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Datta R. Enzymatic degradation of cellulose in soil: A review. Heliyon 2024; 10:e24022. [PMID: 38234915 PMCID: PMC10792583 DOI: 10.1016/j.heliyon.2024.e24022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 12/13/2023] [Accepted: 01/02/2024] [Indexed: 01/19/2024] Open
Abstract
Cellulose degradation is a critical process in soil ecosystems, playing a vital role in nutrient cycling and organic matter decomposition. Enzymatic degradation of cellulosic biomass is the most sustainable and green method of producing liquid biofuel. It has gained intensive research interest with future perspective as the majority of terrestrial lignocellulose biomass has a great potential to be used as a source of bioenergy. However, the recalcitrant nature of lignocellulose limits its use as a source of energy. Noteworthy enough, enzymatic conversion of cellulose biomass could be a leading future technology. Fungal enzymes play a central role in cellulose degradation. Our understanding of fungal cellulases has substantially redirected in the past few years with the discovery of a new class of enzymes and Cellulosome. Efforts have been made from time to time to develop an economically viable method of cellulose degradation. This review provides insights into the current state of knowledge regarding cellulose degradation in soil and identifies areas where further research is needed.
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Affiliation(s)
- Rahul Datta
- Department of Geology and Pedology, Faculty of Forestry and Wood Technology. Mendel University In Brno, Czech Republic
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2
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Zulkernain NH, Uvarajan T, Ng CC. Roles and significance of chelating agents for potentially toxic elements (PTEs) phytoremediation in soil: A review. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 341:117926. [PMID: 37163837 DOI: 10.1016/j.jenvman.2023.117926] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 04/04/2023] [Accepted: 04/10/2023] [Indexed: 05/12/2023]
Abstract
Phytoremediation is a biological remediation technique known for low-cost technology and environmentally friendly approach, which employs plants to extract, stabilise, and transform various compounds, such as potentially toxic elements (PTEs), in the soil or water. Recent developments in utilising chelating agents soil remediation have led to a renewed interest in chelate-induced phytoremediation. This review article summarises the roles of various chelating agents and the mechanisms of chelate-induced phytoremediation. This paper also discusses the recent findings on the impacts of chelating agents on PTEs uptake and plant growth and development in phytoremediation. It was found that the chelating agents have increased the rate of metal absorption and translocation up to 45% from roots to the aboveground plant parts during PTEs phytoremediation. Besides, it was also explored that the plants may experience some phytotoxicity after adding chelating agents to the soil. However, due to the leaching potential of synthetic chelating agents, the use of organic chelants have been explored to be used in PTEs phytoremediation. Finally, this paper also presents comprehensive insights on the significance of using chelating agents through SWOT analysis to discuss the advantages and limitations of chelate-induced phytoremediation.
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Affiliation(s)
- Nur Hanis Zulkernain
- China-ASEAN College of Marine Sciences, Xiamen University, Malaysia (XMUM), Sepang, Selangor Darul Ehsan, Malaysia; School of Postgraduate Studies, Research and Internationalisation, Faculty of Integrated Life Sciences, Quest International University, Malaysia
| | - Turkeswari Uvarajan
- School of Postgraduate Studies, Research and Internationalisation, Faculty of Integrated Life Sciences, Quest International University, Malaysia
| | - Chuck Chuan Ng
- China-ASEAN College of Marine Sciences, Xiamen University, Malaysia (XMUM), Sepang, Selangor Darul Ehsan, Malaysia.
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3
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Xu H, Fu B, Lei J, Kang H, Wang J, Huang X, Zhu F. Soil microbial communities and their co-occurrence networks in response to long-term Pb-Zn contaminated soil in southern China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:26687-26702. [PMID: 36369447 DOI: 10.1007/s11356-022-23962-1] [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: 07/14/2022] [Accepted: 10/29/2022] [Indexed: 06/16/2023]
Abstract
Mining causes extreme heavy metal (HM) contamination to surrounding environments and poses threats to soil microbial community. The effects of HMs on soil microbial communities are not only related to their total amounts but also associated with the distribution of chemical fractions. However, the effects of chemical fractions on soil microbes and their interactions remain largely unclear. Here we investigated soil physicochemical properties and bacterial and fungal communities of soil samples from the control area and lightly (L), moderately (M), and heavily (H) contaminated areas, respectively, which were collected from long-term Pb-Zn slag contamination area in the southern China. The results showed that bacterial and fungal community composition and structure were significantly affected by HMs, while community diversity was not significantly affected by HMs. The critical environmental factor affecting bacterial and fungal communities was pH, and the impacts of chemical fractions on their changes were more significant than the total amounts of HMs. Variance partitioning analysis (VPA) revealed fungal community changes were mostly driven by HM total amounts, but bacterial community changes were mostly driven by soil chemical properties. Co-occurrence network indicated that interactions among species of fungal network were sparser than that of bacterial network, but fungal network was more stable, due to a more significant number of keystone taxa and a lower percentage of positive associations. These illustrated that the fungal community might serve as indicator taxa for HM-contaminated status, and specific HM-responsive fungal species such as Triangularia mangenotii, Saitozyma podzolica, and Cladosporium endophytica, and genus Rhizophagus can be considered relevant bioindicators due to their less relative abundance in contaminated areas. Additionally, HM-responsive bacterial OTUs representing five genera within Sulfurifustis, Thiobacillus, Sphingomonas, Qipengyuania, and Sulfurirhabdus were found to be tolerant to HM stress due to their high relative abundance in contaminated levels.
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Affiliation(s)
- Hongyang Xu
- College of Horticulture, Hunan Agricultural University, Changsha, 410128, People's Republic of China
| | - Bingqing Fu
- College of Life Science and Technology, Central-South, University of Forestry and Technology, Changsha, 410004, People's Republic of China
| | - Jiaqi Lei
- College of Landscape Architecture and Art Design, Hunan Agricultural University, Changsha, Hunan, 410128, People's Republic of China
| | - Hui Kang
- Changsha Environmental Protection College, Changsha, 410004, People's Republic of China
| | - Jun Wang
- College of Life Science and Technology, Central-South, University of Forestry and Technology, Changsha, 410004, People's Republic of China
| | - Xinhao Huang
- College of Landscape Architecture and Art Design, Hunan Agricultural University, Changsha, Hunan, 410128, People's Republic of China
| | - Fan Zhu
- College of Landscape Architecture and Art Design, Hunan Agricultural University, Changsha, Hunan, 410128, People's Republic of China.
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4
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Liu J, Li C, Ma W, Liu W, Wu W. Molecular Characterization of Distinct Fungal Communities in the Soil of a Rare Earth Mining Area. MICROBIAL ECOLOGY 2022; 84:1212-1223. [PMID: 34839384 DOI: 10.1007/s00248-021-01931-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 11/15/2021] [Indexed: 06/13/2023]
Abstract
The exploitation of ion-absorbed rare earth elements (REEs) has caused serious ecological destruction and environmental pollution. Effects on soil fungal structure and diversity exerted by mining activities are usually ignored, although fungus is one of the most important components in soil ecosystems. In the present research, quantitative polymerase chain reaction (qPCR) and high-throughput Illumina MiSeq sequencing were conducted to characterize fungal community composition and structure in soil of a rare earth mining area after in situ leaching. Statistical analyses, network, and FUNGuild were used to conduct in-depth analyses. Ascomycota, Basidiomycota, and Glomeromycota were the most abundant phyla in the mining soils. Fungal community structures were stable after leaching practice, but nutrition contents (organic matter, TC, and TN) significantly and positively contributed to fungal abundances and diversities. Saprotrophs in phyla Ascomycota and Basidiomycota were the dominant fungal trophic mode, and they played critical roles in nutrient cycling, transformation processes, and reducing REE toxicity. Symbiotrophs of phyla Glomeromycota contributed to soil aggregation and slowing down nutrient losses after in situ leaching practice. In addition, fungi could regulate the interactions between species to resist the harsh environment of REE toxicity or ammonium caused by in situ leaching practice.
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Affiliation(s)
- Jingjing Liu
- School of Energy and Machinery Engineering, Jiangxi University of Science and Technology, Nanchang, 330013, China.
