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Reid DM, Khadka M, Kahlon S, Chalasani N, Kass K. Severe Shewanella Cellulitis Following Saltwater Exposure in an Elderly Patient. Cureus 2024; 16:e55724. [PMID: 38586666 PMCID: PMC10998643 DOI: 10.7759/cureus.55724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 03/06/2024] [Indexed: 04/09/2024] Open
Abstract
Shewanella algae is an opportunistic Gram-negative bacillus primarily found in marine environments. It can cause a range of infections in humans, from superficial soft tissue infections to more severe conditions like bacteremia, otitis, and hepatobiliary infections. While infections are rare, they can be significant, leading to complications such as sepsis and tissue necrosis. We present the case of severe cellulitis caused by Shewanella in an 88-year-old patient with multiple comorbidities. Following a blue crab pinch and consequent saltwater exposure, the patient developed severe cellulitis, sepsis, delirium, and atrial fibrillation. Despite these complications and the patient's age, a prompt diagnosis and a combination of antibiotic treatments led to a successful recovery. This case is notable for its illustration of the potential severity and diverse clinical presentation of Shewanella infections. It highlights the importance of considering Shewanella as a possible pathogen in cases of saltwater exposure and teaches management in elderly, multi-morbid patients.
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Affiliation(s)
- Devaun M Reid
- Internal Medicine, University of South Florida Morsani College of Medicine, Tampa, USA
| | - Monica Khadka
- Internal Medicine, University of South Florida Morsani College of Medicine, Tampa, USA
| | - Sunny Kahlon
- Internal Medicine, University of South Florida Morsani College of Medicine, Tampa, USA
| | - Nishanth Chalasani
- Internal Medicine, University of South Florida Morsani College of Medicine, Tampa, USA
| | - Kathryn Kass
- Infectious Disease, University of South Florida, Tampa, USA
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2
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Wu YF, Chen J, Xie WY, Peng C, Tang ST, Rosen BP, Kappler A, Zhang J, Zhao FJ. Anoxygenic phototrophic arsenite oxidation by a Rhodobacter strain. Environ Microbiol 2023; 25:1538-1548. [PMID: 36978205 PMCID: PMC10676076 DOI: 10.1111/1462-2920.16380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 03/18/2023] [Indexed: 03/30/2023]
Abstract
Microbially mediated arsenic redox transformations are key for arsenic speciation and mobility in rice paddies. Whereas anaerobic anoxygenic photosynthesis coupled to arsenite (As(III)) oxidation has been widely examined in arsenic-replete ecosystems, it remains unknown whether this light-dependent process exists in paddy soils. Here, we isolated a phototrophic purple bacteria, Rhodobacter strain CZR27, from an arsenic-contaminated paddy soil and demonstrated its capacity to oxidize As(III) to arsenate (As(V)) using malate as a carbon source photosynthetically. Genome sequencing revealed an As(III)-oxidizing gene cluster (aioXSRBA) encoding an As(III) oxidase. Functional analyses showed that As(III) oxidation under anoxic phototrophic conditions correlated with transcription of the large subunit of the As(III) oxidase aioA gene. Furthermore, the non-As(III) oxidizer Rhodobacter capsulatus SB1003 heterologously expressing aioBA from strain CZR27 was able to oxidize As(III), indicating that aioBA was responsible for the observed As(III) oxidation in strain CZR27. Our study provides evidence for the presence of anaerobic photosynthesis-coupled As(III) oxidation in paddy soils, highlighting the importance of light-dependent, microbe-mediated arsenic redox changes in paddy arsenic biogeochemistry.
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Affiliation(s)
- Yi-Fei Wu
- Jiangsu Key Laboratory for Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Jian Chen
- Department of Cellular Biology and Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida 33199, USA
| | - Wan-Ying Xie
- Jiangsu Key Laboratory for Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Chao Peng
- College of Life Sciences, China West Normal University, Nanchong, China
| | - Shi-Tong Tang
- Jiangsu Key Laboratory for Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Barry P. Rosen
- Department of Cellular Biology and Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida 33199, USA
| | - Andreas Kappler
- Geomicrobiology, Department of Geoscience, University of Tuebingen, Tuebingen 72076, Germany
- Cluster of Excellence: EXC 2124: Controlling Microbes to Fight Infection, Tuebingen 72076, Germany
| | - Jun Zhang
- Jiangsu Key Laboratory for Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Fang-Jie Zhao
- Jiangsu Key Laboratory for Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
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3
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Chen Q, Li G, Lu Z, Su Y, Wu B, Shi B. Efficient Mn(II) removal by biological granular activated carbon filtration. JOURNAL OF HAZARDOUS MATERIALS 2023:131877. [PMID: 37344241 DOI: 10.1016/j.jhazmat.2023.131877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 06/06/2023] [Accepted: 06/15/2023] [Indexed: 06/23/2023]
Abstract
Sufficient and sustainable manganese(II) removal is a challenging task to prevent Mn-related drinking water discoloration problems. This study investigated Mn(II) removal by granular activated carbon (GAC) filtration under various conditions. The results showed that biological GAC filter columns could reduce Mn(II) from 400 μg/L to 10 μg/L after a short ripening period, while sand filter columns did not show evident Mn(II) removal function. Water quality changes, pretreatment with NaClO and chemogenic MnOx coating on GAC media surface did not influence the Mn(II) removal capacity of GAC filter columns. 16S rRNA gene sequencing showed that the abundance of potential Mn(II)-oxidizing bacteria in the GAC media was similar to that in the sand media. However, qPCR results indicated that GAC media colonized dramatically more biomass than sand media, resulting in highly effective Mn(II) removal by GAC filter columns. Under chlorinated conditions, GAC filtration underperformed sand filtration in Mn(II) removal, although activated carbon has been reported to be capable of catalyzing Mn(II) oxidation by chlorine. Fast chlorine decay in GAC filter columns made it hard to sustain chemical Mn(II) oxidation and thus led to less Mn(II) removal. This study highlighted the advantage of biological GAC filtration over sand filtration in Mn(II) removal.
