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Yang Y, Liu H, Wang H, Li C, Lv J. Strategies of soil microbial N-cycling in different cadmium contaminated soil with wheat straw return. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 278:116406. [PMID: 38728941 DOI: 10.1016/j.ecoenv.2024.116406] [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: 11/03/2023] [Revised: 04/07/2024] [Accepted: 04/25/2024] [Indexed: 05/12/2024]
Abstract
Cadmium contamination inevitably affects the microbially mediated transformation of nitrogen in soils with wheat straw return. The responses of nitrogen functional microorganisms to cadmium in acidic and alkaline soils under wheat straw returned are still unclear. In this study, quantitative polymerase chain reaction (qPCR) and sequencing of nitrifying and denitrifying bacteria were performed to investigate the effects of wheat straw application on nitrogen conversion in different Cd-contaminated soils during an incubation experiment. Results showed that the presence of Cd decreased the abundance of hao gene catalyzing nitrification and norB gene catalyzing denitrification process, resulting the accumulation of NH4+-N and reduction of NO3--N in the acidic soils. Additionally, Cd-contamination stimulates the nitrification catalyzed by bacterial amoA gene and thus reduced the NH4+-N content in the alkaline soils. Meanwhile, Cd dominated the decrease of NO3--N content by promoting denitrification process catalyzed by nirS gene. Among all nitrifying and denitrifying microorganisms, Nitrosospira are tolerant to Cd stress under alkaline condition but sensitive to acidic condition, which dominantly harbored hao gene in the acidic soils and bacterial amoA gene in the alkaline soils. This study aimed to provide reasonable information for the rational adoption of wheat straw returning strategies to realize nitrogen regulation in Cd-contaminated farmland soil.
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Affiliation(s)
- Yajun Yang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of soil and water conservation Chinese Academy of Sciences & College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, PR China.
| | - Hexiang Liu
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of soil and water conservation Chinese Academy of Sciences & College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Hui Wang
- Xianyang Soil and Fertilizer Workstation, Xianyang, Shaanxi 712000, PR China
| | - Chengjuan Li
- Xianyang Soil and Fertilizer Workstation, Xianyang, Shaanxi 712000, PR China
| | - Jialong Lv
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of soil and water conservation Chinese Academy of Sciences & College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, PR China.
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2
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Han X, Beck K, Bürgmann H, Frey B, Stierli B, Frossard A. Synthetic oligonucleotides as quantitative PCR standards for quantifying microbial genes. Front Microbiol 2023; 14:1279041. [PMID: 37942081 PMCID: PMC10627841 DOI: 10.3389/fmicb.2023.1279041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 10/09/2023] [Indexed: 11/10/2023] Open
Abstract
Real-time quantitative PCR (qPCR) has been widely used to quantify gene copy numbers in microbial ecology. Despite its simplicity and straightforwardness, establishing qPCR assays is often impeded by the tedious process of producing qPCR standards by cloning the target DNA into plasmids. Here, we designed double-stranded synthetic DNA fragments from consensus sequences as qPCR standards by aligning microbial gene sequences (10-20 sequences per gene). Efficiency of standards from synthetic DNA was compared with plasmid standards by qPCR assays for different phylogenetic marker and functional genes involved in carbon (C) and nitrogen (N) cycling, tested with DNA extracted from a broad range of soils. Results showed that qPCR standard curves using synthetic DNA performed equally well to those from plasmids for all the genes tested. Furthermore, gene copy numbers from DNA extracted from soils obtained by using synthetic standards or plasmid standards were comparable. Our approach therefore demonstrates that a synthetic DNA fragment as qPCR standard provides comparable sensitivity and reliability to a traditional plasmid standard, while being more time- and cost-efficient.
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Affiliation(s)
- Xingguo Han
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
| | - Karin Beck
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Helmut Bürgmann
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Beat Frey
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
| | - Beat Stierli
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
| | - Aline Frossard
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
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3
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Wang Y, Zeng X, Zhang Y, Zhang N, Xu L, Wu C. Responses of potential ammonia oxidation and ammonia oxidizers community to arsenic stress in seven types of soil. J Environ Sci (China) 2023; 127:15-29. [PMID: 36522049 DOI: 10.1016/j.jes.2022.02.038] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 02/21/2022] [Accepted: 02/22/2022] [Indexed: 06/17/2023]
Abstract
Soil arsenic contamination is of great concern because of its toxicity to human, crops, and soil microorganisms. However, the impacts of arsenic on soil ammonia oxidizers communities remain unclear. Seven types of soil spiked with 0 or 100 mg arsenic per kg soil were incubated for 180 days and sampled at days 1, 15, 30, 90 and 180. The changes in the community composition and abundance of ammonia oxidizing bacteria (AOB) and ammonia oxidizing archaea (AOA) were analyzed by terminal restriction fragment length polymorphism (T-RFLP) analysis, clone library sequencing, and quantitative PCR (qPCR) targeting amoA gene. Results revealed considerable variations in the potential ammonia oxidation (PAO) rates in different soils, but soil PAO was not consistently significantly inhibited by arsenic, probably due to the low bioavailable arsenic contents or the existence of functional redundancy between AOB and AOA. The variations in AOB and AOA communities were closely associated with the changes in arsenic fractionations. The amoA gene abundances of AOA increased after arsenic addition, whereas AOB decreased, which corroborated the notion that AOA and AOB might occupy different niches in arsenic-contaminated soils. Phylogenetic analysis of amoA gene-encoded proteins revealed that all AOB clone sequences belonged to the genus Nitrosospira, among which those belonging to Nitrosospira cluster 3a were dominant. The main AOA sequence detected belonged to Thaumarchaeal Group 1.1b, which was considered to have a high ability to adapt to environmental changes. Our results provide new insights into the impacts of arsenic on the soil nitrogen cycling.
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Affiliation(s)
- Yanan Wang
- Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Environment, Institute of Environment and Sustainable Development in Agriculture, Ministry of Agriculture and Rural Affairs of the P.R. China, Beijing 100081, China
| | - Xibai Zeng
- Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Environment, Institute of Environment and Sustainable Development in Agriculture, Ministry of Agriculture and Rural Affairs of the P.R. China, Beijing 100081, China.
