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DeCola AC, Toppen LC, Brown KP, Dadkhah A, Rizzo DM, Ziels RM, Scarborough MJ. Microbiome assembly and stability during start-up of a full-scale, two-phase anaerobic digester fed cow manure and mixed organic feedstocks. BIORESOURCE TECHNOLOGY 2024; 394:130247. [PMID: 38158092 DOI: 10.1016/j.biortech.2023.130247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 12/20/2023] [Accepted: 12/20/2023] [Indexed: 01/03/2024]
Abstract
Carbon transformations during anaerobic digestion are mediated by complex microbiomes, but their assembly is poorly understood, especially in full-scale digesters. Gene-centric metagenomics combining functional and taxonomic classification was performed for an on-farm digester during start-up. Cow manure and organic waste pre-treated in a hydrolysis tank were fed to the methane-producing digester and the volatile solids loading rate was slowly increased from 0 to 3.5 kg volatile solids m-3 d-1 over one year. The microbial community in the anaerobic digester exhibited a high ratio of archaea, which were dominated by hydrogenotrophic methanogens. Bacteria in the anaerobic digester had a high abundance of genes for ferredoxin cycling, H2 generation, and more metabolically complex fermentations than in the hydrolysis tank. In total, the results show that a functionally stable microbiome was achieved quickly during start-up and that the microbiome created in the low-pH hydrolysis tank did not persist in the downstream anaerobic digester.
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Affiliation(s)
- Amy C DeCola
- Department of Civil and Environmental Engineering, University of Vermont, Burlington, VT, United States
| | - Lucinda C Toppen
- Department of Civil and Environmental Engineering, University of Vermont, Burlington, VT, United States
| | - Kennedy P Brown
- Department of Civil and Environmental Engineering, University of Vermont, Burlington, VT, United States
| | - Ali Dadkhah
- Department of Civil and Environmental Engineering, University of Vermont, Burlington, VT, United States
| | - Donna M Rizzo
- Department of Civil and Environmental Engineering, University of Vermont, Burlington, VT, United States; Gund Institute for Environment, University of Vermont, Burlington, VT, United States
| | - Ryan M Ziels
- Department of Civil Engineering, University of British Columbia, Vancouver, Canada
| | - Matthew J Scarborough
- Department of Civil and Environmental Engineering, University of Vermont, Burlington, VT, United States; Gund Institute for Environment, University of Vermont, Burlington, VT, United States.
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2
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Deng Z, Chen H, Wang J, Zhang N, Han Z, Xie Y, Zhang X, Fang X, Yu H, Zhang D, Yue Z, Zhang C. Marine Dehalogenator and Its Chaperones: Microbial Duties and Responses in 2,4,6-Trichlorophenol Dechlorination. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023. [PMID: 37478352 DOI: 10.1021/acs.est.3c03738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/23/2023]
Abstract
Marine environments contain diverse halogenated organic compounds (HOCs), both anthropogenic and natural, nourishing a group of versatile organohalide-respiring bacteria (OHRB). Here, we identified a novel OHRB (Peptococcaceae DCH) with conserved motifs but phylogenetically diverse reductive dehalogenase catalytic subunit (RdhAs) from marine enrichment culture. Further analyses clearly demonstrate the horizontal gene transfer of rdhAs among marine OHRB. Moreover, 2,4,6-trichlorophenol (TCP) was dechlorinated to 2,4-dichlorophenol and terminated at 4-chlorophenol in culture. Dendrosporobacter and Methanosarcina were the two dominant genera, and the constructed and verified metabolic pathways clearly demonstrated that the former provided various substrates for other microbes, while the latter drew nutrients, but might provide little benefit to microbial dehalogenation. Furthermore, Dendrosporobacter could readily adapt to TCP, and sporulation-related proteins of Dendrosporobacter were significantly upregulated in TCP-free controls, whereas other microbes (e.g., Methanosarcina and Aminivibrio) became more active, providing insights into how HOCs shape microbial communities. Additionally, sulfate could affect the dechlorination of Peptococcaceae DCH, but not debromination. Considering their electron accessibility and energy generation, the results clearly demonstrate that bromophenols are more suitable than chlorophenols for the enrichment of OHRB in marine environments. This study will greatly enhance our understanding of marine OHRB (rdhAs), auxiliary microbes, and microbial HOC adaptive mechanisms.
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Affiliation(s)
- Zhaochao Deng
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan 316021, Zhejiang, China
| | - Haixin Chen
- BGI-Sanya, BGI-Shenzhen, Sanya 572025, China
| | - Jun Wang
- BGI-Sanya, BGI-Shenzhen, Sanya 572025, China
| | - Ning Zhang
- Department of Environmental Engineering, School of Chemical Engineering and Pharmacy, Henan University of Science and Technology, Luoyang 471000, Henan, China
| | - Zhiqiang Han
- Department of Marine Resources and Environment, Fishery College, Zhejiang Ocean University, Zhoushan 316002, Zhejiang, China
| | - Yeting Xie
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin 541006, Guangxi, China
| | - Xiaoyan Zhang
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin 541006, Guangxi, China
| | | | - Hao Yu
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan 316021, Zhejiang, China
| | - Dongdong Zhang
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan 316021, Zhejiang, China
| | - Zhen Yue
- BGI-Sanya, BGI-Shenzhen, Sanya 572025, China
| | - Chunfang Zhang
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan 316021, Zhejiang, China
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin 541006, Guangxi, China
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3
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Ferreira D, Venceslau SS, Bernardino R, Preto A, Zhang L, Waldbauer JR, Leavitt WD, Pereira IAC. DsrC is involved in fermentative growth and interacts directly with the FlxABCD-HdrABC complex in Desulfovibrio vulgaris Hildenborough. Environ Microbiol 2023; 25:962-976. [PMID: 36602077 DOI: 10.1111/1462-2920.16335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 12/28/2022] [Indexed: 01/06/2023]
Abstract
DsrC is a key protein in dissimilatory sulfur metabolism, where it works as co-substrate of the dissimilatory sulfite reductase DsrAB. DsrC has two conserved cysteines in a C-terminal arm that are converted to a trisulfide upon reduction of sulfite. In sulfate-reducing bacteria, DsrC is essential and previous works suggested additional functions beyond sulfite reduction. Here, we studied whether DsrC also plays a role during fermentative growth of Desulfovibrio vulgaris Hildenborough, by studying two strains where the functionality of DsrC is impaired by a lower level of expression (IPFG07) and additionally by the absence of one conserved Cys (IPFG09). Growth studies coupled with metabolite and proteomic analyses reveal that fermentation leads to lower levels of DsrC, but impairment of its function results in reduced growth by fermentation and a shift towards more fermentative metabolism during sulfate respiration. In both respiratory and fermentative conditions, there is increased abundance of the FlxABCD-HdrABC complex and Adh alcohol dehydrogenase in IPFG09 versus the wild type, which is reflected in higher production of ethanol. Pull-down experiments confirmed a direct interaction between DsrC and the FlxABCD-HdrABC complex, through the HdrB subunit. Dissimilatory sulfur metabolism, where sulfur compounds are used for energy generation, is a key process in the ecology of anoxic environments, and is more widespread among bacteria than previously believed. Two central proteins for this type of metabolism are DsrAB dissimilatory sulfite reductase and its co-substrate DsrC. Using physiological, proteomic and biochemical studies of Desulfovibrio vulgaris Hildenborough and mutants affected in DsrC functionality, we show that DsrC is also relevant for fermentative growth of this model organism and that it interacts directly with the soluble FlxABCD-HdrABC complex that links the NAD(H) pool with dissimilatory sulfite reduction.
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Affiliation(s)
- Delfim Ferreira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Sofia S Venceslau
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Raquel Bernardino
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - André Preto
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Lichun Zhang
- Department of the Geophysical Sciences, University of Chicago, Chicago, Illinois, USA
| | - Jacob R Waldbauer
- Department of the Geophysical Sciences, University of Chicago, Chicago, Illinois, USA
| | - William D Leavitt
- Department of Earth Sciences, Dartmouth College, Hanover, New Hampshire, USA
- Department of Chemistry, Dartmouth College, Hanover, New Hampshire, USA
| | - Inês A C Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
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Qu YN, Rao YZ, Qi YL, Li YX, Li A, Palmer M, Hedlund BP, Shu WS, Evans PN, Nie GX, Hua ZS, Li WJ. Panguiarchaeum symbiosum, a potential hyperthermophilic symbiont in the TACK superphylum. Cell Rep 2023; 42:112158. [PMID: 36827180 DOI: 10.1016/j.celrep.2023.112158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 12/27/2022] [Accepted: 02/09/2023] [Indexed: 02/24/2023] Open
Abstract
The biology of Korarchaeia remains elusive due to the lack of genome representatives. Here, we reconstruct 10 closely related metagenome-assembled genomes from hot spring habitats and place them into a single species, proposed herein as Panguiarchaeum symbiosum. Functional investigation suggests that Panguiarchaeum symbiosum is strictly anaerobic and grows exclusively in thermal habitats by fermenting peptides coupled with sulfide and hydrogen production to dispose of electrons. Due to its inability to biosynthesize archaeal membranes, amino acids, and purines, this species likely exists in a symbiotic lifestyle similar to DPANN archaea. Population metagenomics and metatranscriptomic analyses demonstrated that genes associated with amino acid/peptide uptake and cell attachment exhibited positive selection and were highly expressed, supporting the proposed proteolytic catabolism and symbiotic lifestyle. Our study sheds light on the metabolism, evolution, and potential symbiotic lifestyle of Panguiarchaeum symbiosum, which may be a unique host-dependent archaeon within the TACK superphylum.
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Affiliation(s)
- Yan-Ni Qu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Yang-Zhi Rao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Yan-Ling Qi
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Yu-Xian Li
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Andrew Li
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Marike Palmer
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154, USA; Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Wen-Sheng Shu
- School of Life Sciences, South China Normal University, Guangzhou 510631, PR China
| | - Paul N Evans
- The Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD 4072, Australia
| | - Guo-Xing Nie
- College of Fisheries, Henan Normal University, Xinxiang, China
| | - Zheng-Shuang Hua
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China.
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China; State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, PR China.
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5
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Ugwuanyi IR, Fogel ML, Bowden R, Steele A, De Natale G, Troise C, Somma R, Piochi M, Mormone A, Glamoclija M. Comparative metagenomics at Solfatara and Pisciarelli hydrothermal systems in Italy reveal that ecological differences across substrates are not ubiquitous. Front Microbiol 2023; 14:1066406. [PMID: 36819055 PMCID: PMC9930910 DOI: 10.3389/fmicb.2023.1066406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 01/06/2023] [Indexed: 02/04/2023] Open
Abstract
Introduction Continental hydrothermal systems (CHSs) are geochemically complex, and they support microbial communities that vary across substrates. However, our understanding of these variations across the complete range of substrates in CHS is limited because many previous studies have focused predominantly on aqueous settings. Methods Here we used metagenomes in the context of their environmental geochemistry to investigate the ecology of different substrates (i.e., water, mud and fumarolic deposits) from Solfatara and Pisciarelli. Results and Discussion Results indicate that both locations are lithologically similar with distinct fluid geochemistry. In particular, all substrates from Solfatara have similar chemistry whereas Pisciarelli substrates have varying chemistry; with water and mud from bubbling pools exhibiting high SO4 2- and NH4 + concentrations. Species alpha diversity was found to be different between locations but not across substrates, and pH was shown to be the most important driver of both diversity and microbial community composition. Based on cluster analysis, microbial community structure differed significantly between Pisciarelli substrates but not between Solfatara substrates. Pisciarelli mud pools, were dominated by (hyper)thermophilic archaea, and on average, bacteria dominated Pisciarelli fumarolic deposits and all investigated Solfatara environments. Carbon fixation and sulfur oxidation were the most important metabolic pathways fueled by volcanic outgassing at both locations. Together, results demonstrate that ecological differences across substrates are not a widespread phenomenon but specific to the system. Therefore, this study demonstrates the importance of analyzing different substrates of a CHS to understand the full range of microbial ecology to avoid biased ecological assessments.
