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Zhuo S, Jiang Y, Qi L, Hu Y, Jiang Z, Dong Y, Shi L. The robustness of porin-cytochrome gene clusters from Geobacter metallireducens in extracellular electron transfer. mBio 2024:e0058024. [PMID: 39092920 DOI: 10.1128/mbio.00580-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 07/03/2024] [Indexed: 08/04/2024] Open
Abstract
To investigate their roles in extracellular electron transfer (EET), the porin-cytochrome (pcc) gene clusters Gmet0825-0828, Gmet0908-0910, and Gmet0911-0913 of the Gram-negative bacterium Geobacter metallireducens were deleted. Failure to delete all pcc gene clusters at the same time suggested their essential roles in extracellular reduction of Fe(III)-citrate by G. metallireducens. Deletion of Gmet0825-0828 had no impact on bacterial reduction of Fe(III)-citrate but diminished bacterial reduction of ferrihydrite and abolished anode reduction and direct interspecies electron transfer (DIET) to Methanosarcina barkeri and Geobacter sulfurreducens. Although it had no impact on the bacterial reduction of Fe(III)-citrate, deletion of Gmet0908-0910 delayed ferrihydrite reduction, abolished anode reduction, and diminished DIET. Deletion of Gmet0911-0913 had little impact on DIET but diminished bacterial reductions of Fe(III)-citrate, ferrihydrite, and anodes. Most importantly, deletions of both Gmet0825-0828 and Gmet0908-0910 restored bacterial reduction of ferrihydrite and anodes and DIET. Enhanced expression of Gmet0911-0913 in this double mutant when grown in coculture with G. sulfurreducens ΔhybLΔfdnG suggested that this cluster might compensate for impaired EET functions of deleting Gmet0825-0828 and Gmet0908-0910. Thus, these pcc gene clusters played essential, distinct, overlapping, and compensatory roles in EET of G. metallireducens that are difficult to characterize as deletion of some clusters affected expression of others. The robustness of these pcc gene clusters enabled G. metallireducens to mediate EET to different acceptors for anaerobic growth even when two of its three pcc gene clusters were inactivated by mutation. The results from this investigation provide new insights into the roles of pcc gene clusters in bacterial EET. IMPORTANCE The Gram-negative bacterium Geobacter metallireducens is of environmental and biotechnological significance. Crucial to the unique physiology of G. metallireducens is its extracellular electron transfer (EET) capability. This investigation sheds new light on the robust roles of the three porin-cytochrome (pcc) gene clusters, which are directly involved in EET across the bacterial outer membrane, in the EET of G. metallireducens. In addition to their essential roles, these gene clusters also play distinct, overlapping, and compensatory roles in the EET of G. metallireducens. The distinct roles of the pcc gene clusters enable G. metallireducens to mediate EET to a diverse group of electron acceptors for anaerobic respirations. The overlapping and compensatory roles of the pcc gene clusters enable G. metallireducens to maintain and restore its EET capability for anaerobic growth when one or two of its three pcc gene clusters are deleted from the genome.
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Affiliation(s)
- Shiyan Zhuo
- Department of Biological Sciences and Technology, School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Yongguang Jiang
- Department of Biological Sciences and Technology, School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Lei Qi
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yidan Hu
- Department of Biological Sciences and Technology, School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Zhou Jiang
- Department of Biological Sciences and Technology, School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Yiran Dong
- Department of Biological Sciences and Technology, School of Environmental Studies, China University of Geosciences, Wuhan, China
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
- State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution, Ministry of Ecology and Environment, China University of Geosciences, Wuhan, China
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, China University of Geosciences, Wuhan, China
| | - Liang Shi
- Department of Biological Sciences and Technology, School of Environmental Studies, China University of Geosciences, Wuhan, China
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
- State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution, Ministry of Ecology and Environment, China University of Geosciences, Wuhan, China
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, China University of Geosciences, Wuhan, China
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Harnisch F, Deutzmann JS, Boto ST, Rosenbaum MA. Microbial electrosynthesis: opportunities for microbial pure cultures. Trends Biotechnol 2024; 42:1035-1047. [PMID: 38431514 PMCID: PMC11310912 DOI: 10.1016/j.tibtech.2024.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 02/05/2024] [Accepted: 02/05/2024] [Indexed: 03/05/2024]
Abstract
Microbial electrosynthesis (MES) is an emerging technology that couples renewable electricity to microbial production processes. Although advances in MES performance have been driven largely by microbial mixed cultures, we see a great limitation in the diversity, and hence value, of products that can be achieved in undefined mixed cultures. By contrast, metabolic control of pure cultures and genetic engineering could greatly expand the scope of MES, and even of broader electrobiotechnology, to include targeted high-value products. To leverage this potential, we advocate for more efforts and activities to develop engineered electroactive microbes for synthesis, and we highlight the need for a standardized electrobioreactor infrastructure that allows the establishment and engineering of electrobioprocesses with these novel biocatalysts.
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Affiliation(s)
- Falk Harnisch
- Department of Microbial Biotechnology, Helmholtz Centre for Environmental Research GmbH, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Jörg S Deutzmann
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, USA
| | - Santiago T Boto
- Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knöll-Institute, Adolf Reichwein Strasse 23, 07745 Jena, Germany; Institute of Microbiology, Faculty for Biological Sciences, Friedrich-Schiller-University Jena, Neugasse 23, 07743 Jena, Germany
| | - Miriam A Rosenbaum
- Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knöll-Institute, Adolf Reichwein Strasse 23, 07745 Jena, Germany; Institute of Microbiology, Faculty for Biological Sciences, Friedrich-Schiller-University Jena, Neugasse 23, 07743 Jena, Germany.
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Stewart DI, Vasconcelos EJR, Burke IT, Baker A. Metagenomes from microbial populations beneath a chromium waste tip give insight into the mechanism of Cr (VI) reduction. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 931:172507. [PMID: 38657818 DOI: 10.1016/j.scitotenv.2024.172507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 04/04/2024] [Accepted: 04/13/2024] [Indexed: 04/26/2024]
Abstract
Dumped Chromium Ore Processing Residue (COPR) at legacy sites poses a threat to health through leaching of toxic Cr(VI) into groundwater. Previous work implicates microbial activity in reducing Cr(VI) to less mobile and toxic Cr(III), but the mechanism has not been explored. To address this question a combined metagenomic and geochemical study was undertaken. Soil samples from below the COPR waste were used to establish anaerobic microcosms which were challenged with Cr(VI), with or without acetate as an electron donor, and incubated for 70 days. Cr was rapidly reduced in both systems, which also reduced nitrate, nitrite then sulfate, but this sequence was accelerated in the acetate amended microcosms. 16S rRNA gene sequencing revealed that the original soil sample was diverse but both microcosm systems became less diverse by the end of the experiment. A high proportion of 16S rRNA gene reads and metagenome-assembled genomes (MAGs) with high completeness could not be taxonomically classified, highlighting the distinctiveness of these alkaline Cr impacted systems. Examination of the coding capacity revealed widespread capability for metal tolerance and Fe uptake and storage, and both populations possessed metabolic capability to degrade a wide range of organic molecules. The relative abundance of genes for fatty acid degradation was 4× higher in the unamended compared to the acetate amended system, whereas the capacity for dissimilatory sulfate metabolism was 3× higher in the acetate amended system. We demonstrate that naturally occurring in situ bacterial populations have the metabolic capability to couple acetate oxidation to sequential reduction of electron acceptors which can reduce Cr(VI) to less mobile and toxic Cr(III), and that microbially produced sulfide may be important in reductive precipitation of chromate. This capability could be harnessed to create a Cr(VI) trap-zone beneath COPR tips without the need to disturb the waste.
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Affiliation(s)
- Douglas I Stewart
- School of Civil Engineering, University of Leeds, Leeds LS2 9JT, UK.
| | | | - Ian T Burke
- School of Earth and Environment, University of Leeds, Leeds LS2 9JT, UK.
| | - Alison Baker
- School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK.
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Masuda Y, Mise K, Xu Z, Zhang Z, Shiratori Y, Senoo K, Itoh H. Global soil metagenomics reveals distribution and predominance of Deltaproteobacteria in nitrogen-fixing microbiome. MICROBIOME 2024; 12:95. [PMID: 38790049 PMCID: PMC11127431 DOI: 10.1186/s40168-024-01812-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 04/09/2024] [Indexed: 05/26/2024]
Abstract
BACKGROUND Biological nitrogen fixation is a fundamental process sustaining all life on earth. While distribution and diversity of N2-fixing soil microbes have been investigated by numerous PCR amplicon sequencing of nitrogenase genes, their comprehensive understanding has been hindered by lack of de facto standard protocols for amplicon surveys and possible PCR biases. Here, by fully leveraging the planetary collections of soil shotgun metagenomes along with recently expanded culture collections, we evaluated the global distribution and diversity of terrestrial diazotrophic microbiome. RESULTS After the extensive analysis of 1,451 soil metagenomic samples, we revealed that the Anaeromyxobacteraceae and Geobacteraceae within Deltaproteobacteria are ubiquitous groups of diazotrophic microbiome in the soils with different geographic origins and land usage types, with particular predominance in anaerobic soils (paddy soils and sediments). CONCLUSION Our results indicate that Deltaproteobacteria is a core bacterial taxon in the potential soil nitrogen fixation population, especially in anaerobic environments, which encourages a careful consideration on deltaproteobacterial diazotrophs in understanding terrestrial nitrogen cycling. Video Abstract.
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Affiliation(s)
- Yoko Masuda
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.
| | - Kazumori Mise
- National Institute of Advanced Industrial Science and Technology (AIST) Hokkaido, 2-17-2-1 Tsukisamu-higashi, Toyohira, Sapporo, Hokkaido, 062-8517, Japan.
| | - Zhenxing Xu
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Zhengcheng Zhang
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yutaka Shiratori
- Niigata Agricultural Research Institute, 857 Nagakura-machi, Nagaoka, Niigata, 940-0826, Japan
| | - Keishi Senoo
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Hideomi Itoh
- National Institute of Advanced Industrial Science and Technology (AIST) Hokkaido, 2-17-2-1 Tsukisamu-higashi, Toyohira, Sapporo, Hokkaido, 062-8517, Japan.
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Li X, Huang X, Hu X, Chong Y. Effects of hematite on two types of dissolved organic compounds in lignocellulosic anaerobic hydrolysate: Lignin-derived aromatic compounds and denitrifying carbon sources. BIORESOURCE TECHNOLOGY 2024; 399:130606. [PMID: 38499201 DOI: 10.1016/j.biortech.2024.130606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 03/06/2024] [Accepted: 03/15/2024] [Indexed: 03/20/2024]
Abstract
The utilization of anaerobic hydrolysate from agroforestry wastes is limited by dissolved lignin and aromatics, which have received insufficient attention despite their potential as excellent carbon sources for denitrification. This study aims to investigate the influence of hematite on lignin-derived aromatic compounds and denitrifying carbon sources, as well as to identify iron-reducing bacteria that utilize lignin-derived aromatic compounds as electron donors. The findings revealed that hematite facilitated the anaerobic fermentation of plant biomass, resulting in the production of small molecular organic acids. Moreover, biodegradation of lignin-derived aromatic compounds led to the formation of phenolic acids, while an increased generation of denitrifying carbon sources enhanced nitrogen removal efficiency by 13.84 %. Additionally, due to adsorption by hematite and subsequent microbial degradation, there was a significant improvement (40.32%) in color removal rate within denitrification effluent. Notably, Azonexus strains were hypothesized to be involved in Fe(Ⅲ) reduction coupled with aromatic compounds oxidation.
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Affiliation(s)
- Xinjing Li
- Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Xiangwei Huang
- Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Xingbao Hu
- Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Yunxiao Chong
- Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China.
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Xie J, Zhao Z, Coker VS, O'Driscoll B, Cai R, Haigh SJ, Holmes SM, Lloyd JR. Bioproduction of cerium-bearing magnetite and application to improve carbon-black supported platinum catalysts. J Nanobiotechnology 2024; 22:203. [PMID: 38659001 PMCID: PMC11041677 DOI: 10.1186/s12951-024-02464-x] [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: 10/09/2023] [Accepted: 04/04/2024] [Indexed: 04/26/2024] Open
Abstract
BACKGROUND Biogeochemical processing of metals including the fabrication of novel nanomaterials from metal contaminated waste streams by microbial cells is an area of intense interest in the environmental sciences. RESULTS Here we focus on the fate of Ce during the microbial reduction of a suite of Ce-bearing ferrihydrites with between 0.2 and 4.2 mol% Ce. Cerium K-edge X-ray absorption near edge structure (XANES) analyses showed that trivalent and tetravalent cerium co-existed, with a higher proportion of tetravalent cerium observed with increasing Ce-bearing of the ferrihydrite. The subsurface metal-reducing bacterium Geobacter sulfurreducens was used to bioreduce Ce-bearing ferrihydrite, and with 0.2 mol% and 0.5 mol% Ce, an Fe(II)-bearing mineral, magnetite (Fe(II)(III)2O4), formed alongside a small amount of goethite (FeOOH). At higher Ce-doping (1.4 mol% and 4.2 mol%) Fe(III) bioreduction was inhibited and goethite dominated the final products. During microbial Fe(III) reduction Ce was not released to solution, suggesting Ce remained associated with the Fe minerals during redox cycling, even at high Ce loadings. In addition, Fe L2,3 X-ray magnetic circular dichroism (XMCD) analyses suggested that Ce partially incorporated into the Fe(III) crystallographic sites in the magnetite. The use of Ce-bearing biomagnetite prepared in this study was tested for hydrogen fuel cell catalyst applications. Platinum/carbon black electrodes were fabricated, containing 10% biomagnetite with 0.2 mol% Ce in the catalyst. The addition of bioreduced Ce-magnetite improved the electrode durability when compared to a normal Pt/CB catalyst. CONCLUSION Different concentrations of Ce can inhibit the bioreduction of Fe(III) minerals, resulting in the formation of different bioreduction products. Bioprocessing of Fe-minerals to form Ce-containing magnetite (potentially from waste sources) offers a sustainable route to the production of fuel cell catalysts with improved performance.
