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Taipale SJ, Vesamäki J, Kautonen P, Kukkonen JVK, Biasi C, Nissinen R, Tiirola M. Biodegradation of microplastic in freshwaters: A long-lasting process affected by the lake microbiome. Environ Microbiol 2023; 25:2669-2680. [PMID: 36054230 DOI: 10.1111/1462-2920.16177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 08/11/2022] [Indexed: 11/29/2022]
Abstract
Plastics have been produced for over a century, but definitive evidence of complete plastic biodegradation in different habitats, particularly freshwater ecosystems, is still missing. Using 13 C-labelled polyethylene microplastics (PE-MP) and stable isotope analysis of produced gas and microbial membrane lipids, we determined the biodegradation rate and fate of carbon in PE-MP in different freshwater types. The biodegradation rate in the humic-lake waters was much higher (0.45% ± 0.21% per year) than in the clear-lake waters (0.07% ± 0.06% per year) or the artificial freshwater medium (0.02% ± 0.02% per year). Complete biodegradation of PE-MP was calculated to last 100-200 years in humic-lake waters, 300-4000 years in clear-lake waters, and 2000-20,000 years in the artificial freshwater medium. The concentration of 18:1ω7, characteristic phospholipid fatty acid in Alpha- and Gammaproteobacteria, was a predictor of faster biodegradation of PE. Uncultured Acetobacteraceae and Comamonadaceae among Alpha- and Gammaproteobacteria, respectively, were major bacteria related to the biodegradation of PE-MP. Overall, it appears that microorganisms in humic lakes with naturally occurring refractory polymers are more adept at decomposing PE than those in other waters.
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Affiliation(s)
- Sami J Taipale
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Jussi Vesamäki
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Petra Kautonen
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Jussi V K Kukkonen
- Department of Environmental and Biological Science, University of Eastern Finland, Finland
| | - Christina Biasi
- Department of Environmental and Biological Science, University of Eastern Finland, Finland
| | - Riitta Nissinen
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Marja Tiirola
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
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2
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Dyksma S, Pester M. Oxygen respiration and polysaccharide degradation by a sulfate-reducing acidobacterium. Nat Commun 2023; 14:6337. [PMID: 37816749 PMCID: PMC10564751 DOI: 10.1038/s41467-023-42074-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 09/25/2023] [Indexed: 10/12/2023] Open
Abstract
Sulfate-reducing microorganisms represent a globally important link between the sulfur and carbon cycles. Recent metagenomic surveys expanded the diversity of microorganisms putatively involved in sulfate reduction underscoring our incomplete understanding of this functional guild. Here, we use genome-centric metatranscriptomics to study the energy metabolism of Acidobacteriota that carry genes for dissimilation of sulfur compounds in a long-term continuous culture running under alternating anoxic and oxic conditions. Differential gene expression analysis reveals the unique metabolic flexibility of a pectin-degrading acidobacterium to switch from sulfate to oxygen reduction when shifting from anoxic to oxic conditions. The combination of facultative anaerobiosis and polysaccharide degradation expands the metabolic versatility among sulfate-reducing microorganisms. Our results highlight that sulfate reduction and aerobic respiration are not mutually exclusive in the same organism, sulfate reducers can mineralize organic polymers, and anaerobic mineralization of complex organic matter is not necessarily a multi-step process involving different microbial guilds but can be bypassed by a single microbial species.
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Affiliation(s)
- Stefan Dyksma
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Department of Microorganisms, Braunschweig, Germany.
| | - Michael Pester
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Department of Microorganisms, Braunschweig, Germany.
- Technical University of Braunschweig, Institute of Microbiology, Braunschweig, Germany.
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3
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Mitzscherling J, Genderjahn S, Schleicher AM, Bartholomäus A, Kallmeyer J, Wagner D. Clay-associated microbial communities and their relevance for a nuclear waste repository in the Opalinus Clay rock formation. Microbiologyopen 2023; 12:e1370. [PMID: 37642485 PMCID: PMC10333725 DOI: 10.1002/mbo3.1370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 06/19/2023] [Accepted: 06/23/2023] [Indexed: 08/31/2023] Open
Abstract
Microorganisms are known to be natural agents of biocorrosion and mineral transformation, thereby potentially affecting the safety of deep geological repositories used for high-level nuclear waste storage. To better understand how resident microbial communities of the deep terrestrial biosphere may act on mineralogical and geochemical characteristics of insulating clays, we analyzed their structure and potential metabolic functions, as well as site-specific mineralogy and element composition from the dedicated Mont Terri underground research laboratory, Switzerland. We found that the Opalinus Clay formation is mainly colonized by Alphaproteobacteria, Firmicutes, and Bacteroidota, which are known for corrosive biofilm formation. Potential iron-reducing bacteria were predominant in comparison to methanogenic archaea and sulfate-reducing bacteria. Despite microbial communities in Opalinus Clay being in majority homogenous, site-specific mineralogy and geochemistry conditions have selected for subcommunities that display metabolic potential for mineral dissolution and transformation. Our findings indicate that the presence of a potentially low-active mineral-associated microbial community must be further studied to prevent effects on the repository's integrity over the long term.
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Affiliation(s)
- Julia Mitzscherling
- GFZ German Research Centre for Geosciences, Section GeomicrobiologyPotsdamGermany
| | - Steffi Genderjahn
- GFZ German Research Centre for Geosciences, Section GeomicrobiologyPotsdamGermany
| | - Anja M. Schleicher
- GFZ German Research Centre for Geosciences, Section Inorganic and Isotope GeochemistryPotsdamGermany
| | | | - Jens Kallmeyer
- GFZ German Research Centre for Geosciences, Section GeomicrobiologyPotsdamGermany
| | - Dirk Wagner
- GFZ German Research Centre for Geosciences, Section GeomicrobiologyPotsdamGermany
- Institute of GeosciencesUniversity of PotsdamPotsdamGermany
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4
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Jiao Y, An L, Wang W, Ma J, Wu C, Wu X. Microbial communities and their roles in the Cenozoic sulfurous oil reservoirs in the Southwestern Qaidam Basin, Western China. Sci Rep 2023; 13:7988. [PMID: 37198206 DOI: 10.1038/s41598-023-33978-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 04/21/2023] [Indexed: 05/19/2023] Open
Abstract
The latest discovery of sulfurous natural gas marked a breakthrough in the Cenozoic natural gas exploration in the southwestern margin of Qaidam Basin. The 16S rRNA analyses were performed on the crude oil samples from H2S-rich reservoirs in the Yuejin, Shizigou and Huatugou profiles, to understand the sulfurous gas origin, which was also integrated with carbon and hydrogen isotopes of alkane and sulfur isotopes of H2S collected from the Yingxiongling Area. Results show that the microorganisms in samples can survive in the hypersaline reservoirs, and can be classified into multiple phyla, including Proteobacteria, Planctomycetes, Firmicutes, Bacteroidetes, and Haloanaerobiaeota. Methanogens are abundant in all of the three profiles, while sulfate-reducing bacteria are abundant in Yuejin and Huatugou profiles, contributing to the methane and H2S components in the natural gas. The carbon, hydrogen and sulfur isotopes of sulfurous natural gas in the Yingxiongling Area show that the natural gas is a mixture of coal-type gas and oil-type gas, which was primarily derived from thermal degradation, and natural gas from the Yuejin and Huatugou profiles also originated from biodegradation. The isotopic analysis agrees well with the 16S rRNA results, i.e., H2S-rich natural gas from the Cenozoic reservoirs in the southwest margin of the Qaidam Basin was primarily of thermal genesis, with microbial genesis of secondary importance.
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Affiliation(s)
- Yue Jiao
- The Laboratory of Orogenic Belts and Crustal Evolution, School of Earth and Space Science, Peking University, Beijing, 100871, China
| | - Liyun An
- College of Architecture and Environment, Sichuan University, Chengdu, 610065, China
| | - Wei Wang
- The No. 1 Oil Extraction Plant, Qinghai Oilfield Company, PetroChina, Haixi, 817000, Qinghai, China
| | - Jian Ma
- The Laboratory of Orogenic Belts and Crustal Evolution, School of Earth and Space Science, Peking University, Beijing, 100871, China
| | - Chaodong Wu
- The Laboratory of Orogenic Belts and Crustal Evolution, School of Earth and Space Science, Peking University, Beijing, 100871, China.
| | - Xiaolei Wu
- College of Engineering, Peking University, Beijing, 100871, China
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5
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Seder-Colomina M, Mangeret A, Bauda P, Brest J, Stetten L, Merrot P, Julien A, Diez O, Barker E, Billoir E, Poupin P, Thouvenot A, Cazala C, Morin G. Influence of microorganisms on uranium release from mining-impacted lake sediments under various oxygenation conditions. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2022; 24:1830-1843. [PMID: 36082760 DOI: 10.1039/d2em00104g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Microbial processes can be involved in the remobilization of uranium (U) from reduced sediments under O2 reoxidation events such as water table fluctuations. Such reactions could be typically encountered after U-bearing sediment dredging operations. Solid U(IV) species may thus reoxidize into U(VI) that can be released in pore waters in the form of aqueous complexes with organic and inorganic ligands. Non-uraninite U(IV) species may be especially sensitive to reoxidation and remobilization processes. Nevertheless, little is known regarding the effect of microbially mediated processes on the behaviour of U under these conditions.
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Affiliation(s)
- Marina Seder-Colomina
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-ENV/SEDRE, 31 avenue de la Division Leclerc, 92260 Fontenay-aux-Roses, France.
| | - Arnaud Mangeret
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-ENV/SEDRE, 31 avenue de la Division Leclerc, 92260 Fontenay-aux-Roses, France.
| | - Pascale Bauda
- Université de Lorraine, CNRS, LIEC, F-57000 Metz, France
| | - Jessica Brest
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), UMR 7590 CNRS-Sorbonne Université -MNHN-IRD, case 115, 4 place Jussieu, 75252 Paris Cedex 5, France
| | - Lucie Stetten
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-ENV/SEDRE, 31 avenue de la Division Leclerc, 92260 Fontenay-aux-Roses, France.
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), UMR 7590 CNRS-Sorbonne Université -MNHN-IRD, case 115, 4 place Jussieu, 75252 Paris Cedex 5, France
| | - Pauline Merrot
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), UMR 7590 CNRS-Sorbonne Université -MNHN-IRD, case 115, 4 place Jussieu, 75252 Paris Cedex 5, France
| | - Anthony Julien
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-ENV/SEDRE, 31 avenue de la Division Leclerc, 92260 Fontenay-aux-Roses, France.
| | - Olivier Diez
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-ENV/SEDRE, 31 avenue de la Division Leclerc, 92260 Fontenay-aux-Roses, France.
| | - Evelyne Barker
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-ENV/SEDRE, 31 avenue de la Division Leclerc, 92260 Fontenay-aux-Roses, France.
| | - Elise Billoir
- Université de Lorraine, CNRS, LIEC, F-57000 Metz, France
| | - Pascal Poupin
- Université de Lorraine, CNRS, LIEC, F-57000 Metz, France
| | | | - Charlotte Cazala
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-ENV/SEDRE, 31 avenue de la Division Leclerc, 92260 Fontenay-aux-Roses, France.
| | - Guillaume Morin
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), UMR 7590 CNRS-Sorbonne Université -MNHN-IRD, case 115, 4 place Jussieu, 75252 Paris Cedex 5, France
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6
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Meier AB, Oppermann S, Drake HL, Schmidt O. The root zone of graminoids: A niche for H2-consuming acetogens in a minerotrophic peatland. Front Microbiol 2022; 13:978296. [PMID: 35992704 PMCID: PMC9391049 DOI: 10.3389/fmicb.2022.978296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 07/19/2022] [Indexed: 11/13/2022] Open
Abstract
The importance of acetogens for H2 turnover and overall anaerobic degradation in peatlands remains elusive. In the well-studied minerotrophic peatland fen Schlöppnerbrunnen, H2-consuming acetogens are conceptualized to be largely outcompeted by iron reducers, sulfate reducers, and hydrogenotrophic methanogens in bulk peat soil. However, in root zones of graminoids, fermenters thriving on rhizodeposits and root litter might temporarily provide sufficient H2 for acetogens. In the present study, root-free peat soils from around the roots of Molinia caerulea and Carex rostrata (i.e., two graminoids common in fen Schlöpnnerbrunnen) were anoxically incubated with or without supplemental H2 to simulate conditions of high and low H2 availability in the fen. In unsupplemented soil treatments, H2 concentrations were largely below the detection limit (∼10 ppmV) and possibly too low for acetogens and methanogens, an assumption supported by the finding that neither acetate nor methane substantially accumulated. In the presence of supplemental H2, acetate accumulation exceeded CH4 accumulation in Molinia soil whereas acetate and methane accumulated equally in Carex soil. However, reductant recoveries indicated that initially, additional unknown processes were involved either in H2 consumption or the consumption of acetate produced by H2-consuming acetogens. 16S rRNA and 16S rRNA gene analyses revealed that potential acetogens (Clostridium, Holophagaceae), methanogens (Methanocellales, Methanobacterium), iron reducers (Geobacter), and physiologically uncharacterized phylotypes (Acidobacteria, Actinobacteria, Bacteroidetes) were stimulated by supplemental H2 in soil treatments. Phylotypes closely related to clostridial acetogens were also active in soil-free Molinia and Carex root treatments with or without supplemental H2. Due to pronounced fermentation activities, H2 consumption was less obvious in root treatments, and acetogens likely thrived on root organic carbon and fermentation products (e.g., ethanol) in addition to H2. Collectively, the data highlighted that in fen Schlöppnerbrunnen, acetogens are associated to graminoid roots and inhabit the peat soil around the roots, where they have to compete for H2 with methanogens and iron reducers. Furthermore, the study underscored that the metabolically flexible acetogens do not rely on H2, potentially a key advantage over other H2 consumers under the highly dynamic conditions characteristic for the root-zones of graminoids in peatlands.
