1
|
Schwarz IA, Alsaqri B, Lekbach Y, Henry K, Gorman S, Woodard T, Dion L, Real L, Holmes DE, Smith JA, Lovley DR. Lack of physiological evidence for cytochrome filaments functioning as conduits for extracellular electron transfer. mBio 2024; 15:e0069024. [PMID: 38717196 PMCID: PMC11077965 DOI: 10.1128/mbio.00690-24] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 03/08/2024] [Indexed: 05/12/2024] Open
Abstract
Extracellular cytochrome filaments are proposed to serve as conduits for long-range extracellular electron transfer. The primary functional physiological evidence has been the reported inhibition of Geobacter sulfurreducens Fe(III) oxide reduction when the gene for the filament-forming cytochrome OmcS is deleted. Here we report that the OmcS-deficient strain from that original report reduces Fe(III) oxide as well as the wild-type, as does a triple mutant in which the genes for the other known filament-forming cytochromes were also deleted. The triple cytochrome mutant displayed filaments with the same 3 nm diameter morphology and conductance as those produced by Escherichia coli heterologously expressing the G. sulfurreducens PilA pilin gene. Fe(III) oxide reduction was inhibited when the pilin gene in cytochrome-deficient mutants was modified to yield poorly conductive 3 nm diameter filaments. The results are consistent with the concept that 3 nm diameter electrically conductive pili (e-pili) are required for G. sulfurreducens long-range extracellular electron transfer. In contrast, rigorous physiological functional evidence is lacking for cytochrome filaments serving as conduits for long-range electron transport. IMPORTANCE Unraveling microbial extracellular electron transfer mechanisms has profound implications for environmental processes and advancing biological applications. This study on Geobacter sulfurreducens challenges prevailing beliefs on cytochrome filaments as crucial components thought to facilitate long-range electron transport. The discovery of an OmcS-deficient strain's unexpected effectiveness in Fe(III) oxide reduction prompted a reevaluation of the key conduits for extracellular electron transfer. By exploring the impact of genetic modifications on G. sulfurreducens' performance, this research sheds light on the importance of 3-nm diameter electrically conductive pili in Fe(III) oxide reduction. Reassessing these mechanisms is essential for uncovering the true drivers of extracellular electron transfer in microbial systems, offering insights that could revolutionize applications across diverse fields.
Collapse
Affiliation(s)
- Ingrid A. Schwarz
- Department of Biomolecular Sciences, Central Connecticut State University, New Britain, Connecticut, USA
| | - Baha Alsaqri
- Department of Biomolecular Sciences, Central Connecticut State University, New Britain, Connecticut, USA
| | - Yassir Lekbach
- Department of Microbiology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Kathryn Henry
- Department of Physical and Biological Sciences, Western New England University, Springfield, Massachusetts, USA
| | - Sydney Gorman
- Department of Physical and Biological Sciences, Western New England University, Springfield, Massachusetts, USA
| | - Trevor Woodard
- Department of Microbiology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Laura Dion
- Department of Physical and Biological Sciences, Western New England University, Springfield, Massachusetts, USA
| | - Lauren Real
- Department of Biomolecular Sciences, Central Connecticut State University, New Britain, Connecticut, USA
| | - Dawn E. Holmes
- Department of Microbiology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
- Department of Physical and Biological Sciences, Western New England University, Springfield, Massachusetts, USA
| | - Jessica A. Smith
- Department of Biomolecular Sciences, Central Connecticut State University, New Britain, Connecticut, USA
- Department of Microbiology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Derek R. Lovley
- Department of Microbiology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| |
Collapse
|
2
|
Gupta S, Thokchom SD, Kapoor R. Arbuscular mycorrhiza fungus alleviates arsenic mediated disturbances in tricarboxylic acid cycle and nitrogen metabolism in Triticum aestivum L. Plant Physiol Biochem 2023; 197:107631. [PMID: 36965318 DOI: 10.1016/j.plaphy.2023.03.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [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: 01/01/2023] [Revised: 02/18/2023] [Accepted: 03/05/2023] [Indexed: 06/18/2023]
Abstract
Utilization of arbuscular mycorrhizal (AM) fungi (AMF) as a sustainable strategy in redeeming arsenic (As) toxicity in plants is a promising approach. Low As accumulation, restoration of physiological processes, and As tolerance by AMF have been documented in crop plants. However, to comprehend AM-mediated As tolerance in plants, understanding the biochemical responses of host to the symbiont is crucial. The study evaluated the effect of an AM fungus, Rhizophagus intraradices on tricarboxylic acid cycle (TCA) and nitrogen metabolism of Triticum aestivum under three As concentrations (0, 25, and 50 mg As kg-1 soil). Results showed that TCA cycle and nitrogen metabolism were severely impaired by As that resulted into a higher C/N ratio. However, colonization by R. intraradices attenuated As mediated alterations in TCA cycle by augmenting the activity of pyruvate dehydrogenase that provided sufficient substrate for the TCA cycle. Furthermore, mycorrhizal (M) plants reinstated the activities of isocitrate dehydrogenase, succinate dehydrogenase, fumarase, and malate dehydrogenase even under high As level. Although citrate synthase and oxoglutarate dehydrogenase activities declined upon As exposure in M-plants, these were nevertheless higher than their non-mycorrhizal (NM) counterparts, ensuring higher levels of citric acid and succinic acid in M-plants. AM colonization also moderated the As-mediated disturbances in nitrogen assimilation by augmenting the activity of nitrate reductase, nitrite reductase, glutamine synthase, and glutamine-2-oxoglutarate amino transferase. Overall findings of the study point out that colonization by R. intraradices favourably regulated the TCA cycle and nitrogen metabolism and confronted As-mediated alterations in C/N ratio.
Collapse
Affiliation(s)
- Samta Gupta
- Department of Botany, University of Delhi, Delhi, 110007, India
| | | | - Rupam Kapoor
- Department of Botany, University of Delhi, Delhi, 110007, India.
| |
Collapse
|
3
|
Zhuang Z, Yang G, Zhuang L. Exopolysaccharides matrix affects the process of extracellular electron transfer in electroactive biofilm. Sci Total Environ 2022; 806:150713. [PMID: 34606863 DOI: 10.1016/j.scitotenv.2021.150713] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [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: 06/11/2021] [Revised: 08/19/2021] [Accepted: 09/27/2021] [Indexed: 05/20/2023]
Abstract
The applications of bioelectrochemical systems (BESs) in the field of environment and energy are achieved through the bioelectrocatalytic process of electroactive biofilms. As a primary component of biofilm, the role of exopolysaccharides in electroactive biofilm in BESs is poorly understood. This study constructed an exopolysaccharides-deficient Geobacter sulfurreducens-based BES to explore the role of exopolysaccharides in electroactive biofilm. Compared with the wild type, the mutant biofilm expressing less exopolysaccharides decreased the capacity of current generation. In the mutant biofilm, the content of exopolysaccharides decreased significantly, resulting in a thinner biofilm and lower cell viability compared with the wild-type biofilm. However, the mutant with overexpressed pili developed a mature biofilm with extended time, which indicating the importance of exopolysaccharides for early biofilm formation and the compensatory role of pili in biofilm formation. The mutant biofilm had less content of c-type cytochromes (c-Cyts) and lower electrochemical activity of extracellular polymeric substances than the wild-type biofilm, suggesting a function of exopolysaccharides anchoring extracellular c-Cyts that essential to extracellular electron transfer (EET) in electroactive biofilms. Our findings demonstrated the essential role of exopolysaccharides in the process of EET in electroactive biofilm, which contributed to a better understanding and optimization of the performance of BESs.
Collapse
Affiliation(s)
- Zheng Zhuang
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, China
| | - Guiqin Yang
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, China
| | - Li Zhuang
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, China.
| |
Collapse
|
4
|
Liu X, Holmes DE, Walker DJF, Li Y, Meier D, Pinches S, Woodard TL, Smith JA. Cytochrome OmcS is not essential for extracellular electron transport via conductive pili in Geobacter sulfurreducens strain KN400. Appl Environ Microbiol 2021;:AEM0162221. [PMID: 34669448 DOI: 10.1128/AEM.01622-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The multi-heme c-type cytochrome OmcS is one of the central components for extracellular electron transport in Geobacter sulfurreducens strain DL-1, but its role in other microbes, including other strains of G. sulfurreducens is currently a matter of debate. Therefore, we investigated the function of OmcS in G. sulfurreducens strain KN400, which is even more effective in extracellular electron transfer than strain DL-1. We found that deleting omcS from strain KN400 did not negatively impact the rate of Fe(III) oxide reduction and that the cells expressed conductive filaments. Replacing the wild-type pilin gene with the aro-5 pilin gene eliminated the OmcS-deficient strain's ability for electron transport to insoluble electron acceptors and diminished filament conductivity. These results are consistent with the concept that electrically conductive pili are the primary conduit for long-range electron transfer in G. sulfurreducens and closely related species. These findings, coupled with the lack of OmcS homologs in most other microbes capable of extracellular electron transfer, suggest that OmcS is not a common critical component for extracellular electron transfer. Importance OmcS has been widely studied and noted to be one of the key components for extracellular electron exchange by Geobacter sulfurreducens strain DL-1. However, the true importance of OmcS warrants further investigation as it is well-known that very few bacteria, even within the Geobacteraceae family, contain OmcS homologs, and many bacteria capable of extracellular electron transfer lack an abundance of any type of outer-surface c-type cytochrome. In addition, there is much debate regarding the importance of OmcS filaments in the mechanism of extracellular electron transport to insoluble electron acceptors by G. sulfurreducens. It has been suggested that filaments comprised of OmcS, rather than e-pili, are the predominant conductive filaments expressed by G. sulfurreducens. However, the results presented in this manuscript, along with multiple other lines of evidence, indicate that OmcS filaments cannot be the primary conductive protein nanowires expressed by G. sulfurreducens.
Collapse
|
5
|
Andrade A, Hernández-Eligio A, Tirado AL, Vega-Alvarado L, Olvera M, Morett E, Juárez K. Specialization of the Reiterated Copies of the Heterodimeric Integration Host Factor Genes in Geobacter sulfurreducens. Front Microbiol 2021; 12:626443. [PMID: 33737919 PMCID: PMC7962754 DOI: 10.3389/fmicb.2021.626443] [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: 11/05/2020] [Accepted: 01/14/2021] [Indexed: 12/13/2022] Open
Abstract
Integration host factor (IHF) is a widely distributed small heterodimeric protein member of the bacterial Nucleoid-Associated Proteins (NAPs), implicated in multiple DNA regulatory processes. IHF recognizes a specific DNA sequence and induces a large bend of the nucleic acid. IHF function has been mainly linked with the regulation of RpoN-dependent promoters, where IHF commonly recognizes a DNA sequence between the enhancer-binding region and the promoter, facilitating a close contact between the upstream bound activator and the promoter bound, RNA polymerase. In most proteobacteria, the genes encoding IHF subunits (ihfA and ihfB) are found in a single copy. However, in some Deltaproteobacteria, like Geobacter sulfurreducens, those genes are duplicated. To date, the functionality of IHF reiterated encoding genes is unknown. In this work, we achieved the functional characterization of the ihfA-1, ihfA-2, ihfB-1, and ihfB-2 from G. sulfurreducens. Unlike the ΔihfA-2 or ΔihfB-1 strains, single gene deletion in ihfA-1 or ihfB-2, provokes an impairment in fumarate and Fe(III) citrate reduction. Accordingly, sqRT-PCR experiments showed that ihfA-1 and ihfB-2 were expressed at higher levels than ihfA-2 and ihfB-1. In addition, RNA-Seq analysis of the ΔihfA-1 and ΔihfB-2 strains revealed a total of 89 and 122 differentially expressed genes, respectively. Furthermore, transcriptional changes in 25 genes were shared in both mutant strains. Among these genes, we confirmed the upregulation of the pilA-repressor, GSU1771, and downregulation of the triheme-cytochrome (pgcA) and the aconitate hydratase (acnA) genes by RT-qPCR. EMSA experiments also demonstrated the direct binding of IHF to the upstream promoter regions of GSU1771, pgcA and acnA. PilA changes in ΔihfA-1 and ΔihfB-2 strains were also verified by immunoblotting. Additionally, heme-staining of subcellular fractions in ΔihfA-1 and ΔihfB-2 strains revealed a remarkable deficit of c-type cytochromes. Overall, our data indicate that at least during fumarate and Fe(III) citrate reduction, the functional IHF regulator is likely assembled by the products of ihfA-1 and ihfB-2. Also, a role of IHF controlling expression of multiple genes (other than RpoN-dependent) affects G. sulfurreducens physiology and extracellular electron transfer.
