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Hoover RL, Keffer JL, Polson SW, Chan CS. Gallionellaceae pangenomic analysis reveals insight into phylogeny, metabolic flexibility, and iron oxidation mechanisms. mSystems 2023; 8:e0003823. [PMID: 37882557 PMCID: PMC10734462 DOI: 10.1128/msystems.00038-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 09/20/2023] [Indexed: 10/27/2023] Open
Abstract
IMPORTANCE Neutrophilic iron-oxidizing bacteria (FeOB) produce copious iron (oxyhydr)oxides that can profoundly influence biogeochemical cycles, notably the fate of carbon and many metals. To fully understand environmental microbial iron oxidation, we need a thorough accounting of iron oxidation mechanisms. In this study, we show the Gallionellaceae FeOB genomes encode both characterized iron oxidases as well as uncharacterized multiheme cytochromes (MHCs). MHCs are predicted to transfer electrons from extracellular substrates and likely confer metabolic capabilities that help Gallionellaceae occupy a range of different iron- and mineral-rich niches. Gallionellaceae appear to specialize in iron oxidation, so it would be advantageous for them to have multiple mechanisms to oxidize various forms of iron, given the many iron minerals on Earth, as well as the physiological and kinetic challenges faced by FeOB. The multiple iron/mineral oxidation mechanisms may help drive the widespread ecological success of Gallionellaceae.
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Affiliation(s)
- Rene L. Hoover
- Microbiology Graduate Program, University of Delaware, Newark, Delaware, USA
- Department of Earth Sciences, University of Delaware, Newark, Delaware, USA
| | - Jessica L. Keffer
- Department of Earth Sciences, University of Delaware, Newark, Delaware, USA
| | - Shawn W. Polson
- Department of Computer and Information Sciences, University of Delaware, Newark, Delaware, USA
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware, USA
| | - Clara S. Chan
- Microbiology Graduate Program, University of Delaware, Newark, Delaware, USA
- Department of Earth Sciences, University of Delaware, Newark, Delaware, USA
- School of Marine Science and Policy, University of Delaware, Newark, Delaware, USA
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Chan CS, Dykes GE, Hoover RL, Limmer MA, Seyfferth AL. Gallionellaceae in rice root plaque: metabolic roles in iron oxidation, nutrient cycling, and plant interactions. Appl Environ Microbiol 2023; 89:e0057023. [PMID: 38009924 PMCID: PMC10734482 DOI: 10.1128/aem.00570-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 09/18/2023] [Indexed: 11/29/2023] Open
Abstract
IMPORTANCE In waterlogged soils, iron plaque forms a reactive barrier between the root and soil, collecting phosphate and metals such as arsenic and cadmium. It is well established that iron-reducing bacteria solubilize iron, releasing these associated elements. In contrast, microbial roles in plaque formation have not been clear. Here, we show that there is a substantial population of iron oxidizers in plaque, and furthermore, that these organisms (Sideroxydans and Gallionella) are distinguished by genes for plant colonization and nutrient fixation. Our results suggest that iron-oxidizing and iron-reducing bacteria form and remodel iron plaque, making it a dynamic system that represents both a temporary sink for elements (P, As, Cd, C, etc.) as well as a source. In contrast to abiotic iron oxidation, microbial iron oxidation results in coupled Fe-C-N cycling, as well as microbe-microbe and microbe-plant ecological interactions that need to be considered in soil biogeochemistry, ecosystem dynamics, and crop management.
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Affiliation(s)
- Clara S. Chan
- Department of Earth Sciences, University of Delaware, Newark, Delaware, USA
- School of Marine Science and Policy, University of Delaware, Newark, Delaware, USA
- Microbiology Graduate Program, University of Delaware, Newark, Delaware, USA
- Delaware Biotechnology Institute, Newark, Delaware, USA
| | - Gretchen E. Dykes
- Microbiology Graduate Program, University of Delaware, Newark, Delaware, USA
- Delaware Biotechnology Institute, Newark, Delaware, USA
- Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware, USA
| | - Rene L. Hoover
- Department of Earth Sciences, University of Delaware, Newark, Delaware, USA
- Microbiology Graduate Program, University of Delaware, Newark, Delaware, USA
- Delaware Biotechnology Institute, Newark, Delaware, USA
| | - Matt A. Limmer
- Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware, USA
| | - Angelia L. Seyfferth
- Department of Earth Sciences, University of Delaware, Newark, Delaware, USA
- Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware, USA
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Baker IR, Matzen SL, Schuler CJ, Toner BM, Girguis PR. Aerobic iron-oxidizing bacteria secrete metabolites that markedly impede abiotic iron oxidation. PNAS Nexus 2023; 2:pgad421. [PMID: 38111821 PMCID: PMC10727123 DOI: 10.1093/pnasnexus/pgad421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 11/29/2023] [Indexed: 12/20/2023]
Abstract
Iron is one of the Earth's most abundant elements and is required for essentially all forms of life. Yet, iron's reactivity with oxygen and poor solubility in its oxidized form (Fe3+) mean that it is often a limiting nutrient in oxic, near-neutral pH environments like Earth's ocean. In addition to being a vital nutrient, there is a diversity of aerobic organisms that oxidize ferrous iron (Fe2+) to harness energy for growth and biosynthesis. Accordingly, these organisms rely on access to co-existing Fe2+ and O2 to survive. It is generally presumed that such aerobic iron-oxidizing bacteria (FeOB) are relegated to low-oxygen regimes where abiotic iron oxidation rates are slower, yet some FeOB live in higher oxygen environments where they cannot rely on lower oxygen concentrations to overcome abiotic competition. We hypothesized that FeOB chemically alter their environment to limit abiotic interactions between Fe2+ and O2. To test this, we incubated the secreted metabolites (collectively known as the exometabolome) of the deep-sea iron- and hydrogen-oxidizing bacterium Ghiorsea bivora TAG-1 with ferrous iron and oxygen. We found that this FeOB's iron-oxidizing exometabolome markedly impedes the abiotic oxidation of ferrous iron, increasing the half-life of Fe2+ 100-fold from ∼3 to ∼335 days in the presence of O2, while the exometabolome of TAG-1 grown on hydrogen had no effect. Moreover, the few precipitates that formed in the presence of TAG-1's iron-oxidizing exometabolome were poorly crystalline, compared with the abundant iron particles that mineralized in the absence of abiotic controls. We offer an initial exploration of TAG-1's iron-oxidizing exometabolome and discuss potential key contributors to this process. Overall, our findings demonstrate that the exometabolome as a whole leads to a sustained accumulation of ferrous iron in the presence of oxygen, consequently altering the redox equilibrium. This previously unknown adaptation likely enables these microorganisms to persist in an iron-oxidizing and iron-precipitating world and could have impacts on the bioavailability of iron to FeOB and other life in iron-limiting environments.