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Affiliation(s)
- Jinxin Xie
- Department of Earth and Environmental Sciences, The University of Manchester, Manchester, UK.
| | - Ziyu Zhao
- Department of Chemical Engineering, The University of Manchester, Manchester, UK
| | - Victoria S Coker
- Department of Earth and Environmental Sciences, The University of Manchester, Manchester, UK
| | - Brian O'Driscoll
- Department of Earth and Environmental Sciences, The University of Manchester, Manchester, UK
- Department of Earth and Environmental Sciences, The University of Ottawa, Ottawa, Canada
| | - Rongsheng Cai
- Department of Materials, The University of Manchester, Manchester, UK
| | - Sarah J Haigh
- Department of Materials, The University of Manchester, Manchester, UK
| | - Stuart M Holmes
- Department of Chemical Engineering, The University of Manchester, Manchester, UK
| | - Jonathan R Lloyd
- Department of Earth and Environmental Sciences, The University of Manchester, Manchester, UK.
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Han S, Yang S, Tang R, Xie CJ, Liu X, Liu GH, Zhou SG. Two novel Fe(III)-reducing bacteria, Geothrix campi sp. nov. and Geothrix mesophila sp. nov., isolated from paddy soils. Antonie Van Leeuwenhoek 2024; 117:68. [PMID: 38630330 DOI: 10.1007/s10482-024-01967-9] [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: 07/14/2023] [Accepted: 04/08/2024] [Indexed: 04/19/2024]
Abstract
In this research, two novel Fe(III)-reducing bacteria, SG10T and SG198T of genus Geothrix, were isolated from the rice field of Fujian Agriculture and Forestry University in Fuzhou, Fujian Province, China. Strains SG10T and SG198T were strictly anaerobic, rod-shaped and Gram-stain-negative. The two novel strains exhibited iron reduction ability, utilizing various single organic acid as the elector donor and Fe(III) as a terminal electron acceptor. Strains SG10T and SG198T showed the highest 16S rRNA sequences similarities to the type strains of Geothrix oryzisoli SG189T (99.0-99.5%) and Geothrix paludis SG195T (99.0-99.7%), respectively. The phylogenetic trees based on the 16S rRNA gene and genome 120 conserved core genes showed that strains SG10T and SG198T belong to the genus Geothrix. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the phylogenetic neighbors and the two isolated strains were 86.1-94.3% and 30.7-59.5%, respectively. The major fatty acids were iso-C15:0, anteiso-C15:0, C16:0 and iso-C13:0 3OH, and MK-8 was the main respiratory quinone. According to above results, the two strains were assigned to the genus Geothrix with the names Geothrix campi sp. nov. and Geothrix mesophila sp. nov. Type strains are SG10T (= GDMCC 1.3406 T = JCM 39331 T) and SG198T (= GDMCC 62910 T = KCTC 25635 T), respectively.
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Affiliation(s)
- Shuang Han
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, People's Republic of China
| | - Shang Yang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, People's Republic of China
| | - Rong Tang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, People's Republic of China
| | - Cheng-Jie Xie
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, People's Republic of China
| | - Xing Liu
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, People's Republic of China
| | - Guo-Hong Liu
- Institute of Resources, Environment and Soil Fertilizer, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, 350003, People's Republic of China.
| | - Shun-Gui Zhou
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, People's Republic of China.
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Holmes DE, Woodard TL, Smith JA, Musat F, Lovley DR. Electrobiocorrosion by microbes without outer-surface cytochromes. MLIFE 2024; 3:110-118. [PMID: 38827509 PMCID: PMC11139208 DOI: 10.1002/mlf2.12111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/14/2023] [Accepted: 12/03/2023] [Indexed: 06/04/2024]
Abstract
Anaerobic microbial corrosion of iron-containing metals causes extensive economic damage. Some microbes are capable of direct metal-to-microbe electron transfer (electrobiocorrosion), but the prevalence of electrobiocorrosion among diverse methanogens and acetogens is poorly understood because of a lack of tools for their genetic manipulation. Previous studies have suggested that respiration with 316L stainless steel as the electron donor is indicative of electrobiocorrosion, because, unlike pure Fe0, 316L stainless steel does not abiotically generate H2 as an intermediary electron carrier. Here, we report that all of the methanogens (Methanosarcina vacuolata, Methanothrix soehngenii, and Methanobacterium strain IM1) and acetogens (Sporomusa ovata and Clostridium ljungdahlii) evaluated respired with pure Fe0 as the electron donor, but only M. vacuolata, Mx. soehngenii, and S. ovata were capable of stainless steel electrobiocorrosion. The electrobiocorrosive methanogens required acetate as an additional energy source in order to produce methane from stainless steel. Cocultures of S. ovata and Mx. soehngenii demonstrated how acetogens can provide acetate to methanogens during corrosion. Not only was Methanobacterium strain IM1 not capable of electrobiocorrosion, but it also did not accept electrons from Geobacter metallireducens, an effective electron-donating partner for direct interspecies electron transfer to all methanogens that can directly accept electrons from Fe0. The finding that M. vacuolata, Mx. soehngenii, and S. ovata are capable of electrobiocorrosion, despite a lack of the outer-surface c-type cytochromes previously found to be important in other electrobiocorrosive microbes, demonstrates that there are multiple microbial strategies for making electrical contact with Fe0.
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Affiliation(s)
- Dawn E. Holmes
- Department of MicrobiologyUniversity of Massachusetts AmherstAmherstMassachusettsUSA
- Department of Physical and Biological ScienceWestern New England UniversitySpringfieldMassachusettsUSA
| | - Trevor L. Woodard
- Department of MicrobiologyUniversity of Massachusetts AmherstAmherstMassachusettsUSA
| | - Jessica A. Smith
- Department of MicrobiologyUniversity of Massachusetts AmherstAmherstMassachusettsUSA
- Department of Biomolecular SciencesCentral Connecticut State UniversityNew BritainConnecticutUSA
| | - Florin Musat
- Department of Biology, Section for MicrobiologyAarhus UniversityAarhusDenmark
- Department of Molecular Biology and Biotechnology, Faculty of Biology and GeologyBabeş‐Bolyai UniversityCluj‐NapocaRomania
| | - Derek R. Lovley
- Department of MicrobiologyUniversity of Massachusetts AmherstAmherstMassachusettsUSA
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Tang R, Yang S, Narsing Rao MP, Xie CJ, Han S, Yang QE, Rensing C, Liu GH, Yuan Y, Zhou SG. Three Fe(III)-reducing and nitrogen-fixing bacteria, Anaeromyxobacter terrae sp. nov., Anaeromyxobacter oryzisoli sp. nov. and Anaeromyxobacter soli sp. nov., isolated from paddy soil. Int J Syst Evol Microbiol 2024; 74. [PMID: 38323900 DOI: 10.1099/ijsem.0.006268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2024] Open
Abstract
Three microaerophilic bacterial strains, designated SG22T, SG63T and SG29T were isolated from paddy soils in PR China. Cells of these strains were Gram-staining-negative and long rod-shaped. SG22T, SG63T and SG29T showed the highest 16S rRNA gene sequence similarities with the members of the genus Anaeromyxobacter. The results of phylogenetic and phylogenomic analysis also indicated that these strains clustered with members of the genus Anaeromyxobacter. The main respiratory menaquinone of SG22T, SG63T and SG29T was MK-8 and the major fatty acids were iso-C15 : 0, iso-C17 : 0 and C16 : 0. SG22T, SG29T and SG63T not only possessed iron reduction ability but also harboured genes (nifHDK) encoding nitrogenase. The genomic DNA G+C contents of SG22T, SG63T and SG29T ranged from 73.3 to 73.5 %. The average nucleotide identity (ANI) and digital DNA-DNA hybridisation (dDDH) values between SG22T, SG63T and SG29T and the closely related species of the genus Anaeromyxobacter were lower than the cut-off values (dDDH 70 % and ANI 95-96 %) for prokaryotic species delineation. On the basis of these results, strains SG22T, SG63T and SG29T represent three novel species within the genus Anaeromyxobacter, for which the names Anaeromyxobacter terrae sp. nov., Anaeromyxobacter oryzisoli sp. nov. and Anaeromyxobacter soli sp. nov., are proposed. The type strains are SG22T (= GDMCC 1.3185T = JCM 35581T), SG63T (= GDMCC 1.2914T = JCM 35124T) and SG29T (= GDMCC 1.2911T = JCM 35123T).
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Affiliation(s)
- Rong Tang
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, PR China
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Shang Yang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Manik Prabhu Narsing Rao
- Instituto de Ciencias Aplicadas, Facultad de Ingeniería, Universidad Autónoma de Chile, Sede Talca, Talca 3460000, Chile
| | - Cheng-Jie Xie
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Shuang Han
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Qiu-E Yang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Christopher Rensing
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Guo-Hong Liu
- Agricultural Bio-resources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
| | - Yong Yuan
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, PR China
| | - Shun-Gui Zhou
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
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10
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Veerubhotla R, Marzocchi U. Examining the resistance and resilience of anode-respiring Shewanella oneidensis biohybrid using microsensors. CHEMOSPHERE 2024; 350:141109. [PMID: 38176592 DOI: 10.1016/j.chemosphere.2024.141109] [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: 08/09/2023] [Revised: 12/09/2023] [Accepted: 01/01/2024] [Indexed: 01/06/2024]
Abstract
Immobilizing electro-active microbes within polymer matrices (thereby forming biohybrids) is a promising approach to accelerate microbial attachment to electrodes and increase the biofilm robustness. However, little is known on the fine scale chemical environment that develops within the electro-active biohybrids. Herein, we develop a biohybrid by immobilizing a culture of Shewanella oneidensis MR1 in agar matrix on the surface of a graphite electrode poised at +0.25 V. The resulting bioanode (3-6 mm thick) was grown under anoxic conditions and produced a steady current of 40 μA. Oxygen and pH distribution within the biohybrid were characterized in-situ using microsensors. As Shewanella is a facultative aerobe, it will halt the current production in the presence of oxygen. Thus, in addition, we investigated the alteration of the microenvironment during and after aeration of the medium to evaluate the oxygen tolerance of the system. During aeration, oxygen was effectively consumed in the top layers of the biofilm, leaving a 400-900 μm thick anoxic zone on the anode surface, that sustained >60% of the initial current. Current production recovered to pre-oxic condition within 5 h after the aeration was stopped, showing that immobilization can promote both high resistance and resilience of the system. Despite the absence of strong buffering conditions, pH profiles indicated a maximum drop of 0.2 units across the biohybrid. Characterizing the chemical microenvironment helps to elucidate the mechanistic functioning of artificial biofilms and hold a great potential for the designing of future, more effective biohybrid electrodes.
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Affiliation(s)
- Ramya Veerubhotla
- Aarhus University Center for Water Technology WATEC, Department of Biology, Aarhus University, Denmark.
| | - Ugo Marzocchi
- Aarhus University Center for Water Technology WATEC, Department of Biology, Aarhus University, Denmark; Center for Electromicrobiology CEM, Department of Biology, Aarhus University, Denmark
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11
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Vigneron A, Guyoneaud R, Goñi-Urriza M. Genome-Centric Metatranscriptomics Reveals Multiple Co-occurring Routes for Hydrocarbon Degradation in Chronically Contaminated Marine Microbial Mats. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:1551-1562. [PMID: 38197744 DOI: 10.1021/acs.est.3c08386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
Long-term hydrocarbon pollution is a devious threat to aquatic and marine ecosystems. However, microbial responses to chronic pollution remain poorly understood. Combining genome-centric metagenomic and metatranscriptomic analyses of microbial mat samples that experienced chronic hydrocarbon pollution for more than 80 years, we analyzed the transcriptomic activity of alkane and aromatic hydrocarbon degradation pathways at the population level. Consistent with the fluctuating and stratified redox conditions of the habitat, both aerobic and anaerobic hydrocarbon degradation pathways were expressed by taxonomically and metabolically contrasted lineages including members of Bacteroidiales, Desulfobacteraceae, Pseudomonadales; Alcanivoraceae and Halieaceae populations with (photo)-heterotrophic, sulfur- and organohalide-based metabolisms, providing evidence for the co-occurrence and activity of aerobic and anaerobic hydrocarbon degradation pathways in shallow marine microbial mats. In addition, our results suggest that aerobic alkane degradation in long-term pollution involved bacterial families that are naturally widely distributed in marine habitats, but hydrocarbon concentration and composition were found to be a strong structuring factor of their intrafamily diversity and transcriptomic activities.
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Affiliation(s)
- Adrien Vigneron
- Université de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau 64053, France
| | - Rémy Guyoneaud
- Université de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau 64053, France
| | - Marisol Goñi-Urriza
- Université de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau 64053, France
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12
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Yang G, Lin C, Hou T, Wu X, Fang Y, Yao S, Zhuang L, Yuan Y. The survival strategy of direct interspecies electron transfer-capable coculture under electron donor-limited environments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:168223. [PMID: 37926263 DOI: 10.1016/j.scitotenv.2023.168223] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 10/08/2023] [Accepted: 10/28/2023] [Indexed: 11/07/2023]
Abstract
Direct interspecies electron transfer (DIET) has been considered as an effective mechanism for interspecies electron exchange in microbial syntrophy. Understanding DIET-capable syntrophic associations under energy-limited environments is important because these conditions more closely approximate those found in natural subsurface environments than in the batch cultures in the laboratory. This study, investigated the metabolic dynamics and electron transfer mechanisms in DIET-capable syntrophic coculture of Geobacter metallireducens and Geobacter sulfurreducens under electron donor-limited condition. The wild-coculture and the mutant-coculture with a citrate synthase-deficient G. sulfurreducens exhibited similar rates of syntrophic metabolism under ethanol-limited and ethanol-replete conditions. Transcriptomic analyses revealed that, in the mutant-coculture in which interspecies electron exchange was the sole electron source for G. sulfurreducens, the transcription of genes associated with uptake hydrogenase in G. sulfurreducens were significantly repressed and thus DIET tended to be the preferred mode of interspecies electron exchange under electron donor-limited condition. To overcome electron donor limitation, c-type cytochromes in the coculture actively moved from outer membrane to extracellular environment, potentially via increased secretion of outer-membrane vesicles. These results suggested a preferred electron transfer mechanism for DIET-capable syntrophic communities' survival in the electron donor-limited environments, providing valuable insights into the biogeochemical processes mediated by DIET in natural and engineered environments.