| | - Yang Zhang
- Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Environment, Institute of Environment and Sustainable Development in Agriculture, Ministry of Agriculture and Rural Affairs of the P.R. China, Beijing 100081, China
| | - Nan Zhang
- Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Environment, Institute of Environment and Sustainable Development in Agriculture, Ministry of Agriculture and Rural Affairs of the P.R. China, Beijing 100081, China
| | - Liyang Xu
- Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Environment, Institute of Environment and Sustainable Development in Agriculture, Ministry of Agriculture and Rural Affairs of the P.R. China, Beijing 100081, China
| | - Cuixia Wu
- Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Environment, Institute of Environment and Sustainable Development in Agriculture, Ministry of Agriculture and Rural Affairs of the P.R. China, Beijing 100081, China
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4
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Frey B, Rast BM, Qi W, Stierli B, Brunner I. Long-term mercury contamination does not affect the microbial gene potential for C and N cycling in soils but enhances detoxification gene abundance. Front Microbiol 2022; 13:1034138. [PMID: 36274742 PMCID: PMC9581213 DOI: 10.3389/fmicb.2022.1034138] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 09/20/2022] [Indexed: 11/13/2022] Open
Abstract
Soil microorganisms are key transformers of mercury (Hg), a toxic and widespread pollutant. It remains uncertain, however, how long-term exposure to Hg affects crucial microbial functions, such as litter decomposition and nitrogen cycling. Here, we used a metagenomic approach to investigate the state of soil functions in an agricultural floodplain contaminated with Hg for more than 80 years. We sampled soils along a gradient of Hg contamination (high, moderate, low). Hg concentrations at the highly contaminated site (36 mg kg–1 dry soil on average) were approximately 10 times higher than at the moderately contaminated site (3 mg kg–1 dry soil) and more than 100 times higher than at the site with low contamination (0.25 mg kg–1 dry soil; corresponding to the natural background concentration in Switzerland). The analysis of the CAZy and NCyc databases showed that carbon and nitrogen cycling was not strongly affected with high Hg concentrations, although a significant change in the beta-diversity of the predicted genes was observed. The only functional classes from the CAZy database that were significantly positively overrepresented under higher Hg concentrations were genes involved in pectin degradation, and from the NCyc database dissimilatory nitrate reduction and N-fixation. When comparing between low and high Hg concentrations the genes of the EggNOG functional category of inorganic ion transport and metabolism, two genes encoding Hg transport proteins and one gene involved in heavy metal transport detoxification were among those that were highly significantly overrepresented. A look at genes specifically involved in detoxification of Hg species, such as the mer and hgc genes, showed a significant overrepresentation when Hg contamination was increased. Normalized counts of these genes revealed a dominant role for the phylum Proteobacteria. In particular, most counts for almost all mer genes were found in Betaproteobacteria. In contrast, hgc genes were most abundant in Desulfuromonadales. Overall, we conclude from this metagenomic analysis that long-term exposure to high Hg triggers shifts in the functional beta-diversity of the predicted microbial genes, but we do not see a dramatic change or breakdown in functional capabilities, but rather functional redundancy.
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Affiliation(s)
- Beat Frey
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
- *Correspondence: Beat Frey,
| | - Basil M. Rast
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Weihong Qi
- FGCZ Functional Genomics Center Zurich, ETH Zürich and University of Zürich, Zürich, Switzerland
- SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Beat Stierli
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Ivano Brunner
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
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5
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Guo H, Gu J, Wang X, Song Z, Nasir M, Tuo X. Elucidating the microbiological characteristics of cyromazine affecting the nitrogen cycle during aerobic composting of pig manure. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 764:142812. [PMID: 33071140 DOI: 10.1016/j.scitotenv.2020.142812] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 09/28/2020] [Accepted: 09/29/2020] [Indexed: 06/11/2023]
Abstract
Cyromazine as insect growth inhibitor have been frequently detected in the environment, which show a potential threat to environment and soil health. Nitrogen is an essential component of all living organisms and the main nutrient limiting life on our planet. In this study, quantitative polymerase chain reaction (qPCR) and sequencing of nitrifying and denitrifying bacteria were conducted to investigate the dynamic effects of cyromazine on nitrogen conversion during laboratory-based composting. Results showed that the presence of cyromazine significantly reduced the abundance of amoA gene during the thermophilic phase of composting (p < 0.01), resulting in lower oxidation of NH4+-N. The archaea amoA gene was more resistant to cyromazine. The nirK gene was more abundant than the nirS gene during composting and was significantly reduced only under high concentrations of cyromazine (p < 0.01). The high dose of cyromazine (15 mg/kg) severely damaged the nitrogen fixation capacity of compost products. Cyromazine exhibited an inhibition effect on richness (ACE, Chao) of nitrifying and denitrifying microorganisms during the thermophilic period, while increased the diversity (shannon) at all stages of composting. Pseudomonas_formosensis was the core denitrifiers that harbored nosZ gene, Nitrosomonas_eutropha and Nitrosospira_sp_Nl5 were the dominant nitrifier that harbored amoA gene, and these species have a negative response to cyromazine. Network analysis indicated that the dominant bacteria harboring amoA and nosZ genes were hubs of nitrogen oxidation and reduction processes. Structural equation modeling revealed that NO2--N conversion played a crucial role in driving denitrification, and increase of NH4+-N content was attributed to the inhibition of nitrification and denitrification during composting caused by cyromazine.
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Affiliation(s)
- Honghong Guo
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jie Gu
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China; Research Center of Recycle Agricultural Engineering and Technology of Shaanxi Province, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Xiaojuan Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zilin Song
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Mubasher Nasir
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiaxia Tuo
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
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6
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Herzog C, Hartmann M, Frey B, Stierli B, Rumpel C, Buchmann N, Brunner I. Microbial succession on decomposing root litter in a drought-prone Scots pine forest. ISME JOURNAL 2019; 13:2346-2362. [PMID: 31123321 PMCID: PMC6776048 DOI: 10.1038/s41396-019-0436-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 04/16/2019] [Accepted: 05/03/2019] [Indexed: 12/21/2022]
Abstract
Decomposition is a major flux of the carbon cycle in forest soils and understanding the involved processes is a key for budgeting carbon turnover. Decomposition is constrained by the presence of biological agents such as microorganisms and the underlying environmental conditions such as water availability. A metabarcoding approach of ribosomal markers was chosen to study the succession of bacterial and fungal decomposers on root litter. Litterbags containing pine roots were buried in a pine forest for two years and sequentially sampled. Decomposition and the associated communities were surveyed under ambient dry and long-term irrigation conditions. Early decomposition stages were characterized by the presence of fast-cycling microorganisms such as Bacteroidetes and Helotiales, which were then replaced by more specialized bacteria and litter-associated or parasitic groups such as Acidobacteria, white rots, and Pleosporales. This succession was likely driven by a decrease of easily degradable carbohydrates and a relative increase in persistent compounds such as lignin. We hypothesize that functional redundancy among the resident microbial taxa caused similar root decomposition rates in control and irrigated forest soils. These findings have important implications for drought-prone Alpine forests as frequent drought events reduce litter fall, but not litter decomposition, potentially resulting in lower carbon stocks.
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Affiliation(s)
- Claude Herzog
- Swiss Federal Research Institute WSL, CH-8903, Birmensdorf, Switzerland.,ETH Zürich, CH-8092, Zürich, Switzerland
| | - Martin Hartmann
- Swiss Federal Research Institute WSL, CH-8903, Birmensdorf, Switzerland.,ETH Zürich, CH-8092, Zürich, Switzerland
| | - Beat Frey
- Swiss Federal Research Institute WSL, CH-8903, Birmensdorf, Switzerland
| | - Beat Stierli
- Swiss Federal Research Institute WSL, CH-8903, Birmensdorf, Switzerland
| | - Cornelia Rumpel
- Centre Nationale de Recherche Scientifique (CNRS), Institute of Ecology and Environment (IEES), Thiverval-Grignon, 78850, France
| | | | - Ivano Brunner
- Swiss Federal Research Institute WSL, CH-8903, Birmensdorf, Switzerland.