- Jiangxi Key Laboratory of Mining & Metallurgy Environmental Pollution Control, Ganzhou, 341099, China.
| | - Chun Li
- School of Energy and Machinery Engineering, Jiangxi University of Science and Technology, Nanchang, 330013, China
| | - Wendan Ma
- School of Energy and Machinery Engineering, Jiangxi University of Science and Technology, Nanchang, 330013, China
| | - Wei Liu
- College of Chemistry and Environmental Science, Hebei University, Baoding, 071002, China
| | - Weixiang Wu
- Institute of Environmental Science and Technology, Zhejiang University, Hangzhou, 310030, People's Republic of China
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5
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Iqbal A, Ali I, Yuan P, Khan R, Liang H, Wei S, Jiang L. Combined Application of Manure and Chemical Fertilizers Alters Soil Environmental Variables and Improves Soil Fungal Community Composition and Rice Grain Yield. Front Microbiol 2022; 13:856355. [PMID: 35910624 PMCID: PMC9330912 DOI: 10.3389/fmicb.2022.856355] [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: 01/17/2022] [Accepted: 06/14/2022] [Indexed: 11/13/2022] Open
Abstract
Soil microorganisms play vital roles in energy flow and soil nutrient cycling and, thus, are important for crop production. A detailed understanding of the complex responses of microbial communities to diverse organic manure and chemical fertilizers (CFs) is crucial for agroecosystem sustainability. However, little is known about the response of soil fungal communities and soil nutrients to manure and CFs, especially under double-rice cropping systems. In this study, we investigated the effects of the application of combined manure and CFs to various fertilization strategies, such as no N fertilizer (Neg-CF); 100% chemical fertilizer (Pos-CF); 60% cattle manure (CM) + 40% CF (high-CM); 30% CM + 70% CF (low-CM); 60% poultry manure (PM) + 40% CF (high-PM), and 30% PM + 70% CF (low-PM) on soil fungal communities' structure and diversity, soil environmental variables, and rice yield. Results showed that synthetic fertilizer plus manure addition significantly increased the soil fertility and rice grain yield compared to sole CFs' application. Moreover, the addition of manure significantly changed the soil fungal community structure and increased the relative abundance of fungi such as phyla Ascomycota, Basidiomycota, Mortierellomycota, and Rozellomycota. The relative abundances dramatically differed at each taxonomic level, especially between manured and non-manured regimes. Principal coordinates analysis (PCoA) exhibited greater impacts of the addition of manure amendments than CFs on fungal community distributions. Redundancy analysis showed that the dominant fungal phyla were positively correlated with soil pH, soil organic C (SOC), total N, and microbial biomass C, and the fungal community structure was strongly affected by SOC. Network analysis explored positive relationships between microorganisms and could increase their adaptability in relevant environments. In addition, the structural equation model (SEM) shows the relationship between microbial biomass, soil nutrients, and rice grain yield. The SEM showed that soil nutrient contents and their availability directly affect rice grain yield, while soil fungi indirectly affect grain yield through microbial biomass production and nutrient levels. Our results suggest that manure application combined with CFs altered soil biochemical traits and soil fungal community structure and counteracted some of the adverse effects of the synthetic fertilizer. Overall, the findings of this research suggest that the integrated application of CF and manure is a better approach for improving soil health and rice yield.
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Affiliation(s)
- Anas Iqbal
- College of Life Science and Technology, Guangxi University, Nanning, China
- College of Agriculture, Guangxi University, Nanning, China
| | - Izhar Ali
- College of Agriculture, Guangxi University, Nanning, China
| | - Pengli Yuan
- College of Agriculture, Guangxi University, Nanning, China
| | - Rayyan Khan
- Key Laboratory of Tobacco Biology and Processing, Ministry of Agriculture and Rural Affairs, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - He Liang
- College of Agriculture, Guangxi University, Nanning, China
| | - Shanqing Wei
- College of Agriculture, Guangxi University, Nanning, China
| | - Ligeng Jiang
- College of Life Science and Technology, Guangxi University, Nanning, China
- College of Agriculture, Guangxi University, Nanning, China
- *Correspondence: Ligeng Jiang
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Zhang K, Tappero R, Ruytinx J, Branco S, Liao HL. Disentangling the role of ectomycorrhizal fungi in plant nutrient acquisition along a Zn gradient using X-ray imaging. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 801:149481. [PMID: 34467922 DOI: 10.1016/j.scitotenv.2021.149481] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/01/2021] [Accepted: 08/01/2021] [Indexed: 06/13/2023]
Abstract
Zinc (Zn) is a plant essential micronutrient involved in a wide range of cellular processes. Ectomycorrhizal fungi (EMF) are known to play a critical role in regulating plant Zn status. However, how EMF control uptake and translocation of Zn and other nutrients in plant roots under different Zn conditions is not well known. Using X-ray fluorescence imaging, we found the EMF species Suillus luteus increased pine root Zn acquisition under low Zn concentrations and reduced its accumulation under higher Zn levels. By contrast, non-mycorrhizal pine roots exposed to high Zn indiscriminately take up and translocate Zn to root tissues, leading to Zn stress. Regardless of S. luteus inoculation, the absorption pattern of Ca and Cu was similar to Zn. Compared to Ca and Cu, effects of S. luteus on Fe acquisition were more marked, leading to a negative association between Zn addition and Fe concentration within EMF roots. Besides, higher nutrient accumulation in the fungal sheath, compared to hyphae inhabiting between intercellular space of cortex cells, implies the fungal sheath serves as a barrier to regulate nutrient transportation into fungal Hartig net. Our results demonstrate the crucial roles EMF play in plant nutrient uptake and how fungal partners ameliorate soil chemical conditions either by increasing or decreasing element uptake.
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Affiliation(s)
- Kaile Zhang
- North Florida Research and Education Center, University of Florida, Quincy, FL 32351, USA; Soil and Water Science Department, University of Florida, Gainesville, FL 32611, USA
| | - Ryan Tappero
- Brookhaven National Laboratory, NSLS-II, Upton, NY 11973, USA
| | - Joske Ruytinx
- Research Groups Microbiology and Plant Genetics, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussel, Belgium
| | - Sara Branco
- Department of Integrative Biology, University of Colorado Denver, Denver, CO 80204, USA
| | - Hui-Ling Liao
- North Florida Research and Education Center, University of Florida, Quincy, FL 32351, USA; Soil and Water Science Department, University of Florida, Gainesville, FL 32611, USA.
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7
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Advances in the Role of Dark Septate Endophytes in the Plant Resistance to Abiotic and Biotic Stresses. J Fungi (Basel) 2021; 7:jof7110939. [PMID: 34829226 PMCID: PMC8622582 DOI: 10.3390/jof7110939] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/29/2021] [Accepted: 11/02/2021] [Indexed: 02/06/2023] Open
Abstract
Endophytic fungi have been studied in recent decades to understand how they interact with their hosts, the types of relationships they establish, and the potential effects of this interaction. Dark septate endophytes (DSE) are isolated from healthy plants and form melanised structures in the roots, including inter- and intracellular hyphae and microsclerotia, causing low host specificity and covering a wide geographic range. Many studies have revealed beneficial relationships between DSE and their hosts, such as enhanced plant growth, nutrient uptake, and resistance to biotic and abiotic stress. Furthermore, in recent decades, studies have revealed the ability of DSE to mitigate the negative effects of crop diseases, thereby highlighting DSE as potential biocontrol agents of plant diseases (BCAs). Given the importance of these fungi in nature, this article is a review of the role of DSE as BCAs. The findings of increasing numbers of studies on these fungi and their relationships with their plant hosts are also discussed to enable their use as a tool for the integrated management of crop diseases and pests.
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8
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Clary Sage Cultivation and Mycorrhizal Inoculation Influence the Rhizosphere Fungal Community of an Aged Trace-Element Polluted Soil. Microorganisms 2021; 9:microorganisms9061333. [PMID: 34205382 PMCID: PMC8234821 DOI: 10.3390/microorganisms9061333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/16/2021] [Accepted: 06/17/2021] [Indexed: 11/17/2022] Open
Abstract
Soil fungal communities play a central role in natural systems and agroecosystems. As such, they have attracted significant research interest. However, the fungal microbiota of aromatic plants, such as clary sage (Salvia sclarea L.), remain unexplored. This is especially the case in trace element (TE)-polluted conditions and within the framework of phytomanagement approaches. The presence of high concentrations of TEs in soils can negatively affect not only microbial diversity and community composition but also plant establishment and growth. Hence, the objective of this study is to investigate the soil fungal and arbuscular mycorrhizal fungi (AMF) community composition and their changes over time in TE-polluted soils in the vicinity of a former lead smelter and under the cultivation of clary sage. We used Illumina MiSeq amplicon sequencing to evaluate the effects of in situ clary sage cultivation over two successive years, combined or not with exogenous AMF inoculation, on the rhizospheric soil and root fungal communities. We obtained 1239 and 569 fungal amplicon sequence variants (ASV), respectively, in the rhizospheric soil and roots of S. sclarea under TE-polluted conditions. Remarkably, 69 AMF species were detected at our experimental site, belonging to 12 AMF genera. Furthermore, the inoculation treatment significantly shaped the fungal communities in soil and increased the number of AMF ASVs in clary sage roots. In addition, clary sage cultivation over successive years could be one of the explanatory parameters for the inter-annual variation in both fungal and AMF communities in the soil and root biotopes. Our data provide new insights on fungal and AMF communities in the rhizospheric soil and roots of an aromatic plant, clary sage, grown in TE-polluted agricultural soil.