Collapse
Affiliation(s)
- Angel Andrade
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico.,Departamento de Microbiología, Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey, Mexico
| | - Alberto Hernández-Eligio
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico.,CONACYT, Ciudad de México, Mexico
| | - Ana Lilia Tirado
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Leticia Vega-Alvarado
- Instituto de Ciencias Aplicadas y Tecnología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México, Mexico
| | - Maricela Olvera
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Enrique Morett
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Katy Juárez
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| |
Collapse
|
6
|
Huang C, Liu Q, Li ZL, Ma XD, Hou YN, Ren NQ, Wang AJ. Relationship between functional bacteria in a denitrification desulfurization system under autotrophic, heterotrophic, and mixotrophic conditions. Water Res 2021; 188:116526. [PMID: 33125994 DOI: 10.1016/j.watres.2020.116526] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [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: 08/05/2020] [Revised: 10/08/2020] [Accepted: 10/14/2020] [Indexed: 06/11/2023]
Abstract
The denitrification desulfurization system can be used to remediate wastewater containing carbon, nitrogen, and sulfur. However, the relationship between autotrophic and heterotrophic bacteria remains poorly understood. To better understand the roles and relations of core bacteria, an expanded granular sludge bed (EGSB) reactor was continuously operated under autotrophic (stage I), heterotrophic (stage II) and mixotrophic (stages III-VII) conditions with a 490-day period. Stage IV represented the excellent S0 recovery rate (69.5%). The different trophic conditions caused the obvious succession of dominant bacterial genera. Autotrophic environment (stage I) enriched mostly Thiobacillus, and heterotrophic environment (stage II) was dominated with Azoarcus and Pseudomonas. Thauera, Arcobacter and Azoarcus became the predominant genera under mixotrophic conditions (stage III-VII). Strains belonged to these core genera were further isolated, and all seven isolates were confirmed with denitrifying sulfur oxidation capacity. Heterotrophic strain HDD1 (genus of Thauera) possessed both the highest sulfide degradation and S0 recovery rates. Expression levels of cbbM and gltA genes were positively related with the autotrophic and heterotrophic conditions, respectively. NirK gene was highly expressed between log 3.7-log 4.3 during the entire run. Expression of both sqr and soxB genes were closely related with sulfur conversion. More than 57.5% of S0 recovery rate could be obtained as sqr gene expression was greater than log 3.2, and while, sulfate was the primary form as soxB gene expression higher than log 3.9. The correlation between core microbial genera was very low from network, indicating a complex and non-specific mutualistic network between bacterial functional groups under each nutrient condition, and a stable coexistence state was possibly formed through utilizing each the secondary or waste metabolites in the mixotrophic conditions. This relationship was beneficial to the stability of the microbial community structure in the denitrification desulfurization system.
Collapse
Affiliation(s)
- Cong Huang
- Tianjin Insitute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Qian Liu
- Research Center for Eco-environmental Engineering, Dongguan University of Technology, Dongguan, 523808, China
| | - Zhi-Ling Li
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China.
| | - Xiao-Dan Ma
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Ya-Nan Hou
- Tianjin Insitute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Nan-Qi Ren
- Tianjin Insitute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Ai-Jie Wang
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China; Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
| |
Collapse
|
7
|
Mollaei M, Timmers PHA, Suarez-Diez M, Boeren S, van Gelder AH, Stams AJM, Plugge CM. Comparative proteomics of Geobacter sulfurreducens PCA T in response to acetate, formate and/or hydrogen as electron donor. Environ Microbiol 2020; 23:299-315. [PMID: 33185968 PMCID: PMC7894505 DOI: 10.1111/1462-2920.15311] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 10/19/2020] [Accepted: 11/06/2020] [Indexed: 12/11/2022]
Abstract
Geobacter sulfurreducens is a model bacterium to study the degradation of organic compounds coupled to the reduction of Fe(III). The response of G. sulfurreducens to the electron donors acetate, formate, hydrogen and a mixture of all three with Fe(III) citrate as electron acceptor was studied using comparative physiological and proteomic approaches. Variations in the supplied electron donors resulted in differential abundance of proteins involved in the citric acid cycle (CAC), gluconeogenesis, electron transport, and hydrogenases and formate dehydrogenase. Our results provided new insights into the electron donor metabolism of G. sulfurreducens. Remarkably, formate was the preferred electron donor compared to acetate, hydrogen, or acetate plus hydrogen. When hydrogen was the electron donor, formate was formed, which was associated with a high abundance of formate dehydrogenase. Notably, abundant proteins of two CO2 fixation pathways (acetyl-CoA pathway and the reversed oxidative CAC) corroborated chemolithoautotrophic growth of G. sulfurreducens with formate or hydrogen and CO2 , and provided novel insight into chemolithoautotrophic growth of G. sulfurreducens.
Collapse
Affiliation(s)
- Monir Mollaei
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Leeuwarden, The Netherlands.,Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Peer H A Timmers
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Leeuwarden, The Netherlands.,Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, The Netherlands
| | - Sjef Boeren
- Laboratory of Biochemistry, Wageningen University & Research, Wageningen, The Netherlands
| | - Antonie H van Gelder
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Alfons J M Stams
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands.,Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Caroline M Plugge
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Leeuwarden, The Netherlands.,Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| |
Collapse
|
8
|
Tentori EF, Richardson RE. Methane Monooxygenase Gene Transcripts as Quantitative Biomarkers of Methanotrophic Activity in Methylosinus trichosporium OB3b. Appl Environ Microbiol 2020; 86:e01048-20. [PMID: 32948519 DOI: 10.1128/AEM.01048-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 09/10/2020] [Indexed: 01/20/2023] Open
Abstract
Methanotrophic microorganisms are characterized by their ability to oxidize methane. Globally they have a significant impact on methane emissions by attenuating net methane fluxes to the atmosphere in natural and engineered systems, though the populations are dynamic in their activity level in soils and waters. Methanotrophs oxidize methane using methane monooxygenase (MMO) enzymes, and selected subunit genes of the most common MMOs, specifically pmoA and mmoX, are used as biomarkers for the presence and abundance of populations of bacterial methanotrophs. The relative expression of these biomarker genes is dependent on copper-to-biomass ratios. Empirically derived quantitative relationships between methane oxidation biomarker transcript amounts and methanotrophic activity could facilitate determination of methane oxidation rates. In this study, pure cultures of a model type II methanotroph, Methylosinus trichosporium OB3b, were grown in hollow-fiber membrane bioreactors (HFMBR) under different steady-state methane oxidation conditions. Methanotroph biomass (DNA based) and methane oxidation biomarker mRNA transcript amounts were determined using quantitative PCR (qPCR) and reverse transcription-PCR (RT-qPCR), respectively. Under both copper-present and copper-limited conditions, per-cell pmoA mRNA transcript levels positively correlated with measured per-cell methane oxidation rates across 3 orders of magnitude. These correlations, if maintained across different methanotrophs, could prove valuable for inferring in situ oxidation rates of methanotrophs and understanding the dynamics of their impact on net methane emissions.IMPORTANCE Methanotrophs are naturally occurring microorganisms capable of oxidizing methane and have an impact on global net methane emissions. The genes pmoA and mmoX are used as biomarkers for bacterial methanotrophs. Quantitative relationships between transcript amounts of these genes and methane oxidation rates could facilitate estimation of methanotrophic activity. In this study, a strong correlation was observed between per-cell pmoA transcript levels and per-cell methane oxidation rates for pure cultures of the aerobic methanotroph M. trichosporium OB3b grown in bioreactors. If similar relationships exist across different methanotrophs, they could prove valuable for inferring in situ oxidation rates of methanotrophs and better understanding their impact on net methane emissions.
Collapse
|
9
|
Zhuang Z, Yang G, Mai Q, Guo J, Liu X, Zhuang L. Physiological potential of extracellular polysaccharide in promoting Geobacter biofilm formation and extracellular electron transfer. Sci Total Environ 2020; 741:140365. [PMID: 32610234 DOI: 10.1016/j.scitotenv.2020.140365] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [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: 05/13/2020] [Revised: 06/17/2020] [Accepted: 06/17/2020] [Indexed: 06/11/2023]
Abstract
Geobacter sulfurreducens biofilms have promising applications in renewable energy, pollutant bioremediation, and bioelectronic applications. Genetically manipulating G. sulfurreducens biofilms is an effective strategy to improve the capacity of extracellular electron transfer (EET). Extracellular polysaccharide, a sticky component surrounding microbes, plays an important role in EET. Herein, we constructed a mutant of G. sulfurreducens strain PCA overexpressing the gene GSU1501 (part of the ATP-dependent exporter of the polysaccharide biosynthesis gene operon), designated strain PCA-1501, to increase EET capacity. Experimental results showed that the overexpression of GSU1501 increased extracellular polysaccharide secretion by 25.5%, which promoted the formation of biofilm with higher thickness and viability, as well as the content of extracellular c-type cytochromes. Compared with the control strain, the mutant showed a higher capacity of Fe(III) oxide reduction and current generation (increased by 20.4% and 22.2%, respectively). Interestingly, the overexpression of GSU1501 hindered the pili formation by reducing the transcription level of pilA; a compensatory relationship between extracellular polysaccharide and pili in promoting biofilm formation deserves further investigation. This study provides a feasible method to promote the EET capacity of G. sulfurreducens biofilms, which benefit their bioelectrochemical applications.
Collapse
Affiliation(s)
- Zheng Zhuang
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 511443, China
| | - Guiqin Yang
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 511443, China
| | - Qijun Mai
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 511443, China
| | - Junhui Guo
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 511443, China
| | - Xing Liu
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Li Zhuang
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 511443, China.
| |
Collapse
|
10
|
Zhang T, Shi XC, Ding R, Xu K, Tremblay PL. The hidden chemolithoautotrophic metabolism of Geobacter sulfurreducens uncovered by adaptation to formate. ISME J 2020; 14:2078-2089. [PMID: 32398660 DOI: 10.1038/s41396-020-0673-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 04/24/2020] [Accepted: 04/29/2020] [Indexed: 02/01/2023]
Abstract
Multiple Fe(III)-reducing Geobacter species including the model Geobacter sulfurreducens are thought to be incapable of carbon dioxide fixation. The discovery of the reversed oxidative tricarboxylic acid cycle (roTCA) for CO2 reduction with citrate synthase as key enzyme raises the possibility that G. sulfurreducens harbors the metabolic potential for chemolithoautotrophic growth. We investigate this hypothesis by transferring G. sulfurreducens PCA serially with Fe(III) as electron acceptor and formate as electron donor and carbon source. The evolved strain T17-3 grew chemolithoautotrophically with a 2.7-fold population increase over 48 h and a Fe(III) reduction rate of 417.5 μM h-1. T17-3 also grew with CO2 as carbon source. Mutations in T17-3 and enzymatic assays point to an adaptation process where the succinyl-CoA synthetase, which is inactive in the wild-type, became active to complete the roTCA cycle. Deletion of the genes coding for the succinyl-CoA synthetase in T17-3 prevented growth with formate as substrate. Enzymatic assays also showed that the citrate synthase can perform the necessary cleavage of citrate for the functional roTCA cycle. These results demonstrate that G. sulfurreducens after adaptation reduced CO2 via the roTCA cycle. This previously hidden metabolism can be harnessed for biotechnological applications and suggests hidden ecological functions for Geobacter.
Collapse
Affiliation(s)
- Tian Zhang
- State Key Laboratory of Silicate Materials for Architectures, Wuhan University of Technology, Wuhan, 430070, PR China. .,School of Materials Science and Engineering, Wuhan University of Technology, Wuhan, 430070, PR China. .,School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, Wuhan, 430070, PR China.
| | - Xiao-Chen Shi
- State Key Laboratory of Silicate Materials for Architectures, Wuhan University of Technology, Wuhan, 430070, PR China.,School of Materials Science and Engineering, Wuhan University of Technology, Wuhan, 430070, PR China.,School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, Wuhan, 430070, PR China
| | - Ran Ding
- State Key Laboratory of Silicate Materials for Architectures, Wuhan University of Technology, Wuhan, 430070, PR China.,School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, Wuhan, 430070, PR China
| | - Kai Xu
- Center for Material Research and Analysis, Wuhan University of Technology, Wuhan, 430070, PR China
| | - Pier-Luc Tremblay
- State Key Laboratory of Silicate Materials for Architectures, Wuhan University of Technology, Wuhan, 430070, PR China. .,School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, Wuhan, 430070, PR China.
| |
Collapse
|
11
|
Yang G, Huang L, Yu Z, Liu X, Chen S, Zeng J, Zhou S, Zhuang L. Anode potentials regulate Geobacter biofilms: New insights from the composition and spatial structure of extracellular polymeric substances. Water Res 2019; 159:294-301. [PMID: 31102858 DOI: 10.1016/j.watres.2019.05.027] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [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: 09/10/2018] [Revised: 04/20/2019] [Accepted: 05/08/2019] [Indexed: 06/09/2023]
Abstract
The extracellular electron transfer (EET) efficiency in bioelectrochemical systems has been proven to be dependent on anode potentials. To explore the underlying mechanism, previous studies have mainly focused on EET conduit and bacterial biomass but rarely concerned with the role of extracellular polymeric substances (EPS) surrounding electroactive cells. In this study, the response of Geobacter biofilms to anode potentials was investigated with a special emphasis on the mechanistic role of EPS. The electrochemical activities and cell viabilities of Geobacter soli biofilms were simultaneously attenuated at 0.4 and 0.6 V compared to -0.2 and 0 V. It was found that the biofilms (especially the biofilm region closer to electrode surface) grown at -0.2 and 0 V produced relatively more extracellular redox-active proteins and less extracellular polysaccharides, which conferred higher electron accepting/donating capacities to EPS and consequently facilitated EET. Meanwhile, electrically nonconductive extracellular polysaccharide-dominated interior layers were formed in the biofilms grown at 0.4 and 0.6 V, which limited direct EET but might serve as physical barriers for protecting cells in these biofilms from the increasing stress by poised electrodes. These results demonstrated that the production of EPS under different anode potentials might be finely regulated by cells to keep balance between EET efficiency and cell-protection. This study provides a new insight to investigate the Geobacter biofilms coping with various environments, and is useful for optimizing electrochemical activity of anode biofilms.