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Affiliation(s)
- Qi Chen
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Institute of Environmental and Municipal Engineering, North China University of Water Resources and Electric Power, Zhengzhou 450045, China
| | - Guiwei Li
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
| | - Zhili Lu
- Institute of Environmental and Municipal Engineering, North China University of Water Resources and Electric Power, Zhengzhou 450045, China
| | - Yuliang Su
- Zhuhai Water Environment Holdings Group Ltd., Zhuhai, Guangdong 519000, China
| | - Bin Wu
- Zhuhai Water Environment Holdings Group Ltd., Zhuhai, Guangdong 519000, China
| | - Baoyou Shi
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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4
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Jia L, Zhou Q, Li Y, Wu W. Application of manganese oxides in wastewater treatment: Biogeochemical Mn cycling driven by bacteria. CHEMOSPHERE 2023:139219. [PMID: 37327824 DOI: 10.1016/j.chemosphere.2023.139219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/05/2023] [Accepted: 06/13/2023] [Indexed: 06/18/2023]
Abstract
Manganese oxides (MnOx) are recognized as a strongest oxidant and adsorbent, of which composites have been proved to be effective in the removal of contaminants from wastewater. This review provides a comprehensive analysis of Mn biochemistry in water environment including Mn oxidation and Mn reduction. The recent research on the application of MnOx in the wastewater treatment was summarized, including the involvement of organic micropollutant degradation, the transformation of nitrogen and phosphorus, the fate of sulfur and the methane mitigation. In addition to the adsorption capacity, the Mn cycling mediated by Mn(II) oxidizing bacteria and Mn(IV) reducing bacteria is the driving force for the MnOx utilization. The common category, characteristics and functions of Mn microorganisms in recent studies were also reviewed. Finally, the discussion on the influence factors, microbial response, reaction mechanism and potential risk of MnOx application in pollutants' transformation were proposed, which might be the promising opportunities for the future investigation of MnOx application in wastewater treatment.
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Affiliation(s)
- Lixia Jia
- Department of Environmental Science, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, PR China
| | - Qi Zhou
- Department of Environmental Science, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, PR China
| | - Yuanwei Li
- Department of Environmental Science, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, PR China
| | - Weizhong Wu
- Department of Environmental Science, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, PR China; The Key Laboratory of Water and Sediment Sciences (Peking University), Ministry of Education, Beijing, 100871, China.
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5
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Mineralogical and Genomic Constraints on the Origin of Microbial Mn Oxide Formation in Complexed Microbial Community at the Terrestrial Hot Spring. Life (Basel) 2022; 12:life12060816. [PMID: 35743847 PMCID: PMC9224936 DOI: 10.3390/life12060816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/18/2022] [Accepted: 05/26/2022] [Indexed: 11/17/2022] Open
Abstract
Manganese (Mn) oxides are widespread on the surface environments of the modern Earth. The role of microbial activities in the formation of Mn oxides has been discussed for several decades. However, the mechanisms of microbial Mn oxidation, and its role in complex microbial communities in natural environments, remain uncertain. Here, we report the geochemical, mineralogical, and metagenomic evidence for biogenic Mn oxides, found in Japanese hot spring sinters. The low crystallinity of Mn oxides, and their spatial associations with organic matter, support the biogenic origin of Mn oxides. Specific multicopper oxidases (MCOs), which are considered Mn-oxidizing enzymes, were identified using metagenomic analyses. Nanoscale nuggets of copper sulfides were, also, discovered in the organic matter in Mn-rich sinters. A part of these copper sulfides most likely represents traces of MCOs, and this is the first report of traces of Mn-oxidizing enzyme in geological samples. Metagenomic analyses, surprisingly, indicated a close association of Mn oxides, not only in aerobic but also in anaerobic microbial communities. These new findings offer the unique and unified positions of Mn oxides, with roles that have not been ignored, to sustain anaerobic microbial communities in hot spring environments.
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6
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Min D, Cheng L, Liu JQ, Liu DF, Li WW, Yu HQ. Ligand-Assisted Formation of Soluble Mn(III) and Bixbyite-like Mn 2O 3 by Shewanella putrefaciens CN32. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:3812-3820. [PMID: 35226466 DOI: 10.1021/acs.est.2c00342] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Functional material synthesis through biomineralization is effective and environmentally friendly. Biomineralized manganese (Mn) oxides are important for remediation and energy storage. Manganese(II) biomineralization is achieved by a diverse group of bacteria. We show that in the presence of oxygen the dissimilatory manganese-reducing bacterium Shewanella putrefaciens CN32 can oxidize Mn(II). The Mn(II) oxidation was accelerated with the increase in the initial Mn(II) concentration from 0.5 to 3 mM. The reaction was mainly associated with a cell-free filtrate, rather than the direct enzymatic oxidation or indirect oxidation by reactive oxygen species or macrocyclic siderophores. Instead, indirect oxidization of Mn(II) into soluble Mn(III) and bixbyite-like Mn2O3 via microbially produced extracellular ligands (molecular weights of 1-3 kDa) was identified. This work broadens our view about microbial Mn(II) oxidation and unveils the important roles of Shewanella species in the geochemical cycling of manganese.
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Affiliation(s)
- Di Min
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Lei Cheng
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Jia-Qi Liu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Dong-Feng Liu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Wen-Wei Li
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Han-Qing Yu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
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7
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McCormick NE, Earle M, Ha C, Hakes L, Evans A, Anderson L, Stoddart AK, Langille MGI, Gagnon GA. Biological and physico-chemical mechanisms accelerating the acclimation of Mn-removing biofilters. WATER RESEARCH 2021; 207:117793. [PMID: 34715404 DOI: 10.1016/j.watres.2021.117793] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 10/17/2021] [Accepted: 10/18/2021] [Indexed: 06/13/2023]
Abstract
This study investigated treatment strategies which accelerated the acclimation of new Mn-removing biofilters to help utilities respond to changing Mn regulations, such as the recent introduction of a health-based maximum acceptable concentration and a reduction in the aesthetic objective for Mn in drinking water by Health Canada. Bench-scale filters of either GAC or anthracite media were fed with applied water containing Mn (17-61 μg/L) from a full-scale plant over 294 days. Treatment strategies included the addition of H2O2 (1 mg/L) and/or an increase in pH from 6.8 to 7.5 through the addition of NaOH. The potential physico-chemical and biological mechanisms responsible for accelerated biofilter acclimation under the various redox conditions were investigated through thermodynamic modelling, to predict homogeneous Mn oxide formation, and 16S rRNA gene amplicon sequencing, to characterize the microbial community within the filters. GAC filters treated with NaOH, and both H2O2 and NaOH, were the first to acclimate (< 20 μg/L Mn in filter effluent) after 59 and 63 days respectively, while the ambient GAC filter took almost 3 times as long to acclimate (168 days), and the anthracite filters which received the same chemically adjusted water took almost 4 times as long (226 and 251 days, respectively). The accelerated acclimation in the treated GAC filters was likely due to physico-chemical oxidation via three potential mechanisms: (1) homogeneous oxidation of dissolved Mn(II) to Mn(III)/Mn(IV) oxides and the subsequent removal of oxides from solution through adherence to the GAC surface, (2) adsorption of dissolved Mn(II) to GAC and subsequent homogeneous or biological oxidation, or (3) formation of colloidal Mn(III)/Mn(IV) oxides and subsequent adsorption of dissolved Mn(II) to the Mn colloids. In the untreated GAC filter and all anthracite filters, which did not benefit from improved redox conditions or an active surface, physico-chemical mechanisms alone were insufficient for consistent Mn removal to less than 20 μg/L. Acclimation in these filters was delayed until a microbiome enriched with bacteria capable of biological nitrification and Mn oxidation evolved within the filters. The acclimated microbiome was consistent between GAC and anthracite filters and was significantly different from the non-acclimated microbiome (p < 0.001) initially formed during the early operation of the filters. Interestingly, treatment with NaOH, and NaOH and H2O2, which accelerated physico-chemical oxidation in GAC filters, was observed to delay the development of biological oxidation in anthracite filters, and thus deferred acclimation. Although some filters took longer to acclimate than others, once acclimation was reached all filters had a similar microbiome and were able to consistently remove Mn to below 20 µg/L.
