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Wang HY, Yu ZG, Zhou FW, Hernandez JC, Grandjean A, Biester H, Xiao KQ, Knorr KH. Microbial communities and functions are structured by vertical geochemical zones in a northern peatland. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 950:175273. [PMID: 39111416 DOI: 10.1016/j.scitotenv.2024.175273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 07/31/2024] [Accepted: 08/02/2024] [Indexed: 08/10/2024]
Abstract
Northern peatlands are important carbon pools; however, differences in the structure and function of microbiomes inhabiting contrasting geochemical zones within these peatlands have rarely been emphasized. Using 16S rRNA gene sequencing, metagenomic profiling, and detailed geochemical analyses, we investigated the taxonomic composition and genetic potential across various geochemical zones of a typical northern peatland profile in the Changbai Mountains region (Northeastern China). Specifically, we focused on elucidating the turnover of organic carbon, sulfur (S), nitrogen (N), and methane (CH4). Three geochemical zones were identified and characterized according to porewater and solid-phase analyses: the redox interface (<10 cm), shallow peat (10-100 cm), and deep peat (>100 cm). The redox interface and upper shallow peat demonstrated a high availability of labile carbon, which decreased toward deeper peat. In deep peat, anaerobic respiration and methanogenesis were likely constrained by thermodynamics, rather than solely driven by available carbon, as the acetate concentrations reached 90 μmol·L-1. Both the microbial community composition and metabolic potentials were significantly different (p < 0.05) among the redox interface, shallow peat, and deep peat. The redox interface demonstrated a close interaction between N, S, and CH4 cycling, mainly driven by Thermodesulfovibrionia, Bradyrhizobium, and Syntrophorhabdia metagenome-assembled genomes (MAGs). The archaeal Bathyarchaeia were indicated to play a significant role in the organic carbon, N, and S cycling in shallow peat. Although constrained by anaerobic respiration and methanogenesis, deep peat exhibited a higher metabolic potential for organic carbon degradation, primarily mediated by Acidobacteriota. In terms of CH4 turnover, subsurface peat (10-20 cm) was a CH4 production hotspot, with a net turnover rate of ∼2.9 nmol·cm-3·d-1, while the acetoclastic, hydrogenotrophic, and methylotrophic methanogenic pathways all potentially contributed to CH4 production. The results of this study improve our understanding of biogeochemical cycles and CH4 turnover along peatland profiles.
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Affiliation(s)
- Hong-Yan Wang
- Key Laboratory of Hydrometeorological Disaster Mechanism and Warning, Ministry of Water Resources, School of Hydrology and Water Resources, Nanjing University of Information Science and Technology, Nanjing 210044, China; State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Zhi-Guo Yu
- Key Laboratory of Hydrometeorological Disaster Mechanism and Warning, Ministry of Water Resources, School of Hydrology and Water Resources, Nanjing University of Information Science and Technology, Nanjing 210044, China.
| | - Feng-Wu Zhou
- Department of Environmental Science and Engineering, Fudan University, Shanghai, China
| | - Julio-Castillo Hernandez
- Department of Microbiology and Biochemistry, University of the Free State, Bloemfontein, South Africa
| | - Annkathrin Grandjean
- University of Münster, Institute for Landscape Ecology, Ecohydrology and Biogeochemistry Group, Heisenbergstr. 2, Münster 48149, Germany
| | - Harald Biester
- Institut für Geoökologie, Technische Universitat Braunschweig, Langer Kamp 19C, Braunschweig 38106, Germany
| | - Ke-Qing Xiao
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Klaus-Holger Knorr
- University of Münster, Institute for Landscape Ecology, Ecohydrology and Biogeochemistry Group, Heisenbergstr. 2, Münster 48149, Germany.
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Peixoto S, Morgado RG, Prodana M, Cardoso DN, Malheiro C, Neves J, Santos C, Khodaparast Z, Pavlaki MD, Rodrigues S, Rodrigues SM, Henriques I, Loureiro S. Responses of soil microbiome to copper-based materials (nano and bulk) for agricultural applications: An indoor-mesocosm experiment. NANOIMPACT 2024; 34:100506. [PMID: 38626862 DOI: 10.1016/j.impact.2024.100506] [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: 01/16/2024] [Revised: 04/07/2024] [Accepted: 04/08/2024] [Indexed: 04/21/2024]
Abstract
The foreseen increasing application of copper-based nanomaterials (Cu-NMs), replacing or complementing existing Cu-agrochemicals, may negatively impact the soil microbiome. Thus, we studied the effects on soil microbiome function and composition of nano copper oxide (nCuO) or copper hydroxide NMs in a commercial (Kocide®3000) or a lab-synthetized formulation (nCu(OH)2) or bulk copper hydroxide (Cu(OH)2-B), at the commonly recommended Cu dose of 50 mg(Cu)kg-1 soil. Microbial responses were studied over 28 days in a designed indoor mesocosm. On day-28, in comparison to non-treated soil (CT), all Cu-treatments led to a reduction in dehydrogenase (95% to 68%), arylsulfatase (41% to 27%), and urease (40% to 20%) activity. There was a 32% increase in the utilization of carbon substrates in the nCuO-treatment and an increased abundance of viable bacteria in the nCu(OH)2-treatment (75% of heterotrophic and 69% of P-solubilizing bacteria). The relative abundance of Acidobacteria [Kocide®3000, nCuO, and Cu(OH)2-B treatments] and Flavobacteriia [nCu(OH)2-treatment] was negatively affected by Cu exposure. The abundance of Cu-tolerant bacteria increased in soils treated with Kocide®3000 (Clostridia) and nCu(OH)2 (Gemmatimonadetes). All Cu-treated soils exhibited a reduced abundance of denitrification-related genes (0.05% of nosZ gene). The DTPA-extractable pool of ionic Cu(II) varied among treatments: Cu(OH)2-B > Kocide®3000 ∼ nCuO>nCu(OH)2, which may explain changes on the soil microbiome composition, at the genera and OTU levels. Thus, our study revealed that Cu-materials (nano and bulk) influence the soil microbiome with implications on its ecological role. It highlights the importance of assessing the impact of Cu-materials under dynamic and complex exposure scenarios and emphasizes the need for specific regulatory frameworks for NMs.
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Affiliation(s)
- Sara Peixoto
- CESAM-Centre for Environmental and Marine Studies & Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Rui G Morgado
- CESAM-Centre for Environmental and Marine Studies & Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Marija Prodana
- CESAM-Centre for Environmental and Marine Studies & Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Diogo N Cardoso
- CESAM-Centre for Environmental and Marine Studies & Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Catarina Malheiro
- CESAM-Centre for Environmental and Marine Studies & Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Joana Neves
- CESAM-Centre for Environmental and Marine Studies & Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Cátia Santos
- CESAM-Centre for Environmental and Marine Studies & Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Zahra Khodaparast
- CESAM-Centre for Environmental and Marine Studies & Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Maria D Pavlaki
- CESAM-Centre for Environmental and Marine Studies & Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Sandra Rodrigues
- CESAM & Department of Environment and Planning, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Sónia M Rodrigues
- CESAM & Department of Environment and Planning, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Isabel Henriques
- University of Coimbra, CEF- Centro de Ecologia Funcional & Department of Life Sciences, Faculty of Sciences and Technology, Portugal.
| | - Susana Loureiro
- CESAM-Centre for Environmental and Marine Studies & Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
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Cui X, He J, Chu Z, Ruan X, Jiang Z, Jiang W, Xin X, Pang H, Zou X. Effects of exogenous N-acyl homoserine lactones (AHLs) on methanogenic activities and microbial community differences during anaerobic digestion. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 355:120449. [PMID: 38432012 DOI: 10.1016/j.jenvman.2024.120449] [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: 10/25/2023] [Revised: 02/02/2024] [Accepted: 02/20/2024] [Indexed: 03/05/2024]
Abstract
N-acyl homoserine lactones (AHLs) function as signaling molecules influencing microbial community dynamics. This study investigates the impact of exogenously applied AHLs on methane production during waste-activated sludge (WAS) anaerobic digestion (AD). Nine AHL types, ranging from 10-4 to 10 μg/g VSS, were applied, comparing microbial community composition under optimal AHL concentrations. Firmicutes, Bacteroidetes, Chloroflexi, and Proteobacteria were identified in anaerobic digesters with C4-HSL, C6-HSL, and C8-HSL. Compared to the control, Halobacterota increased by 19.25%, 20.87%, and 9.33% with C7-HSL, C10-HSL, and C12-HSL. Exogenous C7-HSL enhanced the relative abundance of Methanosarcina, Romboutsia, Sedimentibacter, Proteiniclasticum, Christensenellaceae_R-7_group. C10-HSL increased Methanosarcina abundance. C4-HSL, C6-HSL, C8-HSL, C10-HSL, and C12-HSL showed potential to increase unclassified_Firmicutes. Functional Annotation of Prokaryotic Taxa (FAPROTAX) predicted AHLs' impact on related functional genes, providing insights into their role in AD methanogenesis regulation. This study aimed to enhance the understanding of the influence of different types of exogenous AHLs on AD and provide technical support for regulating the methanogenesis efficiency of AD by exogenous AHLs.
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Affiliation(s)
- Xinxin Cui
- School of Civil Engineering, Guangzhou University, 230 Zhonghuan West Road, Guangzhou 510006, China.
| | - Junguo He
- School of Civil Engineering, Guangzhou University, 230 Zhonghuan West Road, Guangzhou 510006, China.
| | - Zhaorui Chu
- School of Civil Engineering, Guangzhou University, 230 Zhonghuan West Road, Guangzhou 510006, China
| | - Xian Ruan
- School of Civil Engineering, Guangzhou University, 230 Zhonghuan West Road, Guangzhou 510006, China
| | - Zhifeng Jiang
- School of Civil Engineering, Guangzhou University, 230 Zhonghuan West Road, Guangzhou 510006, China
| | - Weixun Jiang
- School of Civil Engineering, Guangzhou University, 230 Zhonghuan West Road, Guangzhou 510006, China
| | - Xiaodong Xin
- Research Center for Eco-Environmental Engineering, Dongguan University of Technology, 1 Daxue Road, Dongguan 523808, China
| | - Heliang Pang
- School of Environmental and Municipal Engineering, Xi 'an University of Architecture and Technology, 13 Yanta Road Middle Section, Xi 'an 710055, China
| | - Xiang Zou
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, 73 Huanghe Road, Harbin 150090, China
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Hou XY, Qiao WT, Gu JD, Liu CY, Hussain MM, Du DL, Zhou Y, Wang YF, Li Q. Reforestation of Cunninghamia lanceolata changes the relative abundances of important prokaryotic families in soil. Front Microbiol 2024; 15:1312286. [PMID: 38414777 PMCID: PMC10896735 DOI: 10.3389/fmicb.2024.1312286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 01/25/2024] [Indexed: 02/29/2024] Open
Abstract
Over the past decades, many forests have been converted to monoculture plantations, which might affect the soil microbial communities that are responsible for governing the soil biogeochemical processes. Understanding how reforestation efforts alter soil prokaryotic microbial communities will therefore inform forest management. In this study, the prokaryotic communities were comparatively investigated in a secondary Chinese fir forest (original) and a reforested Chinese fir plantation (reforested from a secondary Chinese fir forest) in Southern China. The results showed that reforestation changed the structure of the prokaryotic community: the relative abundances of important prokaryotic families in soil. This might be caused by the altered soil pH and organic matter content after reforestation. Soil profile layer depth was an important factor as the upper layers had a higher diversity of prokaryotes than the lower ones (p < 0.05). The composition of the prokaryotic community presented a seasonality characteristic. In addition, the results showed that the dominant phylum was Acidobacteria (58.86%) with Koribacteraceae (15.38%) as the dominant family in the secondary Chinese fir forest and the reforested plantation. Furthermore, soil organic matter, total N, hydrolyzable N, and NH 4 + - N were positively correlated with prokaryotic diversity (p < 0.05). Also, organic matter and NO 3 - - N were positively correlated to prokaryotic abundance (p < 0.05). This study demonstrated that re-forest transformation altered soil properties, which lead to the changes in microbial composition. The changes in microbial community might in turn influence biogeochemical processes and the environmental variables. The study could contribute to forest management and policy-making.
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Affiliation(s)
- Xue-Yan Hou
- Institute of Environmental Health and Ecological Security, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
| | - Wen-Tao Qiao
- Institute of Environmental Health and Ecological Security, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
| | - Ji-Dong Gu
- Environmental Engineering, Guangdong Technion Israel Institute of Technology, Shantou, China
| | - Chao-Ying Liu
- Institute of Environmental Health and Ecological Security, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
| | - Muhammad Mahroz Hussain
- Institute of Environmental Health and Ecological Security, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
| | - Dao-Lin Du
- Jingjiang College, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
| | - Yi Zhou
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, China
| | - Yong-Feng Wang
- Institute of Environmental Health and Ecological Security, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
| | - Qian Li
- Institute of Environmental Health and Ecological Security, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
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Wang H, Xu Y, Kumar A, Knorr KH, Zhao X, Perez JPH, Sun G, Yu ZG. Temperature and organic carbon quality control the anaerobic carbon mineralization in peat profiles via modulating microbes: A case study of Changbai Mountain. ENVIRONMENTAL RESEARCH 2023; 237:116904. [PMID: 37595828 DOI: 10.1016/j.envres.2023.116904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/01/2023] [Accepted: 08/15/2023] [Indexed: 08/20/2023]
Abstract
Peatlands account for a significant fraction of the global carbon stock. However, the complex interplay of abiotic and biotic factors governing anaerobic carbon mineralization in response to warming remains unclear. In this study, peat sediments were collected from a typical northern peatland-Changbai Mountain to investigate the behavior and mechanism of anaerobic carbon mineralization in response to depth (0-200 cm) and temperature (5 °C, 15 °C and 20 °C), by integrating geochemical and microbial analysis. Several indices including humification indexes (HI), aromaticity, and water extractable organic carbon (WEOC) components were applied to evaluate carbon quality, while 16S rRNA sequencing was used to measure microbial composition. Regardless of temperature, degradations of carbon quality and associated reduction in microbial abundance as well as diversity resulted in a decrease in anaerobic carbon mineralization (both CO2 and CH4) towards greater depth. Warming either from 5 °C to 15 °C or 20 °C significantly increased anaerobic carbon mineralization in all depth profiles by improving carbon availability. Enhanced carbon availabilities were mediated by the change in microbial composition (p < 0.01) and an increase in metabolic activities, which was particularly evident in the enhanced β-glucosidase activity and microbial collaborations. A remarkable increase of over 10-fold in the relative abundance of the Geothrix genus was observed under warming. Overall, warming resulted in an enhanced contribution of CH4 emission and a higher ratio of hydrogenotrophic methanogenesis, as evidenced by carbon isotope fractionation factors. In addition, deep peat soils (>100 cm) with recalcitrant carbon demonstrated greater temperature sensitivity (Q10: ∼2.0) than shallow peat soils (Q10:∼1.2) when temperature increased from 15 °C to 20 °C. The findings of this study have significantly deepened our understanding for mechanisms of carbon quality and microbe-driven anaerobic carbon mineralization in peatlands under global warming.