Collapse
Affiliation(s)
- Guiqin Yang
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou, 510632, China
| | - Lingyan Huang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhen Yu
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangzhou, 510650, China
| | - Xiaoming Liu
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangzhou, 510650, China
| | - Shanshan Chen
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jianxiong Zeng
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Shungui Zhou
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Li Zhuang
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou, 510632, China.
| |
Collapse
|
12
|
Tsuchiya T, Ehara A, Kasahara Y, Hamamura N, Amachi S. Expression of Genes and Proteins Involved in Arsenic Respiration and Resistance in Dissimilatory Arsenate-Reducing Geobacter sp. Strain OR-1. Appl Environ Microbiol 2019; 85:e00763-19. [PMID: 31101608 DOI: 10.1128/AEM.00763-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 05/08/2019] [Indexed: 12/13/2022] Open
Abstract
The reduction of arsenate [As(V)] to arsenite [As(III)] by dissimilatory As(V)-reducing bacteria, such as Geobacter spp., may play a significant role in arsenic release from anaerobic sediments into groundwater. The biochemical and molecular mechanisms by which these bacteria cope with this toxic element remain unclear. In this study, the expression of several genes involved in arsenic respiration (arr) and resistance (ars) was determined using Geobacter sp. strain OR-1, the only cultured Geobacter strain capable of As(V) respiration. In addition, proteins expressed differentially under As(V)-respiring conditions were identified by semiquantitative proteomic analysis. Dissimilatory As(V) reductase (Arr) of strain OR-1 was localized predominantly in the periplasmic space, and the transcription of its gene (arrA) was upregulated under As(V)-respiring conditions. The transcription of the detoxifying As(V) reductase gene (arsC) was also upregulated, but its induction required 500 times higher concentration of As(III) (500 μM) than did the arrA gene. Comparative proteomic analysis revealed that in addition to the Arr and Ars proteins, proteins involved in the following processes were upregulated under As(V)-respiring conditions: (i) protein folding and assembly for rescue of proteins with oxidative damage, (ii) DNA replication and repair for restoration of DNA breaks, (iii) anaplerosis and gluconeogenesis for sustainable energy production and biomass formation, and (iv) protein and nucleotide synthesis for the replacement of damaged proteins and nucleotides. These results suggest that strain OR-1 copes with arsenic stress by orchestrating pleiotropic processes that enable this bacterium to resist and actively metabolize arsenic.IMPORTANCE Dissimilatory As(V)-reducing bacteria, such as Geobacter spp., play significant roles in arsenic release and contamination in groundwater and threaten the health of people worldwide. However, the biochemical and molecular mechanisms by which these bacteria cope with arsenic toxicity remain unclear. In this study, it was found that both respiratory and detoxifying As(V) reductases of a dissimilatory As(V)-reducing bacterium, Geobacter sp. strain OR-1, were upregulated under As(V)-respiring conditions. In addition, various proteins expressed specifically or more abundantly in strain OR-1 under arsenic stress were identified. Strain OR-1 actively metabolizes arsenic while orchestrating various metabolic processes that repair oxidative damage caused by arsenic. Such information is useful in assessing and identifying possible countermeasures for the prevention of microbial arsenic release in nature.
Collapse
|
13
|
Abstract
The family Geobacteraceae, with its only valid genus Geobacter, comprises deltaproteobacteria ubiquitous in soil, sediments, and subsurface environments where metal reduction is an active process. Research for almost three decades has provided novel insights into environmental processes and biogeochemical reactions not previously known to be carried out by microorganisms. At the heart of the environmental roles played by Geobacter bacteria is their ability to integrate redox pathways and regulatory checkpoints that maximize growth efficiency with electron donors derived from the decomposition of organic matter while respiring metal oxides, particularly the often abundant oxides of ferric iron. This metabolic specialization is complemented by versatile metabolic reactions, respiratory chains, and sensory networks that allow specific members to adaptively respond to environmental cues to integrate organic and inorganic contaminants in their oxidative and reductive metabolism, respectively. Thus, Geobacteraceae are important members of the microbial communities that degrade hydrocarbon contaminants under iron-reducing conditions and that contribute, directly or indirectly, to the reduction of radionuclides, toxic metals, and oxidized species of nitrogen. Their ability to produce conductive pili as nanowires for discharging respiratory electrons to solid-phase electron acceptors and radionuclides, or for wiring cells in current-harvesting biofilms highlights the unique physiological traits that make these organisms attractive biological platforms for bioremediation, bioenergy, and bioelectronics application. Here we review some of the most notable physiological features described in Geobacter species since the first model representatives were recovered in pure culture. We provide a historical account of the environmental research that has set the foundation for numerous physiological studies and the laboratory tools that had provided novel insights into the role of Geobacter in the functioning of microbial communities from pristine and contaminated environments. We pay particular attention to latest research, both basic and applied, that has served to expand the field into new directions and to advance interdisciplinary knowledge. The electrifying physiology of Geobacter, it seems, is alive and well 30 years on.
Collapse
|
14
|
Li D, Li J, Liu D, Ma X, Cheng L, Li W, Qian C, Mu Y, Yu H. Potential regulates metabolism and extracellular respiration of electroactiveGeobacterbiofilm. Biotechnol Bioeng 2019; 116:961-971. [DOI: 10.1002/bit.26928] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Revised: 11/26/2018] [Accepted: 01/17/2019] [Indexed: 01/02/2023]
Affiliation(s)
- Dao‐Bo Li
- Department of Applied ChemistryUniversity of Science and Technology of ChinaHefei China
| | - Jie Li
- Department of Applied ChemistryUniversity of Science and Technology of ChinaHefei China
| | - Dong‐Feng Liu
- Department of Applied ChemistryUniversity of Science and Technology of ChinaHefei China
| | - Xin Ma
- School of Life Sciences, University of Science and Technology of ChinaHefei China
| | - Lei Cheng
- School of Life Sciences, University of Science and Technology of ChinaHefei China
| | - Wen‐Wei Li
- Department of Applied ChemistryUniversity of Science and Technology of ChinaHefei China
| | - Chen Qian
- Department of Applied ChemistryUniversity of Science and Technology of ChinaHefei China
| | - Yang Mu
- Department of Applied ChemistryUniversity of Science and Technology of ChinaHefei China
| | - Han‐Qing Yu
- Department of Applied ChemistryUniversity of Science and Technology of ChinaHefei China
| |
Collapse
|
15
|
Zhang L, Fan J, Feng G, Declerck S. The arbuscular mycorrhizal fungus Rhizophagus irregularis MUCL 43194 induces the gene expression of citrate synthase in the tricarboxylic acid cycle of the phosphate-solubilizing bacterium Rahnella aquatilis HX2. Mycorrhiza 2019; 29:69-75. [PMID: 30368606 DOI: 10.1007/s00572-018-0871-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [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: 07/30/2018] [Accepted: 10/19/2018] [Indexed: 06/08/2023]
Abstract
An increasing number of studies have demonstrated that arbuscular mycorrhizal fungi can cooperate with other soil microorganisms, e.g., bacteria, which develop near or on the surface of the extraradical hyphae where they perform multiple functions. However, the mechanisms involved in this privileged relationship are still poorly known. In the present study, we investigated how the arbuscular mycorrhizal fungus Rhizophagus irregularis MUCL 43194 influences the three pace-making enzymes (i.e., citrate synthase, isocitrate dehydrogenase, and α-oxoglutarate dehydrogenase) of the tricarboxylic acid (TCA) cycle in the phosphate-solubilizing bacterium Rahnella aquatilis HX2. The study was conducted under strict in vitro culture conditions and analysis made at the transcriptional level. Results showed that R. irregularis induced the expression of the gene-encoding citrate synthase (gltA), the pace-making enzyme involved in the first step of the TCA cycle, in R. aquatilis at all time points of observation (i.e., 1, 6, 12, 24, 48, and 72 h). The expression of the gene-encoding isocitrate dehydrogenase (icd) significantly decreased at 6, 12, 24, 48, and 72 h and the expression of the gene-encoding α-oxoglutarate dehydrogenase E1 component (kgdhc) significantly increased at 1, 6, and 48 h. The above results suggested that R. irregularis may influence the level of adenosine triphosphate production in R. aquatilis and thus the metabolism of the bacterium by stimulating the expression of gltA involved in the TCA cycle. Our results suggest a fine-tuned dialog between R. irregularis MUCL 43194 and R. aquatilis HX2 and emphasize the complexity of the interactions that might take place at the hyphal surface of arbuscular mycorrhizal fungi hosting communities of microbes.
Collapse
Affiliation(s)
- Lin Zhang
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
- Earth and Life Institute, Applied microbiology, Mycology, Université catholique de Louvain, Croix du sud 2, bte L7.05.06, 1348, Louvain-la-Neuve, Belgium
| | - Jiequn Fan
- Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China
| | - Gu Feng
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China.
| | - Stéphane Declerck
- Earth and Life Institute, Applied microbiology, Mycology, Université catholique de Louvain, Croix du sud 2, bte L7.05.06, 1348, Louvain-la-Neuve, Belgium
| |
Collapse
|
16
|
Holmes DE, Orelana R, Giloteaux L, Wang LY, Shrestha P, Williams K, Lovley DR, Rotaru AE. Potential for Methanosarcina to Contribute to Uranium Reduction during Acetate-Promoted Groundwater Bioremediation. Microb Ecol 2018; 76:660-667. [PMID: 29500492 PMCID: PMC6132540 DOI: 10.1007/s00248-018-1165-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [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: 12/14/2017] [Accepted: 02/16/2018] [Indexed: 05/06/2023]
Abstract
Previous studies of acetate-promoted bioremediation of uranium-contaminated aquifers focused on Geobacter because no other microorganisms that can couple the oxidation of acetate with U(VI) reduction had been detected in situ. Monitoring the levels of methyl CoM reductase subunit A (mcrA) transcripts during an acetate-injection field experiment demonstrated that acetoclastic methanogens from the genus Methanosarcina were enriched after 40 days of acetate amendment. The increased abundance of Methanosarcina corresponded with an accumulation of methane in the groundwater. In order to determine whether Methanosarcina species could be participating in U(VI) reduction in the subsurface, cell suspensions of Methanosarcina barkeri were incubated in the presence of U(VI) with acetate provided as the electron donor. U(VI) was reduced by metabolically active M. barkeri cells; however, no U(VI) reduction was observed in inactive controls. These results demonstrate that Methanosarcina species could play an important role in the long-term bioremediation of uranium-contaminated aquifers after depletion of Fe(III) oxides limits the growth of Geobacter species. The results also suggest that Methanosarcina have the potential to influence uranium geochemistry in a diversity of anaerobic sedimentary environments.
Collapse
Affiliation(s)
- Dawn E Holmes
- Department of Physical and Biological Science, Western New England University, Springfield, MA, USA.
- Department of Microbiology, University of Massachusetts Amherst, Amherst, MA, USA.
| | - Roberto Orelana
- Department of Microbiology, University of Massachusetts Amherst, Amherst, MA, USA
| | - Ludovic Giloteaux
- Department of Molecular Biology and Genetics, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, USA
| | - Li-Ying Wang
- Department of Microbiology, University of Massachusetts Amherst, Amherst, MA, USA
| | - Pravin Shrestha
- Energy Biosciences Institute, University of California Berkeley, Berkeley, CA, USA
| | | | - Derek R Lovley
- Department of Microbiology, University of Massachusetts Amherst, Amherst, MA, USA
| | | |
Collapse
|
17
|
Ishii S, Suzuki S, Tenney A, Nealson KH, Bretschger O. Comparative metatranscriptomics reveals extracellular electron transfer pathways conferring microbial adaptivity to surface redox potential changes. ISME J 2018; 12:2844-63. [PMID: 30050163 DOI: 10.1038/s41396-018-0238-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 04/12/2018] [Accepted: 06/30/2018] [Indexed: 01/15/2023]
Abstract
Some microbes can capture energy through redox reactions with electron flow to solid-phase electron acceptors, such as metal-oxides or poised electrodes, via extracellular electron transfer (EET). While diverse oxide minerals, exhibiting different surface redox potentials, are widely distributed on Earth, little is known about how microbes sense and use the minerals. Here we show electrochemical, metabolic, and transcriptional responses of EET-active microbial communities established on poised electrodes to changes in the surface redox potentials (as electron acceptors) and surrounding substrates (as electron donors). Combination of genome-centric stimulus-induced metatranscriptomics and metabolic pathway investigation revealed that nine Geobacter/Pelobacter microbes performed EET activity differently according to their preferable surface potentials and substrates. While the Geobacter/Pelobacter microbes coded numerous numbers of multi-heme c-type cytochromes and conductive e-pili, wide variations in gene expression were seen in response to altering surrounding substrates and surface potentials, accelerating EET via poised electrode or limiting EET via an open circuit system. These flexible responses suggest that a wide variety of EET-active microbes utilizing diverse EET mechanisms may work together to provide such EET-active communities with an impressive ability to handle major changes in surface potential and carbon source availability.
