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He Z, Chen J, Yuan S, Chen S, Hu Y, Zheng Y, Li D. Iron Plaque: A Shield against Soil Contamination and Key to Sustainable Agriculture. PLANTS (BASEL, SWITZERLAND) 2024; 13:1476. [PMID: 38891285 PMCID: PMC11174575 DOI: 10.3390/plants13111476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 05/14/2024] [Accepted: 05/22/2024] [Indexed: 06/21/2024]
Abstract
Soils play a dominant role in supporting the survival and growth of crops and they are also extremely important for human health and food safety. At present, the contamination of soil by heavy metals remains a globally concerning environmental issue that needs to be resolved. In the environment, iron plaque, naturally occurring on the root surface of wetland plants, is found to be equipped with an excellent ability at blocking the migration of heavy metals from soils to plants, which can be further developed as an environmentally friendly strategy for soil remediation to ensure food security. Because of its large surface-to-volume porous structure, iron plaque exhibits high binding affinity to heavy metals. Moreover, iron plaque can be seen as a reservoir to store nutrients to support the growth of plants. In this review, the formation process of iron plaque, the ecological role that iron plaque plays in the environment and the interaction between iron plaque, plants and microbes, are summarized.
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Affiliation(s)
- Zeping He
- School of Life Sciences and Chemistry, Hunan University of Technology, Zhuzhou 412007, China; (Z.H.); (S.Y.); (S.C.); (Y.Z.)
| | - Jinyuan Chen
- School of Life Sciences and Chemistry, Hunan University of Technology, Zhuzhou 412007, China; (Z.H.); (S.Y.); (S.C.); (Y.Z.)
| | - Shilin Yuan
- School of Life Sciences and Chemistry, Hunan University of Technology, Zhuzhou 412007, China; (Z.H.); (S.Y.); (S.C.); (Y.Z.)
| | - Sha Chen
- School of Life Sciences and Chemistry, Hunan University of Technology, Zhuzhou 412007, China; (Z.H.); (S.Y.); (S.C.); (Y.Z.)
- Hunan Provincial Engineering Research Center of Lily Germplasm Resource Innovation and Deep Processing, Hunan University of Technology, Zhuzhou 412007, China
- Zhuzhou City Joint Laboratory of Environmental Microbiology and Plant Resources Utilization, Hunan University of Technology, Zhuzhou 412007, China
| | - Yuanyi Hu
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha 410125, China;
- National Center of Technology Innovation for Saline-Alkali Tolerant Rice in Sanya, Sanya 572000, China
| | - Yi Zheng
- School of Life Sciences and Chemistry, Hunan University of Technology, Zhuzhou 412007, China; (Z.H.); (S.Y.); (S.C.); (Y.Z.)
| | - Ding Li
- School of Life Sciences and Chemistry, Hunan University of Technology, Zhuzhou 412007, China; (Z.H.); (S.Y.); (S.C.); (Y.Z.)
- Hunan Provincial Engineering Research Center of Lily Germplasm Resource Innovation and Deep Processing, Hunan University of Technology, Zhuzhou 412007, China
- Zhuzhou City Joint Laboratory of Environmental Microbiology and Plant Resources Utilization, Hunan University of Technology, Zhuzhou 412007, China
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Chen C, Fang Y, Zhou D. Selective pressure of PFOA on microbial community: Enrichment of denitrifiers harboring ARGs and the transfer of ferric-electrons. WATER RESEARCH 2023; 233:119813. [PMID: 36863277 DOI: 10.1016/j.watres.2023.119813] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 02/23/2023] [Accepted: 02/24/2023] [Indexed: 06/18/2023]
Abstract
Perfluorooctanoic acid (PFOA), a class of permanent organic pollutants, is frequently detected in surface and ground water, with the latter made up primarily of porous media (such as soils, sediments, and aquifers) that harbor microbial communities. Therefore, we investigated the effects of PFOA on water ecosystems and found that, under stimulation by 2.4 μM PFOA, denitrifiers were significantly enriched due to their hosting antibiotic resistant genes (ARGs), which were 1.45 times more abundant than the control. Furthermore, denitrifying metabolism was enhanced by Fe(II) electron donation. Specifically, 2.4 μM PFOA significantly enhanced the removal of total inorganic nitrogen by 178.6%. The microbial community became predominated by denitrifying bacteria (67.8% abundance). Notably, the nitrate-reduction ferrous-oxidizing (NRFO) bacteria Dechloromonas, Acidovorax, Bradyrhizorium, etc. were significantly enriched. The selective pressures of PFOA driving the enrichment of denitrifiers were twofold. First, the toxic PFOA induced denitrifying bacteria to produce ARGs, mainly including the efflux (occupying 55.4%) and antibiotic inactivation (occupying 41.2%) types, which improved microbial tolerance to PFOA. The risk of horizontal ARGs transmission was elevated as the overall number of horizontally transmissible ARGs increased by 47.1%. Second, Fe(II) electrons were transported via the porin-cytochrome c extracellular electrons transfer system (EET), promoting the expression of nitrate reductases, which in turn further enhanced denitrification. In summary, PFOA regulated the microbial community structure and influenced microbial TN removal functions and increased the contribution of ARGs by the denitrifier hosts, but the PFOA-induced production of ARGs may pose a serious ecological threat that needs to be comprehensively investigated.
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Affiliation(s)
- Congli Chen
- Engineering Research Center of Low-Carbon Treatment and Green Development of Polluted Water in Northeast China, Ministry of Education, Northeast Normal University, Changchun 130117, China; Jilin Engineering Lab for Water Pollution Control and Resources Recovery, Northeast Normal University, Changchun 130117, China; School of Environment, Northeast Normal University, Changchun 130117, China
| | - Yuanping Fang
- Engineering Research Center of Low-Carbon Treatment and Green Development of Polluted Water in Northeast China, Ministry of Education, Northeast Normal University, Changchun 130117, China; Jilin Engineering Lab for Water Pollution Control and Resources Recovery, Northeast Normal University, Changchun 130117, China; School of Environment, Northeast Normal University, Changchun 130117, China
| | - Dandan Zhou
- Engineering Research Center of Low-Carbon Treatment and Green Development of Polluted Water in Northeast China, Ministry of Education, Northeast Normal University, Changchun 130117, China; Jilin Engineering Lab for Water Pollution Control and Resources Recovery, Northeast Normal University, Changchun 130117, China; School of Environment, Northeast Normal University, Changchun 130117, China.
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Yu L, Adamson P, Lay Yap P, Tung T, Makar S, Turra M, Higgins G, Losic D. From Biowaste to Lab-Bench: Low-Cost Magnetic Iron Oxide Nanoparticles for RNA Extraction and SARS-CoV-2 Diagnostics. BIOSENSORS 2023; 13:196. [PMID: 36831962 PMCID: PMC9953475 DOI: 10.3390/bios13020196] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/12/2023] [Accepted: 01/19/2023] [Indexed: 06/18/2023]
Abstract
The gold standard for diagnostics of SARS-CoV-2 (COVID-19) virus is based on real-time polymerase chain reaction (RT-PCR) using centralized PCR facilities and commercial viral RNA extraction kits. One of the key components of these kits are magnetic beads composed of silica coated magnetic iron oxide (Fe2O3 or Fe3O4) nanoparticles, needed for the selective extraction of RNA. At the beginning of the pandemic in 2019, due to a high demand across the world there were severe shortages of many reagents and consumables, including these magnetic beads required for testing for SARS-CoV-2. Laboratories needed to source these products elsewhere, preferably at a comparable or lower cost. Here, we describe the development of a simple, low-cost and scalable preparation of magnetic nanoparticles (MNPs) from biowaste and demonstrate their successful application in viral RNA extraction and the detection of COVID-19. These MNPs have a unique nanoplatelet shape with a high surface area, which are beneficial features, expected to provide improved RNA adsorption, better dispersion and processing ability compared with commercial spherical magnetic beads. Their performance in COVID-19 RNA extraction was evaluated in comparison with commercial magnetic beads and the results presented here showed comparable results for high throughput PCR analysis. The presented magnetic nanoplatelets generated from biomass waste are safe, low-cost, simple to produce in large scale and could provide a significantly reduced cost of nucleic acid extraction for SARS-CoV-2 and other DNA and RNA viruses.
