The Experts below are selected from a list of 981 Experts worldwide ranked by ideXlab platform
Jillian F Banfield - One of the best experts on this subject based on the ideXlab platform.
-
Communicated by K. Horikoshi
2013Co-Authors: Jillian F Banfield, Jennifer L. Macalady, Æ Martha, M. Vestling, David Baumler, Æ Nick, Boekelheide Æ Charles, W. Kaspar, Æ J. F. BanfieldAbstract:Tetraether-linked membrane monolayers in Ferroplasma spp: a key to survival in aci
-
Comparative genomics in acid mine drainage biofilm communities reveals metabolic and structural differentiation of co-occurring archaea
BMC genomics, 2013Co-Authors: Alexis P Yelton, Luis R. Comolli, Nicholas B. Justice, Cindy J. Castelle, Vincent J. Denef, Brian C. Thomas, Jillian F BanfieldAbstract:Background: Metal sulfide mineral dissolution during bioleaching and acid mine drainage (AMD) formation creates an environment that is inhospitable to most life. Despite dominance by a small number of bacteria, AMD microbial biofilm communities contain a notable variety of coexisting and closely related Euryarchaea, most of which have defied cultivation efforts. For this reason, we used metagenomics to analyze variation in gene content that may contribute to niche differentiation among co-occurring AMD archaea. Our analyses targeted members of the Thermoplasmatales and related archaea. These results greatly expand genomic information available for this archaeal order. Results: We reconstructed near-complete genomes for uncultivated, relatively low abundance organisms A-, E-, and Gplasma, members of Thermoplasmatales order, and for a novel organism, Iplasma. Genomic analyses of these organisms, as well as Ferroplasma type I and II, reveal that all are facultative aerobic heterotrophs with the ability to use many of the same carbon substrates, including methanol. Most of the genomes share genes for toxic metal resistance and surface-layer production. Only Aplasma and Eplasma have a full suite of flagellar genes whereas all but the Ferroplasma spp. have genes for pili production. Cryogenic-electron microscopy (cryo-EM) and tomography (cryo-ET) strengthen these metagenomics-based ultrastructural predictions. Notably, only Aplasma, Gplasma and the Ferroplasma spp. have predicted iron oxidation genes and Eplasma and Iplasma lack most genes for cobalamin, valine, (iso)leucine and histidine synthesis. Conclusion: The Thermoplasmatales AMD archaea share a large number of metabolic capabilities. All of the uncultivated organisms studied here (A-, E-, G-, and Iplasma) are metabolically very similar to characterized Ferroplasma spp., differentiating themselves mainly in their genetic capabilities for biosynthesis, motility, and possibly iron oxidation. These results indicate that subtle, but important genomic differences, coupled with unknown differences in gene expression, distinguish these organisms enough to allow for co-existence. Overall this study reveals shared features of organisms from the Thermoplasmatales lineage and provides new insights into the functioning of AMD communities.
-
Genetic exchange across a species boundary in the archaeal genus Ferroplasma.
Genetics, 2007Co-Authors: John M. Eppley, Gene W. Tyson, Wayne M. Getz, Jillian F BanfieldAbstract:Speciation as the result of barriers to genetic exchange is the foundation for the general biological species concept. However, the relevance of genetic exchange for defining microbial species is uncertain. In fact, the extent to which microbial populations comprise discrete clusters of evolutionarily related organisms is generally unclear. Metagenomic data from an acidophilic microbial community enabled a genomewide, comprehensive investigation of variation in individuals from two coexisting natural archaeal populations. Individuals are clustered into species-like groups in which cohesion appears to be maintained by homologous recombination. We quantified the dependence of recombination frequency on sequence similarity genomewide and found a decline in recombination with increasing evolutionary distance. Both inter- and intralineage recombination frequencies have a log-linear dependence on sequence divergence. In the declining phase of interspecies genetic exchange, recombination events cluster near the origin of replication and are localized by tRNAs and short regions of unusually high sequence similarity. The breakdown of genetic exchange with increasing sequence divergence could contribute to, or explain, the establishment and preservation of the observed population clusters in a manner consistent with the biological species concept.
-
Sulfate requirement for heterotrophic growth of "Ferroplasma acidarmanus" strain fer1.
Research in microbiology, 2005Co-Authors: David J. Baumler, Jillian F Banfield, Kwang Cheol Jeong, Brian G. Fox, Charles W. KasparAbstract:Abstract Growth of the acidophilic archaeon, “Ferroplasma acidarmanus” strain fer1, in a laboratory medium (primary constituents, FeSO4 72 mM and 0.02% yeast extract) is minimal. A survey of the annotated genome revealed metabolic transporters for Ni2+, sugars, and amino acids. Accordingly, the concentration of yeast extract was increased to 0.1% and the addition of 2 mM Ni(NH4)2(SO4)2 significantly enhanced the cultivation of strain fer1. The maximum optical density in the modified fer1 medium (mfer) was OD 492 = 0.27 with 1010 viable cells / ml as determined by a most-probable-number method, which exceeds previously reported viable cells / ml by >100-fold. Strain fer1 displayed chemolithotrophic growth with Fe2+ in mfer containing 100 mM FeSO4 or FeCl2. In the absence of Fe2+, heterotrophic growth occurred with one of the following salts (100 mM): ZnSO4, MnSO4, MgSO4, (NH4)2SO4, or Fe2(SO4)3, and did not occur with (100 mM): ZnCl2, MnCl2, MgCl2, NH4Cl, or FeCl3. Escaping headspace gas from strain fer1 cultures formed a precipitate in a zinc acetate trap. Sulfide was absent in the precipitate but zinc and sulfur were detected. These data demonstrate that SO4 is required for heterotrophic growth of strain fer1 and may have a role in the global sulfur cycle.