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Affiliation(s)
- Isabel R Baker
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Sarick L Matzen
- Department of Soil, Water, and Climate, University of Minnesota Twin Cities, Saint Paul, MN 55108, USA
| | - Christopher J Schuler
- Department of Earth and Environmental Sciences, University of Minnesota Twin Cities, Saint Paul, MN 55108, USA
| | - Brandy M Toner
- Department of Soil, Water, and Climate, University of Minnesota Twin Cities, Saint Paul, MN 55108, USA
- Department of Earth and Environmental Sciences, University of Minnesota Twin Cities, Saint Paul, MN 55108, USA
| | - Peter R Girguis
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
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Lee WS, Aziz HA, Tajarudin HA. Removal of Fe and Mn from the groundwater by using zeolite with Rossellomorea sp. Water Environ Res 2023; 95:e10913. [PMID: 37475142 DOI: 10.1002/wer.10913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 07/04/2023] [Accepted: 07/13/2023] [Indexed: 07/22/2023]
Abstract
Groundwater is one of the alternatives to surface water that can be used for drinking water; however, it normally exists with high iron and manganese content. In this study, a column study was conducted to observe the elimination of iron (Fe) and manganese (Mn) in the groundwater under different retention times by using zeolite immobilized with iron-oxidizing bacteria (IOB). Rossellomorea sp., representing an IOB, was found from the isolation process and was further cultured in the laboratory for immobilization into the natural zeolite as replacement materials for the sand filter. When the zeolite assisted with the Rossellomorea sp. was used, the elimination of Fe and Mn were 99.34% and 88.92%, respectively, compared to the removal of Fe and Mn, which were 93.62% and 93.73%, respectively, for media without immobilization. The presence of Rossellomorea sp. enhances the Fe oxidation, resulting in high removal of Fe. The Thomas and Yoon-Nelson models were performed in both raw zeolite and zeolite with IOB. The total coliform (most probable number [MPN]) increased from 70.8 to 307.6 MPN/100 mL because of the Rossellomorea sp. present that promotes the growth of coliform bacteria. In conclusion, the immobilization of zeolite with IOB is a potential technique to extract the Fe and Mn in the groundwater. PRACTITIONER POINTS: Zeolite incorporated with Rossellomorea sp. has higher removal performance of Fe, whereas the removal of Mn reduced compared to the raw zeolite. The presence of Rossellomorea sp. enhances the oxidation of ferrous iron and improves the removal of Fe in the groundwater because the ferric iron is the priority ion to be exchanged. The removal of UV254 increase when Rossellomorea sp. present in the zeolite because the Rossellomorea sp. consume the natural organic matter as carbon source.
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Affiliation(s)
- Wen Si Lee
- School of Civil Engineering, Engineering Campus, Universiti Sains Malaysia, Nibong Tebal, Malaysia
| | - Hamidi Abdul Aziz
- School of Civil Engineering, Engineering Campus, Universiti Sains Malaysia, Nibong Tebal, Malaysia
- Solid Waste Management Cluster, Engineering Campus, Universiti Sains Malaysia, Nibong Tebal, Malaysia
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He Y, Zeng X, Xu F, Shao Z. Diversity of Mixotrophic Neutrophilic Thiosulfate- and Iron-Oxidizing Bacteria from Deep-Sea Hydrothermal Vents. Microorganisms 2022; 11:microorganisms11010100. [PMID: 36677390 PMCID: PMC9861301 DOI: 10.3390/microorganisms11010100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/22/2022] [Accepted: 12/22/2022] [Indexed: 01/04/2023] Open
Abstract
At deep-sea hydrothermal vents, sulfur oxidation and iron oxidation are of the highest importance to microbial metabolisms, which are thought to contribute mainly in chemolithoautotrophic groups. In this study, 17 mixotrophic neutrophilic thiosulfate- and iron-oxidizing bacteria were isolated from hydrothermal fields on the Carlsberg Ridge in the Indian Ocean, nine to the γ-proteobacteria (Halomonas (4), Pseudomonas (2), Marinobacter (2), and Rheinheimera (1)), seven to the α-proteobacteria (Thalassospira, Qipengyuania, Salipiger, Seohaeicola, Martelella, Citromicrobium, and Aurantimonas), and one to the Actinobacteria (Agromyces), as determined by their 16S rRNA and genome sequences. The physiological characterization of these isolates revealed wide versatility in electron donors (Fe(II) and Mn(II), or thiosulfate) and a variety of lifestyles as lithotrophic or heterotrophic, microaerobic, or anaerobic. As a representative strain, Pseudomonas sp. IOP_13 showed its autotrophic gowth from 105 cells/ml to 107 cells/ml;carbon dioxide fixation capacity with the δ13CVPDB in the biomass increased from -27.42‱ to 3460.06‱; the thiosulfate-oxidizing ability with produced SO42- increased from 60 mg/L to 287 mg/L; and the iron-oxidizing ability with Fe(II) decreased from 10 mM to 5.2 mM. In addition, iron-oxide crust formed outside the cells. Gene coding for energy metabolism involved in possible iron, manganese, and sulfur oxidation, and denitrification was identified by their genome analysis. This study sheds light on the function of the mixotrophic microbial community in the iron/manganese/sulfur cycles and the carbon fixation of the hydrothermal fields.
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Qian Z, Wu C, Pan W, Xiong X, Xia L, Li W. Arsenic Transformation in Soil-Rice System Affected by Iron-Oxidizing Strain ( Ochrobactrum sp.) and Related Soil Metabolomics Analysis. Front Microbiol 2022; 13:794950. [PMID: 35256871 PMCID: PMC8897285 DOI: 10.3389/fmicb.2022.794950] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 01/14/2022] [Indexed: 11/29/2022] Open
Abstract
Iron-oxidizing bacteria (FeOB) could oxidize Fe(II) and mediate biomineralization, which provides the possibility for its potential application in arsenic (As) remediation. In the present study, a strain named Ochrobactrum EEELCW01 isolated previously, was inoculated into paddy soils to investigate the effect of FeOB inoculation on the As migration and transformation in paddy soils. The results showed that inoculation of Ochrobactrum sp. increased the proportion of As in iron-aluminum oxide binding fraction, which reduced the As bioavailability in paddy soils and effectively reduced the As accumulation in rice tissues. Moreover, the inoculation of iron oxidizing bacteria increased the abundance of KD4-96, Pedosphaeraceae and other bacteria in the soils, which could reduce the As toxicity in the soil through biotransformation. The abundance of metabolites such as carnosine, MG (0:0/14:0/0:0) and pantetheine 4'-phosphate increased in rhizosphere soils inoculated with FeOB, which indicated that the defense ability of soil-microorganism-plant system against peroxidation caused by As was enhanced. This study proved that FeOB have the potential application in remediation of As pollution in paddy soil, FeOB promotes the formation of iron oxide in paddy soil, and then adsorbed and coprecipitated with arsenic. On the other hand, the inoculation of Ochrobactrum sp. change soil microbial community structure and soil metabolism, increase the abundance of FeOB in soil, promote the biotransformation process of As in soil, and enhance the resistance of soil to peroxide pollution (As pollution).