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Lemmel F, Maunoury-Danger F, Leyval C, Cébron A. Altered fungal communities in contaminated soils from French industrial brownfields. JOURNAL OF HAZARDOUS MATERIALS 2021; 406:124296. [PMID: 33268205 DOI: 10.1016/j.jhazmat.2020.124296] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 10/14/2020] [Accepted: 10/14/2020] [Indexed: 05/20/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) and metals are contaminants of industrial brownfield soils. Pollutants can have harmful effects on fungi, which are major actors of soil functioning. Our objective was to highlight fungal selection following long-term contamination of soils. Fungal diversity was assessed on 30 top-soil samples from ten sites gathered in three groups with different contamination levels and physico-chemical characteristics: 1) uncontaminated controls, 2) slag heaps displaying high PAH and moderate metal contaminations, and 3) settling ponds displaying high metal and intermediate PAH contaminations. Although fungal abundance and richness were similar among the soil groups, the diversity and evenness indices were lower for the slag heap group. Fungal diversity differed among soil groups at the phylum and OTU levels, and indicator species were identified. The relative abundance of Agaricomycetes, Saccharomycetes, Leotiomycetes and Chytridiomycota was higher in the control soils than in the two groups of contaminated soils. Cryptomycota LKM11 representatives were favoured in the slag heap and settling pond groups, and their relative abundance was correlated to the zinc and lead contamination levels. Dothideomycetes - positively linked to PAH contamination - and Eurotiomycetes were specific to the slag heap group. Pucciniomycetes and especially Gymnosporangium members were favoured in the settling pond soils.
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Affiliation(s)
- Florian Lemmel
- Université de Lorraine, CNRS, LIEC, Nancy F-54000, France
| | | | - Corinne Leyval
- Université de Lorraine, CNRS, LIEC, Nancy F-54000, France
| | - Aurélie Cébron
- Université de Lorraine, CNRS, LIEC, Nancy F-54000, France.
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10
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Liu C, Duan C, Meng X, Yue M, Zhang H, Wang P, Xiao Y, Hou Z, Wang Y, Pan Y. Cadmium pollution alters earthworm activity and thus leaf-litter decomposition and soil properties. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 267:115410. [PMID: 32866867 DOI: 10.1016/j.envpol.2020.115410] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 07/17/2020] [Accepted: 08/08/2020] [Indexed: 06/11/2023]
Abstract
It has been reported that heavy metal contamination can affect litter decomposition and soil properties through its impact on microbial communities. However, it is still unclear whether the expected changes in earthworm activities in responses to heavy metal contamination could affect these properties. Therefore, we quantified earthworm (Eisenia fetida) responses in survival rate to lethal cadmium (Cd) concentrations (0, 50, 100, 150, 200, 250, and 300 mg L-1), and in burrowing ability, physiological characteristics, and feeding rate (on poplar leaf litter) to sub-lethal Cd concentrations (0, 15, 30, and 45 mg kg-1). Finally, sub-lethal influences of Cd on the decomposition rate of poplar leaf litter and on soil properties were investigated in the present of E. fetida. The 12-, 24-, 36-, and 48-h LC50 of Cd for E. fetida were 276.0, 208.6, 192.6, 179.8 mg L-1, respectively. With increasing Cd concentration, malondialdehyde was stimulated, superoxide dismutase first increased and then decreased, while feeding rate, total borrowing length, and maximum burrowing depth consistently decreased. Consequently, leaf-litter decomposition rate and soil nutrient concentrations generally decreased with increasing Cd concentration. Our results indicate that, by affecting earthworm activities, Cd inhibited leaf-litter decomposition and led to the degradation of soil fertility. This study highlights the importance of earthworms in mediating soil functions under heavy metal stress.
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Affiliation(s)
- Change Liu
- School of Ecology and Environmental Sciences & Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments, Yunnan University, Kunming, Yunnan, 650091, China; School of Ecology and Environmental Sciences, Yunnan University, Kunming, 650091, China
| | - Changqun Duan
- School of Ecology and Environmental Sciences & Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments, Yunnan University, Kunming, Yunnan, 650091, China; School of Ecology and Environmental Sciences, Yunnan University, Kunming, 650091, China
| | - Xianghuai Meng
- School of Ecology and Environmental Sciences & Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments, Yunnan University, Kunming, Yunnan, 650091, China; School of Ecology and Environmental Sciences, Yunnan University, Kunming, 650091, China
| | - Minhui Yue
- School of Ecology and Environmental Sciences & Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments, Yunnan University, Kunming, Yunnan, 650091, China; School of Ecology and Environmental Sciences, Yunnan University, Kunming, 650091, China
| | - Hao Zhang
- School of Life Science, Yunnan Normal University, Kunming, 650500, China
| | - Peng Wang
- School of Ecology and Environmental Sciences & Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments, Yunnan University, Kunming, Yunnan, 650091, China; School of Ecology and Environmental Sciences, Yunnan University, Kunming, 650091, China
| | - Yanlan Xiao
- School of Ecology and Environmental Sciences & Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments, Yunnan University, Kunming, Yunnan, 650091, China; School of Ecology and Environmental Sciences, Yunnan University, Kunming, 650091, China
| | - Zhiyong Hou
- Dongting Lake Station for Wetland Ecosystem Research, Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha, 410125, China
| | - Yuanfeng Wang
- School of Ecology and Environmental Sciences & Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments, Yunnan University, Kunming, Yunnan, 650091, China; School of Ecology and Environmental Sciences, Yunnan University, Kunming, 650091, China
| | - Ying Pan
- School of Ecology and Environmental Sciences & Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments, Yunnan University, Kunming, Yunnan, 650091, China; School of Ecology and Environmental Sciences, Yunnan University, Kunming, 650091, China.
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11
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Czaplicki LM, Redfern LK, Cooper EM, Ferguson PL, Vilgalys R, Gunsch CK. Investigating the mycobiome of the Holcomb Creosote Superfund Site. CHEMOSPHERE 2020; 252:126208. [PMID: 32229362 PMCID: PMC7242165 DOI: 10.1016/j.chemosphere.2020.126208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 12/20/2019] [Accepted: 02/12/2020] [Indexed: 06/10/2023]
Abstract
Even though many fungi are known to degrade a range of organic chemicals and may be advantageous for targeting hydrophobic chemicals with low bioavailability due to their ability to secrete extracellular enzymes, fungi are not commonly leveraged in the context of bioremediation. Here we sought to examine the fungal microbiome (mycobiome) at a model creosote polluted site to determine if fungi were prevalent under high PAH contamination conditions as well as to identify potential mycostimulation targets. Several significant positive associations were detected between OTUs and mid-to high-molecular weight PAHs. Several OTUs were closely related to taxa that have previously been identified in culture-based studies as PAH degraders. In particular, members belonging to the Ascomycota phylum were the most diverse at higher PAH concentrations suggesting this phylum may be promising biostimulation targets. There were nearly three times more positive correlations as compared to negative correlations, suggesting that creosote-tolerance is more common than creosote-sensitivity in the fungal community. Future work including shotgun metagenomic analysis would help confirm the presence of specific degradation genes. Overall this study suggests that mycobiome and bacterial microbiome analyses should be performed in parallel to devise the most optimal in situ biostimulation treatment strategies.
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Affiliation(s)
- Lauren M Czaplicki
- Pratt School of Engineering, Department of Civil and Environmental Engineering, Duke University, Durham, NC, 27713, USA
| | - Lauren K Redfern
- Pratt School of Engineering, Department of Civil and Environmental Engineering, Duke University, Durham, NC, 27713, USA
| | - Ellen M Cooper
- Nicholas School of the Environment, Duke University, Durham, NC, 27713, USA
| | - P Lee Ferguson
- Nicholas School of the Environment, Duke University, Durham, NC, 27713, USA
| | - Rytas Vilgalys
- Department of Biology, Duke University, Durham, NC, 27713, USA
| | - Claudia K Gunsch
- Pratt School of Engineering, Department of Civil and Environmental Engineering, Duke University, Durham, NC, 27713, USA.