-
Tetraether-linked membrane monolayers in Ferroplasma spp: a key to survival in acid
Extremophiles, 2004Co-Authors: Jennifer L. Macalady, David Baumler, Charles W. Kaspar, Martha M. Vestling, Nick Boekelheide, Jillian F BanfieldAbstract:Ferroplasma acidarmanus thrives in hot, extremely low pH, metal-rich solutions associated with dissolving metal sulfide ore deposits. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and thin layer chromatography analyses of F. acidarmanus membranes indicate that tetraether lipids predominate, with at least three core lipid structures. NMR measurements indicate that the cytoplasmic pH of F. acidarmanus is ~5.6. The optimal growth pH is ~1.2, and the lowest growth pH is ~0.0. Thus, these organisms maintain pH gradients across their membranes that approach 5 pH units. Tetraether lipids were originally thought to be specifically associated with thermophiles but are now known to be widely distributed within the archaeal domain. Our data, in combination with recently published results for thermophilic and mesothermophilic acidophilic archaea, indicate that there may be a stronger association between tetraether lipids and tolerance to acid and/or large metal ion gradients.
Weimin Zeng - One of the best experts on this subject based on the ideXlab platform.
-
effects of ph value on the expression of key iron sulfur oxidation genes during bioleaching of chalcopyrite on thermophilic condition
Annals of Microbiology, 2019Co-Authors: Tangjian Peng, Guanzhou Qiu, Dan Zhou, Yanan Liu, Weimin ZengAbstract:Physicochemical factors such pH value would affect the microbial metabolism during chalcopyrite bioleaching. To this end, the effects of pH on the expression of critical functional genes during bioleaching were evaluated. A mixed culture of moderate thermophiles was used for chalcopyrite bioleaching at initial pH values of 1.0, 2.0, and 3.0, and bioleaching processes were monitored via measuring the physicochemical parameters. Quantitative real-time PCR assay was used to monitor the dynamics of microbial community structures and the expression of critical iron/sulfur oxidation genes (4Fe-4S ferredoxin and sulfate adenylyltransferase genes, respectively). Redundancy analysis and calculation of correlation coefficients were used to reveal linkages between gene expression and various physicochemical factors. The leaching processes at initial pH of 1.0 and 3.0 were prolonged compared with that at initial pH of 2.0. It was shown that Sulfobacillus thermosulfidooxidans and Acidithiobacillus caldus were the dominant species during the early stage in free and attached cells, respectively, while Ferroplasma thermophilum became predominant in the later phase. The gene expression in Sulfobacillus thermosulfidooxidans and Ferroplasma thermophilum was greatly affected by pH values. On the other hand, the relationship between pH and gene expression in Acidithiobacillus caldus was not significant. The study unraveled the importance of pH value on chalcopyrite bioleaching, and pH selectively influenced the expression of key functional genes of some specific species.
-
Effects of pH value on the expression of key iron/sulfur oxidation genes during bioleaching of chalcopyrite on thermophilic condition
Annals of Microbiology, 2019Co-Authors: Tangjian Peng, Guanzhou Qiu, Dan Zhou, Liu Yanan, Yu Runlan, Weimin ZengAbstract:Physicochemical factors such pH value would affect the microbial metabolism during chalcopyrite bioleaching. To this end, the effects of pH on the expression of critical functional genes during bioleaching were evaluated. A mixed culture of moderate thermophiles was used for chalcopyrite bioleaching at initial pH values of 1.0, 2.0, and 3.0, and bioleaching processes were monitored via measuring the physicochemical parameters. Quantitative real-time PCR assay was used to monitor the dynamics of microbial community structures and the expression of critical iron/sulfur oxidation genes (4Fe-4S ferredoxin and sulfate adenylyltransferase genes, respectively). Redundancy analysis and calculation of correlation coefficients were used to reveal linkages between gene expression and various physicochemical factors. The leaching processes at initial pH of 1.0 and 3.0 were prolonged compared with that at initial pH of 2.0. It was shown that Sulfobacillus thermosulfidooxidans and Acidithiobacillus caldus were the dominant species during the early stage in free and attached cells, respectively, while Ferroplasma thermophilum became predominant in the later phase. The gene expression in Sulfobacillus thermosulfidooxidans and Ferroplasma thermophilum was greatly affected by pH values. On the other hand, the relationship between pH and gene expression in Acidithiobacillus caldus was not significant. The study unraveled the importance of pH value on chalcopyrite bioleaching, and pH selectively influenced the expression of key functional genes of some specific species.
-
the shift of microbial community under the adjustment of initial and processing ph during bioleaching of chalcopyrite concentrate by moderate thermophiles
Bioresource Technology, 2014Co-Authors: Runlan Yu, Weimin Zeng, Dan Zhou, Guohua Gu, Miao ChenAbstract:The shift of microbial community under the adjustment of different pH was analyzed by denaturing gradient gel electrophoresis (DGGE). The results indicated, at initial pH 1.0, 2.0 and 3.0, the copper extraction in 22 days amounted to 84.6%, 88.2% and 77.5%, respectively; however, when the initial pH was 2.0, processing pH was adjusted to 1.0 and 3.0 on day 16, the copper extraction in 32 days was 85% and 62.6%, respectively. DGGE analysis showed Acidithiobacillus caldus, Leptospirillum ferriphilum, Sulfobacillus thermosulfidooxidans and Ferroplasma thermophilum existed in bioleaching systems. At initial pH 1.0 and 3.0, S. thermosulfidooxidans and A. caldus were main microorganisms. While at initial pH 2.0, L. ferriphilum, A. caldus and S. thermosulfidooxidans were always detected. At processing pH 1.0 and 3.0, the adjustment of pH greatly inhibited the growth of L. ferriphilum; it was also found microbial community would recover gradually only if pH stimulation did not fatally affect microorganisms.