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Affiliation(s)
- Ziyan Qian
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
- School of Metallurgy and Environment, Central South University, Changsha, China
| | - Chuan Wu
- School of Metallurgy and Environment, Central South University, Changsha, China
- Department of Science and Environmental Studies, The Education University of Hong Kong, Tai Po, Hong Kong SAR, China
| | - Weisong Pan
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Xiaoran Xiong
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Libing Xia
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Waichin Li
- Department of Science and Environmental Studies, The Education University of Hong Kong, Tai Po, Hong Kong SAR, China
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Anaya-Garzon J, Hubau A, Joulian C, Guezennec AG. Bioleaching of E-Waste: Influence of Printed Circuit Boards on the Activity of Acidophilic Iron-Oxidizing Bacteria. Front Microbiol 2021; 12:669738. [PMID: 34489879 PMCID: PMC8416503 DOI: 10.3389/fmicb.2021.669738] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 07/12/2021] [Indexed: 11/29/2022] Open
Abstract
Bioleaching is a promising strategy to recover valuable metals from spent printed circuit boards (PCBs). The performance of the process is catalyzed by microorganisms, which the toxic effect of PCBs can inhibit. This study aimed to investigate the capacity of an acidophilic iron-oxidizing culture, mainly composed of Leptospirillum ferriphilum, to oxidize iron in PCB-enriched environments. The culture pre-adapted to 1% (w/v) PCB content successfully thrived in leachates with the equivalent of 6% of PCBs, containing 8.5 g L–1 Cu, 8 g L–1 Fe, 1 g L–1 Zn, 92 mg L–1 Ni, 12.6 mg L–1 Pb, and 4.4 mg L–1 Co, among other metals. However, the inhibiting effect of PCBs limited the microbial activity by delaying the onset of the exponential iron oxidation. Successive subcultures boosted the activity of the culture by reducing this delay by up to 2.6 times under batch conditions. Subcultures also favored the rapid establishment of high microbial activity in continuous mode.
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Affiliation(s)
- Juan Anaya-Garzon
- Bureau de Recherches Géologiques et Minières, Orléans, France.,Chimie ParisTech, PSL Research University, CNRS, Institut de Recherche de Chimie Paris, Paris, France
| | - Agathe Hubau
- Bureau de Recherches Géologiques et Minières, Orléans, France
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Abstract
Freshwater iron mats are dynamic geochemical environments with broad ecological diversity, primarily formed by the iron-oxidizing bacteria. The community features functional groups involved in biogeochemical cycles for iron, sulfur, carbon, and nitrogen. Despite this complexity, iron mat communities provide an excellent model system for exploring microbial ecological interactions and ecological theories in situ Syntrophies and competition between the functional groups in iron mats, how they connect cycles, and the maintenance of these communities by taxons outside bacteria (the eukaryota, archaea, and viruses) have been largely unstudied. Here, we review what is currently known about freshwater iron mat communities, the taxa that reside there, and the interactions between these organisms, and we propose ways in which future studies may uncover exciting new discoveries. For example, the archaea in these mats may play a greater role than previously thought as they are diverse and widespread in iron mats based on 16S rRNA genes and include methanogenic taxa. Studies with a holistic view of the iron mat community members focusing on their diverse interactions will expand our understanding of community functions, such as those involved in pollution removal. To begin addressing questions regarding the fundamental interactions and to identify the conditions in which they occur, more laboratory culturing techniques and coculture studies, more network and keystone species analyses, and the expansion of studies to more freshwater iron mat systems are necessary. Increasingly accessible bioinformatic, geochemical, and culturing tools now open avenues to address the questions that we pose herein.
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Affiliation(s)
- Chequita N Brooks
- Department of Biology, East Carolina University, Greenville, North Carolina, USA
| | - Erin K Field
- Department of Biology, East Carolina University, Greenville, North Carolina, USA
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Price KA, Garrison CE, Richards N, Field EK. A Shallow Water Ferrous-Hulled Shipwreck Reveals a Distinct Microbial Community. Front Microbiol 2020; 11:1897. [PMID: 32973699 PMCID: PMC7466744 DOI: 10.3389/fmicb.2020.01897] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 07/20/2020] [Indexed: 12/12/2022] Open
Abstract
Shipwrecks act as artificial reefs and provide a solid surface in aquatic systems for many different forms of life to attach to, especially microbial communities, making them a hotspot of biogeochemical cycling. Depending on the microbial community and surrounding environment, they may either contribute to the wreck’s preservation or deterioration. Even within a single wreck, preservation and deterioration processes may vary, suggesting that the microbial community may also vary. This study aimed to identify the differences through widespread sampling of the microbial communities associated with the Pappy Lane shipwreck (NC shipwreck site #PAS0001), a shallow water ferrous-hulled shipwreck in Pamlico Sound, North Carolina to determine if there are differences across the wreck as well as from its surrounding environment. Loose shipwreck debris, drilled shipcores, surrounding sediment, and seawater samples were collected from the Pappy Lane shipwreck to characterize the microbial communities on and around the shipwreck. Results indicated that the shipwreck samples were more similar to each other than the surrounding sediment and aquatic environments suggesting they have made a specialized niche associated with the shipwreck. There were differences between the microbial community across the shipwreck, including between visibly corroded and non-corroded shipwreck debris pieces. Relative abundance estimates for neutrophilic iron-oxidizing bacteria (FeOB), an organism that may contribute to deterioration through biocorrosion, revealed they are present across the shipwreck and at highest abundance on the samples containing visible corrosion products. Zetaproteobacteria, a known class of marine iron-oxidizers, were also found in higher abundance on shipwreck samples with visible corrosion. A novel Zetaproteobacteria strain, Mariprofundus ferrooxydans O1, was isolated from one of the shipwreck pieces and its genome analyzed to elucidate the functional potential of the organism. In addition to iron oxidation pathways, the isolate has the genomic potential to perform carbon fixation in both high and low oxygen environments, as well as perform nitrogen fixation, contributing to the overall biogeochemical cycling of nutrients and metals in the shipwreck ecosystem. By understanding the microbial communities associated with shallow water ferrous-hulled shipwrecks, better management strategies and preservation plans can be put into place to preserve these artificial reefs and non-renewable cultural resources.
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Affiliation(s)
- Kyra A Price
- Department of Biology, East Carolina University, Greenville, NC, United States
| | - Cody E Garrison
- Department of Biology, East Carolina University, Greenville, NC, United States
| | - Nathan Richards
- Program in Maritime Studies, Department of History, East Carolina University, Greenville, NC, United States
| | - Erin K Field
- Department of Biology, East Carolina University, Greenville, NC, United States
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Vardanyan N, Sevoyan G, Navasardyan T, Vardanyan A. Recovery of valuable metals from polymetallic mine tailings by natural microbial consortium. Environ Technol 2019; 40:3467-3472. [PMID: 29781399 DOI: 10.1080/09593330.2018.1478454] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 05/14/2018] [Indexed: 06/08/2023]
Abstract
Possibilities for the recovery of non-ferrous and precious metals from Kapan polymetallic mine tailings (Armenia) were studied. The aim of this paper was to study the possibilities of bioleaching of samples of concentrated tailings by the natural microbial consortium of drainage water. The extent of extraction of metals from the samples of concentrated tailings by natural microbial consortium reached 41-55% and 53-73% for copper and zinc, respectively. Metal leaching efficiencies of pure culture Leptospirillum ferrooxidans Teg were higher, namely 47-93% and 73-81% for copper and zinc, respectively. The content of gold in solid phase of tailings increased about 7-16% and 2-9% after bio-oxidation process by L. ferrooxidans Teg and natural microbial consortium, respectively. It was shown that bioleaching of the samples of tailings could be performed using the natural consortium of drainage water. However, to increase the intensity of the recovery of valuable metals, natural consortium of drainage water combined with iron-oxidizing L. ferrooxidans Teg has been proposed.