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Affiliation(s)
- Le Yu
- School of Chemical Engineering and Advanced Materials, University of Adelaide, Adelaide, SA 5005, Australia
- ARC Hub for Graphene Enabled Industry Transformation, The University of Adelaide, Adelaide, SA 5005, Australia
| | | | - Pei Lay Yap
- School of Chemical Engineering and Advanced Materials, University of Adelaide, Adelaide, SA 5005, Australia
- ARC Hub for Graphene Enabled Industry Transformation, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Tran Tung
- School of Chemical Engineering and Advanced Materials, University of Adelaide, Adelaide, SA 5005, Australia
- ARC Hub for Graphene Enabled Industry Transformation, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Shaheer Makar
- School of Chemical Engineering and Advanced Materials, University of Adelaide, Adelaide, SA 5005, Australia
- ARC Hub for Graphene Enabled Industry Transformation, The University of Adelaide, Adelaide, SA 5005, Australia
- Faculty of Pharmacy, Assiut University, Assiut 71526, Egypt
| | - Mark Turra
- SA Pathology, Adelaide, SA 5000, Australia
| | | | - Dusan Losic
- School of Chemical Engineering and Advanced Materials, University of Adelaide, Adelaide, SA 5005, Australia
- ARC Hub for Graphene Enabled Industry Transformation, The University of Adelaide, Adelaide, SA 5005, Australia
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Chen Y, Li X, Liu T, Li F, Sun W, Young LY, Huang W. Metagenomic analysis of Fe(II)-oxidizing bacteria for Fe(III) mineral formation and carbon assimilation under microoxic conditions in paddy soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 851:158068. [PMID: 35987227 DOI: 10.1016/j.scitotenv.2022.158068] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 08/08/2022] [Accepted: 08/12/2022] [Indexed: 06/15/2023]
Abstract
Microbially mediated Fe(II) oxidation is prevalent and thought to be central to many biogeochemical processes in paddy soils. However, we have limited insights into the Fe(II) oxidation process in paddy fields, considered the world's largest engineered wetland, where microoxic conditions are ubiquitous. In this study, microaerophilic Fe(II) oxidizing bacteria (FeOB) from paddy soil were enriched in gradient tubes with FeS, FeCO3, and Fe3(PO4)2 as iron sources to investigate their capacity for Fe(II) oxidation and carbon assimilation. Results showed that the highest rate of Fe(II) oxidation (k = 0.836 mM d-1) was obtained in the FeCO3 tubes, and cells grown in the Fe3(PO4)2 tubes yielded maximum assimilation amounts of 13C-NaHCO3 of 1.74% on Day 15. Amorphous Fe(III) oxides were found in all the cell bands with iron substrates as a result of microbial Fe(II) oxidation. Metagenomics analysis of the enriched microbes targeted genes encoding iron oxidase Cyc2, oxygen-reducing terminal oxidase, and ribulose-bisphosphate carboxylase, with results indicated that the potential Fe(II) oxidizers include nitrate-reducing FeOB (Dechloromonas and Thiobacillus), Curvibacter, and Magnetospirillum. By combining cultivation-dependent and metagenomic approaches, our results found a number of FeOB from paddy soil under microoxic conditions, which provide insight into the complex biogeochemical interactions of iron and carbon within paddy fields. The contribution of the FeOB to the element cycling in rice-growing regions deserves further investigation.
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Affiliation(s)
- Yating Chen
- Institute for Disaster Management and Reconstruction, Sichuan University-Hong Kong Polytechnic University, Chengdu 610207, China
| | - Xiaomin Li
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China.
| | - Tongxu Liu
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Fangbai Li
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China.
| | - Weimin Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Lily Y Young
- Department of Environmental Sciences, Rutgers University, New Brunswick, NJ 08901, USA
| | - Weilin Huang
- Department of Environmental Sciences, Rutgers University, New Brunswick, NJ 08901, USA
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Demaret L, Hutchinson IB, Ingley R, Edwards HGM, Fagel N, Compere P, Javaux EJ, Eppe G, Malherbe C. Fe-Rich Fossil Vents as Mars Analog Samples: Identification of Extinct Chimneys in Miocene Marine Sediments Using Raman Spectroscopy, X-Ray Diffraction, and Scanning Electron Microscopy-Energy Dispersive X-Ray Spectroscopy. ASTROBIOLOGY 2022; 22:1081-1098. [PMID: 35704291 DOI: 10.1089/ast.2021.0128] [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: 06/15/2023]
Abstract
On Earth, the circulation of Fe-rich fluids in hydrothermal environments leads to characteristic iron mineral deposits, reflecting the pH and redox chemical conditions of the hydrothermal system, and is often associated with chemotroph microorganisms capable of deriving energy from chemical gradients. On Mars, iron-rich hydrothermal sites are considered to be potentially important astrobiological targets for searching evidence of life during exploration missions, such as the Mars 2020 and the ExoMars 2022 missions. In this study, an extinct hydrothermal chimney from the Jaroso hydrothermal system (SE Spain), considered an interesting geodynamic and mineralogical terrestrial analog for Mars, was analyzed using Raman spectroscopy, X-ray diffraction, and scanning electron microscopy coupled with energy dispersive X-ray spectroscopy. The sample consists of a fossil vent in a Miocene shallow-marine sedimentary deposit composed of a marl substrate, an iron-rich chimney pipe, and a central space filled with backfilling deposits and vent condensates. The iron crust is particularly striking due to the combined presence of molecular and morphological indications of a microbial colonization, including mineral microstructures (e.g., stalks, filaments), iron oxyhydroxide phases (altered goethite, ferrihydrite), and organic signatures (carotenoids, organopolymers). The clear identification of pigments by resonance Raman spectroscopy and the preservation of organics in association with iron oxyhydroxides by Raman microimaging demonstrate that the iron crust was indeed colonized by microbial communities. These analyses confirm that Raman spectroscopy is a powerful tool for documenting the habitability of such historical hydrothermal environments. Finally, based on the results obtained, we propose that the ancient iron-rich hydrothermal pipes should be recognized as singular terrestrial Mars analog specimens to support the preparatory work for robotic in situ exploration missions to Mars, as well as during the subsequent interpretation of data returned by those missions.
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Affiliation(s)
- Lucas Demaret
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liege, Liege, Belgium
- Early Life Traces & Evolution-Astrobiology, UR Astrobiology, University of Liege, Liege, Belgium
| | - Ian B Hutchinson
- Department of Physics and Astronomy, University of Leicester, Leicester, United Kingdom
| | - Richard Ingley
- Department of Physics and Astronomy, University of Leicester, Leicester, United Kingdom
| | - Howell G M Edwards
- Department of Physics and Astronomy, University of Leicester, Leicester, United Kingdom
| | - Nathalie Fagel
- Laboratory Argiles, Géochimie et Environnements Sédimentaires, University of Liege, Liege, Belgium
| | - Philippe Compere
- Laboratory of Functional and Evolutionary Morphology, UR FOCUS, and Centre for Applied Research and Education in Microscopy (CAREM), University of Liege, Liege, Belgium
| | - Emmanuelle J Javaux
- Early Life Traces & Evolution-Astrobiology, UR Astrobiology, University of Liege, Liege, Belgium
| | - Gauthier Eppe
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liege, Liege, Belgium
| | - Cédric Malherbe
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liege, Liege, Belgium
- Early Life Traces & Evolution-Astrobiology, UR Astrobiology, University of Liege, Liege, Belgium
- Department of Physics and Astronomy, University of Leicester, Leicester, United Kingdom
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PioABC-Dependent Fe(II) Oxidation during Photoheterotrophic Growth on an Oxidized Carbon Substrate Increases Growth Yield. Appl Environ Microbiol 2022; 88:e0097422. [PMID: 35862670 PMCID: PMC9361825 DOI: 10.1128/aem.00974-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Microorganisms that carry out Fe(II) oxidation play a major role in biogeochemical cycling of iron in environments with low oxygen. Fe(II) oxidation has been largely studied in the context of autotrophy. Here, we show that the anoxygenic phototroph, Rhodopseudomonas palustris CGA010, carries out Fe(II) oxidation during photoheterotrophic growth with an oxidized carbon source, malate, leading to an increase in cell yield and allowing more carbon to be directed to cell biomass. We probed the regulatory basis for this by transcriptome sequencing (RNA-seq) and found that the expression levels of the known pioABC Fe(II) oxidation genes in R. palustris depended on the redox-sensing two-component system, RegSR, and the oxidation state of the carbon source provided to cells. This provides the first mechanistic demonstration of mixotrophic growth involving reducing power generated from both Fe(II) oxidation and carbon assimilation. IMPORTANCE The simultaneous use of carbon and reduced metals such as Fe(II) by bacteria is thought to be widespread in aquatic environments, and a mechanistic description of this process could improve our understanding of biogeochemical cycles. Anoxygenic phototrophic bacteria like Rhodopseudomonas palustris typically use light for energy and organic compounds as both a carbon and an electron source. They can also use CO2 for carbon by carbon dioxide fixation when electron-rich compounds like H2, thiosulfate, and Fe(II) are provided as electron donors. Here, we show that Fe(II) oxidation can be used in another context to promote higher growth yields of R. palustris when the oxidized carbon compound malate is provided. We further established the regulatory mechanism underpinning this observation.