-
Effect of pulp density on planktonic and attached community dynamics during bioleaching of chalcopyrite by a moderately thermophilic microbial culture under uncontrolled conditions
Minerals Engineering, 2014Co-Authors: Yuguang Wang, Weimin Zeng, Guanzhou Qiu, Lijuan Zhang, Lili Wan, Xinhua Chen, Zhu Chen, Hongbo ZhouAbstract:Abstract An enriched and adapted moderately thermophilic culture showed good performance during bioleaching of chalcopyrite under uncontrolled conditions. The copper extractions were up to 85.0%, 77.3% and 56.3% at pulp densities of 10%, 15% and 20% (w/v) within 22 days, respectively. The real-time quantitative PCR was employed to monitor planktonic and attached community dynamics during bioleaching of chalcopyrite by the moderately thermophilic microbial culture. Only three species, including Acidithiobacillus caldus , Sulfobacillus acidophilus and Ferroplasma thermophilum , were detected during the whole bioleaching process. The results show that pulp density had significant effects on planktonic and attached microbial community dynamics. The succession of attached cells was different from community dynamics of their planktonic counterparts. F. thermophilum and A. caldus preferred to attach to mineral surface, especially at pulp densities of 15% and 20%.
-
Bioleaching of chalcopyrite by defined mixed moderately thermophilic consortium including a marine acidophilic halotolerant bacterium
Bioresource Technology, 2012Co-Authors: Yuguang Wang, Weimin Zeng, Lijuan Zhang, Xinhua Chen, Lijun Su, Junzi Wu, Hongbo ZhouAbstract:Abstract A defined mixed moderately thermophilic consortium including three terrestrial microorganisms ( Leptospirillum ferriphilum , Acidithiobacillus caldus and Ferroplasma thermophilum ) and a marine acidophilic halotolerant bacterium ( Sulfobacillus sp. TPY) was constructed to evaluate its ability for bioleaching of chalcopyrite with the addition of sodium chloride (NaCl), and the community dynamics was monitored by real-time quantitative PCR (qPCR). It was found that Sulfobacillus sp. TPY was able to tolerate 2% (w/v) NaCl, while other three microorganisms were suppressed when the concentration of NaCl was higher than 0.35%. The results suggested that NaCl below certain concentration could improve copper extraction by using pure cultures or the consortium to bioleach chalcopyrite. Community dynamics analysis during bioleaching at 0.1% NaCl showed that Sulfobacillus sp. TPY was predominant species during the whole bioleaching process, L. ferriphilum and A. caldus were less at any time compared with Sulfobacillus sp. TPY. F. thermophilum had never been dominant species even in the final stage.
Hongbo Zhou - One of the best experts on this subject based on the ideXlab platform.
-
Insight to the early-stage adsorption mechanism of moderately thermophilic consortia and intensified bioleaching of chalcopyrite
Biochemical Engineering Journal, 2019Co-Authors: Liu Ronghui, Chen Jing, Wenbo Zhou, Haina Cheng, Hongbo ZhouAbstract:Abstract Biofilm plays an important role on chalcopyrite bioleaching and early-stage adsorption of cells are essential for biofilm formation. In this study, the interspecies interaction and the early adsorption behavior of moderately thermophilic consortia (Ferroplasma thermophilum, Leptospirillum ferriphilum and Acidithiobacillus caldus) were investigated. qPCR and Confocal laser scanning microscopy (CLSM) were adopted in this study. The bacterial adsorption experiments showed that three pure culture could attach properly on chalcopyrite within a short time and the equilibrium data was well fitted with both Langmuir and Freundlich models. Meanwhile, compared to Ferroplasma thermophilum, Leptospirillum ferriphilum and Acidithiobacillus caldus showed coadsorption relationship and owned competitive adavantages in the binary culture system. The adsorption of both Leptospirillum ferriphilum and Acidithiobacillus caldus together promoted the attachment of Ferroplasma thermophilum. The intensified bioleaching assays based on this attachment mechanism showed that the bioaugmentation of the advanced leaching stage by adapated Ferroplasma thermophilum significantly accelerated copper extraction. Confocal laser scanning microscopy (CLSM) results confirmed the improved biofilm formation by bioaugmentation with adapted Ferroplasma thermophilum. Furthermore, a mechanism model for intensifying chalcopyrite bioleaching by biofilm was established. The results revealed that attachment was complicated but provided an efficient approach to intensify chalcopyrite bioleaching.