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Affiliation(s)
- Narine Vardanyan
- Department of Microbiology, SPC "Armbiotechnology" of the National Academy of Sciences of Armenia , Yerevan , Armenia
| | - Garegin Sevoyan
- Department of Chemical, Biological and Environmental Technologies, Armenian National Polytechnic University , Yerevan , Armenia
| | | | - Arevik Vardanyan
- Department of Microbiology, SPC "Armbiotechnology" of the National Academy of Sciences of Armenia , Yerevan , Armenia
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Garrison CE, Price KA, Field EK. Environmental Evidence for and Genomic Insight into the Preference of Iron-Oxidizing Bacteria for More-Corrosion-Resistant Stainless Steel at Higher Salinities. Appl Environ Microbiol 2019; 85:e00483-19. [PMID: 31076431 DOI: 10.1128/AEM.00483-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 05/07/2019] [Indexed: 11/20/2022] Open
Abstract
Iron-oxidizing bacteria (FeOB) are some of the initial colonizing organisms during microbially influenced corrosion of steel infrastructure. To better understand the abiotic conditions under which FeOB colonize steel, an environmental study was conducted to determine the effects of salinity, temperature, dissolved oxygen levels, and steel type on FeOB colonization. Stainless steel (304 and 316 [i.e., 304SS and 316SS]) was used to determine the potential susceptibility of these specialized corrosion-resistant steels. Steel coupon deployments along salinity gradients in two river systems revealed attachment by FeOB at all sites, with greater abundance of FeOB at higher salinities and on 316SS, compared to 304SS. This may be due to the presence of molybdenum in 316SS, potentially providing a selective advantage for FeOB colonization. A novel Zetaproteobacteria species, Mariprofundus erugo, was isolated from these stainless steel samples. Genes for molybdenum utilization and uptake and reactive oxygen species protection were found within its genome, supporting the evidence from our FeOB abundance data; they may represent adaptations of FeOB for colonization of surfaces of anthropogenic iron sources such as stainless steel. These results reveal environmental conditions under which FeOB colonize steel surfaces most abundantly, and they provide the framework needed to develop biocorrosion prevention strategies for stainless steel infrastructure in coastal estuarine areas.IMPORTANCE Colonization of FeOB on corrosion-resistant stainless steel types (304SS and 316SS) has been quantified from environmental deployments along salinity gradients in estuarine environments. Greater FeOB abundance at higher salinities and on the more-corrosion-resistant 316SS suggests that there may be a higher risk of biocorrosion at higher salinities and there may be a selective advantage from certain stainless steel alloy metals, such as molybdenum, for FeOB colonization. A novel species of FeOB described here was isolated from our stainless steel coupon deployments, and its genome sequence supports our environmental data, as genes involved in the potential selectiveness toward surface colonization of stainless steel might lead to higher rates of biocorrosion of manmade aquatic infrastructure. These combined results provide environmental constraints for FeOB colonization on anthropogenic iron sources and build on previous frameworks for biocorrosion prevention strategies.
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12
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Hottenstein JD, Neilson JW, Gil-Loaiza J, Root RA, White SA, Chorover J, Maier RM. Soil Microbiome Dynamics During Pyritic Mine Tailing Phytostabilization: Understanding Microbial Bioindicators of Soil Acidification. Front Microbiol 2019; 10:1211. [PMID: 31275251 PMCID: PMC6593306 DOI: 10.3389/fmicb.2019.01211] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 05/13/2019] [Indexed: 11/17/2022] Open
Abstract
Challenges to the reclamation of pyritic mine tailings arise from in situ acid generation that severely constrains the growth of natural revegetation. While acid mine drainage (AMD) microbial communities are well-studied under highly acidic conditions, fewer studies document the dynamics of microbial communities that generate acid from pyritic material under less acidic conditions that can allow establishment and support of plant growth. This research characterizes the taxonomic composition dynamics of microbial communities present during a 6-year compost-assisted phytostabilization field study in extremely acidic pyritic mine tailings. A complementary microcosm experiment was performed to identify successional community populations that enable the acidification process across a pH gradient. Taxonomic profiles of the microbial populations in both the field study and microcosms reveal shifts in microbial communities that play pivotal roles in facilitating acidification during the transition between moderately and highly acidic conditions. The potential co-occurrence of organoheterotrophic and lithoautotrophic energy metabolisms during acid generation suggests the importance of both groups in facilitating acidification. Taken together, this research suggests that key microbial populations associated with pH transitions could be used as bioindicators for either sustained future plant growth or for acid generation conditions that inhibit further plant growth.
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Affiliation(s)
- John D Hottenstein
- Department of Soil, Water and Environmental Science, The University of Arizona, Tucson, AZ, United States
| | - Julie W Neilson
- Department of Soil, Water and Environmental Science, The University of Arizona, Tucson, AZ, United States
| | - Juliana Gil-Loaiza
- Department of Soil, Water and Environmental Science, The University of Arizona, Tucson, AZ, United States
| | - Robert A Root
- Department of Soil, Water and Environmental Science, The University of Arizona, Tucson, AZ, United States
| | - Scott A White
- Department of Soil, Water and Environmental Science, The University of Arizona, Tucson, AZ, United States
| | - Jon Chorover
- Department of Soil, Water and Environmental Science, The University of Arizona, Tucson, AZ, United States
| | - Raina M Maier
- Department of Soil, Water and Environmental Science, The University of Arizona, Tucson, AZ, United States
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Borilova S, Mandl M, Zeman J, Kucera J, Pakostova E, Janiczek O, Tuovinen OH. Can Sulfate Be the First Dominant Aqueous Sulfur Species Formed in the Oxidation of Pyrite by Acidithiobacillus ferrooxidans? Front Microbiol 2019; 9:3134. [PMID: 30619202 PMCID: PMC6305575 DOI: 10.3389/fmicb.2018.03134] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 12/04/2018] [Indexed: 11/13/2022] Open
Abstract
According to the literature, pyrite (FeS2) oxidation has been previously determined to involve thiosulfate as the first aqueous intermediate sulfur product, which is further oxidized to sulfate. In the present study, pyrite oxidation by Acidithiobacillus ferrooxidans was studied using electrochemical and metabolic approaches in an effort to extend existing knowledge on the oxidation mechanism. Due to the small surface area, the reaction rate of a compact pyrite electrode in the form of polycrystalline pyrite aggregate in A. ferrooxidans suspension was very slow at a spontaneously formed high redox potential. The slow rate made it possible to investigate the oxidation process in detail over a term of 100 days. Using electrochemical parameters from polarization curves and levels of released iron, the number of exchanged electrons per pyrite molecule was estimated. The values close to 14 and 2 electrons were determined for the oxidation with and without bacteria, respectively. These results indicated that sulfate was the dominant first aqueous sulfur species formed in the presence of bacteria and elemental sulfur was predominantly formed without bacteria. The stoichiometric calculations are consistent with high iron-oxidizing activities of bacteria that continually keep the released iron in the ferric form, resulting in a high redox potential. The sulfur entity of pyrite was oxidized to sulfate by Fe3+ without intermediate thiosulfate under these conditions. Cell attachment on the corroded pyrite electrode surface was documented although pyrite surface corrosion by Fe3+ was evident without bacterial participation. Attached cells may be important in initiating the oxidation of the pyrite surface to release iron from the mineral. During the active phase of oxidation of a pyrite concentrate sample, the ATP levels in attached and planktonic bacteria were consistent with previously established ATP content of iron-oxidizing cells. No significant upregulation of three essential genes involved in energy metabolism of sulfur compounds was observed in the planktonic cells, which represented the dominant biomass in the pyrite culture. The study demonstrated the formation of sulfate as the first dissolved sulfur species with iron-oxidizing bacteria under high redox potential conditions. Minor aqueous sulfur intermediates may be formed but as a result of side reactions.