Collapse
|
18
|
Holmes DE, Shrestha PM, Walker DJF, Dang Y, Nevin KP, Woodard TL, Lovley DR. Metatranscriptomic Evidence for Direct Interspecies Electron Transfer between Geobacter and Methanothrix Species in Methanogenic Rice Paddy Soils. Appl Environ Microbiol 2017; 83:e00223-17. [PMID: 28258137 DOI: 10.1128/AEM.00223-17] [Citation(s) in RCA: 154] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 02/24/2017] [Indexed: 01/04/2023] Open
Abstract
The possibility that Methanothrix (formerly Methanosaeta) and Geobacter species cooperate via direct interspecies electron transfer (DIET) in terrestrial methanogenic environments was investigated in rice paddy soils. Genes with high sequence similarity to the gene for the PilA pilin monomer of the electrically conductive pili (e-pili) of Geobacter sulfurreducens accounted for over half of the PilA gene sequences in metagenomic libraries and 42% of the mRNA transcripts in RNA sequencing (RNA-seq) libraries. This abundance of e-pilin genes and transcripts is significant because e-pili can serve as conduits for DIET. Most of the e-pilin genes and transcripts were affiliated with Geobacter species, but sequences most closely related to putative e-pilin genes from genera such as Desulfobacterium, Deferribacter, Geoalkalibacter, and Desulfobacula, were also detected. Approximately 17% of all metagenomic and metatranscriptomic bacterial sequences clustered with Geobacter species, and the finding that Geobacter spp. were actively transcribing growth-related genes indicated that they were metabolically active in the soils. Genes coding for e-pilin were among the most highly transcribed Geobacter genes. In addition, homologs of genes encoding OmcS, a c-type cytochrome associated with the e-pili of G. sulfurreducens and required for DIET, were also highly expressed in the soils. Methanothrix species in the soils highly expressed genes for enzymes involved in the reduction of carbon dioxide to methane. DIET is the only electron donor known to support CO2 reduction in Methanothrix Thus, these results are consistent with a model in which Geobacter species were providing electrons to Methanothrix species for methane production through electrical connections of e-pili.IMPORTANCEMethanothrix species are some of the most important microbial contributors to global methane production, but surprisingly little is known about their physiology and ecology. The possibility that DIET is a source of electrons for Methanothrix in methanogenic rice paddy soils is important because it demonstrates that the contribution that Methanothrix makes to methane production in terrestrial environments may extend beyond the conversion of acetate to methane. Furthermore, defined coculture studies have suggested that when Methanothrix species receive some of their energy from DIET, they grow faster than when acetate is their sole energy source. Thus, Methanothrix growth and metabolism in methanogenic soils may be faster and more robust than generally considered. The results also suggest that the reason that Geobacter species are repeatedly found to be among the most metabolically active microorganisms in methanogenic soils is that they grow syntrophically in cooperation with Methanothrix spp., and possibly other methanogens, via DIET.
Collapse
|
19
|
Dranguet P, Le Faucheur S, Cosio C, Slaveykova VI. Influence of chemical speciation and biofilm composition on mercury accumulation by freshwater biofilms. Environ Sci Process Impacts 2017; 19:38-49. [PMID: 27942649 DOI: 10.1039/c6em00493h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Mercury (Hg) is a pollutant of high concern for aquatic systems due to the biomagnification of its methylated form along the food chain. However, in contrast to other metals, gaining knowledge of its bioavailable forms for aquatic microorganisms remains challenging, making Hg risk assessment difficult. Ubiquitous and sessile freshwater biofilms are well known to accumulate and to transform Hg present in their ambient environment. The present study thus aims to evaluate whether non-extractable (proxy of intracellular) Hg accumulated by biofilms could be a good indicator of Hg bioavailability for microorganisms in freshwater. To that end, the link between Hg concentration and speciation, as well as biofilm composition (percentage of abiotic, biotic, chlorophyll and phycocyanin-fractions and abundance of dsrA, gcs, merA and hgcA bacterial genes) and biofilm Hg accumulation was examined. The studied biofilms were grown on artificial substrata in four reservoirs along the Olt River (Romania), which was contaminated by Hg coming from chlor-alkali plant effluents. The 0.45 μm-filterable Hg concentrations in ambient waters were measured and inorganic IHg speciation was modelled. Biofilms were analyzed for their non-extractable IHg and methylmercury (MeHg) contents as well as for their composition. The non-extractable IHg content was related, but not significantly, to the concentration of total IHg (r2 = 0.88, p = 0.061) whereas a significant correlation was found with the predicted IHg concentration that is not bound to dissolved organic matter (r2 = 0.95, p = 0.027), despite its extremely low concentrations (10-25 M), showing a limitation of the thermodynamic Hg modelling to predict Hg bioavailability. The studied biofilms were different in biomass and composition and a principal component analysis showed that the non-extractable IHg content correlated with the abundance of the merA and hgcA genes, while MeHg accumulation was only linked with the abundance of the rRNA 16S gene. The present study suggests that non-extractable IHg concentrations in biofilms are a useful proxy of IHg bioavailable forms in waters whereas the hgcA and merA genes are good biomarkers of both biofilm IHg exposure and bioavailability.
Collapse
Affiliation(s)
- P Dranguet
- University of Geneva, Faculty of Science, Earth and Environmental Sciences, Department F.-A. Forel for Environmental and Aquatic Sciences, Uni Carl Vogt, 66 Bvd. Carl Vogt, CH-1211 Geneva, Switzerland.
| | - S Le Faucheur
- University of Geneva, Faculty of Science, Earth and Environmental Sciences, Department F.-A. Forel for Environmental and Aquatic Sciences, Uni Carl Vogt, 66 Bvd. Carl Vogt, CH-1211 Geneva, Switzerland.
| | - C Cosio
- University of Geneva, Faculty of Science, Earth and Environmental Sciences, Department F.-A. Forel for Environmental and Aquatic Sciences, Uni Carl Vogt, 66 Bvd. Carl Vogt, CH-1211 Geneva, Switzerland.
| | - V I Slaveykova
- University of Geneva, Faculty of Science, Earth and Environmental Sciences, Department F.-A. Forel for Environmental and Aquatic Sciences, Uni Carl Vogt, 66 Bvd. Carl Vogt, CH-1211 Geneva, Switzerland.
| |
Collapse
|
20
|
Speers AM, Schindler BD, Hwang J, Genc A, Reguera G. Genetic Identification of a PilT Motor in Geobacter sulfurreducens Reveals a Role for Pilus Retraction in Extracellular Electron Transfer. Front Microbiol 2016; 7:1578. [PMID: 27799920 PMCID: PMC5065972 DOI: 10.3389/fmicb.2016.01578] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [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: 07/01/2016] [Accepted: 09/21/2016] [Indexed: 12/13/2022] Open
Abstract
The metal-reducing bacterium Geobacter sulfurreducens requires the expression of conductive pili to reduce iron oxides and to wire electroactive biofilms, but the role of pilus retraction in these functions has remained elusive. Here we show that of the four PilT proteins encoded in the genome of G. sulfurreducens, PilT3 powered pilus retraction in planktonic cells of a PilT-deficient strain of P. aeruginosa and restored the dense mutant biofilms to wild-type levels. Furthermore, PilT3 and PilT4 rescued the twitching motility defect of the PilT-deficient mutant. However, PilT4 was the only paralog whose inactivation in G. sulfurreducens lead to phenotypes associated with the hyperpiliation of non-retractile mutants such as enhanced adhesion and biofilm-forming abilities. In addition, PilT4 was required to reduce iron oxides. Taken together, the results indicate that PilT4 is the motor ATPase of G. sulfurreducens pili and reveal a previously unrecognized role for pilus retraction in extracellular electron transfer, a strategy that confers on Geobacter spp. an adaptive advantage for metal reduction in the natural environment.
Collapse
Affiliation(s)
- Allison M Speers
- Department of Microbiology and Molecular Genetics, Michigan State University East Lansing, MI, USA
| | - Bryan D Schindler
- Department of Microbiology and Molecular Genetics, Michigan State University East Lansing, MI, USA
| | - Jihwan Hwang
- Department of Microbiology and Molecular Genetics, Michigan State University East Lansing, MI, USA
| | - Aycin Genc
- Department of Microbiology and Molecular Genetics, Michigan State University East Lansing, MI, USA
| | - Gemma Reguera
- Department of Microbiology and Molecular Genetics, Michigan State University East Lansing, MI, USA
| |
Collapse
|
21
|
Ueki T, Nevin KP, Woodard TL, Lovley DR. Genetic switches and related tools for controlling gene expression and electrical outputs of Geobacter sulfurreducens. J Ind Microbiol Biotechnol 2016; 43:1561-1575. [PMID: 27659960 DOI: 10.1007/s10295-016-1836-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Accepted: 09/11/2016] [Indexed: 01/04/2023]
Abstract
Physiological studies and biotechnology applications of Geobacter species have been limited by a lack of genetic tools. Therefore, potential additional molecular strategies for controlling metabolism were explored. When the gene for citrate synthase, or acetyl-CoA transferase, was placed under the control of a LacI/IPTG regulator/inducer system, cells grew on acetate only in the presence of IPTG. The TetR/AT system could also be used to control citrate synthase gene expression and acetate metabolism. A strain that required IPTG for growth on D-lactate was constructed by placing the gene for D-lactate dehydrogenase under the control of the LacI/IPTG system. D-Lactate served as an inducer in a strain in which a D-lactate responsive promoter and transcription repressor were used to control citrate synthase expression. Iron- and potassium-responsive systems were successfully incorporated to regulate citrate synthase expression and growth on acetate. Linking the appropriate degradation tags on the citrate synthase protein made it possible to control acetate metabolism with either the endogenous ClpXP or exogenous Lon protease and tag system. The ability to control current output from Geobacter biofilms and the construction of an AND logic gate for acetate metabolism suggested that the tools developed may be applicable for biosensor and biocomputing applications.
Collapse
Affiliation(s)
- Toshiyuki Ueki
- Department of Microbiology, University of Massachusetts, Morrill Science Center IV North, 639 North Pleasant Street, Amherst, MA, 01003, USA.
| | - Kelly P Nevin
- Department of Microbiology, University of Massachusetts, Morrill Science Center IV North, 639 North Pleasant Street, Amherst, MA, 01003, USA
| | - Trevor L Woodard
- Department of Microbiology, University of Massachusetts, Morrill Science Center IV North, 639 North Pleasant Street, Amherst, MA, 01003, USA
| | - Derek R Lovley
- Department of Microbiology, University of Massachusetts, Morrill Science Center IV North, 639 North Pleasant Street, Amherst, MA, 01003, USA
| |
Collapse
|
22
|
Araújo WL, Santos DS, Dini-Andreote F, Salgueiro-Londoño JK, Camargo-Neves AA, Andreote FD, Dourado MN. Genes related to antioxidant metabolism are involved in Methylobacterium mesophilicum-soybean interaction. Antonie Van Leeuwenhoek 2015; 108:951-63. [PMID: 26238382 DOI: 10.1007/s10482-015-0548-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2015] [Accepted: 07/24/2015] [Indexed: 10/23/2022]
Abstract
The genus Methylobacterium is composed of pink-pigmented methylotrophic bacterial species that are widespread in natural environments, such as soils, stream water and plants. When in association with plants, this genus colonizes the host plant epiphytically and/or endophytically. This association is known to promote plant growth, induce plant systemic resistance and inhibit plant infection by phytopathogens. In the present study, we focused on evaluating the colonization of soybean seedling-roots by Methylobacterium mesophilicum strain SR1.6/6. We focused on the identification of the key genes involved in the initial step of soybean colonization by methylotrophic bacteria, which includes the plant exudate recognition and adaptation by planktonic bacteria. Visualization by scanning electron microscopy revealed that M. mesophilicum SR1.6/6 colonizes soybean roots surface effectively at 48 h after inoculation, suggesting a mechanism for root recognition and adaptation before this period. The colonization proceeds by the development of a mature biofilm on roots at 96 h after inoculation. Transcriptomic analysis of the planktonic bacteria (with plant) revealed the expression of several genes involved in membrane transport, thus confirming an initial metabolic activation of bacterial responses when in the presence of plant root exudates. Moreover, antioxidant genes were mostly expressed during the interaction with the plant exudates. Further evaluation of stress- and methylotrophic-related genes expression by qPCR showed that glutathione peroxidase and glutathione synthetase genes were up-regulated during the Methylobacterium-soybean interaction. These findings support that glutathione (GSH) is potentially a key molecule involved in cellular detoxification during plant root colonization. In addition to methylotrophic metabolism, antioxidant genes, mainly glutathione-related genes, play a key role during soybean exudate recognition and adaptation, the first step in bacterial colonization.
Collapse
Affiliation(s)
- Welington Luiz Araújo
- LABMEM/NAP-BIOP, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes, 1374 -Ed. Biomédicas II, Cidade Universitária, São Paulo, SP, 05508-900, Brazil,
| | | | | | | | | | | | | |
Collapse
|
23
|
Heinzelmann SM, Villanueva L, Sinke-Schoen D, Sinninghe Damsté JS, Schouten S, van der Meer MTJ. Impact of metabolism and growth phase on the hydrogen isotopic composition of microbial fatty acids. Front Microbiol 2015; 6:408. [PMID: 26005437 PMCID: PMC4424904 DOI: 10.3389/fmicb.2015.00408] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [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: 11/05/2014] [Accepted: 04/19/2015] [Indexed: 12/12/2022] Open
Abstract
Microorganisms are involved in all elemental cycles and therefore it is important to study their metabolism in the natural environment. A recent technique to investigate this is the hydrogen isotopic composition of microbial fatty acids, i.e., heterotrophic microorganisms produce fatty acids enriched in deuterium (D) while photoautotrophic and chemoautotrophic microorganisms produce fatty acids depleted in D compared to the water in the culture medium (growth water). However, the impact of factors other than metabolism have not been investigated. Here, we evaluate the impact of growth phase compared to metabolism on the hydrogen isotopic composition of fatty acids of different environmentally relevant microorganisms with heterotrophic, photoautotrophic and chemoautotrophic metabolisms. Fatty acids produced by heterotrophs are enriched in D compared to growth water with εlipid/water between 82 and 359‰ when grown on glucose or acetate, respectively. Photoautotrophs (εlipid/water between −149 and −264‰) and chemoautotrophs (εlipid/water between −217 and −275‰) produce fatty acids depleted in D. Fatty acids become, in general, enriched by between 4 and 46‰ with growth phase which is minor compared to the influence of metabolisms. Therefore, the D/H ratio of fatty acids is a promising tool to investigate community metabolisms in nature.