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Sackett JD, Kamble N, Leach E, Schuelke T, Wilbanks E, Rowe AR. Genome-Scale Mutational Analysis of Cathode-Oxidizing Thioclava electrotropha ElOx9 T. Front Microbiol 2022; 13:909824. [PMID: 35756027 PMCID: PMC9226611 DOI: 10.3389/fmicb.2022.909824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/17/2022] [Indexed: 11/13/2022] Open
Abstract
Extracellular electron transfer (EET) – the process by which microorganisms transfer electrons across their membrane(s) to/from solid-phase materials – has implications for a wide range of biogeochemically important processes in marine environments. Though EET is thought to play an important role in the oxidation of inorganic minerals by lithotrophic organisms, the mechanisms involved in the oxidation of solid particles are poorly understood. To explore the genetic basis of oxidative EET, we utilized genomic analyses and transposon insertion mutagenesis screens (Tn-seq) in the metabolically flexible, lithotrophic Alphaproteobacterium Thioclava electrotropha ElOx9T. The finished genome of this strain is 4.3 MB, and consists of 4,139 predicted ORFs, 54 contain heme binding motifs, and 33 of those 54 are predicted to localize to the cell envelope or have unknown localizations. To begin to understand the genetic basis of oxidative EET in ElOx9T, we constructed a transposon mutant library in semi-rich media which was comprised of >91,000 individual mutants encompassing >69,000 unique TA dinucleotide insertion sites. The library was subjected to heterotrophic growth on minimal media with acetate and autotrophic oxidative EET conditions on indium tin oxide coated glass electrodes poised at –278 mV vs. SHE or un-poised in an open circuit condition. We identified 528 genes classified as essential under these growth conditions. With respect to electrochemical conditions, 25 genes were essential under oxidative EET conditions, and 29 genes were essential in both the open circuit control and oxidative EET conditions. Though many of the genes identified under electrochemical conditions are predicted to be localized in the cytoplasm and lack heme binding motifs and/or homology to known EET proteins, we identified several hypothetical proteins and poorly characterized oxidoreductases that implicate a novel mechanism(s) for EET that warrants further study. Our results provide a starting point to explore the genetic basis of novel oxidative EET in this marine sediment microbe.
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Affiliation(s)
- Joshua D Sackett
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, United States
| | - Nitin Kamble
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, United States
| | - Edmund Leach
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, United States
| | - Taruna Schuelke
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Elizabeth Wilbanks
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Annette R Rowe
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, United States
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She J, Liu J, He H, Zhang Q, Lin Y, Wang J, Yin M, Wang L, Wei X, Huang Y, Chen C, Lin W, Chen N, Xiao T. Microbial response and adaption to thallium contamination in soil profiles. JOURNAL OF HAZARDOUS MATERIALS 2022; 423:127080. [PMID: 34523503 DOI: 10.1016/j.jhazmat.2021.127080] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/09/2021] [Accepted: 08/27/2021] [Indexed: 06/13/2023]
Abstract
Thallium (Tl) is a trace metal with high toxicity. Comprehensive investigation of spatial distribution of Tl and microorganism is still limited in soils from mining area. In this study, 16S rRNA sequencing and network analysis were used for deciphering the co-occurrence patterns of bacterial communities in two different types of soil profiles around a typical Tl-bearing pyrite mine. The results showed that geochemical parameters (such as pH, S, Tl, Fe and TOM) were the driving forces for shaping the vertical distribution of microbial community. According to network analysis, a wide diversity of microbial modules were present in both soil profiles and affected by depth, significantly associated with variations in Tl geochemical fractionation. Phylogenetic information further unveiled that the microbial modules were mainly dominated by Fe reducing bacteria (FeRB), Fe oxidizing bacteria (FeOB), S oxidizing bacteria and Mn reducing bacteria. The results of metagenome indicated that Fe, Mn and S cycle in soil are closely involved in the biogeochemical cycle of Tl. The findings of co-occurrence patterns in the bacterial network and correlation between microorganisms and different geochemical fractions of Tl may benefit the strategy of bioremediation of Tl-contaminated soils with indigenous microbes.
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Affiliation(s)
- Jingye She
- Key Laboratory of Water Quality and Conservation in the Pearl River Delta, Ministry of Education, Guangdong Provincial Key Laboratory of Radionuclides Pollution Control and Resources, School of Environmental Science and Engineering, Guangzhou University, Guangzhou, China
| | - Juan Liu
- Key Laboratory of Water Quality and Conservation in the Pearl River Delta, Ministry of Education, Guangdong Provincial Key Laboratory of Radionuclides Pollution Control and Resources, School of Environmental Science and Engineering, Guangzhou University, Guangzhou, China; Key Laboratory of Mineralogy and Metallogeny, Chinese Academy of Sciences and Guangdong Provincial Key Laboratory of Mineral Physics and Materials, Guangzhou Institute of Geochemistry, Guangzhou 510640, China
| | - Hongping He
- Key Laboratory of Mineralogy and Metallogeny, Chinese Academy of Sciences and Guangdong Provincial Key Laboratory of Mineral Physics and Materials, Guangzhou Institute of Geochemistry, Guangzhou 510640, China
| | - Qiong Zhang
- Department of Earth Sciences, University of Oxford, Oxford, UK
| | - Yuyang Lin
- Key Laboratory of Water Quality and Conservation in the Pearl River Delta, Ministry of Education, Guangdong Provincial Key Laboratory of Radionuclides Pollution Control and Resources, School of Environmental Science and Engineering, Guangzhou University, Guangzhou, China
| | - Jin Wang
- Key Laboratory of Water Quality and Conservation in the Pearl River Delta, Ministry of Education, Guangdong Provincial Key Laboratory of Radionuclides Pollution Control and Resources, School of Environmental Science and Engineering, Guangzhou University, Guangzhou, China.
