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Liu ZY, Yang R, Xiang XY, Niu LL, Yin DX. Enhancement of phytoextraction efficiency coupling Pteris vittata with low-dose biochar in arsenic-contaminated soil. INTERNATIONAL JOURNAL OF PHYTOREMEDIATION 2023; 25:1810-1818. [PMID: 37066697 DOI: 10.1080/15226514.2023.2199876] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Phytoremediation of arsenic (As) by Pteris vittata (P. vittata) is a cost-effective and environmentally friendly method for restoring As-contaminated sites. However, the phytoextraction efficiency is low in some cases, such as clay soil, thus biochar was applied to enhance the efficiency of As extraction. The paper investigated the effect of biochar on soil characteristic, As mobility, and As uptake in P. vittata with a 90-day greenhouse experiment. Biochar derived from rice straw was added at rates of 0.5, 1.5, and 4% (w/w). The results showed that, under biochar amendment, soil pH raised from 5.24 to 6.03 and 4.91 to 5.85, soil dissolved organic carbon (DOC) increased 11.1-46.1% and 2.8-11.2%, respectively, in rhizosphere and bulk soils. Biochar also increased soil catalase (CAT) activity significantly, especially for the rhizosphere soil. Besides, biochar increased the labile As in the soils and transfer coefficient from roots to aboveground, thereby enhancing As accumulation by P. vittata tissues. The accumulation of As in fronds of P. vittata was up to 350 mg kg-1 in 1.5% biochar, which was more than twice the control and far beyond other biochar treatments. The results indicate that biochar addition is favorable to improve phytoremediation of P. vittata in As-contaminated soil and 1.5% (w/w) biochar may be a reasonable application ratio, thus providing an effective solution to enhance the efficiency of As phytoextraction.
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Affiliation(s)
- Zhou-Yu Liu
- School of Resources and Environment, Anhui Agricultural University, Hefei, China
| | - Rui Yang
- School of Resources and Environment, Anhui Agricultural University, Hefei, China
| | - Xue-Ying Xiang
- College of Environmental Sciences and Engineering, Peking University, Beijing, China
| | - Li-Lu Niu
- School of Resources and Environment, Anhui Agricultural University, Hefei, China
| | - Dai-Xia Yin
- School of Resources and Environment, Anhui Agricultural University, Hefei, China
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Xu Q, Fu H, Zhu B, Hussain HA, Zhang K, Tian X, Duan M, Xie X, Wang L. Potassium Improves Drought Stress Tolerance in Plants by Affecting Root Morphology, Root Exudates and Microbial Diversity. Metabolites 2021; 11:metabo11030131. [PMID: 33668385 PMCID: PMC7996290 DOI: 10.3390/metabo11030131] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 02/14/2021] [Accepted: 02/20/2021] [Indexed: 11/16/2022] Open
Abstract
Potassium (K) reduces the deleterious effects of drought stress on plants. However, this mitigation has been studied mainly in the aboveground plant pathways, while the effect of K on root-soil interactions in the underground part is still underexplored. Here, we conducted the experiments to investigate how K enhances plant resistance and tolerance to drought by controlling rhizosphere processes. Three culture methods (sand, water, and soil) evaluated two rapeseed cultivars’ root morphology, root exudates, soil nutrients, and microbial community structure under different K supply levels and water conditions to construct a defensive network of the underground part. We found that K supply increased the root length and density and the organic acids secretion. The organic acids were significantly associated with the available potassium decomposition, in order of formic acid > malonic acid > lactic acid > oxalic acid > citric acid. However, the mitigation had the hormesis effect, as the appropriate range of K facilitated the morphological characteristic and physiological function of the root system with increases of supply levels, while the excessive input of K could hinder the plant growth. The positive effect of K-fertilizer on soil pH, available phosphorus and available potassium content, and microbial diversity index was more significant under the water stress. The rhizosphere nutrients and pH further promoted the microbial community development by the structural equation modeling, while the non-rhizosphere nutrients had an indirect negative effect on microbes. In short, K application could alleviate drought stress on the growth and development of plants by regulating the morphology and secretion of roots and soil ecosystems.