Collapse
Affiliation(s)
- Sandra M Heinzelmann
- Department of Marine Organic Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research Den Burg, Netherlands
| | - Laura Villanueva
- Department of Marine Organic Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research Den Burg, Netherlands
| | - Danielle Sinke-Schoen
- Department of Marine Organic Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research Den Burg, Netherlands
| | - Jaap S Sinninghe Damsté
- Department of Marine Organic Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research Den Burg, Netherlands ; Department of Earth Sciences, Faculty of Geosciences, Utrecht University Utrecht, Netherlands
| | - Stefan Schouten
- Department of Marine Organic Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research Den Burg, Netherlands ; Department of Earth Sciences, Faculty of Geosciences, Utrecht University Utrecht, Netherlands
| | - Marcel T J van der Meer
- Department of Marine Organic Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research Den Burg, Netherlands
| |
Collapse
|
24
|
Rose ND, Regan JM. Changes in phosphorylation of adenosine phosphate and redox state of nicotinamide-adenine dinucleotide (phosphate) in Geobacter sulfurreducens in response to electron acceptor and anode potential variation. Bioelectrochemistry 2015; 106:213-20. [PMID: 25857596 DOI: 10.1016/j.bioelechem.2015.03.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 03/03/2015] [Accepted: 03/16/2015] [Indexed: 01/28/2023]
Abstract
Geobacter sulfurreducens is one of the dominant bacterial species found in biofilms growing on anodes in bioelectrochemical systems. The intracellular concentrations of reduced and oxidized forms of nicotinamide-adenine dinucleotide (NADH and NAD(+), respectively) and nicotinamide-adenine dinucleotide phosphate (NADPH and NADP(+), respectively) as well as adenosine triphosphate (ATP), adenosine diphosphate (ADP), and adenosine monophosphate (AMP) were measured in G. sulfurreducens using fumarate, Fe(III)-citrate, or anodes poised at different potentials (110, 10, -90, and -190 mV (vs. SHE)) as the electron acceptor. The ratios of CNADH/CNAD+ (0.088±0.022) and CNADPH/CNADP+ (0.268±0.098) were similar under all anode potentials tested and with Fe(III)-citrate (reduced extracellularly). Both ratios significantly increased with fumarate as the electron acceptor (0.331±0.094 for NAD and 1.96±0.37 for NADP). The adenylate energy charge (the fraction of phosphorylation in intracellular adenosine phosphates) was maintained near 0.47 under almost all conditions. Anode-growing biofilms demonstrated a significantly higher molar ratio of ATP/ADP relative to suspended cultures grown on fumarate or Fe(III)-citrate. These results provide evidence that the cellular location of reduction and not the redox potential of the electron acceptor controls the intracellular redox potential in G. sulfurreducens and that biofilm growth alters adenylate phosphorylation.
Collapse
Affiliation(s)
- Nicholas D Rose
- College of Engineering, Department of Civil and Environmental Engineering, The Pennsylvania State University, 212 Sackett Building, State College, PA 16802, USA.
| | - John M Regan
- College of Engineering, Department of Civil and Environmental Engineering, The Pennsylvania State University, 212 Sackett Building, State College, PA 16802, USA.
| |
Collapse
|
25
|
Holmes DE, Giloteaux L, Chaurasia AK, Williams KH, Luef B, Wilkins MJ, Wrighton KC, Thompson CA, Comolli LR, Lovley DR. Evidence of Geobacter-associated phage in a uranium-contaminated aquifer. ISME J 2015; 9:333-46. [PMID: 25083935 PMCID: PMC4303627 DOI: 10.1038/ismej.2014.128] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2014] [Revised: 05/27/2014] [Accepted: 06/14/2014] [Indexed: 11/08/2022]
Abstract
Geobacter species may be important agents in the bioremediation of organic and metal contaminants in the subsurface, but as yet unknown factors limit the in situ growth of subsurface Geobacter well below rates predicted by analysis of gene expression or in silico metabolic modeling. Analysis of the genomes of five different Geobacter species recovered from contaminated subsurface sites indicated that each of the isolates had been infected with phage. Geobacter-associated phage sequences were also detected by metagenomic and proteomic analysis of samples from a uranium-contaminated aquifer undergoing in situ bioremediation, and phage particles were detected by microscopic analysis in groundwater collected from sediment enrichment cultures. Transcript abundance for genes from the Geobacter-associated phage structural proteins, tail tube Gp19 and baseplate J, increased in the groundwater in response to the growth of Geobacter species when acetate was added, and then declined as the number of Geobacter decreased. Western blot analysis of a Geobacter-associated tail tube protein Gp19 in the groundwater demonstrated that its abundance tracked with the abundance of Geobacter species. These results suggest that the enhanced growth of Geobacter species in the subsurface associated with in situ uranium bioremediation increased the abundance and activity of Geobacter-associated phage and show that future studies should focus on how these phages might be influencing the ecology of this site.
Collapse
Affiliation(s)
- Dawn E Holmes
- Department of Microbiology, University of Massachusetts Amherst, Amherst, MA, USA
- Western New England University, Springfield, MA, USA
| | - Ludovic Giloteaux
- Department of Microbiology, University of Massachusetts Amherst, Amherst, MA, USA
| | - Akhilesh K Chaurasia
- Department of Microbiology, University of Massachusetts Amherst, Amherst, MA, USA
| | | | - Birgit Luef
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Earth and Planetary Sciences, University of California, Berkeley, Berkeley, CA, USA
| | | | - Kelly C Wrighton
- Department of Earth and Planetary Sciences, University of California, Berkeley, Berkeley, CA, USA
| | - Courtney A Thompson
- Department of Microbiology, University of Massachusetts Amherst, Amherst, MA, USA
| | - Luis R Comolli
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Derek R Lovley
- Department of Microbiology, University of Massachusetts Amherst, Amherst, MA, USA
| |
Collapse
|
26
|
Orellana R, Hixson KK, Murphy S, Mester T, Sharma ML, Lipton MS, Lovley DR. Proteome of Geobacter sulfurreducens in the presence of U(VI). Microbiology (Reading) 2014; 160:2607-2617. [DOI: 10.1099/mic.0.081398-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Geobacter species often play an important role in the in situ bioremediation of uranium-contaminated groundwater, but little is known about how these microbes avoid uranium toxicity. To evaluate this further, the proteome of Geobacter sulfurreducens exposed to 100 µM U(VI) acetate was compared to control cells not exposed to U(VI). Of the 1363 proteins detected from these cultures, 203 proteins had higher abundance during exposure to U(VI) compared with the control cells and 148 proteins had lower abundance. U(VI)-exposed cultures expressed lower levels of proteins involved in growth, protein and amino acid biosynthesis, as well as key central metabolism enzymes as a result of the deleterious effect of U(VI) on the growth of G. sulfurreducens. In contrast, proteins involved in detoxification, such as several efflux pumps belonging to the RND (resistance–nodulation–cell division) family, and membrane protection, and other proteins, such as chaperones and proteins involved in secretion systems, were found in higher abundance in cells exposed to U(VI). Exposing G. sulfurreducens to U(VI) resulted in a higher abundance of many proteins associated with the oxidative stress response, such as superoxide dismutase and superoxide reductase. A strain in which the gene for superoxide dismutase was deleted grew more slowly than the WT strain in the presence of U(VI), but not in its absence. The results suggested that there is no specific mechanism for uranium detoxification. Rather, multiple general stress responses are induced, which presumably enable Geobacter species to tolerate high uranium concentrations.
Collapse
Affiliation(s)
- Roberto Orellana
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA
| | - Kim K. Hixson
- Environmental Molecular Sciences Laboratory and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Sean Murphy
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA
| | - Tünde Mester
- Department of Ophthalmology and Visual Sciences, University of Michigan Medical School, Kellogg Eye Center, Ann Arbor, MI 48105, USA
| | - Manju L. Sharma
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA
| | - Mary S. Lipton
- Environmental Molecular Sciences Laboratory and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Derek R. Lovley
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA
| |
Collapse
|
27
|
Holmes DE, Giloteaux L, Orellana R, Williams KH, Robbins MJ, Lovley DR. Methane production from protozoan endosymbionts following stimulation of microbial metabolism within subsurface sediments. Front Microbiol 2014; 5:366. [PMID: 25147543 PMCID: PMC4123621 DOI: 10.3389/fmicb.2014.00366] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [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: 04/24/2014] [Accepted: 07/01/2014] [Indexed: 11/13/2022] Open
Abstract
Previous studies have suggested that protozoa prey on Fe(III)- and sulfate-reducing bacteria that are enriched when acetate is added to uranium contaminated subsurface sediments to stimulate U(VI) reduction. In order to determine whether protozoa continue to impact subsurface biogeochemistry after these acetate amendments have stopped, 18S rRNA and ß-tubulin sequences from this phase of an in situ uranium bioremediation field experiment were analyzed. Sequences most similar to Metopus species predominated, with the majority of sequences most closely related to M. palaeformis, a cilitated protozoan known to harbor methanogenic symbionts. Quantification of mcrA mRNA transcripts in the groundwater suggested that methanogens closely related to Metopus endosymbionts were metabolically active at this time. There was a strong correlation between the number of mcrA transcripts from the putative endosymbiotic methanogen and Metopus ß-tubulin mRNA transcripts during the course of the field experiment, suggesting that the activity of the methanogens was dependent upon the activity of the Metopus species. Addition of the eukaryotic inhibitors cyclohexamide and colchicine to laboratory incubations of acetate-amended subsurface sediments significantly inhibited methane production and there was a direct correlation between methane concentration and Metopus ß-tubulin and putative symbiont mcrA gene copies. These results suggest that, following the stimulation of subsurface microbial growth with acetate, protozoa harboring methanogenic endosymbionts become important members of the microbial community, feeding on moribund biomass and producing methane.
Collapse
Affiliation(s)
- Dawn E Holmes
- Department of Microbiology, University of Massachusetts Amherst, MA, USA ; Physical and Biological Sciences, Western New England University Springfield, MA, USA
| | - Ludovic Giloteaux
- Department of Microbiology, University of Massachusetts Amherst, MA, USA
| | - Roberto Orellana
- Department of Microbiology, University of Massachusetts Amherst, MA, USA
| | | | | | - Derek R Lovley
- Department of Microbiology, University of Massachusetts Amherst, MA, USA
| |
Collapse
|
28
|
Malvankar NS, King GM, Lovley DR. Centimeter-long electron transport in marine sediments via conductive minerals. ISME J 2014; 9:527-31. [PMID: 25050525 DOI: 10.1038/ismej.2014.131] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2014] [Revised: 06/16/2014] [Accepted: 06/18/2014] [Indexed: 11/09/2022]
Abstract
Centimeter-long electron conduction through marine sediments, in which electrons derived from sulfide in anoxic sediments are transported to oxygen in surficial sediments, may have an important influence on sediment geochemistry. Filamentous bacteria have been proposed to mediate the electron transport, but the filament conductivity could not be verified and other mechanisms are possible. Surprisingly, previous investigations have never actually measured the sediment conductivity or its basic physical properties. Here we report direct measurements that demonstrate centimeter-long electron flow through marine sediments, with conductivities sufficient to account for previously estimated electron fluxes. Conductivity was lost for oxidized sediments, which contrasts with the previously described increase in the conductivity of microbial biofilms upon oxidation. Adding pyrite to the sediments significantly enhanced the conductivity. These results suggest that the role of conductive minerals, which are more commonly found in sediments than centimeter-long microbial filaments, need to be considered when modeling marine sediment biogeochemistry.
Collapse
Affiliation(s)
- Nikhil S Malvankar
- 1] Department of Physics, University of Massachusetts, Amherst, Amherst, MA, USA [2] Department of Microbiology, University of Massachusetts, Amherst, Amherst, MA, USA
| | - Gary M King
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Derek R Lovley
- Department of Microbiology, University of Massachusetts, Amherst, Amherst, MA, USA
| |
Collapse
|
29
|
Smith JA, Tremblay PL, Shrestha PM, Snoeyenbos-West OL, Franks AE, Nevin KP, Lovley DR. Going wireless: Fe(III) oxide reduction without pili by Geobacter sulfurreducens strain JS-1. Appl Environ Microbiol 2014; 80:4331-40. [PMID: 24814783 DOI: 10.1128/AEM.01122-14] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Previous studies have suggested that the conductive pili of Geobacter sulfurreducens are essential for extracellular electron transfer to Fe(III) oxides and for optimal long-range electron transport through current-producing biofilms. The KN400 strain of G. sulfurreducens reduces poorly crystalline Fe(III) oxide more rapidly than the more extensively studied DL-1 strain. Deletion of the gene encoding PilA, the structural pilin protein, in strain KN400 inhibited Fe(III) oxide reduction. However, low rates of Fe(III) reduction were detected after extended incubation (>30 days) in the presence of Fe(III) oxide. After seven consecutive transfers, the PilA-deficient strain adapted to reduce Fe(III) oxide as fast as the wild type. Microarray, whole-genome resequencing, proteomic, and gene deletion studies indicated that this adaptation was associated with the production of larger amounts of the c-type cytochrome PgcA, which was released into the culture medium. It is proposed that the extracellular cytochrome acts as an electron shuttle, promoting electron transfer from the outer cell surface to Fe(III) oxides. The adapted PilA-deficient strain competed well with the wild-type strain when both were grown together on Fe(III) oxide. However, when 50% of the culture medium was replaced with fresh medium every 3 days, the wild-type strain outcompeted the adapted strain. A possible explanation for this is that the necessity to produce additional PgcA, to replace the PgcA being continually removed, put the adapted strain at a competitive disadvantage, similar to the apparent selection against electron shuttle-producing Fe(III) reducers in many anaerobic soils and sediments. Despite increased extracellular cytochrome production, the adapted PilA-deficient strain produced low levels of current, consistent with the concept that long-range electron transport through G. sulfurreducens biofilms is more effective via pili.