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Affiliation(s)
- Hongyan Wang
- School of Hydrology and Water Resources, Nanjing University of Information Science and Technology, Nanjing, 210044, China; Key Laboratory of Watershed Earth Surface Processes and Ecological Security, Zhejiang Normal University, Jinhua, 321004, China; State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Yijie Xu
- School of Hydrology and Water Resources, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Amit Kumar
- School of Hydrology and Water Resources, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Klaus-Holger Knorr
- University of Münster, Institute for Landscape Ecology, Ecohydrology and Biogeochemistry Group, Heisenbergstr. 2, Münster, 48149, Germany
| | - Xiaoning Zhao
- School of Geographical Sciences, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Jeffrey Paulo H Perez
- Sec. 3.2 Organic Geochemistry, GFZ German Research Centre for Geosciences, Telegrafenberg, 14473, Potsdam, Germany
| | - Guoxin Sun
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Zhi-Guo Yu
- School of Hydrology and Water Resources, Nanjing University of Information Science and Technology, Nanjing, 210044, China.
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Seward J, Bräuer S, Beckett P, Roy-Léveillée P, Emilson E, Watmough S, Basiliko N. Recovery of Smelter-Impacted Peat and Sphagnum Moss: a Microbial Perspective. MICROBIAL ECOLOGY 2023; 86:2894-2903. [PMID: 37632540 DOI: 10.1007/s00248-023-02289-5] [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: 05/17/2023] [Accepted: 08/15/2023] [Indexed: 08/28/2023]
Abstract
Peatlands store approximately one-half of terrestrial soil carbon and one-tenth of non-glacial freshwater. Some of these important ecosystems are located near heavy metal emitting smelters. To improve the understanding of smelter impacts and potential recovery after initial pollution controls in the 1970s (roughly 50 years of potential recovery), we sampled peatlands along a distance gradient of 134 km from a smelter in Sudbury, Ontario, Canada, an area with over a century of nickel (Ni) and copper (Cu) mining activity. This work is aimed at evaluating potential shifts in bacterial and archaeal community structures in Sphagnum moss and its underlying peat within smelter-impacted poor fens. In peat, total Ni and Cu concentrations were higher (0.062-0.067 and 0.110-0.208 mg/g, respectively) at sites close to the smelter and exponentially dropped with distance from the smelter. This exponential decrease in Ni concentrations was also observed in Sphagnum. 16S rDNA amplicon sequencing showed that peat and Sphagnum moss host distinct microbiomes with peat accommodating a more diverse community structure. The microbiomes of Sphagnum were dominated by Proteobacteria (62.5%), followed by Acidobacteria (11.9%), with no observable trends with distance from the smelter. Dominance of Acidobacteria (32.4%) and Proteobacteria (29.6%) in peat was reported across all sites. No drift in taxonomy was seen across the distance gradient or from the reference sites, suggesting a potential microbiome recovery toward that of the reference peatlands microbiomes after decades of pollution controls. These results advance the understanding of peat and Sphagnum moss microbiomes, as well as depict the sensitivities and the resilience of peatland ecosystems.
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Affiliation(s)
- James Seward
- Vale Living with Lakes Centre and the School of Natural Sciences, Laurentian University, 935 Ramsey Lake Rd, Sudbury, ON, P3E 2C6, Canada.
| | - Suzanna Bräuer
- Department of Biology, Appalachian State University, 572 Rivers Street, Boone, NC, 28608, USA
| | - Peter Beckett
- Vale Living with Lakes Centre and the School of Natural Sciences, Laurentian University, 935 Ramsey Lake Rd, Sudbury, ON, P3E 2C6, Canada
| | - Pascale Roy-Léveillée
- Department of Geography, Université Laval, Pavillon Abitibi-Price, Quebec, G1V 0A6, Canada
| | - Erik Emilson
- Natural Resources Canada, Great Lakes Forestry Centre, 1219 Queen St. East, Sault Ste. Marie, ON, P6A 2E5, Canada
| | - Shaun Watmough
- School of the Environment, Trent University, Peterborough, Ontario, Canada
| | - Nathan Basiliko
- Department of Natural Resources Management, Lakehead University, 955 Oliver Rd., Thunder Bay, ON, P7B 5E1, Canada
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Coluccia M, Besaury L. Acidobacteria members harbour an abundant and diverse carbohydrate-active enzymes (cazyme) and secreted proteasome repertoire, key factors for potential efficient biomass degradation. Mol Genet Genomics 2023:10.1007/s00438-023-02045-x. [PMID: 37335345 DOI: 10.1007/s00438-023-02045-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 06/05/2023] [Indexed: 06/21/2023]
Abstract
The Acidobacteria phylum is a very abundant group (20-30% of microbial communities in soil ecosystems); however, little is known about these microorganisms and their ability to degrade the biomass and lignocellulose due to the difficulty of culturing them. We, therefore, bioinformatically studied the content of lignocellulolytic enzymes (total and predicted secreted enzymes) and secreted peptidases in an in silico library containing 41 Acidobacteria genomes. The results showed a high abundance and diversity of total and secreted Carbohydrate-Active enzymes (cazyme) families among the Acidobacteria compared to known previous degraders. Indeed, the relative abundance of cazymes in some genomes represented more than 6% of the gene coding proteins with at least 300 cazymes. The same observation was made with the predicted secreted peptidases with several families of secreted peptidases, which represented at least 1.5% of the gene coding proteins in several genomes. These results allowed us to highlight the lignocellulolytic potential of the Acidobacteria phylum in the degradation of lignocellulosic biomass, which could explain its high abundance in the environment.
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Affiliation(s)
- Marion Coluccia
- Université de Reims Champagne Ardenne, INRAE, FARE, UMR A 614, Chaire AFERE, 51097, Reims, France
| | - Ludovic Besaury
- Université de Reims Champagne Ardenne, INRAE, FARE, UMR A 614, Chaire AFERE, 51097, Reims, France.
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Fu L, Xie R, Ma D, Zhang M, Liu L. Variations in soil microbial community structure and extracellular enzymatic activities along a forest-wetland ecotone in high-latitude permafrost regions. Ecol Evol 2023; 13:e10205. [PMID: 37332520 PMCID: PMC10269122 DOI: 10.1002/ece3.10205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 06/02/2023] [Accepted: 06/05/2023] [Indexed: 06/20/2023] Open
Abstract
Permafrost degradation by global warming is expected to alter the hydrological processes, which results in changes in vegetation species composition and gives rise to community succession. Ecotones are sensitive transition areas between ecosystem boundaries, attract particular interest due to their ecological importance and prompt responses to the environmental variables. However, the characteristics of soil microbial communities and extracellular enzymes along the forest-wetland ecotone in high-latitude permafrost region remain poorly understood. In this study, we evaluated the variations of soil bacterial and fungal community structures and soil extracellular enzymatic activities of 0-10 cm and 10-20 cm soil layers in five different wetland types along environmental gradients, including Larix gmelinii swamp (LY), Betula platyphylla swamp (BH), Alnus sibirica var. hirsute swamp (MCY), thicket swamp (GC), and tussock swamp (CC). The relative abundances of some dominant bacterial (Actinobacteria and Verrucomicrobia) and fungal (Ascomycota and Basidiomycota) phyla differed significantly among different wetlands, while bacterial and fungal alpha diversity was not strongly affected by soil depth. PCoA results showed that vegetation type, rather than soil depth explained more variation of soil microbial community structure. β-glucosidase and β-N-acetylglucosaminidase activities were significantly lower in GC and CC than in LY, BH, and MCY, while acid phosphatase activity was significantly higher in BH and GC than LY and CC. Altogether, the data suggest that soil moisture content (SMC) was the most important environmental factor contributing to the bacterial and fungal communities, while extracellular enzymatic activities were closely related to soil total organic carbon (TOC), nitrate nitrogen (NO3--N) and total phosphorus (TP).
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Affiliation(s)
- Lingyu Fu
- College of Geographical SciencesHarbin Normal UniversityHarbinChina
| | - Ruifeng Xie
- College of Geographical SciencesHarbin Normal UniversityHarbinChina
| | - Dalong Ma
- College of Geographical SciencesHarbin Normal UniversityHarbinChina
| | - Man Zhang
- College of Geographical SciencesHarbin Normal UniversityHarbinChina
| | - Lin Liu
- College of Geographical SciencesHarbin Normal UniversityHarbinChina
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Nong H, Liu J, Chen J, Zhao Y, Wu L, Tang Y, Liu W, Yang G, Xu Z. Woody plants have the advantages in the phytoremediation process of manganese ore with the help of microorganisms. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 863:160995. [PMID: 36535473 DOI: 10.1016/j.scitotenv.2022.160995] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 12/09/2022] [Accepted: 12/13/2022] [Indexed: 06/17/2023]
Abstract
The serious ecological damage caused by mining activities cannot be ignored. The use of an environmentally friendly restoration method to rebuild the vegetation and soil environment in the mining area has attracted more and more attention. This paper aims to study soil quality as well as vegetation characteristics of four woody species including Pinus massoniana (P. massoniana), Broussonetia papyrifera (B. papyrifera), Koelreuteria paniculata (K. paniculata), Osmanthus fragrans (O. fragrans), and two herbaceous species including Setaria viridis (S. viridis) and Cynodon dactylon (C. dactylon). In addition, we further clarified the effects of B. papyrifera and K. paniculata on soil nutrients and microbial communities after restoration. The results showed that the vegetation restoration area had better soil quality and plant community diversity, and the woody plants restoration effect were better. Compared with slag, B. papyrifera and K. paniculata remediation could improve soil pH and mitigate heavy metal contamination in mining areas, but was not effective in enhancing Soil Organic Matter (SOM), Total Nitrogen (TN), Total Potassium (TK) and Total Phosphorus (TP). In addition, the abundance and diversity of soil bacterial communities were increased. Of all the study sites, Proteobacteria had the greatest dominance. Vegetation restoration resulted in an increase in the relative abundance of Acidobacteria, while a decrease in Actinobacteria, Cyanobacteria and Firmicutes. With the restoration of vegetation, the increase of pH, the change of TN, SOM, TK, TP and the mitigation of Manganese (Mn) pollution were the main reasons affecting the soil microbial community. This study has great significance for understanding the ecological changes in the mining area after artificially mediated vegetation restoration, including changes in soil environment, plant community and microbial community, and woody plants will be more encouraged for the restoration of manganese mining areas.
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Affiliation(s)
- Huijiao Nong
- Hunan Research Center of Engineering Technology for Utilization of Environmental and Resources Plant, Central South University of Forestry and Technology, Changsha 410004, Hunan, China; Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Beijing 100081, China
| | - Jun Liu
- Hunan Research Center of Engineering Technology for Utilization of Environmental and Resources Plant, Central South University of Forestry and Technology, Changsha 410004, Hunan, China
| | - Junzhi Chen
- College of Forestry, Northwest A & F University, Yangling 712100, Shanxi, China
| | - Yunlin Zhao
- Hunan Research Center of Engineering Technology for Utilization of Environmental and Resources Plant, Central South University of Forestry and Technology, Changsha 410004, Hunan, China
| | - Liang Wu
- Hunan Research Center of Engineering Technology for Utilization of Environmental and Resources Plant, Central South University of Forestry and Technology, Changsha 410004, Hunan, China
| | - Yongcheng Tang
- Hunan Research Center of Engineering Technology for Utilization of Environmental and Resources Plant, Central South University of Forestry and Technology, Changsha 410004, Hunan, China
| | - Wensheng Liu
- Hunan Research Center of Engineering Technology for Utilization of Environmental and Resources Plant, Central South University of Forestry and Technology, Changsha 410004, Hunan, China
| | - Guiyan Yang
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Beijing 100081, China; College of Forestry, Northwest A & F University, Yangling 712100, Shanxi, China
| | - Zhenggang Xu
- Hunan Research Center of Engineering Technology for Utilization of Environmental and Resources Plant, Central South University of Forestry and Technology, Changsha 410004, Hunan, China; College of Forestry, Northwest A & F University, Yangling 712100, Shanxi, China.
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10
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Sui X, Frey B, Yang L, Liu Y, Zhang R, Ni H, Li MH. Soil Acidobacterial community composition changes sensitively with wetland degradation in northeastern of China. Front Microbiol 2022; 13:1052161. [PMID: 36620014 PMCID: PMC9816132 DOI: 10.3389/fmicb.2022.1052161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 12/08/2022] [Indexed: 12/24/2022] Open
Abstract
Acidobacteria are a major component of the soil bacteria and are conducted for many soil functions, and the soil Acidobacterial structure and diversity are affected by climate changes and human activities. However, soil Acidobacterial structure and diversity in wetland ecosystems are still limited recognized. The current study aimed to study the Acidobacterial community and diversity in relation to soil environmental factors along a typical degradation series from primitive wetland to forest in a representative fresh wetland in northeastern China. In this research, we assessed the soil Acidobacterial community composition, using Illumina MiSeq sequencing along a typical degradation series from primitive wetland to forest in a representative fresh wetland in northeastern China. The soil physico chemical properties changed significantly among the eight degrade stages (p < 0.05). The α diversity index (Shannon and Chao1 index) of soil Acidobacteria changed significantly between different degradation stages (p < 0.05). Principal Coordinates Analysis (PCoA) revealed that the soil acidobacteiral communities obviously separated into wetland group and forest group. The most abundant subgroups of Acidobacteria accounted for 31% (Gp1), 5% (Gp2), 12% (Gp3), 2% (Gp4), 5% (Gp6), and 2% (Gp7) in soils within eight successional series. The compositions of soil Acidobacteria in wetland stages were significantly affected by soil moisture content, soil total nitrogen and available nitrogen contents, while those in forest stages were significantly driven by soil pH, soil organic carbon, total nitrogen, available phosphorus and soil moisture content. Our results indicated that the soil Acidobacterial community was mainly structured by soil physico chemical parameters, and wetland degradation towards forests will greatly influence the soil Acidobacterial structure and thus the wetland functions.