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Affiliation(s)
- Sarka Borilova
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czechia
| | - Martin Mandl
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czechia
| | - Josef Zeman
- Department of Geological Sciences, Faculty of Science, Masaryk University, Brno, Czechia
| | - Jiri Kucera
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czechia
| | - Eva Pakostova
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czechia
| | - Oldrich Janiczek
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czechia
| | - Olli H Tuovinen
- Department of Microbiology, The Ohio State University, Columbus, OH, United States
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14
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Laroche E, Casiot C, Fernandez-Rojo L, Desoeuvre A, Tardy V, Bruneel O, Battaglia-Brunet F, Joulian C, Héry M. Dynamics of Bacterial Communities Mediating the Treatment of an As-Rich Acid Mine Drainage in a Field Pilot. Front Microbiol 2018; 9:3169. [PMID: 30627121 PMCID: PMC6309452 DOI: 10.3389/fmicb.2018.03169] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 12/07/2018] [Indexed: 12/31/2022] Open
Abstract
Passive treatment based on iron biological oxidation is a promising strategy for Arsenic (As)-rich acid mine drainage (AMD) remediation. In the present study, we characterized by 16S rRNA metabarcoding the bacterial diversity in a field-pilot bioreactor treating extremely As-rich AMD in situ, over a 6 months monitoring period. Inside the bioreactor, the bacterial communities responsible for iron and arsenic removal formed a biofilm (“biogenic precipitate”) whose composition varied in time and space. These communities evolved from a structure at first similar to the one of the feed water used as an inoculum to a structure quite similar to the natural biofilm developing in situ in the AMD. Over the monitoring period, iron-oxidizing bacteria always largely dominated the biogenic precipitate, with distinct populations (Gallionella, Ferrovum, Leptospirillum, Acidithiobacillus, Ferritrophicum), whose relative proportions extensively varied among time and space. A spatial structuring was observed inside the trays (arranged in series) composing the bioreactor. This spatial dynamic could be linked to the variation of the physico-chemistry of the AMD water between the raw water entering and the treated water exiting the pilot. According to redundancy analysis (RDA), the following parameters exerted a control on the bacterial communities potentially involved in the water treatment process: dissolved oxygen, temperature, pH, dissolved sulfates, arsenic and Fe(II) concentrations and redox potential. Appreciable arsenite oxidation occurring in the bioreactor could be linked to the stable presence of two distinct monophylogenetic groups of Thiomonas related bacteria. The ubiquity and the physiological diversity of the bacteria identified, as well as the presence of bacteria of biotechnological relevance, suggested that this treatment system could be applied to the treatment of other AMD.
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Affiliation(s)
- Elia Laroche
- HydroSciences Montpellier, CNRS, IRD, University of Montpellier, Montpellier, France.,BRGM, Geomicrobiology and Environmental Monitoring Unit, Orléans, France
| | - Corinne Casiot
- HydroSciences Montpellier, CNRS, IRD, University of Montpellier, Montpellier, France
| | - Lidia Fernandez-Rojo
- HydroSciences Montpellier, CNRS, IRD, University of Montpellier, Montpellier, France
| | - Angélique Desoeuvre
- HydroSciences Montpellier, CNRS, IRD, University of Montpellier, Montpellier, France
| | - Vincent Tardy
- HydroSciences Montpellier, CNRS, IRD, University of Montpellier, Montpellier, France
| | - Odile Bruneel
- HydroSciences Montpellier, CNRS, IRD, University of Montpellier, Montpellier, France
| | | | - Catherine Joulian
- BRGM, Geomicrobiology and Environmental Monitoring Unit, Orléans, France
| | - Marina Héry
- HydroSciences Montpellier, CNRS, IRD, University of Montpellier, Montpellier, France
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15
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Khalifa A, Nakasuji Y, Saka N, Honjo H, Asakawa S, Watanabe T. Ferrigenium kumadai gen. nov., sp. nov., a microaerophilic iron-oxidizing bacterium isolated from a paddy field soil. Int J Syst Evol Microbiol 2018; 68:2587-2592. [PMID: 29944111 DOI: 10.1099/ijsem.0.002882] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
An iron-oxidizing bacterium, designated strain An22T, which was isolated from a paddy field soil in Anjo, Japan, was described taxonomically. Strain An22T was motile by a single polar flagellum, curved-rod, Gram-negative bacterium that was able to grow at 12-37 °C (optimally at 25-30 °C) and at pH 5.2-6.8 (pH 5.9-6.1). The strain grew microaerobically and autotrophically by oxidizing ferrous iron, but did not form stalks, a unique structure of iron oxides. The major cellular fatty acids were C16 : 0 and C16 : 1ω7c/C16 : 1ω6c. The major respiratory quinones were UQ-10 and UQ-8. The strain possessed ribulose-1,5-bisphosphate carboxylase/oxygenase indicating an autotrophic nature via the Calvin-Benson-Bassham cycle. The total DNA G+C content was 61.4 mol%. 16S rRNA gene sequence analysis revealed that strain An22T was affiliated with the class Betaproteobacteria and clustered with iron-oxidizing bacteria, Gallionella ferrugineaJohan (94.8 % similarity) and Ferriphaselus amnicola OYT1T (94.4 %) in the family Gallionellaceae. Based on the low 16S rRNA gene sequence similarity to the phylogenetically closest genera and the combination of unique morphological, physiological and biochemical characteristics, strain An22T represents a novel genus and species within the family Gallionellaceae, for which the name Ferrigenium kumadai gen. nov., sp. nov. is proposed. The type strain is An22T (=JCM 30584T=NBRC 112974T=ATCC TSD-51T).