Collapse
|
30
|
Dourado MN, Bogas AC, Pomini AM, Andreote FD, Quecine MC, Marsaioli AJ, Araújo WL. Methylobacterium-plant interaction genes regulated by plant exudate and quorum sensing molecules. Braz J Microbiol 2014; 44:1331-9. [PMID: 24688531 PMCID: PMC3958207 DOI: 10.1590/s1517-83822013000400044] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [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: 06/11/2012] [Accepted: 04/04/2013] [Indexed: 11/21/2022] Open
Abstract
Bacteria from the genus Methylobacterium interact symbiotically (endophytically and epiphytically) with different plant species. These interactions can promote plant growth or induce systemic resistance, increasing plant fitness. The plant colonization is guided by molecular communication between bacteria-bacteria and bacteria-plants, where the bacteria recognize specific exuded compounds by other bacteria (e.g. homoserine molecules) and/or by the plant roots (e.g. flavonoids, ethanol and methanol), respectively. In this context, the aim of this study was to evaluate the effect of quorum sensing molecules (N-acyl-homoserine lactones) and plant exudates (including ethanol) in the expression of a series of bacterial genes involved in Methylobacterium-plant interaction. The selected genes are related to bacterial metabolism (mxaF), adaptation to stressful environment (crtI, phoU and sss), to interactions with plant metabolism compounds (acdS) and pathogenicity (patatin and phoU). Under in vitro conditions, our results showed the differential expression of some important genes related to metabolism, stress and pathogenesis, thereby AHL molecules up-regulate all tested genes, except phoU, while plant exudates induce only mxaF gene expression. In the presence of plant exudates there is a lower bacterial density (due the endophytic and epiphytic colonization), which produce less AHL, leading to down regulation of genes when compared to the control. Therefore, bacterial density, more than plant exudate, influences the expression of genes related to plant-bacteria interaction.
Collapse
Affiliation(s)
| | | | - Armando M Pomini
- Departamento de Química, Universidade Estadual de Maringá, Maringá, PR, Brazil
| | - Fernando Dini Andreote
- Departamento de Ciências do Solos, Escola Superior de Agricultura "Luiz de Queiróz", Universidade de São Paulo, Piracicaba, SP, Brazil
| | | | - Anita J Marsaioli
- Instituto de Química, Universidade de Campinas, Campinas, São Paulo, Brazil
| | - Welington Luiz Araújo
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, SP, Brazil
| |
Collapse
|
31
|
Zhang T, Tremblay PL, Chaurasia AK, Smith JA, Bain TS, Lovley DR. Anaerobic benzene oxidation via phenol in Geobacter metallireducens. Appl Environ Microbiol 2013; 79:7800-6. [PMID: 24096430 DOI: 10.1128/AEM.03134-13] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Anaerobic activation of benzene is expected to represent a novel biochemistry of environmental significance. Therefore, benzene metabolism was investigated in Geobacter metallireducens, the only genetically tractable organism known to anaerobically degrade benzene. Trace amounts (<0.5 μM) of phenol accumulated in cultures of Geobacter metallireducens anaerobically oxidizing benzene to carbon dioxide with the reduction of Fe(III). Phenol was not detected in cell-free controls or in Fe(II)- and benzene-containing cultures of Geobacter sulfurreducens, a Geobacter species that cannot metabolize benzene. The phenol produced in G. metallireducens cultures was labeled with (18)O during growth in H2(18)O, as expected for anaerobic conversion of benzene to phenol. Analysis of whole-genome gene expression patterns indicated that genes for phenol metabolism were upregulated during growth on benzene but that genes for benzoate or toluene metabolism were not, further suggesting that phenol was an intermediate in benzene metabolism. Deletion of the genes for PpsA or PpcB, subunits of two enzymes specifically required for the metabolism of phenol, removed the capacity for benzene metabolism. These results demonstrate that benzene hydroxylation to phenol is an alternative to carboxylation for anaerobic benzene activation and suggest that this may be an important metabolic route for benzene removal in petroleum-contaminated groundwaters, in which Geobacter species are considered to play an important role in anaerobic benzene degradation.
Collapse
|
32
|
Orellana R, Leavitt JJ, Comolli LR, Csencsits R, Janot N, Flanagan KA, Gray AS, Leang C, Izallalen M, Mester T, Lovley DR. U(VI) reduction by diverse outer surface c-type cytochromes of Geobacter sulfurreducens. Appl Environ Microbiol 2013; 79:6369-74. [PMID: 23934497 DOI: 10.1128/AEM.02551-13] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Early studies with Geobacter sulfurreducens suggested that outer-surface c-type cytochromes might play a role in U(VI) reduction, but it has recently been suggested that there is substantial U(VI) reduction at the surface of the electrically conductive pili known as microbial nanowires. This phenomenon was further investigated. A strain of G. sulfurreducens, known as Aro-5, which produces pili with substantially reduced conductivity reduced U(VI) nearly as well as the wild type, as did a strain in which the gene for PilA, the structural pilin protein, was deleted. In order to reduce rates of U(VI) reduction to levels less than 20% of the wild-type rates, it was necessary to delete the genes for the five most abundant outer surface c-type cytochromes of G. sulfurreducens. X-ray absorption near-edge structure spectroscopy demonstrated that whereas 83% ± 10% of the uranium associated with wild-type cells correspond to U(IV) after 4 h of incubation, with the quintuple mutant, 89% ± 10% of uranium was U(VI). Transmission electron microscopy and X-ray energy dispersion spectroscopy revealed that wild-type cells did not precipitate uranium along pili as previously reported, but U(IV) was precipitated at the outer cell surface. These findings are consistent with those of previous studies, which have suggested that G. sulfurreducens requires outer-surface c-type cytochromes but not pili for the reduction of soluble extracellular electron acceptors.
Collapse
|
33
|
Holmes DE, Giloteaux L, Williams KH, Wrighton KC, Wilkins MJ, Thompson CA, Roper TJ, Long PE, Lovley DR. Enrichment of specific protozoan populations during in situ bioremediation of uranium-contaminated groundwater. ISME J 2013; 7:1286-98. [PMID: 23446832 PMCID: PMC3695288 DOI: 10.1038/ismej.2013.20] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [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: 09/25/2012] [Revised: 01/07/2013] [Accepted: 01/10/2013] [Indexed: 11/09/2022]
Abstract
The importance of bacteria in the anaerobic bioremediation of groundwater polluted with organic and/or metal contaminants is well recognized and in some instances so well understood that modeling of the in situ metabolic activity of the relevant subsurface microorganisms in response to changes in subsurface geochemistry is feasible. However, a potentially significant factor influencing bacterial growth and activity in the subsurface that has not been adequately addressed is protozoan predation of the microorganisms responsible for bioremediation. In field experiments at a uranium-contaminated aquifer located in Rifle, CO, USA, acetate amendments initially promoted the growth of metal-reducing Geobacter species, followed by the growth of sulfate reducers, as observed previously. Analysis of 18S rRNA gene sequences revealed a broad diversity of sequences closely related to known bacteriovorous protozoa in the groundwater before the addition of acetate. The bloom of Geobacter species was accompanied by a specific enrichment of sequences most closely related to the ameboid flagellate, Breviata anathema, which at their peak accounted for over 80% of the sequences recovered. The abundance of Geobacter species declined following the rapid emergence of B. anathema. The subsequent growth of sulfate-reducing Peptococcaceae was accompanied by another specific enrichment of protozoa, but with sequences most similar to diplomonadid flagellates from the family Hexamitidae, which accounted for up to 100% of the sequences recovered during this phase of the bioremediation. These results suggest a prey-predator response with specific protozoa responding to increased availability of preferred prey bacteria. Thus, quantifying the influence of protozoan predation on the growth, activity and composition of the subsurface bacterial community is essential for predictive modeling of in situ uranium bioremediation strategies.
Collapse
Affiliation(s)
- Dawn E Holmes
- Department of Microbiology, Morrill Science Center IVN, University of Massachusetts Amherst, Amherst, MA 01003, USA.
| | | | | | | | | | | | | | | | | |
Collapse
|
34
|
Vargas M, Malvankar NS, Tremblay PL, Leang C, Smith JA, Patel P, Snoeyenbos-West O, Nevin KP, Lovley DR. Aromatic amino acids required for pili conductivity and long-range extracellular electron transport in Geobacter sulfurreducens. mBio 2013; 4:e00105-13. [PMID: 23481602 DOI: 10.1128/mBio.00105-13] [Citation(s) in RCA: 112] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
It has been proposed that Geobacter sulfurreducens requires conductive pili for long-range electron transport to Fe(III) oxides and for high-density current production in microbial fuel cells. In order to investigate this further, we constructed a strain of G. sulfurreducens, designated Aro-5, which produced pili with diminished conductivity. This was accomplished by modifying the amino acid sequence of PilA, the structural pilin protein. An alanine was substituted for each of the five aromatic amino acids in the carboxyl terminus of PilA, the region in which G. sulfurreducens PilA differs most significantly from the PilAs of microorganisms incapable of long-range extracellular electron transport. Strain Aro-5 produced pili that were properly decorated with the multiheme c-type cytochrome OmcS, which is essential for Fe(III) oxide reduction. However, pili preparations of the Aro-5 strain had greatly diminished conductivity and Aro-5 cultures were severely limited in their capacity to reduce Fe(III) compared to the control strain. Current production of the Aro-5 strain, with a graphite anode serving as the electron acceptor, was less than 10% of that of the control strain. The conductivity of the Aro-5 biofilms was 10-fold lower than the control strain’s. These results demonstrate that the pili of G. sulfurreducens must be conductive in order for the cells to be effective in extracellular long-range electron transport. Extracellular electron transfer by Geobacter species plays an important role in the biogeochemistry of soils and sediments and has a number of bioenergy applications. For example, microbial reduction of Fe(III) oxide is one of the most geochemically significant processes in anaerobic soils, aquatic sediments, and aquifers, and Geobacter organisms are often abundant in such environments. Geobacter sulfurreducens produces the highest current densities of any known pure culture, and close relatives are often the most abundant organisms colonizing anodes in microbial fuel cells that harvest electricity from wastewater or aquatic sediments. The finding that a strain of G. sulfurreducens that produces pili with low conductivity is limited in these extracellular electron transport functions provides further insight into these environmentally significant processes.
Collapse
|
35
|
Giloteaux L, Holmes DE, Williams KH, Wrighton KC, Wilkins MJ, Montgomery AP, Smith JA, Orellana R, Thompson CA, Roper TJ, Long PE, Lovley DR. Characterization and transcription of arsenic respiration and resistance genes during in situ uranium bioremediation. ISME J 2013; 7:370-83. [PMID: 23038171 PMCID: PMC3554400 DOI: 10.1038/ismej.2012.109] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [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: 05/11/2012] [Revised: 08/01/2012] [Accepted: 08/01/2012] [Indexed: 11/09/2022]
Abstract
The possibility of arsenic release and the potential role of Geobacter in arsenic biogeochemistry during in situ uranium bioremediation was investigated because increased availability of organic matter has been associated with substantial releases of arsenic in other subsurface environments. In a field experiment conducted at the Rifle, CO study site, groundwater arsenic concentrations increased when acetate was added. The number of transcripts from arrA, which codes for the α-subunit of dissimilatory As(V) reductase, and acr3, which codes for the arsenic pump protein Acr3, were determined with quantitative reverse transcription-PCR. Most of the arrA (>60%) and acr3-1 (>90%) sequences that were recovered were most similar to Geobacter species, while the majority of acr3-2 (>50%) sequences were most closely related to Rhodoferax ferrireducens. Analysis of transcript abundance demonstrated that transcription of acr3-1 by the subsurface Geobacter community was correlated with arsenic concentrations in the groundwater. In contrast, Geobacter arrA transcript numbers lagged behind the major arsenic release and remained high even after arsenic concentrations declined. This suggested that factors other than As(V) availability regulated the transcription of arrA in situ, even though the presence of As(V) increased the transcription of arrA in cultures of Geobacter lovleyi, which was capable of As(V) reduction. These results demonstrate that subsurface Geobacter species can tightly regulate their physiological response to changes in groundwater arsenic concentrations. The transcriptomic approach developed here should be useful for the study of a diversity of other environments in which Geobacter species are considered to have an important influence on arsenic biogeochemistry.