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Affiliation(s)
- Ifeoma R. Ugwuanyi
- Department of Earth and Environmental Sciences, Rutgers University, Newark, NJ, United States,Ifeoma R. Ugwuanyi, ✉
| | - Marilyn L. Fogel
- EDGE Institute, University of California, Riverside, Riverside, CA, United States
| | - Roxane Bowden
- Earth and Planets Laboratory, Carnegie Institution for Science, Washington, DC, United States
| | - Andrew Steele
- Earth and Planets Laboratory, Carnegie Institution for Science, Washington, DC, United States
| | - Giuseppe De Natale
- Istituto Nazionale di Geofisica e Vulcanologia, Osservatorio Vesuviano, Naples, Italy,Consiglio Nazionale delle Ricerche INO, Naples, Italy
| | - Claudia Troise
- Istituto Nazionale di Geofisica e Vulcanologia, Osservatorio Vesuviano, Naples, Italy,Consiglio Nazionale delle Ricerche INO, Naples, Italy
| | - Renato Somma
- Istituto Nazionale di Geofisica e Vulcanologia, Osservatorio Vesuviano, Naples, Italy,Consiglio Nazionale delle Ricerche IRISS, Naples, Italy
| | - Monica Piochi
- Istituto Nazionale di Geofisica e Vulcanologia, Osservatorio Vesuviano, Naples, Italy
| | - Angela Mormone
- Istituto Nazionale di Geofisica e Vulcanologia, Osservatorio Vesuviano, Naples, Italy
| | - Mihaela Glamoclija
- Department of Earth and Environmental Sciences, Rutgers University, Newark, NJ, United States,*Correspondence: Mihaela Glamoclija, ✉
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6
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Pelmenschikov V, Ferreira D, Venceslau SS, Hildebrandt P, Pereira IAC, Todorovic S. Substrate-Dependent Conformational Switch of the Noncubane [4Fe-4S] Cluster in Heterodisulfide Reductase HdrB. J Am Chem Soc 2023; 145:7-11. [PMID: 36542731 DOI: 10.1021/jacs.2c10885] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The noncubane [4Fe-4S] cluster identified in the active site of heterodisulfide reductase (HdrB) displays a unique geometry among Fe-S cofactors found in metalloproteins. Here we employ resonance Raman (RR) spectroscopy and density functional theory (DFT) calculations to probe structural, electronic, and vibrational properties of the noncubane cluster in HdrB from a non-methanogenic Desulfovibrio vulgaris (Dv) Hildenborough organism. The immediate protein environment of the two neighboring clusters in DvHdrB is predicted using homology modeling. We demonstrate that in the absence of substrate, the oxidized [4Fe-4S]3+ cluster adopts a "closed" conformation. Upon substrate coordination at the "special" iron center, the cluster core translates to an "open" structure, facilitated by the "supernumerary" cysteine ligand switch from iron-bridging to iron-terminal mode. The observed RR fingerprint of the noncubane cluster, supported by Fe-S vibrational mode analysis, will advance future studies of enzymes containing this unusual cofactor.
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Affiliation(s)
| | - Delfim Ferreira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, 2780-157 Oeiras, Portugal
| | - Sofia S Venceslau
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, 2780-157 Oeiras, Portugal
| | - Peter Hildebrandt
- Institut für Chemie, Technische Universität Berlin, 10623 Berlin, Germany
| | - Inês A C Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, 2780-157 Oeiras, Portugal
| | - Smilja Todorovic
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, 2780-157 Oeiras, Portugal
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7
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Ramírez GA, Keshri J, Vahrson I, Garber AI, Berrang ME, Cox NA, González-Cerón F, Aggrey SE, Oakley BB. Cecal Microbial Hydrogen Cycling Potential Is Linked to Feed Efficiency Phenotypes in Chickens. Front Vet Sci 2022; 9:904698. [PMID: 35799838 PMCID: PMC9255636 DOI: 10.3389/fvets.2022.904698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 05/19/2022] [Indexed: 11/24/2022] Open
Abstract
In chickens, early life exposure to environmental microbes has long-lasting impacts on gastrointestinal (GI) microbiome development and host health and growth, via mechanisms that remain uncharacterized. In this study, we demonstrated that administrating a fecal microbiome transplant (FMT) from adults to day-of-hatch chicks results in significantly higher body mass of birds and decreased residual feed intake (RFI), implying enhanced feed efficiency, at 6 weeks of age. To assess the potential mechanisms through which FMT affects adult bird phenotype, we combined 16 S rRNA gene amplification, metagenomic, and comparative genomic approaches to survey the composition and predicted activities of the resident microbiome of various GI tract segments. Early life FMT exposure had a long-lasting significant effect on the microbial community composition and function of the ceca but not on other GI segments. Within the ceca of 6-week-old FMT birds, hydrogenotrophic microbial lineages and genes were most differentially enriched. The results suggest that thermodynamic regulation in the cecum, in this case via hydrogenotrophic methanogenic and sulfur-cycling lineages, potentially serving as hydrogen sinks, may enhance fermentative efficiency and dietary energy harvest capacity. Our study provides a specific mechanism of action through which early-life microbiome transplants modulate market-relevant phenotypes in poultry and, thereby, may represent a significant advance toward microbiome-focused sustainable agriculture.
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Affiliation(s)
- Gustavo Antonio Ramírez
- College of Veterinary Medicine, Western University of Health Sciences, Pomona, CA, United States
- Leon H. Charney School of Marine Sciences, Haifa University, Haifa, Israel
| | - Jitendra Keshri
- College of Veterinary Medicine, Western University of Health Sciences, Pomona, CA, United States
| | - Isabella Vahrson
- College of Veterinary Medicine, Western University of Health Sciences, Pomona, CA, United States
| | - Arkadiy I. Garber
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Mark E. Berrang
- Poultry Microbiological Safety and Processing Research Unit, USDA Agricultural Research Service, Athens, GA, United States
| | - Nelson A. Cox
- Poultry Microbiological Safety and Processing Research Unit, USDA Agricultural Research Service, Athens, GA, United States
| | - Fernando González-Cerón
- Departamento de Zootecnia, Chapingo Autonomous University, Estado de Mexico, Mexico
- NutriGenomics Laboratory, Department of Poultry Science, University of Georgia, Athens, GA, United States
| | - Samuel E. Aggrey
- NutriGenomics Laboratory, Department of Poultry Science, University of Georgia, Athens, GA, United States
| | - Brian B. Oakley
- College of Veterinary Medicine, Western University of Health Sciences, Pomona, CA, United States
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8
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Phylogenomic Analysis of Metagenome-Assembled Genomes Deciphered Novel Acetogenic Nitrogen-Fixing Bathyarchaeota from Hot Spring Sediments. Microbiol Spectr 2022; 10:e0035222. [PMID: 35647693 PMCID: PMC9241837 DOI: 10.1128/spectrum.00352-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This study describes the phylogenomic analysis and metabolic insights of metagenome-assembled genomes (MAGs) retrieved from hot spring sediment samples. The metagenome-assembled sequences recovered three near-complete genomes belonging to the archaeal phylum. Analysis of genome-wide core genes and 16S rRNA-based phylogeny placed the ILS200 and ILS300 genomes within the uncultivated and largely understudied bathyarchaeal phylum, whereas ILS100 represented the phylum Thaumarchaeota. The average nucleotide identity (ANI) of the bin ILS100 was 76% with Nitrososphaeria_archaeon_isolate_SpSt-1069. However, the bins ILS200 and ILS300 showed ANI values of 75% and 70% with Candidatus_Bathyarchaeota_archaeon_isolate_DRTY-6_2_bin_115 and Candidatus_Bathyarchaeota_archaeon_BA1_ba1_01, respectively. The genomic potential of Bathyarchaeota bins ILS200 and ILS300 showed genes necessary for the Wood-Ljungdahl pathway, and the gene encoding the methyl coenzyme M reductase (mcr) complex essential for methanogenesis was absent. The metabolic potential of the assembled genomes included genes involved in nitrogen assimilation, including nitrogenase and the genes necessary for the urea cycle. The presence of these genes suggested the metabolic potential of Bathyarchaeota to fix nitrogen under extreme environments. In addition, the ILS200 and ILS300 genomes carried genes involved in the tricarboxylic acid (TCA) cycle, glycolysis, and degradation of organic carbons. Finally, we conclude that the reconstructed Bathyarchaeota bins are autotrophic acetogens and organo-heterotrophs. IMPORTANCE We describe the Bathyarchaeota bins that are likely to be acetogens with a wide range of metabolic potential. These bins did not exhibit methanogenic machinery, suggesting methane production may not occur by all subgroup lineages of Bathyarchaeota. Phylogenetic analysis support that both ILS200 and ILS300 belonged to the Bathyarchaeota. The discovery of new bathyarchaeotal MAGs provides additional knowledge for understanding global carbon and nitrogen metabolism under extreme conditions.
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9
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Wells M, Basu P, Stolz JF. The physiology and evolution of microbial selenium metabolism. Metallomics 2021; 13:6261189. [PMID: 33930157 DOI: 10.1093/mtomcs/mfab024] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 04/21/2021] [Accepted: 04/22/2021] [Indexed: 12/27/2022]
Abstract
Selenium is an essential trace element whose compounds are widely metabolized by organisms from all three domains of life. Moreover, phylogenetic evidence indicates that selenium species, along with iron, molybdenum, tungsten, and nickel, were metabolized by the last universal common ancestor of all cellular lineages, primarily for the synthesis of the 21st amino acid selenocysteine. Thus, selenium metabolism is both environmentally ubiquitous and a physiological adaptation of primordial life. Selenium metabolic reactions comprise reductive transformations both for assimilation into macromolecules and dissimilatory reduction of selenium oxyanions and elemental selenium during anaerobic respiration. This review offers a comprehensive overview of the physiology and evolution of both assimilatory and dissimilatory selenium metabolism in bacteria and archaea, highlighting mechanisms of selenium respiration. This includes a thorough discussion of our current knowledge of the physiology of selenocysteine synthesis and incorporation into proteins in bacteria obtained from structural biology. Additionally, this is the first comprehensive discussion in a review of the incorporation of selenium into the tRNA nucleoside 5-methylaminomethyl-2-selenouridine and as an inorganic cofactor in certain molybdenum hydroxylase enzymes. Throughout, conserved mechanisms and derived features of selenium metabolism in both domains are emphasized and discussed within the context of the global selenium biogeochemical cycle.
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Affiliation(s)
- Michael Wells
- Department of Biological Sciences, Duquesne University, Pittsburgh, PA 15282, USA
| | - Partha Basu
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, USA
| | - John F Stolz
- Department of Biological Sciences, Duquesne University, Pittsburgh, PA 15282, USA
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10
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Zinke LA, Evans PN, Santos-Medellín C, Schroeder AL, Parks DH, Varner RK, Rich VI, Tyson GW, Emerson JB. Evidence for non-methanogenic metabolisms in globally distributed archaeal clades basal to the Methanomassiliicoccales. Environ Microbiol 2020; 23:340-357. [PMID: 33185945 DOI: 10.1111/1462-2920.15316] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 11/05/2020] [Accepted: 11/09/2020] [Indexed: 12/21/2022]
Abstract
Recent discoveries of mcr and mcr-like genes in genomes from diverse archaeal lineages suggest that methane metabolism is an ancient pathway with a complicated evolutionary history. One conventional view is that methanogenesis is an ancestral metabolism of the class Thermoplasmata. Through comparative genomic analysis of 12 Thermoplasmata metagenome-assembled genomes (MAGs) basal to the Methanomassiliicoccales, we show that these microorganisms do not encode the genes required for methanogenesis. Further analysis of 770 Ca. Thermoplasmatota genomes/MAGs found no evidence of mcrA homologues outside of the Methanomassiliicoccales. Together, these results suggest that methanogenesis was laterally acquired by an ancestor of the Methanomassiliicoccales. The 12 analysed MAGs include representatives from four orders basal to the Methanomassiliicoccales, including a high-quality MAG that likely represents a new order, Ca. Lunaplasma lacustris ord. nov. sp. nov. These MAGs are predicted to use diverse energy conservation pathways, including heterotrophy, sulfur and hydrogen metabolism, denitrification, and fermentation. Two lineages are widespread among anoxic, sedimentary environments, whereas Ca. Lunaplasma lacustris has thus far only been detected in alpine caves and subarctic lake sediments. These findings advance our understanding of the metabolic potential, ecology, and global distribution of the Thermoplasmata and provide insight into the evolutionary history of methanogenesis within the Ca. Thermoplasmatota.
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Affiliation(s)
- Laura A Zinke
- Department of Plant Pathology, University of California, Davis, CA, USA
| | - Paul N Evans
- The Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Qld, 4072, Australia
| | | | - Alena L Schroeder
- Department of Plant Pathology, University of California, Davis, CA, USA
| | - Donovan H Parks
- The Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Qld, 4072, Australia
| | - Ruth K Varner
- Earth Systems Research Center, Institute for the Study of Earth, Oceans and Space, University of New Hampshire, Durham, NH, USA.,Department of Earth Sciences, University of New Hampshire, Durham, NH, USA
| | - Virginia I Rich
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | - Gene W Tyson
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Brisbane, Qld, 4102, Australia
| | - Joanne B Emerson
- Department of Plant Pathology, University of California, Davis, CA, USA
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11
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Liu YF, Chen J, Liu ZL, Shou LB, Lin DD, Zhou L, Yang SZ, Liu JF, Li W, Gu JD, Mu BZ. Anaerobic Degradation of Paraffins by Thermophilic Actinobacteria under Methanogenic Conditions. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:10610-10620. [PMID: 32786606 DOI: 10.1021/acs.est.0c02071] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Microbial anaerobic alkane degradation is a key process in subsurface oil reservoirs and anoxic environments contaminated with petroleum, with a major impact on global carbon cycling. However, the thermophiles capable of water-insoluble paraffins (>C17) degradation under methanogenic conditions has remained understudied. Here, we established thermophilic (55 °C) n-paraffins-degrading (C21-C30) cultures from an oil reservoir. After over 900 days of incubation, the even-numbered n-paraffins were biodegraded to methane. The bacterial communities are dominated by a novel class-level lineage of actinobacteria, 'Candidatus Syntraliphaticia'. These 'Ca. Syntraliphaticia'-like metagenome-assembled genomes (MAGs) encode a complete alkylsuccinate synthases (ASS) gene operon, as well as hydrogenases and formate dehydrogenase, and several enzymes potentially involved in alkyl-CoA oxidation and the Wood-Ljungdahl pathway. Metatranscriptomic analysis suggests that n-paraffins are activated via fumarate addition reaction, and oxidized into carbon dioxide, hydrogen/formate and acetate by 'Ca. Syntraliphaticia', that could be further converted to methane by the abundant hydrogenotrophic and acetoclastic methanogens. We also found a divergent methyl-CoM reductase-like complex (MCR) and a canonical MCR in two MAGs representing 'Ca. Methanosuratus' (within candidate phylum Verstraetearchaeota), indicating the capability of methane and short-chain alkane metabolism in the oil reservoir. Ultimately, this result offers new insights into the degradability and the mechanisms of n-paraffins under methanogenic conditions at high temperatures.