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7
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Luo J, Liu Y, Tao Q, Hou Q, Wu K, Song Y, Liu Y, Guo X, Li J, Hashmi MLUR, Liang Y, Li T. Successive phytoextraction alters ammonia oxidation and associated microbial communities in heavy metal contaminated agricultural soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 664:616-625. [PMID: 30763842 DOI: 10.1016/j.scitotenv.2019.01.315] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Revised: 01/22/2019] [Accepted: 01/24/2019] [Indexed: 06/09/2023]
Abstract
Phytoextraction is an attractive strategy for remediation of soils contaminated by heavy metal (HM), yet the effects of this practice on biochemical processes involved in soil nutrient cycling remain unknown. Here we investigated the impact of successive phytoextraction with a Cd/Zn co-hyperaccumulator Sedum alfredii (Crassulaceae) on potential nitrification rates (PNRs), abundance and composition of nitrifying communities and functional genes associated with nitrification using archaeal and bacterial 16S rRNA gene profiling and quantitative real-time PCR. The PNRs in rhizosphere were significantly (P < 0.05) lower than in the unplanted soils, and decreased markedly with planting time. The decrease of PNR was more paralleled by changes in numbers of copy and transcript of archaeal amoA gene than the bacterial counterpart. Phylogenetic analysis revealed that phytoextraction induced shifts in community structure of soil group 1.1b lineage-dominated ammonia-oxidizing archaea (AOA), Nitrosospira cluster 3-like ammonia-oxidizing bacteria (AOB) and Nitrospira-like nitrite-oxidizing bacteria (NOB). A strong positive correlation was observed between amoA gene transcript numbers and PNRs, whereas root exudates showed negative effect on PNR. This effect was further corroborated by incubation test with the concentrated root exudates of S. alfredii. Partial least squares path model demonstrated that PNR was predominantly controlled by number of AOA amoA gene transcripts which were strongly influenced by root exudation and HM level in soil. Our result reveals that successive phytoextraction of agricultural soil contaminated by HMs using S. alfredii could inhibit ammonia oxidation and thereby reduce nitrogen loss.
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Affiliation(s)
- Jipeng Luo
- Ministry of Education Key Laboratory of Environmental Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yuying Liu
- Ministry of Education Key Laboratory of Environmental Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Qi Tao
- Ministry of Education Key Laboratory of Environmental Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Qiong Hou
- Ministry of Education Key Laboratory of Environmental Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Keren Wu
- Ministry of Education Key Laboratory of Environmental Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yuchao Song
- Ministry of Education Key Laboratory of Environmental Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yuankun Liu
- Ministry of Education Key Laboratory of Environmental Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xinyu Guo
- Ministry of Education Key Laboratory of Environmental Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jinxing Li
- Ministry of Education Key Laboratory of Environmental Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Muhammad Laeeq Ur Rehman Hashmi
- Ministry of Education Key Laboratory of Environmental Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yongchao Liang
- Ministry of Education Key Laboratory of Environmental Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Tingqiang Li
- Ministry of Education Key Laboratory of Environmental Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China.
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8
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Touceda-González M, Prieto-Fernández Á, Renella G, Giagnoni L, Sessitsch A, Brader G, Kumpiene J, Dimitriou I, Eriksson J, Friesl-Hanl W, Galazka R, Janssen J, Mench M, Müller I, Neu S, Puschenreiter M, Siebielec G, Vangronsveld J, Kidd PS. Microbial community structure and activity in trace element-contaminated soils phytomanaged by Gentle Remediation Options (GRO). ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2017; 231:237-251. [PMID: 28802993 DOI: 10.1016/j.envpol.2017.07.097] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 07/28/2017] [Accepted: 07/28/2017] [Indexed: 06/07/2023]
Abstract
Gentle remediation options (GRO) are based on the combined use of plants, associated microorganisms and soil amendments, which can potentially restore soil functions and quality. We studied the effects of three GRO (aided-phytostabilisation, in situ stabilisation and phytoexclusion, and aided-phytoextraction) on the soil microbial biomass and respiration, the activities of hydrolase enzymes involved in the biogeochemical cycles of C, N, P, and S, and bacterial community structure of trace element contaminated soils (TECS) from six field trials across Europe. Community structure was studied using denaturing gradient gel electrophoresis (DGGE) fingerprinting of Bacteria, α- and β-Proteobacteria, Actinobacteria and Streptomycetaceae, and sequencing of DGGE bands characteristic of specific treatments. The number of copies of genes involved in ammonia oxidation and denitrification were determined by qPCR. Phytomanagement increased soil microbial biomass at three sites and respiration at the Biogeco site (France). Enzyme activities were consistently higher in treated soils compared to untreated soils at the Biogeco site. At this site, microbial biomass increased from 696 to 2352 mg ATP kg-1 soil, respiration increased from 7.4 to 40.1 mg C-CO2 kg-1 soil d-1, and enzyme activities were 2-11-fold higher in treated soils compared to untreated soil. Phytomanagement induced shifts in the bacterial community structure at both, the total community and functional group levels, and generally increased the number of copies of genes involved in the N cycle (nirK, nirS, nosZ, and amoA). The influence of the main soil physico-chemical properties and trace element availability were assessed and eventual site-specific effects elucidated. Overall, our results demonstrate that phytomanagement of TECS influences soil biological activity in the long term.
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Affiliation(s)
- M Touceda-González
- Instituto de Investigaciones Agrobiológicas de Galicia (IIAG), Consejo Superior de Investigaciones Científicas (CSIC), Aptdo. 122, Santiago de Compostela 15780, Spain.