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Affiliation(s)
- Guiqin Yang
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, China
| | - Canfen Lin
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, China
| | - Tiqun Hou
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, China
| | - Xian Wu
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, China
| | - Yanlun Fang
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, China
| | - Sijie Yao
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, China
| | - Li Zhuang
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, China.
| | - Yong Yuan
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
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13
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Newman-Portela AM, Krawczyk-Bärsch E, Lopez-Fernandez M, Bok F, Kassahun A, Drobot B, Steudtner R, Stumpf T, Raff J, Merroun ML. Biostimulation of indigenous microbes for uranium bioremediation in former U mine water: multidisciplinary approach assessment. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:7227-7245. [PMID: 38157180 PMCID: PMC10821841 DOI: 10.1007/s11356-023-31530-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 12/09/2023] [Indexed: 01/03/2024]
Abstract
Characterizing uranium (U) mine water is necessary to understand and design an effective bioremediation strategy. In this study, water samples from two former U-mines in East Germany were analysed. The U and sulphate (SO42-) concentrations of Schlema-Alberoda mine water (U: 1 mg/L; SO42-: 335 mg/L) were 2 and 3 order of magnitude higher than those of the Pöhla sample (U: 0.01 mg/L; SO42-: 0.5 mg/L). U and SO42- seemed to influence the microbial diversity of the two water samples. Microbial diversity analysis identified U(VI)-reducing bacteria (e.g. Desulfurivibrio) and wood-degrading fungi (e.g. Cadophora) providing as electron donors for the growth of U-reducers. U-bioreduction experiments were performed to screen electron donors (glycerol, vanillic acid, and gluconic acid) for Schlema-Alberoda U-mine water bioremediation purpose. Thermodynamic speciation calculations show that under experimental conditions, U(VI) is not coordinated to the amended electron donors. Glycerol was the best-studied electron donor as it effectively removed 99% of soluble U, 95% of Fe, and 58% of SO42- from the mine water, probably by biostimulation of indigenous microbes. Vanillic acid removed 90% of U, and no U removal occurred using gluconic acid.
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Affiliation(s)
- Antonio M Newman-Portela
- Department of Microbiology, Faculty of Science, University of Granada, Avda. Fuentenueva S/N, 18071, Granada, Spain.
- Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328, Dresden, Germany.
| | - Evelyn Krawczyk-Bärsch
- Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328, Dresden, Germany
| | - Margarita Lopez-Fernandez
- Department of Microbiology, Faculty of Science, University of Granada, Avda. Fuentenueva S/N, 18071, Granada, Spain
| | - Frank Bok
- Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328, Dresden, Germany
| | - Andrea Kassahun
- WISMUT GmbH, Jagdschänkenstraße 29, 09117, Chemnitz, Germany
| | - Björn Drobot
- Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328, Dresden, Germany
| | - Robin Steudtner
- Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328, Dresden, Germany
| | - Thorsten Stumpf
- Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328, Dresden, Germany
| | - Johannes Raff
- Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328, Dresden, Germany
| | - Mohamed L Merroun
- Department of Microbiology, Faculty of Science, University of Granada, Avda. Fuentenueva S/N, 18071, Granada, Spain
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Ghafouri M, Pourjafar F, Ghobadi Nejad Z, Yaghmaei S. Biological treatment of triclosan using a novel strain of Enterobacter cloacae and introducing naphthalene dioxygenase as an effective enzyme. JOURNAL OF HAZARDOUS MATERIALS 2023; 459:131833. [PMID: 37473572 DOI: 10.1016/j.jhazmat.2023.131833] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 05/22/2023] [Accepted: 06/09/2023] [Indexed: 07/22/2023]
Abstract
In recent years, triclosan (TCS) has been widely used as an antibacterial agent in personal care products due to the spread of the Coronavirus. TSC is an emerging contaminant, and due to its stability and toxicity, it cannot be completely degraded through traditional wastewater treatment methods. In this study, a novel strain of Enterobacter cloacae was isolated and identified that can grow in high TCS concentrations. Also, we introduced naphthalene dioxygenase as an effective enzyme in TCS biodegradation, and its role during the removal process was investigated along with the laccase enzyme. The change of cell surface hydrophobicity during TCS removal revealed that a glycolipid biosurfactant called rhamnolipid was involved in TCS removal, leading to enhanced biodegradation of TCS. The independent variables, such as initial TCS concentration, pH, removal duration, and temperature, were optimized using the response surface method (RSM). As a result, the maximum TCS removal (97%) was detected at a pH value of 7 and a temperature of 32 °C after 9 days and 12 h of treatment. Gas chromatography-mass spectrometry (GC/MS) analysis showed five intermediate products and a newly proposed pathway for TCS degradation. Finally, the phytotoxicity experiment conducted on Cucumis sativus and Lens culinaris seeds demonstrated an increase in germination power and growth of stems and roots in comparison to untreated water. These results indicate that the final treated water was less toxic.
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Affiliation(s)
- Mahsa Ghafouri
- Department of Chemical and Petroleum Engineering, Sharif University of Technology, Tehran, Iran
| | - Fatemeh Pourjafar
- Department of Chemical and Petroleum Engineering, Sharif University of Technology, Tehran, Iran
| | - Zahra Ghobadi Nejad
- Biochemical & Bioenvironmental Research Center, Sharif University of Technology, Azadi Avenue, P.O Box 11155-1399, Tehran, Iran
| | - Soheila Yaghmaei
- Department of Chemical and Petroleum Engineering, Sharif University of Technology, Tehran, Iran; Biochemical & Bioenvironmental Research Center, Sharif University of Technology, Azadi Avenue, P.O Box 11155-1399, Tehran, Iran.
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15
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Yamashita T, Yamashita Y, Takano M, Sato N, Nakano S, Yokoyama H. 3D Printed lattice-structured metal electrodes for enhanced current production in bioelectrochemical systems. ENVIRONMENTAL TECHNOLOGY 2023; 44:3229-3235. [PMID: 35302914 DOI: 10.1080/09593330.2022.2056083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 03/10/2022] [Indexed: 06/14/2023]
Abstract
Bioelectrochemical systems (BESs) are emerging techniques that use biological production of current for versatile activities, including energy recovery and bioremediation. The development of high-performance three-dimensional (3D) electrodes has attracted attention for facilitating current production in BESs. Carbon-based electrodes have been commonly used in BESs, but metal electrodes are not generally employed because of their low biocompatibility with microbes. In this study, 3D stainless-steel electrodes, composed of octahedral lattice, were fabricated using the 3D printing technique. Heat treatment was conducted to form an iron-oxide layer on the electrode surface for increasing biocompatibility. Another crucial parameter that determines current production is the pitch length of a lattice electrode as it affects the surface area and substrate diffusion. The pitch length was optimized by testing the lattice electrodes with pitches ranging from 1.5 mm to 6.0 mm. The highest current, obtained with the 3.0 mm-pitch electrode, was 50% higher than that obtained with common 3D carbon-felt electrodes. These results demonstrate the usefulness of 3D lattice-structured metal electrodes in BESs.
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Affiliation(s)
- Takahiro Yamashita
- Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization, Tsukuba, Japan
| | | | | | - Naoko Sato
- Advanced Manufacturing Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Shizuka Nakano
- Advanced Manufacturing Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Hiroshi Yokoyama
- Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization, Tsukuba, Japan
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16
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Zhou J, Smith JA, Li M, Holmes DE. Methane production by Methanothrix thermoacetophila via direct interspecies electron transfer with Geobacter metallireducens. mBio 2023; 14:e0036023. [PMID: 37306514 PMCID: PMC10470525 DOI: 10.1128/mbio.00360-23] [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] [Accepted: 04/13/2023] [Indexed: 06/13/2023] Open
Abstract
Methanothrix is widely distributed in natural and artificial anoxic environments and plays a major role in global methane emissions. It is one of only two genera that can form methane from acetate dismutation and through participation in direct interspecies electron transfer (DIET) with exoelectrogens. Although Methanothrix is a significant member of many methanogenic communities, little is known about its physiology. In this study, transcriptomics helped to identify potential routes of electron transfer during DIET between Geobacter metallireducens and Methanothrix thermoacetophila. Additions of magnetite to cultures significantly enhanced growth by acetoclastic methanogenesis and by DIET, while granular activated carbon (GAC) amendments impaired growth. Transcriptomics suggested that the OmaF-OmbF-OmcF porin complex and the octaheme outer membrane c-type cytochrome encoded by Gmet_0930, were important for electron transport across the outer membrane of G. metallireducens during DIET with Mx. thermoacetophila. Clear differences in the metabolism of Mx. thermoacetophila when grown via DIET or acetate dismutation were not apparent. However, genes coding for proteins involved in carbon fixation, the sheath fiber protein MspA, and a surface-associated quinoprotein, SqpA, were highly expressed in all conditions. Expression of gas vesicle genes was significantly lower in DIET- than acetate-grown cells, possibly to facilitate better contact between membrane-associated redox proteins during DIET. These studies reveal potential electron transfer mechanisms utilized by both Geobacter and Methanothrix during DIET and provide important insights into the physiology of Methanothrix in anoxic environments. IMPORTANCE Methanothrix is a significant methane producer in a variety of methanogenic environments including soils and sediments as well as anaerobic digesters. Its abundance in these anoxic environments has mostly been attributed to its high affinity for acetate and its ability to grow by acetoclastic methanogenesis. However, Methanothrix species can also generate methane by directly accepting electrons from exoelectrogenic bacteria through direct interspecies electron transfer (DIET). Methane production through DIET is likely to further increase their contribution to methane production in natural and artificial environments. Therefore, acquiring a better understanding of DIET with Methanothrix will help shed light on ways to (i) minimize microbial methane production in natural terrestrial environments and (ii) maximize biogas formation by anaerobic digesters treating waste.
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Affiliation(s)
- Jinjie Zhou
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
- Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong, China
- Department of Microbiology, University of Massachusetts‐Amherst, Amherst, Massachusetts, USA
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
| | - Jessica A. Smith
- Department of Microbiology, University of Massachusetts‐Amherst, Amherst, Massachusetts, USA
- Department of Biomolecular Sciences, Central Connecticut State University, New Britain, Connecticut, USA
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
| | - Dawn E. Holmes
- Department of Microbiology, University of Massachusetts‐Amherst, Amherst, Massachusetts, USA
- Department of Physical and Biological Science, Western New England University, Springfield, Massachusetts, USA
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17
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Smith JA, Holmes DE, Woodard TL, Li Y, Liu X, Wang LY, Meier D, Schwarz IA, Lovley DR. Detrimental impact of the Geobacter metallireducens type VI secretion system on direct interspecies electron transfer. Microbiol Spectr 2023; 11:e0094123. [PMID: 37650614 PMCID: PMC10580878 DOI: 10.1128/spectrum.00941-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 07/02/2023] [Indexed: 09/01/2023] Open
Abstract
Direct interspecies electron transfer (DIET) is important in anaerobic communities of environmental and practical significance. Other than the need for close physical contact for electrical connections, the interactions of DIET partners are poorly understood. Type VI secretion systems (T6SSs) typically kill competitive microbes. Surprisingly, Geobacter metallireducens highly expressed T6SS genes when DIET-based co-cultures were initiated with Geobacter sulfurreducens. T6SS gene expression was lower when the electron shuttle anthraquinone-2,6-disulfonate was added to alleviate the need for interspecies contact. Disruption of hcp, the G. metallireducens gene for the main T6SS needle-tube protein subunit, and the most highly upregulated gene in DIET-grown cells eliminated the long lag periods required for the initiation of DIET. The mutation did not aid DIET in the presence of granular-activated carbon (GAC), consistent with the fact that DIET partners do not make physical contact when electrically connected through conductive materials. The hcp-deficient mutant also established DIET quicker with Methanosarcina barkeri. However, the mutant also reduced Fe(III) oxide faster than the wild-type strain, a phenotype not expected from the loss of the T6SS. Quantitative PCR revealed greater gene transcript abundance for key components of extracellular electron transfer in the hcp-deficient mutant versus the wild-type strain, potentially accounting for the faster Fe(III) oxide reduction and impact on DIET. The results highlight that interspecies interactions beyond electrical connections may influence DIET effectiveness. The unexpected increase in the expression of genes for extracellular electron transport components when hcp was deleted emphasizes the complexities in evaluating the electromicrobiology of highly adaptable Geobacter species. IMPORTANCE Direct interspecies electron transfer is an alternative to the much more intensively studied process of interspecies H2 transfer as a mechanism for microbes to share electrons during the cooperative metabolism of energy sources. DIET is an important process in anaerobic soils and sediments generating methane, a significant greenhouse gas. Facilitating DIET can accelerate and stabilize the conversion of organic wastes to methane biofuel in anaerobic digesters. Therefore, a better understanding of the factors controlling how fast DIET partnerships are established is expected to lead to new strategies for promoting this bioenergy process. The finding that when co-cultured with G. sulfurreducens, G. metallireducens initially expressed a type VI secretion system, a behavior not conducive to interspecies cooperation, illustrates the complexity of establishing syntrophic relationships.
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Affiliation(s)
- Jessica A. Smith
- Department of Microbiology, University of Massachusetts Amherst, Morrill IV N Science Center, Amherst, Massachusetts, USA
- Department of Biomolecular Sciences, Central Connecticut State University, New Britain, Connecticut, USA
| | - Dawn E. Holmes
- Department of Microbiology, University of Massachusetts Amherst, Morrill IV N Science Center, Amherst, Massachusetts, USA
- Department of Physical and Biological Sciences, Western New England University, Springfield, Massachusetts, USA
| | - Trevor L. Woodard
- Department of Microbiology, University of Massachusetts Amherst, Morrill IV N Science Center, Amherst, Massachusetts, USA
| | - Yang Li
- Department of Microbiology, University of Massachusetts Amherst, Morrill IV N Science Center, Amherst, Massachusetts, USA
- School of Ocean Science and Technology, Dalian University of Technology, Panjin, Liaoning, China
| | - Xinying Liu
- Department of Microbiology, University of Massachusetts Amherst, Morrill IV N Science Center, Amherst, Massachusetts, USA
- College of Environmental Science and Engineering, Beijing Forestry University, Beijing, China
| | - Li-Ying Wang
- Department of Microbiology, University of Massachusetts Amherst, Morrill IV N Science Center, Amherst, Massachusetts, USA
| | - David Meier
- Department of Microbiology, University of Massachusetts Amherst, Morrill IV N Science Center, Amherst, Massachusetts, USA
| | - Ingrid A. Schwarz
- Department of Biomolecular Sciences, Central Connecticut State University, New Britain, Connecticut, USA
| | - Derek R. Lovley
- Department of Microbiology, University of Massachusetts Amherst, Morrill IV N Science Center, Amherst, Massachusetts, USA
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Zhang B, Shi S, Tang R, Qiao C, Yang M, You Z, Shao S, Wu D, Yu H, Zhang J, Cao Y, Li F, Song H. Recent advances in enrichment, isolation, and bio-electrochemical activity evaluation of exoelectrogenic microorganisms. Biotechnol Adv 2023; 66:108175. [PMID: 37187358 DOI: 10.1016/j.biotechadv.2023.108175] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 05/10/2023] [Accepted: 05/10/2023] [Indexed: 05/17/2023]
Abstract
Exoelectrogenic microorganisms (EEMs) catalyzed the conversion of chemical energy to electrical energy via extracellular electron transfer (EET) mechanisms, which underlay diverse bio-electrochemical systems (BES) applications in clean energy development, environment and health monitoring, wearable/implantable devices powering, and sustainable chemicals production, thereby attracting increasing attentions from academic and industrial communities in the recent decades. However, knowledge of EEMs is still in its infancy as only ~100 EEMs of bacteria, archaea, and eukaryotes have been identified, motivating the screening and capture of new EEMs. This review presents a systematic summarization on EEM screening technologies in terms of enrichment, isolation, and bio-electrochemical activity evaluation. We first generalize the distribution characteristics of known EEMs, which provide a basis for EEM screening. Then, we summarize EET mechanisms and the principles underlying various technological approaches to the enrichment, isolation, and bio-electrochemical activity of EEMs, in which a comprehensive analysis of the applicability, accuracy, and efficiency of each technology is reviewed. Finally, we provide a future perspective on EEM screening and bio-electrochemical activity evaluation by focusing on (i) novel EET mechanisms for developing the next-generation EEM screening technologies, and (ii) integration of meta-omics approaches and bioinformatics analyses to explore nonculturable EEMs. This review promotes the development of advanced technologies to capture new EEMs.