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Affiliation(s)
- Yi-Fan Liu
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P.R. China
- Engineering Research Center of MEOR, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P. R. China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, P.R. China
| | - Jing Chen
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P.R. China
- Engineering Research Center of MEOR, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P. R. China
| | - Zhong-Lin Liu
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P.R. China
- Engineering Research Center of MEOR, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P. R. China
| | - Li-Bin Shou
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P.R. China
- Engineering Research Center of MEOR, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P. R. China
| | - Dan-Dan Lin
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P.R. China
- Engineering Research Center of MEOR, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P. R. China
| | - Lei Zhou
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P.R. China
- Engineering Research Center of MEOR, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P. R. China
| | - Shi-Zhong Yang
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P.R. China
- Engineering Research Center of MEOR, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P. R. China
| | - Jin-Feng Liu
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P.R. China
- Engineering Research Center of MEOR, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P. R. China
| | - Wei Li
- National Engineering Laboratory for Industrial Wastewater Treatment, School of Resources and Environmental Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P. R. China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, P.R. China
| | - Ji-Dong Gu
- Environmental Engineering, Guangdong Technion Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong 515063, P.R. China
| | - Bo-Zhong Mu
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P.R. China
- Engineering Research Center of MEOR, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P. R. China
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12
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Ernst C, Kayastha K, Koch T, Venceslau SS, Pereira IAC, Demmer U, Ermler U, Dahl C. Structural and spectroscopic characterization of a HdrA-like subunit from Hyphomicrobium denitrificans. FEBS J 2020; 288:1664-1678. [PMID: 32750208 DOI: 10.1111/febs.15505] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 07/03/2020] [Accepted: 07/31/2020] [Indexed: 02/01/2023]
Abstract
Many bacteria and archaea employ a novel pathway of sulfur oxidation involving an enzyme complex that is related to the heterodisulfide reductase (Hdr or HdrABC) of methanogens. As a first step in the biochemical characterization of Hdr-like proteins from sulfur oxidizers (sHdr), we structurally analyzed the recombinant sHdrA protein from the Alphaproteobacterium Hyphomicrobium denitrificans at 1.4 Å resolution. The sHdrA core structure is similar to that of methanogenic HdrA (mHdrA) which binds the electron-bifurcating flavin adenine dinucleotide (FAD), the heart of the HdrABC-[NiFe]-hydrogenase catalyzed reaction. Each sHdrA homodimer carries two FADs and two [4Fe-4S] clusters being linked by electron conductivity. Redox titrations monitored by electron paramagnetic resonance and visible spectroscopy revealed a redox potential between -203 and -188 mV for the [4Fe-4S] center. The potentials for the FADH•/FADH- and FAD/FADH• pairs reside between -174 and -156 mV and between -81 and -19 mV, respectively. The resulting stable semiquinone FADH• species already detectable in the visible and electron paramagnetic resonance spectra of the as-isolated state of sHdrA is incompatible with basic principles of flavin-based electron bifurcation such that the sHdr complex does not apply this new mode of energy coupling. The inverted one-electron FAD redox potentials of sHdr and mHdr are clearly reflected in the different FAD-polypeptide interactions. According to this finding and the assumption that the sHdr complex forms an asymmetric HdrAA'B1C1B2C2 hexamer, we tentatively propose a mechanism that links protein-bound sulfane oxidation to sulfite on HdrB1 with NAD+ reduction via lipoamide disulfide reduction on HdrB2. The FAD of HdrA thereby serves as an electron storage unit. DATABASE: Structural data are available in PDB database under the accession number 6TJR.
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Affiliation(s)
- Corvin Ernst
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | | | - Tobias Koch
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Sofia S Venceslau
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Inês A C Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Ulrike Demmer
- Max-Planck-Institut für Biophysik, Frankfurt, Germany
| | - Ulrich Ermler
- Max-Planck-Institut für Biophysik, Frankfurt, Germany
| | - Christiane Dahl
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
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13
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Dillon ML, Hawes I, Jungblut AD, Mackey TJ, Eisen JA, Doran PT, Sumner DY. Environmental control on the distribution of metabolic strategies of benthic microbial mats in Lake Fryxell, Antarctica. PLoS One 2020; 15:e0231053. [PMID: 32282803 PMCID: PMC7153904 DOI: 10.1371/journal.pone.0231053] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 03/15/2020] [Indexed: 11/19/2022] Open
Abstract
Ecological theories posit that heterogeneity in environmental conditions greatly affects community structure and function. However, the degree to which ecological theory developed using plant- and animal-dominated systems applies to microbiomes is unclear. Investigating the metabolic strategies found in microbiomes are particularly informative for testing the universality of ecological theories because microorganisms have far wider metabolic capacity than plants and animals. We used metagenomic analyses to explore the relationships between the energy and physicochemical gradients in Lake Fryxell and the metabolic capacity of its benthic microbiome. Statistical analysis of the relative abundance of metabolic marker genes and gene family diversity shows that oxygenic photosynthesis, carbon fixation, and flavin-based electron bifurcation differentiate mats growing in different environmental conditions. The pattern of gene family diversity points to the likely importance of temporal environmental heterogeneity in addition to resource gradients. Overall, we found that the environmental heterogeneity of photosynthetically active radiation (PAR) and oxygen concentration ([O2]) in Lake Fryxell provide the framework by which metabolic diversity and composition of the community is structured, in accordance with its phylogenetic structure. The organization of the resulting microbial ecosystems are consistent with the maximum power principle and the species sorting model.
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Affiliation(s)
- Megan L. Dillon
- Ecology Department, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America
- Department of Earth and Planetary Sciences, University of California, Davis, Davis, California, United States of America
| | - Ian Hawes
- Coastal Marine Field Station, University of Waikato, Hamilton, Waikato, New Zealand
| | - Anne D. Jungblut
- Life Sciences Department, Natural History Museum, London, England, United Kingdom
| | - Tyler J. Mackey
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Jonathan A. Eisen
- Department of Evolution and Ecology, University of California, Davis, Davis, California, United States of America
| | - Peter T. Doran
- Geology and Geophysics Department, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Dawn Y. Sumner
- Department of Earth and Planetary Sciences, University of California, Davis, Davis, California, United States of America
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14
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Abstract
Current understanding of the diversity, biology, and ecology of Archaea is very limited, especially considering how few of the known phyla have been cultured or genomically explored. The reconstruction of “Ca. Methanomixophus” MAGs not only expands the known range of metabolic versatility of the members of Archaeoglobi but also suggests that the phylogenetic distribution of MCR and MTR complexes is even wider than previously anticipated. Euryarchaeal lineages have been believed to have a methanogenic last common ancestor. However, members of euryarchaeal Archaeoglobi have long been considered nonmethanogenic and their evolutionary history remains elusive. Here, three high-quality metagenomic-assembled genomes (MAGs) retrieved from high-temperature oil reservoir and hot springs, together with three newly assembled Archaeoglobi MAGs from previously reported hot spring metagenomes, are demonstrated to represent a novel genus of Archaeoglobaceae, “Candidatus Methanomixophus.” All “Ca. Methanomixophus” MAGs encode an M methyltransferase (MTR) complex and a traditional type of methyl-coenzyme M reductase (MCR) complex, which is different from the divergent MCR complexes found in “Ca. Polytropus marinifundus.” In addition, “Ca. Methanomixophus dualitatem” MAGs preserve the genomic capacity for dissimilatory sulfate reduction. Comparative phylogenetic analysis supports a laterally transferred origin for an MCR complex and vertical heritage of the MTR complex in this lineage. Metatranscriptomic analysis revealed concomitant in situ activity of hydrogen-dependent methylotrophic methanogenesis and heterotrophic fermentation within populations of “Ca. Methanomixophus hydrogenotrophicum” in a high-temperature oil reservoir. IMPORTANCE Current understanding of the diversity, biology, and ecology of Archaea is very limited, especially considering how few of the known phyla have been cultured or genomically explored. The reconstruction of “Ca. Methanomixophus” MAGs not only expands the known range of metabolic versatility of the members of Archaeoglobi but also suggests that the phylogenetic distribution of MCR and MTR complexes is even wider than previously anticipated.
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15
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Colman DR, Lindsay MR, Amenabar MJ, Boyd ES. The Intersection of Geology, Geochemistry, and Microbiology in Continental Hydrothermal Systems. ASTROBIOLOGY 2019; 19:1505-1522. [PMID: 31592688 DOI: 10.1089/ast.2018.2016] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Decompressional boiling of ascending hydrothermal waters and separation into a vapor (gas) and a liquid phase drive extensive variation in the geochemical composition of hot spring waters. Yet little is known of how the process of phase separation influences the distribution of microbial metabolisms in springs. Here, we determined the variation in protein coding genes in 51 metagenomes from chemosynthetic hot spring communities that span geochemical gradients in Yellowstone National Park. The 51 metagenomes could be divided into 5 distinct groups that correspond to low and high temperatures and acidic and circumneutral/alkaline springs. A fifth group primarily comprised metagenomes from springs with moderate acidity and that are influenced by elevated volcanic gas input. Protein homologs putatively involved in the oxidation of sulfur compounds, a process that leads to acidification of spring waters, in addition to those involved in the reduction of sulfur compounds were enriched in metagenomes from acidic springs sourced by vapor phase gases. Metagenomes from springs with evidence for elevated volcanic gas input were enriched in protein homologs putatively involved in oxidation of those gases, including hydrogen and methane. Finally, metagenomes from circumneutral/alkaline springs sourced by liquid phase waters were enriched in protein homologs putatively involved in heterotrophy and respiration of oxidized nitrogen compounds and oxygen. These results indicate that the geological process of phase separation shapes the ecology of thermophilic communities through its influence on the availability of nutrients in the form of gases, solutes, and minerals. Microbial acidification of hot spring waters further influences the kinetic and thermodynamic stabilities of nutrients and their bioavailability. These data therefore provide an important framework to understand how geological processes have shaped the evolutionary history of chemosynthetic thermophiles and how these organisms, in turn, have shaped their geochemical environments.
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Affiliation(s)
- Daniel R Colman
- Department of Microbiology & Immunology, Montana State University, Bozeman, Montana
| | - Melody R Lindsay
- Department of Microbiology & Immunology, Montana State University, Bozeman, Montana
| | | | - Eric S Boyd
- Department of Microbiology & Immunology, Montana State University, Bozeman, Montana
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16
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Boyd JA, Jungbluth SP, Leu AO, Evans PN, Woodcroft BJ, Chadwick GL, Orphan VJ, Amend JP, Rappé MS, Tyson GW. Divergent methyl-coenzyme M reductase genes in a deep-subseafloor Archaeoglobi. THE ISME JOURNAL 2019; 13:1269-1279. [PMID: 30651609 PMCID: PMC6474303 DOI: 10.1038/s41396-018-0343-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 11/29/2018] [Accepted: 12/11/2018] [Indexed: 12/28/2022]
Abstract
The methyl-coenzyme M reductase (MCR) complex is a key enzyme in archaeal methane generation and has recently been proposed to also be involved in the oxidation of short-chain hydrocarbons including methane, butane, and potentially propane. The number of archaeal clades encoding the MCR continues to grow, suggesting that this complex was inherited from an ancient ancestor, or has undergone extensive horizontal gene transfer. Expanding the representation of MCR-encoding lineages through metagenomic approaches will help resolve the evolutionary history of this complex. Here, a near-complete Archaeoglobi metagenome-assembled genome (MAG; Ca. Polytropus marinifundus gen. nov. sp. nov.) was recovered from the deep subseafloor along the Juan de Fuca Ridge flank that encodes two divergent McrABG operons similar to those found in Ca. Bathyarchaeota and Ca. Syntrophoarchaeum MAGs. Ca. P. marinifundus is basal to members of the class Archaeoglobi, and encodes the genes for β-oxidation, potentially allowing an alkanotrophic metabolism similar to that proposed for Ca. Syntrophoarchaeum. Ca. P. marinifundus also encodes a respiratory electron transport chain that can potentially utilize nitrate, iron, and sulfur compounds as electron acceptors. Phylogenetic analysis suggests that the Ca. P. marinifundus MCR operons were horizontally transferred, changing our understanding of the evolution and distribution of this complex in the Archaea.
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Affiliation(s)
- Joel A Boyd
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia
| | - Sean P Jungbluth
- Center for Dark Energy Biosphere Investigations, University of Southern California, Los Angeles, CA, USA
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Andy O Leu
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia
| | - Paul N Evans
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia
| | - Ben J Woodcroft
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia
| | - Grayson L Chadwick
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
| | - Victoria J Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
| | - Jan P Amend
- Departments of Earth Sciences and Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Michael S Rappé
- Hawaii Institute of Marine Biology, University of Hawaii at Manoa, Kaneohe, HI, USA
| | - Gene W Tyson
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia.