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Affiliation(s)
- Anja B. Meier
- Department of Ecological Microbiology, University of Bayreuth, Bayreuth, Germany
| | - Sindy Oppermann
- Department of Ecological Microbiology, University of Bayreuth, Bayreuth, Germany
| | - Harold L. Drake
- Department of Ecological Microbiology, University of Bayreuth, Bayreuth, Germany
| | - Oliver Schmidt
- Department of Ecological Microbiology, University of Bayreuth, Bayreuth, Germany
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
- *Correspondence: Oliver Schmidt,
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7
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Uptake of Phytoplankton-Derived Carbon and Cobalamins by Novel Acidobacteria Genera in Microcystis Blooms Inferred from Metagenomic and Metatranscriptomic Evidence. Appl Environ Microbiol 2022; 88:e0180321. [PMID: 35862730 PMCID: PMC9317899 DOI: 10.1128/aem.01803-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Interactions between bacteria and phytoplankton can influence primary production, community composition, and algal bloom development. However, these interactions are poorly described for many consortia, particularly for freshwater bloom-forming cyanobacteria. Here, we assessed the gene content and expression of two uncultivated Acidobacteria from Lake Erie Microcystis blooms. These organisms were targeted because they were previously identified as important catalase producers in Microcystis blooms, suggesting that they protect Microcystis from H2O2. Metatranscriptomics revealed that both Acidobacteria transcribed genes for uptake of organic compounds that are known cyanobacterial products and exudates, including lactate, glycolate, amino acids, peptides, and cobalamins. Expressed genes for amino acid metabolism and peptide transport and degradation suggest that use of amino acids and peptides by Acidobacteria may regenerate nitrogen for cyanobacteria and other organisms. The Acidobacteria genomes lacked genes for biosynthesis of cobalamins but expressed genes for its transport and remodeling. This indicates that the Acidobacteria obtained cobalamins externally, potentially from Microcystis, which has a complete gene repertoire for pseudocobalamin biosynthesis; expressed them in field samples; and produced pseudocobalamin in axenic culture. Both Acidobacteria were detected in Microcystis blooms worldwide. Together, the data support the hypotheses that uncultured and previously unidentified Acidobacteria taxa exchange metabolites with phytoplankton during harmful cyanobacterial blooms and influence nitrogen available to phytoplankton. Thus, novel Acidobacteria may play a role in cyanobacterial physiology and bloom development. IMPORTANCE Interactions between heterotrophic bacteria and phytoplankton influence competition and successions between phytoplankton taxa, thereby influencing ecosystem-wide processes such as carbon cycling and algal bloom development. The cyanobacterium Microcystis forms harmful blooms in freshwaters worldwide and grows in buoyant colonies that harbor other bacteria in their phycospheres. Bacteria in the phycosphere and in the surrounding community likely influence Microcystis physiology and ecology and thus the development of freshwater harmful cyanobacterial blooms. However, the impacts and mechanisms of interaction between bacteria and Microcystis are not fully understood. This study explores the mechanisms of interaction between Microcystis and uncultured members of its phycosphere in situ with population genome resolution to investigate the cooccurrence of Microcystis and freshwater Acidobacteria in blooms worldwide.
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8
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Liu SH, Lee KY. Performance of a packed-bed anode bio-electrochemical reactor for power generation and for removal of gaseous acetone. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 314:115062. [PMID: 35436710 DOI: 10.1016/j.jenvman.2022.115062] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 03/23/2022] [Accepted: 04/08/2022] [Indexed: 06/14/2023]
Abstract
The packed anode bioelectrochemical system (Pa-BES) developed in this study is a type of BES that introduces waste gas into a cathode and then into an anode, thereby providing the cathode with sufficient oxygen and reducing the amount of oxygen to the anode to promote the output of electricity. When the empty-bed residence time was 45 s and the liquid flowrate was 35 mL/s, the system achieved optimal performance. Under these conditions, removal efficiency, mineralization efficiency, voltage output, and power density were 93.86%, 93.37%, 296.3 mV, and 321.12 mW/m3, respectively. The acetone in the waste gas was almost completely converted into carbon dioxide, indicating that Pa-BES can effectively remove acetone and has the potential to be used in practical situations. A cyclic voltammetry analysis revealed that the packings exhibited clear redox peaks, indicating that the Pa-BES has outstanding biodegradation and power generation abilities. Through microbial community dynamics, numerous organics degraders, electrochemically active bacteria, nitrifying and denitrifying bacteria were found, and the spatial distribution of these microbes were identified. Among them, Xanthobacter, Bryobacter, Mycobacteriums and Terrimonawas were able to decompose acetone or other organic substances, with Xanthobacter dominating. Bacterium_OLB10 and Ferruginibacter are the electrochemically active bacteria in Pa-BES, while Ferruginibacter is the most abundant in the main anode, which is responsible for electron collection and transfer.
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Affiliation(s)
- Shu-Hui Liu
- Department of Safety, Health and Environmental Engineering, National Yunlin University of Science and Technology, Yunlin, 64002, Taiwan, ROC.
| | - Kun-Yan Lee
- Department of Safety, Health and Environmental Engineering, National Yunlin University of Science and Technology, Yunlin, 64002, Taiwan, ROC
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9
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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: 0] [Impact Index Per Article: 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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10
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Wu Q, Jiang X, Wu H, Zou L, Wang L, Shi J. Effects and Mechanisms of Copper Oxide Nanoparticles with Regard to Arsenic Availability in Soil-Rice Systems: Adsorption Behavior and Microbial Response. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:8142-8154. [PMID: 35654440 DOI: 10.1021/acs.est.2c01393] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Copper oxide nanoparticles (CuO NPs) are widely used as fungicides in agriculture. Arsenic (As) is a ubiquitous contaminant in paddy soil. The present study was focused on the adsorption behavior of CuO NPs with regard to As as well as the characteristics of the microbial community changes in As-contaminated soil-rice systems in response to CuO NPs. The study found that CuO NPs could be a temporary sink of As in soil; a high dose of CuO NPs promoted the release of As from crystalline iron oxide, which increased the As content in the liquid phase. The study also found that the As bioavailability changed significantly when the dose of CuO NPs was higher than 50 mg kg-1 in the soil-rice system. The addition of 100 mg kg-1 CuO NPs increased the microbial diversity and the abundance of genes involved in As cycling, decreased the abundance of Fe(III)-reducing bacteria and sulfate-reducing genes, and decreased As accumulation in grains. Treatment with 500 mg kg-1 CuO NPs increased the abundance of Fe(III)-reducing bacteria and sulfate-reducing genes, decreased Fe plaques, and increased As accumulation in rice. The adverse effects of CuO NPs on crops and associated risks need to be considered carefully.
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Affiliation(s)
- Qianhua Wu
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
- Key Laboratory for Water Pollution Control and Environmental Safety, Zhejiang University, Hangzhou 310058, China
| | - Xiaohan Jiang
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
- Key Laboratory for Water Pollution Control and Environmental Safety, Zhejiang University, Hangzhou 310058, China
| | - Hanxin Wu
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
- Key Laboratory for Water Pollution Control and Environmental Safety, Zhejiang University, Hangzhou 310058, China
| | - Lina Zou
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
- Key Laboratory for Water Pollution Control and Environmental Safety, Zhejiang University, Hangzhou 310058, China
| | - Lubin Wang
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
- Key Laboratory for Water Pollution Control and Environmental Safety, Zhejiang University, Hangzhou 310058, China
| | - Jiyan Shi
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
- Key Laboratory for Water Pollution Control and Environmental Safety, Zhejiang University, Hangzhou 310058, China
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11
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Sanchez-Huerta C, Fortunato L, Leiknes T, Hong PY. Influence of biofilm thickness on the removal of thirteen different organic micropollutants via a Membrane Aerated Biofilm Reactor (MABR). JOURNAL OF HAZARDOUS MATERIALS 2022; 432:128698. [PMID: 35349844 DOI: 10.1016/j.jhazmat.2022.128698] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 03/09/2022] [Accepted: 03/11/2022] [Indexed: 06/14/2023]
Abstract
The presence of organic micropollutants (OMPs) in natural water bodies has become an emerging concern due to their fast dissemination into natural water sources, high persistence, ubiquitous nature, and detrimental impact on the environment and human health. This study evaluated the Membrane Aerated Biofilm Reactor (MABR) efficiency in the removal of 13 OMPs commonly reported in water. Results demonstrated that OMPs removal is dependent on biofilm thickness and bacterial cell density, microbial community composition and physicochemical properties of OMPs. Effective removals of ammonium and organic carbon (COD, >50%), acetaminophen (70%) and triclosan (99%) were obtained even at early stages of biofilm development (thickness < 0.33 mm, 2.9 ×105 cell mL-1). An increase in biofilm thickness and cell density (1.02 mm, 2.2 ×106 cell mL-1) enhanced the system performance. MABR achieved over 90% removal of nonpolar, hydrophobic and hydrophilic OMPs and 22-69% removal of negatively charged and acidic OMPs. Relative abundances of Zoogloea, Aquabacterium, Leucobacter, Runella, and Paludilbaculum bacteria correlated with the removal of certain OMPs. In addition, MABR achieved up to 96% nitrification and 80% overall COD removal by the end of the experiment. The findings from this study demonstrated MABRs to be a feasible option to treat municipal wastewater polluted by OMPs.
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Affiliation(s)
- C Sanchez-Huerta
- Environmental Science and Engineering Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia; Water Desalination and Reuse Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia.
| | - L Fortunato
- Environmental Science and Engineering Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia; Water Desalination and Reuse Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - T Leiknes
- Environmental Science and Engineering Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - P-Y Hong
- Environmental Science and Engineering Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia; Water Desalination and Reuse Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
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12
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Yang ZN, Liu ZS, Wang KH, Liang ZL, Abdugheni R, Huang Y, Wang RH, Ma HL, Wang XK, Yang ML, Zhang BG, Li DF, Jiang CY, Corvini PFX, Liu SJ. Soil microbiomes divergently respond to heavy metals and polycyclic aromatic hydrocarbons in contaminated industrial sites. ENVIRONMENTAL SCIENCE AND ECOTECHNOLOGY 2022; 10:100169. [PMID: 36159729 PMCID: PMC9488039 DOI: 10.1016/j.ese.2022.100169] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 03/14/2022] [Accepted: 03/14/2022] [Indexed: 05/19/2023]
Abstract
Contaminated sites from electronic waste (e-waste) dismantling and coking plants feature high concentrations of heavy metals (HMs) and/or polycyclic aromatic hydrocarbons (PAHs) in soil. Mixed contamination (HMs + PAHs) hinders land reclamation and affects the microbial diversity and function of soil microbiomes. In this study, we analyzed HM and PAH contamination from an e-waste dismantling plant and a coking plant and evaluated the influences of HM and PAH contamination on soil microbiomes. It was noticed that HMs and PAHs were found in all sites, although the major contaminants of the e-waste dismantling plant site were HMs (such as Cu at 5,947.58 ± 433.44 mg kg-1, Zn at 4,961.38 ± 436.51 mg kg-1, and Mn at 2,379.07 ± 227.46 mg kg-1), and the major contaminants of the coking plant site were PAHs (such as fluorene at 11,740.06 ± 620.1 mg kg-1, acenaphthylene at 211.69 ± 7.04 mg kg-1, and pyrene at 183.14 ± 18.89 mg kg-1). The microbiomes (diversity and abundance) of all sites were determined via high-throughput sequencing of 16S rRNA genes, and redundancy analysis was conducted to investigate the relations between soil microbiomes and contaminants. The results showed that the microbiomes of the contaminated sites divergently responded to HMs and PAHs. The abundances of the bacterial genera Sulfuritalea, Pseudomonas, and Sphingobium were positively related to PAHs, while the abundances of the bacterial genera Bryobacter, Nitrospira, and Steroidobacter were positively related to HMs. This study promotes an understanding of how soil microbiomes respond to single and mixed contamination with HMs and PAHs.