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Affiliation(s)
- Qiwen Xu
- Key Laboratory of Eco-Environments in Three Gorges Reservoir Region, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (Q.X.); (B.Z.); (K.Z.); (X.T.); (M.D.); (X.X.)
| | - Hao Fu
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China;
| | - Bo Zhu
- Key Laboratory of Eco-Environments in Three Gorges Reservoir Region, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (Q.X.); (B.Z.); (K.Z.); (X.T.); (M.D.); (X.X.)
| | - Hafiz Athar Hussain
- Key Laboratory of Eco-Environments in Three Gorges Reservoir Region, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (Q.X.); (B.Z.); (K.Z.); (X.T.); (M.D.); (X.X.)
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Correspondence: (H.A.H.); (L.W.)
| | - Kangping Zhang
- Key Laboratory of Eco-Environments in Three Gorges Reservoir Region, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (Q.X.); (B.Z.); (K.Z.); (X.T.); (M.D.); (X.X.)
| | - Xiaoqing Tian
- Key Laboratory of Eco-Environments in Three Gorges Reservoir Region, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (Q.X.); (B.Z.); (K.Z.); (X.T.); (M.D.); (X.X.)
| | - Meichun Duan
- Key Laboratory of Eco-Environments in Three Gorges Reservoir Region, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (Q.X.); (B.Z.); (K.Z.); (X.T.); (M.D.); (X.X.)
| | - Xiaoyu Xie
- Key Laboratory of Eco-Environments in Three Gorges Reservoir Region, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (Q.X.); (B.Z.); (K.Z.); (X.T.); (M.D.); (X.X.)
| | - Longchang Wang
- Key Laboratory of Eco-Environments in Three Gorges Reservoir Region, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (Q.X.); (B.Z.); (K.Z.); (X.T.); (M.D.); (X.X.)
- Correspondence: (H.A.H.); (L.W.)
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Herrera Paredes S, Lebeis SL. Giving back to the community: microbial mechanisms of plant–soil interactions. Funct Ecol 2016. [DOI: 10.1111/1365-2435.12684] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sur Herrera Paredes
- Department of Biology Howard Hughes Medical Institute, Curriculum in Bioinformatics and Computational Biology University of North Carolina Chapel Hill North Carolina 27599‐3280 USA
| | - Sarah L. Lebeis
- Department of Microbiology University of Tennessee Knoxville Tennessee 37996‐0845 USA
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Haichar FEZ, Heulin T, Guyonnet JP, Achouak W. Stable isotope probing of carbon flow in the plant holobiont. Curr Opin Biotechnol 2016; 41:9-13. [PMID: 27019410 DOI: 10.1016/j.copbio.2016.02.023] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Revised: 02/19/2016] [Accepted: 02/23/2016] [Indexed: 01/27/2023]
Abstract
Microbial communities associated with a plant host, constituting a holobiont, affect the physiology and growth of the plant via metabolites that are mainly derived from their photosynthates. The structure and function of active microbial communities that assimilate root exudates can be tracked by using stable isotope probing (SIP) approaches. This article reviews results from ongoing SIP research in plant-microbe interactions, with a specific focus on investigating the fate of fresh and recalcitrant carbon in the rhizosphere with 13C enriched-root exudates, in addition to identifying key players in carbon cycling. Finally, we discuss new SIP applications that have the potential to identify novel enzymes implicated in rhizoremediation or plant genes dedicated to root exudation by combining SIP approaches and genome wide associations studies.
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Affiliation(s)
- Feth El Zahar Haichar
- Université Lyon1, CNRS, UMR5557, INRA, USC1364, Ecologie Microbienne, 69622 Villeurbanne, France.