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17
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Delforno TP, Macedo TZ, Midoux C, Lacerda GV, Rué O, Mariadassou M, Loux V, Varesche MBA, Bouchez T, Bize A, Oliveira VM. Comparative metatranscriptomic analysis of anaerobic digesters treating anionic surfactant contaminated wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 649:482-494. [PMID: 30176460 DOI: 10.1016/j.scitotenv.2018.08.328] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 08/23/2018] [Accepted: 08/24/2018] [Indexed: 06/08/2023]
Abstract
Three distinct biological reactors fed with synthetic medium (UASB_Control), synthetic medium and linear alkylbenzene sulfonate (LAS; UASB_SL), and real laundry wastewater (UASB_LW) were compared using a metatranscriptomic approach to determine putative bioindicator genes and taxonomies associated to all steps of anaerobic LAS biodegradation pathway. A homemade bioinformatics pipeline combined with an R workflow was developed to perform the RNAseq data analysis. UASB_SL and UASB_LW showed similar values of LAS biological degradation (~47%) and removal (53-55%). Rarefaction analysis revealed that 1-2 million reads were sufficient to access the whole functional capacity. In the first step of LAS biodegradation pathway, fumarate reductase subunit C was detected and taxonomically assigned to the genus Syntrophobacter (0.002% - UASB_SL; 0.0015% - UASB_LW; not detected - UASB_Control). In the second step, many enzymes related to beta-oxidation were observed and most of them with low relative abundance in UASB Control and taxonomically related with Smithella, Acinetobacter and Syntrophorhabdus. For the ring cleavage step, the abundance of 6 OCH CoA hydrolase putative gene was ten times higher in UASB_SL and UASB_LW when compared to UASB_Control, and assigned to Desulfomonile and Syntrophorhabdus. Finally, the adenylylsulfate reductase, taxonomically related with Desulfovibrio and Desulfomonile, was observed in the desulfonation step with the highest relative abundance in UASB_LW.
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Affiliation(s)
- Tiago P Delforno
- Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), Campinas University - UNICAMP, Campinas, SP CEP 13081-970, Brazil.
| | - Thais Z Macedo
- Laboratory of Biological Processes, Department of Hydraulics and Sanitation, Engineering School of São Carlos, University of São Paulo (EESC - USP) Campus II, São Carlos, SP CEP 13563-120, Brazil
| | - Cédric Midoux
- Irstea, UR HBAN, F-92761 Antony, France; Mathématiques et Informatique Appliquées du Génome à l'Environnement - MaIAGE, UR1404, INRA, 78352 Jouy-en-Josas, France
| | - Gileno V Lacerda
- Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), Campinas University - UNICAMP, Campinas, SP CEP 13081-970, Brazil
| | - Olivier Rué
- Mathématiques et Informatique Appliquées du Génome à l'Environnement - MaIAGE, UR1404, INRA, 78352 Jouy-en-Josas, France
| | - Mahendra Mariadassou
- Mathématiques et Informatique Appliquées du Génome à l'Environnement - MaIAGE, UR1404, INRA, 78352 Jouy-en-Josas, France
| | - Valentin Loux
- Mathématiques et Informatique Appliquées du Génome à l'Environnement - MaIAGE, UR1404, INRA, 78352 Jouy-en-Josas, France
| | - Maria B A Varesche
- Laboratory of Biological Processes, Department of Hydraulics and Sanitation, Engineering School of São Carlos, University of São Paulo (EESC - USP) Campus II, São Carlos, SP CEP 13563-120, Brazil
| | | | | | - Valéria M Oliveira
- Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), Campinas University - UNICAMP, Campinas, SP CEP 13081-970, Brazil
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18
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Wang R, Lin JQ, Liu XM, Pang X, Zhang CJ, Yang CL, Gao XY, Lin CM, Li YQ, Li Y, Lin JQ, Chen LX. Sulfur Oxidation in the Acidophilic Autotrophic Acidithiobacillus spp. Front Microbiol 2019; 9:3290. [PMID: 30687275 PMCID: PMC6335251 DOI: 10.3389/fmicb.2018.03290] [Citation(s) in RCA: 107] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 12/18/2018] [Indexed: 12/12/2022] Open
Abstract
Sulfur oxidation is an essential component of the earth's sulfur cycle. Acidithiobacillus spp. can oxidize various reduced inorganic sulfur compounds (RISCs) with high efficiency to obtain electrons for their autotrophic growth. Strains in this genus have been widely applied in bioleaching and biological desulfurization. Diverse sulfur-metabolic pathways and corresponding regulatory systems have been discovered in these acidophilic sulfur-oxidizing bacteria. The sulfur-metabolic enzymes in Acidithiobacillus spp. can be categorized as elemental sulfur oxidation enzymes (sulfur dioxygenase, sulfur oxygenase reductase, and Hdr-like complex), enzymes in thiosulfate oxidation pathways (tetrathionate intermediate thiosulfate oxidation (S4I) pathway, the sulfur oxidizing enzyme (Sox) system and thiosulfate dehydrogenase), sulfide oxidation enzymes (sulfide:quinone oxidoreductase) and sulfite oxidation pathways/enzymes. The two-component systems (TCSs) are the typical regulation elements for periplasmic thiosulfate metabolism in these autotrophic sulfur-oxidizing bacteria. Examples are RsrS/RsrR responsible for S4I pathway regulation and TspS/TspR for Sox system regulation. The proposal of sulfur metabolic and regulatory models provide new insights and overall understanding of the sulfur-metabolic processes in Acidithiobacillus spp. The future research directions and existing barriers in the bacterial sulfur metabolism are also emphasized here and the breakthroughs in these areas will accelerate the research on the sulfur oxidation in Acidithiobacillus spp. and other sulfur oxidizers.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Jian-Qun Lin
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Lin-Xu Chen
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
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19
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Hua ZS, Qu YN, Zhu Q, Zhou EM, Qi YL, Yin YR, Rao YZ, Tian Y, Li YX, Liu L, Castelle CJ, Hedlund BP, Shu WS, Knight R, Li WJ. Genomic inference of the metabolism and evolution of the archaeal phylum Aigarchaeota. Nat Commun 2018; 9:2832. [PMID: 30026532 PMCID: PMC6053391 DOI: 10.1038/s41467-018-05284-4] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 06/13/2018] [Indexed: 12/30/2022] Open
Abstract
Microbes of the phylum Aigarchaeota are widely distributed in geothermal environments, but their physiological and ecological roles are poorly understood. Here we analyze six Aigarchaeota metagenomic bins from two circumneutral hot springs in Tengchong, China, to reveal that they are either strict or facultative anaerobes, and most are chemolithotrophs that can perform sulfide oxidation. Applying comparative genomics to the Thaumarchaeota and Aigarchaeota, we find that they both originated from thermal habitats, sharing 1154 genes with their common ancestor. Horizontal gene transfer played a crucial role in shaping genetic diversity of Aigarchaeota and led to functional partitioning and ecological divergence among sympatric microbes, as several key functional innovations were endowed by Bacteria, including dissimilatory sulfite reduction and possibly carbon monoxide oxidation. Our study expands our knowledge of the possible ecological roles of the Aigarchaeota and clarifies their evolutionary relationship to their sister lineage Thaumarchaeota.
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Affiliation(s)
- Zheng-Shuang Hua
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Yan-Ni Qu
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Qiyun Zhu
- Department of Pediatrics, University of California San Diego, La Jolla, CA, 92093, USA
| | - En-Min Zhou
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Yan-Ling Qi
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Yi-Rui Yin
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Yang-Zhi Rao
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Ye Tian
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Yu-Xian Li
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Lan Liu
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Cindy J Castelle
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA.,Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
| | - Wen-Sheng Shu
- School of Life Sciences, South China Normal University, 510631, Guangzhou, China
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, 92093, USA.,Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, 92093, USA.,Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, 92093, USA
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China. .,College of Fisheries, Henan Normal University, 453007, Xinxiang, China.
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Sedano-Núñez VT, Boeren S, Stams AJM, Plugge CM. Comparative proteome analysis of propionate degradation by Syntrophobacter fumaroxidans in pure culture and in coculture with methanogens. Environ Microbiol 2018; 20:1842-1856. [PMID: 29611893 PMCID: PMC5947623 DOI: 10.1111/1462-2920.14119] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 03/20/2018] [Accepted: 03/24/2018] [Indexed: 11/28/2022]
Abstract
Syntrophobacter fumaroxidans is a sulfate-reducing bacterium able to grow on propionate axenically or in syntrophic interaction with methanogens or other sulfate-reducing bacteria. We performed a proteome analysis of S. fumaroxidans growing with propionate axenically with sulfate or fumarate, and in syntrophy with Methanospirillum hungatei, Methanobacterium formicicum or Desulfovibrio desulfuricans. Special attention was put on the role of hydrogen and formate in interspecies electron transfer (IET) and energy conservation. Formate dehydrogenase Fdh1 and hydrogenase Hox were the main confurcating enzymes used for energy conservation. In the periplasm, Fdh2 and hydrogenase Hyn play an important role in reverse electron transport associated with succinate oxidation. Periplasmic Fdh3 and Fdh5 were involved in IET. The sulfate reduction pathway was poorly regulated and many enzymes associated with sulfate reduction (Sat, HppA, AprAB, DsrAB and DsrC) were abundant even at conditions where sulfate was not present. Proteins similar to heterodisulfide reductases (Hdr) were abundant. Hdr/Flox was detected in all conditions while HdrABC/HdrL was exclusively detected when sulfate was available; these complexes most likely confurcate electrons. Our results suggest that S. fumaroxidans mainly used formate for electron release and that different confurcating mechanisms were used in its sulfidogenic metabolism.
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Affiliation(s)
- Vicente T Sedano-Núñez
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, Wageningen, The Netherlands
| | - Sjef Boeren
- Laboratory of Biochemistry, Wageningen University & Research, Stippeneng 4, Wageningen, The Netherlands
| | - Alfons J M Stams
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, Wageningen, The Netherlands.,Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga, 4710-057, Portugal
| | - Caroline M Plugge
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, Wageningen, The Netherlands
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21
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Diversity of Sulfur-Oxidizing and Sulfur-Reducing Microbes in Diverse Ecosystems. ADVANCES IN SOIL MICROBIOLOGY: RECENT TRENDS AND FUTURE PROSPECTS 2018. [DOI: 10.1007/978-981-10-6178-3_4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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22
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Wagner T, Koch J, Ermler U, Shima S. Methanogenic heterodisulfide reductase (HdrABC-MvhAGD) uses two noncubane [4Fe-4S] clusters for reduction. Science 2017; 357:699-703. [DOI: 10.1126/science.aan0425] [Citation(s) in RCA: 120] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Accepted: 07/25/2017] [Indexed: 12/15/2022]
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Broman E, Sjöstedt J, Pinhassi J, Dopson M. Shifts in coastal sediment oxygenation cause pronounced changes in microbial community composition and associated metabolism. MICROBIOME 2017; 5:96. [PMID: 28793929 PMCID: PMC5549381 DOI: 10.1186/s40168-017-0311-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 07/18/2017] [Indexed: 05/25/2023]
Abstract
BACKGROUND A key characteristic of eutrophication in coastal seas is the expansion of hypoxic bottom waters, often referred to as 'dead zones'. One proposed remediation strategy for coastal dead zones in the Baltic Sea is to mix the water column using pump stations, circulating oxygenated water to the sea bottom. Although microbial metabolism in the sediment surface is recognized as key in regulating bulk chemical fluxes, it remains unknown how the microbial community and its metabolic processes are influenced by shifts in oxygen availability. Here, coastal Baltic Sea sediments sampled from oxic and anoxic sites, plus an intermediate area subjected to episodic oxygenation, were experimentally exposed to oxygen shifts. Chemical, 16S rRNA gene, metagenomic, and metatranscriptomic analyses were conducted to investigate changes in chemistry fluxes, microbial community structure, and metabolic functions in the sediment surface. RESULTS Compared to anoxic controls, oxygenation of anoxic sediment resulted in a proliferation of bacterial populations in the facultative anaerobic genus Sulfurovum that are capable of oxidizing toxic sulfide. Furthermore, the oxygenated sediment had higher amounts of RNA transcripts annotated as sqr, fccB, and dsrA involved in sulfide oxidation. In addition, the importance of cryptic sulfur cycling was highlighted by the oxidative genes listed above as well as dsvA, ttrB, dmsA, and ddhAB that encode reductive processes being identified in anoxic and intermediate sediments turned oxic. In particular, the intermediate site sediments responded differently upon oxygenation compared to the anoxic and oxic site sediments. This included a microbial community composition with more habitat generalists, lower amounts of RNA transcripts attributed to methane oxidation, and a reduced rate of organic matter degradation. CONCLUSIONS These novel data emphasize that genetic expression analyses has the power to identify key molecular mechanisms that regulate microbial community responses upon oxygenation of dead zones. Moreover, these results highlight that microbial responses, and therefore ultimately remediation efforts, depend largely on the oxygenation history of sites. Furthermore, it was shown that re-oxygenation efforts to remediate dead zones could ultimately be facilitated by in situ microbial molecular mechanisms involved in removal of toxic H2S and the potent greenhouse gas methane.