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Větrovský T, Morais D, Kohout P, Lepinay C, Algora C, Awokunle Hollá S, Bahnmann BD, Bílohnědá K, Brabcová V, D'Alò F, Human ZR, Jomura M, Kolařík M, Kvasničková J, Lladó S, López-Mondéjar R, Martinović T, Mašínová T, Meszárošová L, Michalčíková L, Michalová T, Mundra S, Navrátilová D, Odriozola I, Piché-Choquette S, Štursová M, Švec K, Tláskal V, Urbanová M, Vlk L, Voříšková J, Žifčáková L, Baldrian P. GlobalFungi, a global database of fungal occurrences from high-throughput-sequencing metabarcoding studies. Sci Data 2020; 7:228. [PMID: 32661237 PMCID: PMC7359306 DOI: 10.1038/s41597-020-0567-7] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 06/05/2020] [Indexed: 02/08/2023] Open
Abstract
Fungi are key players in vital ecosystem services, spanning carbon cycling, decomposition, symbiotic associations with cultivated and wild plants and pathogenicity. The high importance of fungi in ecosystem processes contrasts with the incompleteness of our understanding of the patterns of fungal biogeography and the environmental factors that drive those patterns. To reduce this gap of knowledge, we collected and validated data published on the composition of soil fungal communities in terrestrial environments including soil and plant-associated habitats and made them publicly accessible through a user interface at https://globalfungi.com . The GlobalFungi database contains over 600 million observations of fungal sequences across > 17 000 samples with geographical locations and additional metadata contained in 178 original studies with millions of unique nucleotide sequences (sequence variants) of the fungal internal transcribed spacers (ITS) 1 and 2 representing fungal species and genera. The study represents the most comprehensive atlas of global fungal distribution, and it is framed in such a way that third-party data addition is possible.
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Affiliation(s)
- Tomáš Větrovský
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Daniel Morais
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Petr Kohout
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Clémentine Lepinay
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Camelia Algora
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Sandra Awokunle Hollá
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Barbara Doreen Bahnmann
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Květa Bílohnědá
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Vendula Brabcová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Federica D'Alò
- Laboratory of Systematic Botany and Mycology, University of Tuscia, Largo dell'Università snc, Viterbo, 01100, Italy
| | - Zander Rainier Human
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Mayuko Jomura
- Department of Forest Science and Resources, College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa, Japan
| | - Miroslav Kolařík
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Jana Kvasničková
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Salvador Lladó
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Rubén López-Mondéjar
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Tijana Martinović
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Tereza Mašínová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Lenka Meszárošová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Lenka Michalčíková
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Tereza Michalová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Sunil Mundra
- Department of Biology, United Arab Emirates University, Al Ain, Abu Dhabi, United Arab Emirates
- Section for Genetics and Evolutionary Biology, University of Oslo, Blindernveien 31, 0316, Oslo, Norway
| | - Diana Navrátilová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Iñaki Odriozola
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Sarah Piché-Choquette
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Martina Štursová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Karel Švec
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Vojtěch Tláskal
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Michaela Urbanová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Lukáš Vlk
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Jana Voříšková
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Lucia Žifčáková
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Petr Baldrian
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic.
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Chen Z, Wang Q, Ma J, Zou P, Yu Q, Jiang L. Fungal community composition change and heavy metal accumulation in response to the long-term application of anaerobically digested slurry in a paddy soil. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 196:110453. [PMID: 32229326 DOI: 10.1016/j.ecoenv.2020.110453] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 03/04/2020] [Accepted: 03/06/2020] [Indexed: 06/10/2023]
Abstract
Anaerobically digested slurry (ADS) has been widely used as a liquid fertilizer in agroecosystems. However, there is scant information on the effects of successive ADS applications on heavy metals (HMs) accumulation and fungal community composition in paddy soils. In this study, we conducted a field experiment over 10 years to assess the changes in soil HMs and fungal community composition under the long-term application of ADS in a paddy field. The four treatments were (1) no fertilizer (CK); (2) mineral fertilizer and 270 kg N ha-1 from urea (MF); (3) 270 kg N ha-1 from ADS (ADS1); and (4) 540 kg N ha-1 from ADS (ADS2). The results revealed that ADS application improved paddy soil fertility compared to that under the MF treatment by increasing soil organic C (SOC), total N (TN) and available potassium (AK). Long-term application of ADS significantly increased soil total and available Zn (TZn and AZn) concentrations as compared to those under the MF treatment. However, there were no significant differences in the total and available Cu concentrations or the total Pb concentration between the ADS and MF treatments. Sequence analysis showed that application of ADS increased the fungal richness indexes (Chao1 and ACE) compared to MF treatment. Principal coordinate analysis (PCoA) showed that the soil fungal community compositions were significantly separated by high levels of ADS application. Long-term application of ADS increased the relative abundance of classes Sordariomycetes, Dothideomycetes and Agaricomycetes by 20.8-29.0%, 107.3-141.4% and 289.5-387.5%, respectively, but decreased that of Pezizomycetes by 14.0-33.0% compared to that under the MF treatment. At the genus level, compared to those under the MF treatment, the relative abundances of Pyrenochaetopsis and Myrothecium were significantly increased by the application of ADS, but those of Mrakia and Tetracladium were significantly decreased. Redundancy analysis (RDA) revealed that SOC, AZn and AP were the three most important factors affecting the fungal community composition of the paddy soil. Our findings suggested that fungal community composition could be affected by changes in the chemical properties and heavy metal contents of paddy soil under high application of ADS in the long term.
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Affiliation(s)
- Zhaoming Chen
- Institute of Environmental Resources and Soil Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Qiang Wang
- Institute of Environmental Resources and Soil Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.
| | - Junwei Ma
- Institute of Environmental Resources and Soil Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Ping Zou
- Institute of Environmental Resources and Soil Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Qiaogang Yu
- Institute of Environmental Resources and Soil Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Lina Jiang
- Institute of Environmental Resources and Soil Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
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14
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Yu X, Ding Z, Ji Y, Zhao J, Liu X, Tian J, Wu N, Fan Y. An operon consisting of a P-type ATPase gene and a transcriptional regulator gene responsible for cadmium resistances in Bacillus vietamensis 151-6 and Bacillus marisflavi 151-25. BMC Microbiol 2020; 20:18. [PMID: 31964334 PMCID: PMC6975044 DOI: 10.1186/s12866-020-1705-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 01/13/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Cadmium (Cd) is a severely toxic heavy metal to most microorganisms. Many bacteria have developed Cd2+ resistance. RESULTS In this study, we isolated two different Cd2+ resistance Bacillus sp. strains, Bacillus vietamensis 151-6 and Bacillus marisflavi 151-25, which could be grown in the presence of Cd2+ at concentration up to 0.3 mM and 0.8 mM, respectively. According to the genomic sequencing, transcriptome analysis under cadmium stress, and other related experiments, a gene cluster in plasmid p25 was found to be a major contributor to Cd2+ resistance in B. marisflavi 151-25. The cluster in p25 contained orf4802 and orf4803 which encodes an ATPase transporter and a transcriptional regulator protein, respectively. Although 151-6 has much lower Cd2+ resistance than 151-25, they contained similar gene cluster, but in different locations. A gene cluster on the chromosome containing orf4111, orf4112 and orf4113, which encodes an ATPase transporter, a cadmium efflux system accessory protein and a cadmium resistance protein, respectively, was found to play a major role on the Cd2+ resistance for B. vietamensis 151-6. CONCLUSIONS This work described cadmium resistance mechanisms in newly isolated Bacillus vietamensis 151-6 and Bacillus marisflavi 151-25. Based on homologies to the cad system (CadA-CadC) in Staphylococcus aureus and analysis of transcriptome under Cd2+ induction, we inferred that the mechanisms of cadmium resistance in B. marisflavi 151-25 was as same as the cad system in S. aureus. Although Bacillus vietamensis 151-6 also had the similar gene cluster to B. marisflavi 151-25 and S. aureus, its transcriptional regulatory mechanism of cadmium resistance was not same. This study explored the cadmium resistance mechanism for B. vietamensis 151-6 and B. marisflavi 151-25 and has expanded our understanding of the biological effects of cadmium.