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Affiliation(s)
- Ashraf Khalifa
- 1Biological Sciences Department, Faculty of Sciences, King Faisal University, Al-Ahsaa, Saudi Arabia.,2Botany and Microbiology Department, Faculty of Sciences, Beni-Suef University, Beni-Suef 65211, Egypt
| | - Yuta Nakasuji
- 3School of Agricultural Sciences, Nagoya University, Furocho, Chikusa, Nagoya 464-8601, Japan.,†Present address: Ichibiki Co., Ltd., Atsuta, Nagoya, Aichi 456-0018, Japan
| | - Norikuni Saka
- 4Crop Institute, Aichi Agricultural Research Center, Anjo, Aichi 446-0066, Japan.,‡Present address: Aichi Agricultural Research Center, Nagakute, Aichi 480-1103, Japan
| | - Hiroki Honjo
- 4Crop Institute, Aichi Agricultural Research Center, Anjo, Aichi 446-0066, Japan.,§Present address: Higashi Mikawa Agriculture, Forestry, and Fisheries Office, Toyohashi, Aichi 440-0833, Japan
| | - Susumu Asakawa
- 5Graduate School of Bioagricultural Sciences, Nagoya University, Furocho, Chikusa, Nagoya 464-8601, Japan
| | - Takeshi Watanabe
- 5Graduate School of Bioagricultural Sciences, Nagoya University, Furocho, Chikusa, Nagoya 464-8601, Japan
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Fleming EJ, Woyke T, Donatello RA, Kuypers MMM, Sczyrba A, Littmann S, Emerson D. Insights into the Fundamental Physiology of the Uncultured Fe-Oxidizing Bacterium Leptothrix ochracea. Appl Environ Microbiol 2018; 84:e02239-17. [PMID: 29453262 DOI: 10.1128/AEM.02239-17] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 02/10/2018] [Indexed: 01/23/2023] Open
Abstract
Leptothrix ochracea is known for producing large volumes of iron oxyhydroxide sheaths that alter wetland biogeochemistry. For over a century, these delicate structures have fascinated microbiologists and geoscientists. Because L. ochracea still resists long-term in vitro culture, the debate regarding its metabolic classification dates back to 1885. We developed a novel culturing technique for L. ochracea using in situ natural waters and coupled this with single-cell genomics and nanoscale secondary-ion mass spectrophotometry (nanoSIMS) to probe L. ochracea's physiology. In microslide cultures L. ochracea doubled every 5.7 h and had an absolute growth requirement for ferrous iron, the genomic capacity for iron oxidation, and a branched electron transport chain with cytochromes putatively involved in lithotrophic iron oxidation. Additionally, its genome encoded several electron transport chain proteins, including a molybdopterin alternative complex III (ACIII), a cytochrome bd oxidase reductase, and several terminal oxidase genes. L. ochracea contained two key autotrophic proteins in the Calvin-Benson-Bassham cycle, a form II ribulose bisphosphate carboxylase, and a phosphoribulose kinase. L. ochracea also assimilated bicarbonate, although calculations suggest that bicarbonate assimilation is a small fraction of its total carbon assimilation. Finally, L. ochracea's fundamental physiology is a hybrid of those of the chemolithotrophic Gallionella-type iron-oxidizing bacteria and the sheathed, heterotrophic filamentous metal-oxidizing bacteria of the Leptothrix-Sphaerotilus genera. This allows L. ochracea to inhabit a unique niche within the neutrophilic iron seeps.IMPORTANCE Leptothrix ochracea was one of three groups of organisms that Sergei Winogradsky used in the 1880s to develop his hypothesis on chemolithotrophy. L. ochracea continues to resist cultivation and appears to have an absolute requirement for organic-rich waters, suggesting that its true physiology remains unknown. Further, L. ochracea is an ecological engineer; a few L. ochracea cells can generate prodigious volumes of iron oxyhydroxides, changing the ecosystem's geochemistry and ecology. Therefore, to determine L. ochracea's basic physiology, we employed new single-cell techniques to demonstrate that L. ochracea oxidizes iron to generate energy and, despite having predicted genes for autotrophic growth, assimilates a fraction of the total CO2 that autotrophs do. Although not a true chemolithoautotroph, L. ochracea's physiological strategy allows it to be flexible and to extensively colonize iron-rich wetlands.
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17
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Chiu BK, Kato S, McAllister SM, Field EK, Chan CS. Novel Pelagic Iron-Oxidizing Zetaproteobacteria from the Chesapeake Bay Oxic-Anoxic Transition Zone. Front Microbiol 2017; 8:1280. [PMID: 28769885 PMCID: PMC5513912 DOI: 10.3389/fmicb.2017.01280] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 06/26/2017] [Indexed: 01/11/2023] Open
Abstract
Chemolithotrophic iron-oxidizing bacteria (FeOB) could theoretically inhabit any environment where Fe(II) and O2 (or nitrate) coexist. Until recently, marine Fe-oxidizing Zetaproteobacteria had primarily been observed in benthic and subsurface settings, but not redox-stratified water columns. This may be due to the challenges that a pelagic lifestyle would pose for Zetaproteobacteria, given low Fe(II) concentrations in modern marine waters and the possibility that Fe oxyhydroxide biominerals could cause cells to sink. However, we recently cultivated Zetaproteobacteria from the Chesapeake Bay oxic–anoxic transition zone, suggesting that they can survive and contribute to biogeochemical cycling in a stratified estuary. Here we describe the isolation, characterization, and genomes of two new species, Mariprofundus aestuarium CP-5 and Mariprofundus ferrinatatus CP-8, which are the first Zetaproteobacteria isolates from a pelagic environment. We looked for adaptations enabling strains CP-5 and CP-8 to overcome the challenges of living in a low Fe redoxcline with frequent O2 fluctuations due to tidal mixing. We found that the CP strains produce distinctive dreadlock-like Fe oxyhydroxide structures that are easily shed, which would help cells maintain suspension in the water column. These oxides are by-products of Fe(II) oxidation, likely catalyzed by the putative Fe(II) oxidase encoded by the cyc2 gene, present in both CP-5 and CP-8 genomes; the consistent presence of cyc2 in all microaerophilic FeOB and other FeOB genomes supports its putative role in Fe(II) oxidation. The CP strains also have two gene clusters associated with biofilm formation (Wsp system and the Widespread Colonization Island) that are absent or rare in other Zetaproteobacteria. We propose that biofilm formation enables the CP strains to attach to FeS particles and form flocs, an advantageous strategy for scavenging Fe(II) and developing low [O2] microenvironments within more oxygenated waters. However, the CP strains appear to be adapted to somewhat higher concentrations of O2, as indicated by the presence of genes encoding aa3-type cytochrome c oxidases, but not the cbb3-type found in all other Zetaproteobacteria isolate genomes. Overall, our results reveal adaptations for life in a physically dynamic, low Fe(II) water column, suggesting that niche-specific strategies can enable Zetaproteobacteria to live in any environment with Fe(II).
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Affiliation(s)
- Beverly K Chiu
- Department of Geological Sciences, University of Delaware, NewarkDE, United States
| | - Shingo Kato
- Project Team for Development of New-Generation Research Protocol for Submarine Resources, Japan Agency for Marine-Earth Science and TechnologyKanagawa, Japan
| | - Sean M McAllister
- School of Marine Science and Policy, University of Delaware, NewarkDE, United States
| | - Erin K Field
- Department of Biology, East Carolina University, GreenvilleNC, United States
| | - Clara S Chan
- Department of Geological Sciences, University of Delaware, NewarkDE, United States.,School of Marine Science and Policy, University of Delaware, NewarkDE, United States
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18
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Hoshino T, Kuratomi T, Morono Y, Hori T, Oiwane H, Kiyokawa S, Inagaki F. Ecophysiology of Zetaproteobacteria Associated with Shallow Hydrothermal Iron-Oxyhydroxide Deposits in Nagahama Bay of Satsuma Iwo-Jima, Japan. Front Microbiol 2016; 6:1554. [PMID: 26793184 PMCID: PMC4707226 DOI: 10.3389/fmicb.2015.01554] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 12/22/2015] [Indexed: 11/13/2022] Open
Abstract
Previous studies of microbial communities in deep-sea hydrothermal ferric deposits have demonstrated that members of Zetaproteobacteria play significant ecological roles in biogeochemical iron-cycling. However, the ecophysiological characteristics and interaction between other microbial members in the habitat still remain largely unknown. In this study, we investigated microbial communities in a core sample obtained from shallow hydrothermal iron-oxyhydroxide deposits at Nagahama Bay of Satsuma Iwo-Jima, Japan. Scanning electron microscopic observation showed numerous helical stalk structures, suggesting the occurrence of iron-oxidizing bacteria. Analysis of 16S rRNA gene sequences indicated the co-occurrence of iron-oxidizing Zetaproteobacteria and iron-reducing bacteria such as the genera Deferrisoma and Desulfobulbus with strong correlations on the sequence abundance. CARD-FISH indicated that the numbers of Zetaproteobacteria were not always consistent to the frequency of stalk structures. In the stalk-abundant layers with relatively small numbers of Zetaproteobacteria cells, accumulation of polyphosphate was observed inside Zetaproteobacteria cells, whereas no polyphosphate grains were observed in the topmost layers with fewer stalks and abundant Zetaproteobacteria cells. These results suggest that Zetaproteobacteria store intracellular polyphosphates during active iron oxidation that contributes to the mineralogical growth and biogeochemical iron cycling.