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Affiliation(s)
- Elias Broman
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Johanna Sjöstedt
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
- Present address: Department of Biology/Aquatic ecology, Lund University, Sölvesgatan 37, 223 62 Lund, Sweden
- Present address: Centre for Ocean Life, Institute for Aquatic Resources, Technical University of Denmark, 2900 Charlottenlund, Denmark
| | - Jarone Pinhassi
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
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24
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Urbieta MS, Rascovan N, Vázquez MP, Donati E. Genome analysis of the thermoacidophilic archaeon Acidianus copahuensis focusing on the metabolisms associated to biomining activities. BMC Genomics 2017; 18:445. [PMID: 28587624 PMCID: PMC5461723 DOI: 10.1186/s12864-017-3828-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 05/30/2017] [Indexed: 11/21/2022] Open
Abstract
Background Several archaeal species from the order Sulfolobales are interesting from the biotechnological point of view due to their biomining capacities. Within this group, the genus Acidianus contains four biomining species (from ten known Acidianus species), but none of these have their genome sequenced. To get insights into the genetic potential and metabolic pathways involved in the biomining activity of this group, we sequenced the genome of Acidianus copahuensis ALE1 strain, a novel thermoacidophilic crenarchaeon (optimum growth: 75 °C, pH 3) isolated from the volcanic geothermal area of Copahue at Neuquén province in Argentina. Previous experimental characterization of A. copahuensis revealed a high biomining potential, exhibited as high oxidation activity of sulfur and sulfur compounds, ferrous iron and sulfide minerals (e.g.: pyrite). This strain is also autotrophic and tolerant to heavy metals, thus, it can grow under adverse conditions for most forms of life with a low nutrient demand, conditions that are commonly found in mining environments. Results In this work we analyzed the genome of Acidianus copahuensis and describe the genetic pathways involved in biomining processes. We identified the enzymes that are most likely involved in growth on sulfur and ferrous iron oxidation as well as those involved in autotrophic carbon fixation. We also found that A. copahuensis genome gathers different features that are only present in particular lineages or species from the order Sulfolobales, some of which are involved in biomining. We found that although most of its genes (81%) were found in at least one other Sulfolobales species, it is not specifically closer to any particular species (60–70% of proteins shared with each of them). Although almost one fifth of A. copahuensis proteins are not found in any other Sulfolobales species, most of them corresponded to hypothetical proteins from uncharacterized metabolisms. Conclusion In this work we identified the genes responsible for the biomining metabolisms that we have previously observed experimentally. We provide a landscape of the metabolic potentials of this strain in the context of Sulfolobales and propose various pathways and cellular processes not yet fully understood that can use A. copahuensis as an experimental model to further understand the fascinating biology of thermoacidophilic biomining archaea. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3828-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- María Sofía Urbieta
- CINDEFI (CCT La Plata-CONICET, UNLP), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calle 47 y 115, 1900, La Plata, Argentina. .,, Calle 50, entre 115 y 116, N° 227, La Plata, Buenos Aires, Argentina.
| | - Nicolás Rascovan
- Instituto de Agrobiotecnología de Rosario (INDEAR), CONICET, Predio CCT, Rosario, Argentina
| | - Martín P Vázquez
- Instituto de Agrobiotecnología de Rosario (INDEAR), CONICET, Predio CCT, Rosario, Argentina
| | - Edgardo Donati
- CINDEFI (CCT La Plata-CONICET, UNLP), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calle 47 y 115, 1900, La Plata, Argentina
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25
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Genomic reconstruction of multiple lineages of uncultured benthic archaea suggests distinct biogeochemical roles and ecological niches. ISME JOURNAL 2017; 11:1118-1129. [PMID: 28085154 DOI: 10.1038/ismej.2016.189] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 11/10/2016] [Accepted: 11/19/2016] [Indexed: 01/14/2023]
Abstract
Genomic bins belonging to multiple archaeal lineages were recovered from distinct redox regimes in sediments of the White Oak River estuary. The reconstructed archaeal genomes were identified as belonging to the rice cluster subgroups III and V (RC-III, RC-V), the Marine Benthic Group D (MBG-D), and a newly described archaeal class, the Theionarchaea. The metabolic capabilities of these uncultured archaea were inferred and indicated a common capability for extracellular protein degradation, supplemented by other pathways. The multiple genomic bins within the MBG-D archaea shared a nearly complete reductive acetyl-CoA pathway suggesting acetogenic capabilities. In contrast, the RC-III metabolism appeared centered on the degradation of detrital proteins and production of H2, whereas the RC-V archaea lacked capabilities for protein degradation and uptake, and appeared to be specialized on carbohydrate fermentation. The Theionarchaea appeared as complex metabolic hybrids; encoding a complete tricarboxylic acid cycle permitting carbon (acetyl-CoA) oxidation, together with a complete reductive acetyl-CoA pathway and sulfur reduction by a sulfhydrogenase. The differentiated inferred capabilities of these uncultured archaeal lineages indicated lineage-specific linkages with the nitrogen, carbon and sulfur cycles. The predicted metabolisms of these archaea suggest preferences for distinct geochemical niches within the estuarine sedimentary environment.
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Mardanov AV, Beletsky AV, Kadnikov VV, Slobodkin AI, Ravin NV. Genome Analysis of Thermosulfurimonas dismutans, the First Thermophilic Sulfur-Disproportionating Bacterium of the Phylum Thermodesulfobacteria. Front Microbiol 2016; 7:950. [PMID: 27379079 PMCID: PMC4911364 DOI: 10.3389/fmicb.2016.00950] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 06/02/2016] [Indexed: 11/17/2022] Open
Abstract
Thermosulfurimonas dismutans S95T, isolated from a deep-sea hydrothermal vent is the first bacterium of the phylum Thermodesulfobacteria reported to grow by the disproportionation of elemental sulfur, sulfite, or thiosulfate with carbon dioxide as the sole carbon source. In contrast to its phylogenetically close relatives, which are dissimilatory sulfate-reducers, T. dismutans is unable to grow by sulfate respiration. The features of this organism and its 2,1 Mb draft genome sequence are described in this report. Genome analysis revealed that the T. dismutans genome contains the set of genes for dissimilatory sulfate reduction including ATP sulfurylase, the AprA and B subunits of adenosine-5′-phosphosulfate reductase, and dissimilatory sulfite reductase. The oxidation of elemental sulfur to sulfite could be enabled by APS reductase-associated electron transfer complex QmoABC and heterodisulfide reductase. The genome also contains several membrane-linked molybdopterin oxidoreductases that are thought to be involved in sulfur metabolism as subunits of thiosulfate, polysulfide, or tetrathionate reductases. Nitrate could be used as an electron acceptor and reduced to ammonium, as indicated by the presence of periplasmic nitrate and nitrite reductases. Autotrophic carbon fixation is enabled by the Wood–Ljungdahl pathway, and the complete set of genes that is required for nitrogen fixation is also present in T. dismutans. Overall, our results provide genomic insights into energy and carbon metabolism of chemolithoautotrophic sulfur-disproportionating bacterium that could be important primary producer in microbial communities of deep-sea hydrothermal vents.
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Affiliation(s)
- Andrey V Mardanov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences Moscow, Russia
| | - Alexey V Beletsky
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences Moscow, Russia
| | - Vitaly V Kadnikov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences Moscow, Russia
| | - Alexander I Slobodkin
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences Moscow, Russia
| | - Nikolai V Ravin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences Moscow, Russia
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27
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Borrel G, Adam PS, Gribaldo S. Methanogenesis and the Wood-Ljungdahl Pathway: An Ancient, Versatile, and Fragile Association. Genome Biol Evol 2016; 8:1706-11. [PMID: 27189979 PMCID: PMC4943185 DOI: 10.1093/gbe/evw114] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Methanogenesis coupled to the Wood–Ljungdahl pathway is one of the most ancient metabolisms for energy generation and carbon fixation in the Archaea. Recent results are sensibly changing our view on the diversity of methane-cycling capabilities in this Domain of Life. The availability of genomic sequences from uncharted branches of the archaeal tree has highlighted the existence of novel methanogenic lineages phylogenetically distant to previously known ones, such as the Methanomassiliicoccales. At the same time, phylogenomic analyses have suggested a methanogenic ancestor for all Archaea, implying multiple independent losses of this metabolism during archaeal diversification. This prediction has been strengthened by the report of genes involved in methane cycling in members of the Bathyarchaeota (a lineage belonging to the TACK clade), representing the first indication of the presence of methanogenesis outside of the Euryarchaeota. In light of these new data, we discuss how the association between methanogenesis and the Wood–Ljungdahl pathway appears to be much more flexible than previously thought, and might provide information on the processes that led to loss of this metabolism in many archaeal lineages. The combination of environmental microbiology, experimental characterization and phylogenomics opens up exciting avenues of research to unravel the diversity and evolutionary history of fundamental metabolic pathways.
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Affiliation(s)
- Guillaume Borrel
- Department of Microbiology, Unité De Biologie Moléculaire Du Gène Chez Les Extrêmophiles, Institut Pasteur, Paris, France
| | - Panagiotis S Adam
- Department of Microbiology, Unité De Biologie Moléculaire Du Gène Chez Les Extrêmophiles, Institut Pasteur, Paris, France Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Simonetta Gribaldo
- Department of Microbiology, Unité De Biologie Moléculaire Du Gène Chez Les Extrêmophiles, Institut Pasteur, Paris, France
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Lazar CS, Baker BJ, Seitz K, Hyde AS, Dick GJ, Hinrichs KU, Teske AP. Genomic evidence for distinct carbon substrate preferences and ecological niches of Bathyarchaeota in estuarine sediments. Environ Microbiol 2016; 18:1200-11. [PMID: 26626228 DOI: 10.1111/1462-2920.13142] [Citation(s) in RCA: 158] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 11/19/2015] [Accepted: 11/19/2015] [Indexed: 11/28/2022]
Abstract
Investigations of the biogeochemical roles of benthic Archaea in marine sediments are hampered by the scarcity of cultured representatives. In order to determine their metabolic capacity, we reconstructed the genomic content of four widespread uncultured benthic Archaea recovered from estuary sediments at 48% to 95% completeness. Four genomic bins were found to belong to different subgroups of the former Miscellaneous Crenarcheota Group (MCG) now called Bathyarchaeota: MCG-6, MCG-1, MCG-7/17 and MCG-15. Metabolic predictions based on gene content of the different genome bins indicate that subgroup 6 has the ability to hydrolyse extracellular plant-derived carbohydrates, and that all four subgroups can degrade detrital proteins. Genes encoding enzymes involved in acetate production as well as in the reductive acetyl-CoA pathway were detected in all four genomes inferring that these Archaea are organo-heterotrophic and autotrophic acetogens. Genes involved in nitrite reduction were detected in all Bathyarchaeota subgroups and indicate a potential for dissimilatory nitrite reduction to ammonium. Comparing the genome content of the different Bathyarchaeota subgroups indicated preferences for distinct types of carbohydrate substrates and implicitly, for different niches within the sedimentary environment.
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Affiliation(s)
- Cassandre Sara Lazar
- University of North Carolina Chapel Hill, Marine Sciences, Chapel Hill, NC, USA.,Organic Geochemistry Group, MARUM Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, Bremen, Germany.,Institute of Ecology, Friedrich Schiller University Jena, Dornburger Straße 159, 07743, Jena, Germany
| | - Brett J Baker
- University of Texas Austin, Department of Marine Science, Marine Science Institute, Port Aransas, TX, 78383, USA
| | - Kiley Seitz
- University of Texas Austin, Department of Marine Science, Marine Science Institute, Port Aransas, TX, 78383, USA
| | - Andrew S Hyde
- University of North Carolina Chapel Hill, Marine Sciences, Chapel Hill, NC, USA
| | - Gregory J Dick
- University of Michigan, Earth and Environmental Sciences, Ann Arbor, MI, 48109, USA
| | - Kai-Uwe Hinrichs
- Organic Geochemistry Group, MARUM Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, Bremen, Germany
| | - Andreas P Teske
- University of North Carolina Chapel Hill, Marine Sciences, Chapel Hill, NC, USA
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Latorre M, Ehrenfeld N, Cortés MP, Travisany D, Budinich M, Aravena A, González M, Bobadilla-Fazzini RA, Parada P, Maass A. Global transcriptional responses of Acidithiobacillus ferrooxidans Wenelen under different sulfide minerals. BIORESOURCE TECHNOLOGY 2016; 200:29-34. [PMID: 26476161 DOI: 10.1016/j.biortech.2015.09.110] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 09/28/2015] [Accepted: 09/29/2015] [Indexed: 06/05/2023]
Abstract
In order to provide new information about the adaptation of Acidithiobacillus ferrooxidans during the bioleaching process, the current analysis presents the first report of the global transcriptional response of the native copper mine strain Wenelen (DSM 16786) oxidized under different sulfide minerals. Microarrays were used to measure the response of At. ferrooxidans Wenelen to shifts from iron supplemented liquid cultures (reference state) to the addition of solid substrates enriched in pyrite or chalcopyrite. Genes encoding for energy metabolism showed a similar transcriptional profile for the two sulfide minerals. Interestingly, four operons related to sulfur metabolism were over-expressed during growth on a reduced sulfur source. Genes associated with metal tolerance (RND and ATPases type P) were up-regulated in the presence of pyrite or chalcopyrite. These results suggest that At. ferrooxidans Wenelen presents an efficient transcriptional system developed to respond to environmental conditions, namely the ability to withstand high copper concentrations.