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Affiliation(s)
- N E McCormick
- Centre for Water Resources Studies, Department of Civil and Resource Engineering, Dalhousie University, Halifax, NS, Canada.
| | - M Earle
- Centre for Water Resources Studies, Department of Civil and Resource Engineering, Dalhousie University, Halifax, NS, Canada
| | - C Ha
- Alameda County Water District, Freemont, CA, USA
| | - L Hakes
- Alameda County Water District, Freemont, CA, USA
| | - A Evans
- Arcadis US, Inc., Austin, TX, USA
| | - L Anderson
- Centre for Water Resources Studies, Department of Civil and Resource Engineering, Dalhousie University, Halifax, NS, Canada
| | - A K Stoddart
- Centre for Water Resources Studies, Department of Civil and Resource Engineering, Dalhousie University, Halifax, NS, Canada
| | - M G I Langille
- Department of Pharmacology, Dalhousie University, Halifax, NS, Canada
| | - G A Gagnon
- Centre for Water Resources Studies, Department of Civil and Resource Engineering, Dalhousie University, Halifax, NS, Canada
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8
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Zhang L, Fang W, Li X, Lu W, Li J. Strong linkages between dissolved organic matter and the aquatic bacterial community in an urban river. WATER RESEARCH 2020; 184:116089. [PMID: 32693265 DOI: 10.1016/j.watres.2020.116089] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 06/16/2020] [Accepted: 06/19/2020] [Indexed: 06/11/2023]
Abstract
Aquatic bacterial communities play an important role in biogeochemical cycling in river ecosystems; however, knowledge of the linkages between bacterial communities and dissolved organic matter (DOM) in urban rivers is limited. Here, 16S rRNA amplicon sequencing and parallel factor (PARAFAC) modeling of excitation-emission fluorescence spectroscopy were used to analyze the compositions, co-occurrence patterns, and interactions with chromophoric DOM (CDOM) of bacterial communities in urban river water samples influenced by different human activities. The results revealed that two protein-like components accounted for 65.2 ± 9.56% of the total variability in all three fluorescence components, which suggests that CDOM in urban rivers is mainly a microbial source. In addition to pH and DO, CDOM is also an important factor affecting bacterial community structure, and the main classes (Gammaproteobacteria and Clostridia) and genera (Limnohabitans and Alpinimonas) showed strong positive correlations with terrestrial humic-like C1 and tryptophan-like C2, respectively. When autotrophic and heterotrophic bacteria coexist in urban rivers, the production and degradation of CDOM will occur simultaneously. Furthermore, the riverine bacterial co-occurrence network had a nonrandom modular structure, which was mainly driven by classification correlation and bacterial function. The high abundance of genes related to xenobiotic metabolism, carbon metabolism and nitrogen metabolism in the urban river indicated that anthropogenic activity may be the dominant selective force altering the bacterial communities. Overall, our results provide a novel view for the assembly of bacterial communities in urban river ecosystems under the influence of different human activities.
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Affiliation(s)
- Lei Zhang
- School of Civil Engineering and Architecture, Chuzhou University, Chuzhou, 239000, China.
| | - Wangkai Fang
- School of Civil Engineering and Architecture, Chuzhou University, Chuzhou, 239000, China
| | - Xingchen Li
- School of Civil Engineering and Architecture, Chuzhou University, Chuzhou, 239000, China
| | - Wenxuan Lu
- Fisheries Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230036, China
| | - Jing Li
- Fisheries Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230036, China
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9
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Mitchell SL, Hudson-Smith NV, Cahill MS, Reynolds BN, Frand SD, Green CM, Wang C, Hang MN, Hernandez RT, Hamers RJ, Feng ZV, Haynes CL, Carlson EE. Chronic exposure to complex metal oxide nanoparticles elicits rapid resistance in Shewanella oneidensis MR-1. Chem Sci 2019; 10:9768-9781. [PMID: 32055346 PMCID: PMC6993611 DOI: 10.1039/c9sc01942a] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 08/29/2019] [Indexed: 12/20/2022] Open
Abstract
Engineered nanoparticles are incorporated into numerous emerging technologies because of their unique physical and chemical properties. Many of these properties facilitate novel interactions, including both intentional and accidental effects on biological systems. Silver-containing particles are widely used as antimicrobial agents and recent evidence indicates that bacteria rapidly become resistant to these nanoparticles. Much less studied is the chronic exposure of bacteria to particles that were not designed to interact with microorganisms. For example, previous work has demonstrated that the lithium intercalated battery cathode nanosheet, nickel manganese cobalt oxide (NMC), is cytotoxic and causes a significant delay in growth of Shewanella oneidensis MR-1 upon acute exposure. Here, we report that S. oneidensis MR-1 rapidly adapts to chronic NMC exposure and is subsequently able to survive in much higher concentrations of these particles, providing the first evidence of permanent bacterial resistance following exposure to nanoparticles that were not intended as antibacterial agents. We also found that when NMC-adapted bacteria were subjected to only the metal ions released from this material, their specific growth rates were higher than when exposed to the nanoparticle. As such, we provide here the first demonstration of bacterial resistance to complex metal oxide nanoparticles with an adaptation mechanism that cannot be fully explained by multi-metal adaptation. Importantly, this adaptation persists even after the organism has been grown in pristine media for multiple generations, indicating that S. oneidensis MR-1 has developed permanent resistance to NMC.