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Affiliation(s)
- Xin Sui
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin, China
- Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region, School of Life Sciences, Heilongjiang University, Harbin, China
- Snow and Landscape Research WSLSwiss Federal Institute for Forest, , Birmensdorf, Switzerland
- Institute of Nature and Ecology, Heilongjiang Academy of Sciences, Harbin, China
| | - Beat Frey
- Snow and Landscape Research WSLSwiss Federal Institute for Forest, , Birmensdorf, Switzerland
| | - Libin Yang
- Institute of Nature and Ecology, Heilongjiang Academy of Sciences, Harbin, China
| | - Yingnan Liu
- Institute of Nature and Ecology, Heilongjiang Academy of Sciences, Harbin, China
| | - Rongtao Zhang
- Institute of Nature and Ecology, Heilongjiang Academy of Sciences, Harbin, China
| | - Hongwei Ni
- Heilongjiang Academy of Forestry, Harbin, China
| | - Mai-He Li
- Snow and Landscape Research WSLSwiss Federal Institute for Forest, , Birmensdorf, Switzerland
- Key Laboratory of Geographical Processes and Ecological Security in Changbai Mountains, Ministry of Education, School of Geographical Sciences, Northeast Normal University, Changchun, China
- School of Life Science, Hebei University, Baoding, China
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11
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Liu F, Ji M, Xiao L, Wang X, Diao Y, Dan Y, Wang H, Sang W, Zhang Y. Organics composition and microbial analysis reveal the different roles of biochar and hydrochar in affecting methane oxidation from paddy soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 843:157036. [PMID: 35772551 DOI: 10.1016/j.scitotenv.2022.157036] [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: 05/02/2022] [Revised: 06/20/2022] [Accepted: 06/24/2022] [Indexed: 06/15/2023]
Abstract
Biochar and hydrochar, as valuable and eco-friendly soil remediation materials from greenwaste, have potential to enhance methane oxidation in paddy soil. But the mechanism of biomass carbon on the improvement of methane-oxidizing bacteria communities in paddy soil has not been adequately elucidated. In the present study, the effect of different-temperature rice straw-based biomass carbon (RB400, RB600, RH250 and RH300) on methane oxidation were investigated by analyzing the soil dissolved organic matter (DOM), physicochemical properties and changes in microbial community structure. The results of the 17-day incubation experiment showed that the methane oxidation rate increased under all types of biomass carbon in the first 6 days. The enhancement of methane oxidation rate was more pronounced for biochar compared to hydrochar, with RB600 being the most effective treatment. The result of excitation-emission matrix (EEM) fluorescence spectroscopy showed that less DOM were released from the soil in the biochar treatments compared to the hydrochar treatments and protein-like were detected only in the hydrochar group. Microbial analysis further showed that hydrochar inhibited the growth of Bacillus, Methylobacter, and Methylocystis, while RB600 significantly increased the relative abundance of methanotrophs (responsible for methane oxidation), such as Methylocystis and Methylobacter, which was consistent with their different effects on the methane oxidation rate. Moreover, from the analysis of principal component analysis (PCA) and canonical correspondence analysis (CCA), Methylobacter and Methylocystis were negatively respond to H/C of biomass carbon. The present study provides a deeper understanding of the effect of biomass carbon obtained by different processes on methane oxidation when applied to soil from the perspective of organic matter and microbial communities.
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Affiliation(s)
- Feihong Liu
- Textile Pollution Controlling Engineering Center of Ministry of Environmental Protection, College of Environmental Science and Engineering, Donghua University, Shanghai 201620, China
| | - Mengyuan Ji
- Department of Biology, University of Padua, 35131 Padova, Italy
| | - Lurui Xiao
- Textile Pollution Controlling Engineering Center of Ministry of Environmental Protection, College of Environmental Science and Engineering, Donghua University, Shanghai 201620, China
| | - Xiaoxia Wang
- Textile Pollution Controlling Engineering Center of Ministry of Environmental Protection, College of Environmental Science and Engineering, Donghua University, Shanghai 201620, China
| | - Yinzhu Diao
- Textile Pollution Controlling Engineering Center of Ministry of Environmental Protection, College of Environmental Science and Engineering, Donghua University, Shanghai 201620, China
| | - Yitong Dan
- Textile Pollution Controlling Engineering Center of Ministry of Environmental Protection, College of Environmental Science and Engineering, Donghua University, Shanghai 201620, China
| | - Huan Wang
- Textile Pollution Controlling Engineering Center of Ministry of Environmental Protection, College of Environmental Science and Engineering, Donghua University, Shanghai 201620, China
| | - Wenjing Sang
- Textile Pollution Controlling Engineering Center of Ministry of Environmental Protection, College of Environmental Science and Engineering, Donghua University, Shanghai 201620, China.
| | - Yalei Zhang
- College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
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12
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GWAS, MWAS and mGWAS provide insights into precision agriculture based on genotype-dependent microbial effects in foxtail millet. Nat Commun 2022; 13:5913. [PMID: 36207301 PMCID: PMC9546826 DOI: 10.1038/s41467-022-33238-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 09/09/2022] [Indexed: 11/09/2022] Open
Abstract
Genetic and environmental factors collectively determine plant growth and yield. In the past 20 years, genome-wide association studies (GWAS) have been conducted on crops to decipher genetic loci that contribute to growth and yield, however, plant genotype appears to be insufficient to explain the trait variations. Here, we unravel the associations between genotypic, phenotypic, and rhizoplane microbiota variables of 827 foxtail millet cultivars by an integrated GWAS, microbiome-wide association studies (MWAS) and microbiome genome-wide association studies (mGWAS) method. We identify 257 rhizoplane microbial biomarkers associated with six key agronomic traits and validated the microbial-mediated growth effects on foxtail millet using marker strains isolated from the field. The rhizoplane microbiota composition is mainly driven by variations in plant genes related to immunity, metabolites, hormone signaling and nutrient uptake. Among these, the host immune gene FLS2 and transcription factor bHLH35 are widely associated with the microbial taxa of the rhizoplane. We further uncover a plant genotype-microbiota interaction network that contributes to phenotype plasticity. The microbial-mediated growth effects on foxtail millet are dependent on the host genotype, suggesting that precision microbiome management could be used to engineer high-yielding cultivars in agriculture systems.
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13
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Panis F, Rompel A. The Novel Role of Tyrosinase Enzymes in the Storage of Globally Significant Amounts of Carbon in Wetland Ecosystems. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:11952-11968. [PMID: 35944157 PMCID: PMC9454253 DOI: 10.1021/acs.est.2c03770] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/01/2022] [Accepted: 07/05/2022] [Indexed: 05/30/2023]
Abstract
Over the last millennia, wetlands have been sequestering carbon from the atmosphere via photosynthesis at a higher rate than releasing it and, therefore, have globally accumulated 550 × 1015 g of carbon, which is equivalent to 73% of the atmospheric carbon pool. The accumulation of organic carbon in wetlands is effectuated by phenolic compounds, which suppress the degradation of soil organic matter by inhibiting the activity of organic-matter-degrading enzymes. The enzymatic removal of phenolic compounds by bacterial tyrosinases has historically been blocked by anoxic conditions in wetland soils, resulting from waterlogging. Bacterial tyrosinases are a subgroup of oxidoreductases that oxidatively remove phenolic compounds, coupled to the reduction of molecular oxygen to water. The biochemical properties of bacterial tyrosinases have been investigated thoroughly in vitro within recent decades, while investigations focused on carbon fluxes in wetlands on a macroscopic level have remained a thriving yet separated research area so far. In the wake of climate change, however, anoxic conditions in wetland soils are threatened by reduced rainfall and prolonged summer drought. This potentially allows tyrosinase enzymes to reduce the concentration of phenolic compounds, which in turn will increase the release of stored carbon back into the atmosphere. To offer compelling evidence for the novel concept that bacterial tyrosinases are among the key enzymes influencing carbon cycling in wetland ecosystems first, bacterial organisms indigenous to wetland ecosystems that harbor a TYR gene within their respective genome (tyr+) have been identified, which revealed a phylogenetically diverse community of tyr+ bacteria indigenous to wetlands based on genomic sequencing data. Bacterial TYR host organisms covering seven phyla (Acidobacteria, Actinobacteria, Bacteroidetes, Firmicutes, Nitrospirae, Planctomycetes, and Proteobacteria) have been identified within various wetland ecosystems (peatlands, marshes, mangrove forests, bogs, and alkaline soda lakes) which cover a climatic continuum ranging from high arctic to tropic ecosystems. Second, it is demonstrated that (in vitro) bacterial TYR activity is commonly observed at pH values characteristic for wetland ecosystems (ranging from pH 3.5 in peatlands and freshwater swamps to pH 9.0 in soda lakes and freshwater marshes) and toward phenolic compounds naturally present within wetland environments (p-coumaric acid, gallic acid, protocatechuic acid, p-hydroxybenzoic acid, caffeic acid, catechin, and epicatechin). Third, analyzing the available data confirmed that bacterial host organisms tend to exhibit in vitro growth optima at pH values similar to their respective wetland habitats. Based on these findings, it is concluded that, following increased aeration of previously anoxic wetland soils due to climate change, TYRs are among the enzymes capable of reducing the concentration of phenolic compounds present within wetland ecosystems, which will potentially destabilize vast amounts of carbon stored in these ecosystems. Finally, promising approaches to mitigate the detrimental effects of increased TYR activity in wetland ecosystems and the requirement of future investigations of the abundance and activity of TYRs in an environmental setting are presented.
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14
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Xu M, Dai W, Zhao Z, Zheng J, Huang F, Mei C, Huang S, Liu C, Wang P, Xiao R. Effect of rice straw biochar on three different levels of Cd-contaminated soils: Cd availability, soil properties, and microbial communities. CHEMOSPHERE 2022; 301:134551. [PMID: 35405191 DOI: 10.1016/j.chemosphere.2022.134551] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 03/31/2022] [Accepted: 04/05/2022] [Indexed: 06/14/2023]
Abstract
Biochar can be effective in immobilizing soil cadmium (Cd), but the difference in its immobilization mechanisms for different levels of Cd-contaminated soils was overlooked. In this study, rice straw biochar (BC) was added to three Cd-contaminated soils following 180 days of incubation, in the process of which the dynamic changes of Cd speciation, soil properties and microbial community diversity were determined. BC could significantly reduce the ratio of acid-soluble in the three soils, especially in light and medium Cd-contaminated soils by more than 20%. The addition of biochar could significantly increase the soil pH, soil organic matter, cation exchange capacity, and the activities of catalase, but decrease the richness and diversity of bacterial communities in all soils. The associations between microbial communities were inhibited in light and medium Cd-contaminated soils, but promoted in heavy Cd-contaminated soils. Furthermore, the main pathway of BC effect on soil Cd availability was also analyzed by partial least squares model (PLS-PM), which indicated that BC indirectly reduced Cd availability mainly by regulating the microbial community in light Cd-contaminated soil, whereas BC directly reduced Cd availability primarily by its own adsorption in medium and heavy Cd-contaminated soils. This research deepened understanding of the mechanisms of stabilization of Cd by biochar for agricultural soils.
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Affiliation(s)
- Meili Xu
- Guangdong Industrial Contaminated Site Remediation Technology and Equipment Engineering Research Center, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou, 510006, PR China
| | - Weijie Dai
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Zilin Zhao
- Guangdong Industrial Contaminated Site Remediation Technology and Equipment Engineering Research Center, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou, 510006, PR China
| | - Jiatong Zheng
- Guangdong Industrial Contaminated Site Remediation Technology and Equipment Engineering Research Center, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou, 510006, PR China
| | - Fei Huang
- Guangdong Industrial Contaminated Site Remediation Technology and Equipment Engineering Research Center, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou, 510006, PR China.
| | - Chuang Mei
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, PR China
| | - Shuting Huang
- Guangdong Industrial Contaminated Site Remediation Technology and Equipment Engineering Research Center, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou, 510006, PR China
| | - Chufan Liu
- Shenzhen Academy of Environmental Science, Shenzhen, 518001, PR China
| | - Peng Wang
- Guangdong Industrial Contaminated Site Remediation Technology and Equipment Engineering Research Center, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou, 510006, PR China
| | - Rongbo Xiao
- Guangdong Industrial Contaminated Site Remediation Technology and Equipment Engineering Research Center, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou, 510006, PR China.