| | - Á Prieto-Fernández
- Instituto de Investigaciones Agrobiológicas de Galicia (IIAG), Consejo Superior de Investigaciones Científicas (CSIC), Aptdo. 122, Santiago de Compostela 15780, Spain
| | - G Renella
- University of Florence, Department of Agrifood Production and Environmental Sciences, P.le delle Cascine 18, I-50144 Florence, Italy
| | - L Giagnoni
- University of Florence, Department of Agrifood Production and Environmental Sciences, P.le delle Cascine 18, I-50144 Florence, Italy
| | - A Sessitsch
- AIT Austrian Institute of Technology GmbH, Center for Health & Bioresources, 3430 Tulln, Austria
| | - G Brader
- AIT Austrian Institute of Technology GmbH, Center for Health & Bioresources, 3430 Tulln, Austria
| | - J Kumpiene
- Luleå University of Technology, Waste Science & Technology, SE-97187 Luleå, Sweden
| | - I Dimitriou
- Swedish University of Agriculture Sciences, Department of Crop Production Ecology, SE-750 07 Uppsala, Sweden
| | - J Eriksson
- Swedish University of Agriculture Sciences, Department of Soil and Environment, SE-750 07 Uppsala, 17, Sweden
| | - W Friesl-Hanl
- AIT Austrian Institute of Technology GmbH, Center for Energy, 3430 Tulln, Austria
| | - R Galazka
- Institute of Soil Science and Plant Cultivation, State Research Institute, Czartoryskich 8, 24-100 Pulawy, Poland
| | - J Janssen
- Hasselt University, Centre for Environmental Sciences, 23 Agoralaan building D, B-3590 Diepenbeek, Belgium
| | - M Mench
- BIOGECO, INRA, Univ. Bordeaux, 33615 Pessac, France
| | - I Müller
- Saxon State Office for Environment, Agriculture and Geology, Pillnitzer Platz 3, 01326 Dresden Pillnitz, Germany
| | - S Neu
- Saxon State Office for Environment, Agriculture and Geology, Pillnitzer Platz 3, 01326 Dresden Pillnitz, Germany
| | - M Puschenreiter
- University of Natural Resources and Life Sciences Vienna - BOKU, Department of Forest and Soil Sciences, 3430 Tulln, Austria
| | - G Siebielec
- Institute of Soil Science and Plant Cultivation, State Research Institute, Czartoryskich 8, 24-100 Pulawy, Poland
| | - J Vangronsveld
- Hasselt University, Centre for Environmental Sciences, 23 Agoralaan building D, B-3590 Diepenbeek, Belgium
| | - P S Kidd
- Instituto de Investigaciones Agrobiológicas de Galicia (IIAG), Consejo Superior de Investigaciones Científicas (CSIC), Aptdo. 122, Santiago de Compostela 15780, Spain
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9
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Structural and functional variability in root-associated bacterial microbiomes of Cd/Zn hyperaccumulator Sedum alfredii. Appl Microbiol Biotechnol 2017; 101:7961-7976. [PMID: 28894921 DOI: 10.1007/s00253-017-8469-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 07/08/2017] [Accepted: 07/30/2017] [Indexed: 01/27/2023]
Abstract
Interactions between roots and microbes affect plant's resistance to abiotic stress. However, the structural and functional variation of root-associated microbiomes and their effects on metal accumulation in hyperaccumulators remain poorly understood. Here, we characterize the root-associated microbiota of a hyperaccumulating (HP) and a non-hyperaccumulating (NHP) genotype of Sedum alfredii by 16S ribosomal RNA gene profiling. We show that distinct microbiomes are observed in four spatially separable compartments: the bulk soil, rhizosphere, rhizoplane, and endosphere. Both the rhizosphere and rhizoplane were preferentially colonized by Proteobacteria, and the endosphere by Actinobacteria. The rhizosphere and endophytic microbiomes were dominated by the family of Sphingomonadaceae and Streptomycetaceae, respectively, which benefited for their survival and adaptation. The bacterial α-diversity decreases along the spatial gradient from the rhizosphere to the endosphere. Soil type and compartment were strongest determinants of root-associated community variation, and host genotype explained a small, but significant amount of variation. The enrichment of Bacteroidetes and depletion of Firmicutes and Planctomycetes in the HP endosphere compared with that of the NHP genotype may affect metal hyperaccumulation. Program PICRUSt predicted moderate functional differences in bacterial consortia across rhizocompartments and soil types. The functional categories involved in membrane transporters (specifically ATP-binding cassette transporters) and energy metabolism were overrepresented in endosphere of HP in comparison with NHP genotypes. Taken together, our study reveals substantial variation in structure and function of microbiomes colonizing different compartments, with the endophytic microbiota potentially playing an important role in heavy metal hyperaccumulation.
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10
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Hartmann M, Brunner I, Hagedorn F, Bardgett RD, Stierli B, Herzog C, Chen X, Zingg A, Graf-Pannatier E, Rigling A, Frey B. A decade of irrigation transforms the soil microbiome of a semi-arid pine forest. Mol Ecol 2017; 26:1190-1206. [DOI: 10.1111/mec.13995] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Revised: 11/18/2016] [Accepted: 12/19/2016] [Indexed: 01/17/2023]
Affiliation(s)
- Martin Hartmann
- Swiss Federal Research Institute WSL; 8903 Birmensdorf Switzerland
| | - Ivano Brunner
- Swiss Federal Research Institute WSL; 8903 Birmensdorf Switzerland
| | - Frank Hagedorn
- Swiss Federal Research Institute WSL; 8903 Birmensdorf Switzerland
| | - Richard D. Bardgett
- School of Earth and Environmental Sciences; Michael Smith Building; The University of Manchester; M13 9PT Manchester UK
| | - Beat Stierli
- Swiss Federal Research Institute WSL; 8903 Birmensdorf Switzerland
| | - Claude Herzog
- Swiss Federal Research Institute WSL; 8903 Birmensdorf Switzerland
- Swiss Federal Institute of Technology ETH; 8092 Zürich Switzerland
| | - Xiamei Chen
- Swiss Federal Research Institute WSL; 8903 Birmensdorf Switzerland
| | - Andreas Zingg
- Swiss Federal Research Institute WSL; 8903 Birmensdorf Switzerland
| | | | - Andreas Rigling
- Swiss Federal Research Institute WSL; 8903 Birmensdorf Switzerland
| | - Beat Frey
- Swiss Federal Research Institute WSL; 8903 Birmensdorf Switzerland
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11
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Wang P, Di HJ, Cameron KC, Tan Q, Podolyan A, Zhao X, McLaren RG, Hu C. The response of ammonia-oxidizing microorganisms to trace metals and urine in two grassland soils in New Zealand. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:2476-2483. [PMID: 27817146 DOI: 10.1007/s11356-016-8030-1] [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: 08/05/2016] [Accepted: 11/01/2016] [Indexed: 06/06/2023]
Abstract
An incubation experiment was conducted to investigate the response of ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), and the nitrification rate to the contamination of Cu, Zn, and Cd in two New Zealand grassland soils. The soils spiked with different concentrations of Cu (20 and 50 mg kg-1), Zn (20 and 50 mg kg-1), and Cd (2 and 10 mg kg-1) were incubated for 14 days and then treated with 500 mg kg-1 urine-N before continuing incubation for a total of 115 days. Soils were sampled at intervals throughout the incubation. The nitrification rate in soils at each sampling period was determined, and the abundance of AOB and AOA was measured by real-time quantification polymerase chain reaction (qPCR) assay of the amoA gene copy numbers. The results revealed that moderate trace metal stress did not significantly affect the abundance of AOB and AOA in the two soils, probably due to the high organic matter content of the soils which would have reduced the toxic effect of the metals. Nitrification rates were much greater and the observable nitrification period was much shorter in the dairy farm (DF) soil, in which the AOB and AOA abundances were greater than those of the mixed cropping farm (MF) soil. AOB were shown to grow under high nitrogen conditions, whereas AOA were shown to grow under low N environments, with different metal concentrations. Therefore, nitrogen status rather than metal applications was the main determining factor for AOB and AOA growth in the two soils studied.