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Affiliation(s)
- Stephanie L Mitchell
- Department of Chemistry , University of Minnesota , 207 Pleasant St. SE , Minneapolis , MN 55455 , USA .
| | - Natalie V Hudson-Smith
- Department of Chemistry , University of Minnesota , 207 Pleasant St. SE , Minneapolis , MN 55455 , USA .
| | - Meghan S Cahill
- Department of Chemistry , University of Minnesota , 207 Pleasant St. SE , Minneapolis , MN 55455 , USA .
| | - Benjamin N Reynolds
- Department of Biochemistry, Molecular Biology, and Biophysics , University of Minnesota , 321 Church Street SE , Minneapolis , Minnesota 55454 , USA
| | - Seth D Frand
- Chemistry Department , Augsburg University , 2211 Riverside Ave , Minneapolis , MN 55454 , USA
| | - Curtis M Green
- Department of Chemistry , University of Wisconsin-Madison , 1101 University Avenue , Madison , WI 53706 , USA
| | - Chenyu Wang
- Department of Chemistry , University of Wisconsin-Madison , 1101 University Avenue , Madison , WI 53706 , USA
| | - Mimi N Hang
- Department of Chemistry , University of Wisconsin-Madison , 1101 University Avenue , Madison , WI 53706 , USA
| | - Rodrigo Tapia Hernandez
- Chemistry Department , Augsburg University , 2211 Riverside Ave , Minneapolis , MN 55454 , USA
| | - Robert J Hamers
- Department of Chemistry , University of Wisconsin-Madison , 1101 University Avenue , Madison , WI 53706 , USA
| | - Z Vivian Feng
- Chemistry Department , Augsburg University , 2211 Riverside Ave , Minneapolis , MN 55454 , USA
| | - Christy L Haynes
- Department of Chemistry , University of Minnesota , 207 Pleasant St. SE , Minneapolis , MN 55455 , USA .
| | - Erin E Carlson
- Department of Chemistry , University of Minnesota , 207 Pleasant St. SE , Minneapolis , MN 55455 , USA .
- Department of Biochemistry, Molecular Biology, and Biophysics , University of Minnesota , 321 Church Street SE , Minneapolis , Minnesota 55454 , USA
- Department of Medicinal Chemistry , University of Minnesota , 208 Harvard Street SE , Minneapolis , 55454 , USA
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10
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Electrons selective uptake of a metal-reducing bacterium Shewanella oneidensis MR-1 from ferrocyanide. Biosens Bioelectron 2019; 142:111571. [DOI: 10.1016/j.bios.2019.111571] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 08/01/2019] [Accepted: 08/03/2019] [Indexed: 12/24/2022]
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11
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Thomas PJ, Boller AJ, Satagopan S, Tabita FR, Cavanaugh CM, Scott KM. Isotope discrimination by form IC RubisCO from
Ralstonia eutropha
and
Rhodobacter sphaeroides
, metabolically versatile members of ‘
Proteobacteria
’ from aquatic and soil habitats. Environ Microbiol 2018; 21:72-80. [DOI: 10.1111/1462-2920.14423] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 09/18/2018] [Indexed: 11/29/2022]
Affiliation(s)
- Phaedra J. Thomas
- Department of Integrative Biology University of South Florida Tampa FL USA
| | - Amanda J. Boller
- Department of Integrative Biology University of South Florida Tampa FL USA
| | - Sriram Satagopan
- Department of Microbiology The Ohio State University Columbus OH USA
| | - F. Robert Tabita
- Department of Microbiology The Ohio State University Columbus OH USA
| | - Colleen M. Cavanaugh
- Department of Organismic and Evolutionary Biology Harvard University Cambridge MA USA
| | - Kathleen M. Scott
- Department of Integrative Biology University of South Florida Tampa FL USA
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Fan YY, Li BB, Yang ZC, Cheng YY, Liu DF, Yu HQ. Abundance and diversity of iron reducing bacteria communities in the sediments of a heavily polluted freshwater lake. Appl Microbiol Biotechnol 2018; 102:10791-10801. [PMID: 30334090 DOI: 10.1007/s00253-018-9443-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 08/19/2018] [Accepted: 10/07/2018] [Indexed: 12/27/2022]
Abstract
Iron reduction mediated by Fe(III)-reducing bacteria (FeRB) occurs in aqueous environments and plays an essential role in removing contaminates in polluted freshwater lakes. Two model FeRB species, Shewanella and Geobacter, have been intensively studied because of their functions in bioremediation, iron reduction, and bioelectricity production. However, the abundance and community diversity of Shewanella and Geobacter in eutrophic freshwater lakes remain largely unknown. In this work, the distribution, abundance and biodiversity of Shewanella, Geobacter and other FeRB in the sediments of a heavily polluted lake, Chaohu Lake, China, across four successive seasons were investigated. Shewanella, Geobacter, and other FeRB were found to be widely distributed in the sediment of this heavily eutrophic lake. Geobacter was abundant with at least one order of magnitude more than Shewanella in cold seasons. Three Shewanella-related operational taxonomic units were detected and sixty one Geobacter-related operational taxonomic units were grouped into three phylogenetic clades. Thiobacillus, Desulfuromonas and Geobacter were identified as the main members of FeRB in the lake sediments. Interestingly, nutrients like carbon, nitrogen, and phosphorus were found to be the key factors governing the abundance and diversity of FeRB. Total FeRB, as well as Geobacter and Shewanella, were more abundant in the heavily eutrophic zone than those in the lightly eutrophic zone. The abundance and diversity of FeRB in the sediments of freshwater lakes were highly related with the degree of eutrophication, which imply that FeRB might have a great potential in alleviating the eutrophication and contamination in aqueous environments.
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Affiliation(s)
- Yang-Yang Fan
- School of Life Sciences, University of Science & Technology of China, Hefei, 230026, China
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Chemistry, University of Science & Technology of China, Hefei, 230026, China
| | - Bing-Bing Li
- School of Life Sciences, University of Science & Technology of China, Hefei, 230026, China
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Chemistry, University of Science & Technology of China, Hefei, 230026, China
| | - Zong-Chuang Yang
- School of Life Sciences, University of Science & Technology of China, Hefei, 230026, China
| | - Yuan-Yuan Cheng
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Chemistry, University of Science & Technology of China, Hefei, 230026, China
| | - Dong-Feng Liu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Chemistry, University of Science & Technology of China, Hefei, 230026, China.