| | - Meiling Yin
- Key Laboratory of Water Quality and Conservation in the Pearl River Delta, Ministry of Education, Guangdong Provincial Key Laboratory of Radionuclides Pollution Control and Resources, School of Environmental Science and Engineering, Guangzhou University, Guangzhou, China
| | - Lulu Wang
- Key Laboratory of Water Quality and Conservation in the Pearl River Delta, Ministry of Education, Guangdong Provincial Key Laboratory of Radionuclides Pollution Control and Resources, School of Environmental Science and Engineering, Guangzhou University, Guangzhou, China
| | - Xudong Wei
- Key Laboratory of Water Quality and Conservation in the Pearl River Delta, Ministry of Education, Guangdong Provincial Key Laboratory of Radionuclides Pollution Control and Resources, School of Environmental Science and Engineering, Guangzhou University, Guangzhou, China
| | - Yeliang Huang
- Key Laboratory of Water Quality and Conservation in the Pearl River Delta, Ministry of Education, Guangdong Provincial Key Laboratory of Radionuclides Pollution Control and Resources, School of Environmental Science and Engineering, Guangzhou University, Guangzhou, China
| | - Changzhi Chen
- Key Laboratory of Water Quality and Conservation in the Pearl River Delta, Ministry of Education, Guangdong Provincial Key Laboratory of Radionuclides Pollution Control and Resources, School of Environmental Science and Engineering, Guangzhou University, Guangzhou, China
| | - Wenli Lin
- Key Laboratory of Water Quality and Conservation in the Pearl River Delta, Ministry of Education, Guangdong Provincial Key Laboratory of Radionuclides Pollution Control and Resources, School of Environmental Science and Engineering, Guangzhou University, Guangzhou, China
| | - Nan Chen
- Key Laboratory of Water Quality and Conservation in the Pearl River Delta, Ministry of Education, Guangdong Provincial Key Laboratory of Radionuclides Pollution Control and Resources, School of Environmental Science and Engineering, Guangzhou University, Guangzhou, China
| | - Tangfu Xiao
- Key Laboratory of Water Quality and Conservation in the Pearl River Delta, Ministry of Education, Guangdong Provincial Key Laboratory of Radionuclides Pollution Control and Resources, School of Environmental Science and Engineering, Guangzhou University, Guangzhou, China; State Key Laboratory of Geohazard Prevention and Geoenvironment Protection, Chengdu University of Technology, Chengdu, China
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Pecoraro L, Wang X, Shah D, Song X, Kumar V, Shakoor A, Tripathi K, Ramteke PW, Rani R. Biosynthesis Pathways, Transport Mechanisms and Biotechnological Applications of Fungal Siderophores. J Fungi (Basel) 2021; 8:21. [PMID: 35049961 PMCID: PMC8781417 DOI: 10.3390/jof8010021] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 12/21/2021] [Accepted: 12/21/2021] [Indexed: 11/16/2022] Open
Abstract
Iron (Fe) is the fourth most abundant element on earth and represents an essential nutrient for life. As a fundamental mineral element for cell growth and development, iron is available for uptake as ferric ions, which are usually oxidized into complex oxyhydroxide polymers, insoluble under aerobic conditions. In these conditions, the bioavailability of iron is dramatically reduced. As a result, microorganisms face problems of iron acquisition, especially under low concentrations of this element. However, some microbes have evolved mechanisms for obtaining ferric irons from the extracellular medium or environment by forming small molecules often regarded as siderophores. Siderophores are high affinity iron-binding molecules produced by a repertoire of proteins found in the cytoplasm of cyanobacteria, bacteria, fungi, and plants. Common groups of siderophores include hydroxamates, catecholates, carboxylates, and hydroximates. The hydroxamate siderophores are commonly synthesized by fungi. L-ornithine is a biosynthetic precursor of siderophores, which is synthesized from multimodular large enzyme complexes through non-ribosomal peptide synthetases (NRPSs), while siderophore-Fe chelators cell wall mannoproteins (FIT1, FIT2, and FIT3) help the retention of siderophores. S. cerevisiae, for example, can express these proteins in two genetically separate systems (reductive and nonreductive) in the plasma membrane. These proteins can convert Fe (III) into Fe (II) by a ferrous-specific metalloreductase enzyme complex and flavin reductases (FREs). However, regulation of the siderophore through Fur Box protein on the DNA promoter region and its activation or repression depend primarily on the Fe availability in the external medium. Siderophores are essential due to their wide range of applications in biotechnology, medicine, bioremediation of heavy metal polluted environments, biocontrol of plant pathogens, and plant growth enhancement.
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Affiliation(s)
- Lorenzo Pecoraro
- School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, Tianjin 300072, China; (X.W.); (D.S.); (X.S.); (A.S.); (R.R.)
| | - Xiao Wang
- School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, Tianjin 300072, China; (X.W.); (D.S.); (X.S.); (A.S.); (R.R.)
| | - Dawood Shah
- School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, Tianjin 300072, China; (X.W.); (D.S.); (X.S.); (A.S.); (R.R.)
- Institute of Biotechnology and Genetic Engineering, The University of Agriculture Peshawar, Peshawar 25000, Pakistan
| | - Xiaoxuan Song
- School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, Tianjin 300072, China; (X.W.); (D.S.); (X.S.); (A.S.); (R.R.)
| | - Vishal Kumar
- Department of Food Science and Technology, Yeungnam University, Gyongsan 38541, Korea;
| | - Abdul Shakoor
- School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, Tianjin 300072, China; (X.W.); (D.S.); (X.S.); (A.S.); (R.R.)
- College of Geography and Environmental Science, Henan University, Kaifeng 475004, China
| | - Keshawanand Tripathi
- Center for Conservation and Utilization of Blue-Green Algae, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India;
| | - Pramod W. Ramteke
- Faculty of Life Sciences, Mandsaur University, Mandsaur 458001, India;
| | - Rupa Rani
- School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, Tianjin 300072, China; (X.W.); (D.S.); (X.S.); (A.S.); (R.R.)
- Department of Environmental Science and Engineering, Indian Institute of Technology (Indian School of Mines), Dhanbad 826004, India
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10
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Complete Genome Sequence of Halomonas sp. Strain FeN2, a Novel Cathode-Oxidizing Bacterium Isolated from Catalina Harbor Sediments. Microbiol Resour Announc 2021; 10:e0086221. [PMID: 34792381 PMCID: PMC8601139 DOI: 10.1128/mra.00862-21] [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] [Indexed: 11/20/2022] Open
Abstract
We report the complete, closed, circular genome of Halomonas sp. strain FeN2, a metabolically versatile electrotroph that was isolated from Catalina Harbor sediments. The 4.8-Mb genome contains 4,286 protein-coding genes and has complete glycolytic, tricarboxylic acid, glyoxylate, pentose phosphate, and reductive pentose phosphate pathways. FeN2 also contains genes for aerobic and anaerobic (denitrification) respiration.
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11
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Huang YM, Straub D, Blackwell N, Kappler A, Kleindienst S. Meta-omics Reveal Gallionellaceae and Rhodanobacter Species as Interdependent Key Players for Fe(II) Oxidation and Nitrate Reduction in the Autotrophic Enrichment Culture KS. Appl Environ Microbiol 2021; 87:e0049621. [PMID: 34020935 PMCID: PMC8276803 DOI: 10.1128/aem.00496-21] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 05/16/2021] [Indexed: 01/04/2023] Open
Abstract
Nitrate reduction coupled to Fe(II) oxidation (NRFO) has been recognized as an environmentally important microbial process in many freshwater ecosystems. However, well-characterized examples of autotrophic nitrate-reducing Fe(II)-oxidizing bacteria are rare, and their pathway of electron transfer as well as their interaction with flanking community members remain largely unknown. Here, we applied meta-omics (i.e., metagenomics, metatranscriptomics, and metaproteomics) to the nitrate-reducing Fe(II)-oxidizing enrichment culture KS growing under autotrophic or heterotrophic conditions and originating from freshwater sediment. We constructed four metagenome-assembled genomes with an estimated completeness of ≥95%, including the key players of NRFO in culture KS, identified as Gallionellaceae sp. and Rhodanobacter sp. The Gallionellaceae sp. and Rhodanobacter sp. transcripts and proteins likely involved in Fe(II) oxidation (e.g., mtoAB, cyc2, and mofA), denitrification (e.g., napGHI), and oxidative phosphorylation (e.g., respiratory chain complexes I to V) along with Gallionellaceae sp. transcripts and proteins for carbon fixation (e.g., rbcL) were detected. Overall, our results indicate that in culture KS, the Gallionellaceae sp. and Rhodanobacter sp. are interdependent: while Gallionellaceae sp. fixes CO2 and provides organic compounds for Rhodanobacter sp., Rhodanobacter sp. likely detoxifies NO through NO reduction and completes denitrification, which cannot be performed by Gallionellaceae sp. alone. Additionally, the transcripts and partial proteins of cbb3- and aa3-type cytochrome c suggest the possibility for a microaerophilic lifestyle of the Gallionellaceae sp., yet culture KS grows under anoxic conditions. Our findings demonstrate that autotrophic NRFO is performed through cooperation among denitrifying and Fe(II)-oxidizing bacteria, which might resemble microbial interactions in freshwater environments. IMPORTANCE Nitrate-reducing Fe(II)-oxidizing bacteria are widespread in the environment, contribute to nitrate removal, and influence the fate of the greenhouse gases nitrous oxide and carbon dioxide. The autotrophic growth of nitrate-reducing Fe(II)-oxidizing bacteria is rarely investigated and not fully understood. The most prominent model system for this type of study is the enrichment culture KS. To gain insights into the metabolism of nitrate reduction coupled to Fe(II) oxidation in the absence of organic carbon and oxygen, we performed metagenomic, metatranscriptomic, and metaproteomic analyses of culture KS and identified Gallionellaceae sp. and Rhodanobacter sp. as interdependent key Fe(II) oxidizers in culture KS. Our work demonstrates that autotrophic nitrate reduction coupled to Fe(II) oxidation is not performed by an individual strain but is a cooperation of at least two members of the bacterial community in culture KS. These findings serve as a foundation for our understanding of nitrate-reducing Fe(II)-oxidizing bacteria in the environment.