-
Influence of bioaugmentation with Ferroplasma thermophilum on chalcopyrite bioleaching and microbial community structure
Hydrometallurgy, 2014Co-Authors: Lijuan Zhang, Yuguang Wang, Lili Wan, Feng Mao, Wei Zhang, Xinhua Chen, Hongbo ZhouAbstract:Abstract Ferroplasma spp. are cell wall-deficient, extremely acidophilic and iron-oxidising archaea that have considerable biotechnological potential for bioleaching processes. The current study focuses on investigating the ecological importance of mixotrophic Ferroplasma thermophilum L1 during chalcopyrite bioleaching and the feasibility of bioaugmentation with this archaeon to improve the extraction of copper from chalcopyrite. Bioaugmentation consisted of the addition of highly concentrated F . thermophilum (with different inoculum concentrations) into the two defined bioleaching systems that represented the early and advanced chalcopyrite bioleaching stages. The evolution of bioleaching performance, microbial community structure and leached solid residues after bioaugmentation were compared with those in the conventional (control) bioleaching experiment. The results of bioaugmentation undertaken at the early stage showed that the growth of Leptospirillum ferriphilum and Acidithiobacillus caldus were promoted after bioaugmentation, which, in turn, assisted F . thermophilum in surviving under the same conditions. Concurrently, the mineral dissolving and copper extraction rates were significantly accelerated, especially in the ‘Fer-1/1’ test that was bioaugmented with the highest addition amount. After 24 days, 90.2% of the total copper was leached out, which was higher than the value (83.4%) obtained in the control. The untimely formation of a ‘Jarosite’ passivation layer decreased the rate of copper release at the later stage of the ‘Fer-1/1’ test. The bioaugmentation of the advanced leaching stage was detrimental to the chalcopyrite dissolution; the number of added F . thermophilum cells negatively correlated with the copper recovery. The poor bioleaching was also primarily associated with the formation of iron precipitation due to the increased cell numbers of iron oxidisers. These findings indicate that different bioaugmented treatments with F . thermophilum clearly influenced chalcopyrite leaching and the microbial community. Bioaugmentation could be a useful remedy to accelerate chalcopyrite dissolution.
-
Effect of pulp density on planktonic and attached community dynamics during bioleaching of chalcopyrite by a moderately thermophilic microbial culture under uncontrolled conditions
Minerals Engineering, 2014Co-Authors: Yuguang Wang, Weimin Zeng, Guanzhou Qiu, Lijuan Zhang, Lili Wan, Xinhua Chen, Zhu Chen, Hongbo ZhouAbstract:Abstract An enriched and adapted moderately thermophilic culture showed good performance during bioleaching of chalcopyrite under uncontrolled conditions. The copper extractions were up to 85.0%, 77.3% and 56.3% at pulp densities of 10%, 15% and 20% (w/v) within 22 days, respectively. The real-time quantitative PCR was employed to monitor planktonic and attached community dynamics during bioleaching of chalcopyrite by the moderately thermophilic microbial culture. Only three species, including Acidithiobacillus caldus , Sulfobacillus acidophilus and Ferroplasma thermophilum , were detected during the whole bioleaching process. The results show that pulp density had significant effects on planktonic and attached microbial community dynamics. The succession of attached cells was different from community dynamics of their planktonic counterparts. F. thermophilum and A. caldus preferred to attach to mineral surface, especially at pulp densities of 15% and 20%.
-
Bioleaching of chalcopyrite by defined mixed moderately thermophilic consortium including a marine acidophilic halotolerant bacterium
Bioresource Technology, 2012Co-Authors: Yuguang Wang, Weimin Zeng, Lijuan Zhang, Xinhua Chen, Lijun Su, Junzi Wu, Hongbo ZhouAbstract:Abstract A defined mixed moderately thermophilic consortium including three terrestrial microorganisms ( Leptospirillum ferriphilum , Acidithiobacillus caldus and Ferroplasma thermophilum ) and a marine acidophilic halotolerant bacterium ( Sulfobacillus sp. TPY) was constructed to evaluate its ability for bioleaching of chalcopyrite with the addition of sodium chloride (NaCl), and the community dynamics was monitored by real-time quantitative PCR (qPCR). It was found that Sulfobacillus sp. TPY was able to tolerate 2% (w/v) NaCl, while other three microorganisms were suppressed when the concentration of NaCl was higher than 0.35%. The results suggested that NaCl below certain concentration could improve copper extraction by using pure cultures or the consortium to bioleach chalcopyrite. Community dynamics analysis during bioleaching at 0.1% NaCl showed that Sulfobacillus sp. TPY was predominant species during the whole bioleaching process, L. ferriphilum and A. caldus were less at any time compared with Sulfobacillus sp. TPY. F. thermophilum had never been dominant species even in the final stage.
-
community structure and dynamics of the free and attached microorganisms during moderately thermophilic bioleaching of chalcopyrite concentrate
Bioresource Technology, 2010Co-Authors: Weimin Zeng, Hongbo Zhou, Miao Chen, Juanhua Peng, Weiliang Chao, Yansheng ZhangAbstract:A mixed culture of moderately thermophiles showed good performance in bioleaching of chalcopyrite. Its community structure was investigated by amplified ribosomal DNA restriction analysis. The result shows that Leptospirillum ferriphilum and Acidithiobacillus caldus were the predominant bacteria and Ferroplasma thermophilum, the only archaea, could be always detected during bioleaching. Therefore, real-time PCR assay was performed to monitor these microorganisms’ dynamics in the solution and on the mineral surface. It is shown that both in the solution and on the mineral surface, A. caldus was the dominant species at the early stage and L. ferriphilum was the predominant species at the later stage. The amount of the same species exhibited different variation trends in the solution and on the mineral surface. The amount of attached L. ferriphilum increased faster than that of the free one, and the amount of attached F. thermophilum kept at a stable level while the free one increased rapidly at the end.