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Affiliation(s)
- Baocai Zhang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Sicheng Shi
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Rui Tang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Chunxiao Qiao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Meiyi Yang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Zixuan You
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Shulin Shao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Deguang Wu
- Department of Brewing Engineering, Moutai Institute, Luban Ave, Renhuai 564507, Guizhou, PR China
| | - Huan Yu
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Junqi Zhang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Yingxiu Cao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Feng Li
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China.
| | - Hao Song
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China.
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Xie J, Coker VS, O'Driscoll B, Cai R, Haigh SJ, Lloyd JR. Microbial Reduction of Antimony(V)-Bearing Ferrihydrite by Geobacter sulfurreducens. Appl Environ Microbiol 2023; 89:e0217522. [PMID: 36853045 PMCID: PMC10057881 DOI: 10.1128/aem.02175-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 02/05/2023] [Indexed: 03/01/2023] Open
Abstract
The reduction of Sb(V)-bearing ferrihydrite by Geobacter sulfurreducens was studied to determine the fate of the metalloid in Fe-rich systems undergoing redox transformations. Sb(V) added at a range of concentrations adsorbed readily to ferrihydrite, and the loadings had a pronounced impact on the rate and extent of Fe(III) reduction and the products formed. Magnetite dominated at low (0.5 and 1 mol%) Sb(V) concentrations, with crystallite sizes decreasing at higher Sb loadings: 37-, 25-, and 17-nm particles for no-Sb, 0.5% Sb, and 1% Sb samples, respectively. In contrast, goethite was the dominant end product for samples with higher antimony loadings (2 and 5 mol%), with increased goethite grain size in the 5% Sb sample. Inductively coupled mass spectrometry (ICP-MS) analysis confirmed that Sb was not released to solution during the bioreduction process, and X-ray photoelectron spectroscopy (XPS) analyses showed that no Sb(III) was formed throughout the experiments, confirming that the Fe(III)-reducing bacterium Geobacter sulfurreducens cannot reduce Sb(V) enzymatically or via biogenic Fe(II). These findings suggest that Fe (bio)minerals have a potential role in limiting antimony pollution in the environment, even when undergoing redox transformations. IMPORTANCE Antimony is an emerging contaminant that shares chemical characteristics with arsenic. Metal-reducing bacteria (such as Geobacter sulfurreducens) can cause the mobilization of arsenic from Fe(III) minerals under anaerobic conditions, causing widespread contamination of aquifers worldwide. This research explores whether metal-reducing bacteria can drive the mobilization of antimony under similar conditions. In this study, we show that G. sulfurreducens cannot reduce Sb(V) directly or cause Sb release during the bioreduction of the Fe(III) mineral ferrihydrite [although the sorbed Sb(V) did alter the Fe(II) mineral end products formed]. Overall, this study highlights the tight associations between Fe and Sb in environmental systems, suggesting that the microbial reduction of Fe(III)/Sb mineral assemblages may not lead to Sb release (in stark contrast to the mobilization of As in iron-rich systems) and offers potential Fe-based remediation options for Sb-contaminated environments.
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Affiliation(s)
- Jinxin Xie
- Williamson Research Centre for Molecular Environmental Science, Department of Earth and Environmental Science, The University of Manchester, Manchester, United Kingdom
| | - Victoria S. Coker
- Williamson Research Centre for Molecular Environmental Science, Department of Earth and Environmental Science, The University of Manchester, Manchester, United Kingdom
| | - Brian O'Driscoll
- Williamson Research Centre for Molecular Environmental Science, Department of Earth and Environmental Science, The University of Manchester, Manchester, United Kingdom
- Department of Earth and Environmental Sciences, The University of Ottawa, Ottawa, Canada
| | - Rongsheng Cai
- Department of Materials, The University of Manchester, Manchester, United Kingdom
| | - Sarah J. Haigh
- Department of Materials, The University of Manchester, Manchester, United Kingdom
| | - Jonathan R. Lloyd
- Williamson Research Centre for Molecular Environmental Science, Department of Earth and Environmental Science, The University of Manchester, Manchester, United Kingdom
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Zhao X, Teng Z, Wang G, Luo W, Guo Y, Ji X, Hu W, Li M. Anaerobic syntrophic system composed of phosphate solubilizing bacteria and dissimilatory iron reducing bacteria induces cadmium immobilization via secondary mineralization. JOURNAL OF HAZARDOUS MATERIALS 2023; 446:130702. [PMID: 36587597 DOI: 10.1016/j.jhazmat.2022.130702] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/12/2022] [Accepted: 12/28/2022] [Indexed: 06/17/2023]
Abstract
Secondary mineralization is a promising method for remediating cadmium (Cd) pollution in sediments, but the poor stability of Cd-containing secondary minerals is a bottleneck that limits the development of this approach. The existence of phosphate can enhance the formation of stable secondary minerals and points a new direction for Cd immobilization. In this research, a novel syntrophic system composed of phosphate solubilizing bacteria (PSB) and dissimilatory iron reducing bacteria (DIRB) was established and the effect and mechanism of Cd immobilization in the system were also explored. The results showed that under the conditions of DIRB:PSB (V:V)= 3:1, syntrophic bacteria dosage of 5% and glucose dosage of 5 g/L, Cd incorporated in the secondary minerals could account for about 60% of the total Cd. In the pH range of 5-9, alkaline environment was conducive to the immobilization of Cd and the percentage of combined Cd was up to 58%, while the combined Cd in secondary minerals decreased from 62% to 56% with the increase of initial Cd concentration from 0.1 to 0.3 mmol/L. In addition, XRD, XPS, Mössbauer and other characterization results showed that secondary minerals, such as Cd exchange hydroxyapatite (Cd-HAP) and kryzhanovskite (Fe3(PO4)2(OH)3) were formed in this new system. The established syntrophic system of PSB and DIRB is thus a prospective bioremediation technology for Cd immobilization in sediments and can avoid the potential risk might be caused by the addition of phosphorus-containing materials.
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Affiliation(s)
- Xin Zhao
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing 100083, China; Engineering Research Center for Water Pollution Source Control & Eco-remediation, College of Environmental Science and Engineering, Beijing Forestry University, Beijing 100083, China
| | - Zedong Teng
- Innovation Academy for Green Manufacture, National Engineering Research Center of Green Recycling for Strategic Metal Resources, Key Laboratory of Green Process and Engineering, Beijing 100190, China; Engineering Research Centre of Process Pollution Control, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
| | - Gongting Wang
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing 100083, China; Engineering Research Center for Water Pollution Source Control & Eco-remediation, College of Environmental Science and Engineering, Beijing Forestry University, Beijing 100083, China
| | - Wenqing Luo
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing 100083, China; Engineering Research Center for Water Pollution Source Control & Eco-remediation, College of Environmental Science and Engineering, Beijing Forestry University, Beijing 100083, China
| | - Yali Guo
- Shanghai Investigation, Design & Research Institute Co., Ltd., Shanghai 200335, China; YANGTZE Eco-Environment Engineering Research Center (Shanghai), China Three Gorges Corporation, Shanghai 200335, China
| | - Xiaonan Ji
- Shanghai Investigation, Design & Research Institute Co., Ltd., Shanghai 200335, China; YANGTZE Eco-Environment Engineering Research Center (Shanghai), China Three Gorges Corporation, Shanghai 200335, China
| | - Wei Hu
- Shanghai Investigation, Design & Research Institute Co., Ltd., Shanghai 200335, China; YANGTZE Eco-Environment Engineering Research Center (Shanghai), China Three Gorges Corporation, Shanghai 200335, China
| | - Min Li
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing 100083, China; Engineering Research Center for Water Pollution Source Control & Eco-remediation, College of Environmental Science and Engineering, Beijing Forestry University, Beijing 100083, China.
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Han S, Tang R, Yang S, Xie CJ, Narsing Rao MP, Rensing C, Liu GH, Zhou SG. Geothrix oryzisoli sp. nov., a ferric iron-reducing bacterium isolated from paddy soil. Antonie Van Leeuwenhoek 2023; 116:477-486. [PMID: 36897496 DOI: 10.1007/s10482-023-01817-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 02/18/2023] [Indexed: 03/11/2023]
Abstract
An anaerobic, Gram-staining-negative, rod-shaped, Fe(III)-reducing strain, designated SG189T, was isolated from paddy soil in Fujian Province, China. Growth occurred at 20-35 ℃ (optimum 30 ℃), pH 6.5-8.0 (optimum 7.0) and 0-0.2% (w/v) NaCl (optimum 0%). The strain SG189T showed the highest 16S rRNA sequences similarities to the type strains of Geothrix fermentans DSM 14018T (98.9%), "Geothrix terrae" SG184T (99.0%) and "Geothrix alkalitolerans" SG263T (99.3%). ANI and dDDH values between strain SG189T and the most closely related Geothrix species were 86.5-87.1% and 31.5-32.9%, which lower than the cut-off values (ANI 95-96% and dDDH 70%) for prokaryotic species delineation. Further, genome-based phylogenomic trees constructed using 81 core genes (UBCG2) and 120 conserved genes (GTDB) showed that strain SG189T formed a clade with members of the genus Geothrix. The menaquinone was shown to be MK-8, and the major fatty acids were iso-C15:0 and iso-C13:0 3OH. The genomic DNA G + C content was 68.2%. Additionally, we found that strain SG189T possessed ability to reduce ferric iron, and strain SG189T could reduce 10 mM of ferric citrate in 10 days with lactate as the sole electron donor. Based on the observed physiological and biochemical properties, chemotaxonomic characteristics, ANI and dDDH values, SG189T represents a novel species of the genus Geothrix, for which the name Geothrix oryzisoli sp. nov. is proposed. The type strain is SG189T (= GDMCC 1.3408T = JCM 39324T).
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Affiliation(s)
- Shuang Han
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China
| | - Rong Tang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China
| | - Shang Yang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China
| | - Cheng-Jie Xie
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China
| | - Manik Prabhu Narsing Rao
- Programa de Doctorado en Ciencias Aplicadas, Universidad Autónoma de Chile, Talca, 3460000, Chile
| | - Christopher Rensing
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China
| | - Guo-Hong Liu
- Agricultural Bio-Resources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, Fujian, People's Republic of China.
| | - Shun-Gui Zhou
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China.
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Saha A, Gupta A, Sar P. Metagenome based analysis of groundwater from arsenic contaminated sites of West Bengal revealed community diversity and their metabolic potential. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART A, TOXIC/HAZARDOUS SUBSTANCES & ENVIRONMENTAL ENGINEERING 2023; 58:91-106. [PMID: 36852697 DOI: 10.1080/10934529.2023.2173919] [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: 03/17/2022] [Revised: 01/18/2023] [Accepted: 01/20/2023] [Indexed: 06/18/2023]
Abstract
The study of microbial community in groundwater systems is considered to be essential to improve our understanding of arsenic (As) biogeochemical cycling in aquifers, mainly as it relates to the fate and transport of As. The present study was conducted to determine the microbial community composition and its functional potential using As-contaminated groundwater from part of the Bengal Delta Plain (BDP) in West Bengal, India. Geochemical analyses indicated low to moderate dissolved oxygen (0.42-3.02 mg/L), varying As (2.5-311 µg/L) and Fe (0.19-1.2 mg/L) content, while low concentrations of total organic carbon (TOC), total inorganic carbon (TIC), nitrate, and sulfate were detected. Proteobacteria was the most abundant phylum, while the indiscriminate presence of an array of archaeal phyla, Euryarchaeota, Crenarchaeota, Nanoarchaeota, etc., was noteworthy. The core community members were affiliated to Sideroxydans, Acidovorax, Pseudoxanthomonas, Brevundimonas, etc. However, diversity assessed over multiple seasons indicated a shift from Sideroxydans to Pseudomonas or Brevundimonas dominant community, suggestive of microbial response to seasonally fluctuating geochemical stimuli. Taxonomy-based functional potential showed prospects for As biotransformation, methanogenesis, sulfate respiration, denitrification, etc. Thus, this study strengthened existing reports from this region by capturing the less abundant or difficult-to-culture taxa collectively forming a major fraction of the microbial community.