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Affiliation(s)
- Pengcheng Wang
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
- The Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Hong J Di
- Centre for Soil and Environmental Research, Lincoln University, Christchurch, New Zealand.
| | - Keith C Cameron
- Centre for Soil and Environmental Research, Lincoln University, Christchurch, New Zealand
| | - Qiling Tan
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Andriy Podolyan
- Centre for Soil and Environmental Research, Lincoln University, Christchurch, New Zealand
| | - Xiaohu Zhao
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Ron G McLaren
- Centre for Soil and Environmental Research, Lincoln University, Christchurch, New Zealand
| | - Chengxiao Hu
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, China.
- The Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China.
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12
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Yin Y, Song W, Gu J, Zhang K, Qian X, Zhang X, Zhang Y, Li Y, Wang X. Effects of copper on the abundance and diversity of ammonia oxidizers during dairy cattle manure composting. BIORESOURCE TECHNOLOGY 2016; 221:181-187. [PMID: 27639237 DOI: 10.1016/j.biortech.2016.09.016] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 08/31/2016] [Accepted: 09/04/2016] [Indexed: 06/06/2023]
Abstract
This study investigated the effects of adding Cu(II) at two exposure levels (50 and 500mgkg-1, i.e., Cu50 and Cu500 treatments, respectively) on the activity of ammonia-oxidizing microorganisms during dairy cattle manure composting. The results showed that the pH, NH4+-N, NO3--N, and potential ammonia oxidation values were inhibited significantly by the addition of Cu(II). Furthermore, the abundances of the ammonia-oxidizing archaea (AOA) amoA gene and ammonia-oxidizing bacteria (AOB) amoA gene were determined by quantitative PCR, and their compositions were evaluated by denaturing gradient gel electrophoresis (DGGE). AOA was the dominant ammonia oxidizing microorganism, of which the abundance was much higher than AOB during composting. Cu50 and Cu500 had significant inhibitory effects on the abundance of the amoA gene. The DGGE profile and statistical analysis showed that Cu(II) changed the AOA and AOB community structure and diversity, where Nitrosomonas and Crenarchaeota dominated throughout the composting process.
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Affiliation(s)
- Yanan Yin
- College of Resources and Environmental Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Wen Song
- College of Science, Northwest A&F University, Yangling 712100, China
| | - Jie Gu
- College of Resources and Environmental Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Kaiyu Zhang
- College of Resources and Environmental Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xun Qian
- College of Resources and Environmental Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xin Zhang
- College of Science, Northwest A&F University, Yangling 712100, China
| | - Yajun Zhang
- College of Resources and Environmental Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yang Li
- College of Resources and Environmental Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiaojuan Wang
- College of Resources and Environmental Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
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13
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Hartmann M, Niklaus PA, Zimmermann S, Schmutz S, Kremer J, Abarenkov K, Lüscher P, Widmer F, Frey B. Resistance and resilience of the forest soil microbiome to logging-associated compaction. ISME JOURNAL 2013; 8:226-44. [PMID: 24030594 DOI: 10.1038/ismej.2013.141] [Citation(s) in RCA: 123] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Revised: 07/15/2013] [Accepted: 07/15/2013] [Indexed: 02/01/2023]
Abstract
Soil compaction is a major disturbance associated with logging, but we lack a fundamental understanding of how this affects the soil microbiome. We assessed the structural resistance and resilience of the microbiome using a high-throughput pyrosequencing approach in differently compacted soils at two forest sites and correlated these findings with changes in soil physical properties and functions. Alterations in soil porosity after compaction strongly limited the air and water conductivity. Compaction significantly reduced abundance, increased diversity, and persistently altered the structure of the microbiota. Fungi were less resistant and resilient than bacteria; clayey soils were less resistant and resilient than sandy soils. The strongest effects were observed in soils with unfavorable moisture conditions, where air and water conductivities dropped well below 10% of their initial value. Maximum impact was observed around 6-12 months after compaction, and microbial communities showed resilience in lightly but not in severely compacted soils 4 years post disturbance. Bacteria capable of anaerobic respiration, including sulfate, sulfur, and metal reducers of the Proteobacteria and Firmicutes, were significantly associated with compacted soils. Compaction detrimentally affected ectomycorrhizal species, whereas saprobic and parasitic fungi proportionally increased in compacted soils. Structural shifts in the microbiota were accompanied by significant changes in soil processes, resulting in reduced carbon dioxide, and increased methane and nitrous oxide emissions from compacted soils. This study demonstrates that physical soil disturbance during logging induces profound and long-lasting changes in the soil microbiome and associated soil functions, raising awareness regarding sustainable management of economically driven logging operations.
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Affiliation(s)
- Martin Hartmann
- 1] Forest Soils and Biogeochemistry, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland [2] Molecular Ecology, Research Station Agroscope Reckenholz-Tänikon ART, Zurich, Switzerland
| | - Pascal A Niklaus
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Stephan Zimmermann
- Forest Soils and Biogeochemistry, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Stefan Schmutz
- Forest Soils and Biogeochemistry, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Johann Kremer
- Forest Work Science and Applied Informatics, Technical University of Munich, Freising, Germany
| | | | - Peter Lüscher
- Forest Soils and Biogeochemistry, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Franco Widmer
- Molecular Ecology, Research Station Agroscope Reckenholz-Tänikon ART, Zurich, Switzerland
| | - Beat Frey
- Forest Soils and Biogeochemistry, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
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14
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Zumsteg A, Schmutz S, Frey B. Identification of biomass utilizing bacteria in a carbon-depleted glacier forefield soil by the use of 13C DNA stable isotope probing. ENVIRONMENTAL MICROBIOLOGY REPORTS 2013; 5:424-437. [PMID: 23754723 DOI: 10.1111/1758-2229.12027] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Accepted: 12/13/2012] [Indexed: 06/02/2023]
Abstract
As Alpine glaciers are retreating rapidly, bare soils with low organic C and N contents are becoming exposed. Carbon availability is a key factor regulating microbial diversity and ecosystem functioning in these soils. The aim of this study was to investigate how bacterial activity, community structure and composition are influenced by organic carbon availability. Bare soils were supplied with (13)C-labelled fungal (Penicillium sp.) and green algal (Chlorella sp.) biomass and the CO2 evolution and its δ(13)C signature were monitored up to 60 days. These organisms have previously been isolated near the glacier terminus. DNA stable isotope probing followed by T-RFLP profiling and sequencing of 16S rRNA genes was employed to identify consumers able to assimilate carbon from these biomass amendments. Higher respiration and higher bacterial activity indicated a more efficient utilization of algal cells than fungal cells. Flavobacterium sp. predominantly incorporated fungal-derived C, whereas the algal-derived C was mainly incorporated by Acidobacteria and Proteobacteria. This study emphasizes the important role of both fungal and algal biomass in increasing the carbon pool in recently deglaciated bare soils, as only 20% of the added C was respired as CO2, and the rest, we presume, remained in the soil.