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Affiliation(s)
- Xiaoxia Yu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zundan Ding
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yangyang Ji
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.,College of Life Science and Technology, Jinan University, Guangzhou, Guangdong, China
| | - Jintong Zhao
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoqing Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jian Tian
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Ningfeng Wu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Yunliu Fan
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
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15
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Assress HA, Selvarajan R, Nyoni H, Ntushelo K, Mamba BB, Msagati TAM. Diversity, Co-occurrence and Implications of Fungal Communities in Wastewater Treatment Plants. Sci Rep 2019; 9:14056. [PMID: 31575971 PMCID: PMC6773715 DOI: 10.1038/s41598-019-50624-z] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 09/17/2019] [Indexed: 01/15/2023] Open
Abstract
Three wastewater treatment plants (WWTPs) located in Gauteng province in South Africa were investigated to determine the diversity, co-occurrence and implications of their fungal communities using illumina sequencing platform and network analysis. Phylogenetic taxonomy revealed that members of the fungal communities were assigned to 6 phyla and 361 genera. Basidiomycota and Ascomycota were the most abundant phyla, dominated by the genera Naumovozyma, Pseudotomentella, Derxomyces, Ophiocordyceps, Pulchromyces and Paecilomyces. Phylogenetic analysis revealed the existence of fungal OTUs related to class lineages such as Agaricomycetes, Eurotiomycetes and Sordariomycetes indicating new fungal diversity in WWTPs. Dominant and rare fungal genera that can potentially be used in bioremediation such as Trichoderma, Acremonium, Talaromyces, Paecilomyces, cladophialophora and Saccharomyces were detected. Conversely, genera whose members are known to be pathogenic to human and plant such as Olpidium, Paecilomyces, Aspergillus, Rhodotorula, Penicillium, Candida, Synchytrium, Phyllosticta and Mucor were also detected in all WWTPs. Phylotype analysis confirmed that some fungal phylotypes were highly similar to the reported fungal pathogens of concern. Co-occurrence network analysis revealed that the fungal genera such as Minimedusa, Glomus, Circinella, Coltricia, Caloplaca, Phylosticta, Peziza, Candida, and Hydnobolites were the major networking hub in the WWTPs. The overall results in this study highlighted that WWTPs represent a potential source of beneficial fungi for bioremediation of pollutants in the ecosystem and the need to consider human and plant fungal pathogens during safety evaluation of treated wastewater for reuse.
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Affiliation(s)
- Hailemariam Abrha Assress
- University of South Africa, College of Science Engineering and Technology, Nanotechnology and Water Sustainability Research Unit, UNISA Science Campus, Florida, 1709, Johannesburg, South Africa
| | - Ramganesh Selvarajan
- University of South Africa, College of Agriculture and Environmental sciences, UNISA Science Florida, 1709, Johannesburg, South Africa
| | - Hlengilizwe Nyoni
- University of South Africa, College of Science Engineering and Technology, Nanotechnology and Water Sustainability Research Unit, UNISA Science Campus, Florida, 1709, Johannesburg, South Africa
| | - Khayalethu Ntushelo
- University of South Africa, College of Agriculture and Environmental sciences, UNISA Science Florida, 1709, Johannesburg, South Africa
| | - Bhekie B Mamba
- University of South Africa, College of Science Engineering and Technology, Nanotechnology and Water Sustainability Research Unit, UNISA Science Campus, Florida, 1709, Johannesburg, South Africa.,State Key Laboratory of Seperation and Membranes, Membrane Processes, National Center for International Joint Research on Membrane Science and Technologya, Tianjing, 300387, People's Republic of China
| | - Titus A M Msagati
- University of South Africa, College of Science Engineering and Technology, Nanotechnology and Water Sustainability Research Unit, UNISA Science Campus, Florida, 1709, Johannesburg, South Africa.
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Berthelot C, Leyval C, Chalot M, Blaudez D. Interactions between dark septate endophytes, ectomycorrhizal fungi and root pathogens in vitro. FEMS Microbiol Lett 2019; 366:5531311. [DOI: 10.1093/femsle/fnz158] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 07/10/2019] [Indexed: 12/22/2022] Open
Abstract
ABSTRACTDark septate endophytes (DSEs) are widely distributed worldwide and can promote plant growth. Therefore, they are considered potentially important plant allies, especially in stressful environments. Previous studies have reported that DSEs cohabit roots with other microorganisms such as ectomycorrhizal (ECM), endophytic and pathogenic fungi/oomycetes. However, interactions between different DSE species have not yet been reported, and studies on the interactions between DSEs and other fungi are scarce. Using a simple and reproducible pairwise growth assay in vitro, we studied the synergistic/antagonistic interactions between eight DSEs, two ECM fungi and three root pathogens. Most of the DSE/DSE outcomes were neutral. Interestingly, we identified several DSE strains acting in synergy with other strains, as well as strains that could potentially act as biocontrol agents. Notably, three metal-tolerant DSE strains, namely, Cadophora sp., Leptodontidium sp. and Phialophora mustea, could decrease the growth of the root phytopathogens Pythium intermedium, Phytophthora citricola and Heterobasidion annosum. The present data are discussed in the general context of the use of fungal consortia as inocula in the tree-based phytomanagement of marginal lands.
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Affiliation(s)
| | - Corinne Leyval
- Université de Lorraine, CNRS, LIEC, F-54000 Nancy, France
| | - Michel Chalot
- Université de Bourgogne Franche-Comté, UMR CNRS 6249 Laboratoire Chrono-environnement, F-25211 Montbéliard, France
- Université de Lorraine, F-54000 Nancy, France
| | - Damien Blaudez
- Université de Lorraine, CNRS, LIEC, F-54000 Nancy, France
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Gil-Martínez M, López-García Á, Domínguez MT, Navarro-Fernández CM, Kjøller R, Tibbett M, Marañón T. Ectomycorrhizal Fungal Communities and Their Functional Traits Mediate Plant-Soil Interactions in Trace Element Contaminated Soils. FRONTIERS IN PLANT SCIENCE 2018; 9:1682. [PMID: 30515182 PMCID: PMC6255936 DOI: 10.3389/fpls.2018.01682] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 10/29/2018] [Indexed: 06/09/2023]
Abstract
There is an increasing consensus that microbial communities have an important role in mediating ecosystem processes. Trait-based ecology predicts that the impact of the microbial communities on ecosystem functions will be mediated by the expression of their traits at community level. The link between the response of microbial community traits to environmental conditions and its effect on plant functioning is a gap in most current microbial ecology studies. In this study, we analyzed functional traits of ectomycorrhizal fungal species in order to understand the importance of their community assembly for the soil-plant relationships in holm oak trees (Quercus ilex subsp. ballota) growing in a gradient of exposure to anthropogenic trace element (TE) contamination after a metalliferous tailings spill. Particularly, we addressed how the ectomycorrhizal composition and morphological traits at community level mediate plant response to TE contamination and its capacity for phytoremediation. Ectomycorrhizal fungal taxonomy and functional diversity explained a high proportion of variance of tree functional traits, both in roots and leaves. Trees where ectomycorrhizal fungal communities were dominated by the abundant taxa Hebeloma cavipes and Thelephora terrestris showed a conservative root economics spectrum, while trees colonized by rare taxa presented a resource acquisition strategy. Conservative roots presented ectomycorrhizal functional traits characterized by high rhizomorphs formation and low melanization which may be driven by resource limitation. Soil-to-root transfer of TEs was explained substantially by the ectomycorrhizal fungal species composition, with the highest transfer found in trees whose roots were colonized by Hebeloma cavipes. Leaf phosphorus was related to ectomycorrhizal species composition, specifically higher leaf phosphorus was related to the root colonization by Thelephora terrestris. These findings support that ectomycorrhizal fungal community composition and their functional traits mediate plant performance in metal-contaminated soils, and have a high influence on plant capacity for phytoremediation of contaminants. The study also corroborates the overall effects of ectomycorrhizal fungi on ecosystem functioning through their mediation over the plant economics spectrum.
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Affiliation(s)
- Marta Gil-Martínez
- Department for Protection of the Soil, Plant and Water System, Institute of Natural Resources and Agrobiology of Seville, Spanish National Research Council, Seville, Spain
| | | | - María T. Domínguez
- Área de Edafología y Química Agricola, Departamento de Cristalografía, Mineralogía y Química Agrícola, Universidad de Sevilla, Seville, Spain
| | - Carmen M. Navarro-Fernández
- Department for Protection of the Soil, Plant and Water System, Institute of Natural Resources and Agrobiology of Seville, Spanish National Research Council, Seville, Spain
| | - Rasmus Kjøller
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Mark Tibbett
- Centre for Agri-Environmental Research and Soil Research Centre, School of Agriculture, Policy and Development, University of Reading, Reading, United Kingdom
| | - Teodoro Marañón
- Department for Protection of the Soil, Plant and Water System, Institute of Natural Resources and Agrobiology of Seville, Spanish National Research Council, Seville, Spain
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18
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Parmar S, Li Q, Wu Y, Li X, Yan J, Sharma VK, Wei Y, Li H. Endophytic fungal community of Dysphania ambrosioides from two heavy metal-contaminated sites: evaluated by culture-dependent and culture-independent approaches. Microb Biotechnol 2018; 11:1170-1183. [PMID: 30256529 PMCID: PMC6196397 DOI: 10.1111/1751-7915.13308] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 07/30/2018] [Accepted: 08/01/2018] [Indexed: 01/26/2023] Open
Abstract
Endophytic fungal communities of Dysphania ambrosioides, a hyperaccumulator growing at two Pb-Zn-contaminated sites, were investigated through culture-dependent and culture-independent approaches. A total of 237 culturable endophytic fungi (EF) were isolated from 368 tissue (shoot and roots) segments, and the colonization rate (CR) ranged from 9.64% to 65.98%. The isolates were identified to 43 taxa based on morphological characteristics and rDNA ITS sequence analysis. Among them, 13 taxa (30.23%) were common in plant tissues from both sites; however, dominant EF were dissimilar. In culture-dependent study, 1989 OTUs were obtained through Illumina Miseq sequencing, and dominant EF were almost same in plant tissues from both sites. However, some culturable EF were not observed in total endophytic communities. We suggest that combination of both culture-dependent and culture-independent methods will provide more chances for the precise estimation of endophytic fungal community than using either of them. The tissue had more influence on the culturable fungal community structure, whereas the location had more influence on the total fungal community structure (including culturable and unculturable). Both culture-dependent and culture-independent studies illustrated that endophytic fungal communities of D. ambrosioides varied across the sites, which suggested that HM concentration of the soil may have some influence on endophytic fungal diversity.