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Affiliation(s)
- Anumeha Saha
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
| | - Abhishek Gupta
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
| | - Pinaki Sar
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
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23
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Grey A, Costeira R, Lorenzo E, O’Kane S, McCaul MV, McCarthy T, Jordan SF, Allen CCR, Kelleher BP. Geochemical properties of blue carbon sediments through an elevation gradient: study of an anthropogenically impacted coastal lagoon. BIOGEOCHEMISTRY 2023; 162:381-408. [PMID: 36873378 PMCID: PMC9971090 DOI: 10.1007/s10533-022-00974-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 09/06/2022] [Indexed: 06/18/2023]
Abstract
UNLABELLED Global research is showing that coastal blue carbon ecosystems are vulnerable to climate change driven threats including accelerated sea-level rise and prolonged periods of drought. Furthermore, direct anthropogenic impacts present immediate threats through deterioration of coastal water quality, land reclamation, long-term impact to sediment biogeochemical cycling. These threats will invariably alter the future efficacy of carbon (C) sequestration processes and it is imperative that currently existing blue carbon habitats be protected. Knowledge of underlying biogeochemical, physical and hydrological interactions occurring in functioning blue carbon habitats is essential for developing strategies to mitigate threats, and promote conditions to optimise C sequestration/storage. In this current work, we investigated how sediment geochemistry (0-10 cm depth) responds to elevation, an edaphic factor driven by long-term hydrological regimes consequently exerting control over particle sedimentation rates and vegetation succession. This study was performed in an anthropogenically impacted blue carbon habitat along a coastal ecotone encompassing an elevation gradient transect from intertidal sediments (un-vegetated and covered daily by tidal water), through vegetated salt marsh sediments (periodically covered by spring tides and flooding events), on Bull Island, Dublin Bay. We determined the quantity and distributions of bulk geochemical characteristics in sediments through the elevation gradient, including total organic carbon (TOC), total nitrogen (TN), total metals, silt, clay, and also, 16 individual polyaromatic hydrocarbon's (PAH's) as an indication of anthropogenic input. Elevation measurements for sample sites were determined on this gradient using a LiDAR scanner accompanied by an IGI inertial measurement unit (IMU) on board a light aircraft. Considering the gradient from the Tidal mud zone (T), through the low-mid marsh (M) to the most elevated upper marsh (H), there were significant differences between all zones for many measured environmental variables. The results of significance testing using Kruskal-Wallis analysis revealed, that %C, %N, PAH (µg/g), Mn (mg/kg), TOC:NH4 + and pH are significantly different between all zones on the elevation gradient. The highest values for all these variables exists (excluding pH which followed a reverse trend) in zone H, decreasing in zone M and lowest in the un-vegetated zone T. TC content is 16 fold higher overall in vegetated (3.43 -21.84%) than uninhabited (0.21-0.56%) sediments. TN was over 50 times higher (0.24-1.76%), more specifically increasing in % mass on approach to the upper salt marsh with distance from the tidal flats sediments zone T (0.002-0.05%). Clay and silt distributions were greatest in vegetated sediments, increasing in % content towards upper marsh zones The retention of water, metals, PAHs, mud, chloride ions, NH4 +, PO4 3- and SO4 2- increased with elevated C concentrations, concurrently where pH significantly decreased. Sediments were categorized with respect to PAH contamination where all SM samples were placed in the high polluted category. The results highlight the ability of Blue C sediments to immobilise increasing levels of C, N, and metals, and PAH with over time and with both lateral and vertical expansion. This study provides a valuable data set for an anthropogenically impacted blue carbon habitat predicted to suffer from sea-level rise and exponential urban development. GRAPHICAL ABSTRACT Summarized results from this study demonstrating the geochemical changes through an elevation gradient, with a transect encompassing intertidal sediments through supratidal salt marsh sediments within Bull Island's blue carbon lagoon zones. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s10533-022-00974-0.
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Affiliation(s)
- Anthony Grey
- School of Chemical Sciences, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Ricardo Costeira
- The School of Biological Sciences, Queen’s University Belfast, Belfast, N. Ireland
| | - Emmaline Lorenzo
- Department of Chemistry, University of Kansas, Lawrence, KS 66045 USA
| | - Sean O’Kane
- National Centre for Geocomputation, Maynooth University, Kildare, Ireland
| | - Margaret V. McCaul
- Insight SFI Research Centre for Data Analytics, Dublin City University, Dublin, Ireland
| | - Tim McCarthy
- National Centre for Geocomputation, Maynooth University, Kildare, Ireland
| | - Sean F. Jordan
- Insight SFI Research Centre for Data Analytics, Dublin City University, Dublin, Ireland
| | | | - Brian P. Kelleher
- School of Chemical Sciences, Dublin City University, Glasnevin, Dublin 9, Ireland
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Sujathan S, Singh A. Investigation of Potential Drivers of Elevated Uranium Prevalence in Indian Groundwaters with a Unified Speciation Model. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:1970-1986. [PMID: 36693168 DOI: 10.1021/acs.est.2c08524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Elevated uranium (U) (>WHO limit of 30 μg L-1) in Indian groundwaters is primarily considered geogenic, but the specific mineralogical sources and mechanisms for U mobilization are poorly understood. In this contribution, statistical and geochemical analyses of well-constrained metadata of Indian groundwater quality (n = 342 of 8543) were performed to identify key parameters and processes that influence U concentrations. For geochemical predictions, a unified speciation model was developed from a carefully compiled and updated thermodynamic database of inorganic, organic (Stockholm Humic model), and surface complexation reactions and associated constants. Critical U contamination was found at shallow depths (<100 m) within the Indo-Gangetic plain, as determined by bivariate nonparametric Kendall's Taub and probability-based association tests. Analysis of aquifer redox states, multivariate hierarchical clusters, and principal components indicated that U contamination was predominant not just in oxic but mixed (oxic-anoxic) aquifers under high Fe, Mn, and SO4 concentrations, presumably due to U release from dissolution of Fe/Mn oxides or Fe sulfides and silicate weathering. Most groundwaters were undersaturated with respect to relevant U-bearing solids despite being supersaturated with respect to atmospheric CO2 (average pCO2 of reported dissolved inorganic carbonate (DIC) data = 10-1.57 atm). Yet, dissolved U did not appear to be mass limited, as predicted solubilities from reported sediment concentrations of U were ∼3 orders of magnitude higher. Integration of surface complexation models of U on typical aquifer adsorbents, ferrihydrite, goethite, and manganese dioxide, was necessary to explain dissolved U concentrations. Uranium contamination probabilities with increasing dissolved Ca and Mn exhibited minima at equilibrium solubilities of calcite [∼50 mg L-1] and rhodochrosite [∼0.14 mg L-1], respectively, at an average groundwater pH of ∼7.5. A potential indirect control of such U-free carbonate solids on U mobilization was suggested. For locations (n = 37) where dissolved organic carbon was also reported, organic complexes of U contributed negligibly to dominant U speciation at the groundwater pH. Overall, the unified model suggested competitive dissolution-precipitation and adsorption-desorption controls on U speciation. The model provides a quantitative framework that can be extended to understand dominant mobilization mechanisms of geogenic U in aquifers worldwide after suitable modifications to the relevant aquifer parameters.
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Affiliation(s)
- Surya Sujathan
- Department of Civil Engineering, Center for Environmental Science and Engineering, Indian Institute of Technology Kanpur, Kanpur 208016, Uttar Pradesh, India
| | - Abhas Singh
- Department of Civil Engineering, Center for Environmental Science and Engineering, Indian Institute of Technology Kanpur, Kanpur 208016, Uttar Pradesh, India
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25
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Xie L, Yoshida N, Meng L. Polyphasic Characterization of Geotalea uranireducens NIT-SL11 Newly Isolated from a Complex of Sewage Sludge and Microbially Reduced Graphene Oxide. Microorganisms 2023; 11:microorganisms11020349. [PMID: 36838314 PMCID: PMC9961858 DOI: 10.3390/microorganisms11020349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 01/25/2023] [Accepted: 01/27/2023] [Indexed: 02/03/2023] Open
Abstract
Graphene oxide (GO), a chemically oxidized sheet of graphite, has been used as a conductive carbon carrier of microbes to boost various bioelectrochemical reactions. However, the types of microbes that can reduce GO have rarely been investigated. In this study, a strain of GO-reducing bacteria, named NIT-SL11, which was obtained from a hydrogel of microbially reduced GO and anaerobic sludge that converts sewage to electricity, was phylogenically identified as a novel strain of Geotalea uraniireducens. Considering the current lack of information on the electrogenic ability of the bacterium and its physicochemical and chemotaxonomic characteristics, the polyphasic characterization of the Geotalea uraniireducens strain NIT-SL11 was performed. NIT-SL11 utilized various organic acids, such as lactate, benzoate, and formate, as electron donors and exhibited respiration using GO, electrodes, fumarate, and malate. The strain contained C16:1ω7c and C16:0 as the major fatty acids and MK-8 and 9 as the major respiratory quinones. The complete genome of NIT-SL11 was 4.7 Mbp in size with a G+C content of 60.9%, and it encoded 80 putative c-type cytochromes and 23 type IV pili-related proteins. The possible extracellular electron transfer (EET) pathways of the strain were the porin-cytochrome (Pcc) EET pathway and type IV pili-based pathway.
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26
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Grey A, Costeira R, Lorenzo E, O’Kane S, McCaul MV, McCarthy T, Jordan SF, Allen CCR, Kelleher BP. Biogeochemical properties of blue carbon sediments influence the distribution and monomer composition of bacterial polyhydroxyalkanoates (PHA). BIOGEOCHEMISTRY 2023; 162:359-380. [PMID: 36873379 PMCID: PMC9971093 DOI: 10.1007/s10533-022-01008-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 11/25/2022] [Indexed: 06/18/2023]
Abstract
UNLABELLED Coastal wetlands are highly efficient 'blue carbon' sinks which contribute to mitigating climate change through the long-term removal of atmospheric CO2 and capture of carbon (C). Microorganisms are integral to C sequestration in blue carbon sediments and face a myriad of natural and anthropogenic pressures yet their adaptive responses are poorly understood. One such response in bacteria is the alteration of biomass lipids, specifically through the accumulation of polyhydroxyalkanoates (PHAs) and alteration of membrane phospholipid fatty acids (PLFA). PHAs are highly reduced bacterial storage polymers that increase bacterial fitness in changing environments. In this study, we investigated the distribution of microbial PHA, PLFA profiles, community structure and response to changes in sediment geochemistry along an elevation gradient from intertidal to vegetated supratidal sediments. We found highest PHA accumulation, monomer diversity and expression of lipid stress indices in elevated and vegetated sediments where C, nitrogen (N), PAH and heavy metals increased, and pH was significantly lower. This was accompanied by a reduction in bacterial diversity and a shift to higher abundances of microbial community members favouring complex C degradation. Results presented here describe a connection between bacterial PHA accumulation, membrane lipid adaptation, microbial community composition and polluted C rich sediments. GRAPHICAL ABSTRACT Geochemical, microbiological and polyhydroxyalkanoate (PHA) gradient in a blue carbon zone. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s10533-022-01008-5.
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Affiliation(s)
- Anthony Grey
- School of Chemical Sciences, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Ricardo Costeira
- The School of Biological Sciences, Queen’s University Belfast, Belfast, Northern Ireland
| | - Emmaline Lorenzo
- Department of Chemistry, University of Kansas, Lawrence, 66045 USA
| | - Sean O’Kane
- National Centre for Geocomputation, Maynooth University, Maynooth, Ireland
| | - Margaret V. McCaul
- Insight SFI Research Centre for Data Analytics, Dublin City University, Dublin 4, Ireland
| | - Tim McCarthy
- National Centre for Geocomputation, Maynooth University, Maynooth, Ireland
| | - Sean F. Jordan
- Insight SFI Research Centre for Data Analytics, Dublin City University, Dublin 4, Ireland
| | | | - Brian P. Kelleher
- School of Chemical Sciences, Dublin City University, Glasnevin, Dublin 9, Ireland
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27
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Yan M, Zhu C, Li B, Su S, Li H. Manure application facilitated electrokinetic remediation of antibiotic-arsenic co-contaminated paddy soil. JOURNAL OF HAZARDOUS MATERIALS 2023; 441:129897. [PMID: 36084469 DOI: 10.1016/j.jhazmat.2022.129897] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/04/2022] [Accepted: 08/31/2022] [Indexed: 06/15/2023]
Abstract
The co-existence of antibiotics and heavy metals in soil with manure application poses high risk to both environment and human health, and thus effective remediation methods are in urgent need. This study investigated the synergistic effects of electrokinetic remediation (EKR) on antibiotic resistance and arsenic (As) in co-contaminated paddy soils. EKR treatments in soil amended with pig manure (EKR-PD) showed better remediation efficiency compared with that without pig manure. In detail, the content of available As and the abundance of antibiotic-resistant bacteria (ARB) decreased by 25.2 %-41.4 % and 9.5 %-21.1 % after 7-d remediation, respectively, due to a relatively higher current density for EKR-PD. The role of the electric field contributed to 33.9 % of antibiotic degradation. Antibiotic resistance genes (ARGs) with ribosomal-protection and enzymatic-deactivation types were easier to remove, with the removal ratio of 37.8 %-41.6 % in EKR-PD. Brevundimonas was the most significantly different species during remediation. Bacillus and Clostridium_ sensu_stricto_1 were potential host bacteria of ARGs in the electric field. Membrane transport might be an effective strategy for microorganisms to respond to the stress of both electric field and co-contaminated environments. This study supports the potential role of EKR in the co-contamination of heavy metals and antibiotic resistance under manure application.
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Affiliation(s)
- Mengmeng Yan
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Changxiong Zhu
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Binxu Li
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Shiming Su
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Hongna Li
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China.
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28
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Fei Y, Chen S, Wang Z, Chen T, Zhang B. Woodchip-sulfur based mixotrophic biotechnology for hexavalent chromium detoxification in the groundwater. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 324:116298. [PMID: 36179473 DOI: 10.1016/j.jenvman.2022.116298] [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: 06/29/2022] [Revised: 08/26/2022] [Accepted: 09/14/2022] [Indexed: 06/16/2023]
Abstract
This study investigated groundwater hexavalent chromium (Cr(VI)) decontamination by a biological permeable reactive barrier (bio-PRB), where a woodchip-elemental sulfur [S(0)] based mixotrophic process was established. 89.0 ± 0.27% of Cr(VI) was removed from the synthetic groundwater after 72 h at a concentration of 50 mg/L during the preliminary batch experiment. The impact of geochemical and hydrodynamic conditions Cr(VI) removal was investigated in the bio-PRB over 225 days. Although elevated Cr(VI) (i.e., 75 mg/L), addition of nitrate and short hydraulic retention time reduced the Cr(VI) removal, 87.2 ± 2.09% of Cr(VI) removal was accomplished. Characterization of the solids indicated that the soluble Cr(VI) was converted and immobilized as the insoluble trivalent chromium [Cr(III)]. 16S rRNA gene based sequencing results suggested that micromolecules produced by woodchip cellulose hydrolyzing- and sulfur oxidizing bacteria were further used by functional Cr(VI) removal bacteria (e.g., Geobacteraceae and Pseudomonas). The extracellular protein and humic-like substances in extracellular polymeric substances (EPS) can bind toxic Cr(VI) through carboxyl and hydroxyl groups, and reduce Cr(VI) in an enzymatic manner. The preliminary finding of this study provided a potential way to utilize agricultural waste for in-situ Cr(VI) contaminated-groundwater remediation.