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Affiliation(s)
- Anita Zumsteg
- Forest Soils and Biogeochemistry, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
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15
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Rieder SR, Brunner I, Daniel O, Liu B, Frey B. Methylation of mercury in earthworms and the effect of mercury on the associated bacterial communities. PLoS One 2013; 8:e61215. [PMID: 23577209 PMCID: PMC3618111 DOI: 10.1371/journal.pone.0061215] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Accepted: 03/07/2013] [Indexed: 11/24/2022] Open
Abstract
Methylmercury compounds are very toxic for most organisms. Here, we investigated the potential of earthworms to methylate inorganic-Hg. We hypothesized that the anaerobic and nutrient-rich conditions in the digestive tracts of earthworm's promote the methylation of Hg through the action of their gut bacteria. Earthworms were either grown in sterile soils treated with an inorganic (HgCl2) or organic (CH3HgCl) Hg source, or were left untreated. After 30 days of incubation, the total-Hg and methyl-Hg concentrations in the soils, earthworms, and their casts were analyzed. The impact of Hg on the bacterial community compositions in earthworms was also studied. Tissue concentrations of methyl-Hg in earthworms grown in soils treated with inorganic-Hg were about six times higher than in earthworms grown in soils without Hg. Concentrations of methyl-Hg in the soils and earthworm casts remained at significantly lower levels suggesting that Hg was mainly methylated in the earthworms. Bacterial communities in earthworms were mostly affected by methyl-Hg treatment. Terminal-restriction fragments (T-RFs) affiliated to Firmicutes were sensitive to inorganic and methyl-Hg, whereas T-RFs related to Betaproteobacteria were tolerant to the Hg treatments. Sulphate-reducing bacteria were detected in earthworms but not in soils.
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Affiliation(s)
- Stephan Raphael Rieder
- Rhizosphere Processes Group, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
- Institute for Biogeochemistry and Pollutant Dynamics, ETH Zürich, Zürich, Switzerland
| | - Ivano Brunner
- Rhizosphere Processes Group, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Otto Daniel
- Ecotoxicology Group, Agroscope Changins-Wädenswil, Wädenswil, Switzerland
| | - Bian Liu
- Medicine-Pulmonary, Allergy and Critical Care, Columbia University, New York, New York, United States
| | - Beat Frey
- Rhizosphere Processes Group, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
- * E-mail:
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16
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Ollivier J, Wanat N, Austruy A, Hitmi A, Joussein E, Welzl G, Munch JC, Schloter M. Abundance and diversity of ammonia-oxidizing prokaryotes in the root-rhizosphere complex of Miscanthus × giganteus grown in heavy metal-contaminated soils. MICROBIAL ECOLOGY 2012; 64:1038-1046. [PMID: 22688859 DOI: 10.1007/s00248-012-0078-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Accepted: 05/23/2012] [Indexed: 06/01/2023]
Abstract
Mine wastes have been considered as a source of heavy metal (HM) contamination in the environment and negatively impact many important ecosystem services provided by soils. Plants like Miscanthus, which tolerate high HM concentrations in soil, are often used for phytoremediation and provide the possibility to use these soils at least for the production of energy crops. However, it is not clear if plant growth at these sites is limited by the availability of nutrients, mainly nitrogen, as microbes in soil might be affected by the contaminant. Therefore, in this study, we investigated in a greenhouse experiment the response of ammonia-oxidizing microbes in the root-rhizosphere complex of Miscanthus × giganteus grown in soils with different levels of long-term arsenic (As) and lead (Pb) contamination. Quantitative PCR of the ammonia monooxigenease gene (amoA) was performed to assess the abundance of ammonia-oxidizing bacteria (AOB) and archaea (AOA) at two different points of plant growth. Furthermore, bulk soil samples before planting were analyzed. In addition, terminal restriction fragment length polymorphism (T-RFLP) analysis was used to investigate the diversity of archaeal amoA amplicons. Whereas high concentrations of As and Pb in soil (83 and 15 g/kg, respectively) resulted independent from plant growth in a clear reduction of AOA and AOB compared to the control soils with lower HM contents, in soils with contamination levels of 10 g/kg As and 0.2 g/kg Pb, only AOB were negatively affected in bulk soil samples. Diversity analysis of archaeal amoA genes revealed clear differences in T-RFLP patterns in response to the degree of HM contamination. Therefore, our results could clearly prove the different response patterns of AOA and AOB in HM-contaminated soils and the development of archaeal amoA phylotypes which are more tolerant towards HMs in soil samples from the areas that were impacted the most by mining waste, which could contribute to functional redundancy of ammonia-oxidizing microbes in soils and stability of nitrification pattern.
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Affiliation(s)
- Julien Ollivier
- Technical University Munich, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany.
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17
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Regier N, Frey B, Converse B, Roden E, Grosse-Honebrink A, Bravo AG, Cosio C. Effect of Elodea nuttallii roots on bacterial communities and MMHg proportion in a Hg polluted sediment. PLoS One 2012; 7:e45565. [PMID: 23029102 PMCID: PMC3444453 DOI: 10.1371/journal.pone.0045565] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Accepted: 08/20/2012] [Indexed: 11/19/2022] Open
Abstract
The objective of this study was to assess the effect of a rooted macrophyte Elodea nuttallii on rhizosphere bacterial communities in Hg contaminated sediments. Specimens of E. nuttallii were exposed to sediments from the Hg contaminated Babeni reservoir (Olt River, Romania) in our microcosm. Plants were allowed to grow for two months until they occupied the entirety of the sediments. Total Hg and MMHg were analysed in sediments where an increased MMHg percentage of the total Hg in pore water of rhizosphere sediments was found. E. nuttallii roots also significantly changed the bacterial community structure in rhizosphere sediments compared to bulk sediments. Deltaproteobacteria dominated the rhizosphere bacterial community where members of Geobacteraceae within the Desulfuromonadales and Desulfobacteraceae were identified. Two bacterial operational taxonomic units (OTUs) which were phylogenetically related to sulfate-reducing bacteria (SRB) became abundant in the rhizosphere. We suggest that these phylotypes could be potentially methylating bacteria and might be responsible for the higher MMHg percentage of the total Hg in rhizosphere sediments. However, SRB were not significantly favoured in rhizosphere sediments as shown by qPCR. Our findings support the hypothesis that rooted macrophytes created a microenvironment favorable for Hg methylation. The presence of E. nuttallii in Hg contaminated sediments should therefore not be overlooked.