| | - Han-Qing Yu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Chemistry, University of Science & Technology of China, Hefei, 230026, China
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13
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Li BB, Cheng YY, Fan YY, Liu DF, Fang CY, Wu C, Li WW, Yang ZC, Yu HQ. Estimates of abundance and diversity of Shewanella genus in natural and engineered aqueous environments with newly designed primers. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 637-638:926-933. [PMID: 29763873 DOI: 10.1016/j.scitotenv.2018.05.051] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 05/04/2018] [Accepted: 05/04/2018] [Indexed: 06/08/2023]
Abstract
Shewanella species have a diverse respiratory ability and wide distribution in environments and play an important role in bioremediation and the biogeochemical cycles of elements. Primers with more accuracy and broader coverage are required with consideration of the increasing number of Shewanella species and evaluation of their roles in various environments. In this work, a new primer set of 640F/815R was developed to quantify the abundance of Shewanella species in natural and engineered environments. In silico tools for primer evaluation, quantitative polymerase chain reaction (qPCR) and clone library results showed that 640F/815R had a higher specificity and coverage than the previous primers in quantitative analysis of Shewanella. Another newly developed primer pair of 211F/815cR was also adopted to analyze the Shewanella diversity and demonstrated to be the best candidate in terms of specificity and coverage. We detected more Shewanella-related species in freshwater environments and found them to be substantially different from those in marine environments. Abundance and diversity of Shewanella species in wastewater treatment plants were largely affected by the process and operating conditions. Overall, this study suggests that investigations of abundance and diversity of Shewanella in various environments are of great importance to evaluate their ecophysiology and potential ecological roles.
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Affiliation(s)
- Bing-Bing Li
- School of Life Sciences, University of Science & Technology of China, Hefei 230026, China; CAS Key Laboratory of Urban Pollutant Conversion, Department of Chemistry, University of Science & Technology of China, Hefei 230026, China
| | - Yuan-Yuan Cheng
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Chemistry, University of Science & Technology of China, Hefei 230026, China
| | - Yang-Yang Fan
- School of Life Sciences, University of Science & Technology of China, Hefei 230026, China
| | - Dong-Feng Liu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Chemistry, University of Science & Technology of China, Hefei 230026, China
| | - Cai-Yun Fang
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Chemistry, University of Science & Technology of China, Hefei 230026, China
| | - Chao Wu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Chemistry, University of Science & Technology of China, Hefei 230026, China
| | - Wen-Wei Li
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Chemistry, University of Science & Technology of China, Hefei 230026, China
| | - Zong-Chuang Yang
- School of Life Sciences, University of Science & Technology of China, Hefei 230026, China
| | - Han-Qing Yu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Chemistry, University of Science & Technology of China, Hefei 230026, China.
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Gat D, Mazar Y, Cytryn E, Rudich Y. Origin-Dependent Variations in the Atmospheric Microbiome Community in Eastern Mediterranean Dust Storms. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:6709-6718. [PMID: 28422476 DOI: 10.1021/acs.est.7b00362] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Microorganisms carried by dust storms are transported through the atmosphere and may affect human health and the functionality of microbial communities in various environments. Characterizing the dust-borne microbiome in dust storms of different origins or that followed different trajectories provides valuable data to improve our understanding of global health and environmental impacts. We present a comparative study on the diversity of dust-borne bacterial communities in dust storms from three distinct origins (North Africa, Syria and Saudi Arabia) and compare them with local bacterial communities sampled on clear days, all collected at a single location: Rehovot, Israel. Storms from different dust origins exhibited distinct bacterial communities, with signature bacterial taxa. Dust storms were characterized by a lower abundance of selected antibiotic resistance genes (ARGs) compared with ambient dust, asserting that the origin of these genes is local and possibly anthropogenic. With the progression of the storm, the storm-borne bacterial community showed increasing resemblance to ambient dust, suggesting mixing with local dust. These results show, for the first time, that dust storms from different sources display distinct bacterial communities, suggesting possible diverse effects on the environment and public health.
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Affiliation(s)
- Daniella Gat
- Department of Earth and Planetary Sciences, Weizmann Institute of Science , Rehovot 7610001, Israel
| | - Yinon Mazar
- Department of Earth and Planetary Sciences, Weizmann Institute of Science , Rehovot 7610001, Israel
| | - Eddie Cytryn
- Institute of Soil, Water and Environmental Sciences, The Volcani Center, Agriculture Research Organization , Rishon Lezion 7528809, Israel
| | - Yinon Rudich
- Department of Earth and Planetary Sciences, Weizmann Institute of Science , Rehovot 7610001, Israel
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15
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Marcus DN, Pinto A, Anantharaman K, Ruberg SA, Kramer EL, Raskin L, Dick GJ. Diverse manganese(II)-oxidizing bacteria are prevalent in drinking water systems. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:120-128. [PMID: 27935222 DOI: 10.1111/1758-2229.12508] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 11/22/2016] [Indexed: 06/06/2023]
Abstract
Manganese (Mn) oxides are highly reactive minerals that influence the speciation, mobility, bioavailability and toxicity of a wide variety of organic and inorganic compounds. Although Mn(II)-oxidizing bacteria are known to catalyze the formation of Mn oxides, little is known about the organisms responsible for Mn oxidation in situ, especially in engineered environments. Mn(II)-oxidizing bacteria are important in drinking water systems, including in biofiltration and water distribution systems. Here, we used cultivation dependent and independent approaches to investigate Mn(II)-oxidizing bacteria in drinking water sources, a treatment plant and associated distribution system. We isolated 29 strains of Mn(II)-oxidizing bacteria and found that highly similar 16S rRNA gene sequences were present in all culture-independent datasets and dominant in the studied drinking water treatment plant. These results highlight a potentially important role for Mn(II)-oxidizing bacteria in drinking water systems, where biogenic Mn oxides may affect water quality in terms of aesthetic appearance, speciation of metals and oxidation of organic and inorganic compounds. Deciphering the ecology of these organisms and the factors that regulate their Mn(II)-oxidizing activity could yield important insights into how microbial communities influence the quality of drinking water.
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Affiliation(s)
- Daniel N Marcus
- Department of Earth and Environmental Science, University of Michigan, Ann Arbor, MI, USA
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Ameet Pinto
- Department of Civil and Environmental Engineering, Northeastern University, Boston, MA, USA
| | - Karthik Anantharaman
- Department of Earth and Environmental Science, University of Michigan, Ann Arbor, MI, USA
| | - Steven A Ruberg
- Great Lakes Environmental Research Laboratory, National Oceanic and Atmospheric Administration, Ann Arbor, MI, USA
| | - Eva L Kramer
- Department of Earth and Environmental Science, University of Michigan, Ann Arbor, MI, USA
| | - Lutgarde Raskin
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Gregory J Dick
- Department of Earth and Environmental Science, University of Michigan, Ann Arbor, MI, USA
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Abstract
The importance of manganese in the physiology of marine microbes, the biogeochemistry of the ocean and the health of microbial communities of past and present is emerging. Manganese is distributed widely throughout the global ocean, taking the form of an essential antioxidant (Mn2+), a potent oxidant (Mn3+) and strong adsorbent (Mn oxides) sequestering disproportionately high levels of trace metals and nutrients in comparison to the surrounding seawater. Manganese is, in fact, linked to nearly all other elemental cycles and intricately involved in the health, metabolism and function of the ocean's microbiome. Here, we briefly review the diversity of microbes and pathways responsible for the transformation of Mn within the three Mn pools and their distribution within the marine environment. Despite decades of interrogation, we still have much to learn about the players, mechanisms and consequences of the Mn cycle, and new and exciting discoveries are being made at a rapid rate. What is clear is the dynamic and ever-inspiring complexity of reactions involving Mn, and the acknowledgement that microorganisms are the catalytic engine driving the Mn cycle.