| | - Thierry Heulin
- Laboratory of Microbial Ecology of the Rhizosphere and Extreme Environments (LEMIRE), Aix-Marseille Université, CEA, CNRS, UMR 7265 Biosciences and biotechnology Institute of Aix-Marseille (BIAM), ECCOREV FR 3098, CEA/Cadarache, St-Paul-lez-Durance, France
| | - Julien P Guyonnet
- Université Lyon1, CNRS, UMR5557, INRA, USC1364, Ecologie Microbienne, 69622 Villeurbanne, France
| | - Wafa Achouak
- Laboratory of Microbial Ecology of the Rhizosphere and Extreme Environments (LEMIRE), Aix-Marseille Université, CEA, CNRS, UMR 7265 Biosciences and biotechnology Institute of Aix-Marseille (BIAM), ECCOREV FR 3098, CEA/Cadarache, St-Paul-lez-Durance, France
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Applications and impacts of stable isotope probing for analysis of microbial interactions. Appl Microbiol Biotechnol 2014; 98:4817-28. [PMID: 24715147 DOI: 10.1007/s00253-014-5705-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2013] [Revised: 03/17/2014] [Accepted: 03/17/2014] [Indexed: 10/25/2022]
Abstract
Probing the interactions between microbes and their environment with stable isotopes became a powerful technique over the last years. While quadruple mass spectrometry or isotope ratio mass spectrometry (IRMS) require at least 300,000 bacterial cells, analysis at the single-cell level is possible with secondary ion mass spectrometry (SIMS) or Raman microspectrometry. While SIMS needs enrichments of more than 0.1 and Raman microscopy of more than 25 at.-%, IRMS can deal with 0.0001 at.-%. To find out who eats what, one has to discern between the different species in a community. Several methods have been introduced to discern between the different taxa in microbial communities, e.g., by using fatty acids as biomarkers, density centrifugation of DNA/RNA, or fluorescent in situ hybridization (FISH) with phylogenetic probes. While the biomarker approach can be coupled with the high sensitivity of the IRMS, the DNA approach gives in general a better phylogenetic resolution of the metabolic active microbes. A combination of both is the separation via coupling of FISH-probes to magnetic beads or fluorescent assisted cell sorting (FACS) of stained cells leading to fractions which can be analyzed by IRMS. Applying these techniques over a time course can reveal the metabolic kinetics and food webs. In this review, the different methods are presented with examples and their advantages and disadvantages are discussed. An outlook on the combination of the various techniques and their applications in microbial ecology is given.
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Yevdokimov IV, Larionova AA, Stulin AF. Turnover of “new” and “old” carbon in soil microbial biomass. Microbiology (Reading) 2013. [DOI: 10.1134/s0026261713040036] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Culture-Independent Molecular Tools for Soil and Rhizosphere Microbiology. DIVERSITY-BASEL 2013. [DOI: 10.3390/d5030581] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Dias ACF, Dini-Andreote F, Hannula SE, Andreote FD, Pereira e Silva MDC, Salles JF, de Boer W, van Veen J, van Elsas JD. Different selective effects on rhizosphere bacteria exerted by genetically modified versus conventional potato lines. PLoS One 2013; 8:e67948. [PMID: 23844136 PMCID: PMC3700926 DOI: 10.1371/journal.pone.0067948] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Accepted: 05/23/2013] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND In this study, we assessed the actively metabolizing bacteria in the rhizosphere of potato using two potato cultivars, i.e. the genetically-modified (GM) cultivar Modena (having tubers with altered starch content) and the near-isogenic non-GM cultivar Karnico. To achieve our aims, we pulse-labelled plants at EC90 stage with (13)C-CO2 and analysed their rhizosphere microbial communities 24 h, 5 and 12 days following the pulse. In the analyses, phospholipid fatty acid/stable isotope probing (PLFA-SIP) as well as RNA-SIP followed by reverse transcription and PCR-DGGE and clone library analysis, were used to determine the bacterial groups that actively respond to the root-released (13)C labelled carbonaceous compounds. METHODOLOGY/PRINCIPAL FINDINGS The PLFA-SIP data revealed major roles of bacteria in the uptake of root-released (13)C carbon, which grossly increased with time. Gram-negative bacteria, including members of the genera Pseudomonas and Burkholderia, were strong accumulators of the (13)C-labeled compounds at the two cultivars, whereas Gram-positive bacteria were lesser responders. PCR-DGGE analysis of cDNA produced from the two cultivar types showed that these had selected different bacterial, alpha- and betaproteobacterial communities at all time points. Moreover, an effect of time was observed, indicating dynamism in the structure of the active bacterial communities. PCR-DGGE as well as clone library analyses revealed that the main bacterial responders at cultivar Karnico were taxonomically affiliated with the genus Pseudomonas, next to Gluconacetobacter and Paracoccus. Cultivar Modena mainly attracted Burkholderia, next to Moraxella-like (Moraxellaceae family) and Sphingomonas types. CONCLUSIONS/SIGNIFICANCE Based on the use of Pseudomonas and Burkholderia as proxies for differentially-selected bacterial genera, we conclude that the selective forces exerted by potato cultivar Modena on the active bacterial populations differed from those exerted by cultivar Karnico.