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15
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Huber KJ, Pester M, Eichorst SA, Navarrete AA, Foesel BU. Editorial: Acidobacteria – Towards Unraveling the Secrets of a Widespread, Though Enigmatic, Phylum. Front Microbiol 2022; 13:960602. [PMID: 35814658 PMCID: PMC9267355 DOI: 10.3389/fmicb.2022.960602] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Katharina J. Huber
- Department Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Michael Pester
- Department Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- Institute for Microbiology, Technical University of Braunschweig, Braunschweig, Germany
| | - Stephanie A. Eichorst
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Acacio A. Navarrete
- Graduate Program in Environmental Sciences, University Brazil, São Paulo, Brazil
| | - Bärbel U. Foesel
- Working Group Biobank, Research Unit Molecular Epidemiology, Institute of Epidemiology, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
- *Correspondence: Bärbel U. Foesel
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16
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Fu L, Wu C, Zuo J, Zhou Y, Yang J. Residual ozone in microorganisms enhanced organics removal and shaped microbial community. CHEMOSPHERE 2021; 278:130322. [PMID: 33831684 DOI: 10.1016/j.chemosphere.2021.130322] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 03/06/2021] [Accepted: 03/15/2021] [Indexed: 06/12/2023]
Abstract
The residual ozone played an important role in enhancing the organics removal by stimulate subsequent biological processes. However, how the residual ozone affects the biological process is not well studied. In this work, a pilot scale integrated O3-BAF, ordinary BAF and separated O3-BAF were compared in advanced treatment of real bio-treated petrochemical wastewater. Results showed that residual ozone with 0.05-0.10 mg L-1 in the BAF demonstrated relatively high chemical oxygen demand (COD) removal efficiency of 48.4%, which was 1.5-fold higher than that obtained by separated O3-BAF and 3-fold higher than that obtained by ordinary BAF. The stimulative effect of low dosage of O3 on biological treatment additionally donated 33.9% of the COD removal in the BAF. The COD removal amount per dosage of ozone reached 5.30 mg-COD/mg-O3. The biofilm thickness in the integrated O3-BAF was reduced by 30-50% while the dehydrogenase activity (DHA) was improved by 500%, indicating the stimulate effect on the bioactivity. Additionally, Illumina HiSeq sequencing of 16S rRNA gene amplicons demonstrated significant microbial diversity decreasing. Specially, Gemmatimonadetes and Bacteroidetes are the dominate microorganism in the integrated O3-BAF, having a positive correlation with the proper residual ozone, and increased by 5.4% and 4.2% in comparison with the separated O3-BAF, respectively. The residual ozone higher than 0.22 mg L-1 showed inhibition effect on the bioactivity. In summary, the control of residual ozone introduced to BAF was crucial for stimulative effects and manager the microbial community in the integrated O3-BAF, which still need further detail research.
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Affiliation(s)
- Liya Fu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China; Research Center of Environmental Pollution Control Engineering Technology, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China; School of Environment, Tsinghua University, Beijing, 100084, China
| | - Changyong Wu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China; Research Center of Environmental Pollution Control Engineering Technology, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China.
| | - Jian'e Zuo
- Research Center of Environmental Pollution Control Engineering Technology, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Yuexi Zhou
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China; Research Center of Environmental Pollution Control Engineering Technology, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China; School of Environment, Tsinghua University, Beijing, 100084, China.
| | - Jin Yang
- School of Chemical and Environmental Engineering, China University of Mining and Technology, Beijing, 100083, China
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17
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Ghezzi D, Filippini M, Cappelletti M, Firrincieli A, Zannoni D, Gargini A, Fedi S. Molecular characterization of microbial communities in a peat-rich aquifer system contaminated with chlorinated aliphatic compounds. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:23017-23035. [PMID: 33438126 DOI: 10.1007/s11356-020-12236-3] [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: 07/24/2020] [Accepted: 12/25/2020] [Indexed: 06/12/2023]
Abstract
In an aquifer-aquitard system in the subsoil of the city of Ferrara (Emilia-Romagna region, northern Italy) highly contaminated with chlorinated aliphatic toxic organics such as trichloroethylene (TCE) and tetrachloroethylene (PCE), a strong microbial-dependent dechlorination activity takes place during migration of contaminants through shallow organic-rich layers with peat intercalations. The in situ microbial degradation of chlorinated ethenes, formerly inferred by the utilization of contaminant concentration profiles and Compound-Specific Isotope Analysis (CSIA), was here assessed using Illumina sequencing of V4 hypervariable region of 16S rRNA gene and by clone library analysis of dehalogenase metabolic genes. Taxon-specific investigation of the microbial communities catalyzing the chlorination process revealed the presence of not only dehalogenating genera such as Dehalococcoides and Dehalobacter but also of numerous other groups of non-dehalogenating bacteria and archaea thriving on diverse metabolisms such as hydrolysis and fermentation of complex organic matter, acidogenesis, acetogenesis, and methanogenesis, which can indirectly support the reductive dechlorination process. Besides, the diversity of genes encoding some reductive dehalogenases was also analyzed. Geochemical and 16S rRNA and RDH gene analyses, as a whole, provided insights into the microbial community complexity and the distribution of potential dechlorinators. Based on the data obtained, a possible network of metabolic interactions has been hypothesized to obtain an effective reductive dechlorination process.
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Affiliation(s)
- Daniele Ghezzi
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, Via Irnerio 42, 40126, Bologna, Italy
- Laboratory of NanoBiotechnology, IRCSS Istituto Ortopedico Rizzoli, via di Barbiano 1/10, 40136, Bologna, Italy
| | - Maria Filippini
- Department of Biological, Geological and Environmental Sciences, Alma Mater Studiorum University of Bologna, via Zamboni 67, 40126, Bologna, Italy
| | - Martina Cappelletti
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, Via Irnerio 42, 40126, Bologna, Italy
| | - Andrea Firrincieli
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, Via Irnerio 42, 40126, Bologna, Italy
| | - Davide Zannoni
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, Via Irnerio 42, 40126, Bologna, Italy
| | - Alessandro Gargini
- Department of Biological, Geological and Environmental Sciences, Alma Mater Studiorum University of Bologna, via Zamboni 67, 40126, Bologna, Italy
| | - Stefano Fedi
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, Via Irnerio 42, 40126, Bologna, Italy.
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18
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Undisturbed Soil Pedon under Birch Forest: Characterization of Microbiome in Genetic Horizons. SOIL SYSTEMS 2021. [DOI: 10.3390/soilsystems5010014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Vast areas of land in the forest-steppe of West Siberia are occupied by birch forests, the most common ecosystems there. However, currently, little is known about the microbiome composition in the underlying soil, especially along a sequence of soil genetic horizons. The study aimed at inventorying microbiome in genetic horizons of a typical Phaeozem under undisturbed birch forest in West Siberia. Bacteria and fungi were studied using 16S rRNA genes’ and ITS2 amplicon sequencing with Illumina MiSeq. Proteobacteria and Acidobacteria together accounted for two-thirds of the operational taxonomic units (OTUs) numbers and half of the sequences in each genetic horizon. Acidobacteria predominated in eluvial environments, whereas Proteobacteria, preferred topsoil. The fungal sequences were dominated by Ascomycota and Basidiomycota phyla. Basidiomycota was the most abundant in the topsoil, whereas Ascomycota increased down the soil profile. Thelephoraceae family was the most abundant in the A horizon, whereas the Pyronemataceae family dominants in the AEl horizon, ultimately prevailing in the subsoil. We conclude that soil genetic horizons shape distinct microbiomes, therefore soil horizontation should be accounted for while studying undisturbed soils. This study, representing the first description of bacterio- and mycobiomes in genetic horizons of the Phaeozem profile, provides a reference for future research.
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19
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Costa OYA, Kuramae EE. The influence of agar brands and micronutrients in the growth optimization of Granulicella sp. (Acidobacteriota). J Microbiol Methods 2021; 181:106148. [PMID: 33484740 DOI: 10.1016/j.mimet.2021.106148] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 01/04/2021] [Accepted: 01/12/2021] [Indexed: 11/25/2022]
Abstract
Acidobacteriota are highly abundant in soils, however, few cultured representatives are available. The purity of the reagents can influence microbial growth in laboratory conditions and successful isolation. Here we investigated the impact of different agar brands in culture medium and advocate that agar origin should be carefully considered for Acidobacteriota strains growth and microbial isolation.
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Affiliation(s)
- Ohana Y A Costa
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, Droevendaalsesteeg 10, 6708, PB, Wageningen, the Netherlands.
| | - Eiko E Kuramae
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, Droevendaalsesteeg 10, 6708, PB, Wageningen, the Netherlands; Institute of Environmental Biology, Ecology and Biodiversity, Utrecht University, 3584, CH, Utrecht, the Netherlands
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20
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Cheng X, Yun Y, Wang H, Ma L, Tian W, Man B, Liu C. Contrasting bacterial communities and their assembly processes in karst soils under different land use. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 751:142263. [PMID: 33181984 DOI: 10.1016/j.scitotenv.2020.142263] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 09/03/2020] [Accepted: 09/05/2020] [Indexed: 06/11/2023]
Abstract
Structure and assembly processes of soil bacterial communities under different land use at karst areas remained poorly understood to date. To address this issue, soil samples from arable land and pristine forest over a karst cave, located in the acid rain impacted area, Hubei province, were collected and subjected to high-throughput sequencing and multivariate statistical analysis. Bacterial communities and functions remarkably distinguished between soils under different land use. Both edaphic properties (the content of SO42-, C/N, pH, TN) and weathering processes, such as Si concentration, Mg/Al and Ca/Al, significantly impacted on soil bacterial community structures. Variable selections were predominant ecological processes, and pH and SO42- concentration were of significance in community assembly. Random molecular ecological network analysis revealed a more stable and complex microbial network in the forest ecosystem, which can quickly response to environmental change. Forest soil bacteria were mainly phototrophs, involving in C and N cycles, whereas those in arable soils were mainly chemoheterotrophs, capable of degrading organic fertilizers due to anthropogenic activities as confirmed by the analysis of keystone taxa, indicators and functional prediction. These results reveal that land use constructed soil bacterial communities in different aspects such as the structure, potential functions, microbial interactions and correlations with environmental variables. To our knowledge, this is the first report on bacterial community assembly in karst soils under different land use which enhances our understanding about how land use impact on microbial interaction and community assembly processes.
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Affiliation(s)
- Xiaoyu Cheng
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China; School of Environmental Studies, China University of Geosciences, Wuhan 430074, China
| | - Yuan Yun
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China; College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Hongmei Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China; School of Environmental Studies, China University of Geosciences, Wuhan 430074, China; Laboratory of Basin Hydrology and Wetland Eco-restoration, China University of Geosciences, Wuhan 430074, China.
| | - Liyuan Ma
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China; School of Environmental Studies, China University of Geosciences, Wuhan 430074, China
| | - Wen Tian
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China; School of Environmental Studies, China University of Geosciences, Wuhan 430074, China
| | - Baiying Man
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China; College of Life Science, Shangrao Normal University, Shangrao 334001, China
| | - Chaoyang Liu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China; School of Environmental Studies, China University of Geosciences, Wuhan 430074, China
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Guo A, Pan C, Ma J, Bao Y. Linkage of antibiotic resistance genes, associated bacteria communities and metabolites in the wheat rhizosphere from chlorpyrifos-contaminated soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 741:140457. [PMID: 32615437 DOI: 10.1016/j.scitotenv.2020.140457] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 06/19/2020] [Accepted: 06/21/2020] [Indexed: 05/28/2023]
Abstract
Rhizosphere is a crucial site for the proliferation of antibiotic resistance genes (ARGs) in agricultural soil. Pesticide contamination is ubiquitous in soil, such as chlorpyrifos as one of the most commonly used pesticides. However, limited knowledge is reported about ARGs profiles changes and the driving mechanism of ARGs prevalence in rhizosphere soil after adding pesticide. In this study, irrespective of chlorpyrifos presence, the abundances of ARGs (tetM, tetO, tetQ, tetW, tetX, sul1 and sul2) and intI1 in rhizosphere soil of wheat were obviously higher than those in bulk soil. 20.0 mg·kg-1 chlorpyrifos significantly increased the abundance of total ARGs and intI1 in bulk soil, respectively, at day 50 and 100, but not in rhizosphere soil. Rhizosphere influence on ARGs was far greater than chlorpyrifos. ARGs and intI1 abundances were higher at day 50 than ones at day 100. C/N ratio and NO3--N content, which were affected by rhizosphere and cultivation time, significantly explained the increased ARGs. Compared to bulk soil, rhizosphere shifted host bacteria of tetracycline resistance genes (TRGs), intI1 at genus level, and host bacteria of sul1, sul2 at phylum level. Rhizosphere simplified the linkage of ARGs, host bacteria and metabolites. Bacterial communities played important roles in the variation of ARGs and intI1, and the difference in the distribution of potential hosts between bulk and rhizosphere soil was related to metabolites abundance and composition. These results provide valuable information for understanding the linkage of ARGs, associated bacteria communities and metabolites in the wheat rhizosphere soil.
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Affiliation(s)
- Aiyun Guo
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education)/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin, 300350, China
| | - Chengrong Pan
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education)/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin, 300350, China
| | - Jinyu Ma
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education)/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin, 300350, China
| | - Yanyu Bao
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education)/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin, 300350, China.
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22
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Egorova DA, Voronina OL, Solovyev AI, Kunda MS, Aksenova EI, Ryzhova NN, Danilova KV, Rykova VS, Scherbakova AA, Semenov AN, Polyakov NB, Grumov DA, Shevlyagina NV, Dolzhikova IV, Romanova YM, Gintsburg AL. Integrated into Environmental Biofilm Chromobacterium vaccinii Survives Winter with Support of Bacterial Community. Microorganisms 2020; 8:E1696. [PMID: 33143246 PMCID: PMC7716238 DOI: 10.3390/microorganisms8111696] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 09/30/2020] [Accepted: 10/29/2020] [Indexed: 12/27/2022] Open
Abstract
Chromobacterium species are common in tropical and subtropical zones in environmental samples according to numerous studies. Here, we describe an environmental case of resident Chromobacterium vaccinii in biofilms associated with Carex spp. roots in Moscow region, Russia (warm-summer humid continental climate zone). We performed broad characterization of individual properties as well as surrounding context for better understanding of the premise of C. vaccinii survival during the winter season. Genome properties of isolated strains propose some insights into adaptation to habit and biofilm mode of life, including social cheaters carrying ΔluxR mutation. Isolated C. vaccinii differs from previously described strains in some biochemical properties and some basic characteristics like fatty acid composition as well as unique genome features. Despite potential to modulate membrane fluidity and presence of several genes responsible for cold shock response, isolated C. vaccinii did not survive during exposure to 4 °C, while in the complex biofilm sample, it was safely preserved for at least half a year in vitro at 4 °C. The surrounding bacterial community within the same biofilm with C. vaccinii represented a series of psychrophilic bacterial species, which may share resistance to low temperatures with other species within biofilm and provide C. vaccinii an opportunity to survive during the cold winter season.