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Affiliation(s)
- Zhen-Ni Yang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ze-Shen Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ke-Huan Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zong-Lin Liang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Rashidin Abdugheni
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ye Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Run-Hua Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hong-Lin Ma
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiao-Kang Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Mei-Ling Yang
- School of Life Sciences, Hebei University, Baoding, 071002, Hebei Province, China
| | - Bing-Ge Zhang
- School of Public Health, Xuzhou Medical University, Xuzhou, 221004, Jiangsu Province, China
| | - De-Feng Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Cheng-Ying Jiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- Corresponding author.
| | - Philippe F.-X. Corvini
- School of Life Sciences, University of Applied Sciences and Arts Northwestern Switzerland, Muttenz, 4132, Switzerland
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, 226237, Shandong Province, China
- Corresponding author. State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
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13
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Govindarajan A, Crum M, Adolacion J, Kiaghadi A, Acuña-Gonzalez E, Rifai HS, Willson RC. Sediment and their bacterial communities in an industrialized estuary after Hurricane Harvey. MARINE POLLUTION BULLETIN 2022; 175:113359. [PMID: 35124375 DOI: 10.1016/j.marpolbul.2022.113359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 12/26/2021] [Accepted: 01/15/2022] [Indexed: 06/14/2023]
Abstract
Estuaries experience variable physicochemical conditions, especially after hurricanes and due to anthropogenic sources of pollution. Their microbial communities are not as well understood in terms of community structure and diversity, particularly in response to stresses from pollution and severe events. This study presents a 16S rRNA-based description of sediment microbial communities in the Houston Ship Channel-Galveston Bay estuary after Hurricane Harvey in 2017. A total of 11 sites were sampled, and microbial genomic DNA was isolated from sediment. The presence and abundance of specific bacterial and archaeal taxa in the sediment indicated pollutant inputs from identified legacy sources. The abundance of certain microbial groups was explained by the mobilization of contaminated sediment and sediment transport due to Harvey. Several microorganisms involved in the biodegradation of xenobiotics were observed. The spatial occurrence of Dehalococcoidia, a degrader of persistent polychlorinated compounds, was explained in relation to sediment properties and contaminant concentrations.
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Affiliation(s)
| | - Mary Crum
- Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| | - Jay Adolacion
- School of Engineering and Science, Tecnológico de Monterrey, Monterrey, Mexico
| | - Amin Kiaghadi
- Civil and Environmental Engineering, University of Houston, Houston, TX, USA
| | - Edgar Acuña-Gonzalez
- School of Medicine and Health Sciences, Tecnológico de Monterrey, Monterrey, Mexico
| | - Hanadi S Rifai
- Civil and Environmental Engineering, University of Houston, Houston, TX, USA.
| | - Richard C Willson
- Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
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14
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Wang G, Li Y, Liu J, Chen B, Su H, Liang J, Huang W, Yu K. Comparative Genomics Reveal the Animal-Associated Features of the Acanthopleuribacteraceae Bacteria, and Description of Sulfidibacter corallicola gen. nov., sp., nov. Front Microbiol 2022; 13:778535. [PMID: 35173698 PMCID: PMC8841776 DOI: 10.3389/fmicb.2022.778535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 01/07/2022] [Indexed: 11/13/2022] Open
Abstract
Members of the phylum Acidobacteria are ubiquitous in various environments. Soil acidobacteria have been reported to present a variety of strategies for their success in terrestrial environments. However, owing to lack of pure culture, information on animal-associated acidobacteria are limited, except for those obtained from 16S rRNA genes. To date, only two acidobacteria have been isolated from animals, namely strain M133T obtained from coral Porites lutea and Acanthopleuribacter pedis KCTC 12899T isolated from chiton. Genomics and physiological characteristics of strain M133T and A. pedis KCTC 12899T were compared with 19 other isolates (one strain from each genus) in the phylum Acidobacteria. The results revealed that strain M133T represents a new species in a new genus in the family Acanthopleuribacteraceae. To date, these two Acanthopleuribacteraceae isolates have the largest genomes (10.85–11.79 Mb) in the phylum Acidobacteria. Horizontal gene transfer and gene duplication influenced the structure and plasticity of these large genomes. Dissimilatory nitrate reduction and abundant secondary metabolite biosynthetic gene clusters (including eicosapentaenoic acid de novo biosynthesis) are two distinct features of the Acanthopleuribacteraceae bacteria in the phylum Acidobacteria. The absence of glycoside hydrolases involved in plant polysaccharide degradation and presence of animal disease-related peptidases indicate that these bacteria have evolved to adapt to the animal hosts. In addition to low- and high-affinity respiratory oxygen reductases, enzymes for nitrate to nitrogen, and sulfhydrogenase were also detected in strain M133T, suggesting the capacity and flexibility to grow in aerobic and anaerobic environments. This study highlighted the differences in genome structure, carbohydrate and protein utilization, respiration, and secondary metabolism between animal-associated acidobacteria and other acidobacteria, especially the soil acidobacteria, displaying flexibility and versatility of the animal-associated acidobacteria in environmental adaption.
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Affiliation(s)
- Guanghua Wang
- Guangxi Key Laboratory on the Study of Coral Reefs in the South China Sea, Nanning, China
- Coral Reef Research Center of China, Guangxi University, Nanning, China
- School of Marine Sciences, Guangxi University, Nanning, China
| | - Yuanjin Li
- Guangxi Key Laboratory on the Study of Coral Reefs in the South China Sea, Nanning, China
- Coral Reef Research Center of China, Guangxi University, Nanning, China
- School of Marine Sciences, Guangxi University, Nanning, China
| | - Jianfeng Liu
- Guangxi Key Laboratory on the Study of Coral Reefs in the South China Sea, Nanning, China
- Coral Reef Research Center of China, Guangxi University, Nanning, China
- School of Marine Sciences, Guangxi University, Nanning, China
| | - Biao Chen
- Guangxi Key Laboratory on the Study of Coral Reefs in the South China Sea, Nanning, China
- Coral Reef Research Center of China, Guangxi University, Nanning, China
- School of Marine Sciences, Guangxi University, Nanning, China
| | - Hongfei Su
- Guangxi Key Laboratory on the Study of Coral Reefs in the South China Sea, Nanning, China
- Coral Reef Research Center of China, Guangxi University, Nanning, China
- School of Marine Sciences, Guangxi University, Nanning, China
| | - Jiayuan Liang
- Guangxi Key Laboratory on the Study of Coral Reefs in the South China Sea, Nanning, China
- Coral Reef Research Center of China, Guangxi University, Nanning, China
- School of Marine Sciences, Guangxi University, Nanning, China
| | - Wen Huang
- Guangxi Key Laboratory on the Study of Coral Reefs in the South China Sea, Nanning, China
- Coral Reef Research Center of China, Guangxi University, Nanning, China
- School of Marine Sciences, Guangxi University, Nanning, China
| | - Kefu Yu
- Guangxi Key Laboratory on the Study of Coral Reefs in the South China Sea, Nanning, China
- Coral Reef Research Center of China, Guangxi University, Nanning, China
- School of Marine Sciences, Guangxi University, Nanning, China
- *Correspondence: Kefu Yu,
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15
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Ruhl IA, Sheremet A, Furgason CC, Krause S, Bowers RM, Jarett JK, Tran TM, Grasby SE, Woyke T, Dunfield PF. GAL08, an Uncultivated Group of Acidobacteria, Is a Dominant Bacterial Clade in a Neutral Hot Spring. Front Microbiol 2022; 12:787651. [PMID: 35087491 PMCID: PMC8787282 DOI: 10.3389/fmicb.2021.787651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 11/29/2021] [Indexed: 11/28/2022] Open
Abstract
GAL08 are bacteria belonging to an uncultivated phylogenetic cluster within the phylum Acidobacteria. We detected a natural population of the GAL08 clade in sediment from a pH-neutral hot spring located in British Columbia, Canada. To shed light on the abundance and genomic potential of this clade, we collected and analyzed hot spring sediment samples over a temperature range of 24.2–79.8°C. Illumina sequencing of 16S rRNA gene amplicons and qPCR using a primer set developed specifically to detect the GAL08 16S rRNA gene revealed that absolute and relative abundances of GAL08 peaked at 65°C along three temperature gradients. Analysis of sediment collected over multiple years and locations revealed that the GAL08 group was consistently a dominant clade, comprising up to 29.2% of the microbial community based on relative read abundance and up to 4.7 × 105 16S rRNA gene copy numbers per gram of sediment based on qPCR. Using a medium quality threshold, 25 single amplified genomes (SAGs) representing these bacteria were generated from samples taken at 65 and 77°C, and seven metagenome-assembled genomes (MAGs) were reconstructed from samples collected at 45–77°C. Based on average nucleotide identity (ANI), these SAGs and MAGs represented three separate species, with an estimated average genome size of 3.17 Mb and GC content of 62.8%. Phylogenetic trees constructed from 16S rRNA gene sequences and a set of 56 concatenated phylogenetic marker genes both placed the three GAL08 bacteria as a distinct subgroup of the phylum Acidobacteria, representing a candidate order (Ca. Frugalibacteriales) within the class Blastocatellia. Metabolic reconstructions from genome data predicted a heterotrophic metabolism, with potential capability for aerobic respiration, as well as incomplete denitrification and fermentation. In laboratory cultivation efforts, GAL08 counts based on qPCR declined rapidly under atmospheric levels of oxygen but increased slightly at 1% (v/v) O2, suggesting a microaerophilic lifestyle.
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Affiliation(s)
- Ilona A Ruhl
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Andriy Sheremet
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Chantel C Furgason
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Susanne Krause
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Robert M Bowers
- U.S. Department of Energy Joint Genome Institute, Berkeley, CA, United States
| | - Jessica K Jarett
- U.S. Department of Energy Joint Genome Institute, Berkeley, CA, United States
| | - Triet M Tran
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Stephen E Grasby
- Department of Geoscience, University of Calgary, Calgary, AB, Canada.,Geological Survey of Canada, Calgary, AB, Canada
| | - Tanja Woyke
- U.S. Department of Energy Joint Genome Institute, Berkeley, CA, United States
| | - Peter F Dunfield
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
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16
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Ren Z, Fu X, Zhang G, Li Y, Qin Y, Wang P, Liu X, Lv L. Study on performance and mechanism of enhanced low-concentration ammonia nitrogen removal from low-temperature wastewater by iron-loaded biological activated carbon filter. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 301:113859. [PMID: 34597949 DOI: 10.1016/j.jenvman.2021.113859] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/20/2021] [Accepted: 09/25/2021] [Indexed: 06/13/2023]
Abstract
In order to strengthen the treatment of low-concentration ammonia nitrogen wastewater at low temperature, iron-loaded activated carbon (Fe-AC) with ultrasonic impregnation method was used as the filter material of biofilter process. The performance and mechanism of ammonia nitrogen removal from simulated secondary wastewater by iron-loaded biological activated carbon filter (Fe-BACF) were studied at 10 °C. The characterization results showed that iron was loaded on the surface of AC in the form of Fe2O3, and the specific surface area, total pore volume, pore size and alkaline functional group content of Fe-AC were obviously increased. After the formation of biofilm on the surface of filter media, the average removal rate of ammonia nitrogen by Fe-BACF (97.9%) was significantly higher than that of conventional BACF (87.8%). The improved surface properties increased the number and metabolic activity of microorganisms, and promoted the secretion of EPS on the surface of Fe-BAC. The results of high-throughput sequencing showed that the existence of Fe optimized the bacterial community structure on the surface of Fe-BAC, with the increase of the abundances of psychrophilic bacteria and ammonia nitrogen removal bacteria. The mechanism of enhanced ammonia nitrogen removal by Fe-BACF was the joint action of many factors, among which the main causal relationship was that modification of iron could optimize the number and category of microorganisms on Fe-BAC surface by improving the surface properties, thus improving the biological nitrogen removal ability. Results of this study provided a practical way for the treatment of low ammonia nitrogen wastewater in cold regions.