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Affiliation(s)
- Armando Cavalcante Franco Dias
- Department of Microbial Ecology, Centre for Ecological and Evolutionary Studies (CEES), University of Groningen (RUG), Groningen, The Netherlands
- Department of Soil Science, ESALQ/USP, University of São Paulo, Piracicaba, Brazil
| | - Francisco Dini-Andreote
- Department of Microbial Ecology, Centre for Ecological and Evolutionary Studies (CEES), University of Groningen (RUG), Groningen, The Netherlands
- * E-mail:
| | - Silja Emilia Hannula
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | | | - Michele de Cássia Pereira e Silva
- Department of Microbial Ecology, Centre for Ecological and Evolutionary Studies (CEES), University of Groningen (RUG), Groningen, The Netherlands
| | - Joana Falcão Salles
- Department of Microbial Ecology, Centre for Ecological and Evolutionary Studies (CEES), University of Groningen (RUG), Groningen, The Netherlands
| | - Wietse de Boer
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Johannes van Veen
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Jan Dirk van Elsas
- Department of Microbial Ecology, Centre for Ecological and Evolutionary Studies (CEES), University of Groningen (RUG), Groningen, The Netherlands
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Farrer EC, Herman DJ, Franzova E, Pham T, Suding KN. Nitrogen deposition, plant carbon allocation, and soil microbes: changing interactions due to enrichment. AMERICAN JOURNAL OF BOTANY 2013; 100:1458-70. [PMID: 23804552 DOI: 10.3732/ajb.1200513] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
PREMISE OF THE STUDY Nitrogen (N) inputs to the terrestrial environment have doubled worldwide during the past century. N negatively impacts plant diversity, but it is unknown why some species are more susceptible than others. While it is often assumed that competition drives species decline, N enrichment also strongly affects soil microbial communities. Can these changes affect plant-microbe interactions in ways that differentially influence success of plant species? Furthermore, can altered plant-microbe interactions lead to carbon (C) limitation in plants? METHODS We focused on a species that increases (Deschampsia cespitosa) and one that decreases (Geum rossii) in abundance in N-fertilized plots in alpine tundra. We measured soil microbes using phospholipid fatty acids, and C limitation and transfer using a (13)C tracer experiment, C:N ratios, nonstructural carbohydrates, and leaf preformation. KEY RESULTS While N profoundly influenced microbial communities, this change occurred similarly in association with both plant species. N addition did not alter total C allocation to microbes in either species, but it changed patterns of microbial C acquisition more in Geum, specifically in gram-negative bacteria. Geum showed evidence of C limitation: it allocated less C to storage organs, had lower C:N and carbohydrate stores, and fewer preformed leaves in N plots. CONCLUSIONS Carbon limitation may explain why some species decline with N enrichment, and the decline may be due to physiological responses of plants to N rather than to altered plant-microbe interactions. Global change will alter many processes important in structuring plant communities; noncompetitive mechanisms of species decline may be more widespread than previously thought.
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Affiliation(s)
- Emily C Farrer
- Department of Environmental Science, Policy & Management, University of California, Berkeley, Berkeley, California 94720, USA.