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Affiliation(s)
- Yu-Ming Huang
- Microbial Ecology, Center for Applied Geoscience, University of Tübingen, Tübingen, Germany
- Geomicrobiology, Center for Applied Geoscience, University of Tübingen, Tübingen, Germany
| | - Daniel Straub
- Microbial Ecology, Center for Applied Geoscience, University of Tübingen, Tübingen, Germany
- Quantitative Biology Center (QBiC), University of Tübingen, Tübingen, Germany
| | - Nia Blackwell
- Microbial Ecology, Center for Applied Geoscience, University of Tübingen, Tübingen, Germany
| | - Andreas Kappler
- Geomicrobiology, Center for Applied Geoscience, University of Tübingen, Tübingen, Germany
- Cluster of Excellence, EXC 2124, “Controlling Microbes to Fight Infections,” University of Tübingen, Tübingen, Germany
| | - Sara Kleindienst
- Microbial Ecology, Center for Applied Geoscience, University of Tübingen, Tübingen, Germany
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12
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Tong H, Chen M, Lv Y, Liu C, Zheng C, Xia Y. Changes in the microbial community during microbial microaerophilic Fe(II) oxidation at circumneutral pH enriched from paddy soil. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2021; 43:1305-1317. [PMID: 32975698 DOI: 10.1007/s10653-020-00725-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Accepted: 09/15/2020] [Indexed: 06/11/2023]
Abstract
Fe(II)-oxidizing bacteria (FeOB) are important catalysts for iron cycling in iron-rich marine, groundwater, and freshwater environments. However, few studies have reported the distribution and diversity of these bacteria in flooded paddy soils. This study investigates the microbial structure and diversity of microaerophilic Fe(II)-oxidizing bacteria (mFeOB) and their possible role in Fe(II) oxidation in iron-rich paddy soils. Using enrichment experiments that employed serial transfers, the changes in microaerophilic microbial community were examined via 16S rRNA gene high-throughput sequencing. During enrichments, the Fe(II) oxidation rate decreased as transfers increased, and the maximum rate of Fe(II) oxidation was observed in the first transfer (0.197 mM day-1). Results from X-ray diffraction of minerals and scanning electron microscopy of the cell-mineral aggregates revealed that cell surfaces in all transfers were partly covered with amorphous iron oxide formed by FeOB. After four transfers, the phyla of Proteobacteria had a dominant presence that reached up to 95%. Compared with the original soil, the relative abundances of Cupriavidus, Massilia, Pseudomonas, Ralstonia, Sphingomonas, and Variovorax increased in FeS gradient tubes and became dominant genera after transfers. Cupriavidus, Pseudomonas, and Ralstonia have been identified as FeOB previously. Furthermore, the structure of the microbial community tended to be stable as transfers increased, indicating that other bacterial species might perform important roles in Fe(II) oxidation. These results suggest the potential involvement of mFeOB and these other microorganisms in the Fe(II)-oxidizing process of soils. It will be helpful for future studies to consider their role in related biogeochemical processes, such as transformation of organic matters and heavy metals.
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Affiliation(s)
- Hui Tong
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science and Technology, Guangdong Academy of Sciences, Guangzhou, 510650, China
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, 550081, China
| | - Manjia Chen
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science and Technology, Guangdong Academy of Sciences, Guangzhou, 510650, China
| | - Yahui Lv
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science and Technology, Guangdong Academy of Sciences, Guangzhou, 510650, China
| | - Chengshuai Liu
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, 550081, China.
- CAS Center for Excellence in Quaternary Science and Global Change, Xi'an, 710061, China.
| | - Chunju Zheng
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, 550081, China
| | - Yafei Xia
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, 550081, China
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13
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Engineering lithoheterotrophy in an obligate chemolithoautotrophic Fe(II) oxidizing bacterium. Sci Rep 2021; 11:2165. [PMID: 33495498 PMCID: PMC7835226 DOI: 10.1038/s41598-021-81412-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 01/04/2021] [Indexed: 11/09/2022] Open
Abstract
Neutrophilic Fe(II) oxidizing bacteria like Mariprofundus ferrooxydans are obligate chemolithoautotrophic bacteria that play an important role in the biogeochemical cycling of iron and other elements in multiple environments. These bacteria generally exhibit a singular metabolic mode of growth which prohibits comparative "omics" studies. Furthermore, these bacteria are considered non-amenable to classical genetic methods due to low cell densities, the inability to form colonies on solid medium, and production of copious amounts of insoluble iron oxyhydroxides as their metabolic byproduct. Consequently, the molecular and biochemical understanding of these bacteria remains speculative despite the availability of substantial genomic information. Here we develop the first genetic system in neutrophilic Fe(II) oxidizing bacterium and use it to engineer lithoheterotrophy in M. ferrooxydans, a metabolism that has been speculated but not experimentally validated. This synthetic biology approach could be extended to gain physiological understanding and domesticate other bacteria that grow using a single metabolic mode.
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14
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Duchinski K, Moyer CL, Hager K, Fullerton H. Fine-Scale Biogeography and the Inference of Ecological Interactions Among Neutrophilic Iron-Oxidizing Zetaproteobacteria as Determined by a Rule-Based Microbial Network. Front Microbiol 2019; 10:2389. [PMID: 31708884 PMCID: PMC6823593 DOI: 10.3389/fmicb.2019.02389] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Accepted: 10/02/2019] [Indexed: 12/16/2022] Open
Abstract
Hydrothermal vents, such as those at Lō‘ihi Seamount and the Mariana Arc and back-arc, release iron required to support life from the Earth’s crust. In these ecosystems, bacteria and archaea can oxidize the released iron and therefore play an important role in the biogeochemical cycles of essential nutrients. These organisms often form microbial mats, and the primary producers in these communities can support diverse higher trophic levels. One such class of bacteria are the Zetaproteobacteria. This class of bacteria oxidize iron and commonly produce extracellular iron oxyhydroxide matrices that provide architecture to the microbial mats, so they are considered foundational members of the community and ecosystem engineers. Zetaproteobacteria are responsible for the majority of iron-oxidation in circumneutral, marine, low-oxygen environments. To study the composition of these communities, microbial mats were collected using a biomat sampler, which allows for fine-scale collection of microbial mats. DNA was then extracted and amplified for analysis of the SSU rRNA gene. After quality control and filtering, the SSU rRNA genes from Mariana Arc and Lō‘ihi Seamount microbial mat communities were compared pairwise to determine which site exhibits a greater microbial diversity and how much community overlap exists between the two sites. In-depth analysis was performed with the rule-based microbial network (RMN) algorithm, which identified a possible competitive relationship across oligotypes of a cosmopolitan Zetaproteobacteria operational taxonomic unit (OTU). This result demonstrated the ecological relevance of oligotypes, or fine-scale OTU variants. The oligotype distributions of the cosmopolitan ZetaOTUs varied greatly across the Pacific Ocean. The competitive relationship between dominant oligotypes at Lō‘ihi Seamount and the Mariana Arc and back-arc may be driving their differential distributions across the two regions and may result in species divergence within a cosmopolitan ZetaOTU. This implementation of the RMN algorithm can both predict directional relationships within a community and provide insight to the level at which evolution is occurring across ecosystems.