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Affiliation(s)
- Daria A. Egorova
- N.F. Gamaleya National Research Center of Epidemiology and Microbiology, Ministry of Health, 123098 Moscow, Russia; (A.I.S.); (M.S.K.); (E.I.A.); (N.N.R.); (K.V.D.); (V.S.R.); (A.A.S.); (A.N.S.); (N.B.P.); (D.A.G.); (N.V.S.); (I.V.D.); (Y.M.R.); (A.L.G.)
| | - Olga L. Voronina
- N.F. Gamaleya National Research Center of Epidemiology and Microbiology, Ministry of Health, 123098 Moscow, Russia; (A.I.S.); (M.S.K.); (E.I.A.); (N.N.R.); (K.V.D.); (V.S.R.); (A.A.S.); (A.N.S.); (N.B.P.); (D.A.G.); (N.V.S.); (I.V.D.); (Y.M.R.); (A.L.G.)
| | - Andrey I. Solovyev
- N.F. Gamaleya National Research Center of Epidemiology and Microbiology, Ministry of Health, 123098 Moscow, Russia; (A.I.S.); (M.S.K.); (E.I.A.); (N.N.R.); (K.V.D.); (V.S.R.); (A.A.S.); (A.N.S.); (N.B.P.); (D.A.G.); (N.V.S.); (I.V.D.); (Y.M.R.); (A.L.G.)
| | - Marina S. Kunda
- N.F. Gamaleya National Research Center of Epidemiology and Microbiology, Ministry of Health, 123098 Moscow, Russia; (A.I.S.); (M.S.K.); (E.I.A.); (N.N.R.); (K.V.D.); (V.S.R.); (A.A.S.); (A.N.S.); (N.B.P.); (D.A.G.); (N.V.S.); (I.V.D.); (Y.M.R.); (A.L.G.)
| | - Ekaterina I. Aksenova
- N.F. Gamaleya National Research Center of Epidemiology and Microbiology, Ministry of Health, 123098 Moscow, Russia; (A.I.S.); (M.S.K.); (E.I.A.); (N.N.R.); (K.V.D.); (V.S.R.); (A.A.S.); (A.N.S.); (N.B.P.); (D.A.G.); (N.V.S.); (I.V.D.); (Y.M.R.); (A.L.G.)
| | - Natalia N. Ryzhova
- N.F. Gamaleya National Research Center of Epidemiology and Microbiology, Ministry of Health, 123098 Moscow, Russia; (A.I.S.); (M.S.K.); (E.I.A.); (N.N.R.); (K.V.D.); (V.S.R.); (A.A.S.); (A.N.S.); (N.B.P.); (D.A.G.); (N.V.S.); (I.V.D.); (Y.M.R.); (A.L.G.)
| | - Ksenya V. Danilova
- N.F. Gamaleya National Research Center of Epidemiology and Microbiology, Ministry of Health, 123098 Moscow, Russia; (A.I.S.); (M.S.K.); (E.I.A.); (N.N.R.); (K.V.D.); (V.S.R.); (A.A.S.); (A.N.S.); (N.B.P.); (D.A.G.); (N.V.S.); (I.V.D.); (Y.M.R.); (A.L.G.)
| | - Valentina S. Rykova
- N.F. Gamaleya National Research Center of Epidemiology and Microbiology, Ministry of Health, 123098 Moscow, Russia; (A.I.S.); (M.S.K.); (E.I.A.); (N.N.R.); (K.V.D.); (V.S.R.); (A.A.S.); (A.N.S.); (N.B.P.); (D.A.G.); (N.V.S.); (I.V.D.); (Y.M.R.); (A.L.G.)
| | - Anastasya A. Scherbakova
- N.F. Gamaleya National Research Center of Epidemiology and Microbiology, Ministry of Health, 123098 Moscow, Russia; (A.I.S.); (M.S.K.); (E.I.A.); (N.N.R.); (K.V.D.); (V.S.R.); (A.A.S.); (A.N.S.); (N.B.P.); (D.A.G.); (N.V.S.); (I.V.D.); (Y.M.R.); (A.L.G.)
| | - Andrey N. Semenov
- N.F. Gamaleya National Research Center of Epidemiology and Microbiology, Ministry of Health, 123098 Moscow, Russia; (A.I.S.); (M.S.K.); (E.I.A.); (N.N.R.); (K.V.D.); (V.S.R.); (A.A.S.); (A.N.S.); (N.B.P.); (D.A.G.); (N.V.S.); (I.V.D.); (Y.M.R.); (A.L.G.)
| | - Nikita B. Polyakov
- N.F. Gamaleya National Research Center of Epidemiology and Microbiology, Ministry of Health, 123098 Moscow, Russia; (A.I.S.); (M.S.K.); (E.I.A.); (N.N.R.); (K.V.D.); (V.S.R.); (A.A.S.); (A.N.S.); (N.B.P.); (D.A.G.); (N.V.S.); (I.V.D.); (Y.M.R.); (A.L.G.)
- Vernadsky Institute of Geochemistry and Analytical Chemistry of Russian Academy of Sciences, 119991 Moscow, Russia
| | - Daniil A. Grumov
- N.F. Gamaleya National Research Center of Epidemiology and Microbiology, Ministry of Health, 123098 Moscow, Russia; (A.I.S.); (M.S.K.); (E.I.A.); (N.N.R.); (K.V.D.); (V.S.R.); (A.A.S.); (A.N.S.); (N.B.P.); (D.A.G.); (N.V.S.); (I.V.D.); (Y.M.R.); (A.L.G.)
| | - Natalia V. Shevlyagina
- N.F. Gamaleya National Research Center of Epidemiology and Microbiology, Ministry of Health, 123098 Moscow, Russia; (A.I.S.); (M.S.K.); (E.I.A.); (N.N.R.); (K.V.D.); (V.S.R.); (A.A.S.); (A.N.S.); (N.B.P.); (D.A.G.); (N.V.S.); (I.V.D.); (Y.M.R.); (A.L.G.)
| | - Inna V. Dolzhikova
- N.F. Gamaleya National Research Center of Epidemiology and Microbiology, Ministry of Health, 123098 Moscow, Russia; (A.I.S.); (M.S.K.); (E.I.A.); (N.N.R.); (K.V.D.); (V.S.R.); (A.A.S.); (A.N.S.); (N.B.P.); (D.A.G.); (N.V.S.); (I.V.D.); (Y.M.R.); (A.L.G.)
| | - Yulia M. Romanova
- N.F. Gamaleya National Research Center of Epidemiology and Microbiology, Ministry of Health, 123098 Moscow, Russia; (A.I.S.); (M.S.K.); (E.I.A.); (N.N.R.); (K.V.D.); (V.S.R.); (A.A.S.); (A.N.S.); (N.B.P.); (D.A.G.); (N.V.S.); (I.V.D.); (Y.M.R.); (A.L.G.)
- Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation, 119991 Moscow, Russia
| | - Alexander L. Gintsburg
- N.F. Gamaleya National Research Center of Epidemiology and Microbiology, Ministry of Health, 123098 Moscow, Russia; (A.I.S.); (M.S.K.); (E.I.A.); (N.N.R.); (K.V.D.); (V.S.R.); (A.A.S.); (A.N.S.); (N.B.P.); (D.A.G.); (N.V.S.); (I.V.D.); (Y.M.R.); (A.L.G.)
- Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation, 119991 Moscow, Russia
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23
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Metagenomic Analysis Exploring Taxonomic and Functional Diversity of Soil Microbial Communities in Sugarcane Fields Applied with Organic Fertilizer. BIOMED RESEARCH INTERNATIONAL 2020; 2020:9381506. [PMID: 33145361 PMCID: PMC7596465 DOI: 10.1155/2020/9381506] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 09/22/2020] [Accepted: 09/25/2020] [Indexed: 12/14/2022]
Abstract
Organic fertilizers are critically important to soil fertility, microbial communities, and sustainable agricultural strategies. We compared the effect of two fertilizer groups (organic+chemical fertilizer: OM, chemical fertilizer: CK) on sugarcane growth, by observing the difference in microbial communities and functions, soil nutrient status, and agronomic characters of sugarcane. The results showed that the sugar content and yield of sugarcane increased significantly under organic fertilizer treatment. We believe that the increased soil nutrient status and soil microorganisms are the reasons for this phenomenon. In addition, redundancy analysis (RDA) shows that the soil nutrient condition has a major impact on the soil microbial community. In comparison with CK, the species richness of Acidobacteria, Proteobacteria, Chloroflexi, and Gemmatimonadetes as well as the functional abundance of nucleotide metabolism and energy metabolism increased significantly in the OM field. Moreover, compared with CK, genes related to the absorption and biosynthesis of sulfate were more prominent in OM. Therefore, consecutive organic fertilizer application could be an effective method in reference to sustainable production of sugarcane.
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Lu K, Jin Q, Lin Y, Lu W, Li S, Zhou C, Jin J, Jiang Q, Ling L, Xiao M. Cell-Free Fermentation Broth of Bacillus velezensis Strain S3-1 Improves Pak Choi Nutritional Quality and Changes the Bacterial Community Structure of the Rhizosphere Soil. Front Microbiol 2020; 11:2043. [PMID: 33071994 PMCID: PMC7533579 DOI: 10.3389/fmicb.2020.02043] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 08/03/2020] [Indexed: 11/13/2022] Open
Abstract
Bacillus velezensis is a plant growth-promoting rhizobacteria (PGPR) that has long been proven to improve the growth of plants, and it has been widely used in agriculture. However, in many reports, we observed that during the application of bacterial fluids, it appeared that the effect of the cell-free fermentation broth (CFB) was ignored. The purpose of this study is to compare the effect of the no inoculation treatment (CK), the B. velezensis strain S3-1 treatment (S), the CFB treatment in the Pak choi, soil bacterial community structure, soil enzyme activity, and field soil properties. The results have shown that, compared to the inoculation B. velezensis strain S3-1 treatment and the no-inoculation treatment; the inoculation of the CFB treatment can significantly enhance the soluble protein, soluble solids, ascorbic acid of Pak choi and increase the total phosphorus content and electrical conductivity (EC) in the soil. Based on high-throughput sequencing data, our analysis of soil microbial communities used R, NETWORK, and PICRUSt showed that the CFB treatment can enhance the relative abundance of Acidobacteria in the soil, decrease the abundance of native Bacillus in the soil, change the microbial community structure of the top 50 operational taxonomic units (OTUs), and improve soil microbial carbon metabolism and nitrogen metabolism. Overall, we observed that CFB treatment can also improve plant nutrition and change soil microbial communities. This study provides new insights for the application of microbial fertilizers in agricultural production.
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Affiliation(s)
- Kaiheng Lu
- Shanghai Engineering and Technical Research Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Qing Jin
- Shanghai Engineering and Technical Research Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Yibo Lin
- Shanghai Engineering and Technical Research Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Wenwei Lu
- Shanghai Engineering and Technical Research Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Songshuo Li
- Shanghai Engineering and Technical Research Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Chenhao Zhou
- Shanghai Engineering and Technical Research Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Jieren Jin
- Shanghai Engineering and Technical Research Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Qiuyan Jiang
- Shanghai Engineering and Technical Research Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Lichen Ling
- Shanghai Engineering and Technical Research Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Ming Xiao
- Shanghai Engineering and Technical Research Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, China
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25
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Costa OYA, Oguejiofor C, Zühlke D, Barreto CC, Wünsche C, Riedel K, Kuramae EE. Impact of Different Trace Elements on the Growth and Proteome of Two Strains of Granulicella, Class "Acidobacteriia". Front Microbiol 2020; 11:1227. [PMID: 32625179 PMCID: PMC7315648 DOI: 10.3389/fmicb.2020.01227] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 05/14/2020] [Indexed: 12/24/2022] Open
Abstract
Acidobacteria represents one of the most dominant bacterial groups across diverse ecosystems. However, insight into their ecology and physiology has been hampered by difficulties in cultivating members of this phylum. Previous cultivation efforts have suggested an important role of trace elements for the proliferation of Acidobacteria, however, the impact of these metals on their growth and metabolism is not known. In order to gain insight into this relationship, we evaluated the effect of trace element solution SL10 on the growth of two strains (5B5 and WH15) of Acidobacteria belonging to the genus Granulicella and studied the proteomic responses to manganese (Mn). Granulicella species had highest growth with the addition of Mn, as well as higher tolerance to this metal compared to seven other metal salts. Variations in tolerance to metal salt concentrations suggests that Granulicella sp. strains possess different mechanisms to deal with metal ion homeostasis and stress. Furthermore, Granulicella sp. 5B5 might be more adapted to survive in an environment with higher concentration of several metal ions when compared to Granulicella sp. WH15. The proteomic profiles of both strains indicated that Mn was more important in enhancing enzymatic activity than to protein expression regulation. In the genomic analyses, we did not find the most common transcriptional regulation of Mn homeostasis, but we found candidate transporters that could be potentially involved in Mn homeostasis for Granulicella species. The presence of such transporters might be involved in tolerance to higher Mn concentrations, improving the adaptability of bacteria to metal enriched environments, such as the decaying wood-rich Mn environment from which these two Granulicella strains were isolated.