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Affiliation(s)
- Zhijun Ren
- Tianjin Key Laboratory of Clean Energy and Pollution Control, School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin, 300401, PR China
| | - Xiaolin Fu
- Tianjin Key Laboratory of Clean Energy and Pollution Control, School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin, 300401, PR China
| | - Guangming Zhang
- Tianjin Key Laboratory of Clean Energy and Pollution Control, School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin, 300401, PR China
| | - Yuyou Li
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, Sendai, 980-8579, Japan
| | - Yu Qin
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, Sendai, 980-8579, Japan
| | - Pengfei Wang
- Tianjin Key Laboratory of Clean Energy and Pollution Control, School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin, 300401, PR China
| | - Xiaoyang Liu
- Tianjin Key Laboratory of Clean Energy and Pollution Control, School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin, 300401, PR China
| | - Longyi Lv
- Tianjin Key Laboratory of Clean Energy and Pollution Control, School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin, 300401, PR China.
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17
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Liu Q, Chen Z, Tang J, Luo J, Huang F, Wang P, Xiao R. Cd and Pb immobilisation with iron oxide/lignin composite and the bacterial community response in soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 802:149922. [PMID: 34525730 DOI: 10.1016/j.scitotenv.2021.149922] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 08/03/2021] [Accepted: 08/22/2021] [Indexed: 06/13/2023]
Abstract
Iron oxide is a natural mineral that generally exists in the form of iron oxide-organic complexes (Fe-OM) in soil. Lignin is a naturally occurring polymer that is considered to be an important part of soil carbon cycling. In this study we prepared a composite material (MGE) with iron oxide and lignin based on the Fe-OM present in the soil. MGE was then applied to remediate Cd and Pb in contaminated soil. The results show that DTPA-Cd and DTPA-Pb levels were reduced by 58.87% and 78.09%, respectively. The bacterial community diversity index decreased in the iron oxide (GE) group, but a slight increase was observed in the MGE group. In terms of species composition in the MGE group, the abundance of Proteobacteria, Gemmatimonadota and Acidobacteriota increased, while the abundance of Bacteroidota, Actinobacteriota and Firmicutes decreased. The outcome in the GE group was the opposite. In the MGE group, HCl-Fe2+, HCl-Fe3+, and pH were significantly higher than in the other groups, indicating that MGE stimulated the growth of iron-reducing bacteria (FeRB) and promoted iron redox reactions. Iron oxide could be reduced to Fe2+ due to the activity of FeRB, and then Fe2+ would be oxidised and hydrolysed, which led to an increase in soil pH. Secondary minerals were formed during this process. With the oxidation of Fe2+ and the formation of secondary minerals, Cd and Pb could be stabilised in the oxides and were not easily released through a co-precipitation mechanism.
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Affiliation(s)
- Qianjun Liu
- School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China.
| | - Zhaowei Chen
- School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Jiepeng Tang
- School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Jiayi Luo
- School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Fei Huang
- School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Peng Wang
- School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Rongbo Xiao
- School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China.
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18
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Chen Y, Jia F, Liu Y, Yu W, Cai W, Zhang X, He H, Yao H. The effects of Fe(III) and Fe(II) on anammox process and the Fe-N metabolism. CHEMOSPHERE 2021; 285:131322. [PMID: 34246098 DOI: 10.1016/j.chemosphere.2021.131322] [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: 04/20/2021] [Revised: 06/14/2021] [Accepted: 06/20/2021] [Indexed: 06/13/2023]
Abstract
This study aims to compare the effects of different Fe stress on anammox (anaerobic ammonium oxidation) process, therefore seven identical reactors were operated under different Fe(II)/Fe(III) concentrations. After 38 days of operation, the anammox activity was highest (10.49 ± 0.41 mg-TN/(g-VSS·h)) under conditions of 5 mg/L-Fe(II), while under 30 mg/L-Fe(III) displayed severe inhibition. The results showed that continuous addition of 30 mg/L-Fe(III) would damage the composition of EPS (extracellular polymeric substances) and make anammox bacteria more sensitive to environmental stress. While high Fe(II) concentrations could result in precipitates encasing granular sludge, affecting substrate utilization. Moreover, the results of ΔNO3--N/ΔNH4+-N indicated that Fe(II)-dependent nitrate reduction was induced in reactors added with Fe(II). OM27_clade and norank_f__Burkholderiaceae might be candidates for this process according to the correlation of genera and functional genes (based on the PICRUSt 2 functional prediction). Overall, this research is expected to provide new ideas to the effects of Fe(II)/Fe(III) on anammox and to the practical application of coupled system based on anammox in wastewater treatment.
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Affiliation(s)
- Yao Chen
- Beijing Key Laboratory of Aqueous Typical Pollutants Control and Water Quality Safeguard, Department of Municipal and Environmental Engineering, School of Civil Engineering, Beijing Jiaotong University, Beijing, 100044, PR China
| | - Fangxu Jia
- Beijing Key Laboratory of Aqueous Typical Pollutants Control and Water Quality Safeguard, Department of Municipal and Environmental Engineering, School of Civil Engineering, Beijing Jiaotong University, Beijing, 100044, PR China.
| | - Yingjie Liu
- Beijing Key Laboratory of Aqueous Typical Pollutants Control and Water Quality Safeguard, Department of Municipal and Environmental Engineering, School of Civil Engineering, Beijing Jiaotong University, Beijing, 100044, PR China
| | - Wanrou Yu
- Beijing Key Laboratory of Aqueous Typical Pollutants Control and Water Quality Safeguard, Department of Municipal and Environmental Engineering, School of Civil Engineering, Beijing Jiaotong University, Beijing, 100044, PR China
| | - Weiwei Cai
- Beijing Key Laboratory of Aqueous Typical Pollutants Control and Water Quality Safeguard, Department of Municipal and Environmental Engineering, School of Civil Engineering, Beijing Jiaotong University, Beijing, 100044, PR China
| | - Xiaofan Zhang
- Beijing Key Laboratory of Aqueous Typical Pollutants Control and Water Quality Safeguard, Department of Municipal and Environmental Engineering, School of Civil Engineering, Beijing Jiaotong University, Beijing, 100044, PR China
| | - Haodong He
- Beijing Key Laboratory of Aqueous Typical Pollutants Control and Water Quality Safeguard, Department of Municipal and Environmental Engineering, School of Civil Engineering, Beijing Jiaotong University, Beijing, 100044, PR China
| | - Hong Yao
- Beijing Key Laboratory of Aqueous Typical Pollutants Control and Water Quality Safeguard, Department of Municipal and Environmental Engineering, School of Civil Engineering, Beijing Jiaotong University, Beijing, 100044, PR China
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19
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Behnke GD, Kim N, Zabaloy MC, Riggins CW, Rodriguez-Zas S, Villamil MB. Soil Microbial Indicators within Rotations and Tillage Systems. Microorganisms 2021; 9:1244. [PMID: 34201118 PMCID: PMC8228827 DOI: 10.3390/microorganisms9061244] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/01/2021] [Accepted: 06/06/2021] [Indexed: 01/04/2023] Open
Abstract
Recent advancements in agricultural metagenomics allow for characterizing microbial indicators of soil health brought on by changes in management decisions, which ultimately affect the soil environment. Field-scale studies investigating the microbial taxa from agricultural experiments are sparse, with none investigating the long-term effect of crop rotation and tillage on microbial indicator species. Therefore, our goal was to determine the effect of rotations (continuous corn, CCC; continuous soybean, SSS; and each phase of a corn-soybean rotation, Cs and Sc) and tillage (no-till, NT; and chisel tillage, T) on the soil microbial community composition following 20 years of management. We found that crop rotation and tillage influence the soil environment by altering key soil properties, such as pH and soil organic matter (SOM). Monoculture corn lowered pH compared to SSS (5.9 vs. 6.9, respectively) but increased SOM (5.4% vs. 4.6%, respectively). Bacterial indicator microbes were categorized into two groups: SOM dependent and acidophile vs. N adverse and neutrophile. Fungi preferred the CCC rotation, characterized by low pH. Archaeal indicators were mainly ammonia oxidizers with species occupying niches at contrasting pHs. Numerous indicator microbes are involved with N cycling due to the fertilizer-rich environment, prone to aquatic or gaseous losses.
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Affiliation(s)
- Gevan D. Behnke
- Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA; (G.D.B.); (N.K.); (C.W.R.)
| | - Nakian Kim
- Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA; (G.D.B.); (N.K.); (C.W.R.)
| | - Maria C. Zabaloy
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS, UNS-CONICET), Departamento de Agronomía, Universidad Nacional del Sur, Bahia Blanca B8000, Argentina;
| | - Chance W. Riggins
- Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA; (G.D.B.); (N.K.); (C.W.R.)
| | | | - Maria B. Villamil
- Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA; (G.D.B.); (N.K.); (C.W.R.)
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20
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Awata T, Goto Y, Kuratsuka H, Aoi Y, Ozaki N, Ohashi A, Kindaichi T. Reactor performance and microbial community structure of single-stage partial nitritation anammox membrane bioreactors inoculated with Brocadia and Scalindua enrichment cultures. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2021.107991] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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21
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Yoneda Y, Yamamoto K, Makino A, Tanaka Y, Meng XY, Hashimoto J, Shin-ya K, Satoh N, Fujie M, Toyama T, Mori K, Ike M, Morikawa M, Kamagata Y, Tamaki H. Novel Plant-Associated Acidobacteria Promotes Growth of Common Floating Aquatic Plants, Duckweeds. Microorganisms 2021; 9:1133. [PMID: 34074043 PMCID: PMC8225144 DOI: 10.3390/microorganisms9061133] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 05/20/2021] [Indexed: 11/17/2022] Open
Abstract
Duckweeds are small, fast growing, and starch- and protein-rich aquatic plants expected to be a next generation energy crop and an excellent biomaterial for phytoremediation. Despite such an importance, very little is known about duckweed-microbe interactions that would be a key biological factor for efficient industrial utilization of duckweeds. Here we first report the duckweed growth promoting ability of bacterial strains belonging to the phylum Acidobacteria, the members of which are known to inhabit soils and terrestrial plants, but their ecological roles and plant-microbe interactions remain largely unclear. Two novel Acidobacteria strains, F-183 and TBR-22, were successfully isolated from wild duckweeds and phylogenetically affiliated with subdivision 3 and 6 of the phylum, respectively, based on 16S rRNA gene sequence analysis. In the co-culture experiments with aseptic host plants, the F-183 and TBR-22 strains visibly enhanced growth (frond number) of six duckweed species (subfamily Lemnoideae) up to 1.8-5.1 times and 1.6-3.9 times, respectively, compared with uninoculated controls. Intriguingly, both strains also increased the chlorophyll content of the duckweed (Lemna aequinoctialis) up to 2.4-2.5 times. Under SEM observation, the F-183 and TBR-22 strains were epiphytic and attached to the surface of duckweed. Taken together, our findings suggest that indigenous plant associated Acidobacteria contribute to a healthy growth of their host aquatic plants.
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Affiliation(s)
- Yasuko Yoneda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8566, Ibaraki, Japan; (Y.Y.); (K.Y.); (A.M.); (X.-Y.M.); (Y.K.)
| | - Kyosuke Yamamoto
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8566, Ibaraki, Japan; (Y.Y.); (K.Y.); (A.M.); (X.-Y.M.); (Y.K.)