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Affiliation(s)
| | - Craig L Moyer
- Department of Biology, Western Washington University, Bellingham, WA, United States
| | - Kevin Hager
- Department of Biology, Western Washington University, Bellingham, WA, United States
| | - Heather Fullerton
- Department of Biology, College of Charleston, Charleston, SC, United States
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15
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Exposure to different arsenic species drives the establishment of iron- and sulfur-oxidizing bacteria on rice root iron plaques. World J Microbiol Biotechnol 2019; 35:117. [DOI: 10.1007/s11274-019-2690-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 07/07/2019] [Indexed: 10/26/2022]
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16
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Liu T, Chen D, Li X, Li F. Microbially mediated coupling of nitrate reduction and Fe(II) oxidation under anoxic conditions. FEMS Microbiol Ecol 2019; 95:5371120. [DOI: 10.1093/femsec/fiz030] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 03/06/2019] [Indexed: 11/12/2022] Open
Affiliation(s)
- Tongxu Liu
- Guangzhou Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-environmental Science & Technology, Guangzhou 510650, P. R. China
| | - Dandan Chen
- Guangzhou Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-environmental Science & Technology, Guangzhou 510650, P. R. China
- Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Xiaomin Li
- The Environmental Research Institute, MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, P. R. China
| | - Fangbai Li
- Guangzhou Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-environmental Science & Technology, Guangzhou 510650, P. R. China
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17
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Zhang L, Sun H, Zhang XX, Ren H, Ye L. High diversity of potential nitrate-reducing Fe(II)-oxidizing bacteria enriched from activated sludge. Appl Microbiol Biotechnol 2018; 102:4975-4985. [PMID: 29644429 DOI: 10.1007/s00253-018-8961-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 03/11/2018] [Accepted: 03/21/2018] [Indexed: 11/25/2022]
Abstract
Nitrate-dependent Fe(II) oxidation (NDFO) has been discovered in various environments including activated sludge and can potentially be used to remove nitrate from wastewater. In this study, NDFO sludge was successfully enriched from activated sludge under high Fe(II) concentrations over 100 days and the denitrification rate achieved 1.37 mmol N/(gVSS day). High-throughput sequencing of the bacterial 16S rRNA gene was used to investigate the microbial community structure dynamics during the enrichment process. The results showed that the microbial community changed significantly and high diversity of potential Fe(II)-oxidizing bacteria (FeOB) was observed in the enriched sludge. Thermomonas and Gallionella were the dominant bacterial genera in the enriched sludge and their relative abundances accounted for 9.49 and 4.08%, respectively. Furthermore, it was found that potential FeOB were also abundantly present in activated sludge samples of common municipal wastewater treatment plants. Collectively, this study demonstrated that NDFO could be successfully performed by enriched activated sludge and high diversity of bacteria is involved in this process, and the results also provide baseline information for future research and engineering application of NDFO process.
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Affiliation(s)
- Liangying Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, China
| | - Haohao Sun
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, China
| | - Xu-Xiang Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, China
| | - Hongqiang Ren
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, China
| | - Lin Ye
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, China.
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18
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Usman M, Byrne JM, Chaudhary A, Orsetti S, Hanna K, Ruby C, Kappler A, Haderlein SB. Magnetite and Green Rust: Synthesis, Properties, and Environmental Applications of Mixed-Valent Iron Minerals. Chem Rev 2018; 118:3251-3304. [PMID: 29465223 DOI: 10.1021/acs.chemrev.7b00224] [Citation(s) in RCA: 181] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Mixed-valent iron [Fe(II)-Fe(III)] minerals such as magnetite and green rust have received a significant amount of attention over recent decades, especially in the environmental sciences. These mineral phases are intrinsic and essential parts of biogeochemical cycling of metals and organic carbon and play an important role regarding the mobility, toxicity, and redox transformation of organic and inorganic pollutants. The formation pathways, mineral properties, and applications of magnetite and green rust are currently active areas of research in geochemistry, environmental mineralogy, geomicrobiology, material sciences, environmental engineering, and environmental remediation. These aspects ultimately dictate the reactivity of magnetite and green rust in the environment, which has important consequences for the application of these mineral phases, for example in remediation strategies. In this review we discuss the properties, occurrence, formation by biotic as well as abiotic pathways, characterization techniques, and environmental applications of magnetite and green rust in the environment. The aim is to present a detailed overview of the key aspects related to these mineral phases which can be used as an important resource for researchers working in a diverse range of fields dealing with mixed-valent iron minerals.
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Affiliation(s)
- M Usman
- Environmental Mineralogy, Center for Applied Geosciences , University of Tübingen , 72074 Tübingen , Germany.,Institute of Soil and Environmental Sciences , University of Agriculture , Faisalabad 38040 , Pakistan
| | - J M Byrne
- Geomicrobiology, Center for Applied Geosciences , University of Tübingen , 72074 Tübingen , Germany
| | - A Chaudhary
- Environmental Mineralogy, Center for Applied Geosciences , University of Tübingen , 72074 Tübingen , Germany.,Department of Environmental Science and Engineering , Government College University Faisalabad 38000 , Pakistan
| | - S Orsetti
- Environmental Mineralogy, Center for Applied Geosciences , University of Tübingen , 72074 Tübingen , Germany
| | - K Hanna
- Univ Rennes, École Nationale Supérieure de Chimie de Rennes , CNRS, ISCR - UMR6226 , F-35000 Rennes , France
| | - C Ruby
- Laboratoire de Chimie Physique et Microbiologie pour l'Environnement , UMR 7564 CNRS-Université de Lorraine , 54600 Villers-Lès-Nancy , France
| | - A Kappler
- Geomicrobiology, Center for Applied Geosciences , University of Tübingen , 72074 Tübingen , Germany
| | - S B Haderlein
- Environmental Mineralogy, Center for Applied Geosciences , University of Tübingen , 72074 Tübingen , Germany
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19
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Meyer-Dombard DR, Casar CP, Simon AG, Cardace D, Schrenk MO, Arcilla CA. Biofilm formation and potential for iron cycling in serpentinization-influenced groundwater of the Zambales and Coast Range ophiolites. Extremophiles 2018; 22:407-431. [PMID: 29450709 DOI: 10.1007/s00792-018-1005-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2016] [Accepted: 02/05/2018] [Indexed: 02/01/2023]
Abstract
Terrestrial serpentinizing systems harbor microbial subsurface life. Passive or active microbially mediated iron transformations at alkaline conditions in deep biosphere serpentinizing ecosystems are understudied. We explore these processes in the Zambales (Philippines) and Coast Range (CA, USA) ophiolites, and associated surface ecosystems by probing the relevance of samples acquired at the surface to in situ, subsurface ecosystems, and the nature of microbe-mineral associations in the subsurface. In this pilot study, we use microcosm experiments and batch culturing directed at iron redox transformations to confirm thermodynamically based predictions that iron transformations may be important in subsurface serpentinizing ecosystems. Biofilms formed on rock cores from the Zambales ophiolite on surface and in-pit associations, confirming that organisms from serpentinizing systems can form biofilms in subsurface environments. Analysis by XPS and FTIR confirmed that enrichment culturing utilizing ferric iron growth substrates produced reduced, magnetic solids containing siderite, spinels, and FeO minerals. Microcosms and enrichment cultures supported organisms whose near relatives participate in iron redox transformations. Further, a potential 'principal' microbial community common to solid samples in serpentinizing systems was identified. These results indicate collectively that iron redox transformations should be more thoroughly and universally considered when assessing the function of terrestrial subsurface ecosystems driven by serpentinization.
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Affiliation(s)
- D'Arcy R Meyer-Dombard
- Department of Earth and Environmental Sciences, University of Illinois at Chicago, m/c 186, 845 W. Taylor St., Chicago, IL, 60515, USA.
| | - Caitlin P Casar
- Department of Earth and Environmental Sciences, University of Illinois at Chicago, m/c 186, 845 W. Taylor St., Chicago, IL, 60515, USA
| | - Alexander G Simon
- Department of Earth and Environmental Sciences, University of Illinois at Chicago, m/c 186, 845 W. Taylor St., Chicago, IL, 60515, USA
| | - Dawn Cardace
- Department of Geosciences, University of Rhode Island, Kingston, IL, USA
| | - Matthew O Schrenk
- Department of Earth and Environmental Sciences, Michigan State University, East Lansing, MI, USA
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Carlo A Arcilla
- National Institute of Geological Sciences, University of the Philippines, Diliman, Quezon City, Philippines
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20
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Zecchin S, Corsini A, Martin M, Cavalca L. Influence of water management on the active root-associated microbiota involved in arsenic, iron, and sulfur cycles in rice paddies. Appl Microbiol Biotechnol 2017; 101:6725-6738. [DOI: 10.1007/s00253-017-8382-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 05/25/2017] [Accepted: 06/09/2017] [Indexed: 11/28/2022]
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21
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A universal assay for the detection of siderophore activity in natural waters. Biometals 2016; 29:1085-1095. [PMID: 27815738 DOI: 10.1007/s10534-016-9979-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 10/28/2016] [Indexed: 10/20/2022]
Abstract
Siderophores, a family of biogenic metal chelating agents, play critical roles in the biogeochemical cycling of Fe and other metals by facilitating their solubilization and uptake in circumneutral to alkaline oxic environments. However, because of their small concentrations (ca. nM) and large number of molecular structures, siderophore detection and quantification in environmental samples requires specialized equipment and expertise, and often requires pre-concentration of samples, which may introduce significant bias. The "universal" CAS assay, which was originally designed for use in bacterial cultures, quantifies the iron chelating function of a pool of siderophores but only at concentrations (>2 µM) well above the concentrations estimated to be present in marine, freshwater, and soil samples. In this manuscript, we present a high sensitivity modification of this universal assay (HS-CAS) suitable for detecting and quantifying siderophore activity in the nM concentration range, allowing for direct quantitation of siderophore reactivity in transparent aqueous samples.