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Affiliation(s)
- Shobhika Parmar
- Medical School of Kunming University of Science and TechnologyKunming650500China
| | - Qiaohong Li
- The First People's Hospital of Yunnan ProvinceKunming650032China
- The Affiliated Hospital of Kunming University of Science and TechnologyKunming650500China
| | - Ying Wu
- The First People's Hospital of Yunnan ProvinceKunming650032China
- The Affiliated Hospital of Kunming University of Science and TechnologyKunming650500China
| | - Xinya Li
- Medical School of Kunming University of Science and TechnologyKunming650500China
| | - Jinping Yan
- Medical School of Kunming University of Science and TechnologyKunming650500China
| | - Vijay K. Sharma
- Medical School of Kunming University of Science and TechnologyKunming650500China
| | - Yunlin Wei
- Medical School of Kunming University of Science and TechnologyKunming650500China
| | - Haiyan Li
- Medical School of Kunming University of Science and TechnologyKunming650500China
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Houles A, Vincent B, David M, Ducousso M, Galiana A, Juillot F, Hannibal L, Carriconde F, Fritsch E, Jourand P. Ectomycorrhizal Communities Associated with the Legume Acacia spirorbis Growing on Contrasted Edaphic Constraints in New Caledonia. MICROBIAL ECOLOGY 2018; 76:964-975. [PMID: 29717331 DOI: 10.1007/s00248-018-1193-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 04/12/2018] [Indexed: 06/08/2023]
Abstract
This study aims to characterize the ectomycorrhizal (ECM) communities associated with Acacia spirorbis, a legume tree widely spread in New Caledonia that spontaneously grows on contrasted edaphic constraints, i.e. calcareous, ferralitic and volcano-sedimentary soils. Soil geochemical parameters and diversity of ECM communities were assessed in 12 sites representative of the three mains categories of soils. The ectomycorrhizal status of Acacia spirorbis was confirmed in all studied soils, with a fungal community dominated at 92% by Basidiomycota, mostly represented by/tomentella-thelephora (27.6%), /boletus (15.8%), /sebacina (10.5%), /russula-lactarius (10.5%) and /pisolithus-scleroderma (7.9%) lineages. The diversity and the proportion of the ECM lineages were similar for the ferralitic and volcano-sedimentary soils but significantly different for the calcareous soils. These differences in the distribution of the ECM communities were statistically correlated with pH, Ca, P and Al in the calcareous soils and with Co in the ferralitic soils. Altogether, these data suggest a high capacity of A. spirorbis to form ECM symbioses with a large spectrum of fungi regardless the soil categories with contrasted edaphic parameters.
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Affiliation(s)
- Anne Houles
- CIRAD, UMR082 LSTM, TA A-82/J, Campus International de Baillarguet, 34398 Cedex 5, Montpellier, France
- Koniambo Nickel SAS, Vavouto, BP 679, 98860, Koné, New Caledonia
| | - Bryan Vincent
- IRD, UMR040 LSTM, 98848, Nouméa Cedex, New Caledonia
| | - Magali David
- IRD, UMR206 IMPMC, 98848, Nouméa Cedex, New Caledonia
| | - Marc Ducousso
- CIRAD, UMR082 LSTM, TA A-82/J, Campus International de Baillarguet, 34398 Cedex 5, Montpellier, France.
| | - Antoine Galiana
- CIRAD, UMR082 LSTM, TA A-82/J, Campus International de Baillarguet, 34398 Cedex 5, Montpellier, France
| | - Farid Juillot
- IRD, UMR206 IMPMC, 98848, Nouméa Cedex, New Caledonia
| | | | - Fabian Carriconde
- Institut Agronomique néo-Calédonien (IAC), Axe 2, 98800, Nouméa, New Caledonia
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Huang J, Han Q, Li J. Soil propagule bank of ectomycorrhizal fungi associated with Masson pine (Pinus massoniana) grown in a manganese mine wasteland. PLoS One 2018; 13:e0198628. [PMID: 29870548 PMCID: PMC5988271 DOI: 10.1371/journal.pone.0198628] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 05/22/2018] [Indexed: 11/19/2022] Open
Abstract
Ectomycorrhizal (ECM) fungal propagule bank could facilitate the regeneration and plantation of seedlings in disturbed area. In this study, Masson pine (Pinus massoniana) seedlings were used to bait the ECM fungal propagule bank buried in the soils collected from a manganese (Mn) mine wasteland and a non-polluted area in China. After 6-month growth, we found the seedlings grown in the Mn mine soil (Mn:3200 mg kg-1) did not display any toxicity symptoms. Based on morphotyping and ITS-PCR sequencing, we identified a total of 16 ECM fungal OTUs (operative taxonomic units) at 97% similarity threshold, among which 11 OTUs were recovered in the Mn mine soils and 14 in the non-polluted soil. Two soil types shared 9 OTUs and both of them were dominated by a Tylospora sp. Based on those soil propagule banks in Masson pine forests reported in previous, we speculated that some Atheliaceae species may be preferred in the soil propagule bank of some pine species, such as Masson pine. In addition, NMDS ordination displayed geographical position effects on soil propagule banks in five Masson pine forest from three sites at regional scale. In conclusion, Masson pine ECM seedlings could grow well in the Mn wasteland as a suitable tree species used for reforestation application in Mn mineland, in addition, Mn pollution did not alter the dominant ECM fungal species in the soil propagule banks.
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Affiliation(s)
- Jian Huang
- College of Forestry, Northwest A&F University, Yangling, China
| | - Qisheng Han
- College of Forestry, Northwest A&F University, Yangling, China
- Farmland Irrigation Research Institute, Chinese Academy of Agricultural Sciences, Xinxiang, China
| | - Junjian Li
- Institute of Loess Plateau, Shanxi University, Taiyuan, China
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Berthelot C, Blaudez D, Beguiristain T, Chalot M, Leyval C. Co-inoculation of Lolium perenne with Funneliformis mosseae and the dark septate endophyte Cadophora sp. in a trace element-polluted soil. MYCORRHIZA 2018; 28:301-314. [PMID: 29502186 DOI: 10.1007/s00572-018-0826-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 02/07/2018] [Indexed: 06/08/2023]
Abstract
The presence of dark septate endophytes (DSEs) or arbuscular mycorrhizal fungi (AMF) in plant roots and their effects on plant fitness have been extensively described. However, little is known about their interactions when they are simultaneously colonizing a plant root, especially in trace element (TE)-polluted soils. We therefore investigated the effects of Cadophora sp. and Funneliformis mosseae on ryegrass (Lolium perenne) growth and element uptake in a Cd/Zn/Pb-polluted soil. The experiment included four treatments, i.e., inoculation with Cadophora sp., inoculation with F. mosseae, co-inoculation with Cadophora sp. and F. mosseae, and no inoculation. Ryegrass biomass and shoot Na, P, K, and Mg concentrations significantly increased following AMF inoculation as compared to non-inoculated controls. Similarly, DSE inoculation increased shoot Na concentration, whereas dual inoculation significantly decreased shoot Cd concentration. Moreover, oxidative stress determined by ryegrass leaf malondialdehyde concentration was alleviated both in the AMF and dual inoculation treatments. We used quantitative PCR and microscope observations to quantify colonization rates. They demonstrated that DSEs had no effect on AMF colonization, while AMF colonization slightly decreased DSE frequency. We also monitored fluorescein diacetate (FDA) hydrolysis and alkaline phosphatase (AP) activity in the rhizosphere soils. FDA hydrolysis remained unchanged in the three inoculated treatments, but AMF colonization increased AP activity and P mobility in the soil whereas DSE colonization did not alter AP activity. In this experiment, we unveiled the interactions between two ecologically important fungal groups likely to occur in roots which involved a decrease of oxidative stress and Cd accumulation in shoots. These results open promising perspectives on the fungal-based phytomanagement of TE-contaminated sites by the production of uncontaminated and marketable plant biomass.