Olga V. Golyshina - One of the best experts on this subject based on the ideXlab platform.
-
Metabolic and evolutionary patterns in the extremely acidophilic archaeon Ferroplasma acidiphilum YT.
Scientific reports, 2017Co-Authors: Olga V. Golyshina, Hai Tran, Oleg N. Reva, Sofia Lemak, Alexander F. Yakunin, Alexander Goesmann, Taras Y. Nechitaylo, Violetta Lacono, Francesco Smedile, Alexei SlesarevAbstract:Ferroplasmaceae represent ubiquitous iron-oxidising extreme acidophiles with a number of unique physiological traits. In a genome-based study of Ferroplasma acidiphilum YT, the only species of the genus Ferroplasma with a validly published name, we assessed its central metabolism and genome stability during a long-term cultivation experiment. Consistently with physiology, the genome analysis points to F. acidiphilum YT having an obligate peptidolytic oligotrophic lifestyle alongside with anaplerotic carbon assimilation. This narrow trophic specialisation abridges the sugar uptake, although all genes for glycolysis and gluconeogenesis, including bifunctional unidirectional fructose 1,6-bisphosphate aldolase/phosphatase, have been identified. Pyruvate and 2-oxoglutarate dehydrogenases are substituted by ‘ancient’ CoA-dependent pyruvate and alpha-ketoglutarate ferredoxin oxidoreductases. In the lab culture, after ~550 generations, the strain exhibited the mutation rate of ≥1.3 × 10−8 single nucleotide substitutions per site per generation, which is among the highest values recorded for unicellular organisms. All but one base substitutions were G:C to A:T, their distribution between coding and non-coding regions and synonymous-to-non-synonymous mutation ratios suggest the neutral drift being a prevalent mode in genome evolution in the lab culture. Mutations in nature seem to occur with lower frequencies, as suggested by a remarkable genomic conservation in F. acidiphilum YT variants from geographically distant populations.
-
The aerobic respiratory chain of the acidophilic archaeon Ferroplasma acidiphilum: A membrane-bound complex oxidizing ferrous iron
Biochimica biophysica acta (BBA) - Bioenergetics, 2015Co-Authors: Cindy Castelle, Olga V. Golyshina, Manfred Nimtz, Magali Roger, Marielle Bauzan, Myriam Brugna, Sabrina Lignon, Marie-thérèse Giudici-orticoni, Marianne GuiralAbstract:The extremely acidophilic archaeon Ferroplasma acidiphilum is found in iron-rich biomining environments and is an important micro-organism in naturally occurring microbial communities in acid mine drainage. F. acidiphilum is an iron oxidizer that belongs to the order Thermoplasmatales (Euryarchaeota), which harbors the most extremely acidophilic micro-organisms known so far. At present, little is known about the nature or the structural and functional organization of the proteins in F. acidiphilum that impact the iron biogeochemical cycle. We combine here biochemical and biophysical techniques such as enzyme purification, activity measurements, proteomics and spectroscopy to characterize the iron oxidation pathway(s) in F. acidiphilum. We isolated two respiratory membrane protein complexes: a 850 kDa complex containing an aa3-type cytochrome oxidase and a blue copper protein, which directly oxidizes ferrous iron and reduces molecular oxygen, and a 150 kDa cytochrome ba complex likely composed of a di-heme cytochrome and a Rieske protein. We tentatively propose that both of these complexes are involved in iron oxidation respiratory chains, functioning in the so-called uphill and downhill electron flow pathways, consistent with autotrophic life. The cytochrome ba complex could possibly play a role in regenerating reducing equivalents by a reverse (‘uphill’) electron flow. This study constitutes the first detailed biochemical investigation of the metalloproteins that are potentially directly involved in iron-mediated energy conservation in a member of the acidophilic archaea of the genus Ferroplasma
-
Acidiplasma aeolicum gen. nov., sp. nov., a euryarchaeon of the family Ferroplasmaceae isolated from a hydrothermal pool, and transfer of Ferroplasma cupricumulans to Acidiplasma cupricumulans comb. nov.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 2009Co-Authors: Olga V. Golyshina, Kenneth N. Timmis, Manuel Ferrer, Michail M. Yakimov, Heinrich Lünsdorf, Manfred Nimtz, Victor Wray, Brian J. Tindall, Peter N. GolyshinAbstract:A novel acidophilic, cell-wall-less archaeon, strain VT, was isolated from a hydrothermal pool on Vulcano Island, Italy. The morphology of cells was observed to vary from pleomorphic to coccoid. The temperature range for growth of strain VT was 15–65 °C with an optimum at 45 °C. The pH for growth ranged from pH 0 to 4 with an optimal at pH 1.4–1.6. Strain VT was able to grow aerobically and anaerobically, oxidizing ferrous iron and reducing ferric iron, respectively. The isolate grew chemo-organotrophically with yeast extract and yeast extract with glucose as the sources of energy and carbon. The molar G+C content in the DNA was 36 mol%. 16S rRNA gene sequence analysis demonstrated that strain VT was a member of the family Ferroplasmaceae, order Thermoplasmatales, phylum Euryarchaeota, showing sequence identities of 100 % with Ferroplasma cupricumulans BH2T, 95.4 % with Ferroplasma acidiphilum YT, 94 % with Picrophilus torridus DSM 9790T and 92 % with Picrophilus oshimae DSM 9789T. 16S rRNA gene sequence-based phylogenetic analysis showed that strain VT formed a monophyletic cluster together with F. cupricumulans BH2T and all other thermophilic isolates with available 16S rRNA gene sequences, whereas F. acidiphilum YT formed another cluster with mesophilic isolates within the family Ferroplasmaceae. DNA–DNA hybridization values between strain VT and F. cupricumulans BH2T were well below 70 %, indicating that the two strains belong to separate species. Principal membrane lipids of strain VT were dibiphytanyl-based tetraether lipids containing pentacyclic rings. The polar lipids were dominated by a single phosphoglycolipid derivative based on a galactosyl dibiphytanyl phosphoglycerol tetraether, together with smaller amounts of monoglycosyl and diglycosyl dibiphytanyl ether lipids and the corresponding phosphoglycerol derivatives. The major respiratory quinones present were naphthoquinone derivatives. Given the notable physiological and chemical differences as well as the distinct phylogenetic placement of the new isolate relative to the type species of the genus Ferroplasma, we propose strain VT as a member of a new genus and species, Acidiplasma aeolicum gen. nov., sp. nov. The type strain of Acidiplasma aeolicum is strain VT (=DSM 18409T =JCM 14615T). In addition, we propose to transfer Ferroplasma cupricumulans Hawkes et al. 2008 to the genus Acidiplasma as Acidiplasma cupricumulans comb. nov. (type strain BH2T =DSM 16551T =JCM 13668T).