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22
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Beam JP, Bernstein HC, Jay ZJ, Kozubal MA, Jennings RD, Tringe SG, Inskeep WP. Assembly and Succession of Iron Oxide Microbial Mat Communities in Acidic Geothermal Springs. Front Microbiol 2016; 7:25. [PMID: 26913020 PMCID: PMC4753309 DOI: 10.3389/fmicb.2016.00025] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 01/11/2016] [Indexed: 11/25/2022] Open
Abstract
Biomineralized ferric oxide microbial mats are ubiquitous features on Earth, are common in hot springs of Yellowstone National Park (YNP, WY, USA), and form due to direct interaction between microbial and physicochemical processes. The overall goal of this study was to determine the contribution of different community members to the assembly and succession of acidic high-temperature Fe(III)-oxide mat ecosystems. Spatial and temporal changes in Fe(III)-oxide accretion and the abundance of relevant community members were monitored over 70 days using sterile glass microscope slides incubated in the outflow channels of two acidic geothermal springs (pH = 3–3.5; temperature = 68–75°C) in YNP. Hydrogenobaculum spp. were the most abundant taxon identified during early successional stages (4–40 days), and have been shown to oxidize arsenite, sulfide, and hydrogen coupled to oxygen reduction. Iron-oxidizing populations of Metallosphaera yellowstonensis were detected within 4 days, and reached steady-state levels within 14–30 days, corresponding to visible Fe(III)-oxide accretion. Heterotrophic archaea colonized near 30 days, and emerged as the dominant functional guild after 70 days and in mature Fe(III)-oxide mats (1–2 cm thick). First-order rate constants of Fe(III)-oxide accretion ranged from 0.046 to 0.05 day−1, and in situ microelectrode measurements showed that the oxidation of Fe(II) is limited by the diffusion of O2 into the Fe(III)-oxide mat. The formation of microterracettes also implicated O2 as a major variable controlling microbial growth and subsequent mat morphology. The assembly and succession of Fe(III)-oxide mat communities follows a repeatable pattern of colonization by lithoautotrophic organisms, and the subsequent growth of diverse organoheterotrophs. The unique geochemical signatures and micromorphology of extant biomineralized Fe(III)-oxide mats are also useful for understanding other Fe(II)-oxidizing systems.
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Affiliation(s)
- Jacob P Beam
- Department of Land Resources and Environmental Sciences, Thermal Biology Institute, Montana State University Bozeman, MT, USA
| | - Hans C Bernstein
- Department of Chemical and Biological Engineering, Center for Biofilm Engineering, Montana State UniversityBozeman, MT, USA; Biodetection Science and Biological Science Division, Pacific Northwest National LaboratoryRichland, WA, USA
| | - Zackary J Jay
- Department of Land Resources and Environmental Sciences, Thermal Biology Institute, Montana State UniversityBozeman, MT, USA; Department of Chemical and Biological Engineering, Center for Biofilm Engineering, Montana State UniversityBozeman, MT, USA
| | - Mark A Kozubal
- Department of Land Resources and Environmental Sciences, Thermal Biology Institute, Montana State University Bozeman, MT, USA
| | - Ryan deM Jennings
- Department of Land Resources and Environmental Sciences, Thermal Biology Institute, Montana State University Bozeman, MT, USA
| | - Susannah G Tringe
- United States Department of Energy Joint Genome Institute Walnut Creek, CA, USA
| | - William P Inskeep
- Department of Land Resources and Environmental Sciences, Thermal Biology Institute, Montana State University Bozeman, MT, USA
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Microbial Surface Colonization and Biofilm Development in Marine Environments. Microbiol Mol Biol Rev 2015; 80:91-138. [PMID: 26700108 DOI: 10.1128/mmbr.00037-15] [Citation(s) in RCA: 462] [Impact Index Per Article: 51.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Biotic and abiotic surfaces in marine waters are rapidly colonized by microorganisms. Surface colonization and subsequent biofilm formation and development provide numerous advantages to these organisms and support critical ecological and biogeochemical functions in the changing marine environment. Microbial surface association also contributes to deleterious effects such as biofouling, biocorrosion, and the persistence and transmission of harmful or pathogenic microorganisms and their genetic determinants. The processes and mechanisms of colonization as well as key players among the surface-associated microbiota have been studied for several decades. Accumulating evidence indicates that specific cell-surface, cell-cell, and interpopulation interactions shape the composition, structure, spatiotemporal dynamics, and functions of surface-associated microbial communities. Several key microbial processes and mechanisms, including (i) surface, population, and community sensing and signaling, (ii) intraspecies and interspecies communication and interaction, and (iii) the regulatory balance between cooperation and competition, have been identified as critical for the microbial surface association lifestyle. In this review, recent progress in the study of marine microbial surface colonization and biofilm development is synthesized and discussed. Major gaps in our knowledge remain. We pose questions for targeted investigation of surface-specific community-level microbial features, answers to which would advance our understanding of surface-associated microbial community ecology and the biogeochemical functions of these communities at levels from molecular mechanistic details through systems biological integration.
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Castelle CJ, Roger M, Bauzan M, Brugna M, Lignon S, Nimtz M, Golyshina OV, Giudici-Orticoni MT, Guiral M. The aerobic respiratory chain of the acidophilic archaeon Ferroplasma acidiphilum: A membrane-bound complex oxidizing ferrous iron. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:717-28. [PMID: 25896560 DOI: 10.1016/j.bbabio.2015.04.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 04/07/2015] [Accepted: 04/12/2015] [Indexed: 10/23/2022]
Abstract
The extremely acidophilic archaeon Ferroplasma acidiphilum is found in iron-rich biomining environments and is an important micro-organism in naturally occurring microbial communities in acid mine drainage. F. acidiphilum is an iron oxidizer that belongs to the order Thermoplasmatales (Euryarchaeota), which harbors the most extremely acidophilic micro-organisms known so far. At present, little is known about the nature or the structural and functional organization of the proteins in F. acidiphilum that impact the iron biogeochemical cycle. We combine here biochemical and biophysical techniques such as enzyme purification, activity measurements, proteomics and spectroscopy to characterize the iron oxidation pathway(s) in F. acidiphilum. We isolated two respiratory membrane protein complexes: a 850 kDa complex containing an aa3-type cytochrome oxidase and a blue copper protein, which directly oxidizes ferrous iron and reduces molecular oxygen, and a 150 kDa cytochrome ba complex likely composed of a di-heme cytochrome and a Rieske protein. We tentatively propose that both of these complexes are involved in iron oxidation respiratory chains, functioning in the so-called uphill and downhill electron flow pathways, consistent with autotrophic life. The cytochrome ba complex could possibly play a role in regenerating reducing equivalents by a reverse ('uphill') electron flow. This study constitutes the first detailed biochemical investigation of the metalloproteins that are potentially directly involved in iron-mediated energy conservation in a member of the acidophilic archaea of the genus Ferroplasma.