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Affiliation(s)
- Ohana Y A Costa
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands.,Institute of Biology Leiden, Leiden University, Leiden, Netherlands
| | - Chidinma Oguejiofor
- Department of Soil Science and Meteorology, Michael Okpara University of Agriculture, Umudike, Nigeria
| | - Daniela Zühlke
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Cristine C Barreto
- Genomic Sciences and Biotechnology Program, Catholic University of Brasilia, Distrito Federal, Brazil
| | - Christine Wünsche
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Katharina Riedel
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Eiko E Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands.,Ecology and Biodiversity, Institute of Environmental Biology, Utrecht University, Utrecht, Netherlands
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26
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Li P, Zhang Y, Meng Q, Liu Y, Tuyiringire D, Chen Z, Liang S. Effects of trichloroethylene stress on the microbiological characteristics of Mollisol. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 184:109595. [PMID: 31470249 DOI: 10.1016/j.ecoenv.2019.109595] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Revised: 08/17/2019] [Accepted: 08/20/2019] [Indexed: 06/10/2023]
Abstract
Trichloroethylene (TCE), one of 129 kinds of priority pollutants, is the most common halogenated organic pollutant in the environment. To explore the changes in soil physicochemical properties and biological activities then clarify the effects of these factors on bacterial, fungal and actinomycetes communities in Mollisol under TCE stress is the significance of our research. The results indicated that when TCE concentration was greater than 10 mg kg-1, soil quality declined and soil decomposition of organic matter and cycling of mineral nutrients were inhibited through an effect on soil microbial biomass. Operational taxonomic units (OTUs) richness of the bacteria in Mollisol was altered by TCE contamination. The SChao1 and HShannon indices of bacterial communities in Mollisol decreased when 40 mg kg-1 TCE was applied. Meanwhile, the OTU richness of fungi in Mollisol was altered by TCE contamination. The HShannon indices of the fungal communities in Mollisol were inhibited by higher TCE concentrations (20 and 40 mg kg-1 TCE). TCE altered the content of some bacteria, fungi and actinomycetes involved in soil carbon and nitrogen cycling and metabolism, such as Acidobacteria, Proteobacteria, Planctomycetes, Chytridiomycota, Streptomycetales, Pseudonocardiales, Propionibacteriales and Rhizobiales, and thus influenced nutrient cycling and the process of energy metabolism in Mollisol. In addition, redundancy analysis (RDA) results indicated that physicochemical properties and biological activities under TCE contamination significantly affected soil microbial community composition thus confirming that TCE interfered with the carbon and nitrogen cycling and metabolism of soil microorganisms. The results of this study are of great importance for revealing the effects of TCE stress on the microbiological characteristics of Mollisol, and also provide more useful information for determining the potential ecological risk of organic pollutants in Mollisol.
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Affiliation(s)
- Pengfei Li
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China.
| | - Ying Zhang
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China.
| | - Qingjuan Meng
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Ying Liu
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Diogene Tuyiringire
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Zhaobo Chen
- College of Environment and Resources, Dalian Minzu University, 18 Liaohe West Road, Dalian, 116600, China
| | - Shichao Liang
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
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27
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Zhang W, Bai Y, Ruan X, Yin L. The biological denitrification coupled with chemical reduction for groundwater nitrate remediation via using SCCMs as carbon source. CHEMOSPHERE 2019; 234:89-97. [PMID: 31203045 DOI: 10.1016/j.chemosphere.2019.06.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 05/30/2019] [Accepted: 06/02/2019] [Indexed: 06/09/2023]
Abstract
Renewable additional carbon sources for groundwater denitrification, such as sustainable-releasing compound carbon source materials (SCCMs), are required. This work reports long-term groundwater denitrification with permeable reactive barriers filled with SCCMs; the coupling of biological denitrification and chemical reduction avoided the need for a continuous carbon source supply. Four 370-day lab-scale permeable reactive barrier experiments with four SCCMs showed that NO3- removal efficiency in zero-valent iron (ZVI) SCCMs was higher than in ZVI-free SCCMs. In the ZVI SCCMs, the NO3- removal reaction began quickly in the early stage, owing to ZVI chemical reduction, whereas biological denitrification was lower and incomplete with a NO2- concentration of 0.8 mg L-1 in the ZVI SCCM system. As the chemical reduction efficiency decreased, the biological denitrification efficiency increased, and the highest NO3- removal efficiency was 98.8%. Decreasing the Fe2+concentration decreased ZVI chemical reduction. High-throughput sequencing indicated that the proportion of denitrifying bacteria attached to the SCCMs was up to 34.4% at the family level, leading to the denitrification gene being predominant. Quantitative PCR indicated increased microbial metabolic activity, richer bacterial community diversity, and more bacteria. Long-term monitoring data for SCCMs will help realize the use of biological denitrification coupled with chemical reduction for groundwater NO3- remediation.
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Affiliation(s)
- Wen Zhang
- Key Laboratory of Surficial Geochemistry, Ministry of Education, China; School of Earth Science and Engineering, Nanjing University, 210023, Nanjing, China
| | - Ying Bai
- Key Laboratory of Surficial Geochemistry, Ministry of Education, China; School of Earth Science and Engineering, Nanjing University, 210023, Nanjing, China
| | - Xiaohong Ruan
- Key Laboratory of Surficial Geochemistry, Ministry of Education, China; School of Earth Science and Engineering, Nanjing University, 210023, Nanjing, China.
| | - Lin Yin
- Key Laboratory of Surficial Geochemistry, Ministry of Education, China
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28
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Tian W, Wang H, Xiang X, Wang R, Xu Y. Structural Variations of Bacterial Community Driven by Sphagnum Microhabitat Differentiation in a Subalpine Peatland. Front Microbiol 2019; 10:1661. [PMID: 31396183 PMCID: PMC6667737 DOI: 10.3389/fmicb.2019.01661] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 07/04/2019] [Indexed: 11/13/2022] Open
Abstract
Sphagnum microbiomes play an important role in the northern peatland ecosystems. However, information about above and belowground microbiomes related to Sphagnum at subtropical area remains largely limited. In this study, microbial communities from Sphagnum palustre peat, S. palustre green part, and S. palustre brown part at the Dajiuhu Peatland, in central China were investigated via 16S rRNA gene amplicon sequencing. Results indicated that Alphaproteobacteria was the dominant class in all samples, and the classes Acidobacteria and Gammaproteobacteria were abundant in S. palustre peat and S. palustre brown part samples, respectively. In contrast, the class Cyanobacteria dominated in S. palustre green part samples. Microhabitat differentiation mainly contributes to structural differences of bacterial microbiome. In the S. palustre peat, microbial communities were significantly shaped by water table and total nitrogen content. Our study is a systematical investigation on above and belowground bacterial microbiome in a subalpine Sphagnum peatland and the results offer new knowledge about the distribution of bacterial microbiome associated with different microhabitats in subtropical area.
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Affiliation(s)
- Wen Tian
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Hongmei Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
- Laboratory of Basin Hydrology and Wetland Eco-Restoration, China University of Geosciences, Wuhan, China
| | - Xing Xiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Ruicheng Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Ying Xu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
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29
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Wei Z, Hao Z, Li X, Guan Z, Cai Y, Liao X. The effects of phytoremediation on soil bacterial communities in an abandoned mine site of rare earth elements. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 670:950-960. [PMID: 30921727 DOI: 10.1016/j.scitotenv.2019.03.118] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 03/08/2019] [Accepted: 03/08/2019] [Indexed: 06/09/2023]
Abstract
Overexploitation of rare earth elements (REEs) has caused serious desertification and environmental pollution. The ecological restoration of mining areas has attracted increasing attention in China. Soil microbiota is important for successful ecological remediation of abandoned mine land. In this study, soil samples were collected from a restored REE mine site, and the bacterial community composition and diversity were assessed by Illumina high-throughput sequencing targeting the V3-V4 region of the 16S rRNA gene. Microbiota significantly developed in the remediated land. A total of 663,781 effective 16S rRNA gene sequences were obtained, which were classified into 28 bacterial phyla and 3 archaeal phyla. The dominant phyla across all samples (>5% of total effective sequences) were Proteobacteria, Acidobacteria and Firmicutes. Bacterial diversity indices (OTU number, Shannon index and Chao1 index) of the restored soils were higher than those of the tailings and even surpassed those in the unmined site. Redundancy analysis indicated that soil nutrients (soil organic carbon, available phosphorus and total nitrogen) were the dominant factors, followed by soil pH, affecting bacterial community structure. In general, these results suggested that soil amendment and phytoremediation effectively improved the soil environment of the abandoned mine site, which also increased our understanding of the correlation between microbial variation and soil properties in restored REE mine soils.
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Affiliation(s)
- Zhiwen Wei
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, Jiangsu Normal University, Xuzhou 221116, China
| | - Zhikui Hao
- Institute of Applied Biotechnology, Taizhou Vocational and Technical College, Taizhou 318000, China
| | - Xunhang Li
- The Bioscience and Engineering College, Jiangxi Agriculture University, Nanchang 330045, China
| | - Zhengbing Guan
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Yujie Cai
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Xiangru Liao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China.
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30
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Oshkin IY, Kulichevskaya IS, Rijpstra WIC, Sinninghe Damsté JS, Rakitin AL, Ravin NV, Dedysh SN. Granulicella sibirica sp. nov., a psychrotolerant acidobacterium isolated from an organic soil layer in forested tundra, West Siberia. Int J Syst Evol Microbiol 2019; 69:1195-1201. [PMID: 30775959 DOI: 10.1099/ijsem.0.003290] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
An isolate of strictly aerobic, pale-pink pigmented bacteria, strain AF10T, was obtained from an organic soil layer in forested tundra, Nadym region, West Siberia. Cells of strain AF10T were Gram-negative, non-motile rods that produced an amorphous extracellular polysaccharide-like substance and formed large cell aggregates in old cultures. These bacteria were chemoorganotrophic, mildly acidophilic and psychrotolerant, and grew between pH 3.5 and 7.0 (optimum, pH 4.5-5.0) and at temperatures between 2 and 30 °C. The preferred growth substrates were sugars and some polysaccharides. The major fatty acids were iso-C15 : 0, C16 : 0, C16 : 1∆9 c and 13,16-dimethyl octacosanedioic acid. The genome of strain AF10T was 6.14 Mbp in size and encoded a wide repertoire of carbohydrate active enzymes. The genomic DNA G+C content was 59.8 mol%. Phylogenetic analysis indicated that strain AF10T is a member of the genus Granulicella, family Acidobacteriaceae, but displays 94.4-98.0 % 16S rRNA gene sequence similarity to currently described members of this genus. On the basis of phenotypic, chemotaxonomic, phylogenetic and genomic analyses, we propose to classify this bacterium as representing a novel species of the genus Granulicella, Granulicellasibirica sp. nov. Strain AF10T (=DSM 104461T=VKM B-3276T) is the type strain.
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Affiliation(s)
- Igor Y Oshkin
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Irina S Kulichevskaya
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - W Irene C Rijpstra
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Utrecht University, 1790 AB Den Burg, The Netherlands
| | - Jaap S Sinninghe Damsté
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Utrecht University, 1790 AB Den Burg, The Netherlands.,Faculty of Geosciences, Department of Earth Sciences, Geochemistry, Utrecht University, Utrecht, The Netherlands
| | - Andrey L Rakitin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Nikolai V Ravin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Svetlana N Dedysh
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
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31
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Baldrian P. The known and the unknown in soil microbial ecology. FEMS Microbiol Ecol 2019; 95:5281230. [DOI: 10.1093/femsec/fiz005] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 01/08/2019] [Indexed: 12/22/2022] Open
Affiliation(s)
- Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Vídeňská 1083, 14220 Praha 4, Czech Republic
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32
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Dialogue on the nomenclature and classification of prokaryotes. Syst Appl Microbiol 2019; 42:5-14. [DOI: 10.1016/j.syapm.2018.07.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 06/08/2018] [Accepted: 07/03/2018] [Indexed: 12/16/2022]
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33
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Chen Y, Ding Q, Chao Y, Wei X, Wang S, Qiu R. Structural development and assembly patterns of the root-associated microbiomes during phytoremediation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 644:1591-1601. [PMID: 30743871 DOI: 10.1016/j.scitotenv.2018.07.095] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 07/06/2018] [Accepted: 07/08/2018] [Indexed: 05/20/2023]
Abstract
Successful in situ phytoremediation depends on beneficial interactions between roots and microbes. However, the assembly strategies of root-associated microbiome during phytoremediation are not well known. Here we investigated the assembly patterns of root-associated microbiomes during phytoremediation as well as its regulation by both plants and heavy metals. Plant cultivation and soil amendment increased microbial diversity and restructured microbial communities. Rhizo-compartmentalization was the largest source of variation in root-associated microbiomes, with endosphere being the most independent and exclusive compartment. Soil type explained a larger amount of microbiomes variation in bulk soil and rhizosphere than that in endosphere. A specific core root microbiome was likely to be selected by the metal-tolerant plant H. cannabinus, with Enterobacteriaceae, Pseudomonadaceae and Comamonadaceae which contain a large number of metal-tolerant and plant growth-promoting bacteria (PGPB) being the most abundant families. The root-associated microbial community tended to proceed a niche-assembled patterns and formed a smaller bacterial pool dominant by Proteobacteria, Actinobacteria and Chloroflexi under metal-contaminated conditions. Among these genera, potential metal-tolerant PGPB species have taken up the keystone positions in the microbial co-occurrence networks, revealing their key roles in metal-contaminated environment due to niche selection. We also detected a keystone functional group reducing metal bioavailability which might work as vanguards and devote to maintaining the structure and function of the whole microbial community. In conclusion, this study suggested a specific assembly pattern of root-associated microbiomes of the metal-tolerant plant H. cannabinus during phytoremediation, showing the directional selections of the associated microbiomes by both the plant and metal-contaminated conditions in such a system.