Collapse
Affiliation(s)
- Ludovic Giloteaux
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003-9298, USA.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
36
|
Holmes DE, Giloteaux L, Barlett M, Chavan MA, Smith JA, Williams KH, Wilkins M, Long P, Lovley DR. Molecular analysis of the in situ growth rates of subsurface Geobacter species. Appl Environ Microbiol 2013; 79:1646-53. [PMID: 23275510 DOI: 10.1128/AEM.03263-12] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Molecular tools that can provide an estimate of the in situ growth rate of Geobacter species could improve understanding of dissimilatory metal reduction in a diversity of environments. Whole-genome microarray analyses of a subsurface isolate of Geobacter uraniireducens, grown under a variety of conditions, identified a number of genes that are differentially expressed at different specific growth rates. Expression of two genes encoding ribosomal proteins, rpsC and rplL, was further evaluated with quantitative reverse transcription-PCR (qRT-PCR) in cells with doubling times ranging from 6.56 h to 89.28 h. Transcript abundance of rpsC correlated best (r(2) = 0.90) with specific growth rates. Therefore, expression patterns of rpsC were used to estimate specific growth rates of Geobacter species during an in situ uranium bioremediation field experiment in which acetate was added to the groundwater to promote dissimilatory metal reduction. Initially, increased availability of acetate in the groundwater resulted in higher expression of Geobacter rpsC, and the increase in the number of Geobacter cells estimated with fluorescent in situ hybridization compared well with specific growth rates estimated from levels of in situ rpsC expression. However, in later phases, cell number increases were substantially lower than predicted from rpsC transcript abundance. This change coincided with a bloom of protozoa and increased attachment of Geobacter species to solid phases. These results suggest that monitoring rpsC expression may better reflect the actual rate that Geobacter species are metabolizing and growing during in situ uranium bioremediation than changes in cell abundance.
Collapse
|
37
|
Smith JA, Lovley DR, Tremblay PL. Outer cell surface components essential for Fe(III) oxide reduction by Geobacter metallireducens. Appl Environ Microbiol 2013; 79:901-7. [PMID: 23183974 DOI: 10.1128/AEM.02954-12] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Geobacter species are important Fe(III) reducers in a diversity of soils and sediments. Mechanisms for Fe(III) oxide reduction have been studied in detail in Geobacter sulfurreducens, but a number of the most thoroughly studied outer surface components of G. sulfurreducens, particularly c-type cytochromes, are not well conserved among Geobacter species. In order to identify cellular components potentially important for Fe(III) oxide reduction in Geobacter metallireducens, gene transcript abundance was compared in cells grown on Fe(III) oxide or soluble Fe(III) citrate with whole-genome microarrays. Outer-surface cytochromes were also identified. Deletion of genes for c-type cytochromes that had higher transcript abundance during growth on Fe(III) oxides and/or were detected in the outer-surface protein fraction identified six c-type cytochrome genes, that when deleted removed the capacity for Fe(III) oxide reduction. Several of the c-type cytochromes which were essential for Fe(III) oxide reduction in G. metallireducens have homologs in G. sulfurreducens that are not important for Fe(III) oxide reduction. Other genes essential for Fe(III) oxide reduction included a gene predicted to encode an NHL (Ncl-1-HT2A-Lin-41) repeat-containing protein and a gene potentially involved in pili glycosylation. Genes associated with flagellum-based motility, chemotaxis, and pili had higher transcript abundance during growth on Fe(III) oxide, consistent with the previously proposed importance of these components in Fe(III) oxide reduction. These results demonstrate that there are similarities in extracellular electron transfer between G. metallireducens and G. sulfurreducens but the outer-surface c-type cytochromes involved in Fe(III) oxide reduction are different.
Collapse
|
38
|
Rowe AR, Heavner GL, Mansfeldt CB, Werner JJ, Richardson RE. Relating chloroethene respiration rates in Dehalococcoides to protein and mRNA biomarkers. Environ Sci Technol 2012; 46:9388-9397. [PMID: 22812668 DOI: 10.1021/es300996c] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Molecular biomarkers could provide critical insight into myriad in situ microbial activities. In this study we explore correlations of both mRNA and protein biomarkers with chloroethene respiration rate in Dehalococcoides. In a series of continuously fed dechlorinating mixed-culture microcosm experiments (n = 26), we varied respiratory substrates, substrate ratios and feeding rates. Transcript levels for most biomarkers were responsive down to 0.01× the culture's maximum respiration rate. The dehalogenase TceA and the Ni-Fe hydrogenase HupL transcripts were positively correlated (Pearson's r of 0.89 and 0.88, respectively) with respiration rates on log-log plots between 1.5 and 280 μeeq/L-hr for mRNA abundances of 10(7) to 10(10) transcripts/mL (0.07-230 transcripts/genome). These trends were independent of the types of chloroethene or electron donors fed. Other mRNA target levels plateaued or declined at respiration rates above 5 μeeq/L-hr. Using both relative and absolute protein quantification methods, we found that per-genome protein abundances of most targeted biomarkers did not statistically change over the experimental time frames. However, quantified enzyme levels allowed us to calculate in vivo enzyme-specific rate constants (k(cat)) for the dehalogenases PceA and TceA: 400 and 22 substrate molecules/enzyme-sec, respectively. Overall, these data support the promise of both mRNA and protein biomarkers for estimating process rates through either empirical (mRNA-based) or kinetic (protein-based) models, but they require follow-up studies in other cultures and at active remediation sites.
Collapse
Affiliation(s)
- Annette R Rowe
- Field of Microbiology, Cornell University, Ithaca New York 14853, United States
| | | | | | | | | |
Collapse
|
39
|
Druhan JL, Steefel CI, Molins S, Williams KH, Conrad ME, DePaolo DJ. Timing the onset of sulfate reduction over multiple subsurface acetate amendments by measurement and modeling of sulfur isotope fractionation. Environ Sci Technol 2012; 46:8895-8902. [PMID: 22834766 DOI: 10.1021/es302016p] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Stable isotope fractionations of sulfur are reported for three consecutive years of acetate-enabled uranium bioremediation at the US Department of Energy's Rifle Integrated Field Research Challenge (IFRC) site. The data show a previously undocumented decrease in the time between acetate addition and the onset of sulfate reducing conditions over subsequent amendments, from 20 days in the 2007 experiment to 4 days in the 2009 experiment. Increased sulfide concentrations were observed at the same time as δ(34)S of sulfate enrichment in the first year, but in subsequent years elevated sulfide was detected up to 15 days after increased δ(34)S of sulfate. A biogeochemical reactive transport model is developed which explicitly incorporates the stable isotopes of sulfur to simulate fractionation during the 2007 and 2008 amendments. A model based on an initially low, uniformly distributed population of sulfate reducing bacteria that grow and become spatially variable with time reproduces measured trends in solute concentration and δ(34)S, capturing the change in onset of sulfate reduction in subsequent years. Our results demonstrate a previously unrecognized hysteretic effect in the spatial distribution of biomass growth during stimulated subsurface bioremediation.
Collapse
Affiliation(s)
- Jennifer L Druhan
- Department of Earth and Planetary Science, University of California Berkeley, Berkeley, California 94720, United States.
| | | | | | | | | | | |
Collapse
|
40
|
Akob DM, Lee SH, Sheth M, Küsel K, Watson DB, Palumbo AV, Kostka JE, Chin KJ. Gene Expression Correlates with Process Rates Quantified for Sulfate- and Fe(III)-Reducing Bacteria in U(VI)-Contaminated Sediments. Front Microbiol 2012; 3:280. [PMID: 22908009 PMCID: PMC3415069 DOI: 10.3389/fmicb.2012.00280] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [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: 05/18/2012] [Accepted: 07/18/2012] [Indexed: 11/25/2022] Open
Abstract
Though iron- and sulfate-reducing bacteria are well known for mediating uranium(VI) reduction in contaminated subsurface environments, quantifying the in situ activity of the microbial groups responsible remains a challenge. The objective of this study was to demonstrate the use of quantitative molecular tools that target mRNA transcripts of key genes related to Fe(III) and sulfate reduction pathways in order to monitor these processes during in situ U(VI) remediation in the subsurface. Expression of the Geobacteraceae-specific citrate synthase gene (gltA) and the dissimilatory (bi)sulfite reductase gene (dsrA), were correlated with the activity of iron- or sulfate-reducing microorganisms, respectively, under stimulated bioremediation conditions in microcosms of sediments sampled from the U.S. Department of Energy’s Oak Ridge Integrated Field Research Challenge (OR-IFRC) site at Oak Ridge, TN, USA. In addition, Geobacteraceae-specific gltA and dsrA transcript levels were determined in parallel with the predominant electron acceptors present in moderately and highly contaminated subsurface sediments from the OR-IFRC. Phylogenetic analysis of the cDNA generated from dsrA mRNA, sulfate-reducing bacteria-specific 16S rRNA, and gltA mRNA identified activity of specific microbial groups. Active sulfate reducers were members of the Desulfovibrio, Desulfobacterium, and Desulfotomaculum genera. Members of the subsurface Geobacter clade, closely related to uranium-reducing Geobacter uraniireducens and Geobacter daltonii, were the metabolically active iron-reducers in biostimulated microcosms and in situ core samples. Direct correlation of transcripts and process rates demonstrated evidence of competition between the functional guilds in subsurface sediments. We further showed that active populations of Fe(III)-reducing bacteria and sulfate-reducing bacteria are present in OR-IFRC sediments and are good potential targets for in situ bioremediation.
Collapse
|
41
|
Rotaru C, Woodard TL, Choi S, Nevin KP. Spatial heterogeneity of bacterial communities in sediments from an infiltration basin receiving highway runoff. Microb Ecol 2012; 64:461-473. [PMID: 22391798 DOI: 10.1007/s00248-012-0026-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2011] [Accepted: 02/03/2012] [Indexed: 05/31/2023]
Abstract
The bacterial community diversity of highway runoff-contaminated sediment that had undergone 19 years of acetate-based de-icing agents addition followed by three years of acetate-free de-icing agents was investigated. Analysis of 26 sediment samples from two drilled soil cores by means of 16S rDNA PCR generated 3,402 clones, indicating an overall high bacterial diversity, with no prominent members within the communities. Sequence analyses provided evidences that each sediment sample displayed a specific structure bacterial community. Proteobacteria-affiliated clones (58% and 43% for the two boreholes) predominated in all samples, followed by Actinobacteria (12% and 16%), Firmicutes (7% and 12%) and Chloroflexi (7% and 11%). The subsurface geochemistry complemented the molecular methods to further distinguish ambient and contaminant plume zones. Principal component analysis revealed that the levels of Fe(II) and dissolved oxygen were strongly correlated with bacterial communities. At elevated Fe(II) levels, sequences associated with anaerobic bacteria were detected in high levels. As iron levels declined and oxygen levels increased below the plume bottom, there was a gradual shift in the community structure toward the increase of aerobic bacteria.
Collapse
Affiliation(s)
- Camelia Rotaru
- Civil and Environmental Engineering Department, University of Massachusetts, 18 Marston Hall, Amherst, MA 01003, USA.
| | | | | | | |
Collapse
|
42
|
Franks AE, Glaven RH, Lovley DR. Real-time spatial gene expression analysis within current-producing biofilms. ChemSusChem 2012; 5:1092-1098. [PMID: 22577044 DOI: 10.1002/cssc.201100714] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2011] [Revised: 03/06/2011] [Indexed: 05/31/2023]
Abstract
The expression of genes involved in central metabolism and extracellular electron transfer was examined in real-time in current-producing anode biofilms of Geobacter sulfurreducens. Strains of G. sulfurreducens were generated, in which the expression of the gene for a short half-life fluorescent protein was placed under control of the promoter of the genes of interest. Anode biofilms were grown in a chamber that permitted direct examination of the cell fluorescence with confocal scanning laser microscopy. Studies on nifD and citrate synthase expression in response to environmental changes demonstrated that the reporter system revealed initiation and termination of gene transcription. Uniform expression throughout the biofilms was noted for the genes for citrate synthase; PilA, the structural protein of the conductive pili; and OmcZ, a c-type cytochrome essential for optimal current production, which was localized at the anode-biofilm interface. These results demonstrate that even cells at great distance from the anode, or within expected low-pH zones, are metabolically active and likely to contribute to current production and that there are factors other than gene expression differences influencing the distribution of OmcZ. This real-time reporter approach is likely to be a useful tool in optimizing the design of technologies relying on microbe-electrode interactions.
Collapse
Affiliation(s)
- Ashley E Franks
- Department of Microbiology, University of Massachusetts, Morrill IVN, 639 North Pleasant Street, Amherst, MA, USA.
| | | | | |
Collapse
|
43
|
Abstract
Geobacter sulfurreducens, an Fe(III)-reducing deltaproteobacterium found in anoxic subsurface environments, contains 4 NiFe hydrogenases. Hyb, a periplasmically oriented membrane-bound NiFe hydrogenase, is essential for hydrogen-dependent growth. The functions of the three other hydrogenases are unknown. We show here that the other periplasmically oriented membrane-bound NiFe hydrogenase, Hya, is necessary for growth after exposure to oxidative stress when hydrogen or a highly limiting concentration of acetate is the electron source. The beneficial impact of Hya on growth was dependent on the presence of H(2) in the atmosphere. Moreover, the Hya-deficient strain was more sensitive to the presence of superoxide or hydrogen peroxide. Hya was also required to safeguard Hyb hydrogen oxidation activity after exposure to O(2). Overexpression studies demonstrated that Hya was more resistant to oxidative stress than Hyb. Overexpression of Hya also resulted in the creation of a recombinant strain better fitted for exposure to oxidative stress than wild-type G. sulfurreducens. These results demonstrate that one of the physiological roles of the O(2)-resistant Hya is to participate in the oxidative stress defense of G. sulfurreducens.