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Hannula SE, Boschker HTS, de Boer W, van Veen JA. 13C pulse-labeling assessment of the community structure of active fungi in the rhizosphere of a genetically starch-modified potato (Solanum tuberosum) cultivar and its parental isoline. THE NEW PHYTOLOGIST 2012; 194:784-799. [PMID: 22413848 DOI: 10.1111/j.1469-8137.2012.04089.x] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
• The aim of this study was to gain understanding of the carbon flow from the roots of a genetically modified (GM) amylopectin-accumulating potato (Solanum tuberosum) cultivar and its parental isoline to the soil fungal community using stable isotope probing (SIP). • The microbes receiving (13)C from the plant were assessed through RNA/phospholipid fatty acid analysis with stable isotope probing (PLFA-SIP) at three time-points (1, 5 and 12 d after the start of labeling). The communities of Ascomycota, Basidiomycota and Glomeromycota were analysed separately with RT-qPCR and terminal restriction fragment length polymorphism (T-RFLP). • Ascomycetes and glomeromycetes received carbon from the plant as early as 1 and 5 d after labeling, while basidiomycetes were slower in accumulating the labeled carbon. The rate of carbon allocation in the GM variety differed from that in its parental variety, thereby affecting soil fungal communities. • We conclude that both saprotrophic and mycorrhizal fungi rapidly metabolize organic substrates flowing from the root into the rhizosphere, that there are large differences in utilization of root-derived compounds at a lower phylogenetic level within investigated fungal phyla, and that active communities in the rhizosphere differ between the GM plant and its parental cultivar through effects of differential carbon flow from the plant.
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Affiliation(s)
- S E Hannula
- Netherlands Institute of Ecology (NIOO-KNAW), PO Box 50, 6708 PB Wageningen, the Netherlands
| | - H T S Boschker
- Centre for Estuarine and Marine Ecology, Netherlands Institute of Ecology (NIOO-KNAW), PO Box 140, 4400 AC Yerseke, the Netherlands
| | - W de Boer
- Netherlands Institute of Ecology (NIOO-KNAW), PO Box 50, 6708 PB Wageningen, the Netherlands
| | - J A van Veen
- Netherlands Institute of Ecology (NIOO-KNAW), PO Box 50, 6708 PB Wageningen, the Netherlands
- Insititute of Biology, Leiden University, Leiden, the Netherlands
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Gschwendtner S, Esperschütz J, Buegger F, Reichmann M, Müller M, Munch JC, Schloter M. Effects of genetically modified starch metabolism in potato plants on photosynthate fluxes into the rhizosphere and on microbial degraders of root exudates. FEMS Microbiol Ecol 2011; 76:564-75. [PMID: 21348886 DOI: 10.1111/j.1574-6941.2011.01073.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
A high percentage of photosynthetically assimilated carbon is released into soil via root exudates, which are acknowledged as the most important factor for the development of microbial rhizosphere communities. As quality and quantity of root exudates are dependent on plant genotype, the genetic engineering of plants might also influence carbon partitioning within the plant and thus microbial rhizosphere community structure. In this study, the carbon allocation patterns within the plant-rhizosphere system of a genetically modified amylopectin-accumulating potato line (Solanum tuberosum L.) were linked to microbial degraders of root exudates under greenhouse conditions, using (13)C-CO(2) pulse-chase labelling in combination with phospholipid fatty acid (PLFA) analysis. In addition, GM plants were compared with the parental cultivar as well as a second potato cultivar obtained by classical breeding. Rhizosphere samples were obtained during young leaf developmental and flowering stages. (13)C allocation in aboveground plant biomass, water-extractable organic carbon, microbial biomass carbon and PLFA as well as the microbial community structure in the rhizosphere varied significantly between the natural potato cultivars. However, no differences between the GM line and its parental cultivar were observed. Besides the considerable impact of plant cultivar, the plant developmental stage affected carbon partitioning via the plant into the rhizosphere and, subsequently, microbial communities involved in the transformation of root exudates.
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Affiliation(s)
- Silvia Gschwendtner
- Department of Terrestrial Ecogenetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Soil Ecology, Neuherberg, Germany.
