Yeom J, Han J, Kim J, Park W. Seasonal changes in nitrogen-cycle gene abundances and in bacterial communities in acidic forest soils. J Microbiol 2012; 50:365-73. [PMID: 22752898 DOI: 10.1007/s12275-012-1465-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2011] [Accepted: 02/28/2012] [Indexed: 11/26/2022]
Abstract
The abundance of genes related to the nitrogen biogeochemical cycle and the microbial community in forest soils (bacteria, archaea, fungi) were quantitatively analyzed via real-time PCR using 11 sets of specific primers amplifying nifH, bacterial amoA, archaeal amoA, narG, nirS, nirK, norB, nosZ, bacterial 16S rRNA gene, archaeal 16S rRNA gene, and the ITS sequence of fungi. Soils were sampled from Bukhan Mountain from September of 2010 to July of 2011 (7 times). Bacteria were the predominant microbial community in all samples. However, the abundance of archaeal amoA was greater than bacterial amoA throughout the year. The abundances of nifH, nirS, nirK, and norB genes changed in a similar pattern, while narG and nosZ appeared in sensitive to the environmental changes. Clone libraries of bacterial 16S rRNA genes were constructed from summer and winter soil samples and these revealed that Acidobacteria was the most predominant phylum in acidic forest soil environments in both samples. Although a specific correlation of environmental factor and gene abundance was not verified by principle component analysis, our data suggested that the combination of biological, physical, and chemical characteristics of forest soils created distinct conditions favoring the nitrogen biogeochemical cycle and that bacterial communities in undisturbed acidic forest soils were quite stable during seasonal change.
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Affiliation(s)
- Jaejoon Jung
- Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 136-713, Republic of Korea
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