- Bioproduction Research Institute, AIST, Sapporo 062-8517, Hokkaido, Japan
| | - Ayaka Makino
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8566, Ibaraki, Japan; (Y.Y.); (K.Y.); (A.M.); (X.-Y.M.); (Y.K.)
| | - Yasuhiro Tanaka
- Department of Environmental Sciences, Faculty of Life and Environmental Sciences, University of Yamanashi, Kofu 400-8510, Yamanashi, Japan;
| | - Xian-Ying Meng
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8566, Ibaraki, Japan; (Y.Y.); (K.Y.); (A.M.); (X.-Y.M.); (Y.K.)
| | - Junko Hashimoto
- Japan Biological Informatics Consortium (JBiC), Koto-ku, Tokyo 135-0064, Japan;
| | - Kazuo Shin-ya
- Cellular and Molecular Biotechnology Research Institute, AIST, Koto-ku, Tokyo 135-0064, Japan;
| | - Noriyuki Satoh
- Okinawa Institute of Science, Technology Graduate University (OIST), Kunigami-gun 904-0495, Okinawa, Japan; (N.S.); (M.F.)
| | - Manabu Fujie
- Okinawa Institute of Science, Technology Graduate University (OIST), Kunigami-gun 904-0495, Okinawa, Japan; (N.S.); (M.F.)
| | - Tadashi Toyama
- Department of Civil and Environmental Engineering, Faculty of Engineering, University of Yamanashi, Kofu 400-8511, Yamanashi, Japan; (T.T.); (K.M.)
| | - Kazuhiro Mori
- Department of Civil and Environmental Engineering, Faculty of Engineering, University of Yamanashi, Kofu 400-8511, Yamanashi, Japan; (T.T.); (K.M.)
| | - Michihiko Ike
- Division of Sustainable Energy and Environmental Engineering, Graduate School of Engineering, Osaka University, Suita 565-0871, Osaka, Japan;
| | - Masaaki Morikawa
- Graduate School of Environmental Science, Hokkaido University, Sapporo 060-0810, Hokkaido, Japan;
| | - Yoichi Kamagata
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8566, Ibaraki, Japan; (Y.Y.); (K.Y.); (A.M.); (X.-Y.M.); (Y.K.)
| | - Hideyuki Tamaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8566, Ibaraki, Japan; (Y.Y.); (K.Y.); (A.M.); (X.-Y.M.); (Y.K.)
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8577, Ibaraki, Japan
- Microbiology Research Center for Sustainability (MiCS), University of Tsukuba, Tsukuba 305-8572, Ibaraki, Japan
- Biotechnology Research Center, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
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22
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Abstract
Concrete is an extreme but common environment and is home to microbial communities adapted to alkaline, saline, and oligotrophic conditions. Microbes inside the concrete that makes up buildings or roads have received little attention despite their ubiquity and capacity to interact with the concrete. Because concrete is a composite of materials which have their own microbial communities, we hypothesized that the microbial communities of concrete reflect those of the concrete components and that these communities change as the concrete ages. Here, we used a 16S amplicon study to show how microbial communities change over 2 years of outdoor weathering in two sets of concrete cylinders, one prone to the concrete-degrading alkali-silica reaction (ASR) and the other having the risk of the ASR mitigated. After identifying and removing taxa that were likely laboratory or reagent contaminants, we found that precursor materials, particularly the large aggregate (gravel), were the probable source of ∼50 to 60% of the bacteria observed in the first cylinders from each series. Overall, community diversity decreased over 2 years, with temporarily increased diversity in warmer summer months. We found that most of the concrete microbiome was composed of Proteobacteria, Firmicutes, and Actinobacteria, although community composition changed seasonally and over multiyear time scales and was likely influenced by environmental deposition. Although the community composition between the two series was not significantly different overall, several taxa, including Arcobacter, Modestobacter, Salinicoccus, Rheinheimera, Lawsonella, and Bryobacter, appear to be associated with ASR. IMPORTANCE Concrete is the most-used building material in the world and a biologically extreme environment, with a microbiome composed of bacteria that likely come from concrete precursor materials, aerosols, and environmental deposition. These microbes, though seeded from a variety of materials, are all subject to desiccation, heating, starvation, high salinity, and very high pH. Microbes that survive and even thrive under these conditions can potentially either degrade concrete or contribute to its repair. Thus, understanding which microbes survive in concrete, under what conditions, and for how long has potential implications for biorepair of concrete. Further, methodological pipelines for analyzing concrete microbial communities can be applied to concrete from a variety of structures or with different types of damage to identify bioindicator species that can be used for structural health monitoring and service life prediction.
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Choma M, Tahovská K, Kaštovská E, Bárta J, Růžek M, Oulehle F. Bacteria but not fungi respond to soil acidification rapidly and consistently in both a spruce and beech forest. FEMS Microbiol Ecol 2021; 96:5894924. [PMID: 32815987 DOI: 10.1093/femsec/fiaa174] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 08/18/2020] [Indexed: 11/13/2022] Open
Abstract
Anthropogenically enhanced atmospheric sulphur (S) and nitrogen (N) deposition has acidified and eutrophied forest ecosystems worldwide. However, both S and N mechanisms have an impact on microbial communities and the consequences for microbially driven soil functioning differ. We conducted a two-forest stand (Norway spruce and European beech) field experiment involving acidification (sulphuric acid addition) and N (ammonium nitrate) loading and their combination. For 4 years, we monitored separate responses of soil microbial communities to the treatments and investigated the relationship to changes in the activity of extracellular enzymes. We observed that acidification selected for acidotolerant and oligotrophic taxa of Acidobacteria and Actinobacteria decreased bacterial community richness and diversity in both stands in parallel, disregarding their original dissimilarities in soil chemistry and composition of microbial communities. The shifts in bacterial community influenced the stoichiometry and magnitude of enzymatic activity. The bacterial response to experimental N addition was much weaker, likely due to historically enhanced N availability. Fungi were not influenced by any treatment during 4-year manipulation. We suggest that in the onset of acidification when fungi remain irresponsive, bacterial reaction might govern the changes in soil enzymatic activity.
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Affiliation(s)
- Michal Choma
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - Karolina Tahovská
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - Eva Kaštovská
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - Jiří Bárta
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - Michal Růžek
- Czech Geological Survey, Department of Environmental Geochemistry and Biogeochemistry, Geologická 6, Prague 5, 152 00, Czech Republic.,Department of Physical Geography, Faculty of Science, Charles University, Albertov 6, 128 43 Prague, Czech Republic
| | - Filip Oulehle
- Czech Geological Survey, Department of Environmental Geochemistry and Biogeochemistry, Geologická 6, Prague 5, 152 00, Czech Republic
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24
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Yu J, Widyaningsih E, Park Y, Lee T. Nitrogen removal and microbial community diversity in single-chamber electroactive biofilm reactors with different ratios of the cathode surface area to reactor volume. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 758:143677. [PMID: 33288255 DOI: 10.1016/j.scitotenv.2020.143677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/23/2020] [Accepted: 11/06/2020] [Indexed: 06/12/2023]
Abstract
Removal of nitrogen compounds is particularly important domestic wastewater treatment. Our recent study reported the successful removal of nitrogen in single-chamber electroactive biofilm reactors (EBRs) under aeration-free conditions. We hypothesized that the oxygen diffused from the air-cathode is a key factor in the removal of nitrogen in the EBR. If so, the effect of the penetrated oxygen would vary according to the ratio of the air-cathode surface area to the reactor volume (AV ratio) and the hydraulic retention time (HRT). In this study, single-chamber EBRs with three different AV ratios: 125 m2/m3 (EBR-125), 250 m2/m3 (EBR-250), and 500 m2/m3 (EBR-500) were evaluated for the removal of nitrogen under different HRTs of 0.5-6 h. The higher the AV ratio, the greater the increase in nitrification. The total nitrogen (TN) removal efficiency of EBR-125 and EBR-250 decreased as the HRT decreased, while that of EBR-500 increased. EBR-250 showed the highest TN removal (62.0%) with well-balanced nitrification (83.9%) and denitrification (75.1%) at an HRT of 6 h. However, EBR-500 appeared to be superior for practical application because it showed a comparable TN removal (59%) at a substantially short HRT of 1 h. The microbial communities that were involved in the nitrogen cycle varied according to whether the biofilms were located on the anodes, separators, and cathodes but were similar among EBRs with different AV ratios. Nitrifying bacteria were detected in the biofilms that were presented on the cathodes (approximately 7.8% of the total phylotypes), while denitrifying bacteria were mainly found in biofilm that were located on the anodes (approximately 23.3%). Anammox bacteria were also detected on the anode (approximately 3.7%) and in the separator biofilms (approximately 1.9%) of all the EBRs. These results suggest that both the A/V ratio and the HRT could affect the counter diffusion of substrates (NH4+ and organic compounds) and oxygen in the biofilms and allow interactions between a diversity of microorganisms for the successful removal of nitrogen in EBRs. These findings are expected to aid in the development of new applications using EBR for energy-saving wastewater treatment.
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Affiliation(s)
- Jaecheul Yu
- Department of Civil and Environmental Engineering, Pusan National University, Busan 46241, Republic of Korea
| | - Evy Widyaningsih
- Department of Civil and Environmental Engineering, Pusan National University, Busan 46241, Republic of Korea
| | - Younghyun Park
- Korea Testing & Research Institute, Ulsan 44412, Republic of Korea
| | - Taeho Lee
- Department of Civil and Environmental Engineering, Pusan National University, Busan 46241, Republic of Korea.
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25
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Complete Genome Sequence of Paludibaculum fermentans P105 T, a Facultatively Anaerobic Acidobacterium Capable of Dissimilatory Fe(III) Reduction. Microbiol Resour Announc 2021; 10:10/1/e01313-20. [PMID: 33414319 PMCID: PMC8407742 DOI: 10.1128/mra.01313-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Paludibaculum fermentans P105T is a facultatively anaerobic heterotroph of the phylum Acidobacteria which is capable of dissimilatory Fe(III) reduction. This bacterium is a common inhabitant of wetlands and groundwater bodies. The finished genome of strain P105T is 9.53 Mb in size and contains multiple genes coding for membrane-bound multiheme cytochromes. Paludibaculum fermentans P105T is a facultatively anaerobic heterotroph of the phylum Acidobacteria which is capable of dissimilatory Fe(III) reduction. This bacterium is a common inhabitant of wetlands and groundwater bodies. The finished genome of strain P105T is 9.53 Mb in size and contains multiple genes coding for membrane-bound multiheme cytochromes.
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26
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Siderite-based anaerobic iron cycle driven by autotrophic thermophilic microbial consortium. Sci Rep 2020; 10:21661. [PMID: 33303863 PMCID: PMC7729950 DOI: 10.1038/s41598-020-78605-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 11/27/2020] [Indexed: 11/14/2022] Open
Abstract
Using a sample from a terrestrial hot spring (pH 6.8, 60 °C), we enriched a thermophilic microbial consortium performing anaerobic autotrophic oxidation of hydrothermal siderite (FeCO3), with CO2/bicarbonate as the electron acceptor and the only carbon source, producing green rust and acetate. In order to reproduce Proterozoic environmental conditions during the deposition of banded iron formation (BIF), we incubated the microbial consortium in a bioreactor that contained an unmixed anoxic layer of siderite, perfectly mixed N2/CO2-saturated liquid medium and microoxic (2% O2) headspace. Long-term incubation (56 days) led to the formation of magnetite (Fe3O4) instead of green rust as the main product of Fe(II) oxidation, the precipitation of newly formed metabolically induced siderite in the anoxic zone, and the deposition of hematite (Fe2O3) on bioreactor walls over the oxycline boundary. Acetate was the only metabolic product of CO2/bicarbonate reduction. Thus, we have demonstrated the ability of autotrophic thermophilic microbial consortium to perform a short cycle of iron minerals transformation: siderite–magnetite–siderite, accompanied by magnetite and hematite accumulation. This cycle is believed to have driven the evolution of the early biosphere, leading to primary biomass production and deposition of the main iron mineral association of BIF.
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27
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Luo F, Li Y, Norgbey E, Li R, Ya Z, Nwankwegu AS, Lie H, Sarpong L. A study on the occurrence of black water in reservoirs in Eucalyptus Plantation region. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:34927-34940. [PMID: 32577983 DOI: 10.1007/s11356-020-09613-3] [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: 05/15/2019] [Accepted: 06/04/2020] [Indexed: 06/11/2023]
Abstract
Tianbao reservoir in southern China (surrounded by Eucalyptus plantation) serves as a source of drinking water for the inhabitants. However, the reservoir water experiences black water (BW) of which the cause remains unclear. In this study, field observation and simulated laboratory experiment were conducted to understand the cause of the BW. The diffusive gradient in thin-film (DGT) device monitored the spatial changes in concentration of iron (Fe2+), manganese (Mn2+), sulfide (S2-), and dissolved organic carbon (DOC) at the SWI. The planar optode (PO) showed that hypoxia contributed immensely to the high positive fluxes Fe2+, Mn2+, and S2- measured, which co-precipitated to form black materials (FeS and MnS) at the SWI. The co-precipitation between Fe-S and Mn-S was supported by their significant positive correlation (Fe-S: r > 0.05, p < 0.05, Mn-S: r > 0.2, p < 0.05). Significant reduction (p < 0.05) in tannins concentration from November (strong thermal stratification) to December (weak thermal stratification) indicated that Fe2+ and tannins reacted during the mixing of reservoir water in December due to weak stratification. The simulated experiment confirmed that fresh Eucalyptus leaves produces a significant (p < 0.05) amount of tannins during hypoxia and reacts with Fe2+ to produce black water. A high positive correlation (r > 0.8) between Fe2+ and DOC demonstrated that Fe2+ and DOC combined and contributed to the reservoir water blackening. The study provides a better understanding on the impact of Eucalyptus plantation on water quality and provide guidance for scientific planting of Eucalyptus plantation in reservoir basins in southern China to ensure safe drinking water.