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Affiliation(s)
- Yangmei Fei
- School of Water Resources and Environment, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), Beijing, 100083, PR China
| | - Siming Chen
- School of Water Resources and Environment, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), Beijing, 100083, PR China.
| | - Zhongli Wang
- School of Water Resources and Environment, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), Beijing, 100083, PR China
| | - Tao Chen
- School of Environment, South China Normal University, University Town, Guangzhou, 510006, China.
| | - Baogang Zhang
- School of Water Resources and Environment, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), Beijing, 100083, PR China
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Han S, Tang R, Yang S, Xie CJ, Narsing Rao MP, Liu GH, Zhou SG. Two ferric-reducing bacteria Geothrix terrae sp. nov. and Geothrix alkalitolerans sp. nov., isolated from paddy soil. Arch Microbiol 2022; 204:699. [DOI: 10.1007/s00203-022-03293-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/10/2022] [Accepted: 10/18/2022] [Indexed: 11/12/2022]
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Castro AR, Martins G, Salvador AF, Cavaleiro AJ. Iron Compounds in Anaerobic Degradation of Petroleum Hydrocarbons: A Review. Microorganisms 2022; 10:2142. [PMID: 36363734 PMCID: PMC9695802 DOI: 10.3390/microorganisms10112142] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 10/26/2022] [Accepted: 10/26/2022] [Indexed: 09/22/2023] Open
Abstract
Waste and wastewater containing hydrocarbons are produced worldwide by various oil-based industries, whose activities also contribute to the occurrence of oil spills throughout the globe, causing severe environmental contamination. Anaerobic microorganisms with the ability to biodegrade petroleum hydrocarbons are important in the treatment of contaminated matrices, both in situ in deep subsurfaces, or ex situ in bioreactors. In the latter, part of the energetic value of these compounds can be recovered in the form of biogas. Anaerobic degradation of petroleum hydrocarbons can be improved by various iron compounds, but different iron species exert distinct effects. For example, Fe(III) can be used as an electron acceptor in microbial hydrocarbon degradation, zero-valent iron can donate electrons for enhanced methanogenesis, and conductive iron oxides may facilitate electron transfers in methanogenic processes. Iron compounds can also act as hydrocarbon adsorbents, or be involved in secondary abiotic reactions, overall promoting hydrocarbon biodegradation. These multiple roles of iron are comprehensively reviewed in this paper and linked to key functional microorganisms involved in these processes, to the underlying mechanisms, and to the main influential factors. Recent research progress, future perspectives, and remaining challenges on the application of iron-assisted anaerobic hydrocarbon degradation are highlighted.
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Affiliation(s)
- Ana R. Castro
- CEB—Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
- LABBELS—Associate Laboratory, 4704-553 Braga/Guimarães, Portugal
| | - Gilberto Martins
- CEB—Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
- LABBELS—Associate Laboratory, 4704-553 Braga/Guimarães, Portugal
| | - Andreia F. Salvador
- CEB—Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
- LABBELS—Associate Laboratory, 4704-553 Braga/Guimarães, Portugal
| | - Ana J. Cavaleiro
- CEB—Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
- LABBELS—Associate Laboratory, 4704-553 Braga/Guimarães, Portugal
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31
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Xia Q, Ai Z, Huang W, Yang F, Liu F, Lei Z, Huang W. Recent progress in applications of Feammox technology for nitrogen removal from wastewaters: A review. BIORESOURCE TECHNOLOGY 2022; 362:127868. [PMID: 36049707 DOI: 10.1016/j.biortech.2022.127868] [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] [Received: 07/31/2022] [Revised: 08/24/2022] [Accepted: 08/25/2022] [Indexed: 06/15/2023]
Abstract
Feammox process is crucial for the global nitrogen cycle and has great potentials for the treatment of low COD/NH4+-N wastewaters. This work provides a systematic and comprehensive overview of the Feammox process. Specifically, underlying mechanisms and functional microbes mediating the Feammox process are summarized in detail. And key influencing factors including pH, temperature, dissolved oxygen, organic carbon, source of Fe(III) as well as various electron shuttles are discussed. Additionally, recent development trends and attempts of the Feammox technology in wastewater treatment applications are reviewed, and perspectives for future development are presented. A thorough review of the recent progress in Feammox process is expected to provide valuable information for further process optimization, which is helpful to achieve a more economical operation and better nitrogen removal performance in future field applications.
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Affiliation(s)
- Qing Xia
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province, College of Ecology and Environment, Hainan University, 58 Renmin Avenue, Meilan District, Haikou 570228, China
| | - Ziyin Ai
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province, College of Ecology and Environment, Hainan University, 58 Renmin Avenue, Meilan District, Haikou 570228, China
| | - Wenli Huang
- MOE Key Laboratory of Pollution Process and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, No. 94 Weijin Road, Nankai District, Tianjin 300071, China
| | - Fei Yang
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province, College of Ecology and Environment, Hainan University, 58 Renmin Avenue, Meilan District, Haikou 570228, China
| | - Fei Liu
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province, College of Ecology and Environment, Hainan University, 58 Renmin Avenue, Meilan District, Haikou 570228, China
| | - Zhongfang Lei
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Weiwei Huang
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province, College of Ecology and Environment, Hainan University, 58 Renmin Avenue, Meilan District, Haikou 570228, China.
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Srivastava P, Al-Obaidi SA, Webster G, Weightman AJ, Sapsford DJ. Towards passive bioremediation of dye-bearing effluents using hydrous ferric oxide wastes: Mechanisms, products and microbiology. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 317:115332. [PMID: 35617861 DOI: 10.1016/j.jenvman.2022.115332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 04/14/2022] [Accepted: 05/14/2022] [Indexed: 06/15/2023]
Abstract
A novel, circular economy-inspired approach for the "passive" (non-powered and reagent-free) treatment of dye-bearing effluent is presented. The treatment utilises the biogeochemical interaction of dye-bearing wastewater with hydrous ferric oxide (HFO) bearing sludges. The work presented demonstrates for the first time the reuse of HFO-rich waste sludges from potable water and mine water treatment. The waste was used directly without modification or reagent addition, as media/substrate in simple flow-through reactors for the decolourisation and biodegradation of methyl orange (MO) and mixed dyes textile effluent. Three phases of exploratory proof of concept work were undertaken. Columns containing HFO sludges were challenged with solution of MO, and MO amended with glycerol (Phase I), MO in a synthetic textile effluent recipe (Phase II), and real mixed textile effluent containing a mixture of dyes (Phase III). After an initial lag period extensive decolourisation of dye was observed in all cases at rates comparable with pure strains and engineered bioreactor processes, with evidence of biodegradation beyond simple cleavage of the mono azo chromophore and mineralisation. The microbiology of the initial sludge samples in both cases exhibited a diverse range of iron oxidising and reducing bacteria. However, post experiment the microbiology of sludge evolved from being dominated by Proteobacteria to being dominated by Firmicutes. Distinct changes in the microbial community structure were observed in post-treatment MWTS and WTWS where genera capable of iron and sulphate reduction and/or aromatic amine degradation were identified. Average nitrogen removal rates for the columns ranged from 27.8 to 194 g/m3/day which is higher than engineered sequential anaerobic-aerobic bioreactor. Postulated mechanisms for the fast anaerobic decolourisation, biodegradation, and mineralisation of the dyes (as well nitrogen transformations) include various direct and indirect enzymatic and metabolic reactions, as well as reductive attack by continuously regenerated reductants such as Fe(II), HFO bound Fe(II), FeS, and HS-. The ability of iron reducers to degrade aromatic rings is also considered important in the further biodegradation and complete mineralisation of organic carbon. The study reveals that abundant and ubiquitous HFO-rich waste sludges, can be used without amendment, as a substrate in simple flow-through bioremediation system for the decolourisation and partial biodegradation of dyes in textile effluent.
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Affiliation(s)
- Pallavee Srivastava
- School of Engineering, Cardiff University, Queen's Building, The Parade, Cardiff, CF24 3AA, United Kingdom.
| | - Safaa A Al-Obaidi
- School of Engineering, Cardiff University, Queen's Building, The Parade, Cardiff, CF24 3AA, United Kingdom
| | - Gordon Webster
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, United Kingdom
| | - Andrew J Weightman
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, United Kingdom
| | - Devin J Sapsford
- School of Engineering, Cardiff University, Queen's Building, The Parade, Cardiff, CF24 3AA, United Kingdom
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Holmes DE, Zhou J, Smith JA, Wang C, Liu X, Lovley DR. Different outer membrane c-type cytochromes are involved in direct interspecies electron transfer to Geobacter or Methanosarcina species. MLIFE 2022; 1:272-286. [PMID: 38818222 PMCID: PMC10989804 DOI: 10.1002/mlf2.12037] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 07/21/2022] [Accepted: 07/26/2022] [Indexed: 06/01/2024]
Abstract
Direct interspecies electron transfer (DIET) may be most important in methanogenic environments, but mechanistic studies of DIET to date have primarily focused on cocultures in which fumarate was the terminal electron acceptor. To better understand DIET with methanogens, the transcriptome of Geobacter metallireducens during DIET-based growth with G. sulfurreducens reducing fumarate was compared with G. metallireducens grown in coculture with diverse Methanosarcina. The transcriptome of G. metallireducens cocultured with G. sulfurreducens was significantly different from those with Methanosarcina. Furthermore, the transcriptome of G. metallireducens grown with Methanosarcina barkeri, which lacks outer-surface c-type cytochromes, differed from those of G. metallireducens cocultured with M. acetivorans or M. subterranea, which have an outer-surface c-type cytochrome that serves as an electrical connect for DIET. Differences in G. metallireducens expression patterns for genes involved in extracellular electron transfer were particularly notable. Cocultures with c-type cytochrome deletion mutant strains, ∆Gmet_0930, ∆Gmet_0557 and ∆Gmet_2896, never became established with G. sulfurreducens but adapted to grow with all three Methanosarcina. Two porin-cytochrome complexes, PccF and PccG, were important for DIET; however, PccG was more important for growth with Methanosarcina. Unlike cocultures with G. sulfurreducens and M. acetivorans, electrically conductive pili were not needed for growth with M. barkeri. Shewanella oneidensis, another electroactive microbe with abundant outer-surface c-type cytochromes, did not grow via DIET. The results demonstrate that the presence of outer-surface c-type cytochromes does not necessarily confer the capacity for DIET and emphasize the impact of the electron-accepting partner on the physiology of the electron-donating DIET partner.
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Affiliation(s)
- Dawn E. Holmes
- Department of MicrobiologyUniversity of Massachusetts‐AmherstAmherstMassachusettsUSA
- Department of Physical and Biological ScienceWestern New England UniversitySpringfieldMassachusettsUSA
| | - Jinjie Zhou
- Department of MicrobiologyUniversity of Massachusetts‐AmherstAmherstMassachusettsUSA
- Institute for Advanced StudyShenzhen UniversityShenzhenChina
| | - Jessica A. Smith
- Department of MicrobiologyUniversity of Massachusetts‐AmherstAmherstMassachusettsUSA
- Department of Biomolecular SciencesCentral Connecticut State UniversityNew BritainConnecticutUSA
| | - Caiqin Wang
- Department of MicrobiologyUniversity of Massachusetts‐AmherstAmherstMassachusettsUSA
- College of EnvironmentZhejiang University of TechnologyHangzhouChina
| | - Xinying Liu
- Department of MicrobiologyUniversity of Massachusetts‐AmherstAmherstMassachusettsUSA
- College of Environmental Science and EngineeringBeijing Forestry UniversityBeijingChina
| | - Derek R. Lovley
- Department of MicrobiologyUniversity of Massachusetts‐AmherstAmherstMassachusettsUSA
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Nixon SL, Bonsall E, Cockell CS. Limitations of microbial iron reduction under extreme conditions. FEMS Microbiol Rev 2022; 46:6645348. [PMID: 35849069 PMCID: PMC9629499 DOI: 10.1093/femsre/fuac033] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 06/23/2022] [Accepted: 07/15/2022] [Indexed: 01/09/2023] Open
Abstract
Microbial iron reduction is a widespread and ancient metabolism on Earth, and may plausibly support microbial life on Mars and beyond. Yet, the extreme limits of this metabolism are yet to be defined. To investigate this, we surveyed the recorded limits to microbial iron reduction in a wide range of characterized iron-reducing microorganisms (n = 141), with a focus on pH and temperature. We then calculated Gibbs free energy of common microbially mediated iron reduction reactions across the pH-temperature habitability space to identify thermodynamic limits. Comparing predicted and observed limits, we show that microbial iron reduction is generally reported at extremes of pH or temperature alone, but not when these extremes are combined (with the exception of a small number of acidophilic hyperthermophiles). These patterns leave thermodynamically favourable combinations of pH and temperature apparently unoccupied. The empty spaces could be explained by experimental bias, but they could also be explained by energetic and biochemical limits to iron reduction at combined extremes. Our data allow for a review of our current understanding of the limits to microbial iron reduction at extremes and provide a basis to test more general hypotheses about the extent to which biochemistry establishes the limits to life.
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Affiliation(s)
- Sophie L Nixon
- Corresponding author: Department of Earth and Environmental Sciences, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK. E-mail:
| | - Emily Bonsall
- Biological and Environmental Sciences, University of Stirling, Stirling, FK9 4LA, United Kingdom
| | - Charles S Cockell
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, EH9 3FD, United Kingdom
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Wang Y, You LX, Zhong HL, Wu GK, Li YP, Yang XJ, Wang AJ, Nealson KH, Herzberg M, Rensing C. Au(III)-induced extracellular electron transfer by Burkholderia contaminans ZCC for the bio-recovery of gold nanoparticles. ENVIRONMENTAL RESEARCH 2022; 210:112910. [PMID: 35151659 DOI: 10.1016/j.envres.2022.112910] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 01/15/2022] [Accepted: 02/05/2022] [Indexed: 06/14/2023]
Abstract
The biorecovery of gold (Au) by microbial reduction has received increasing attention, however, the biomolecules involved and the mechanisms by which they operate to produce Au nanoparticles have been not resolved. Here we report that Burkholderia contaminans ZCC is capable of reduction of Au(III) to Au nanoparticles on the cell surface. Exposure of B. contaminans ZCC to Au(III) led to significant changes in the functional group of cell proteins, with approximately 11.1% of the (C-C/C-H) bonds being converted to CO (8.1%) and C-OH (3.0%) bonds and 29.4% of the CO bonds being converted to (C-OH/C-O-C/P-O-C) bonds, respectively. In response to Au(III), B. contaminans ZCC also displayed the ability of extracellular electron transfer (EET) via membrane proteins and could produce reduced riboflavin as verified by electrochemical and liquid chromatography-mass spectrometric results, but did not do so without Au(III) being present. Addition of exogenous reduced riboflavin to the medium suggested that B. contaminans ZCC could utilize indirect EET via riboflavin to enhance the rate of reduction of Au(III). Transcriptional analysis of the riboflavin genes (ribBDEFH) supported the view of the importance of riboflavin in the reduction of Au(III) and its importance in the biorecovery of gold.