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Affiliation(s)
- Colleen M Hansel
- Woods Hole Oceanographic Institution, Woods Hole, MA, United States.
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17
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Production of Manganese Oxide Nanoparticles by Shewanella Species. Appl Environ Microbiol 2016; 82:5402-9. [PMID: 27342559 DOI: 10.1128/aem.00663-16] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 06/21/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Several species of the bacterial genus Shewanella are well-known dissimilatory reducers of manganese under anaerobic conditions. In fact, Shewanella oneidensis is one of the most well studied of all metal-reducing bacteria. In the current study, a number of Shewanella strains were tested for manganese-oxidizing capacity under aerobic conditions. All were able to oxidize Mn(II) and to produce solid dark brown manganese oxides. Shewanella loihica strain PV-4 was the strongest oxidizer, producing oxides at a rate of 20.3 mg/liter/day and oxidizing Mn(II) concentrations of up to 9 mM. In contrast, S. oneidensis MR-1 was the weakest oxidizer tested, producing oxides at 4.4 mg/liter/day and oxidizing up to 4 mM Mn(II). Analysis of products from the strongest oxidizers, i.e., S loihica PV-4 and Shewanella putrefaciens CN-32, revealed finely grained, nanosize, poorly crystalline oxide particles with identical Mn oxidation states of 3.86. The biogenic manganese oxide products could be subsequently reduced within 2 days by all of the Shewanella strains when culture conditions were made anoxic and an appropriate nutrient (lactate) was added. While Shewanella species were detected previously as part of manganese-oxidizing consortia in natural environments, the current study has clearly shown manganese-reducing Shewanella species bacteria that are able to oxidize manganese in aerobic cultures. IMPORTANCE Members of the genus Shewanella are well known as dissimilatory manganese-reducing bacteria. This study shows that a number of species from Shewanella are also capable of manganese oxidation under aerobic conditions. Characterization of the products of the two most efficient oxidizers, S. loihica and S. putrefaciens, revealed finely grained, nanosize oxide particles. With a change in culture conditions, the manganese oxide products could be subsequently reduced by the same bacteria. The ability of Shewanella species both to oxidize and to reduce manganese indicates that the genus plays a significant role in the geochemical cycling of manganese. Due to the high affinity of manganese oxides for binding other metals, these bacteria may also contribute to the immobilization and release of other metals in the environment.
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18
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Mazar Y, Cytryn E, Erel Y, Rudich Y. Effect of Dust Storms on the Atmospheric Microbiome in the Eastern Mediterranean. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:4194-202. [PMID: 27001166 DOI: 10.1021/acs.est.5b06348] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
We evaluated the impact of Saharan dust storms on the local airborne microbiome in a city in the Eastern Mediterranean area. Samples of particles with diameter less than 10 μm were collected during two spring seasons on both dusty and nondusty days. DNA was extracted, and partial 16S rRNA gene amplicons were sequenced using the Illumina platform. Bioinformatic analysis showed the effect of dust events on the diversity of the atmospheric microbiome. The relative abundance of desert soil-associated bacteria increased during dust events, while the relative abundance of anthropogenic-influenced taxa decreased. Quantitative polymerase chain reaction measurements of selected clinically significant antibiotic resistance genes (ARGs) showed that their relative abundance decreased during dust events. The ARG profiles on dust-free days were similar to those in aerosol collected in a poultry house, suggesting a strong agricultural influence on the local ambient profiles. We conclude that dust storms enrich the ambient airborne microbiome with new soil-derived bacteria that disappear as the dust settles, suggesting that the bacteria are transported attached to the dust particles. Dust storms do not seem to be an important vector for transport of probed ARGs.
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Affiliation(s)
- Yinon Mazar
- Department of Earth and Planetary Sciences, Weizmann Institute of Science , Rehovot 76100, Israel
| | - Eddie Cytryn
- Institute of Soil, Water and Environmental Sciences, The Volcani Center, Agriculture Research Organization, Bet Dagan 50250, Israel
| | - Yigal Erel
- The Fredy and Nadine Herrmann Institute of Earth Sciences, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
| | - Yinon Rudich
- Department of Earth and Planetary Sciences, Weizmann Institute of Science , Rehovot 76100, Israel
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19
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Smith MW, Davis RE, Youngblut ND, Kärnä T, Herfort L, Whitaker RJ, Metcalf WW, Tebo BM, Baptista AM, Simon HM. Metagenomic evidence for reciprocal particle exchange between the mainstem estuary and lateral bay sediments of the lower Columbia River. Front Microbiol 2015; 6:1074. [PMID: 26483785 PMCID: PMC4589670 DOI: 10.3389/fmicb.2015.01074] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 09/18/2015] [Indexed: 11/27/2022] Open
Abstract
Lateral bays of the lower Columbia River estuary are areas of enhanced water retention that influence net ecosystem metabolism through activities of their diverse microbial communities. Metagenomic characterization of sediment microbiota from three disparate sites in two brackish lateral bays (Baker and Youngs) produced ∼100 Gbp of DNA sequence data analyzed subsequently for predicted SSU rRNA and peptide-coding genes. The metagenomes were dominated by Bacteria. A large component of Eukaryota was present in Youngs Bay samples, i.e., the inner bay sediment was enriched with the invasive New Zealand mudsnail, Potamopyrgus antipodarum, known for high ammonia production. The metagenome was also highly enriched with an archaeal ammonia oxidizer closely related to Nitrosoarchaeum limnia. Combined analysis of sequences and continuous, high-resolution time series of biogeochemical data from fixed and mobile platforms revealed the importance of large-scale reciprocal particle exchanges between the mainstem estuarine water column and lateral bay sediments. Deposition of marine diatom particles in sediments near Youngs Bay mouth was associated with a dramatic enrichment of Bacteroidetes (58% of total Bacteria) and corresponding genes involved in phytoplankton polysaccharide degradation. The Baker Bay sediment metagenome contained abundant Archaea, including diverse methanogens, as well as functional genes for methylotrophy and taxonomic markers for syntrophic bacteria, suggesting that active methane cycling occurs at this location. Our previous work showed enrichments of similar anaerobic taxa in particulate matter of the mainstem estuarine water column. In total, our results identify the lateral bays as both sources and sinks of biogenic particles significantly impacting microbial community composition and biogeochemical activities in the estuary.