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Affiliation(s)
- Nicole Regier
- F.-A. Forel Institute, Geneva University, Versoix, Switzerland
| | - Beat Frey
- Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Brandon Converse
- Department of Geoscience, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Eric Roden
- Department of Geoscience, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | | | | | - Claudia Cosio
- F.-A. Forel Institute, Geneva University, Versoix, Switzerland
- * E-mail:
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18
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Liu YR, Zheng YM, He JZ. Toxicity of profenofos to the springtail, Folsomia candida, and ammonia-oxidizers in two agricultural soils. ECOTOXICOLOGY (LONDON, ENGLAND) 2012; 21:1126-1134. [PMID: 22362510 DOI: 10.1007/s10646-012-0867-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 02/07/2012] [Indexed: 05/31/2023]
Abstract
Extensive use of organophosphorus insecticide profenofos (PFF) for agricultural and house-hold purposes has led to serious environmental pollution, with potential risk to organisms in the ecosystem. This study examined the toxicity of PFF to the soil springtail Folsomia candida and ammonia-oxidizers through a series of toxicity tests conducted on two agricultural soils. It was found that the survival, reproduction, hsp70 gene expression of F. candida and the soil potential nitrification rate (PNR) were sensitive to the PFF, whereas no apparent change was observed in the abundance of ammonia-oxidizers. The reproduction of F. candida was the most sensitive endpoint (mean 0.10 mg/kg of EC(50) value) for PFF, although the test was more time-consuming. The results of the acute toxicity tests suggested that the survival of F. candida could be considered as the most suitable bioindicator for fast screening of PFF toxicity because of its fast and easy test procedure. In addition, the hsp70 gene expression in F. candida and the PNR could be used as important parameters for assessment of PFF toxicity. The threshold concentration based on the obtained endpoints differed in the two soils, and consequently the soil property should be considered in toxicity assessments of contaminated soils.
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Affiliation(s)
- Yu-Rong Liu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
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19
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Blakney AJC, Patten CL. A plant growth-promoting pseudomonad is closely related to the Pseudomonas syringae complex of plant pathogens. FEMS Microbiol Ecol 2011; 77:546-57. [PMID: 21609343 DOI: 10.1111/j.1574-6941.2011.01136.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Pseudomonas putida GR12-2 is well known as a plant growth-promoting rhizobacterium; however, phylogenetic analysis using the 16S rRNA gene and four housekeeping genes indicated that this strain forms a monophyletic group with the Pseudomonas syringae complex, which is composed of several species of plant pathogens. On the basis of these sequence analyses, we suggest that P. putida GR12-2 be redesignated as P. syringae GR12-2. To compare the ecological roles of P. syringae GR12-2 with its close relatives P. syringae pathovar (pv.) tomato DC3000 and P. syringae pv. syringae B728a, we investigated their ability to cause disease and promote plant growth. When introduced on tobacco or tomato leaves, P. syringae GR12-2 was unable to elicit a hypersensitive response or cause disease, which are characteristic responses of P. syringae DC3000 and B728a, nor were type III secretion system genes required for virulence detected in P. syringae GR12-2 by PCR or DNA hybridization. In contrast to P. syringae GR12-2, neither of the phytopathogens was able to promote root growth when inoculated onto canola seeds. Although commensals and nonpathogens have been reported among the strains of the P. syringae complex, P. syringae GR12-2 is a mutualist and a phytostimulator.
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Affiliation(s)
- Andrew J C Blakney
- Department of Biology, University of New Brunswick, Fredericton, NB, Canada
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20
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Heavy-machinery traffic impacts methane emissions as well as methanogen abundance and community structure in oxic forest soils. Appl Environ Microbiol 2011; 77:6060-8. [PMID: 21742929 DOI: 10.1128/aem.05206-11] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Temperate forest soils are usually efficient sinks for the greenhouse gas methane, at least in the absence of significant amounts of methanogens. We demonstrate here that trafficking with heavy harvesting machines caused a large reduction in CH(4) consumption and even turned well-aerated forest soils into net methane sources. In addition to studying methane fluxes, we investigated the responses of methanogens after trafficking in two different forest sites. Trafficking generated wheel tracks with different impact (low, moderate, severe, and unaffected). We found that machine passes decreased the soils' macropore space and lowered hydraulic conductivities in wheel tracks. Severely compacted soils yielded high methanogenic abundance, as demonstrated by quantitative PCR analyses of methyl coenzyme M reductase (mcrA) genes, whereas these sequences were undetectable in unaffected soils. Even after a year after traffic compression, methanogen abundance in compacted soils did not decline, indicating a stability of methanogens here over time. Compacted wheel tracks exhibited a relatively constant community structure, since we found several persisting mcrA sequence types continuously present at all sampling times. Phylogenetic analysis revealed a rather large methanogen diversity in the compacted soil, and most mcrA gene sequences were mostly similar to known sequences from wetlands. The majority of mcrA gene sequences belonged either to the order Methanosarcinales or Methanomicrobiales, whereas both sites were dominated by members of the families Methanomicrobiaceae Fencluster, with similar sequences obtained from peatland environments. The results show that compacting wet forest soils by heavy machinery causes increases in methane production and release.
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21
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Epelde L, Becerril JM, Kowalchuk GA, Deng Y, Zhou J, Garbisu C. Impact of metal pollution and Thlaspi caerulescens growth on soil microbial communities. Appl Environ Microbiol 2010; 76:7843-53. [PMID: 20935131 PMCID: PMC2988604 DOI: 10.1128/aem.01045-10] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2010] [Accepted: 09/26/2010] [Indexed: 11/20/2022] Open
Abstract
Soil microorganisms drive critical functions in plant-soil systems. As such, various microbial properties have been proposed as indicators of soil functioning, making them potentially useful in evaluating the recovery of polluted soils via phytoremediation strategies. To evaluate microbial responses to metal phytoextraction using hyperaccumulators, a microcosm experiment was carried out to study the impacts of Zn and/or Cd pollution and Thlaspi caerulescens growth on key soil microbial properties: basal respiration; substrate-induced respiration (SIR); bacterial community structure as assessed by PCR-denaturing gradient gel electrophoresis (DGGE); community sizes of total bacteria, ammonia-oxidizing bacteria, and chitin-degrading bacteria as assessed by quantitative PCR (Q-PCR); and functional gene distributions as determined by functional gene arrays (GeoChip). T. caerulescens proved to be suitable for Zn and Cd phytoextraction: shoots accumulated up to 8,211 and 1,763 mg kg(-1) (dry weight [DW]) of Zn and Cd, respectively. In general, Zn pollution led to decreased levels of basal respiration and ammonia-oxidizing bacteria, while T. caerulescens growth increased the values of substrate-induced respiration (SIR) and total bacteria. In soils polluted with 1,000 mg Zn kg(-1) and 250 mg Cd kg(-1) (DW), soil bacterial community profiles and the distribution of microbial functional genes were most affected by the presence of metals. Metal-polluted and planted soils had the highest percentage of unique genes detected via the GeoChip (35%). It was possible to track microbial responses to planting with T. caerulescens and to gain insight into the effects of metal pollution on soilborne microbial communities.