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Affiliation(s)
- Yi Wang
- College of Geography and Environmental Sciences, Zhejiang Normal University, Jinhua, 321004, PR China
| | - Le-Xing You
- College of Geography and Environmental Sciences, Zhejiang Normal University, Jinhua, 321004, PR China.
| | - Hong-Lin Zhong
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, PR China
| | - Gao-Kai Wu
- College of Geography and Environmental Sciences, Zhejiang Normal University, Jinhua, 321004, PR China
| | - Yuan-Ping Li
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, PR China
| | - Xiao-Jun Yang
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, PR China
| | - Ai-Jun Wang
- College of Geography and Environmental Sciences, Zhejiang Normal University, Jinhua, 321004, PR China
| | - Kenneth H Nealson
- Department of Earth Science, University of Southern California, Los Angeles, CA, USA
| | - Martin Herzberg
- Molecular Microbiology, Institute for Biology/Microbiology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120, Halle/Saale, Germany
| | - Christopher Rensing
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, PR China.
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36
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Shi XC, Tremblay PL, Xue M, Song X, Zhang T. Fumarate disproportionation by Geobacter sulfurreducens and its involvement in biocorrosion and interspecies electron transfer. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 827:154251. [PMID: 35245554 DOI: 10.1016/j.scitotenv.2022.154251] [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: 12/10/2021] [Revised: 02/14/2022] [Accepted: 02/26/2022] [Indexed: 06/14/2023]
Abstract
The model electroactive bacterium Geobacter sulfurreducens can acquire electrons directly from solid donors including metals and other species. Reports on this physiology concluding that solid donors are the only electron sources were conducted with fumarate believed to serve exclusively as the terminal electron acceptor (TEA). Here, G. sulfurreducens was repeatedly transferred for adaptation within a growth medium containing only fumarate and no other solid or soluble substrate. The resulting evolved strain grew efficiently with either the C4-dicarboxylate fumarate or malate acting simultaneously as electron donor, carbon source, and electron acceptor via disproportionation. Whole-genome sequencing identified 38 mutations including one in the regulator PilR known to repress the expression of the C4-dicarboxylate antiporter DcuB essential to G. sulfurreducens when growing with fumarate. Futhermore, the PilR mutation was identical to the sole mutation previously reported in an evolved G. sulfurreducens grown in a co-culture assumed to derive energy solely from direct interspecies electron transfer, but cultivated with fumarate as the TEA. When cultivating the fumarate-adapted strain in the presence of stainless steel and fumarate, biocorrosion was observed and bacterial growth was accelerated 2.3 times. These results suggest that G. sulfurreducens can conserve energy concomitantly from C4-dicarboxylate disproportionation and the oxidation of a solid electron donor. This co-metabolic capacity confers an advantage to Geobacter for survival and colonization and explains in part why these microbes are omnipresent in different anaerobic ecosystems.
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Affiliation(s)
- Xiao-Chen Shi
- School of Chemistry, Chemical Engineering, and Life Science, Wuhan University of Technology, Wuhan 430070, PR China; School of Resources and Environmental Engineering, Wuhan University of Technology, Wuhan 430070, PR China; Wuhan University of Technology Advanced Engineering Technology Research Institute of Zhongshan City, Zhongshan 528437, PR China
| | - Pier-Luc Tremblay
- School of Chemistry, Chemical Engineering, and Life Science, Wuhan University of Technology, Wuhan 430070, PR China; State Key Laboratory of Silicate Materials for Architectures, Wuhan University of Technology, Wuhan 430070, PR China; Sanya Science and Education Innovation Park, Wuhan University of Technology, Sanya 572024, PR China
| | - Miao Xue
- Institut WUT-AMU, Wuhan University of Technology, Wuhan 430070, PR China
| | - Xinyi Song
- Institut WUT-AMU, Wuhan University of Technology, Wuhan 430070, PR China
| | - Tian Zhang
- School of Chemistry, Chemical Engineering, and Life Science, Wuhan University of Technology, Wuhan 430070, PR China; School of Resources and Environmental Engineering, Wuhan University of Technology, Wuhan 430070, PR China; Institut WUT-AMU, Wuhan University of Technology, Wuhan 430070, PR China; State Key Laboratory of Silicate Materials for Architectures, Wuhan University of Technology, Wuhan 430070, PR China; Sanya Science and Education Innovation Park, Wuhan University of Technology, Sanya 572024, PR China.
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37
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Zhuang Z, Xia X, Yang G, Zhuang L. The Role of Exopolysaccharides in Direct Interspecies Electron Transfer. Front Microbiol 2022; 13:927246. [PMID: 35783440 PMCID: PMC9244359 DOI: 10.3389/fmicb.2022.927246] [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: 04/24/2022] [Accepted: 05/23/2022] [Indexed: 11/14/2022] Open
Abstract
Direct interspecies electron transfer (DIET) is an effective mechanism for microbial species to exchange electrons cooperatively during syntrophic metabolism. It is generally accepted that DIET is mainly mediated by electrically conductive pili and outer surface c-type cytochromes (c-Cyts). However, as an extracellular matrix is ubiquitous and abundant on the surface of microorganisms, the effect and mechanism of exopolysaccharides on DIET are still unclear. This study constructed a co-culture of exopolysaccharides-deficient Geobacter sulfurreducens with Geobacter metallireducens to explore the role of exopolysaccharides in DIET. Results revealed that the deficiency of exopolysaccharides extended the metabolic period of the co-culture by 44.4% and changed the proportions of each species in the co-culture. The exopolysaccharides-deficient co-culture failed to form large, tight spherical aggregates and the expression of c-Cyts and pili was decreased. The addition of magnetite and granular activated carbon (GAC), respectively, might compensate for the functions of c-Cyts and pili in the first generation of co-culture, but the stimulatory effect on the metabolic stable period co-culture was fairly limited. These findings demonstrate that non-conductive exopolysaccharides are an important component of DIET aggregates and an extracellular matrix for DIET-required c-Cyts.
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38
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Chidiac C, Kim Y, de Lannoy C. Enhanced Pb(II) removal from water using conductive carbonaceous nanomaterials as bacterial scaffolds: An experimental and modelling approach. JOURNAL OF HAZARDOUS MATERIALS 2022; 431:128516. [PMID: 35255332 DOI: 10.1016/j.jhazmat.2022.128516] [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: 12/09/2021] [Revised: 02/14/2022] [Accepted: 02/17/2022] [Indexed: 06/14/2023]
Abstract
This study investigated the abilities of electrochemically active bacteria (EAB) as bio-catalysts for Pb(II) bioreduction in an attached growth reactor. Electrically conductive carbon nanofibers (CNF) were used as bacterial scaffolds to facilitate electron transfer between EAB and Pb(II). Our results demonstrated that the CNF attached growth reactor can remove > 80% and > 90% of Pb(II) from solution at 0.5 mg/L and 5.0 mg/L concentrations, respectively, and maintained Pb(II) levels < 0.10 mg/L over repeated Pb(II) dosages dosed at all concentrations. Experimental measurements by SEM-EDX and ICP-OES provided evidence that Pb(II) was reduced to Pb0, suggesting that Pb(II) was adsorbed onto CNFs, and subsequently bioreduced. Numerical modelling was used to estimate Pb(II) concentrations along the CNFs via capturing Pb(II)'s diffusive transport, and the removal mechanisms governed by EAB and CNF adsorption. The model simulation results demonstrated that Pb(II) bioreduction was dominant in the reactor and the significance of Monod kinetics, biofilm thickness and Pb(II) dosage concentration on its removal. This study is the first to prove EAB's ability to treat Pb(II) from contaminated waters in an attached growth configuration. The findings here demonstrate that CNFs can boost biological treatment efficacies in wastewater and/or water treatment to meet stringent water guidelines.
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Affiliation(s)
- Cassandra Chidiac
- Department of Chemical Engineering, McMaster University, 1280 Main Street West, Hamilton, ON, Canada.
| | - Younggy Kim
- Department of Civil Engineering, McMaster University, Canada.
| | - Charles de Lannoy
- Department of Chemical Engineering, McMaster University, 1280 Main Street West, Hamilton, ON, Canada.
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Thomas GH. Microbial Musings - Spring 2022. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35696259 DOI: 10.1099/mic.0.001205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Gavin H Thomas
- Department of Biology, University of York, York, YO10 5YW, UK
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40
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Pang S, Li N, Luo H, Luo X, Shen T, Yang Y, Jiang J. Autotrophic Fe-Driven Biological Nitrogen Removal Technologies for Sustainable Wastewater Treatment. Front Microbiol 2022; 13:895409. [PMID: 35572701 PMCID: PMC9100419 DOI: 10.3389/fmicb.2022.895409] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 04/08/2022] [Indexed: 11/13/2022] Open
Abstract
Fe-driven biological nitrogen removal (FeBNR) has become one of the main technologies in water pollution remediation due to its economy, safety and mild reaction conditions. This paper systematically summarizes abiotic and biotic reactions in the Fe and N cycles, including nitrate/nitrite-dependent anaerobic Fe(II) oxidation (NDAFO) and anaerobic ammonium oxidation coupled with Fe(III) reduction (Feammox). The biodiversity of iron-oxidizing microorganisms for nitrate/nitrite reduction and iron-reducing microorganisms for ammonium oxidation are reviewed. The effects of environmental factors, e.g., pH, redox potential, Fe species, extracellular electron shuttles and natural organic matter, on the FeBNR reaction rate are analyzed. Current application advances in natural and artificial wastewater treatment are introduced with some typical experimental and application cases. Autotrophic FeBNR can treat low-C/N wastewater and greatly benefit the sustainable development of environmentally friendly biotechnologies for advanced nitrogen control.
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Affiliation(s)
- Suyan Pang
- Key Laboratory of Songliao Aquatic Environment, School of Municipal and Environmental Engineering, Ministry of Education, Jilin Jianzhu University, Changchun, China
| | - Ning Li
- Key Laboratory for City Cluster Environmental Safety and Green Development of the Ministry of Education, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Guangdong Provincial Engineering Technology Research Center for Life and Health of River & Lake, Pearl River Water Resources Research Institute, Pearl River Water Resources Commission of the Ministry of Water Resources, Guangzhou, China
- *Correspondence: Ning Li, ;
| | - Huan Luo
- Guangdong Provincial Engineering Technology Research Center for Life and Health of River & Lake, Pearl River Water Resources Research Institute, Pearl River Water Resources Commission of the Ministry of Water Resources, Guangzhou, China
| | - Xiaonan Luo
- Key Laboratory for City Cluster Environmental Safety and Green Development of the Ministry of Education, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Tong Shen
- Key Laboratory for City Cluster Environmental Safety and Green Development of the Ministry of Education, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Yanan Yang
- Guangdong Provincial Engineering Technology Research Center for Life and Health of River & Lake, Pearl River Water Resources Research Institute, Pearl River Water Resources Commission of the Ministry of Water Resources, Guangzhou, China
| | - Jin Jiang
- Key Laboratory for City Cluster Environmental Safety and Green Development of the Ministry of Education, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
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Cai C, Ni G, Xia J, Zhang X, Zheng Y, He B, Marcellin E, Li W, Pu J, Yuan Z, Hu S. Response of the Anaerobic Methanotrophic Archaeon Candidatus " Methanoperedens nitroreducens" to the Long-Term Ferrihydrite Amendment. Front Microbiol 2022; 13:799859. [PMID: 35509320 PMCID: PMC9058156 DOI: 10.3389/fmicb.2022.799859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 03/10/2022] [Indexed: 11/30/2022] Open
Abstract
Anaerobic methanotrophic (ANME) archaea can drive anaerobic oxidation of methane (AOM) using solid iron or manganese oxides as the electron acceptors, hypothetically via direct extracellular electron transfer (EET). This study investigated the response of Candidatus "Methanoperedens nitroreducens TS" (type strain), an ANME archaeon previously characterized to perform nitrate-dependent AOM, to an Fe(III)-amended condition over a prolonged period. Simultaneous consumption of methane and production of dissolved Fe(II) were observed for more than 500 days in the presence of Ca. "M. nitroreducens TS," indicating that this archaeon can carry out Fe(III)-dependent AOM for a long period. Ca. "M. nitroreducens TS" possesses multiple multiheme c-type cytochromes (MHCs), suggesting that it may have the capability to reduce Fe(III) via EET. Intriguingly, most of these MHCs are orthologous to those identified in Candidatus "Methanoperedens ferrireducens," an Fe(III)-reducing ANME archaeon. In contrast, the population of Ca. "M. nitroreducens TS" declined and was eventually replaced by Ca. "M. ferrireducens," implying niche differentiation between these two ANME archaea in the environment.
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Affiliation(s)
- Chen Cai
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, China
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, St Lucia, QLD, Australia
| | - Gaofeng Ni
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, St Lucia, QLD, Australia
| | - Jun Xia
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, St Lucia, QLD, Australia
| | - Xueqin Zhang
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, St Lucia, QLD, Australia
| | - Yue Zheng
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Bingqing He
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, St Lucia, QLD, Australia
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD, Australia
| | - Esteban Marcellin
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD, Australia
| | - Weiwei Li
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, St Lucia, QLD, Australia
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing, China
| | - Jiaoyang Pu
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, St Lucia, QLD, Australia
| | - Zhiguo Yuan
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, St Lucia, QLD, Australia
| | - Shihu Hu
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, St Lucia, QLD, Australia
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42
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A Short Overview of Biological Fuel Cells. MEMBRANES 2022; 12:membranes12040427. [PMID: 35448397 PMCID: PMC9031071 DOI: 10.3390/membranes12040427] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 04/08/2022] [Accepted: 04/09/2022] [Indexed: 02/04/2023]
Abstract
This short review summarizes the improvements on biological fuel cells (BioFCs) with or without ionomer separation membrane. After a general introduction about the main challenges of modern energy management, BioFCs are presented including microbial fuel cells (MFCs) and enzymatic fuel cells (EFCs). The benefits of BioFCs include the capability to derive energy from waste-water and organic matter, the possibility to use bacteria or enzymes to replace expensive catalysts such as platinum, the high selectivity of the electrode reactions that allow working with less complicated systems, without the need for high purification, and the lower environmental impact. In comparison with classical FCs and given their lower electrochemical performances, BioFCs have, up to now, only found niche applications with low power needs, but they could become a green solution in the perspective of sustainable development and the circular economy. Ion exchange membranes for utilization in BioFCs are discussed in the final section of the review: they include perfluorinated proton exchange membranes but also aromatic polymers grafted with proton or anion exchange groups.