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Affiliation(s)
- Fan Luo
- Key Laboratory of Integrated Regulation and Resources Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China
- Guangdong Provincial Academy of Environmental Science, Guangzhou, 510045, China
| | - Yiping Li
- Key Laboratory of Integrated Regulation and Resources Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China
| | - Eyram Norgbey
- Key Laboratory of Integrated Regulation and Resources Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China.
- College of Engineering, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana.
| | - Ronghui Li
- Key Laboratory of Integrated Regulation and Resources Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China
- Guangxi Institute of Water Resources Research, Nanning, 530023, China
| | - Zhu Ya
- Key Laboratory of Integrated Regulation and Resources Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China
| | - Amechi S Nwankwegu
- Key Laboratory of Integrated Regulation and Resources Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China
| | - Huang Lie
- Key Laboratory of Integrated Regulation and Resources Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China
| | - Linda Sarpong
- Key Laboratory of Integrated Regulation and Resources Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China
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28
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Characterization of sludge reduction and bacterial community dynamics in a pilot-scale multi-stage digester system with prolonged sludge retention time. Bioprocess Biosyst Eng 2020; 43:1171-1183. [PMID: 32112148 DOI: 10.1007/s00449-020-02312-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 02/13/2020] [Indexed: 10/24/2022]
Abstract
Sludge reduction performance and bacterial community dynamics in a pilot-scale multi-stage digester system with prolonged sludge retention time were characterized. Throughout the operation period of 281 days, the total loading sludge and the total digested sludge were 4700 and 3300 kg-MLSS. After 114 days of operation, the residual MLSS (RMLSS) in the reactors for sludge treatment was maintained at 18-25 kg-RMLSS m-3, and the sludge reduction efficiency achieved 95% under the F/M ratio (kg-loading MLSS kg-RMLSS-1) of less than 0.018. Also, among the sludge components, both fixed suspended solids and volatile suspended solids were reduced. Based on the sludge reduction performance and the RNA-based bacterial community characteristics, the combined action of the maintenance metabolism, lysis-cryptic growth, and particulate inorganic matter is proposed as the sludge reduction mechanism in the multi-stage sludge treatment process.
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29
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Taipale SJ, Peltomaa E, Kukkonen JVK, Kainz MJ, Kautonen P, Tiirola M. Tracing the fate of microplastic carbon in the aquatic food web by compound-specific isotope analysis. Sci Rep 2019; 9:19894. [PMID: 31882692 PMCID: PMC6934716 DOI: 10.1038/s41598-019-55990-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 12/04/2019] [Indexed: 02/05/2023] Open
Abstract
Increasing abundance of microplastics (MP) in marine and freshwaters is currently one of the greatest environmental concerns. Since plastics are fairly resistant to chemical decomposition, breakdown and reutilization of MP carbon complexes requires microbial activity. Currently, only a few microbial isolates have been shown to degrade MPs, and direct measurements of the fate of the MP carbon are still lacking. We used compound-specific isotope analysis to track the fate of fully labelled 13C-polyethylene (PE) MP carbon across the aquatic microbial-animal interface. Isotopic values of respired CO2 and membrane lipids showed that MP carbon was partly mineralized and partly used for cell growth. Microbial mineralization and assimilation of PE-MP carbon was most active when inoculated microbes were obtained from highly humic waters, which contain recalcitrant substrate sources. Mixotrophic algae (Cryptomonas sp.) and herbivorous zooplankton (Daphnia magna) used microbial mediated PE-MP carbon in their cell membrane fatty acids. Moreover, heteronanoflagellates and mixotrophic algae sequestered MP carbon for synthesizing essential ω-6 and ω-3 polyunsaturated fatty acids. Thus, this study demonstrates that aquatic micro-organisms can produce, biochemically upgrade, and trophically transfer nutritionally important biomolecules from PE-MP.
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Affiliation(s)
- S J Taipale
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, P.O. Box 35 (YA), 40014, Jyväskylä, Finland.
| | - E Peltomaa
- Faculty of Biological and Environmental Sciences, Ecosystems and Environment Research programme, University of Helsinki, Niemenkatu 73, Lahti, FI-15140, Finland.,Institute of Atmospheric and Earth System Research (INAR)/Forest Sciences, University of Helsinki, Helsinki, Finland
| | - J V K Kukkonen
- Department of Environmental and Biological Sciences, Kuopio Campus, University of Eastern Finland, P.O. Box 1627, FI-70211, Kuopio, Finland
| | - M J Kainz
- WasserCluster - Biological Station Lunz, Danube University Krems, Dr. Carl Kupelwieser Promenade 5, A-3293, Lunz am See, Austria
| | - P Kautonen
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, P.O. Box 35 (YA), 40014, Jyväskylä, Finland
| | - M Tiirola
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, P.O. Box 35 (YA), 40014, Jyväskylä, Finland
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30
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Lin J, He F, Su B, Sun M, Owens G, Chen Z. The stabilizing mechanism of cadmium in contaminated soil using green synthesized iron oxide nanoparticles under long-term incubation. JOURNAL OF HAZARDOUS MATERIALS 2019; 379:120832. [PMID: 31276925 DOI: 10.1016/j.jhazmat.2019.120832] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 04/08/2019] [Accepted: 06/26/2019] [Indexed: 05/02/2023]
Abstract
Despite numerous studies having been conducted on the stabilization of heavy metal contaminated soil, our understanding of the mechanisms involved remains limited. Here green synthesized iron oxide nanoparticles (GION) were applied to stabilize cadmium (Cd) in a contaminated soil. GION not only stabilized soil Cd, but also improved soil properties within one year of incubation. After GION application both the exchangeable and carbonate bound Cd fractions decreased by 14.2-83.5% and 18.3-85.8% respectively, and most of the Cd was translocated to the residual Cd fraction. The application of GION also strongly altered soil bacterial communities. In GION treatments, the abundance of Gemmatimonadetes, Proteobacteria, and Saccharibacteria increased which led to a shift in the dominant bacterial genera from Bacillus to Candidatus koribacter. The variation in bacteria confirmed the restoration of the contaminated soil. The most abundant bacterial genus and species found in GION treatments were related to (i) plant derived biomass decomposition; (ii) ammoxidation and denitrification; and (iii) Fe oxidation. GION application may enhance the formation of larger soil aggregates with anaerobic centers and coprecipitation coupled Fe (II) oxidization, ammoxidation and nitrite reduction followed by Fe mineral ripening may be involved in Cd stabilization. The predominant stabilization mechanism was thus coprecipitation-ripening-stabilization.
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Affiliation(s)
- Jiajiang Lin
- Fujian Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Fujian Normal University, Fuzhou 350007, China
| | - Fengxin He
- Fujian Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Fujian Normal University, Fuzhou 350007, China
| | - Binglin Su
- Fujian Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Fujian Normal University, Fuzhou 350007, China
| | - Mengqiang Sun
- Fujian Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Fujian Normal University, Fuzhou 350007, China
| | - Gary Owens
- Environmental Contaminants Group, Future Industries Institute, University of South Australia, Mawson Lakes, SA, 5095, Australia
| | - Zuliang Chen
- Fujian Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Fujian Normal University, Fuzhou 350007, China; Environmental Contaminants Group, Future Industries Institute, University of South Australia, Mawson Lakes, SA, 5095, Australia.
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31
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Zhang X, Zhao S, Gao J, Lei Y, Yuan Y, Jiang Y, Xu Z, He C. Microbial action and mechanisms for Cr(VI) removal performance by layered double hydroxide modified zeolite and quartz sand in constructed wetlands. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2019; 246:636-646. [PMID: 31212217 DOI: 10.1016/j.jenvman.2019.06.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 05/30/2019] [Accepted: 06/05/2019] [Indexed: 06/09/2023]
Abstract
This study was conducted to evaluate the performance underlying the removal of hexavalent chromium Cr(VI) associated with Zn-layered double hydroxides (Zn-LDHs)-modified substrates utilized in simulated constructed wetlands (CWs) from a microbial perspective. To accomplish this, Zn-LDHs-modified substrates (zeolite and quartz sand (QS)) were synthesized at various Zn2+/Al3+ and Fe3+ molar ratios by co-precipitation under alkaline conditions. The experimental group was then compared with a control group to determine the microbial action responsible for Cr(VI) removal during the Cr(VI) removal experiments. The removal experiment revealed that the average Cr(VI) removal rates of the Zn-LDHs-modified substrates were superior to those of natural substrates. Subsequent evaluation of the microbial structure by Illumina high-throughput sequencing revealed that the relative abundance of Novosphingobium, Brevundimonas, Methylophilus, and Acidovorax related to Cr(VI) removal was relatively high in Zn-LDHs-modified substrates. Moreover, the extracellular polymeric substance (EPS) content was significantly influenced by the Zn-LDHs coating according to the relative microbial experiments. Similar trends were observed in enzyme activity. Taken together, these findings illustrated that the Zn-LDHs coating had a significant impact on microbial action, and the Cr(VI) removal efficiency of the Zn-LDHs-modified QS (zeolite) substrate was better than that of the natural substrate because of intracellular and extracellular removal mechanisms. Briefly, the microbial action of Zn-LDHs-modified QS played an important role in Cr(VI) removal, since the EPS content possessed the appropriate concentrations. Moreover, the microbial activity of ZnAl-LDHs-modified QS (zeolite) may have been higher than that of ZnFe-LDHs-modified QS (zeolite) because Al had a stronger promoting effect on Cr(VI) bio-removal than Fe. Therefore, the microbial Cr(VI) removal supported by ZnAl-LDHs-modified QS is a better choice for CWs.
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Affiliation(s)
- Xiangling Zhang
- School of Civil Engineering and Architecture, Wuhan University of Technology, Wuhan, 430070, China.
| | - Shuangjie Zhao
- School of Civil Engineering and Architecture, Wuhan University of Technology, Wuhan, 430070, China
| | - Jingtian Gao
- School of Civil Engineering and Architecture, Wuhan University of Technology, Wuhan, 430070, China; School of Energy and Environment, Inner Mongolia University of Science & Technology, Baotou, 014010, China
| | - Yu Lei
- School of Civil Engineering and Architecture, Wuhan University of Technology, Wuhan, 430070, China
| | - Ye Yuan
- School of Civil Engineering and Architecture, Wuhan University of Technology, Wuhan, 430070, China
| | - Yinghe Jiang
- School of Civil Engineering and Architecture, Wuhan University of Technology, Wuhan, 430070, China
| | - Zhouying Xu
- School of Civil Engineering and Architecture, Wuhan University of Technology, Wuhan, 430070, China
| | - Chunyan He
- School of Civil Engineering and Architecture, Wuhan University of Technology, Wuhan, 430070, China
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Ouyang B, Lu X, Li J, Liu H. Microbial reductive transformation of iron-rich tailings in a column reactor and its environmental implications to arsenic reactive transport in mining tailings. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 670:1008-1018. [PMID: 31018416 DOI: 10.1016/j.scitotenv.2019.03.285] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Revised: 03/16/2019] [Accepted: 03/19/2019] [Indexed: 06/09/2023]
Abstract
The evolution of iron minerals under buried conditions is one of the most important processes controlling the mineral composition and heavy metal transportation in sediments. Microbial-mediated reduction plays a critical role in iron mineral transformation in natural environment. This study examined the transformation pathways of iron minerals mediated by bacteria and the changes of associated arsenic species in iron-rich mine tailings. Static and column reactions were designed to monitor variations of minerals and released iron and arsenic, a reactive transport model was simulated to support laboratory results. Laboratory experiments showed that major ferric minerals were preferentially dissolved and reduced by dissimilatory iron-reducing bacteria. The released Fe3+ in fluid promoted oxidative dissolution of pyrite and arsenopyrite, and precipitation of oxides and carbonates. The arsenic released to fluid was inferred to be immobilized by both pristine ferrihydrite and newly formed hydrous ferric oxides via surface complexation. The reaction system maintained a steady-state of iron mineral transformation and arsenic (im)mobilization. In the latter stage of column reactor experiments, continuous reaction and removal of dissolved Fe3+ and Fe2+ destabilized the state, leading to arsenic re-location and eventually rising concentration in fluid. The findings implicate that microbial-mediated iron mineral evolution remarkably influence the natural mineral assemblages and the fate of contaminant transport in the environment, and that deposition of iron oxides is essential in environmental protection and pollution recovery.