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Affiliation(s)
- Mauricio Latorre
- Mathomics, Center for Mathematical Modeling, Universidad de Chile, Beauchef 851, 7th Floor, Santiago, Chile; Center for Genome Regulation (Fondap 15090007), Universidad de Chile, Blanco Encalada 2085, Santiago, Chile; Laboratorio de Bioinformática y Expresión Génica, INTA, Universidad de Chile, El Líbano 5524, Macul, Santiago, Chile
| | - Nicole Ehrenfeld
- BioSigma S.A., Loteo Los Libertadores, Lote 106, Colina, Chile; Austral Biotech S.A., Francisco Noguera 41, Santiago, Chile
| | - María Paz Cortés
- Mathomics, Center for Mathematical Modeling, Universidad de Chile, Beauchef 851, 7th Floor, Santiago, Chile; Center for Genome Regulation (Fondap 15090007), Universidad de Chile, Blanco Encalada 2085, Santiago, Chile
| | - Dante Travisany
- Mathomics, Center for Mathematical Modeling, Universidad de Chile, Beauchef 851, 7th Floor, Santiago, Chile; Center for Genome Regulation (Fondap 15090007), Universidad de Chile, Blanco Encalada 2085, Santiago, Chile
| | - Marko Budinich
- Mathomics, Center for Mathematical Modeling, Universidad de Chile, Beauchef 851, 7th Floor, Santiago, Chile; Center for Genome Regulation (Fondap 15090007), Universidad de Chile, Blanco Encalada 2085, Santiago, Chile
| | - Andrés Aravena
- Department of Molecular Biology and Genetics, Istanbul University, Istanbul, Turkey
| | - Mauricio González
- Center for Genome Regulation (Fondap 15090007), Universidad de Chile, Blanco Encalada 2085, Santiago, Chile; Laboratorio de Bioinformática y Expresión Génica, INTA, Universidad de Chile, El Líbano 5524, Macul, Santiago, Chile
| | | | - Pilar Parada
- BioSigma S.A., Loteo Los Libertadores, Lote 106, Colina, Chile
| | - Alejandro Maass
- Mathomics, Center for Mathematical Modeling, Universidad de Chile, Beauchef 851, 7th Floor, Santiago, Chile; Center for Genome Regulation (Fondap 15090007), Universidad de Chile, Blanco Encalada 2085, Santiago, Chile; BioSigma S.A., Loteo Los Libertadores, Lote 106, Colina, Chile; Department of Mathematical Engineering, Universidad de Chile, Beauchef 851, 5th Floor, Santiago, Chile.
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Assessment of the Carbon Monoxide Metabolism of the Hyperthermophilic Sulfate-Reducing Archaeon Archaeoglobus fulgidus VC-16 by Comparative Transcriptome Analyses. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2015; 2015:235384. [PMID: 26345487 PMCID: PMC4543118 DOI: 10.1155/2015/235384] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 06/09/2015] [Accepted: 06/14/2015] [Indexed: 11/23/2022]
Abstract
The hyperthermophilic, sulfate-reducing archaeon, Archaeoglobus fulgidus, utilizes CO as an energy source and it is resistant to the toxic effects of high CO concentrations. Herein, transcription profiles were obtained from A. fulgidus during growth with CO and sulfate or thiosulfate, or without an electron acceptor. This provided a basis for a model of the CO metabolism of A. fulgidus. The model suggests proton translocation by “Mitchell-type” loops facilitated by Fqo catalyzing a Fdred:menaquinone oxidoreductase reaction, as the major mode of energy conservation, rather than formate or H2 cycling during respiratory growth. The bifunctional CODH (cdhAB-2) is predicted to play an ubiquitous role in the metabolism of CO, and a novel nitrate reductase-associated respiratory complex was induced specifically in the presence of sulfate. A potential role of this complex in relation to Fdred and APS reduction is discussed. Multiple membrane-bound heterodisulfide reductase (DsrMK) could promote both energy-conserving and non-energy-conserving menaquinol oxidation. Finally, the FqoF subunit may catalyze a Fdred:F420 oxidoreductase reaction. In the absence of electron acceptor, downregulation of F420H2 dependent steps of the acetyl-CoA pathway is linked to transient formate generation. Overall, carboxidotrophic growth seems as an intrinsic capacity of A. fulgidus with little need for novel resistance or respiratory complexes.
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A Post-Genomic View of the Ecophysiology, Catabolism and Biotechnological Relevance of Sulphate-Reducing Prokaryotes. Adv Microb Physiol 2015. [PMID: 26210106 DOI: 10.1016/bs.ampbs.2015.05.002] [Citation(s) in RCA: 174] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Dissimilatory sulphate reduction is the unifying and defining trait of sulphate-reducing prokaryotes (SRP). In their predominant habitats, sulphate-rich marine sediments, SRP have long been recognized to be major players in the carbon and sulphur cycles. Other, more recently appreciated, ecophysiological roles include activity in the deep biosphere, symbiotic relations, syntrophic associations, human microbiome/health and long-distance electron transfer. SRP include a high diversity of organisms, with large nutritional versatility and broad metabolic capacities, including anaerobic degradation of aromatic compounds and hydrocarbons. Elucidation of novel catabolic capacities as well as progress in the understanding of metabolic and regulatory networks, energy metabolism, evolutionary processes and adaptation to changing environmental conditions has greatly benefited from genomics, functional OMICS approaches and advances in genetic accessibility and biochemical studies. Important biotechnological roles of SRP range from (i) wastewater and off gas treatment, (ii) bioremediation of metals and hydrocarbons and (iii) bioelectrochemistry, to undesired impacts such as (iv) souring in oil reservoirs and other environments, and (v) corrosion of iron and concrete. Here we review recent advances in our understanding of SRPs focusing mainly on works published after 2000. The wealth of publications in this period, covering many diverse areas, is a testimony to the large environmental, biogeochemical and technological relevance of these organisms and how much the field has progressed in these years, although many important questions and applications remain to be explored.
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32
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Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment. Nat Commun 2014; 4:2120. [PMID: 23979677 PMCID: PMC3903129 DOI: 10.1038/ncomms3120] [Citation(s) in RCA: 147] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Accepted: 06/06/2013] [Indexed: 11/08/2022] Open
Abstract
Microorganisms in the subsurface represent a substantial but poorly understood component of the Earth's biosphere. Subsurface environments are complex and difficult to characterize; thus, their microbiota have remained as a 'dark matter' of the carbon and other biogeochemical cycles. Here we deeply sequence two sediment-hosted microbial communities from an aquifer adjacent to the Colorado River, CO, USA. No single organism represents more than ~1% of either community. Remarkably, many bacteria and archaea in these communities are novel at the phylum level or belong to phyla lacking a sequenced representative. The dominant organism in deeper sediment, RBG-1, is a member of a new phylum. On the basis of its reconstructed complete genome, RBG-1 is metabolically versatile. Its wide respiration-based repertoire may enable it to respond to the fluctuating redox environment close to the water table. We document extraordinary microbial novelty and the importance of previously unknown lineages in sediment biogeochemical transformations.
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Venceslau SS, Stockdreher Y, Dahl C, Pereira IAC. The "bacterial heterodisulfide" DsrC is a key protein in dissimilatory sulfur metabolism. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1837:1148-64. [PMID: 24662917 DOI: 10.1016/j.bbabio.2014.03.007] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2013] [Revised: 03/07/2014] [Accepted: 03/13/2014] [Indexed: 12/16/2022]
Abstract
DsrC is a small protein present in organisms that dissimilate sulfur compounds, working as a physiological partner of the DsrAB sulfite reductase. DsrC contains two redox active cysteines in a flexible carboxy-terminal arm that are involved in the process of sulfite reduction or sulfur(1) compound oxidation in sulfur-reducing(2) or sulfur-oxidizing(3) organisms, respectively. In both processes, a disulfide formed between the two cysteines is believed to serve as the substrate of several proteins present in these organisms that are related to heterodisulfide reductases of methanogens. Here, we review the information on DsrC and its possible physiological partners, and discuss the idea that this protein may serve as a redox hub linking oxidation of several substrates to dissimilative sulfur metabolism. In addition, we analyze the distribution of proteins of the DsrC superfamily, including TusE that only requires the last Cys of the C-terminus for its role in the biosynthesis of 2-thiouridine, and a new protein that we name RspA (for regulatory sulfur-related protein) that is possibly involved in the regulation of gene expression and does not need the conserved Cys for its function. This article is part of a Special Issue entitled: 18th European Bioenergetic Conference.
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Affiliation(s)
- S S Venceslau
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Y Stockdreher
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Germany
| | - C Dahl
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Germany
| | - I A C Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
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Hocking WP, Stokke R, Roalkvam I, Steen IH. Identification of key components in the energy metabolism of the hyperthermophilic sulfate-reducing archaeon Archaeoglobus fulgidus by transcriptome analyses. Front Microbiol 2014; 5:95. [PMID: 24672515 PMCID: PMC3949148 DOI: 10.3389/fmicb.2014.00095] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 02/20/2014] [Indexed: 11/23/2022] Open
Abstract
Energy conservation via the pathway of dissimilatory sulfate reduction is present in a diverse group of prokaryotes, but is most comprehensively studied in Deltaproteobacteria. In this study, whole-genome microarray analyses were used to provide a model of the energy metabolism of the sulfate-reducing archaeon Archaeoglobus fulgidus, based on comparative analysis of litoautotrophic growth with H2/CO2 and thiosulfate, and heterotrophic growth on lactate with sulfate or thiosulfate. Only 72 genes were expressed differentially between the cultures utilizing sulfate or thiosulfate, whereas 269 genes were affected by a shift in energy source. We identified co-located gene cluster encoding putative lactate dehydrogenases (LDHs; lldD, dld, lldEFG), also present in sulfate-reducing bacteria. These enzymes may take part in energy conservation in A. fulgidus by specifically linking lactate oxidation with APS reduction via the Qmo complex. High transcriptional levels of Fqo confirm an important role of F420H2, as well as a menaquinone-mediated electron transport chain, during heterotrophic growth. A putative periplasmic thiosulfate reductase was identified by specific up-regulation. Also, putative genes for transport of sulfate and sulfite are discussed. We present a model for hydrogen metabolism, based on the probable bifurcation reaction of the Mvh:Hdl hydrogenase, which may inhibit the utilization of Fdred for energy conservation. Energy conservation is probably facilitated via menaquinone to multiple membrane-bound heterodisulfide reductase (Hdr) complexes and the DsrC protein—linking periplasmic hydrogenase (Vht) to the cytoplasmic reduction of sulfite. The ambiguous roles of genes corresponding to fatty acid metabolism induced during growth with H2 are discussed. Putative co-assimilation of organic acids is favored over a homologous secondary carbon fixation pathway, although both mechanisms may contribute to conserve the amount of Fdred needed during autotrophic growth with H2.
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Affiliation(s)
- William P Hocking
- Department of Biology, Centre for Geobiology, University of Bergen Bergen, Norway
| | - Runar Stokke
- Department of Biology, Centre for Geobiology, University of Bergen Bergen, Norway
| | - Irene Roalkvam
- Department of Biology, Centre for Geobiology, University of Bergen Bergen, Norway
| | - Ida H Steen
- Department of Biology, Centre for Geobiology, University of Bergen Bergen, Norway
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Guiral M, Prunetti L, Aussignargues C, Ciaccafava A, Infossi P, Ilbert M, Lojou E, Giudici-Orticoni MT. The hyperthermophilic bacterium Aquifex aeolicus: from respiratory pathways to extremely resistant enzymes and biotechnological applications. Adv Microb Physiol 2013; 61:125-94. [PMID: 23046953 DOI: 10.1016/b978-0-12-394423-8.00004-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Aquifex aeolicus isolated from a shallow submarine hydrothermal system belongs to the order Aquificales which constitute an important component of the microbial communities at elevated temperatures. This hyperthermophilic chemolithoautotrophic bacterium, which utilizes molecular hydrogen, molecular oxygen, and inorganic sulfur compounds to flourish, uses the reductive TCA cycle for CO(2) fixation. In this review, the intricate energy metabolism of A. aeolicus is described. As the chemistry of sulfur is complex and multiple sulfur species can be generated, A. aeolicus possesses a multitude of different enzymes related to the energy sulfur metabolism. It contains also membrane-embedded [NiFe] hydrogenases as well as oxidases enzymes involved in hydrogen and oxygen utilization. We have focused on some of these proteins that have been extensively studied and characterized as super-resistant enzymes with outstanding properties. We discuss the potential use of hydrogenases in an attractive H(2)/O(2) biofuel cell in replacement of chemical catalysts. Using complete genomic sequence and biochemical data, we present here a global view of the energy-generating mechanisms of A. aeolicus including sulfur compounds reduction and oxidation pathways as well as hydrogen and oxygen utilization.
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Affiliation(s)
- Marianne Guiral
- Unité de Bioénergétique et Ingénierie des Protéines, UMR7281-FR3479, CNRS, Aix-Marseille Université, Marseille, France.