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43
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Aguilar-Muñoz P, Lavergne C, Chamy R, Cabrol L. The biotechnological potential of microbial communities from Antarctic soils and sediments: application to low temperature biogenic methane production. J Biotechnol 2022; 351:38-49. [DOI: 10.1016/j.jbiotec.2022.04.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 04/20/2022] [Accepted: 04/26/2022] [Indexed: 11/24/2022]
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Yang G, Li Y, Lin A, Zhuang L. Geobacter benzoatilyticus sp. nov., a novel benzoate-oxidizing, iron-reducing bacterium isolated from petroleum contaminated soil. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005281] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A strictly anaerobic bacterial strain, designated Jerry-YXT, was isolated from petroleum-contaminated soil sampled in China. Strain Jerry-YXT was a Gram-stain-negative bacterium forming reddish colonies. It grew optimally at 30 °C and pH 7.0, and tolerated 1.0 % (w/v) NaCl. Strain Jerry-YXT was able to use fumarate, ferric citrate and ferrihydrite as electron acceptors, and ethanol, acetate and benzoate as electron donors. The major fatty acids of this strain were C16 : 0 and C16 : 1
ω7c/C16 : 1
ω6c (summed feature 3). The 16S rRNA gene sequence-based phylogenetic analysis placed this strain in the genus
Geobacter
, being most closely related to
Geobacter metallireducens
(98.2 % similarity),
Geobacter hydrogenophilus
(98.1 %) and
Geobacter grbiciae
(98.0 %). The DNA G+C content was 57.6 mol%. The average nucleotide identity and digital DNA–DNA hybridization values between the genomes of strain Jerry-YXT and
G. metallireducens
GS-15T were 81.8 and 35.4 %, respectively. The results of the polyphasic study allowed the genotypic and phenotypic differentiation of strain Jerry-YXT from its closest species, which suggested that strain Jerry-YXT represents a novel species of the genus
Geobacter
. The name for the proposed new species is Geobacter benzoatilyticus sp. nov. The type strain is Jerry-YXT (=MCCC 1K05659T=JCM 39190T).
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Affiliation(s)
- Guiqin Yang
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, PR China
| | - Yanling Li
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, PR China
| | - Annian Lin
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, PR China
| | - Li Zhuang
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, PR China
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45
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Yang S, Liu GH, Tang R, Han S, Xie CJ, Zhou SG. Description of two nitrogen-fixing bacteria, Geomonas fuzhouensis sp. nov. and Geomonas agri sp. nov., isolated from paddy soils. Antonie Van Leeuwenhoek 2022; 115:435-444. [PMID: 35094155 DOI: 10.1007/s10482-021-01704-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 12/21/2021] [Indexed: 12/16/2022]
Abstract
Two strictly anaerobic nitrogen-fixing strains, designated RG17T and RG53T, were isolated from paddy soils in China. Strains RG17T and RG53T showed the highest 16S rRNA gene sequence similarities to the type strain Geomonas paludis (97.9-98.4%). Phylogenetic tree based on 16S rRNA gene sequences showed that two strains clustered with members of the genus Geomonas. Growth of strain RG17T was observed at 20-42 °C, pH 5.5-8.5 and 0-0.3% (w/v) NaCl while strain RG53T growth was observed at 20-42 °C, pH 5.5-9.5 and 0-0.7% (w/v) NaCl. Strains RG17T and RG53T contained MK-8 as main menaquinone and C15:1 ω6c, iso-C15:0, and Summed Feature 3 as the major fatty acids. The genomic DNA G + C content of strains RG17T and RG53T were 61.6 and 60.7%, respectively. The digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values between the isolated strains and the closely related Geomonas species were lower than the cut-off value (dDDH 70% and ANI 95-96%) for prokaryotic species delineation. Both strains possessed nif genes nifHDK and nitrogenase activities. Based on the above results, the two strains represent two novel species of the genus Geomonas, for which the names Geomonas fuzhouensis sp. nov. and Geomonas agri sp. nov., are proposed. The type strains are RG17T (= GDMCC 1.2687T = KTCC 25332T) and RG53T (= GDMCC 1.2630T = KCTC 25331T), respectively.
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Affiliation(s)
- Shang Yang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou City, 350002, Fujian Province, People's Republic of China.,Agricultural Bio-Resources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou City, 350003, Fujian Province, People's Republic of China
| | - Guo-Hong Liu
- Agricultural Bio-Resources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou City, 350003, Fujian Province, People's Republic of China
| | - Rong Tang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou City, 350002, Fujian Province, People's Republic of China.,Agricultural Bio-Resources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou City, 350003, Fujian Province, People's Republic of China
| | - Shuang Han
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou City, 350002, Fujian Province, People's Republic of China.,Agricultural Bio-Resources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou City, 350003, Fujian Province, People's Republic of China
| | - Cheng-Jie Xie
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou City, 350002, Fujian Province, People's Republic of China.,Agricultural Bio-Resources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou City, 350003, Fujian Province, People's Republic of China
| | - Shun-Gui Zhou
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou City, 350002, Fujian Province, People's Republic of China.
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46
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Liu GH, Yang S, Tang R, Xie CJ, Zhou SG. Genome Analysis and Description of Three Novel Diazotrophs Geomonas Species Isolated From Paddy Soils. Front Microbiol 2022; 12:801462. [PMID: 35197944 PMCID: PMC8859169 DOI: 10.3389/fmicb.2021.801462] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 12/14/2021] [Indexed: 12/05/2022] Open
Abstract
Five strictly anaerobic strains, designated RG2T, RG3, RG10T, RF4T, and RG29, were isolated from paddy soils in China. Strains RG2T, RF4T, RG10T, RG3, and RG29 grew at temperatures ranging 5–42°C and pH ranging 5.5–8.5. Strains RG2T, RF4T, RG3, and RG29 could tolerate NaCl up to 0–0.7% (w/v) while strain RG10T could tolerate NaCl up to 0–0.8% (w/v). The isolated strains showed the highest 16S rRNA gene sequence similarities to the type strains of Geomonas terrae Red111T and Geomonas paludis Red736T. In phylogenetic (based on 16S rRNA gene sequence) and phylogenomic trees, strains clustered with the members of the genus Geomonas. Menaquinone-8 was the predominant quinone present in all strains. The major fatty acid profiles of all strains were C15:1 ω6c, C16:0, iso-C15:0, and Summed Feature 3. The digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANI) values between the isolated strains and the closely related Geomonas species were lower than the cutoff value (ANI 95–96% and dDDH 70%) for prokaryotic species delineation. Based on physiological, biochemical, and chemotaxonomic properties, strains RG2T, RG10T, and RF4T could easily be differentiated with the members of the genus Geomonas. Additionally, all the isolated strains possessed nifHDK clusters and catalytic compartments of nitrogenase. Based on the above results, the isolated five strains represent three novel species of the genus Geomonas, for which the names Geomonas oryzisoli sp. nov., Geomonas subterranea sp. nov., and Geomonas nitrogeniifigens sp. nov. are proposed. The type strains are RG10T (= GDMCC1.2537T = KCTC 26318T), RG2T (= GDMCC1.2536T = KCTC 25317T), and RF4T (= GDMCC 1.2547T = KCTC 25316T).
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Affiliation(s)
- Guo-Hong Liu
- Agricultural Bio-Resources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Shang Yang
- Agricultural Bio-Resources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Rong Tang
- Agricultural Bio-Resources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Cheng-Jie Xie
- Agricultural Bio-Resources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shun-Gui Zhou
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
- *Correspondence: Shun-Gui Zhou,
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47
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Lovley DR. Electrotrophy: Other microbial species, iron, and electrodes as electron donors for microbial respirations. BIORESOURCE TECHNOLOGY 2022; 345:126553. [PMID: 34906705 DOI: 10.1016/j.biortech.2021.126553] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/06/2021] [Accepted: 12/08/2021] [Indexed: 06/14/2023]
Abstract
Electrotrophy, the growth of microbes on extracellular electron donors, drives important biogeochemical cycles and has practical applications. Studies of Fe(II)-based electrotrophy have provided foundational cytochrome-based mechanistic models for electron transport into cells. Direct electron uptake from other microbial species, Fe(0), or cathodes is of intense interest due to its potential roles in the production and anaerobic oxidation of methane, corrosion, and bioelectrochemical technologies. Other cells or Fe(0) can serve as the sole electron donor supporting the growth of several Geobacter and methanogen strains that are unable to use H2 as an electron donor, providing strong evidence for electrotrophy. Additional evidence for electrotrophy in Geobacter strains and Methanosarcina acetivorans is a requirement for outer-surface c-type cytochromes. However, in most instances claims for electrotrophy in anaerobes are based on indirect inference and the possibility that H2 is actually the electron donor supporting growth has not been rigorously excluded.
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Affiliation(s)
- Derek R Lovley
- Electrobiomaterials Institute, Key Laboratory for Anisotropy and Texture of Materials (Ministry of Education), Northeastern University, Shenyang 110819, China; Department of Microbiology and Institute for Applied Life Sciences (IALS), University of Massachusetts, Amherst, MA, USA.
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48
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From iron to bacterial electroconductive filaments: Exploring cytochrome diversity using Geobacter bacteria. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2021.214284] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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49
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Jin Z, Zhao Z, Liang L, Zhang Y. Effects of ferroferric oxide on azo dye degradation in a sulfate-containing anaerobic reactor: From electron transfer capacity and microbial community. CHEMOSPHERE 2022; 286:131779. [PMID: 34364225 DOI: 10.1016/j.chemosphere.2021.131779] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 07/15/2021] [Accepted: 08/01/2021] [Indexed: 06/13/2023]
Abstract
Anaerobic decolorization of azo dye in sulfate-containing wastewater has been regarded as an economical and effective method, but it is generally limited by the high concentration of azo dye and accumulation of toxic intermediates. To address this problem, Fe3O4 was added to one of the anaerobic reactors to investigate the effects on system performances. Results showed that AO7 removal rate, COD removal rate, and sulfate reduction were enhanced with the addition of Fe3O4 under various influent AO7 concentrations (153 mgCOD/L - 1787 mgCOD/L). According to the proposed pathway for the degradation of AO7, more intermediates (2-hydroxy-1,4-naphthoquinone, phthalide, 4-methylphenol) were produced in the presence of Fe3O4. The electron transfer capacity of sludge was also increased since Fe3O4 could stimulate to secrete humic acid-like organics in EPS. Microbial analysis showed that iron-reducing bacteria like Clostridium and Geobacter were also enriched, which were capable of azo dye and aromatic compounds degradation.
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Affiliation(s)
- Zhen Jin
- Key Laboratory of Industrial Ecology and Environmental Engineering (Dalian University of Technology), Ministry of Education, School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Zhiqiang Zhao
- Key Laboratory of Industrial Ecology and Environmental Engineering (Dalian University of Technology), Ministry of Education, School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Lianfu Liang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Dalian University of Technology), Ministry of Education, School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Yaobin Zhang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Dalian University of Technology), Ministry of Education, School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China.
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50
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Cupples AM, Thelusmond JR. Predicting the occurrence of monooxygenases and their associated phylotypes in soil microcosms. METHODS IN MICROBIOLOGY 2021; 193:106401. [PMID: 34973287 DOI: 10.1016/j.mimet.2021.106401] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/23/2021] [Accepted: 12/23/2021] [Indexed: 10/19/2022]
Abstract
Cometabolic oxidation involves the oxidation of chemicals often by monooxygenases or dioxygenases and can be a removal process for environmental contaminants such as trichloroethene (TCE) or 1,4-dioxane. Information on the occurrence of these genes and their associated microorganisms in environmental samples has the potential to enhance our understanding of contaminant removal. The overall aims were to 1) ascertain which genes encoding for monooxygenases (from methanotrophs, ammonia oxidizing bacteria and toluene/phenol oxidizers) and other key enzymes are present in soil microcosms and 2) determine which phylotypes are associated with those genes. The approach involved a predictive tool called PICRUSt2 and 16S rRNA gene amplicon datasets from two previous soil microcosm studies. The following targets from the KEGG database were examined: pmo/amo, mmo, dmp/pox/tomA, tmo/tbu/tou, bssABC (and downstream genes), tod, xylM, xylA, gst, dhaA, catE, dbfA1, dbfA2 and phenol 2-monooxygenase. A large number of phylotypes were associated with pmo/amo, while mmo was linked to only five. Several phylotypes were associated with both pmo/amo and mmo. The most dominant microorganism predicted for mmoX was Mycobacterium (also predicted for pmo/amo). A large number of phylotypes were associated with all six genes from the dmp/pox/tomA KEGG group. The taxonomic associations predicted for the tmo/tbu/tou KEGG group were more limited. In both datasets, Geobacter was a key phylotype for benzylsuccinate synthase. The dioxygenase-mediated toluene degradation pathway encoded by todC1C2BA was largely absent, as were the genes (xylM, xylA) encoding for xylene monooxygenase. All other genes investigated were predicted to be present and were associated with a number of microorganisms. Overall, the analysis predicted the genes encoding for sMMO (mmo), T3MO/T3MO/ToMO (tmo/tbu/tou) and benzylsuccinate synthase (bssABC) are present for a limited number of phylotypes compared to those encoding for pMMO/AMO (pmo/amo) and phenol monooxygenase/T2MO (dmp/poxA/tomA). These findings suggest in soils contaminant removal via pMMO/AMO or phenol monooxygenase/T2MO may be common because of the occurrence of these enzymes with a large number of phylotypes.
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Affiliation(s)
- Alison M Cupples
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, USA.
| | - Jean-Rene Thelusmond
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, USA
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