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Affiliation(s)
| | - Damien Blaudez
- Université de Lorraine, CNRS, LIEC, F-54000, Nancy, France
| | | | - Michel Chalot
- Université de Bourgogne Franche-Comté, CNRS, Laboratoire Chrono-Environnement, Pôle Universitaire du Pays de Montbéliard, F-25211, Montbéliard, France
- Université de Lorraine, F-54000, Nancy, France
| | - Corinne Leyval
- Université de Lorraine, CNRS, LIEC, F-54000, Nancy, France.
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22
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Keiblinger KM, Schneider M, Gorfer M, Paumann M, Deltedesco E, Berger H, Jöchlinger L, Mentler A, Zechmeister-Boltenstern S, Soja G, Zehetner F. Assessment of Cu applications in two contrasting soils-effects on soil microbial activity and the fungal community structure. ECOTOXICOLOGY (LONDON, ENGLAND) 2018; 27:217-233. [PMID: 29297133 PMCID: PMC5847031 DOI: 10.1007/s10646-017-1888-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 12/12/2017] [Indexed: 05/20/2023]
Abstract
Copper (Cu)-based fungicides have been used in viticulture to prevent downy mildew since the end of the 19th century, and are still used today to reduce fungal diseases. Consequently, Cu has built up in many vineyard soils, and it is still unclear how this affects soil functioning. The present study aimed to assess the short and medium-term effects of Cu contamination on the soil fungal community. Two contrasting agricultural soils, an acidic sandy loam and an alkaline silt loam, were used for an eco-toxicological greenhouse pot experiment. The soils were spiked with a Cu-based fungicide in seven concentrations (0-5000 mg Cu kg-1 soil) and alfalfa was grown in the pots for 3 months. Sampling was conducted at the beginning and at the end of the study period to test Cu toxicity effects on total microbial biomass, basal respiration and enzyme activities. Fungal abundance was analysed by ergosterol at both samplings, and for the second sampling, fungal community structure was evaluated via ITS amplicon sequences. Soil microbial biomass C as well as microbial respiration rate decreased with increasing Cu concentrations, with EC50 ranging from 76 to 187 mg EDTA-extractable Cu kg-1 soil. Oxidative enzymes showed a trend of increasing activity at the first sampling, but a decline in peroxidase activity was observed for the second sampling. We found remarkable Cu-induced changes in fungal community abundance (EC50 ranging from 9.2 to 94 mg EDTA-extractable Cu kg-1 soil) and composition, but not in diversity. A large number of diverse fungi were able to thrive under elevated Cu concentrations, though within the order of Hypocreales several species declined. A remarkable Cu-induced change in the community composition was found, which depended on the soil properties and, hence, on Cu availability.
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Affiliation(s)
- Katharina M Keiblinger
- Institute of Soil Research, University of Natural Resources and Life Sciences, Vienna, Austria.
| | - Martin Schneider
- Institute of Soil Research, University of Natural Resources and Life Sciences, Vienna, Austria
- AIT Austrian Institute of Technology, Center for Energy, Business Unit Environmental Resources & Technologies, Tulln, Austria
| | - Markus Gorfer
- AIT Austrian Institute of Technology, Center for Health and Bioresources, Business Unit Bioresources, Tulln, Austria
| | - Melanie Paumann
- Institute of Soil Research, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Evi Deltedesco
- Institute of Soil Research, University of Natural Resources and Life Sciences, Vienna, Austria
- AIT Austrian Institute of Technology, Center for Health and Bioresources, Business Unit Bioresources, Tulln, Austria
| | | | - Lisa Jöchlinger
- Institute of Soil Research, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Axel Mentler
- Institute of Soil Research, University of Natural Resources and Life Sciences, Vienna, Austria
| | | | - Gerhard Soja
- AIT Austrian Institute of Technology, Center for Energy, Business Unit Environmental Resources & Technologies, Tulln, Austria
| | - Franz Zehetner
- Institute of Soil Research, University of Natural Resources and Life Sciences, Vienna, Austria
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Crognale S, D'Annibale A, Pesciaroli L, Stazi SR, Petruccioli M. Fungal Community Structure and As-Resistant Fungi in a Decommissioned Gold Mine Site. Front Microbiol 2017; 8:2202. [PMID: 29170658 PMCID: PMC5684174 DOI: 10.3389/fmicb.2017.02202] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 10/26/2017] [Indexed: 01/16/2023] Open
Abstract
Although large quantities of heavy metal laden wastes are released in an uncontrolled manner by gold mining activities with ensuing contamination of the surrounding areas, there is scant information on the mycobiota of gold-mine sites. Thus, the present study was aimed to describe the fungal community structure in three differently As- and Hg-polluted soils collected from the Pestarena decommissioned site by using Illumina® metabarcoding. Fungal richness was found to increase as the contamination level increased while biodiversity was not related to the concentrations of inorganic toxicants. Within the phylum Zygomigota which, irrespective of the contamination level, was predominant in all the soils under study, the most abundant genera were Mucor and Mortierella. The relative abundances of Basidiomycota, instead, tended to raise as the contamination increased; within this phylum the most abundant genera were Cryptococcus and Pseudotomentella. The abundance of Ascomycota, ranging from about 8 to 21%, was not related to the contamination level. The relative abundances of those genera (i.e., Penicillium, Trichoderma, and Chaetomium), the cultivable isolates of which exhibited significant As-resistance, were lower than the set threshold (0.5%). Mass balances obtained from As-exposure experiments with these isolates showed that the main mechanisms involved in counteracting the toxicant were accumulation and, above all, volatilization, the respective extents of which ranged from 0.6 to 5.9% and from 6.4 to 31.2% in dependence of the isolate.
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Affiliation(s)
- Silvia Crognale
- Department for Innovation in Biological Systems, Food and Forestry, University of Tuscia, Viterbo, Italy
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Henderson L, Lilje E, Robinson K, Gleason FH, Lilje O. Chapter 30 Effects of Toxic Metals on Chytrids, Fungal-Like Organisms, and Higher Fungi. Mycology 2017. [DOI: 10.1201/9781315119496-31] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Foulon J, Zappelini C, Durand A, Valot B, Girardclos O, Blaudez D, Chalot M. Environmental metabarcoding reveals contrasting microbial communities at two poplar phytomanagement sites. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 571:1230-40. [PMID: 27474992 DOI: 10.1016/j.scitotenv.2016.07.151] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 07/20/2016] [Accepted: 07/21/2016] [Indexed: 05/06/2023]
Abstract
The aim of the present study is to deepen the current understanding of the microbial communities at two poplar phytomanagement sites to reveal the environmental factors that drive the abundance, diversity and composition of microbial communities. A soil analysis revealed that the two soils displayed contrasting physico-chemical characteristics, with significant lower pH and higher Cd, Zn and Mn CaCl2-extractable fractions at Leforest site, compared with Pierrelaye site. The fungal and bacterial community profiles in the poplar roots and soils were assessed through Illumina MiSeq sequencing. Diversity indices and β-diversity measures illustrated that the root microbial communities were well separated from the soil microbial communities at both sites. A detailed study of the fungal composition showed that Ascomycota dominated the overall fungal communities on poplar soil, the root samples at Pierrelaye, and the unplanted soil at the experimental sites. Conversely, Basidiomycota accounted for a much higher percentage of the fungal community in poplar root samples from the Leforest site. The root bacterial communities were dominated by Alphaproteobacteria and Actinobacteria, and the soil samples were dominated by Alphaproteobacteria and Acidobacteria. The occurrence and dominance of the ectomycorrhizal community at Leforest but not at Pierrelaye is the major feature of our data set. Overall, ectomycorrhizal root symbionts appeared to be highly constrained by soil characteristics at the phytomanagement sites. Our data support the view that mycorrhizal inoculation is needed in highly stressed and nutrient-poor environments.