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Affiliation(s)
- Yanmei Chen
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China; Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Qiaobei Ding
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Yuanqing Chao
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Key Lab of Environmental Pollution Control and Remediation Technology, Guangdong 510275, China.
| | - Xiange Wei
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Key Lab of Environmental Pollution Control and Remediation Technology, Guangdong 510275, China
| | - Shizhong Wang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Key Lab of Environmental Pollution Control and Remediation Technology, Guangdong 510275, China
| | - Rongliang Qiu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Key Lab of Environmental Pollution Control and Remediation Technology, Guangdong 510275, China
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34
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Sun X, Zhou Y, Tan Y, Wu Z, Lu P, Zhang G, Yu F. Restoration with pioneer plants changes soil properties and remodels the diversity and structure of bacterial communities in rhizosphere and bulk soil of copper mine tailings in Jiangxi Province, China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:22106-22119. [PMID: 29802615 DOI: 10.1007/s11356-018-2244-3] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 05/06/2018] [Indexed: 06/08/2023]
Abstract
To unravel the ecological function played by pioneer plants in the practical restoration of mine tailings, it is vital to explore changes of soil characteristics and microbial communities in rhizosphere and bulk soil following the adaptation and survival of plants. In the present study, the diversity and structure of rhizospheric bacterial communities of three pioneer plants in copper mine tailings were investigated by Illumina MiSeq sequencing, and the effects of pioneer plants on soil properties were also evaluated. Significant soil improvement was detected in rhizospheric samples, and Alnus cremastogyne showed higher total organic matter, total nitrogen, and available phosphorus than two other herbaceous plants. Microbial diversity indices in rhizosphere and bulk soil of reclaimed tailings were significantly higher than bare tailings, even the soil properties of bulk soil in reclaimed tailings were not significantly different from those of bare tailings. A detailed taxonomic composition analysis demonstrated that Alphaproteobacteria and Deltaproteobacteria, Chloroflexi, Acidobacteria, and Gemmatimonadetes showed significantly higher relative abundance in rhizosphere and bulk soil. In contrast, Gammaproteobacteria and Firmicutes were abundant in bare tailings, in which Bacillus, Pseudomonas, and Lactococcus made up the majority of the bacterial community (63.04%). Many species within known heavy metal resistance and nutrient regulatory microorganism were identified in reclaimed tailings, and were more abundant among rhizospheric microbes. Hierarchical clustering and principal coordinate analysis (PCoA) analysis demonstrated that the bacterial profiles in the rhizosphere clustered strictly together according to plant types, and were distinguishable from bulk soil. However, we also identified a large shared OTUs that occurred repeatedly and was unaffected by highly diverse soil properties in rhizosphere and bulk samples. Redundancy analysis indicated that water content and Cu and As concentrations were the main environmental regulators of microbial composition. These results suggest that the interactive effect of pioneer plants and harsh soil environmental conditions remodel the specific bacterial communities in rhizosphere and bulk soil in mine tailings. And A. cremastogyne might be approximate candidate for phytoremediation of mine tailings for better soil amelioration effect and relative higher diversity of bacterial community in rhizosphere.
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Affiliation(s)
- Xiaoyan Sun
- Jiangxi Engineering and Technology Research Center for Ecological Remediation of Heavy Metal Pollution, Institute of Biology and Resources, Jiangxi Academy of Sciences, Nanchang, 330096, People's Republic of China.
| | - Yanling Zhou
- Jiangxi Engineering and Technology Research Center for Ecological Remediation of Heavy Metal Pollution, Institute of Biology and Resources, Jiangxi Academy of Sciences, Nanchang, 330096, People's Republic of China
| | - Yinjing Tan
- Jiangxi Engineering and Technology Research Center for Ecological Remediation of Heavy Metal Pollution, Institute of Biology and Resources, Jiangxi Academy of Sciences, Nanchang, 330096, People's Republic of China
| | - Zhaoxiang Wu
- Jiangxi Engineering and Technology Research Center for Ecological Remediation of Heavy Metal Pollution, Institute of Biology and Resources, Jiangxi Academy of Sciences, Nanchang, 330096, People's Republic of China
| | - Ping Lu
- Jiangxi Engineering and Technology Research Center for Ecological Remediation of Heavy Metal Pollution, Institute of Biology and Resources, Jiangxi Academy of Sciences, Nanchang, 330096, People's Republic of China
| | - Guohua Zhang
- Jiangxi Engineering and Technology Research Center for Ecological Remediation of Heavy Metal Pollution, Institute of Biology and Resources, Jiangxi Academy of Sciences, Nanchang, 330096, People's Republic of China
| | - Faxin Yu
- Jiangxi Engineering and Technology Research Center for Ecological Remediation of Heavy Metal Pollution, Institute of Biology and Resources, Jiangxi Academy of Sciences, Nanchang, 330096, People's Republic of China
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35
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Pankratov TA. Bacterial complexes of Khibiny Mountains lichens revealed in Cladonia uncialis, C. portentosa, Alectoria ochroleuca, and Nephroma arcticum. Microbiology (Reading) 2018. [DOI: 10.1134/s0026261718010149] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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36
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Morawe M, Hoeke H, Wissenbach DK, Lentendu G, Wubet T, Kröber E, Kolb S. Acidotolerant Bacteria and Fungi as a Sink of Methanol-Derived Carbon in a Deciduous Forest Soil. Front Microbiol 2017; 8:1361. [PMID: 28790984 PMCID: PMC5523551 DOI: 10.3389/fmicb.2017.01361] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2017] [Accepted: 07/05/2017] [Indexed: 02/03/2023] Open
Abstract
Methanol is an abundant atmospheric volatile organic compound that is released from both living and decaying plant material. In forest and other aerated soils, methanol can be consumed by methanol-utilizing microorganisms that constitute a known terrestrial sink. However, the environmental factors that drive the biodiversity of such methanol-utilizers have been hardly resolved. Soil-derived isolates of methanol-utilizers can also often assimilate multicarbon compounds as alternative substrates. Here, we conducted a comparative DNA stable isotope probing experiment under methylotrophic (only [13C1]-methanol was supplemented) and combined substrate conditions ([12C1]-methanol and alternative multi-carbon [13Cu]-substrates were simultaneously supplemented) to (i) identify methanol-utilizing microorganisms of a deciduous forest soil (European beech dominated temperate forest in Germany), (ii) assess their substrate range in the soil environment, and (iii) evaluate their trophic links to other soil microorganisms. The applied multi-carbon substrates represented typical intermediates of organic matter degradation, such as acetate, plant-derived sugars (xylose and glucose), and a lignin-derived aromatic compound (vanillic acid). An experimentally induced pH shift was associated with substantial changes of the diversity of active methanol-utilizers suggesting that soil pH was a niche-defining factor of these microorganisms. The main bacterial methanol-utilizers were members of the Beijerinckiaceae (Bacteria) that played a central role in a detected methanol-based food web. A clear preference for methanol or multi-carbon substrates as carbon source of different Beijerinckiaceae-affiliated phylotypes was observed suggesting a restricted substrate range of the methylotrophic representatives. Apart from Bacteria, we also identified the yeasts Cryptococcus and Trichosporon as methanol-derived carbon-utilizing fungi suggesting that further research is needed to exclude or prove methylotrophy of these fungi.
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Affiliation(s)
- Mareen Morawe
- Department of Ecological Microbiology, University of BayreuthBayreuth, Germany
| | - Henrike Hoeke
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental ResearchLeipzig, Germany.,Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, University of LeipzigLeipzig, Germany
| | - Dirk K Wissenbach
- Institute of Forensic Medicine, University Hospital JenaJena, Germany
| | - Guillaume Lentendu
- Department of Ecology, University of KaiserslauternKaiserslautern, Germany
| | - Tesfaye Wubet
- Department of Soil Ecology, Helmholtz Centre for Environmental ResearchLeipzig, Germany
| | - Eileen Kröber
- Institute of Landscape Biogeochemistry, Leibniz Centre for Landscape ResearchMüncheberg, Germany
| | - Steffen Kolb
- Department of Ecological Microbiology, University of BayreuthBayreuth, Germany.,Institute of Landscape Biogeochemistry, Leibniz Centre for Landscape ResearchMüncheberg, Germany
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37
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Damsté JSS, Rijpstra WIC, Dedysh SN, Foesel BU, Villanueva L. Pheno- and Genotyping of Hopanoid Production in Acidobacteria. Front Microbiol 2017; 8:968. [PMID: 28642737 PMCID: PMC5462960 DOI: 10.3389/fmicb.2017.00968] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 05/15/2017] [Indexed: 11/28/2022] Open
Abstract
Hopanoids are pentacyclic triterpenoid lipids synthesized by different bacterial groups. Methylated hopanoids were believed to be exclusively synthesized by cyanobacteria and aerobic methanotrophs until the genes encoding for the methylation at the C-2 and C-3 position (hpnP and hpnR) were found to be widespread in the bacterial domain, invalidating their use as specific biomarkers. These genes have been detected in the genome of the Acidobacterium "Ca. Koribacter versatilis," but our knowledge of the synthesis of hopanoids and the presence of genes of their biosynthetic pathway in other member of the Acidobacteria is limited. We analyzed 38 different strains of seven Acidobacteria subdivisions (SDs 1, 3, 4, 6, 8, 10, and 23) for the presence of C30 hopenes and C30+ bacteriohopane polyols (BHPs) using the Rohmer reaction. BHPs and/or C30 hopenes were detected in all strains of SD1 and SD3 but not in SD4 (excepting Chloracidobacterium thermophilum), 6, 8, 10, and 23. This is in good agreement with the presence of genes required for hopanoid biosynthesis in the 31 available whole genomes of cultivated Acidobacteria. All genomes encode the enzymes involved in the non-mevalonate pathway ultimately leading to farnesyl diphosphate but only SD1 and 3 Acidobacteria and C. thermophilum encode all three enzymes required for the synthesis of squalene, its cyclization (shc), and addition and modification of the extended side chain (hpnG, hpnH, hpnI, hpnJ, hpnO). In almost all strains, only tetrafunctionalized BHPs were detected; three strains contained variable relative abundances (up to 45%) of pentafunctionalized BHPs. Only "Ca. K. versatilis" contained methylated hopanoids (i.e., 2,3-dimethyl bishomohopanol), although in low (<10%) amounts. These genes are not present in any other Acidobacterium, consistent with the absence of methylated BHPs in the other examined strains. These data are in agreement with the scattered occurrence of methylated BHPs in other bacterial phyla such as the Alpha-, Beta-, and Gammaproteobacteria and the Cyanobacteria, limiting their biomarker potential. Metagenomes of Acidobacteria were also examined for the presence of genes required for hopanoid biosynthesis. The complete pathway for BHP biosynthesis was evident in SD2 Acidobacteria and a group phylogenetically related to SD1 and SD3, in line with the limited occurrence of BHPs in acidobacterial cultures.
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Affiliation(s)
- Jaap S. Sinninghe Damsté
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Utrecht UniversityDen Burg, Netherlands
- Department of Earth Sciences, Geochemistry, Faculty of Geosciences, Utrecht UniversityUtrecht, Netherlands
| | - W. Irene C. Rijpstra
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Utrecht UniversityDen Burg, Netherlands
| | - Svetlana N. Dedysh
- S. N. Winogradsky Institute of Microbiology, Research Center of Biotechnology of Russian Academy of SciencesMoscow, Russia
| | - Bärbel U. Foesel
- Department of Microbial Ecology and Diversity Research, German Collection of Microorganisms and Cell Cultures (LG)Braunschweig, Germany
| | - Laura Villanueva
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Utrecht UniversityDen Burg, Netherlands
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38
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Wegner CE, Liesack W. Unexpected Dominance of Elusive Acidobacteria in Early Industrial Soft Coal Slags. Front Microbiol 2017; 8:1023. [PMID: 28642744 PMCID: PMC5462947 DOI: 10.3389/fmicb.2017.01023] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 05/22/2017] [Indexed: 11/19/2022] Open
Abstract
Acid mine drainage (AMD) and mine tailing environments are well-characterized ecosystems known to be dominated by organisms involved in iron- and sulfur-cycling. Here we examined the microbiology of industrial soft coal slags that originate from alum leaching, an ecosystem distantly related to AMD environments. Our study involved geochemical analyses, bacterial community profiling, and shotgun metagenomics. The slags still contained high amounts of alum constituents (aluminum, sulfur), which mediated direct and indirect effects on bacterial community structure. Bacterial groups typically found in AMD systems and mine tailings were not present. Instead, the soft coal slags were dominated by uncharacterized groups of Acidobacteria (DA052 [subdivision 2], KF-JG30-18 [subdivision 13]), Actinobacteria (TM214), Alphaproteobacteria (DA111), and Chloroflexi (JG37-AG-4), which have previously been detected primarily in peatlands and uranium waste piles. Shotgun metagenomics allowed us to reconstruct 13 high-quality Acidobacteria draft genomes, of which two genomes could be directly linked to dominating groups (DA052, KF-JG30-18) by recovered 16S rRNA gene sequences. Comparative genomics revealed broad carbon utilization capabilities for these two groups of elusive Acidobacteria, including polysaccharide breakdown (cellulose, xylan) and the competence to metabolize C1 compounds (ribulose monophosphate pathway) and lignin derivatives (dye-decolorizing peroxidases). Equipped with a broad range of efflux systems for metal cations and xenobiotics, DA052 and KF-JG30-18 may have a competitive advantage over other bacterial groups in this unique habitat.
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Affiliation(s)
- Carl-Eric Wegner
- Department of Biogeochemistry, Max Planck Institute for Terrestrial MicrobiologyMarburg, Germany
- Aquatic Geomicrobiology, Institute of Ecology, Friedrich Schiller University JenaJena, Germany
| | - Werner Liesack
- Department of Biogeochemistry, Max Planck Institute for Terrestrial MicrobiologyMarburg, Germany
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39
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The first acidobacterial laccase-like multicopper oxidase revealed by metagenomics shows high salt and thermo-tolerance. Appl Microbiol Biotechnol 2017; 101:6261-6276. [DOI: 10.1007/s00253-017-8345-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2017] [Revised: 05/08/2017] [Accepted: 05/10/2017] [Indexed: 01/10/2023]
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40
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Pankratov TA, Kachalkin AV, Korchikov ES, Dobrovol’skaya TG. Microbial communities of lichens. Microbiology (Reading) 2017. [DOI: 10.1134/s0026261717030134] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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41
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Campanharo JC, Kielak AM, Castellane TCL, Kuramae EE, Lemos EGDM. Optimized medium culture forAcidobacteriasubdivision 1 strains. FEMS Microbiol Lett 2016; 363:fnw245. [DOI: 10.1093/femsle/fnw245] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 06/04/2016] [Accepted: 10/25/2016] [Indexed: 11/13/2022] Open
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42
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Deng Y, Cui X, Dumont MG. Identification of active aerobic methanotrophs in plateau wetlands using DNA stable isotope probing. FEMS Microbiol Lett 2016; 363:fnw168. [PMID: 27369086 DOI: 10.1093/femsle/fnw168] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/27/2016] [Indexed: 01/21/2023] Open
Abstract
Sedge-dominated wetlands on the Qinghai-Tibetan Plateau are methane emission centers. Methanotrophs at these sites play a role in reducing methane emissions, but relatively little is known about the composition of active methanotrophs in these wetlands. Here, we used DNA stable isotope probing to identify the key active aerobic methanotrophs in three sedge-dominated wetlands on the plateau. We found that Methylocystis species were active in two peatlands, Hongyuan and Dangxiong. Methylobacter species were found to be active only in Dangxiong peat. Hongyuan peat had the highest methane oxidation rate, and cross-feeding of carbon from methanotrophs to methylotrophic Hyphomicrobium species was observed. Owing to a low methane oxidation rate during the incubation, the labeling of methanotrophs in Maduo wetland samples was not detected. Our results indicate that there are large differences in the activity of methanotrophs in the wetlands of this region.