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HdrC2 from Acidithiobacillus ferrooxidans owns two iron-sulfur binding motifs but binds only one variable cluster between [4Fe-4S] and [3Fe-4S]. Curr Microbiol 2012; 66:88-95. [PMID: 23053491 DOI: 10.1007/s00284-012-0244-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Accepted: 09/20/2012] [Indexed: 10/27/2022]
Abstract
The heterodisulfide reductase complex HdrABC from Acidithiobacillus ferrooxidans was suggested to own novel features that act in reverse to convert the sulfane sulfur of GS( n )H species (n > 1) into sulfite in sulfur oxidation. The HdrC subunit is potentially encoded by two different highly upregulated genes sharing only 29 % identity in A. ferrooxidans grown in sulfur-containing medium, which were named as HdrC1 and HdrC2, respectively and had been confirmed to contain iron-sulfur cluster by expression and characterization, especially the HdrC1 which had been showed to bind only one [4Fe-4S] cluster by mutations. However, the mutations of the HdrC2 remain to be done and the detailed binding information of it is still unclear. Here, we report the expression, mutations, and molecular modeling of the HdrC2 from A. ferrooxidans. This HdrC2 had two identical motifs (Cx(2)Cx(2)Cx(3)C) containing total of eight cysteine residues potentially for iron-sulfur cluster binding. This purified HdrC2 was exhibited to contain one variable cluster converted between [4Fe-4S] and [3Fe-4S] according to different conditions by the UV-scanning and EPR spectra. The site-directed mutagenesis results of these eight residues further confirmed that the HdrC2 in reduction with Fe(2+) condition loaded only one [4Fe-4S](+) with spin S = 1/2 ligated by the residues of Cys73, Cys109, Cys112, and Cys115; the HdrC2 in natural aeration condition lost the Fe atom ligated by the residue of Cys73 and loaded only one [3Fe-4S](0) with spin S = 0; the HdrC2 in oxidation condition loaded only one [3Fe-4S](+) with spin S = 1/2. Molecular modeling results were also in line with the experiment results.
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Grein F, Ramos AR, Venceslau SS, Pereira IAC. Unifying concepts in anaerobic respiration: insights from dissimilatory sulfur metabolism. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1827:145-60. [PMID: 22982583 DOI: 10.1016/j.bbabio.2012.09.001] [Citation(s) in RCA: 125] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Revised: 09/03/2012] [Accepted: 09/04/2012] [Indexed: 10/27/2022]
Abstract
Behind the versatile nature of prokaryotic energy metabolism is a set of redox proteins having a highly modular character. It has become increasingly recognized that a limited number of redox modules or building blocks appear grouped in different arrangements, giving rise to different proteins and functionalities. This modularity most likely reveals a common and ancient origin for these redox modules, and is obviously reflected in similar energy conservation mechanisms. The dissimilation of sulfur compounds was probably one of the earliest biological strategies used by primitive organisms to obtain energy. Here, we review some of the redox proteins involved in dissimilatory sulfur metabolism, focusing on sulfate reducing organisms, and highlight links between these proteins and others involved in different processes of anaerobic respiration. Noteworthy are links to the complex iron-sulfur molybdoenzyme family, and heterodisulfide reductases of methanogenic archaea. We discuss how chemiosmotic and electron bifurcation/confurcation may be involved in energy conservation during sulfate reduction, and how introduction of an additional module, multiheme cytochromes c, opens an alternative bioenergetic strategy that seems to increase metabolic versatility. Finally, we highlight new families of heterodisulfide reductase-related proteins from non-methanogenic organisms, which indicate a widespread distribution for these protein modules and may indicate a more general involvement of thiol/disulfide conversions in energy metabolism. This article is part of a Special Issue entitled: The evolutionary aspects of bioenergetic systems.
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Affiliation(s)
- Fabian Grein
- Instituto de Tecnologia Quimica e Biologica, Universidade Nova de Lisboa, Oeiras, Portugal
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Expression, purification and molecular modeling of another HdrC from Acidithiobacillus ferrooxidans which binds only one [4Fe-4S] cluster. Curr Microbiol 2012; 65:416-23. [PMID: 22760247 DOI: 10.1007/s00284-012-0173-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Accepted: 05/30/2012] [Indexed: 10/28/2022]
Abstract
The heterodisulfide reductase complex HdrABC from Acidithiobacillus ferrooxidans was predicted to have novel features that work in reverse to catalyse the sulfane sulfur of GSnH species (n > 1) into sulfite in sulfur oxidation. There are two different highly upregulated genes potentially encoding the HdrC subunit in A. ferrooxidans grown in sulfur-containing medium. An HdrC containing iron-sulfur cluster from A. ferrooxidans corresponding to one of the genes had been expressed and biophysically characterized. Comparatively, here we report the cloning, expression, and characterization of another HdrC from A. ferrooxidans. This HdrC was expressed in inclusion bodies in all conditions tested. This purified HdrC displayed brown color and contained the [4Fe-4S] cluster confirmed by the UV-scanning and EPR spectra. This HdrC owned two identical motifs (Cx(2)Cx(2)Cx(3)C) including total of eight cysteine residues for [4Fe-4S] cluster binding. To our surprise, the site-directed mutagenesis results of these eight residues revealed that respective removal of the sulfhydryl group of Cys73, Cys76, Cys79, and Cys37 resulted in the cluster loss, but those of Cys27, Cys30, Cys33, and Cys83 had no influence, which demonstrated that this HdrC bound only one cluster, and it might be responsible for causing the HdrABC in A. ferrooxidans working in reverse. Molecular modeling results also supported the above results and showed that this cluster was ligated by Cys73, Cys76, and Cys79 in one motif and Cys37, however, in another motif.
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Abstract
Dissimilatory sulfate and sulfur reduction evolved billions of years ago and while the bacteria and archaea that use this unique metabolism employ a variety of electron donors, H(2) is most commonly used as the energy source. These prokaryotes use multiheme c-type proteins to shuttle electrons from electron donors, and electron transport complexes presumed to contain b-type hemoproteins contribute to proton charging of the membrane. Numerous sulfate and sulfur reducers use an alternate pathway for heme synthesis and, frequently, uniquely specific axial ligands are used to secure c-type heme to the protein. This review presents some of the types and functional activities of hemoproteins involved in these two dissimilatory reduction pathways.
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40
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Muyzer G, Sorokin DY, Mavromatis K, Lapidus A, Foster B, Sun H, Ivanova N, Pati A, D'haeseleer P, Woyke T, Kyrpides NC. Complete genome sequence of Thioalkalivibrio sp. K90mix. Stand Genomic Sci 2011; 5:341-55. [PMID: 22675584 PMCID: PMC3368412 DOI: 10.4056/sigs.2315092] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Thioalkalivibrio sp. K90mix is an obligately chemolithoautotrophic, natronophilic sulfur-oxidizing bacterium (SOxB) belonging to the family Ectothiorhodospiraceae within the Gammaproteobacteria. The strain was isolated from a mixture of sediment samples obtained from different soda lakes located in the Kulunda Steppe (Altai, Russia) based on its extreme potassium carbonate tolerance as an enrichment method. Here we report the complete genome sequence of strain K90mix and its annotation. The genome was sequenced within the Joint Genome Institute Community Sequencing Program, because of its relevance to the sustainable removal of sulfide from wastewater and gas streams.
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Affiliation(s)
- Gerard Muyzer
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
- Department of Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Dimitry Y. Sorokin
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
| | | | - Alla Lapidus
- Joint Genome Institute, Walnut Creek, California, USA
| | - Brian Foster
- Joint Genome Institute, Walnut Creek, California, USA
| | - Hui Sun
- Joint Genome Institute, Walnut Creek, California, USA
| | | | - Amrita Pati
- Joint Genome Institute, Walnut Creek, California, USA
| | | | - Tanja Woyke
- Joint Genome Institute, Walnut Creek, California, USA
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41
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Thauer RK. Anaerobic oxidation of methane with sulfate: on the reversibility of the reactions that are catalyzed by enzymes also involved in methanogenesis from CO2. Curr Opin Microbiol 2011; 14:292-9. [DOI: 10.1016/j.mib.2011.03.003] [Citation(s) in RCA: 135] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2011] [Revised: 03/13/2011] [Accepted: 03/15/2011] [Indexed: 11/16/2022]
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Ossa D, Oliveira R, Murakami M, Vicentini R, Costa-Filho A, Alexandrino F, Ottoboni L, Garcia O. Expression, purification and spectroscopic analysis of an HdrC: An iron–sulfur cluster-containing protein from Acidithiobacillus ferrooxidans. Process Biochem 2011. [DOI: 10.1016/j.procbio.2011.03.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Rodriguez J, Hiras J, Hanson TE. Sulfite oxidation in chlorobaculum tepidum. Front Microbiol 2011; 2:112. [PMID: 21747809 PMCID: PMC3119408 DOI: 10.3389/fmicb.2011.00112] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2011] [Accepted: 05/09/2011] [Indexed: 12/03/2022] Open
Abstract
The green sulfur bacterium Chlorobaculum tepidum is proposed to oxidize sulfide and elemental sulfur via sulfite as an obligate intermediate. The sulfite pool is predicted to be contained in the cytoplasm and be oxidized by the concerted action of ApsBA, which directly oxidizes sulfite, and QmoABC, which transfers electrons from ApsBA to the quinone pool. Like other green sulfur bacteria, C. tepidum was unable to use exogenously provided sulfite as the sole electron donor. However, exogenous sulfite significantly stimulated the growth yield of sulfide limited batch cultures. The growth of C. tepidum mutant strains, CT0867/qmoB::TnOGm and CT0868/qmoC::TnOGm, was not increased by sulfite. Furthermore, these strains accumulated sulfite and displayed a growth yield decrease when grown on sulfide as the sole electron donor. These results support an obligate, cytoplasmic sulfite intermediate as part of the canonical sulfur oxidation pathway in C. tepidum that requires the Qmo complex for oxidation.
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Affiliation(s)
- Jesse Rodriguez
- Department of Biological Sciences, University of Delaware Newark, DE, USA
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44
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Pereira IAC, Ramos AR, Grein F, Marques MC, da Silva SM, Venceslau SS. A comparative genomic analysis of energy metabolism in sulfate reducing bacteria and archaea. Front Microbiol 2011; 2:69. [PMID: 21747791 PMCID: PMC3119410 DOI: 10.3389/fmicb.2011.00069] [Citation(s) in RCA: 215] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2011] [Accepted: 03/25/2011] [Indexed: 11/13/2022] Open
Abstract
The number of sequenced genomes of sulfate reducing organisms (SRO) has increased significantly in the recent years, providing an opportunity for a broader perspective into their energy metabolism. In this work we carried out a comparative survey of energy metabolism genes found in 25 available genomes of SRO. This analysis revealed a higher diversity of possible energy conserving pathways than classically considered to be present in these organisms, and permitted the identification of new proteins not known to be present in this group. The Deltaproteobacteria (and Thermodesulfovibrio yellowstonii) are characterized by a large number of cytochromes c and cytochrome c-associated membrane redox complexes, indicating that periplasmic electron transfer pathways are important in these bacteria. The Archaea and Clostridia groups contain practically no cytochromes c or associated membrane complexes. However, despite the absence of a periplasmic space, a few extracytoplasmic membrane redox proteins were detected in the Gram-positive bacteria. Several ion-translocating complexes were detected in SRO including H(+)-pyrophosphatases, complex I homologs, Rnf, and Ech/Coo hydrogenases. Furthermore, we found evidence that cytoplasmic electron bifurcating mechanisms, recently described for other anaerobes, are also likely to play an important role in energy metabolism of SRO. A number of cytoplasmic [NiFe] and [FeFe] hydrogenases, formate dehydrogenases, and heterodisulfide reductase-related proteins are likely candidates to be involved in energy coupling through electron bifurcation, from diverse electron donors such as H(2), formate, pyruvate, NAD(P)H, β-oxidation, and others. In conclusion, this analysis indicates that energy metabolism of SRO is far more versatile than previously considered, and that both chemiosmotic and flavin-based electron bifurcating mechanisms provide alternative strategies for energy conservation.
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Affiliation(s)
- Inês A Cardoso Pereira
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa Oeiras, Portugal
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Junier P, Junier T, Podell S, Sims DR, Detter JC, Lykidis A, Han CS, Wigginton NS, Gaasterland T, Bernier-Latmani R. The genome of the Gram-positive metal- and sulfate-reducing bacterium Desulfotomaculum reducens strain MI-1. Environ Microbiol 2011; 12:2738-54. [PMID: 20482743 DOI: 10.1111/j.1462-2920.2010.02242.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Spore-forming, Gram-positive sulfate-reducing bacteria (SRB) represent a group of SRB that dominates the deep subsurface as well as niches in which resistance to oxygen and dessication is an advantage. Desulfotomaculum reducens strain MI-1 is one of the few cultured representatives of that group with a complete genome sequence available. The metabolic versatility of this organism is reflected in the presence of genes encoding for the oxidation of various electron donors, including three- and four-carbon fatty acids and alcohols. Synteny in genes involved in sulfate reduction across all four sequenced Gram-positive SRB suggests a distinct sulfate-reduction mechanism for this group of bacteria. Based on the genomic information obtained for sulfate reduction in D. reducens, the transfer of electrons to the sulfite and APS reductases is proposed to take place via the quinone pool and heterodisulfide reductases respectively. In addition, both H(2) -evolving and H(2) -consuming cytoplasmic hydrogenases were identified in the genome, pointing to potential cytoplasmic H(2) cycling in the bacterium. The mechanism of metal reduction remains unknown.