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Affiliation(s)
- Maria W Smith
- Center for Coastal Margin Observation and Prediction and Institute of Environmental Health, Oregon Health & Science University, Portland OR, USA
| | - Richard E Davis
- Center for Coastal Margin Observation and Prediction and Institute of Environmental Health, Oregon Health & Science University, Portland OR, USA
| | | | - Tuomas Kärnä
- Center for Coastal Margin Observation and Prediction and Institute of Environmental Health, Oregon Health & Science University, Portland OR, USA
| | - Lydie Herfort
- Center for Coastal Margin Observation and Prediction and Institute of Environmental Health, Oregon Health & Science University, Portland OR, USA
| | - Rachel J Whitaker
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana IL, USA
| | - William W Metcalf
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana IL, USA
| | - Bradley M Tebo
- Center for Coastal Margin Observation and Prediction and Institute of Environmental Health, Oregon Health & Science University, Portland OR, USA
| | - António M Baptista
- Center for Coastal Margin Observation and Prediction and Institute of Environmental Health, Oregon Health & Science University, Portland OR, USA
| | - Holly M Simon
- Center for Coastal Margin Observation and Prediction and Institute of Environmental Health, Oregon Health & Science University, Portland OR, USA
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20
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Carmichael SK, Zorn BT, Santelli CM, Roble LA, Carmichael MJ, Bräuer SL. Nutrient input influences fungal community composition and size and can stimulate manganese (II) oxidation in caves. ENVIRONMENTAL MICROBIOLOGY REPORTS 2015; 7:592-605. [PMID: 25865809 DOI: 10.1111/1758-2229.12291] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 04/01/2015] [Indexed: 06/04/2023]
Abstract
Little is known about the fungal role in biogeochemical cycling in oligotrophic ecosystems. This study compared fungal communities and assessed the role of exogenous carbon on microbial community structure and function in two southern Appalachian caves: an anthropogenically impacted cave and a near-pristine cave. Due to carbon input from shallow soils, the anthropogenically impacted cave had an order of magnitude greater fungal and bacterial quantitative-polymerase chain reaction (qPCR) gene copy numbers, had significantly greater community diversity, and was dominated by ascomycotal phylotypes common in early phase, labile organic matter decomposition. Fungal assemblages in the near-pristine cave samples were dominated by Basidiomycota typically found in deeper soils (and/or in late phase, recalcitrant organic matter decomposition), suggesting more oligotrophic conditions. In situ carbon and manganese (II) [Mn(II)] addition over 10 weeks resulted in growth of fungal mycelia followed by increased Mn(II) oxidation. A before/after comparison of the fungal communities indicated that this enrichment increased the quantity of fungal and bacterial cells, yet decreased overall fungal diversity. Anthropogenic carbon sources can therefore dramatically influence the diversity and quantity of fungi, impact microbial community function, and stimulate Mn(II) oxidation, resulting in a cascade of changes that can strongly influence nutrient and trace element biogeochemical cycles in karst aquifers.
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Affiliation(s)
- Sarah K Carmichael
- Department of Geology, Appalachian State University, Boone, NC, 28608, USA
| | - Bryan T Zorn
- Department of Biology, Appalachian State University, Boone, NC, 28608, USA
| | - Cara M Santelli
- Smithsonian Institution, National Museum of Natural History, Washington, DC, 20560, USA
| | - Leigh A Roble
- Department of Geology, University of Maryland, College Park, MD, 20742, USA
| | - Mary J Carmichael
- Department of Biology, Wake Forest University, Winston-Salem, NC, 27109, USA
| | - Suzanna L Bräuer
- Department of Biology, Appalachian State University, Boone, NC, 28608, USA
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21
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Blöthe M, Wegorzewski A, Müller C, Simon F, Kuhn T, Schippers A. Manganese-Cycling Microbial Communities Inside Deep-Sea Manganese Nodules. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:7692-7700. [PMID: 26020127 DOI: 10.1021/es504930v] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Polymetallic nodules (manganese nodules) have been formed on deep sea sediments over millions of years and are currently explored for their economic potential, particularly for cobalt, nickel, copper, and manganese. Here we explored microbial communities inside nodules from the northeastern equatorial Pacific. The nodules have a large connected pore space with a huge inner surface of 120 m(2)/g as analyzed by computer tomography and BET measurements. X-ray photoelectron spectroscopy (XPS) and electron microprobe analysis revealed a complex chemical fine structure. This consisted of layers with highly variable Mn/Fe ratios (<1 to >500) and mainly of turbostratic phyllomanganates such as 7 and 10 Å vernadites alternating with layers of Fe-bearing vernadite (δ-MnO2) epitaxially intergrown with amorphous feroxyhyte (δ-FeOOH). Using molecular 16S rRNA gene techniques (clone libraries, pyrosequencing, and real-time PCR), we show that polymetallic nodules provide a suitable habitat for prokaryotes with an abundant and diverse prokaryotic community dominated by nodule-specific Mn(IV)-reducing and Mn(II)-oxidizing bacteria. These bacteria were not detected in the nodule-surrounding sediment. The high abundance and dominance of Mn-cycling bacteria in the manganese nodules argue for a biologically driven closed manganese cycle inside the nodules relevant for their formation and potential degradation.
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Affiliation(s)
- Marco Blöthe
- †Federal Institute for Geosciences and Natural Resources (BGR), Stilleweg 2, 30655 Hannover, Germany
| | - Anna Wegorzewski
- †Federal Institute for Geosciences and Natural Resources (BGR), Stilleweg 2, 30655 Hannover, Germany
| | - Cornelia Müller
- ‡Leibniz Institute for Applied Geophysics, Stilleweg 2, 30655 Hannover, Germany
| | - Frank Simon
- §Leibniz Institute of Polymer Research Dresden, Hohe Str. 6, 01069 Dresden, Germany
| | - Thomas Kuhn
- †Federal Institute for Geosciences and Natural Resources (BGR), Stilleweg 2, 30655 Hannover, Germany
| | - Axel Schippers
- †Federal Institute for Geosciences and Natural Resources (BGR), Stilleweg 2, 30655 Hannover, Germany
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22
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Tien CJ, Lin MC, Chiu WH, Chen CS. Biodegradation of carbamate pesticides by natural river biofilms in different seasons and their effects on biofilm community structure. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2013; 179:95-104. [PMID: 23665845 DOI: 10.1016/j.envpol.2013.04.009] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Revised: 03/31/2013] [Accepted: 04/01/2013] [Indexed: 06/02/2023]
Abstract
This study investigated the ability of natural river biofilms from different seasons to degrade the carbamate pesticides methomyl, carbaryl and carbofuran in single and multiple pesticide systems, and the effects of these pesticides on algal and bacterial communities within biofilms. Spring biofilms had the lowest biomass of algae and bacteria but showed the highest methomyl degradation (>99%) and dissipation rates, suggesting that they might contain microorganisms with high methomyl degradation abilities. Degradation of carbofuran (54.1-59.5%) by biofilms in four seasons was similar, but low degradation of carbaryl (0-27.5%) was observed. The coexistence of other pesticides was found to cause certain effects on pesticide degradation and primarily resulted in lower diversity of diatoms and bacteria than when using a single pesticide. The tolerant diatoms and bacteria potentially having the ability to degrade test pesticides were identified. River biofilms could be suitable biomaterials or used to isolate degraders for bioremediating pesticide-contaminated water.