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Shi JY, Lin HR, Yuan XF, Chen XC, Shen CF, Chen YX. Enhancement of copper availability and microbial community changes in rice rhizospheres affected by sulfur. Molecules 2011; 16:1409-17. [PMID: 21350394 PMCID: PMC6259926 DOI: 10.3390/molecules16021409] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2011] [Revised: 01/18/2011] [Accepted: 01/20/2011] [Indexed: 11/18/2022] Open
Abstract
The role of sulfur on the availability of Cu and the bacterial community in rice rhizospheres was investigated by pot experiments. With sulfur addition, pH in rhizosphere soil decreased and Mg(NO3)2 extractable Cu increased significantly. The bacterial community composition also changed with sulfur addition. Some specific clones having high similarity to Thiobacillus, which indicated that sulfur oxidation in the rice rhizosphere could increase the availability of Cu. These results suggested that sulfur source which could provide substrate to sulfur oxidizing bacteria and enhance the availability of Cu was not a suitable sulfur fertilizer for Cu polluted soil.
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Affiliation(s)
- Ji-Yan Shi
- Ministry of Agriculture Key Laboratory of Non-point Source Pollution Control, Institute of Environmental Science and Technology, Zhejiang University, Hangzhou 310029, China; E-Mails: (H.-R.L.); (X.-C.C.); (C.-F.S.); (Y.-X.C.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +86-571-86971424, Fax: +86-571-86971898
| | - Hui-Rong Lin
- Ministry of Agriculture Key Laboratory of Non-point Source Pollution Control, Institute of Environmental Science and Technology, Zhejiang University, Hangzhou 310029, China; E-Mails: (H.-R.L.); (X.-C.C.); (C.-F.S.); (Y.-X.C.)
- Department of Environmental Science and Engineering, Xiamen University Tan Kah Kee College, Zhangzhou 363105, China
| | - Xiao-Feng Yuan
- Life Science Department, Zhejiang Chinese Medical University, Hangzhou 310053, China; E-Mail: (X.-F.Y.)
| | - Xin-Cai Chen
- Ministry of Agriculture Key Laboratory of Non-point Source Pollution Control, Institute of Environmental Science and Technology, Zhejiang University, Hangzhou 310029, China; E-Mails: (H.-R.L.); (X.-C.C.); (C.-F.S.); (Y.-X.C.)
| | - Chao-Feng Shen
- Ministry of Agriculture Key Laboratory of Non-point Source Pollution Control, Institute of Environmental Science and Technology, Zhejiang University, Hangzhou 310029, China; E-Mails: (H.-R.L.); (X.-C.C.); (C.-F.S.); (Y.-X.C.)
| | - Ying-Xu Chen
- Ministry of Agriculture Key Laboratory of Non-point Source Pollution Control, Institute of Environmental Science and Technology, Zhejiang University, Hangzhou 310029, China; E-Mails: (H.-R.L.); (X.-C.C.); (C.-F.S.); (Y.-X.C.)
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Cadillo-Quiroz H, Yavitt JB, Zinder SH, Thies JE. Diversity and community structure of Archaea inhabiting the rhizoplane of two contrasting plants from an acidic bog. MICROBIAL ECOLOGY 2010; 59:757-767. [PMID: 20024684 DOI: 10.1007/s00248-009-9628-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2009] [Accepted: 12/05/2009] [Indexed: 05/28/2023]
Abstract
Plant root exudates increase nutrient availability and influence microbial communities including archaeal members. We examined the archaeal community inhabiting the rhizoplane of two contrasting vascular plants, Dulichium arundinaceum and Sarracenia purpurea, from an acidic bog in upstate NY. Multiple archaeal 16S rRNA gene libraries showed that methanogenic Archaea were dominant in the rhizoplane of both plants. In addition, the community structure (evenness) of the rhizoplane was found markedly different from the bulk peat. The archaeal community in peat from the same site has been found dominated by the E2 group, meanwhile the rhizoplane communities on both plants were co-dominated by Methanosarcinaceae (MS), rice cluster (RC)-I, and E2. Complementary T-RFLP analysis confirmed the difference between bulk peat and rhizoplane, and further characterized the dominance pattern of MS, RC-I, and E2. In the rhizoplane, MS was dominant on both plants although as a less variable fraction in S. purpurea. RC-I was significantly more abundant than E2 on S. purpurea, while the opposite was observed on D. arundinaceum, suggesting a plant-specific enrichment. Also, the statistical analyses of T-RFLP data showed that although both plants overlap in their community structure, factors such as plant type, patch location, and time could explain nearly a third of the variability in the dataset. Other factors such as water table, plant replicate, and root depth had a low contribution to the observed variance. The results of this study illustrate the general effects of roots and the specific effects of plant types on their nearby archaeal communities which in bog-inhabiting plants were mainly composed by methanogenic groups.