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Affiliation(s)
- Bingjie Ouyang
- Earth Sciences Department, Dartmouth College, HB6105 Fairchild Hall, Hanover, NH 03755, United States; Key Laboratory of Surficial Geochemistry of Ministry of Education, School of Earth Sciences and Engineering, Nanjing University, Nanjing, Jiangsu 210046, China
| | - Xiancai Lu
- Key Laboratory of Surficial Geochemistry of Ministry of Education, School of Earth Sciences and Engineering, Nanjing University, Nanjing, Jiangsu 210046, China.
| | - Juan Li
- State Key Laboratory for Deposits research, School of Earth Sciences and Engineering, Nanjing University, Nanjing, Jiangsu 210046, China
| | - Huan Liu
- State Key Laboratory for Deposits research, School of Earth Sciences and Engineering, Nanjing University, Nanjing, Jiangsu 210046, China
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Wieczorek AS, Schmidt O, Chatzinotas A, von Bergen M, Gorissen A, Kolb S. Ecological Functions of Agricultural Soil Bacteria and Microeukaryotes in Chitin Degradation: A Case Study. Front Microbiol 2019; 10:1293. [PMID: 31281293 PMCID: PMC6596343 DOI: 10.3389/fmicb.2019.01293] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 05/23/2019] [Indexed: 11/24/2022] Open
Abstract
Chitin provides a valuable carbon and nitrogen source for soil microorganisms and is a major component of particulate organic matter in agricultural soils. To date, there is no information on interaction and interdependence in chitin-degrading soil microbiomes. Since microbial chitin degradation occurs under both oxic and anoxic conditions and both conditions occur simultaneously in soil, the comparison of the active microbiome members under both conditions can reveal key players for the overall degradation in aerated soil. A time-resolved 16S rRNA stable isotope probing experiment was conducted with soil material from the top soil layer of a wheat-covered field. [13CU]-chitin was largely mineralized within 20 days under oxic conditions. Cellvibrio, Massilia, and several Bacteroidetes families were identified as initially active chitin degraders. Subsequently, Planctomycetes and Verrucomicrobia were labeled by assimilation of 13C carbon either from [13CU]-chitin or from 13C-enriched components of primary chitin degraders. Bacterial predators (e.g., Bdellovibrio and Bacteriovorax) were labeled, too, and non-labeled microeukaryotic predators (Alveolata) increased their relative abundance toward the end of the experiment (70 days), indicating that chitin degraders were subject to predation. Trophic interactions differed substantially under anoxic and oxic conditions. Various fermentation types occurred along with iron respiration. While Acidobacteria and Chloroflexi were the first taxa to be labeled, although at a low 13C level, Firmicutes and uncultured Bacteroidetes were predominantly labeled at a much higher 13C level during the later stages, suggesting that the latter two bacterial taxa were mainly responsible for the degradation of chitin and also provided substrates for iron reducers. Eventually, our study revealed that (1) hitherto unrecognized Bacteria were involved in a chitin-degrading microbial food web of an agricultural soil, (2) trophic interactions were substantially shaped by the oxygen availability, and (3) detectable predation was restricted to oxic conditions. The gained insights into trophic interactions foster our understanding of microbial chitin degradation, which is in turn crucial for an understanding of soil carbon dynamics.
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Affiliation(s)
- Adam S Wieczorek
- Department of Ecological Microbiology, University of Bayreuth, Bayreuth, Germany
| | - Oliver Schmidt
- Department of Ecological Microbiology, University of Bayreuth, Bayreuth, Germany
| | - Antonis Chatzinotas
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany.,German Centre for Integrative Biodiversity Research (iDiv), Leipzig, Germany
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany.,Faculty of Biosciences, Pharmacy and Psychology, Institute of Biochemistry, University of Leipzig, Leipzig, Germany.,Department of Chemistry and Bioscience, University of Aalborg, Aalborg, Denmark
| | | | - Steffen Kolb
- Microbial Biogeochemistry, RA Landscape Functioning, Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany
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34
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Liang Z, Siegert M, Fang W, Sun Y, Jiang F, Lu H, Chen GH, Wang S. Blackening and odorization of urban rivers: a bio-geochemical process. FEMS Microbiol Ecol 2019; 94:4780270. [PMID: 29293959 DOI: 10.1093/femsec/fix180] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 12/23/2017] [Indexed: 11/14/2022] Open
Abstract
Urban rivers constitute a major part of urban drainage systems, and play critical roles in connecting other surface waters in urban areas. Black-odorous urban rivers are widely found in developing countries experiencing rapid urbanization, and the mismatch between urbanization and sewage treatment is thought to be the reason. The phenomena of blackening and odorization are likely complex bio-geochemical processes of which the microbial interactions with the environment are not fully understood. Here, we provide an overview of the major chemical compounds, such as iron and sulfur, and their bio-geochemical conversions during blackening and odorization of urban rivers. Scenarios explaining the formation of black-odorous urban rivers are proposed. Finally, we point out knowledge gaps in mechanisms and microbial ecology that need to be addressed to better understand the development of black-odorous urban rivers.
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Affiliation(s)
- Zhiwei Liang
- Environmental Microbiome Research Center and the School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Guangzhou, China
| | - Michael Siegert
- Environmental Microbiome Research Center and the School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Guangzhou, China.,Department of Geoscience, University of Calgary, Calgary, Canada
| | - Wenwen Fang
- Environmental Microbiome Research Center and the School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Guangzhou, China
| | - Yu Sun
- Environmental Microbiome Research Center and the School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Guangzhou, China
| | - Feng Jiang
- School of Chemistry and Environment, South China Normal University, Guangzhou, China
| | - Hui Lu
- Environmental Microbiome Research Center and the School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Guangzhou, China
| | - Guang-Hao Chen
- Department of Civil and Environmental Engineering, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Shanquan Wang
- Environmental Microbiome Research Center and the School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Guangzhou, China
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35
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Dedysh SN, Yilmaz P. Refining the taxonomic structure of the phylum Acidobacteria. Int J Syst Evol Microbiol 2018; 68:3796-3806. [DOI: 10.1099/ijsem.0.003062] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
- Svetlana N. Dedysh
- 1Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Pelin Yilmaz
- 2Microbial Physiology Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
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36
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Hao L, Zhang B, Feng C, Zhang Z, Lei Z, Shimizu K, Cao X, Liu H, Liu H. Microbial vanadium (V) reduction in groundwater with different soils from vanadium ore mining areas. CHEMOSPHERE 2018; 202:272-279. [PMID: 29571148 DOI: 10.1016/j.chemosphere.2018.03.075] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 02/19/2018] [Accepted: 03/11/2018] [Indexed: 06/08/2023]
Abstract
This work investigated the potential of vanadium (V) (V(V)) bioreduction by using soils sampled from four main kinds of vanadium ore mining areas, i.e. vanadium titanomagnetite, stone coal, petroleum associated minerals and uvanite as inocula. During a typical operation cycle of 60 h, the soils from vanadium titanomagnetite area and petroleum associated minerals area exhibited higher V(V) removal efficiencies, about 92.0 ± 2.0% and 91.0 ± 1.9% in comparison to 87.1 ± 1.9% and 69.0 ± 1.1% for the soils from uvanite and stone coal areas, respectively. Results from high-throughput 16 S rRNA gene pyrosequencing analysis reflect the accumulation of Bryobacter and Acidobacteriaceae with capabilities of V(V) reduction, accompanied with other functional species. This study is helpful to search new functional species for V(V) reduction and to develop in situ bioremediations of V(V) polluted groundwater.
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Affiliation(s)
- Liting Hao
- School of Water Resources and Environment, China University of Geosciences Beijing, Key Laboratory of Groundwater Circulation and Evolution (China University of Geosciences Beijing), Ministry of Education, Beijing, 100083, China
| | - Baogang Zhang
- School of Water Resources and Environment, China University of Geosciences Beijing, Key Laboratory of Groundwater Circulation and Evolution (China University of Geosciences Beijing), Ministry of Education, Beijing, 100083, China.
| | - Chuanping Feng
- School of Water Resources and Environment, China University of Geosciences Beijing, Key Laboratory of Groundwater Circulation and Evolution (China University of Geosciences Beijing), Ministry of Education, Beijing, 100083, China
| | - Zhenya Zhang
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305- 8572, Japan
| | - Zhongfang Lei
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305- 8572, Japan
| | - Kazuya Shimizu
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305- 8572, Japan
| | - Xuelong Cao
- School of Water Resources and Environment, China University of Geosciences Beijing, Key Laboratory of Groundwater Circulation and Evolution (China University of Geosciences Beijing), Ministry of Education, Beijing, 100083, China
| | - Hui Liu
- School of Water Resources and Environment, China University of Geosciences Beijing, Key Laboratory of Groundwater Circulation and Evolution (China University of Geosciences Beijing), Ministry of Education, Beijing, 100083, China
| | - Huipeng Liu
- School of Water Resources and Environment, China University of Geosciences Beijing, Key Laboratory of Groundwater Circulation and Evolution (China University of Geosciences Beijing), Ministry of Education, Beijing, 100083, China
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37
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Hausmann B, Pelikan C, Herbold CW, Köstlbacher S, Albertsen M, Eichorst SA, Glavina Del Rio T, Huemer M, Nielsen PH, Rattei T, Stingl U, Tringe SG, Trojan D, Wentrup C, Woebken D, Pester M, Loy A. Peatland Acidobacteria with a dissimilatory sulfur metabolism. THE ISME JOURNAL 2018; 12:1729-1742. [PMID: 29476143 PMCID: PMC6018796 DOI: 10.1038/s41396-018-0077-1] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 12/21/2017] [Accepted: 01/20/2018] [Indexed: 12/25/2022]
Abstract
Sulfur-cycling microorganisms impact organic matter decomposition in wetlands and consequently greenhouse gas emissions from these globally relevant environments. However, their identities and physiological properties are largely unknown. By applying a functional metagenomics approach to an acidic peatland, we recovered draft genomes of seven novel Acidobacteria species with the potential for dissimilatory sulfite (dsrAB, dsrC, dsrD, dsrN, dsrT, dsrMKJOP) or sulfate respiration (sat, aprBA, qmoABC plus dsr genes). Surprisingly, the genomes also encoded DsrL, which so far was only found in sulfur-oxidizing microorganisms. Metatranscriptome analysis demonstrated expression of acidobacterial sulfur-metabolism genes in native peat soil and their upregulation in diverse anoxic microcosms. This indicated an active sulfate respiration pathway, which, however, might also operate in reverse for dissimilatory sulfur oxidation or disproportionation as proposed for the sulfur-oxidizing Desulfurivibrio alkaliphilus. Acidobacteria that only harbored genes for sulfite reduction additionally encoded enzymes that liberate sulfite from organosulfonates, which suggested organic sulfur compounds as complementary energy sources. Further metabolic potentials included polysaccharide hydrolysis and sugar utilization, aerobic respiration, several fermentative capabilities, and hydrogen oxidation. Our findings extend both, the known physiological and genetic properties of Acidobacteria and the known taxonomic diversity of microorganisms with a DsrAB-based sulfur metabolism, and highlight new fundamental niches for facultative anaerobic Acidobacteria in wetlands based on exploitation of inorganic and organic sulfur molecules for energy conservation.
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Affiliation(s)
- Bela Hausmann
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Claus Pelikan
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
| | - Craig W Herbold
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
| | - Stephan Köstlbacher
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
| | - Mads Albertsen
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | - Stephanie A Eichorst
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
| | | | - Martin Huemer
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
| | - Per H Nielsen
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | - Thomas Rattei
- Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
| | - Ulrich Stingl
- Department for Microbiology and Cell Science, Fort Lauderdale Research and Education Center, UF/IFAS, University of Florida, Davie, FL, USA
| | - Susannah G Tringe
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Daniela Trojan
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
| | - Cecilia Wentrup
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
| | - Dagmar Woebken
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
| | - Michael Pester
- Department of Biology, University of Konstanz, Konstanz, Germany.