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Affiliation(s)
- Pilar Junier
- Environmental Microbiology Laboratory, Ecole Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland
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Biochemical characterization of individual components of the Allochromatium vinosum DsrMKJOP transmembrane complex aids understanding of complex function in vivo. J Bacteriol 2010; 192:6369-77. [PMID: 20952577 DOI: 10.1128/jb.00849-10] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The DsrMKJOP transmembrane complex has a most important function in dissimilatory sulfur metabolism and consists of cytoplasmic, periplasmic, and membrane integral proteins carrying FeS centers and b- and c-type cytochromes as cofactors. In this study, the complex was isolated from the purple sulfur bacterium Allochromatium vinosum and individual components were characterized as recombinant proteins. The two integral membrane proteins DsrM and DsrP were successfully produced in Escherichia coli C43(DE3) and C41(DE3), respectively. DsrM was identified as a diheme cytochrome b, and the two hemes were found to be in low-spin state. Their midpoint redox potentials were determined to be +60 and +110 mV. Although no hemes were predicted for DsrP, it was also clearly identified as a b-type cytochrome. To the best of our knowledge, this is the first time that heme binding has been experimentally proven for a member of the NrfD protein family. Both cytochromes were partly reduced after addition of a menaquinol analogue, suggesting interaction with quinones in vivo. DsrO and DsrK were both experimentally proven to be FeS-containing proteins. In addition, DsrK was shown to be membrane associated, and we propose a monotopic membrane anchoring for this protein. Coelution assays provide support for the proposed interaction of DsrK with the soluble cytoplasmic protein DsrC, which might be its substrate. A model for the function of DsrMKJOP in the purple sulfur bacterium A. vinosum is presented.
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Zane GM, Yen HCB, Wall JD. Effect of the deletion of qmoABC and the promoter-distal gene encoding a hypothetical protein on sulfate reduction in Desulfovibrio vulgaris Hildenborough. Appl Environ Microbiol 2010; 76:5500-9. [PMID: 20581180 PMCID: PMC2918943 DOI: 10.1128/aem.00691-10] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2010] [Accepted: 06/18/2010] [Indexed: 12/24/2022] Open
Abstract
The pathway of electrons required for the reduction of sulfate in sulfate-reducing bacteria (SRB) is not yet fully characterized. In order to determine the role of a transmembrane protein complex suggested to be involved in this process, a deletion in Desulfovibrio vulgaris Hildenborough was created by marker exchange mutagenesis that eliminated four genes putatively encoding the QmoABC complex and a hypothetical protein (DVU0851). The Qmo (quinone-interacting membrane-bound oxidoreductase) complex is proposed to be responsible for transporting electrons to the dissimilatory adenosine-5'-phosphosulfate reductase in SRB. In support of the predicted role of this complex, the deletion mutant was unable to grow using sulfate as its sole electron acceptor with a range of electron donors. To explore a possible role for the hypothetical protein in sulfate reduction, a second mutant was constructed that had lost only the gene that codes for the DVU0851 protein. The second constructed mutant grew with sulfate as the sole electron acceptor; however, there was a lag that was not present with the wild-type or complemented strain. Neither deletion strain was significantly impaired for growth with sulfite or thiosulfate as the terminal electron acceptor. Complementation of the Delta(qmoABC-DVU0851) mutant with all four genes or only the qmoABC genes restored its ability to grow by sulfate respiration. These results confirmed the prediction that the Qmo complex is in the electron pathway for sulfate reduction and revealed that no other transmembrane complex could compensate when Qmo was lacking.
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Affiliation(s)
- Grant M. Zane
- University of Missouri, Columbia, Missouri, the Virtual Institute for Microbial Stress and Survival‡
| | - Huei-che Bill Yen
- University of Missouri, Columbia, Missouri, the Virtual Institute for Microbial Stress and Survival‡
| | - Judy D. Wall
- University of Missouri, Columbia, Missouri, the Virtual Institute for Microbial Stress and Survival‡
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Meyerdierks A, Kube M, Kostadinov I, Teeling H, Glöckner FO, Reinhardt R, Amann R. Metagenome and mRNA expression analyses of anaerobic methanotrophic archaea of the ANME-1 group. Environ Microbiol 2009; 12:422-39. [PMID: 19878267 DOI: 10.1111/j.1462-2920.2009.02083.x] [Citation(s) in RCA: 192] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Microbial consortia mediating the anaerobic oxidation of methane with sulfate are composed of methanotrophic Archaea (ANME) and Bacteria related to sulfate-reducing Deltaproteobacteria. Cultured representatives are not available for any of the three ANME clades. Therefore, a metagenomic approach was applied to assess the genetic potential of ANME-1 archaea. In total, 3.4 Mbp sequence information was generated based on metagenomic fosmid libraries constructed directly from a methanotrophic microbial mat in the Black Sea. These sequence data represent, in 30 contigs, about 82-90% of a composite ANME-1 genome. The dataset supports the hypothesis of a reversal of the methanogenesis pathway. Indications for an assimilatory, but not for a dissimilatory sulfate reduction pathway in ANME-1, were found. Draft genome and expression analyses are consistent with acetate and formate as putative electron shuttles. Moreover, the dataset points towards downstream electron-accepting redox components different from the ones known from methanogenic archaea. Whereas catalytic subunits of [NiFe]-hydrogenases are lacking in the dataset, genes for an [FeFe]-hydrogenase homologue were identified, not yet described to be present in methanogenic archaea. Clustered genes annotated as secreted multiheme c-type cytochromes were identified, which have not yet been correlated with methanogenesis-related steps. The genes were shown to be expressed, suggesting direct electron transfer as an additional possible mode to shuttle electrons from ANME-1 to the bacterial sulfate-reducing partner.
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Affiliation(s)
- Anke Meyerdierks
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359 Bremen, Germany.
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Quatrini R, Appia-Ayme C, Denis Y, Jedlicki E, Holmes DS, Bonnefoy V. Extending the models for iron and sulfur oxidation in the extreme acidophile Acidithiobacillus ferrooxidans. BMC Genomics 2009; 10:394. [PMID: 19703284 PMCID: PMC2754497 DOI: 10.1186/1471-2164-10-394] [Citation(s) in RCA: 220] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2009] [Accepted: 08/24/2009] [Indexed: 11/10/2022] Open
Abstract
Background Acidithiobacillus ferrooxidans gains energy from the oxidation of ferrous iron and various reduced inorganic sulfur compounds at very acidic pH. Although an initial model for the electron pathways involved in iron oxidation has been developed, much less is known about the sulfur oxidation in this microorganism. In addition, what has been reported for both iron and sulfur oxidation has been derived from different A. ferrooxidans strains, some of which have not been phylogenetically characterized and some have been shown to be mixed cultures. It is necessary to provide models of iron and sulfur oxidation pathways within one strain of A. ferrooxidans in order to comprehend the full metabolic potential of the pangenome of the genus. Results Bioinformatic-based metabolic reconstruction supported by microarray transcript profiling and quantitative RT-PCR analysis predicts the involvement of a number of novel genes involved in iron and sulfur oxidation in A. ferrooxidans ATCC23270. These include for iron oxidation: cup (copper oxidase-like), ctaABT (heme biogenesis and insertion), nuoI and nuoK (NADH complex subunits), sdrA1 (a NADH complex accessory protein) and atpB and atpE (ATP synthetase F0 subunits). The following new genes are predicted to be involved in reduced inorganic sulfur compounds oxidation: a gene cluster (rhd, tusA, dsrE, hdrC, hdrB, hdrA, orf2, hdrC, hdrB) encoding three sulfurtransferases and a heterodisulfide reductase complex, sat potentially encoding an ATP sulfurylase and sdrA2 (an accessory NADH complex subunit). Two different regulatory components are predicted to be involved in the regulation of alternate electron transfer pathways: 1) a gene cluster (ctaRUS) that contains a predicted iron responsive regulator of the Rrf2 family that is hypothesized to regulate cytochrome aa3 oxidase biogenesis and 2) a two component sensor-regulator of the RegB-RegA family that may respond to the redox state of the quinone pool. Conclusion Bioinformatic analysis coupled with gene transcript profiling extends our understanding of the iron and reduced inorganic sulfur compounds oxidation pathways in A. ferrooxidans and suggests mechanisms for their regulation. The models provide unified and coherent descriptions of these processes within the type strain, eliminating previous ambiguity caused by models built from analyses of multiple and divergent strains of this microorganism.
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Affiliation(s)
- Raquel Quatrini
- Center for Bioinformatics and Genome Biology, MIFAB, Fundación Ciencia para la Vida and Depto. de Ciencias Biologicas, Universidad Andres Bello, Santiago, Chile.
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Strittmatter AW, Liesegang H, Rabus R, Decker I, Amann J, Andres S, Henne A, Fricke WF, Martinez-Arias R, Bartels D, Goesmann A, Krause L, Pühler A, Klenk HP, Richter M, Schüler M, Glöckner FO, Meyerdierks A, Gottschalk G, Amann R. Genome sequence of Desulfobacterium autotrophicum HRM2, a marine sulfate reducer oxidizing organic carbon completely to carbon dioxide. Environ Microbiol 2009; 11:1038-55. [PMID: 19187283 PMCID: PMC2702500 DOI: 10.1111/j.1462-2920.2008.01825.x] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2008] [Accepted: 10/25/2008] [Indexed: 01/23/2023]
Abstract
Sulfate-reducing bacteria (SRB) belonging to the metabolically versatile Desulfobacteriaceae are abundant in marine sediments and contribute to the global carbon cycle by complete oxidation of organic compounds. Desulfobacterium autotrophicum HRM2 is the first member of this ecophysiologically important group with a now available genome sequence. With 5.6 megabasepairs (Mbp) the genome of Db. autotrophicum HRM2 is about 2 Mbp larger than the sequenced genomes of other sulfate reducers (SRB). A high number of genome plasticity elements (> 100 transposon-related genes), several regions of GC discontinuity and a high number of repetitive elements (132 paralogous genes Mbp(-1)) point to a different genome evolution when comparing with Desulfovibrio spp. The metabolic versatility of Db. autotrophicum HRM2 is reflected in the presence of genes for the degradation of a variety of organic compounds including long-chain fatty acids and for the Wood-Ljungdahl pathway, which enables the organism to completely oxidize acetyl-CoA to CO(2) but also to grow chemolithoautotrophically. The presence of more than 250 proteins of the sensory/regulatory protein families should enable Db. autotrophicum HRM2 to efficiently adapt to changing environmental conditions. Genes encoding periplasmic or cytoplasmic hydrogenases and formate dehydrogenases have been detected as well as genes for the transmembrane TpII-c(3), Hme and Rnf complexes. Genes for subunits A, B, C and D as well as for the proposed novel subunits L and F of the heterodisulfide reductases are present. This enzyme is involved in energy conservation in methanoarchaea and it is speculated that it exhibits a similar function in the process of dissimilatory sulfate reduction in Db. autotrophicum HRM2.
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Affiliation(s)
- Axel W Strittmatter
- Göttingen Genomics Laboratory, Georg-August-UniversityGrisebachstr. 8, D-37077 Göttingen, Germany
| | - Heiko Liesegang
- Göttingen Genomics Laboratory, Georg-August-UniversityGrisebachstr. 8, D-37077 Göttingen, Germany
| | - Ralf Rabus
- Max Planck Institute for Marine MicrobiologyCelsiusstr. 1, D-28359 Bremen, Germany
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University OldenburgCarl-von-Ossietzky Str. 9-11, D-26111 Oldenburg, Germany
| | - Iwona Decker
- Göttingen Genomics Laboratory, Georg-August-UniversityGrisebachstr. 8, D-37077 Göttingen, Germany
| | - Judith Amann
- Max Planck Institute for Marine MicrobiologyCelsiusstr. 1, D-28359 Bremen, Germany
| | - Sönke Andres
- Göttingen Genomics Laboratory, Georg-August-UniversityGrisebachstr. 8, D-37077 Göttingen, Germany
| | - Anke Henne
- Göttingen Genomics Laboratory, Georg-August-UniversityGrisebachstr. 8, D-37077 Göttingen, Germany
| | - Wolfgang Florian Fricke
- Göttingen Genomics Laboratory, Georg-August-UniversityGrisebachstr. 8, D-37077 Göttingen, Germany
| | - Rosa Martinez-Arias
- Göttingen Genomics Laboratory, Georg-August-UniversityGrisebachstr. 8, D-37077 Göttingen, Germany
| | - Daniela Bartels
- Center for Biotechnology (CeBiTec), Bielefeld UniversityUniversitätsstr. 37, D-33615 Bielefeld, Germany
| | - Alexander Goesmann
- Center for Biotechnology (CeBiTec), Bielefeld UniversityUniversitätsstr. 37, D-33615 Bielefeld, Germany
| | - Lutz Krause
- Center for Biotechnology (CeBiTec), Bielefeld UniversityUniversitätsstr. 37, D-33615 Bielefeld, Germany
| | - Alfred Pühler
- Lehrstuhl für Genetik, Fakultät für Biologie, Universität BielefeldD-33594 Bielefeld, Germany
| | - Hans-Peter Klenk
- DSMZ – Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbHInhoffenstraße 7 B, D-38124 Braunschweig, Germany
| | - Michael Richter
- Max Planck Institute for Marine MicrobiologyCelsiusstr. 1, D-28359 Bremen, Germany
| | - Margarete Schüler
- Max Planck Institute for Marine MicrobiologyCelsiusstr. 1, D-28359 Bremen, Germany
| | | | - Anke Meyerdierks
- Max Planck Institute for Marine MicrobiologyCelsiusstr. 1, D-28359 Bremen, Germany
| | - Gerhard Gottschalk
- Göttingen Genomics Laboratory, Georg-August-UniversityGrisebachstr. 8, D-37077 Göttingen, Germany
| | - Rudolf Amann
- Max Planck Institute for Marine MicrobiologyCelsiusstr. 1, D-28359 Bremen, Germany
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