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Affiliation(s)
- Hinsby Cadillo-Quiroz
- Department of Microbiology, Cornell University, 270 Wing Hall, Ithaca, NY 14853, USA.
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Stelzer N, Imfeld G, Thullner M, Lehmann J, Poser A, Richnow HH, Nijenhuis I. Integrative approach to delineate natural attenuation of chlorinated benzenes in anoxic aquifers. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2009; 157:1800-1806. [PMID: 19250727 DOI: 10.1016/j.envpol.2009.01.029] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2008] [Revised: 01/26/2009] [Accepted: 01/27/2009] [Indexed: 05/27/2023]
Abstract
Biodegradation of chlorobenzenes was assessed at an anoxic aquifer by combining hydrogeochemistry and stable isotope analyses. In situ microcosm analysis evidenced microbial assimilation of chlorobenzene (MCB) derived carbon and laboratory investigations asserted mineralization of MCB at low rates. Sequential dehalogenation of chlorinated benzenes may affect the isotope signature of single chlorobenzene species due to simultaneous depletion and enrichment of (13)C, which complicates the evaluation of degradation. Therefore, the compound-specific isotope analysis was interpreted based on an isotope balance. The enrichment of the cumulative isotope composition of all chlorobenzenes indicated in situ biodegradation. Additionally, the relationship between hydrogeochemistry and degradation activity was investigated by principal component analysis underlining variable hydrogeochemical conditions associated with degradation activity at the plume scale. Although the complexity of the field site did not allow straightforward assessment of natural attenuation processes, the application of an integrative approach appeared relevant to characterize the in situ biodegradation potential.
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Affiliation(s)
- Nicole Stelzer
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Permoserstr. 15, 04318 Leipzig, Germany
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Wang Y, Ke X, Wu L, Lu Y. Community composition of ammonia-oxidizing bacteria and archaea in rice field soil as affected by nitrogen fertilization. Syst Appl Microbiol 2009; 32:27-36. [DOI: 10.1016/j.syapm.2008.09.007] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2008] [Revised: 08/13/2008] [Accepted: 09/11/2008] [Indexed: 11/27/2022]
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17
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Applying stable isotope probing of phospholipid fatty acids and rRNA in a Chinese rice field to study activity and composition of the methanotrophic bacterial communities in situ. ISME JOURNAL 2008; 2:602-14. [DOI: 10.1038/ismej.2008.34] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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18
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Leveau JHJ, Preston GM. Bacterial mycophagy: definition and diagnosis of a unique bacterial-fungal interaction. THE NEW PHYTOLOGIST 2008; 177:859-876. [PMID: 18086226 DOI: 10.1111/j.1469-8137.2007.02325.x] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
This review analyses the phenomenon of bacterial mycophagy, which we define as a set of phenotypic behaviours that enable bacteria to obtain nutrients from living fungi and thus allow the conversion of fungal into bacterial biomass. We recognize three types of bacterial strategies to derive nutrition from fungi: necrotrophy, extracellular biotrophy and endocellular biotrophy. Each is characterized by a set of uniquely sequential and differently overlapping interactions with the fungal target. We offer a detailed analysis of the nature of these interactions, as well as a comprehensive overview of methodologies for assessing and quantifying their individual contributions to the mycophagy phenotype. Furthermore, we discuss future prospects for the study and exploitation of bacterial mycophagy, including the need for appropriate tools to detect bacterial mycophagy in situ in order to be able to understand, predict and possibly manipulate the way in which mycophagous bacteria affect fungal activity, turnover, and community structure in soils and other ecosystems.
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Affiliation(s)
- Johan H J Leveau
- Netherlands Institute of Ecology (NIOO-KNAW), Heteren, the Netherlands
| | - Gail M Preston
- Department of Plant Sciences, University of Oxford, Oxford, UK
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