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Affiliation(s)
- Julie Foulon
- Laboratoire Chrono-Environnement, UMR 6249, Université de Bourgogne Franche-Comté, Pôle Universitaire du Pays de Montbéliard, 4 place Tharradin, BP 71427, 25211 Montbéliard, France
| | - Cyril Zappelini
- Laboratoire Chrono-Environnement, UMR 6249, Université de Bourgogne Franche-Comté, Pôle Universitaire du Pays de Montbéliard, 4 place Tharradin, BP 71427, 25211 Montbéliard, France
| | - Alexis Durand
- Laboratoire Chrono-Environnement, UMR 6249, Université de Bourgogne Franche-Comté, Pôle Universitaire du Pays de Montbéliard, 4 place Tharradin, BP 71427, 25211 Montbéliard, France
| | - Benoit Valot
- Laboratoire Chrono-Environnement, UMR 6249, Université de Bourgogne Franche-Comté, Pôle Universitaire du Pays de Montbéliard, 4 place Tharradin, BP 71427, 25211 Montbéliard, France
| | - Olivier Girardclos
- Laboratoire Chrono-Environnement, UMR 6249, Université de Bourgogne Franche-Comté, Pôle Universitaire du Pays de Montbéliard, 4 place Tharradin, BP 71427, 25211 Montbéliard, France
| | - Damien Blaudez
- CNRS, LIEC UMR7360, Faculté des Sciences et Technologies, BP70239, 54506 Vandoeuvre-lès-Nancy, France; Université de Lorraine, LIEC UMR7360, Faculté des Sciences et Technologies, BP 70239, 54506 Vandoeuvre-lès-Nancy, France
| | - Michel Chalot
- Laboratoire Chrono-Environnement, UMR 6249, Université de Bourgogne Franche-Comté, Pôle Universitaire du Pays de Montbéliard, 4 place Tharradin, BP 71427, 25211 Montbéliard, France; Université de Lorraine, Faculté des Sciences et Technologies, BP 70239, 54506 Vandoeuvre-les-Nancy, France.
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Foulon J, Zappelini C, Durand A, Valot B, Blaudez D, Chalot M. Impact of poplar-based phytomanagement on soil properties and microbial communities in a metal-contaminated site. FEMS Microbiol Ecol 2016; 92:fiw163. [PMID: 27481257 DOI: 10.1093/femsec/fiw163] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/25/2016] [Indexed: 11/14/2022] Open
Abstract
Despite a long history of use in phytomanagement strategies, the impacts of poplar trees on the structure and function of microbial communities that live in the soil remain largely unknown. The current study combined fungal and bacterial community analyses from different management regimes using Illumina-based sequencing with soil analysis. The poplar phytomanagement regimes led to a significant increase in soil fertility and a decreased bioavailability of Zn and Cd, in concert with changes in the microbial communities. The most notable changes in the relative abundance of taxa and operational taxonomic units unsurprisingly indicated that root and soil constitute distinct ecological microbial habitats, as exemplified by the dominance of Laccaria in root samples. The poplar cultivar was also an important driver, explaining 12% and 6% of the variance in the fungal and bacterial data sets, respectively. The overall dominance of saprophytic fungi, e.g. Penicillium canescens, might be related to the decomposition activities needed at the experimental site. Our data further highlighted that the mycorrhizal colonization of poplar cultivars varies greatly between the species and genotypes, which is exemplified by the dominance of Scleroderma under Vesten samples. Further interactions between fungal and bacterial functional groups stressed the potential of high-throughput sequencing technologies in uncovering the microbial ecology of disturbed environments.
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Affiliation(s)
- Julie Foulon
- Laboratoire Chrono-Environnement, UMR 6249, Université de Bourgogne Franche-Comté, Pôle Universitaire du Pays de Montbéliard, 4 place Tharradin, BP 71427, 25211 Montbéliard, France
| | - Cyril Zappelini
- Laboratoire Chrono-Environnement, UMR 6249, Université de Bourgogne Franche-Comté, Pôle Universitaire du Pays de Montbéliard, 4 place Tharradin, BP 71427, 25211 Montbéliard, France
| | - Alexis Durand
- Laboratoire Chrono-Environnement, UMR 6249, Université de Bourgogne Franche-Comté, Pôle Universitaire du Pays de Montbéliard, 4 place Tharradin, BP 71427, 25211 Montbéliard, France
| | - Benoit Valot
- Laboratoire Chrono-Environnement, UMR 6249, Université de Bourgogne Franche-Comté, Pôle Universitaire du Pays de Montbéliard, 4 place Tharradin, BP 71427, 25211 Montbéliard, France
| | - Damien Blaudez
- CNRS, LIEC UMR7360, Faculté des Sciences et Technologies, BP70239, 54506 Vandoeuvre-lès-Nancy, France Université de Lorraine, LIEC UMR7360, Faculté des Sciences et Technologies, BP 70239, 54506 Vandoeuvre-lès-Nancy, France
| | - Michel Chalot
- Laboratoire Chrono-Environnement, UMR 6249, Université de Bourgogne Franche-Comté, Pôle Universitaire du Pays de Montbéliard, 4 place Tharradin, BP 71427, 25211 Montbéliard, France Université de Lorraine, Faculté des Sciences et Technologies, BP 70239, 54506 Vandoeuvre-les-Nancy, France
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Berthelot C, Leyval C, Foulon J, Chalot M, Blaudez D. Plant growth promotion, metabolite production and metal tolerance of dark septate endophytes isolated from metal-polluted poplar phytomanagement sites. FEMS Microbiol Ecol 2016; 92:fiw144. [PMID: 27364359 DOI: 10.1093/femsec/fiw144] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/21/2016] [Indexed: 02/07/2023] Open
Abstract
Numerous studies address the distribution and the diversity of dark septate endophytes (DSEs) in the literature, but little is known about their ecological role and their effect on host plants, especially in metal-polluted soils. Seven DSE strains belonging to Cadophora, Leptodontidium, Phialophora and Phialocephala were isolated from roots of poplar trees from metal-polluted sites. All strains developed on a wide range of carbohydrates, including cell-wall-related compounds. The strains evenly colonized birch, eucalyptus and ryegrass roots in re-synthesis experiments. Root and shoot growth promotion was observed and was both plant and strain dependent. Two Phialophora and Leptodontidium strains particularly improved plant growth. However, there was no correlation between the level of root colonization by DSEs and the intensity of growth promotion. All strains produced auxin and six also stimulated plant growth through the release of volatile organic compounds (VOCs). SPME-GC/MS analyses revealed four major VOCs emitted by Cadophora and Leptodontidium The strains exhibited growth at high concentrations of several metals. The ability of metal-resistant DSE strains to produce both soluble and volatile compounds for plant growth promotion indicates interesting microbial resources with high potential to support sustainable production of bioenergy crops within the context of the phytomanagement of metal-contaminated sites.
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Affiliation(s)
- Charlotte Berthelot
- CNRS, LIEC UMR7360, Faculté des Sciences et Technologies, Université de Lorraine, BP 70239, F-54506 Vandoeuvre-lès-Nancy, France LIEC UMR7360, Faculté des Sciences et Technologies, Université de Lorraine, BP 70239, F-54506 Vandoeuvre-lès-Nancy, France
| | - Corinne Leyval
- CNRS, LIEC UMR7360, Faculté des Sciences et Technologies, Université de Lorraine, BP 70239, F-54506 Vandoeuvre-lès-Nancy, France LIEC UMR7360, Faculté des Sciences et Technologies, Université de Lorraine, BP 70239, F-54506 Vandoeuvre-lès-Nancy, France
| | - Julie Foulon
- CNRS, UMR6249 Laboratoire Chrono-Environnement, Pôle Universitaire du Pays de Montbéliard, 4 place Tharradin, BP 71427, F-25211, Montbéliard, France UMR6249 Laboratoire Chrono-Environnement, Université de Bourgogne Franche-Comté, Pôle Universitaire du Pays de Montbéliard, 4 place Tharradin, BP 71427, F-25211, Montbéliard, France
| | - Michel Chalot
- CNRS, UMR6249 Laboratoire Chrono-Environnement, Pôle Universitaire du Pays de Montbéliard, 4 place Tharradin, BP 71427, F-25211, Montbéliard, France UMR6249 Laboratoire Chrono-Environnement, Université de Bourgogne Franche-Comté, Pôle Universitaire du Pays de Montbéliard, 4 place Tharradin, BP 71427, F-25211, Montbéliard, France Faculté des Sciences et Technologies, Université de Lorraine, BP 70239, F-54506, Vandoeuvre-lès-Nancy, France
| | - Damien Blaudez
- CNRS, LIEC UMR7360, Faculté des Sciences et Technologies, Université de Lorraine, BP 70239, F-54506 Vandoeuvre-lès-Nancy, France LIEC UMR7360, Faculté des Sciences et Technologies, Université de Lorraine, BP 70239, F-54506 Vandoeuvre-lès-Nancy, France
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Ilyas S, Rehman A, Coelho AV, Sheehan D. Proteomic analysis of an environmental isolate of Rhodotorula mucilaginosa after arsenic and cadmium challenge: Identification of a protein expression signature for heavy metal exposure. J Proteomics 2016; 141:47-56. [DOI: 10.1016/j.jprot.2016.04.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 03/07/2016] [Accepted: 04/14/2016] [Indexed: 10/21/2022]
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Martinová V, van Geel M, Lievens B, Honnay O. Strong differences in Quercus robur-associated ectomycorrhizal fungal communities along a forest-city soil sealing gradient. FUNGAL ECOL 2016. [DOI: 10.1016/j.funeco.2015.12.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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