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Affiliation(s)
- Cindy J Castelle
- CNRS, Aix Marseille Université, BIP UMR 7281, FR 3479, 13402 Marseille, France
| | - Magali Roger
- CNRS, Aix Marseille Université, BIP UMR 7281, FR 3479, 13402 Marseille, France
| | - Marielle Bauzan
- CNRS, Aix Marseille Université, Unité de Fermentation, FR 3479, 13402 Marseille, France
| | - Myriam Brugna
- CNRS, Aix Marseille Université, BIP UMR 7281, FR 3479, 13402 Marseille, France
| | - Sabrina Lignon
- CNRS, Aix Marseille Université, Plate-forme Protéomique MaP IBiSA, FR 3479, 13402 Marseille, France
| | - Manfred Nimtz
- Helmholtz Centre for Infection Research, 7 Inhoffen Strasse, 38124 Braunschweig, Germany
| | - Olga V Golyshina
- Helmholtz Centre for Infection Research, 7 Inhoffen Strasse, 38124 Braunschweig, Germany; School of Biological Sciences, Deiniol Road, LL57 2UW, Bangor, UK
| | | | - Marianne Guiral
- CNRS, Aix Marseille Université, BIP UMR 7281, FR 3479, 13402 Marseille, France.
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Melton ED, Swanner ED, Behrens S, Schmidt C, Kappler A. The interplay of microbially mediated and abiotic reactions in the biogeochemical Fe cycle. Nat Rev Microbiol 2014; 12:797-808. [DOI: 10.1038/nrmicro3347] [Citation(s) in RCA: 503] [Impact Index Per Article: 50.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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26
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Bennett SA, Toner BM, Barco R, Edwards KJ. Carbon adsorption onto Fe oxyhydroxide stalks produced by a lithotrophic iron-oxidizing bacteria. GEOBIOLOGY 2014; 12:146-156. [PMID: 24428517 DOI: 10.1111/gbi.12074] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Accepted: 12/16/2013] [Indexed: 06/03/2023]
Abstract
Iron (Fe)-oxidizing bacteria have the potential to produce morphologically unique structures that may be used as biosignatures in geological deposits. One particular example is Mariprofundus ferrooxydans, which produces extracellular twisted ribbon-like stalks consisting of ferrihydrite, co-located with organic and inorganic elements. It is currently thought that M. ferrooxydans excrete and co-precipitate polysaccharides and Fe simultaneously; however, the cellular production of these polysaccharides has yet to be confirmed. Here, we report on a time-series study that used scanning transmission X-ray microscopy and C 1s and Ca 2p near-edge X-ray adsorption fine structure spectroscopy to investigate production of polysaccharides over the growth cycle of M. ferrooxydans. The production and morphology of twisted iron stalks were consistent with previous observations, but unexpectedly, in the log phase, the carbon content of the stalks was extremely low. It was not until stationary growth phase that a significant component of carbon was detected on the stalks. During the log phase, low levels of carbon, only detectable when the stalks were thin, suggested that M. ferrooxydans produce an extracellular polysaccharide template onto which the Fe precipitates. By stationary phase, the increased carbon association with the stalks was a result of adsorption of organic compounds that were released during osmotic shock post-stalk production. In the environment, elevated concentrations of DOC could adsorb onto the Fe stalks as well as a number of other elements, for example, Si, P, Ca, which, by preventing chemical interactions between the Fe nanoparticles, will prevent structural deformation during recrystallization and preserve the structure of these filaments in the rock record.
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Affiliation(s)
- S A Bennett
- Department of Marine and Environmental Biology, University of Southern California, Los Angeles, CA, USA
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Emerson D, Field EK, Chertkov O, Davenport KW, Goodwin L, Munk C, Nolan M, Woyke T. Comparative genomics of freshwater Fe-oxidizing bacteria: implications for physiology, ecology, and systematics. Front Microbiol 2013; 4:254. [PMID: 24062729 PMCID: PMC3770913 DOI: 10.3389/fmicb.2013.00254] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Accepted: 08/07/2013] [Indexed: 11/16/2022] Open
Abstract
The two microaerophilic, Fe-oxidizing bacteria (FeOB) Sideroxydans ES-1 and Gallionella ES-2 have single circular chromosomes of 3.00 and 3.16 Mb that encode 3049 and 3006 genes, respectively. Multi-locus sequence analysis (MLSA) confirmed the relationship of these two organisms to one another, and indicated they may form a novel order, the Gallionellalaes, within the Betaproteobacteria. Both are adapted for chemolithoautotropy, including pathways for CO2-fixation, and electron transport pathways adapted for growth at low O2-levels, an important adaptation for growing on Fe(II). Both genomes contain Mto-genes implicated in iron-oxidation, as well as other genes that could be involved in Fe-oxidation. Nearly 10% of their genomes are devoted to environmental sensing, signal transduction, and chemotaxis, consistent with their requirement for growing in narrow redox gradients of Fe(II) and O2. There are important differences as well. Sideroxydans ES-1 is more metabolically flexible, and can utilize reduced S-compounds, including thiosulfate, for lithotrophic growth. It has a suite of genes for nitrogen fixation. Gallionella ES-2 contains additional gene clusters for exopolysaccharide production, and has more capacity to resist heavy metals. Both strains contain genes for hemerythrins and globins, but ES-1 has an especially high numbers of these genes that may be involved in oxygen homeostasis, or storage. The two strains share homology with the marine FeOB Mariprofundus ferrooxydans PV-1 in CO2 fixation genes, and respiratory genes. In addition, ES-1 shares a suite of 20 potentially redox active genes with PV-1, as well as a large prophage. Combined these genetic, morphological, and physiological differences indicate that these are two novel species, Sideroxydans lithotrophicus ES-1T (ATCC 700298T; JCM 14762; DSMZ 22444; NCMA B100), and Gallionella capsiferriformans ES-2T (ATCC 700299T; JCM 14763; DSMZ 22445; NCMA B101).
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Affiliation(s)
- David Emerson
- Bigelow Laboratory for Ocean Sciences, East Boothbay Harbor ME, USA
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Electron transport at the microbe-mineral interface: a synthesis of current research challenges. Biochem Soc Trans 2013; 40:1163-6. [PMID: 23176448 DOI: 10.1042/bst20120242] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Many bacterial and archaeal species can couple growth to the respiratory reduction or oxidation of insoluble mineral oxides of transition metals. These solid substrates are abundant electron sinks and sources for life on Earth, but, since they are insoluble in water, they cannot enter the bacterial cells. So, to exploit these electron sinks and sources, specific respiratory electron-transfer mechanisms must overcome the physical limitations associated with electron transfer between a microbe and extracellular metal oxides. Recent microbiological, geochemical, biochemical, spectroscopic and structural work is beginning to shed light on the molecular mechanism and impacts of electron transfer at the microbe-mineral interface from a nanometre to kilometre scale. The research field is attracting attention in applied quarters from those with interests in nanowires, microbial fuel cells, bioremediation and microbial cell factories.
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Singer E, Heidelberg JF, Dhillon A, Edwards KJ. Metagenomic insights into the dominant Fe(II) oxidizing Zetaproteobacteria from an iron mat at Lō´ihi, Hawai´l. Front Microbiol 2013; 4:52. [PMID: 23518919 PMCID: PMC3603346 DOI: 10.3389/fmicb.2013.00052] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Accepted: 02/22/2013] [Indexed: 01/04/2023] Open
Abstract
Zetaproteobacteria are among the most prevalent Fe(II)-oxidizing bacteria (FeOB) at deep-sea hydrothermal vents; however, knowledge about their environmental significance is limited. We provide metagenomic insights into an iron mat at the Lō´ihi Seamount, Hawai´l, revealing novel genomic information of locally dominant Zetaproteobacteria lineages. These lineages were previously estimated to account for ~13% of all local Zetaproteobacteria based on 16S clone library data. Biogeochemically relevant genes include nitrite reductases, which were previously not identified in Zetaproteobacteria, sulfide:quinone oxidases, and ribulose-1,5-bisphosphate carboxylase (RuBisCo). Genes assumed to be involved in Fe(II) oxidation correlate in synteny and share 87% amino acid similarity with those previously identified in the related ZetaproteobacteriumMariprofundus ferrooxydans PV-1. Overall, Zetaproteobacteria genes appear to originate primarily from within the Proteobacteria and the Fe(II)-oxidizing Leptospirillum spp. and are predicted to facilitate adaptation to a deep-sea hydrothermal vent environment in addition to microaerophilic Fe(II) and H2S oxidation. This dataset represents the first metagenomic study of FeOB from an iron oxide mat at a deep-sea hydrothermal habitat.
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Affiliation(s)
- Esther Singer
- Department of Earth Sciences, University of Southern California Los Angeles, CA, USA
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