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Affiliation(s)
- Yongcui Deng
- School of Geography Science Nanjing Normal University, Nanjing 210023, China Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | - Xiaoyong Cui
- College of Life Sciences University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Marc G Dumont
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
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Kielak AM, Cipriano MAP, Kuramae EE. Acidobacteria strains from subdivision 1 act as plant growth-promoting bacteria. Arch Microbiol 2016; 198:987-993. [PMID: 27339258 PMCID: PMC5080364 DOI: 10.1007/s00203-016-1260-2] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 06/09/2016] [Accepted: 06/15/2016] [Indexed: 11/26/2022]
Abstract
Acidobacteria is one of the most abundant phyla in soils and has been detected in rhizosphere mainly based on cultivation-independent approaches such as 16S rRNA gene survey. Although putative interaction of Acidobacteria with plants was suggested, so far no plant–bacterial interactions were shown. Therefore, we performed several in vitro tests to evaluate Acidobacteria–plant interactions and the possible mechanisms involved in such interaction. We observed that Arabidopsis thaliana inoculated with three strains belonging to Acidobacteria subdivision 1 showed increase in biomass of roots and shoots as well as morphological changes in root system. Our results indicate that the plant hormone indole-3-acetic acid production and iron acquisition are plausibly involved in the plant and Acidobacteria interactions. Here, we confirm for the first time that Acidobacteria can actively interact with plants and act as plant growth-promoting bacteria. In addition, we show that Acidobacteria strains produce exopolysaccharide which supports the adhesion of bacteria to the root surfaces.
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Affiliation(s)
- Anna M Kielak
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - Matheus A P Cipriano
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - Eiko E Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands.
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44
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Kielak AM, Barreto CC, Kowalchuk GA, van Veen JA, Kuramae EE. The Ecology of Acidobacteria: Moving beyond Genes and Genomes. Front Microbiol 2016; 7:744. [PMID: 27303369 PMCID: PMC4885859 DOI: 10.3389/fmicb.2016.00744] [Citation(s) in RCA: 451] [Impact Index Per Article: 56.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 05/03/2016] [Indexed: 12/01/2022] Open
Abstract
The phylum Acidobacteria is one of the most widespread and abundant on the planet, yet remarkably our knowledge of the role of these diverse organisms in the functioning of terrestrial ecosystems remains surprisingly rudimentary. This blatant knowledge gap stems to a large degree from the difficulties associated with the cultivation of these bacteria by classical means. Given the phylogenetic breadth of the Acidobacteria, which is similar to the metabolically diverse Proteobacteria, it is clear that detailed and functional descriptions of acidobacterial assemblages are necessary. Fortunately, recent advances are providing a glimpse into the ecology of members of the phylum Acidobacteria. These include novel cultivation and enrichment strategies, genomic characterization and analyses of metagenomic DNA from environmental samples. Here, we couple the data from these complementary approaches for a better understanding of their role in the environment, thereby providing some initial insights into the ecology of this important phylum. All cultured acidobacterial type species are heterotrophic, and members of subdivisions 1, 3, and 4 appear to be more versatile in carbohydrate utilization. Genomic and metagenomic data predict a number of ecologically relevant capabilities for some acidobacteria, including the ability to: use of nitrite as N source, respond to soil macro-, micro nutrients and soil acidity, express multiple active transporters, degrade gellan gum and produce exopolysaccharide (EPS). Although these predicted properties allude to a competitive life style in soil, only very few of these prediction shave been confirmed via physiological studies. The increased availability of genomic and physiological information, coupled to distribution data in field surveys and experiments, should direct future progress in unraveling the ecology of this important but still enigmatic phylum.
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Affiliation(s)
- Anna M Kielak
- Department of Microbial Ecology, The Netherlands Institute of Ecology - Koninklijke Nederlandse Akademie van Wetenschappen Wageningen, Netherlands
| | - Cristine C Barreto
- Graduate Program in Genomic Sciences and Biotechnology, Universidade Católica de Brasília Brasília, Brazil
| | - George A Kowalchuk
- Ecology and Biodiversity Group, University of Utrecht Utrecht, Netherlands
| | - Johannes A van Veen
- Department of Microbial Ecology, The Netherlands Institute of Ecology - Koninklijke Nederlandse Akademie van Wetenschappen Wageningen, Netherlands
| | - Eiko E Kuramae
- Department of Microbial Ecology, The Netherlands Institute of Ecology - Koninklijke Nederlandse Akademie van Wetenschappen Wageningen, Netherlands
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Nikrad MP, Kerkhof LJ, Häggblom MM. The subzero microbiome: microbial activity in frozen and thawing soils. FEMS Microbiol Ecol 2016; 92:fiw081. [PMID: 27106051 DOI: 10.1093/femsec/fiw081] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/17/2016] [Indexed: 01/15/2023] Open
Abstract
Most of the Earth's biosphere is characterized by low temperatures (<5°C) and cold-adapted microorganisms are widespread. These psychrophiles have evolved a complex range of adaptations of all cellular constituents to counteract the potentially deleterious effects of low kinetic energy environments and the freezing of water. Microbial life continues into the subzero temperature range, and this activity contributes to carbon and nitrogen flux in and out of ecosystems, ultimately affecting global processes. Microbial responses to climate warming and, in particular, thawing of frozen soils are not yet well understood, although the threat of microbial contribution to positive feedback of carbon flux is substantial. To date, several studies have examined microbial community dynamics in frozen soils and permafrost due to changing environmental conditions, and some have undertaken the complicated task of characterizing microbial functional groups and how their activity changes with changing conditions, either in situ or by isolating and characterizing macromolecules. With increasing temperature and wetter conditions microbial activity of key microbes and subsequent efflux of greenhouse gases also increase. In this review, we aim to provide an overview of microbial activity in seasonally frozen soils and permafrost. With a more detailed understanding of the microbiological activities in these vulnerable soil ecosystems, we can begin to predict and model future expectations for carbon release and climate change.
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Affiliation(s)
| | - Lee J Kerkhof
- Department of Marine and Coastal Sciences, Rutgers, the State University of New Jersey, New Brunswick, NJ 08901, USA
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Masuda S, Bao Z, Okubo T, Sasaki K, Ikeda S, Shinoda R, Anda M, Kondo R, Mori Y, Minamisawa K. Sulfur Fertilization Changes the Community Structure of Rice Root-, and Soil- Associated Bacteria. Microbes Environ 2016; 31:70-5. [PMID: 26947443 PMCID: PMC4791119 DOI: 10.1264/jsme2.me15170] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Under paddy field conditions, biological sulfur oxidation occurs in the oxidized surface soil layer and rhizosphere, in which oxygen leaks from the aerenchyma system of rice plants. In the present study, we examined community shifts in sulfur-oxidizing bacteria associated with the oxidized surface soil layer and rice roots under different sulfur fertilization conditions based on the 16S ribosomal RNA (rRNA) gene in order to explore the existence of oligotrophic sulfur-oxidizing bacteria in the paddy rice ecosystem. Rice plants were grown in pots with no fertilization (control) or CaCO3 or CaSO4 fertilization. A principal-coordinates analysis (PCoA) showed that CaSO4 fertilization markedly affected bacterial communities associated with rice roots and soil, whereas no significant differences were observed in plant growth among the fertilizer treatments examined. In rice roots, the relative abundance of Acidobacteria, Alphaproteobacteria, Gammaproteobacteria, and TM7 was significantly higher in CaSO4-fertilized pots than in control pots. Alphaproteobacteria, Bradyrhizobiaceae, and Methylocystaceae members were significantly more abundant in CaSO4-fertilized roots than in control roots. On the other hand, the abundance of Actinobacteria and Proteobacteria was lower in CaSO4-fertilized soil than in control soil. These results indicate that the bacteria associated with rice roots and soil responded to the sulfur amendment, suggesting that more diverse bacteria are involved in sulfur oxidation in the rice paddy ecosystem than previously considered.
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Novel isolates double the number of chemotrophic species and allow the first description of higher taxa in Acidobacteria subdivision 4. Syst Appl Microbiol 2015; 38:534-44. [DOI: 10.1016/j.syapm.2015.08.001] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2015] [Revised: 08/10/2015] [Accepted: 08/17/2015] [Indexed: 01/15/2023]
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Jiang YW, Wang J, Chen MH, Lv YY, Qiu LH. Acidipila dinghuensis sp. nov., an acidobacterium isolated from forest soil. Int J Syst Evol Microbiol 2015; 66:76-83. [PMID: 26475169 DOI: 10.1099/ijsem.0.000676] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An aerobic, chemoheterotrophic, non-motile, capsule-forming bacterium designated DHOF10T was isolated from a soil sample collected from the forest of Dinghushan Biosphere Reserve, Guangdong Province, PR China. Strain DHOF10T was able to grow at pH 3.5-8.0 (optimum pH 4.0-4.5) and at 10-37 °C (optimum 28-37 °C). NaCl tolerance was up to 1.0 % (w/v). Major fatty acids consisted of iso-C15 : 0, C18 : 1ω9c and C16 : 1ω7c. The quinone was MK-8 and the DNA G+C content was 56.3 mol%. The polar lipids consisted of phosphatidylethanolamine, an unidentified aminolipid, an unidentified phospholipid, two unidentified aminophospholipids and two unidentified polar lipids. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolate was a member of genus Acidipila of the phylum Acidobacteria, with the highest 16S rRNA gene sequence similarity of 97.3 % to Acidipila rosea AP8T. On the basis of phylogenetic, phenotypic, physiological and chemotaxonomic distinctiveness, strain DHOF10T represents a novel species of the genus Acidipila, for which the name Acidipila dinghuensis sp. nov. is proposed. The type strain is DHOF10T ( = CGMCC 1.13007T = KCTC 42631T).
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Affiliation(s)
- Ya-Wen Jiang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Jia Wang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Mei-Hong Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Ying-Ying Lv
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Li-Hong Qiu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
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Paisie TK, Miller TE, Mason OU. Effects of a ciliate protozoa predator on microbial communities in pitcher plant (Sarracenia purpurea) leaves. PLoS One 2014; 9:e113384. [PMID: 25423622 PMCID: PMC4244144 DOI: 10.1371/journal.pone.0113384] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 10/24/2014] [Indexed: 11/18/2022] Open
Abstract
The aquatic communities found within the water filled leaves of the pitcher plant, Sarracenia purpurea, have a simple trophic structure providing an ideal system to study microscale interactions between protozoan predators and their bacterial prey. In this study, replicate communities were maintained with and without the presence of the bactivorous protozoan, Colpoda steinii, to determine the effects of grazing on microbial communities. Changes in microbial (Archaea and Bacteria) community structure were assessed using iTag sequencing of 16S rRNA genes. The microbial communities were similar with and without the protozoan predator, with>1000 species. Of these species, Archaea were negligible, with Bacteria comprising 99.99% of the microbial community. The Proteobacteria and Bacteroidetes were the most dominant phyla. The addition of a protozoan predator did not have a significant effect on microbial evenness nor richness. However, the presence of the protozoan did cause a significant shift in the relative abundances of a number of bacterial species. This suggested that bactivorous protozoan may target specific bacterial species and/or that certain bacterial species have innate mechanisms by which they evade predators. These findings help to elucidate the effect that trophic structure perturbations have on predator prey interactions in microbial systems.
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Affiliation(s)
- Taylor K Paisie
- Department of Earth, Ocean and Atmospheric Science, Florida State University, Tallahassee, Florida, United States of America
| | - Thomas E Miller
- Department of Biological Science, Florida State University, Tallahassee, Florida, United States of America
| | - Olivia U Mason
- Department of Earth, Ocean and Atmospheric Science, Florida State University, Tallahassee, Florida, United States of America
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The rhizosphere selects for particular groups of acidobacteria and verrucomicrobia. PLoS One 2013; 8:e82443. [PMID: 24349285 PMCID: PMC3862674 DOI: 10.1371/journal.pone.0082443] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Accepted: 10/25/2013] [Indexed: 11/23/2022] Open
Abstract
There is a lack in our current understanding on the putative interactions of species of the phyla of Acidobacteria and Verrucomicrobia with plants. Moreover, progress in this area is seriously hampered by the recalcitrance of members of these phyla to grow as pure cultures. The purpose of this study was to investigate whether particular members of Acidobacteria and Verrucomicrobia are avid colonizers of the rhizosphere. Based on previous work, rhizosphere competence was demonstrated for the Verrucomicrobia subdivision 1 groups of Luteolibacter and Candidatus genus Rhizospheria and it was hypothesized that the rhizosphere is a common habitat for Acidobacteria subdivision 8 (class Holophagae). We assessed the population densities of Bacteria, Verrucomicrobia subdivision 1 groups Luteolibacter and Candidatus genus Rhizospheria and Acidobacteria subdivisions 1, 3, 4, 6 and Holophagae in bulk soil and in the rhizospheres of grass, potato and leek in the same field at different points in time using real-time quantitative PCR. Primers of all seven verrucomicrobial, acidobacterial and holophagal PCR systems were based on 16S rRNA gene sequences of cultivable representatives of the different groups. Luteolibacter, Candidatus genus Rhizospheria, subdivision 6 acidobacteria and Holophaga showed preferences for one or more rhizospheres. In particular, the Holophaga 16S rRNA gene number were more abundant in the leek rhizosphere than in bulk soil and the rhizospheres of grass and potato. Attraction to, and colonization of, leek roots by Holophagae strain CHC25 was further shown in an experimental microcosm set-up. In the light of this remarkable capacity, we propose to coin strain CHC25 Candidatus Porrumbacterium oxyphilus (class Holophagae, Phylum Acidobacteria), the first cultured representative with rhizosphere competence.
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