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Affiliation(s)
- Tatsuhiko Hoshino
- Japan Agency for Marine-Earth Science Technology, Kochi Institute for Core Sample ResearchNankoku, Japan; Japan Agency for Marine-Earth Science Technology, Research and Development Center for Submarine ResourcesNankoku, Japan
| | - Takashi Kuratomi
- Department Earth and Planetary Sciences, Kyushu University Fukuoka, Japan
| | - Yuki Morono
- Japan Agency for Marine-Earth Science Technology, Kochi Institute for Core Sample ResearchNankoku, Japan; Japan Agency for Marine-Earth Science Technology, Research and Development Center for Submarine ResourcesNankoku, Japan
| | - Tomoyuki Hori
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology Tsukuba, Japan
| | | | - Shoichi Kiyokawa
- Department Earth and Planetary Sciences, Kyushu University Fukuoka, Japan
| | - Fumio Inagaki
- Japan Agency for Marine-Earth Science Technology, Kochi Institute for Core Sample ResearchNankoku, Japan; Japan Agency for Marine-Earth Science Technology, Research and Development Center for Submarine ResourcesNankoku, Japan
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19
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Abstract
Primary productivity in at least a third of the sunlit open ocean is thought to be iron-limited. Primary sources of dissolved iron (dFe) to the ocean are hydrothermal venting, flux from the sediments along continental margins, and airborne dust. This article provides a general review of sources of hydrothermal and sedimentary iron to the ocean, and speculates upon the role that iron-cycling microbes play in controlling iron dynamics from these sources. Special attention is paid to iron-oxidizing bacteria (FeOB) that live by oxidizing iron and producing biogenic iron oxides as waste products. The presence and ubiquity of FeOB both at hydrothermal systems and in sediments is only beginning to be appreciated. The biogenic oxides they produce have unique properties that could contribute significantly to the dynamics of dFe in the ocean. Changes in the physical and chemical characteristics of the ocean due to climate change and ocean acidification will undoubtedly impact the microbial iron cycle. A better understanding of the contemporary role of microbes in the iron cycle will help in predicting how these changes could ultimately influence marine primary productivity.
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Affiliation(s)
- David Emerson
- Bigelow Laboratory for Ocean Sciences East Boothbay, ME, USA
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20
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Kato S, Ohkuma M, Powell DH, Krepski ST, Oshima K, Hattori M, Shapiro N, Woyke T, Chan CS. Comparative Genomic Insights into Ecophysiology of Neutrophilic, Microaerophilic Iron Oxidizing Bacteria. Front Microbiol 2015; 6:1265. [PMID: 26617599 PMCID: PMC4643136 DOI: 10.3389/fmicb.2015.01265] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 10/30/2015] [Indexed: 11/13/2022] Open
Abstract
Neutrophilic microaerophilic iron-oxidizing bacteria (FeOB) are thought to play a significant role in cycling of carbon, iron and associated elements in both freshwater and marine iron-rich environments. However, the roles of the neutrophilic microaerophilic FeOB are still poorly understood due largely to the difficulty of cultivation and lack of functional gene markers. Here, we analyze the genomes of two freshwater neutrophilic microaerophilic stalk-forming FeOB, Ferriphaselus amnicola OYT1 and Ferriphaselus strain R-1. Phylogenetic analyses confirm that these are distinct species within Betaproteobacteria; we describe strain R-1 and propose the name F. globulitus. We compare the genomes to those of two freshwater Betaproteobacterial and three marine Zetaproteobacterial FeOB isolates in order to look for mechanisms common to all FeOB, or just stalk-forming FeOB. The OYT1 and R-1 genomes both contain homologs to cyc2, which encodes a protein that has been shown to oxidize Fe in the acidophilic FeOB, Acidithiobacillus ferrooxidans. This c-type cytochrome common to all seven microaerophilic FeOB isolates, strengthening the case for its common utility in the Fe oxidation pathway. In contrast, the OYT1 and R-1 genomes lack mto genes found in other freshwater FeOB. OYT1 and R-1 both have genes that suggest they can oxidize sulfur species. Both have the genes necessary to fix carbon by the Calvin–Benson–Basshom pathway, while only OYT1 has the genes necessary to fix nitrogen. The stalk-forming FeOB share xag genes that may help form the polysaccharide structure of stalks. Both OYT1 and R-1 make a novel biomineralization structure, short rod-shaped Fe oxyhydroxides much smaller than their stalks; these oxides are constantly shed, and may be a vector for C, P, and metal transport to downstream environments. Our results show that while different FeOB are adapted to particular niches, freshwater and marine FeOB likely share common mechanisms for Fe oxidation electron transport and biomineralization pathways.
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Affiliation(s)
- Shingo Kato
- Department of Geological Sciences, University of Delaware, Newark DE, USA ; Japan Collection of Microorganisms, RIKEN BioResource Center Tsukuba, Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Center Tsukuba, Japan
| | - Deborah H Powell
- Delaware Biotechnology Institute, University of Delaware, Newark DE, USA
| | - Sean T Krepski
- Department of Geological Sciences, University of Delaware, Newark DE, USA
| | - Kenshiro Oshima
- Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, University of Tokyo Kashiwa, Japan
| | - Masahira Hattori
- Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, University of Tokyo Kashiwa, Japan
| | - Nicole Shapiro
- Department of Energy Joint Genome Institute, Walnut Creek CA, USA
| | - Tanja Woyke
- Department of Energy Joint Genome Institute, Walnut Creek CA, USA
| | - Clara S Chan
- Department of Geological Sciences, University of Delaware, Newark DE, USA
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21
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Reis MP, Avila MP, Costa PS, Barbosa FAR, Laanbroek HJ, Chartone-Souza E, Nascimento AMA. The influence of human settlement on the distribution and diversity of iron-oxidizing bacteria belonging to the Gallionellaceae in tropical streams. Front Microbiol 2014; 5:630. [PMID: 25505456 PMCID: PMC4241827 DOI: 10.3389/fmicb.2014.00630] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 11/04/2014] [Indexed: 01/20/2023] Open
Abstract
Among the neutrophilic iron-oxidizing bacteria (FeOB), Gallionella is one of the most abundant genera in freshwater environments. By applying qPCR and DGGE based on 16S rRNA gene-directed primers targeting Gallionellaceae, we delineated the composition and abundance of the Gallionellaceae-related FeOB community in streams differentially affected by metal mining, and explored the relationships between these community characteristics and environmental variables. The sampling design included streams historically impacted by mining activity and a non-impacted stream. The sediment and water samples harbored a distinct community represented by Gallionella, Sideroxydans, and Thiobacillus species. Sequences affiliated with Gallionella were exclusively observed in sediments impacted by mining activities, suggesting an adaptation of this genus to these environments. In contrast, Sideroxydans-related sequences were found in all sediments including the mining impacted locations. The highest and lowest relative frequencies of Gallionellaceae-related FeOB were associated with the lowest and highest concentrations of Fe, respectively. The data enclosed here clearly show distinct species-specific ecological niches, with Gallionella species dominating in sediments impacted by anthropogenic activities over Sideroxydans species.