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Affiliation(s)
- Chien-Jung Tien
- Department of Biotechnology, National Kaohsiung Normal University, 62, Shen-Chung Road, Yanchao, Kaohsiung 824, Taiwan
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23
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Smith MW, Zeigler Allen L, Allen AE, Herfort L, Simon HM. Contrasting genomic properties of free-living and particle-attached microbial assemblages within a coastal ecosystem. Front Microbiol 2013; 4:120. [PMID: 23750156 PMCID: PMC3668451 DOI: 10.3389/fmicb.2013.00120] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Accepted: 04/29/2013] [Indexed: 11/22/2022] Open
Abstract
The Columbia River (CR) is a powerful economic and environmental driver in the US Pacific Northwest. Microbial communities in the water column were analyzed from four diverse habitats: (1) an estuarine turbidity maximum (ETM), (2) a chlorophyll maximum of the river plume, (3) an upwelling-associated hypoxic zone, and (4) the deep ocean bottom. Three size fractions, 0.1-0.8, 0.8-3, and 3-200 μm were collected for each habitat in August 2007, and used for DNA isolation and 454 sequencing, resulting in 12 metagenomes of >5 million reads (>1.6 Gbp). To characterize the dominant microorganisms and metabolisms contributing to coastal biogeochemistry, we used predicted peptide and rRNA data. The 3- and 0.8-μm metagenomes, representing particulate fractions, were taxonomically diverse across habitats. The 3-μm size fractions contained a high abundance of eukaryota with diatoms dominating the hypoxic water and plume, while cryptophytes were more abundant in the ETM. The 0.1-μm metagenomes represented mainly free-living bacteria and archaea. The most abundant archaeal hits were observed in the deep ocean and hypoxic water (19% of prokaryotic peptides in the 0.1-μm metagenomes), and were homologous to Nitrosopumilus maritimus (ammonia-oxidizing Thaumarchaeota). Bacteria dominated metagenomes of all samples. In the euphotic zone (estuary, plume and hypoxic ocean), the most abundant bacterial taxa (≥40% of prokaryotic peptides) represented aerobic photoheterotrophs. In contrast, the low-oxygen, deep water metagenome was enriched with sequences for strict and facultative anaerobes. Interestingly, many of the same anaerobic bacterial families were enriched in the 3-μm size fraction of the ETM (2-10X more abundant relative to the 0.1-μm metagenome), indicating possible formation of anoxic microniches within particles. Results from this study provide a metagenome perspective on ecosystem-scale metabolism in an upwelling-influenced river-dominated coastal margin.
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Affiliation(s)
- Maria W. Smith
- Center for Coastal Margin Observation and Prediction, Oregon Health and Science UniversityBeaverton, OR, USA
| | - Lisa Zeigler Allen
- Microbial and Environmental Genomics, J. Craig Venter InstituteSan Diego, CA, USA
| | - Andrew E. Allen
- Microbial and Environmental Genomics, J. Craig Venter InstituteSan Diego, CA, USA
| | - Lydie Herfort
- Center for Coastal Margin Observation and Prediction, Oregon Health and Science UniversityBeaverton, OR, USA
| | - Holly M. Simon
- Center for Coastal Margin Observation and Prediction, Oregon Health and Science UniversityBeaverton, OR, USA
- Division of Environmental and Biomolecular Systems, Department of Science and Engineering, Oregon Health and Science UniversityBeaverton, OR, USA
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24
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Anderson CR, Davis RE, Bandolin NS, Baptista AM, Tebo BM. Analysis of in situ manganese(II) oxidation in the Columbia River and offshore plume: linking Aurantimonas and the associated microbial community to an active biogeochemical cycle. Environ Microbiol 2011; 13:1561-76. [PMID: 21418498 DOI: 10.1111/j.1462-2920.2011.02462.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Columbia River is a major source of dissolved nutrients and trace metals for the west coast of North America. A large proportion of these nutrients are sourced from the Columbia River Estuary, where coastal and terrestrial waters mix and resuspend particulate matter within the water column. As estuarine water is discharged off the coast, it transports the particulate matter, dissolved nutrients and microorganisms forming nutrient-rich and metabolically dynamic plumes. In this study, bacterial manganese oxidation within the plume and estuary was investigated during spring and neap tides. The microbial community proteome was fractionated and assayed for Mn oxidation activity. Proteins from the outer membrane and the loosely bound outer membrane fractions were separated using size exclusion chromatography and Mn(II)-oxidizing eluates were analysed with tandem mass spectrometry to identify potential Mn oxidase protein targets. Multi-copper oxidase (MCO) and haem-peroxidase enzymes were identified in active fractions. T-RFLP profiles and cluster analysis indicates that organisms and bacterial communities capable of oxidizing Mn(II) can be sourced from the Columbia River estuary and nearshore coastal ocean. These organisms are producing up to 10 fM MnO₂ cell⁻¹ day⁻¹. Evidence for the presence of Mn(II)-oxidizing bacterial isolates from the genera Aurantimonas, Rhodobacter, Bacillus and Shewanella was found in T-RFLP profiles. Specific Q-PCR probes were designed to target potential homologues of the Aurantimonas manganese oxidizing peroxidase (Mop). By comparing total Mop homologues, Aurantimonas SSU rRNA and total bacterial SSU rRNA gene copies, it appears that Aurantimonas can only account for ~1.7% of the peroxidase genes quantified. Under the broad assumption that at least some of the peroxidase homologues quantified are involved in manganese oxidation, it is possible that other organisms oxidize manganese via peroxidases.
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Affiliation(s)
- C R Anderson
- Division of Environmental and Biomolecular Systems, Oregon Health & Science University, Beaverton, OR 97006, USA.
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