- Leibniz Institute DSMZ, Braunschweig, Germany.
| | - Alexander Loy
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
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38
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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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Vieira S, Luckner M, Wanner G, Overmann J. Luteitalea pratensis gen. nov., sp. nov. a new member of subdivision 6 Acidobacteria isolated from temperate grassland soil. Int J Syst Evol Microbiol 2017; 67:1408-1414. [PMID: 28141504 DOI: 10.1099/ijsem.0.001827] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Albeit being widespread and abundant in soils worldwide, bacteria of the phylum Acidobacteria have remained grossly understudied due to difficulties in their cultivation and isolation. To date, only 48 species have been validly described, including a single member of the phylogenetically diverse Acidobacteria subdivision 6. Here, we report the polyphasic characterization of strain HEG_-6_39T, a novel representative of Acidobacteria subdivision 6 isolated from a grassland soil in Thuringia, Germany. Cells of HEG_-6_39T are Gram-stain-negative, non-motile, non-spore-forming, non-capsulated short rods that form small dark yellow colonies. This slow growing bacterium is psychrotolerant and grows between 0 and 36 °C. It displays a narrower pH tolerance (5.3-8.3) than most acidobacteria. The strain is an aerobe that grows chemo-organotrophically utilizing mostly sugars and proteinaceous substrates such as peptone, yeast extract, casein hydrolysate and casamino acids as substrates. Diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol and two unknown phospholipids are identified as polar lipids. Major fatty acids are iso-C15 : 0, summed feature 3 (C16 : 1ω6c/C16 : 1ω7c), C18 : 1ω9c and iso-C17 : 1ω9c. The major respiratory quinone is MK-8. The G+C content of the genomic DNA is 64.7 mol%. 16S rRNA gene sequence analysis indicated that this bacterium was related to Vicinamibacter silvestris Ac_5_C6T with 93.6 % sequence similarity. Based on the present taxonomic characterization, strain HEG_-6_39T represents a new species of a novel genus for which the name Luteitalea pratensis gen. nov., sp. nov., is proposed. The type strain of the type species is HEG_-6_39T (=DSM 100886T=KCTC 52215T).
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Affiliation(s)
- Selma Vieira
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Manja Luckner
- Department of Biology I, Biozentrum Ludwig Maximilian University of Munich, Großhaderner Str. 2, 82152, Planegg-Martinsried, Germany
| | - Gerhard Wanner
- Department of Biology I, Biozentrum Ludwig Maximilian University of Munich, Großhaderner Str. 2, 82152, Planegg-Martinsried, Germany
| | - Jörg Overmann
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany.,Braunschweig University of Technology, Braunschweig, Germany
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40
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Dedysh SN, Kulichevskaya IS, Huber KJ, Overmann J. Defining the taxonomic status of described subdivision 3 Acidobacteria: proposal of Bryobacteraceae fam. nov. Int J Syst Evol Microbiol 2017; 67:498-501. [PMID: 27902282 DOI: 10.1099/ijsem.0.001687] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The phylum Acidobacteria represents one of the highly diverse but poorly characterized phylogenetic groups of the domain Bacteria. The taxonomically described acidobacteria belong to 27 genera and 49 species, which represent subdivisions 1, 3, 4, 6, 8, 10 and 23 of this phylum. However, the corresponding family ranks have been defined only for some of these characterized micro-organisms. Here, we suggest the establishment of a novel family, Bryobacteraceae fam. nov., to accommodate taxonomically described members of subdivision 3 Acidobacteria. This family is characterized by Gram-stain-negative, non-spore-forming and non-motile rods, which divide by binary fission. Members of this family are mildly acidophilic, mesophilic, aerobic and facultatively anaerobic chemoheterotrophs that utilize various sugars and polysaccharides. The major fatty acids are iso-C15 : 0 and C16 : 1ω7c; the cells also contain significant amounts of 13,16-dimethyloctacosanedioic (iso-diabolic) acid. Currently, the family comprises the genera Bryobacter and Paludibaculum.
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Affiliation(s)
- Svetlana N Dedysh
- 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
| | - Katharina J Huber
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Jörg Overmann
- Braunschweig University of Technology, Braunschweig, Germany
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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41
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Distinct Anaerobic Bacterial Consumers of Cellobiose-Derived Carbon in Boreal Fens with Different CO2/CH4 Production Ratios. Appl Environ Microbiol 2017; 83:AEM.02533-16. [PMID: 27913414 DOI: 10.1128/aem.02533-16] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 11/28/2016] [Indexed: 11/20/2022] Open
Abstract
Northern peatlands in general have high methane (CH4) emissions, but individual peatlands show considerable variation as CH4 sources. Particularly in nutrient-poor peatlands, CH4 production can be low and exceeded by carbon dioxide (CO2) production from unresolved anaerobic processes. To clarify the role anaerobic bacterial degraders play in this variation, we compared consumers of cellobiose-derived carbon in two fens differing in nutrient status and the ratio of CO2 to CH4 produced. After [13C]cellobiose amendment, the mesotrophic fen produced equal amounts of CH4 and CO2 The oligotrophic fen had lower CH4 production but produced 3 to 59 times more CO2 than CH4 RNA stable-isotope probing revealed that in the mesotrophic fen with higher CH4 production, cellobiose-derived carbon was mainly assimilated by various recognized fermenters of Firmicutes and by Proteobacteria The oligotrophic peat with excess CO2 production revealed a wider variety of cellobiose-C consumers, including Firmicutes and Proteobacteria, but also more unconventional degraders, such as Telmatobacter-related Acidobacteria and subphylum 3 of Verrucomicrobia Prominent and potentially fermentative Planctomycetes and Chloroflexi did not appear to process cellobiose-C. Our results show that anaerobic degradation resulting in different levels of CH4 production can involve distinct sets of bacterial degraders. By distinguishing cellobiose degraders from the total community, this study contributes to defining anaerobic bacteria that process cellulose-derived carbon in peat. Several of the identified degraders, particularly fermenters and potential Fe(III) or humic substance reducers in the oligotrophic peat, represent promising candidates for resolving the origin of excess CO2 production in peatlands. IMPORTANCE Peatlands are major sources of the greenhouse gas methane (CH4), yet in many peatlands, CO2 production from unresolved anaerobic processes exceeds CH4 production. Anaerobic degradation produces the precursors of CH4 production but also represents competing processes. We show that anaerobic degradation leading to high or low CH4 production involved distinct sets of bacteria. Well-known fermenters dominated in a peatland with high CH4 production, while novel and unconventional degraders could be identified in a site where CO2 production greatly exceeds CH4 production. Our results help identify and assign functions to uncharacterized bacteria that promote or inhibit CH4 production and reveal bacteria potentially producing the excess CO2 in acidic peat. This study contributes to understanding the microbiological basis for different levels of CH4 emission from peatlands.
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Ji Y, Angel R, Klose M, Claus P, Marotta H, Pinho L, Enrich-Prast A, Conrad R. Structure and function of methanogenic microbial communities in sediments of Amazonian lakes with different water types. Environ Microbiol 2016; 18:5082-5100. [PMID: 27507000 DOI: 10.1111/1462-2920.13491] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 08/06/2016] [Indexed: 11/28/2022]
Abstract
Tropical lake sediments are a significant source for the greenhouse gas methane. We studied function (pathway, rate) and structure (abundance, taxonomic composition) of the microbial communities (Bacteria, Archaea) leading to methane formation together with the main physicochemical characteristics in the sediments of four clear water, six white water and three black water lakes of the Amazon River system. Concentrations of sulfate and ferric iron, pH and δ13 C of organic carbon were usually higher, while concentrations of carbon, nitrogen and rates of CH4 production were generally lower in white water versus clear water or black water sediments. Copy numbers of bacterial and especially archaeal ribosomal RNA genes also tended to be relatively lower in white water sediments. Hydrogenotrophic methanogenesis contributed 58 ± 16% to total CH4 production in all systems. Network analysis identified six communities, of which four were comprised mostly of bacteria found in all sediment types, while two were mostly in clear water sediment. Terminal restriction fragment length polymorphism (T-RFLP) and pyrosequencing showed that the compositions of the communities differed between the different sediment systems, statistically related to the particular physicochemical conditions and to CH4 production rates. Among the archaea, clear water, white water, and black water sediments contained relatively more Methanomicrobiales, Methanosarcinaceae and Methanocellales, respectively, while Methanosaetaceae were common in all systems. Proteobacteria, Deltaproteobacteria (Myxococcales, Syntrophobacterales, sulfate reducers) in particular, Acidobacteria and Firmicutes were the most abundant bacterial phyla in all sediment systems. Among the other important bacterial phyla, clear water sediments contained relatively more Alphaproteobacteria and Planctomycetes, whereas white water sediments contained relatively more Betaproteobacteria, Firmicutes, Actinobacteria, and Chloroflexi than the respective other sediment systems. The data showed communities of bacteria common to all sediment types, but also revealed microbial groups that were significantly different between the sediment types, which also differed in physicochemical conditions. Our study showed that function of the microbial communities may be understood on the basis of their structures, which in turn are determined by environmental heterogeneity.
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Affiliation(s)
- Yang Ji
- Jiangsu Key Laboratory of Agricultural Meteorology, College of Applied Meteorology, Nanjing University of Information Science & Technology, Ningliu Road 219, Nanjing, 210044, China.,Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, Marburg, 35043, Germany
| | - Roey Angel
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network Chemistry meets Microbiology, University of Vienna, Althanstrasse 14, Vienna, 1090, Austria
| | - Melanie Klose
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, Marburg, 35043, Germany
| | - Peter Claus
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, Marburg, 35043, Germany
| | - Humberto Marotta
- Laboratório de Biogeoquímica, Departamento de Ecologia, Instituto de Biologia, University Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.,Graduated Program in Geosciences (Geochemistry), Graduated Program in Geography, Research Center on Biomass and Water Management (NAB/UFF), Sedimentary Environmental Processes Laboratory (LAPSA/UFF), International Laboratory of Global Change (LINC-Global), Fluminense Federal University (UFF), Niterói, Brazil
| | - Luana Pinho
- Department of Chemical Oceanography, Rio de Janeiro State University, Pavilhão João Lyra Filho, sala 4008 Bloco E, Rua São Francisco Xavier, 524, Maracanã-RJ, 20550-900, Brazil
| | - Alex Enrich-Prast
- Laboratório de Biogeoquímica, Departamento de Ecologia, Instituto de Biologia, University Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.,Department of Environmental Change, Linköping University, Linköping, Sweden
| | - Ralf Conrad
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, Marburg, 35043, Germany
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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: 426] [Impact Index Per Article: 53.3] [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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Huber KJ, Geppert AM, Wanner G, Fösel BU, Wüst PK, Overmann J. The first representative of the globally widespread subdivision 6 Acidobacteria,Vicinamibacter silvestris gen. nov., sp. nov., isolated from subtropical savannah soil. Int J Syst Evol Microbiol 2016; 66:2971-2979. [PMID: 27150379 DOI: 10.1099/ijsem.0.001131] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Members of the phylum Acidobacteria are abundant in a wide variety of soil environments. Despite this, previous cultivation attempts have frequently failed to retrieve representative phylotypes of Acidobacteria, which have, therefore, been discovered by culture-independent methods (13175 acidobacterial sequences in the SILVA database version 123; NR99) and only 47 species have been described so far. Strain Ac_5_C6T represents the first isolate of the globally widespread and abundant subdivision 6 Acidobacteria and is described in the present study. Cells of strain Ac_5_C6T were Gram-stain-negative, immotile rods that divided by binary fission. They formed yellow, extremely cohesive colonies and stable aggregates even in rapidly shaken liquid cultures. Ac_5_C6T was tolerant of a wide range of temperatures (12-40 °C) and pH values (4.7-9.0). It grew chemoorganoheterotrophically on a broad range of substrates including different sugars, organic acids, nucleic acids and complex proteinaceous compounds. The major fatty acids of Ac_5_C6T were iso-C17 : 1 ω9c, C18 : 1 ω7c and iso-C15 : 0. Summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c), iso-C17 : 0 and C16 : 0 were also detected. Phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and an unidentified glycolipid were identified as polar lipids. The major quinone was MK-8. The DNA G+C content of Ac_5_C6T was 65.9 mol%. With 16S rRNA gene sequence similarities of 83-84 %, the closest described relatives were Acidicapsa borealis KA1T, Acidobacterium capsulatum 161T, Granulicella pectinovorans TPB6011T, Occallatibacter riparius 277T and Paludibaculum fermentans P105T. According to the morphological, physiological and molecular characteristics, the novel genus Vicinamibacter gen. nov., and the novel species, Vicinamibacter silvestris sp. nov. (type strain Ac_5_C6T = DSM 29464T = LMG 29035T) are proposed.
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Affiliation(s)
- Katharina J Huber
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Alicia M Geppert
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Gerhard Wanner
- Department of Biology I, Biozentrum Ludwig Maximilian University of Munich, Planegg-Martinsried, Germany
| | - Bärbel U Fösel
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Pia K Wüst
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Jörg Overmann
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.,Technical University Braunschweig, Braunschweig, Germany
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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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