-
Acidiplasma aeolicum gen. nov., sp. nov., a euryarchaeon of the family Ferroplasmaceae isolated from a hydrothermal pool, and transfer of Ferroplasma cupricumulans to Acidiplasma cupricumulans comb. nov.
International journal of systematic and evolutionary microbiology, 2009Co-Authors: Olga V. Golyshina, Kenneth N. Timmis, Manuel Ferrer, Michail M. Yakimov, Heinrich Lünsdorf, Manfred Nimtz, Victor Wray, Brian J. Tindall, Peter N. GolyshinAbstract:A novel acidophilic, cell-wall-less archaeon, strain V(T), was isolated from a hydrothermal pool on Vulcano Island, Italy. The morphology of cells was observed to vary from pleomorphic to coccoid. The temperature range for growth of strain V(T) was 15-65 degrees C with an optimum at 45 degrees C. The pH for growth ranged from pH 0 to 4 with an optimal at pH 1.4-1.6. Strain V(T) was able to grow aerobically and anaerobically, oxidizing ferrous iron and reducing ferric iron, respectively. The isolate grew chemo-organotrophically with yeast extract and yeast extract with glucose as the sources of energy and carbon. The molar G+C content in the DNA was 36 mol%. 16S rRNA gene sequence analysis demonstrated that strain V(T) was a member of the family Ferroplasmaceae, order Thermoplasmatales, phylum Euryarchaeota, showing sequence identities of 100 % with Ferroplasma cupricumulans BH2(T), 95.4 % with Ferroplasma acidiphilum Y(T), 94 % with Picrophilus torridus DSM 9790(T) and 92 % with Picrophilus oshimae DSM 9789(T). 16S rRNA gene sequence-based phylogenetic analysis showed that strain V(T) formed a monophyletic cluster together with F. cupricumulans BH2(T) and all other thermophilic isolates with available 16S rRNA gene sequences, whereas F. acidiphilum Y(T) formed another cluster with mesophilic isolates within the family Ferroplasmaceae. DNA-DNA hybridization values between strain V(T) and F. cupricumulans BH2(T) were well below 70 %, indicating that the two strains belong to separate species. Principal membrane lipids of strain V(T) were dibiphytanyl-based tetraether lipids containing pentacyclic rings. The polar lipids were dominated by a single phosphoglycolipid derivative based on a galactosyl dibiphytanyl phosphoglycerol tetraether, together with smaller amounts of monoglycosyl and diglycosyl dibiphytanyl ether lipids and the corresponding phosphoglycerol derivatives. The major respiratory quinones present were naphthoquinone derivatives. Given the notable physiological and chemical differences as well as the distinct phylogenetic placement of the new isolate relative to the type species of the genus Ferroplasma, we propose strain V(T) as a member of a new genus and species, Acidiplasma aeolicum gen. nov., sp. nov. The type strain of Acidiplasma aeolicum is strain V(T) (=DSM 18409(T) =JCM 14615(T)). In addition, we propose to transfer Ferroplasma cupricumulans Hawkes et al. 2008 to the genus Acidiplasma as Acidiplasma cupricumulans comb. nov. (type strain BH2(T) =DSM 16551(T) =JCM 13668(T)).
-
A purple acidophilic di-ferric DNA ligase from Ferroplasma.
Proceedings of the National Academy of Sciences of the United States of America, 2008Co-Authors: Manuel Ferrer, Olga V. Golyshina, Kenneth N. Timmis, Ana Beloqui, Lars H. Böttger, José Manuel Andreu, Julio Polaina, Antonio L. De Lacey, Alfred X. Trautwein, Peter N. GolyshinAbstract:We describe here an extraordinary purple-colored DNA ligase, LigFa, from the acidophilic ferrous iron-oxidizing archaeon Ferroplasma acidiphilum, a di-ferric enzyme with an extremely low pH activity optimum. Unlike any other DNA ligase studied to date, LigFa contains two Fe3+-tyrosinate centers and lacks any requirement for either Mg2+ or K+ for activity. DNA ligases from closest phylogenetic and ecophysiological relatives have normal pH optima (6.0–7.5), lack iron, and require Mg2+/K+ for activity. Ferric iron retention is pH-dependent, with release resulting in partial protein unfolding and loss of activity. Reduction of the Fe3+ to Fe2+ results in an 80% decrease in DNA substrate binding and an increase in the pH activity optimum to 5.0. DNA binding induces significant conformational change around the iron site(s), suggesting that the ferric irons of LigFa act both as structure organizing and stabilizing elements and as Lewis acids facilitating DNA binding at low pH.