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Affiliation(s)
- Lur Epelde
- Neiker-Tecnalia, Department of Ecosystems, Berreaga 1, E-48160 Derio, Spain, Department of Plant Biology and Ecology, University of the Basque Country, P.O. Box 644, E-48080 Bilbao, Spain, NIOO-Centre for Terrestrial Ecology, P.O. Box 40, 6666 ZG Heteren, Netherlands, Institute of Ecological Science, Vrije Universiteit, De Boelelaan 1085, 1081 HV, Amsterdam, Netherlands, University of Oklahoma, Department of Botany and Microbiology, Institute for Environmental Genomics, Norman, Oklahoma 73019
| | - José M. Becerril
- Neiker-Tecnalia, Department of Ecosystems, Berreaga 1, E-48160 Derio, Spain, Department of Plant Biology and Ecology, University of the Basque Country, P.O. Box 644, E-48080 Bilbao, Spain, NIOO-Centre for Terrestrial Ecology, P.O. Box 40, 6666 ZG Heteren, Netherlands, Institute of Ecological Science, Vrije Universiteit, De Boelelaan 1085, 1081 HV, Amsterdam, Netherlands, University of Oklahoma, Department of Botany and Microbiology, Institute for Environmental Genomics, Norman, Oklahoma 73019
| | - George A. Kowalchuk
- Neiker-Tecnalia, Department of Ecosystems, Berreaga 1, E-48160 Derio, Spain, Department of Plant Biology and Ecology, University of the Basque Country, P.O. Box 644, E-48080 Bilbao, Spain, NIOO-Centre for Terrestrial Ecology, P.O. Box 40, 6666 ZG Heteren, Netherlands, Institute of Ecological Science, Vrije Universiteit, De Boelelaan 1085, 1081 HV, Amsterdam, Netherlands, University of Oklahoma, Department of Botany and Microbiology, Institute for Environmental Genomics, Norman, Oklahoma 73019
| | - Ye Deng
- Neiker-Tecnalia, Department of Ecosystems, Berreaga 1, E-48160 Derio, Spain, Department of Plant Biology and Ecology, University of the Basque Country, P.O. Box 644, E-48080 Bilbao, Spain, NIOO-Centre for Terrestrial Ecology, P.O. Box 40, 6666 ZG Heteren, Netherlands, Institute of Ecological Science, Vrije Universiteit, De Boelelaan 1085, 1081 HV, Amsterdam, Netherlands, University of Oklahoma, Department of Botany and Microbiology, Institute for Environmental Genomics, Norman, Oklahoma 73019
| | - Jizhong Zhou
- Neiker-Tecnalia, Department of Ecosystems, Berreaga 1, E-48160 Derio, Spain, Department of Plant Biology and Ecology, University of the Basque Country, P.O. Box 644, E-48080 Bilbao, Spain, NIOO-Centre for Terrestrial Ecology, P.O. Box 40, 6666 ZG Heteren, Netherlands, Institute of Ecological Science, Vrije Universiteit, De Boelelaan 1085, 1081 HV, Amsterdam, Netherlands, University of Oklahoma, Department of Botany and Microbiology, Institute for Environmental Genomics, Norman, Oklahoma 73019
| | - Carlos Garbisu
- Neiker-Tecnalia, Department of Ecosystems, Berreaga 1, E-48160 Derio, Spain, Department of Plant Biology and Ecology, University of the Basque Country, P.O. Box 644, E-48080 Bilbao, Spain, NIOO-Centre for Terrestrial Ecology, P.O. Box 40, 6666 ZG Heteren, Netherlands, Institute of Ecological Science, Vrije Universiteit, De Boelelaan 1085, 1081 HV, Amsterdam, Netherlands, University of Oklahoma, Department of Botany and Microbiology, Institute for Environmental Genomics, Norman, Oklahoma 73019
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Liu YR, Zheng YM, Shen JP, Zhang LM, He JZ. Effects of mercury on the activity and community composition of soil ammonia oxidizers. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2010; 17:1237-1244. [PMID: 20169414 DOI: 10.1007/s11356-010-0302-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2009] [Accepted: 01/20/2010] [Indexed: 05/28/2023]
Abstract
PURPOSE Experiments were conducted to examine the effects of mercury (Hg) on soil nitrification activities and the microbial communities of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA). METHODS The soil samples spiked with different Hg concentrations were incubated for a period of 1, 2, 4, and 8 weeks in triplicate and the potential nitrification rate (PNR) of the samples was determined. The abundance of AOB and AOA was measured after an 8-week incubation by real-time polymerase chain reaction (PCR) assay of the amoA genes, while the community compositions by cloning and sequencing approaches. RESULTS The soil PNR differed with different incubation periods. It tended to decrease with increasing soil Hg concentrations at week 1, basing on which the half-maximal effective concentration (EC50) was 1.59 mg kg(-1). There was no significant difference in the abundance of AOB or AOA among the treatments. The AOB community was dominated by Nitrosospira-like sequences and more than 70% of the obtained clones were affiliated with the cluster 3a.2. The percentage of cluster 3a.1 in AOB community appeared to a consistent trend of decreasing with ascending soil Hg concentrations. While all the AOA sequences in the clone libraries were grouped into cluster S (soil and sediment origin). CONCLUSIONS This study revealed that Hg could inhibit soil potential nitrification and the extent varied with incubation periods. Soil Hg pollution changed the composition of soil AOB to some extent. These findings will be helpful to recognize the effects of Hg on the activity and community composition of soil ammonia oxidizers.
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Affiliation(s)
- Yu-Rong Liu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
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Thébault A, Frey B, Mitchell EAD, Buttler A. Species-specific effects of polyploidisation and plant traits of Centaurea maculosa and Senecio inaequidens on rhizosphere microorganisms. Oecologia 2010; 163:1011-20. [PMID: 20229242 DOI: 10.1007/s00442-010-1598-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2009] [Accepted: 02/25/2010] [Indexed: 11/24/2022]
Abstract
Invasive plant species represent a threat to terrestrial ecosystems, but their effects on the soil biota and the mechanisms involved are not yet well understood. Many invasive species have undergone polyploidisation, leading to the coexistence of various cytotypes in the native range, whereas, in most cases, only one cytotype is present in the introduced range. Since genetic variation within a species can modify soil rhizosphere communities, we studied the effects of different cytotypes and ranges (native diploid, native tetraploid and introduced tetraploid) of Centaurea maculosa and Senecio inaequidens on microbial biomass carbon, rhizosphere total DNA content and bacterial communities of a standard soil in relation to plant functional traits. There was no overall significant difference in microbial biomass between cytotypes. The variation of rhizosphere total DNA content and bacterial community structure according to cytotype was species specific. The rhizosphere DNA content of S. inaequidens decreased with polyploidisation in the native range but did not vary for C. maculosa. In contrast, the bacterial community structure of C. maculosa was affected by polyploidisation and its diversity increased, whereas there was no significant change for S. inaequidens. Traits of S. inaequidens were correlated to the rhizosphere biota. Bacterial diversity and total DNA content were positively correlated with resource allocation to belowground growth and late flowering, whereas microbial biomass carbon was negatively correlated to investment in reproduction. There were no correlations between traits of the cytotypes of C. maculosa and corresponding rhizosphere soil biota. This study shows that polyploidisation may affect rhizosphere bacterial community composition, but that effects vary among plant species. Such changes may contribute to the success of invasive polyploid genotypes in the introduced range.
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Affiliation(s)
- Aurélie Thébault
- Laboratory of Ecological Systems, Ecole Polytechnique Fédérale de Lausanne, Station 2, 1015 Lausanne, Switzerland.
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