Collapse
|
44
|
Wilkins MJ, Callister SJ, Miletto M, Williams KH, Nicora CD, Lovley DR, Long PE, Lipton MS. Development of a biomarker for Geobacter activity and strain composition; proteogenomic analysis of the citrate synthase protein during bioremediation of U(VI). Microb Biotechnol 2012; 4:55-63. [PMID: 21255372 PMCID: PMC3815795 DOI: 10.1111/j.1751-7915.2010.00194.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Monitoring the activity of target microorganisms during stimulated bioremediation is a key problem for the development of effective remediation strategies. At the US Department of Energy's Integrated Field Research Challenge (IFRC) site in Rifle, CO, the stimulation of Geobacter growth and activity via subsurface acetate addition leads to precipitation of U(VI) from groundwater as U(IV). Citrate synthase (gltA) is a key enzyme in Geobacter central metabolism that controls flux into the TCA cycle. Here, we utilize shotgun proteomic methods to demonstrate that the measurement of gltA peptides can be used to track Geobacter activity and strain evolution during in situ biostimulation. Abundances of conserved gltA peptides tracked Fe(III) reduction and changes in U(VI) concentrations during biostimulation, whereas changing patterns of unique peptide abundances between samples suggested sample-specific strain shifts within the Geobacter population. Abundances of unique peptides indicated potential differences at the strain level between Fe(III)-reducing populations stimulated during in situ biostimulation experiments conducted a year apart at the Rifle IFRC. These results offer a novel technique for the rapid screening of large numbers of proteomic samples for Geobacter species and will aid monitoring of subsurface bioremediation efforts that rely on metal reduction for desired outcomes.
Collapse
Affiliation(s)
- Michael J Wilkins
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99353, USA.
| | | | | | | | | | | | | | | |
Collapse
|
45
|
Cologgi DL, Lampa-Pastirk S, Speers AM, Kelly SD, Reguera G. Extracellular reduction of uranium via Geobacter conductive pili as a protective cellular mechanism. Proc Natl Acad Sci U S A 2011; 108:15248-52. [PMID: 21896750 DOI: 10.1073/pnas.1108616108] [Citation(s) in RCA: 176] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The in situ stimulation of Fe(III) oxide reduction by Geobacter bacteria leads to the concomitant precipitation of hexavalent uranium [U(VI)] from groundwater. Despite its promise for the bioremediation of uranium contaminants, the biological mechanism behind this reaction remains elusive. Because Fe(III) oxide reduction requires the expression of Geobacter's conductive pili, we evaluated their contribution to uranium reduction in Geobacter sulfurreducens grown under pili-inducing or noninducing conditions. A pilin-deficient mutant and a genetically complemented strain with reduced outer membrane c-cytochrome content were used as controls. Pili expression significantly enhanced the rate and extent of uranium immobilization per cell and prevented periplasmic mineralization. As a result, pili expression also preserved the vital respiratory activities of the cell envelope and the cell's viability. Uranium preferentially precipitated along the pili and, to a lesser extent, on outer membrane redox-active foci. In contrast, the pilus-defective strains had different degrees of periplasmic mineralization matching well with their outer membrane c-cytochrome content. X-ray absorption spectroscopy analyses demonstrated the extracellular reduction of U(VI) by the pili to mononuclear tetravalent uranium U(IV) complexed by carbon-containing ligands, consistent with a biological reduction. In contrast, the U(IV) in the pilin-deficient mutant cells also required an additional phosphorous ligand, in agreement with the predominantly periplasmic mineralization of uranium observed in this strain. These findings demonstrate a previously unrecognized role for Geobacter conductive pili in the extracellular reduction of uranium, and highlight its essential function as a catalytic and protective cellular mechanism that is of interest for the bioremediation of uranium-contaminated groundwater.
Collapse
|
46
|
Aklujkar M. Two ATP phosphoribosyltransferase isozymes of Geobacter sulfurreducens contribute to growth in the presence or absence of histidine and under nitrogen fixation conditions. Can J Microbiol 2011; 57:547-58. [PMID: 21774583 DOI: 10.1139/w11-047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Bacteria of the Geobacter clade possess two distinct ATP phosphoribosyltransferases encoded by hisG(L) and hisG(S)+hisZ to catalyze the first reaction of histidine biosynthesis. This very unusual redundancy was investigated by mutational analysis. The hisG(L), hisG(S), and hisZ genes of Geobacter sulfurreducens were deleted, effects on growth and histidine biosynthesis gene expression were evaluated, and deficiencies were complemented with plasmid-borne genes. Both hisG(L) and hisG(S)+hisZ encode functional ATP phosphoribosyltransferases. However, deletion of hisG(L) resulted in no growth defect, whereas deletion of hisG(S) delayed growth when histidine was not provided. Both deletions increased hisZ transcript abundance, and both ΔhisG(S) and ΔhisZ mutations increased hisG(L) transcript abundance. Growth with HisG(L) alone (due to deletion of either hisG(S) or hisZ) was better under nitrogen fixation conditions than when ammonium was provided. Deletion of hisZ caused growth defects under all conditions tested, with or without exogenous sources of histidine, with different patterns of histidine biosynthesis gene expression under each condition. Taken together, the data indicate that G. sulfurreducens depends primarily on the HisG(S)Z isozyme as an ATP phosphoribosyltransferase in histidine biosynthesis, and for other functions when histidine is available; however, HisG(L) also functions as ATP phosphoribosyltransferase, particularly during nitrogen fixation.
Collapse
Affiliation(s)
- Muktak Aklujkar
- Department of Microbiology, University of Massachusetts Amherst, USA.
| |
Collapse
|
47
|
Miletto M, Williams KH, N'Guessan AL, Lovley DR. Molecular analysis of the metabolic rates of discrete subsurface populations of sulfate reducers. Appl Environ Microbiol 2011; 77:6502-9. [PMID: 21764959 DOI: 10.1128/AEM.00576-11] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Elucidating the in situ metabolic activity of phylogenetically diverse populations of sulfate-reducing microorganisms that populate anoxic sedimentary environments is key to understanding subsurface ecology. Previous pure culture studies have demonstrated that the transcript abundance of dissimilatory (bi)sulfite reductase genes is correlated with the sulfate-reducing activity of individual cells. To evaluate whether expression of these genes was diagnostic for subsurface communities, dissimilatory (bi)sulfite reductase gene transcript abundance in phylogenetically distinct sulfate-reducing populations was quantified during a field experiment in which acetate was added to uranium-contaminated groundwater. Analysis of dsrAB sequences prior to the addition of acetate indicated that Desulfobacteraceae, Desulfobulbaceae, and Syntrophaceae-related sulfate reducers were the most abundant. Quantifying dsrB transcripts of the individual populations suggested that Desulfobacteraceae initially had higher dsrB transcripts per cell than Desulfobulbaceae or Syntrophaceae populations and that the activity of Desulfobacteraceae increased further when the metabolism of dissimilatory metal reducers competing for the added acetate declined. In contrast, dsrB transcript abundance in Desulfobulbaceae and Syntrophaceae remained relatively constant, suggesting a lack of stimulation by added acetate. The indication of higher sulfate-reducing activity in the Desulfobacteraceae was consistent with the finding that Desulfobacteraceae became the predominant component of the sulfate-reducing community. Discontinuing acetate additions resulted in a decline in dsrB transcript abundance in the Desulfobacteraceae. These results suggest that monitoring transcripts of dissimilatory (bi)sulfite reductase genes in distinct populations of sulfate reducers can provide insight into the relative rates of metabolism of different components of the sulfate-reducing community and their ability to respond to environmental perturbations.
Collapse
|
48
|
Park I, Kim BC. Homologous overexpression of omcZ, a gene for an outer surface c-type cytochrome of Geobacter sulfurreducens by single-step gene replacement. Biotechnol Lett 2011; 33:2043-8. [DOI: 10.1007/s10529-011-0668-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2011] [Accepted: 06/01/2011] [Indexed: 12/17/2022]
|
49
|
Yun J, Ueki T, Miletto M, Lovley DR. Monitoring the metabolic status of geobacter species in contaminated groundwater by quantifying key metabolic proteins with Geobacter-specific antibodies. Appl Environ Microbiol 2011; 77:4597-602. [PMID: 21551286 DOI: 10.1128/AEM.00114-11] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Simple and inexpensive methods for assessing the metabolic status and bioremediation activities of subsurface microorganisms are required before bioremediation practitioners will adopt molecular diagnosis of the bioremediation community as a routine practice for guiding the development of bioremediation strategies. Quantifying gene transcripts can diagnose important aspects of microbial physiology during bioremediation but is technically challenging and does not account for the impact of translational modifications on protein abundance. An alternative strategy is to directly quantify the abundance of key proteins that might be diagnostic of physiological state. To evaluate this strategy, an antibody-based quantification approach was developed to investigate subsurface Geobacter communities. The abundance of citrate synthase corresponded with rates of metabolism of Geobacter bemidjiensis in chemostat cultures. During in situ bioremediation of uranium-contaminated groundwater the quantity of Geobacter citrate synthase increased with the addition of acetate to the groundwater and decreased when acetate amendments stopped. The abundance of the nitrogen-fixation protein, NifD, increased as ammonium became less available in the groundwater and then declined when ammonium concentrations increased. In a petroleum-contaminated aquifer, the abundance of BamB, an enzyme subunit involved in the anaerobic degradation of mono-aromatic compounds by Geobacter species, increased in zones in which Geobacter were expected to play an important role in aromatic hydrocarbon degradation. These results suggest that antibody-based detection of key metabolic proteins, which should be readily adaptable to standardized kits, may be a feasible method for diagnosing the metabolic state of microbial communities responsible for bioremediation, aiding in the rational design of bioremediation strategies.
Collapse
|
50
|
Tremblay PL, Summers ZM, Glaven RH, Nevin KP, Zengler K, Barrett CL, Qiu Y, Palsson BO, Lovley DR. A c-type cytochrome and a transcriptional regulator responsible for enhanced extracellular electron transfer in Geobacter sulfurreducens revealed by adaptive evolution. Environ Microbiol 2011; 13:13-23. [PMID: 20636372 DOI: 10.1111/j.1462-2920.2010.02302.x] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The stimulation of subsurface microbial metabolism often associated with engineered bioremediation of groundwater contaminants presents subsurface microorganisms, which are adapted for slow growth and metabolism in the subsurface, with new selective pressures. In order to better understand how Geobacter species might adapt to selective pressure for faster metal reduction in the subsurface, Geobacter sulfurreducens was put under selective pressure for rapid Fe(III) oxide reduction. The genomes of two resultant strains with rates of Fe(III) oxide reduction that were 10-fold higher than those of the parent strain were resequenced. Both strains contain either a single base-pair change or a 1 nucleotide insertion in a GEMM riboswitch upstream of GSU1761, a gene coding for the periplasmic c-type cytochrome designated PgcA. GSU1771, a gene coding for a SARP regulator, was also mutated in both strains. Introduction of either of the GEMM riboswitch mutations upstream of pgcA in the wild-type increased the abundance of pgcA transcripts, consistent with increased expression of pgcA in the adapted strains. One of the mutations doubled the rate of Fe(III) oxide reduction. Interruption of GSU1771 doubled the Fe(III) oxide reduction rate. This was associated with an increased in expression of pilA, the gene encoding the structural protein for the pili thought to function as microbial nanowires. The combination of the GSU1771 interruption with either of the pgcA mutations resulted in a strain that reduced Fe(III) as fast as the comparable adapted strain. These results suggest that the accumulation of a small number of beneficial mutations under selective pressure, similar to that potentially present during bioremediation, can greatly enhance the capacity for Fe(III) oxide reduction in G. sulfurreducens. Furthermore, the results emphasize the importance of the c-type cytochrome PgcA and pili in Fe(III) oxide reduction and demonstrate how adaptive evolution studies can aid in the elucidation of complex mechanisms, such as extracellular electron transfer.
Collapse
Affiliation(s)
- Pier-Luc Tremblay
- Department of Microbiology, University of Massachusetts, Amherst, MA, USACenter for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC, USADepartment of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Zarath M Summers
- Department of Microbiology, University of Massachusetts, Amherst, MA, USACenter for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC, USADepartment of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Richard H Glaven
- Department of Microbiology, University of Massachusetts, Amherst, MA, USACenter for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC, USADepartment of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Kelly P Nevin
- Department of Microbiology, University of Massachusetts, Amherst, MA, USACenter for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC, USADepartment of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Karsten Zengler
- Department of Microbiology, University of Massachusetts, Amherst, MA, USACenter for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC, USADepartment of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Christian L Barrett
- Department of Microbiology, University of Massachusetts, Amherst, MA, USACenter for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC, USADepartment of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Yu Qiu
- Department of Microbiology, University of Massachusetts, Amherst, MA, USACenter for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC, USADepartment of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Bernhard O Palsson
- Department of Microbiology, University of Massachusetts, Amherst, MA, USACenter for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC, USADepartment of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Derek R Lovley
- Department of Microbiology, University of Massachusetts, Amherst, MA, USACenter for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC, USADepartment of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| |
Collapse
|