Mark Dopson - One of the best experts on this subject based on the ideXlab platform.
-
A Novel Inorganic Sulfur Compound Metabolizing Ferroplasma-Like Population Is Suggested to Mediate Extracellular Electron Transfer.
Frontiers in microbiology, 2018Co-Authors: Domenico Simone, Daniela Palma, Elias Broman, Stephanie Turner, Mark DopsonAbstract:Mining and processing of metal sulfide ores produces waters containing metals and inorganic sulfur compounds such as tetrathionate and thiosulfate. If released untreated, these sulfur compounds can be oxidized to generate highly acidic wastewaters (termed ‘acid mine drainage’) that cause severe environmental pollution. One potential method to remediate mining wastewaters is the maturing biotechnology of ‘microbial fuel cells’ that offers the sustainable removal of acid generating inorganic sulfur compounds alongside producing an electrical current. Microbial fuel cells exploit the ability of bacterial cells to transfer electrons to a mineral as the terminal electron acceptor during anaerobic respiration by replacing the mineral with a solid anode. In consequence, by substituting natural minerals with electrodes, microbial fuel cells also provide an excellent platform to understand environmental microbe-mineral interactions that are fundamental to element cycling. Previously, tetrathionate degradation coupled to the generation of an electrical current has been demonstrated and here we report a metagenomic and metatranscriptomic analysis of the microbial community. Reconstruction of inorganic sulfur compound metabolism suggested the substrate tetrathionate was metabolized by the Ferroplasma-like and Acidithiobacillus-like populations via multiple pathways. Characterized Ferroplasma species do not utilize inorganic sulfur compounds, suggesting a novel Ferroplasma-like population had been selected. Oxidation of intermediate sulfide, sulfur, thiosulfate and adenylyl-sulfate released electrons and the extracellular electron transfer to the anode was suggested to be dominated by candidate soluble electron shuttles produced by the Ferroplasma-like population. However, as the soluble electron shuttle compounds also have alternative functions within the cell, it cannot be ruled out that acidophiles use novel, uncharacterized mechanisms to mediate extracellular electron transfer. Several populations within the community were suggested to metabolize intermediate inorganic sulfur compounds by multiple pathways, which highlights the potential for mutualistic or symbiotic relationships. This study provided the genetic base for acidophilic microbial fuel cells utilized for the remediation of inorganic sulfur compounds from acid mine drainage.
-
Table_2_A Novel Inorganic Sulfur Compound Metabolizing Ferroplasma-Like Population Is Suggested to Mediate Extracellular Electron Transfer.xlsx
2018Co-Authors: Domenico Simone, Daniela Palma, Elias Broman, Stephanie Turner, Mark DopsonAbstract:Mining and processing of metal sulfide ores produces waters containing metals and inorganic sulfur compounds such as tetrathionate and thiosulfate. If released untreated, these sulfur compounds can be oxidized to generate highly acidic wastewaters [termed ‘acid mine drainage (AMD)’] that cause severe environmental pollution. One potential method to remediate mining wastewaters is the maturing biotechnology of ‘microbial fuel cells’ that offers the sustainable removal of acid generating inorganic sulfur compounds alongside producing an electrical current. Microbial fuel cells exploit the ability of bacterial cells to transfer electrons to a mineral as the terminal electron acceptor during anaerobic respiration by replacing the mineral with a solid anode. In consequence, by substituting natural minerals with electrodes, microbial fuel cells also provide an excellent platform to understand environmental microbe–mineral interactions that are fundamental to element cycling. Previously, tetrathionate degradation coupled to the generation of an electrical current has been demonstrated and here we report a metagenomic and metatranscriptomic analysis of the microbial community. Reconstruction of inorganic sulfur compound metabolism suggested the substrate tetrathionate was metabolized by the Ferroplasma-like and Acidithiobacillus-like populations via multiple pathways. Characterized Ferroplasma species do not utilize inorganic sulfur compounds, suggesting a novel Ferroplasma-like population had been selected. Oxidation of intermediate sulfide, sulfur, thiosulfate, and adenylyl-sulfate released electrons and the extracellular electron transfer to the anode was suggested to be dominated by candidate soluble electron shuttles produced by the Ferroplasma-like population. However, as the soluble electron shuttle compounds also have alternative functions within the cell, it cannot be ruled out that acidophiles use novel, uncharacterized mechanisms to mediate extracellular electron transfer. Several populations within the community were suggested to metabolize intermediate inorganic sulfur compounds by multiple pathways, which highlights the potential for mutualistic or symbiotic relationships. This study provided the genetic base for acidophilic microbial fuel cells utilized for the remediation of inorganic sulfur compounds from AMD.