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Affiliation(s)
- Mariana P Reis
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais Belo Horizonte, Brazil
| | - Marcelo P Avila
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais Belo Horizonte, Brazil
| | - Patrícia S Costa
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais Belo Horizonte, Brazil
| | - Francisco A R Barbosa
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais Belo Horizonte, Brazil
| | - Hendrikus J Laanbroek
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO - KNAW) Wageningen, Netherlands ; Institute of Environmental Biology, Utrecht University Utrecht, Netherlands
| | - Edmar Chartone-Souza
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais Belo Horizonte, Brazil
| | - Andréa M A Nascimento
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais Belo Horizonte, Brazil
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22
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Li X, Mercado R, Kernan T, West AC, Banta S. Addition of citrate to Acidithiobacillus ferrooxidans cultures enables precipitate-free growth at elevated pH and reduces ferric inhibition. Biotechnol Bioeng 2014; 111:1940-8. [PMID: 24771134 DOI: 10.1002/bit.25268] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2014] [Revised: 04/08/2014] [Accepted: 04/15/2014] [Indexed: 11/10/2022]
Abstract
Acidithiobacillus ferrooxidans is an acidophilic chemolithoautotroph that is important in biomining and other biotechnological operations. The cells are able to oxidize inorganic iron, but the insolubility and product inhibition by Fe(3+) complicates characterization of these cultures. Here we explore the growth kinetics of A. ferrooxidans in iron-based medium in a pH range from 1.6 to 2.2. It was found that as the pH was increased from 1.6 to 2.0, the maintenance coefficient decreased while both the growth kinetics and maximum cell yield increased in the precipitate-free, low Fe(2+) concentration medium. In higher iron media a similar trend was observed at low pH, but the formation of precipitates at higher pH (2.0) hampered cell growth and lowered the specific growth rate and maximum cell yield. In order to eliminate ferric precipitates, chelating agents were introduced into the medium. Citric acid was found to be relatively non-toxic and did not appear to interfere with iron oxidation at a maximum concentration of 70 mM. Inclusion of citric acid prevented precipitation and A. ferrooxidans growth parameters resumed their trends as a function of pH. The addition of citrate also decreased the apparent substrate saturation constant (KS ) indicating a reduction in the competitive inhibition of growth by ferric ions. These results indicate that continuous cultures of A. ferrooxidans in the presence of citrate at elevated pH will enable enhanced cell yields and productivities. This will be critical as these cells are used in the development of new biotechnological applications such as electrofuel production.
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Affiliation(s)
- Xiaozheng Li
- Department of Chemical Engineering, Columbia University, 500W 120th Street, New York, New York, 10027
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23
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Abstract
Surfaces of carbon steel (CS) exposed to mixed cultures of iron-oxidizing bacteria (FeOB) and dissimilatory iron-reducing bacteria (FeRB) in seawater media under aerobic conditions were rougher than surfaces of CS exposed to pure cultures of either type of microorganism. The roughened surface, demonstrated by profilometry, is an indication of loss of metal from the surface. In the presence of CS, aerobically grown FeOB produced tight, twisted helical stalks encrusted with iron oxides. When CS was exposed anaerobically in the presence of FeRB, some surface oxides were removed. However, when the same FeOB and FeRB were grown together in an aerobic medium, FeOB stalks were less encrusted with iron oxides and appeared less tightly coiled. These observations suggest that iron oxides on the stalks were reduced and solubilized by the FeRB. Roughened surfaces of CS and denuded stalks were replicated with culture combinations of different species of FeOB and FeRB under three experimental conditions. Measurements of electrochemical polarization resistance established different rates of corrosion of CS in aerobic and anaerobic media, but could not differentiate rate differences between sterile controls and inoculated exposures for a given bulk concentration of dissolved oxygen. Similarly, total iron in the electrolyte could not be used to differentiate treatments. The experiments demonstrate the potential for iron cycling (oxidation and reduction) on corroding CS in aerobic seawater media.
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Affiliation(s)
- Jason S. Lee
- Naval Research Laboratory, Stennis Space Center, MS, USA
| | - Joyce M. McBeth
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | - Richard I. Ray
- Naval Research Laboratory, Stennis Space Center, MS, USA
| | | | - David Emerson
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
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Kato S, Nakamura K, Toki T, Ishibashi JI, Tsunogai U, Hirota A, Ohkuma M, Yamagishi A. Iron-based microbial ecosystem on and below the seafloor: a case study of hydrothermal fields of the southern mariana trough. Front Microbiol 2012; 3:89. [PMID: 22435065 PMCID: PMC3304087 DOI: 10.3389/fmicb.2012.00089] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Accepted: 02/22/2012] [Indexed: 11/13/2022] Open
Abstract
Microbial community structures in deep-sea hydrothermal vents fields are constrained by available energy yields provided by inorganic redox reactions, which are in turn controlled by chemical composition of hydrothermal fluids. In the past two decades, geochemical and microbiological studies have been conducted in deep-sea hydrothermal vents at three geographically different areas of the Southern Mariana Trough (SMT). A variety of geochemical data of hydrothermal fluids and an unparalleled microbiological dataset of various samples (i.e., sulfide structures of active vents, iron-rich mats, borehole fluids, and ambient seawater) are available for comparative analyses. Here, we summarize the geochemical and microbiological characteristics in the SMT and assess the relationship between the microbial community structures and the fluid geochemistry in the SMT by thermodynamic modeling. In the high temperature vent fluids, aerobic sulfide-oxidation has the potential to yield large amounts of bioavailable energy in the vent fluids, which is consistent with the detection of species related to sulfide-oxidizing bacteria (such as Thiomicrospira in the Gammaproteobacteria and Sulfurimonas in the Epsilonproteobacteria). Conversely, the bioavailable energy yield from aerobic iron-oxidation reactions in the low-temperature fluids collected from man-made boreholes and several natural vents were comparable to or higher than those from sulfide-oxidation. This is also consistent with the detection of species related to iron-oxidizing bacteria (Mariprofundus in the Zetaproteobacteria) in such low-temperature samples. The results of combination of microbiological, geochemical, and thermodynamic analyses in the SMT provide novel insights into the presence and significance of iron-based microbial ecosystems in deep-sea hydrothermal fields.
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Affiliation(s)
- Shingo Kato
- Japan Collection of Microorganisms, RIKEN BioResource Center Wako, Saitama, Japan
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