-
A Novel Inorganic Sulfur Compound Metabolizing Ferroplasma-Like Population Is Suggested to Mediate Extracellular Electron Transfer
Frontiers Media S.A., 2018Co-Authors: Domenico Simone, Daniela Palma, Elias Broman, Stephanie Turner, Mark DopsonAbstract:Mining and processing of metal sulfide ores produces waters containing metals and inorganic sulfur compounds such as tetrathionate and thiosulfate. If released untreated, these sulfur compounds can be oxidized to generate highly acidic wastewaters [termed ‘acid mine drainage (AMD)’] that cause severe environmental pollution. One potential method to remediate mining wastewaters is the maturing biotechnology of ‘microbial fuel cells’ that offers the sustainable removal of acid generating inorganic sulfur compounds alongside producing an electrical current. Microbial fuel cells exploit the ability of bacterial cells to transfer electrons to a mineral as the terminal electron acceptor during anaerobic respiration by replacing the mineral with a solid anode. In consequence, by substituting natural minerals with electrodes, microbial fuel cells also provide an excellent platform to understand environmental microbe–mineral interactions that are fundamental to element cycling. Previously, tetrathionate degradation coupled to the generation of an electrical current has been demonstrated and here we report a metagenomic and metatranscriptomic analysis of the microbial community. Reconstruction of inorganic sulfur compound metabolism suggested the substrate tetrathionate was metabolized by the Ferroplasma-like and Acidithiobacillus-like populations via multiple pathways. Characterized Ferroplasma species do not utilize inorganic sulfur compounds, suggesting a novel Ferroplasma-like population had been selected. Oxidation of intermediate sulfide, sulfur, thiosulfate, and adenylyl-sulfate released electrons and the extracellular electron transfer to the anode was suggested to be dominated by candidate soluble electron shuttles produced by the Ferroplasma-like population. However, as the soluble electron shuttle compounds also have alternative functions within the cell, it cannot be ruled out that acidophiles use novel, uncharacterized mechanisms to mediate extracellular electron transfer. Several populations within the community were suggested to metabolize intermediate inorganic sulfur compounds by multiple pathways, which highlights the potential for mutualistic or symbiotic relationships. This study provided the genetic base for acidophilic microbial fuel cells utilized for the remediation of inorganic sulfur compounds from AMD
-
Table_1_A Novel Inorganic Sulfur Compound Metabolizing Ferroplasma-Like Population Is Suggested to Mediate Extracellular Electron Transfer.docx
2018Co-Authors: Domenico Simone, Daniela Palma, Elias Broman, Stephanie Turner, Mark DopsonAbstract:Mining and processing of metal sulfide ores produces waters containing metals and inorganic sulfur compounds such as tetrathionate and thiosulfate. If released untreated, these sulfur compounds can be oxidized to generate highly acidic wastewaters [termed ‘acid mine drainage (AMD)’] that cause severe environmental pollution. One potential method to remediate mining wastewaters is the maturing biotechnology of ‘microbial fuel cells’ that offers the sustainable removal of acid generating inorganic sulfur compounds alongside producing an electrical current. Microbial fuel cells exploit the ability of bacterial cells to transfer electrons to a mineral as the terminal electron acceptor during anaerobic respiration by replacing the mineral with a solid anode. In consequence, by substituting natural minerals with electrodes, microbial fuel cells also provide an excellent platform to understand environmental microbe–mineral interactions that are fundamental to element cycling. Previously, tetrathionate degradation coupled to the generation of an electrical current has been demonstrated and here we report a metagenomic and metatranscriptomic analysis of the microbial community. Reconstruction of inorganic sulfur compound metabolism suggested the substrate tetrathionate was metabolized by the Ferroplasma-like and Acidithiobacillus-like populations via multiple pathways. Characterized Ferroplasma species do not utilize inorganic sulfur compounds, suggesting a novel Ferroplasma-like population had been selected. Oxidation of intermediate sulfide, sulfur, thiosulfate, and adenylyl-sulfate released electrons and the extracellular electron transfer to the anode was suggested to be dominated by candidate soluble electron shuttles produced by the Ferroplasma-like population. However, as the soluble electron shuttle compounds also have alternative functions within the cell, it cannot be ruled out that acidophiles use novel, uncharacterized mechanisms to mediate extracellular electron transfer. Several populations within the community were suggested to metabolize intermediate inorganic sulfur compounds by multiple pathways, which highlights the potential for mutualistic or symbiotic relationships. This study provided the genetic base for acidophilic microbial fuel cells utilized for the remediation of inorganic sulfur compounds from AMD.
-
Biofilm development in the extremely acidophilic archaeon ‘Ferroplasma acidarmanus’ Fer1
Extremophiles, 2010Co-Authors: Craig Baker-austin, Margaret Wexler, Philip L. Bond, Joanna Potrykus, Mark DopsonAbstract:‘ Ferroplasma acidarmanus ’ Fer1 is an iron-oxidizing extreme acidophile isolated from the Iron Mountain mine, California, USA. This archaeon is predominantly found in biofilm-associated structures in the environment, and produces two distinct biofilm morphologies. Bioinformatic analysis of the ‘ F. acidarmanus ’ Fer1 genome identified genes annotated as involved in attachment and biofilm formation. No putative quorum sensing signaling genes were identified and no N -acyl homoserine lactone-like compounds were found in ‘ F. acidarmanus ’ Fer1 biofilm supernatant. Scanning confocal microscopy analysis of biofilm development on the surface of pyrite demonstrated the temporal and spatial development of biofilm growth. Furthermore, two-dimensional polyacrylamide gel electrophoresis was used to examine differential protein expression patterns between biofilm and planktonic populations. Ten up-regulated proteins were identified that included six enzymes associated with anaerobic growth, suggesting that the dominating phenotype in the mature biofilm was associated with anaerobic modes of growth. This report increases our knowledge of the genetic and proteomic basis of biofilm formation in an extreme acidophilic archaeon.