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Ramayandi, Sagita ND, Li F. Impact of coexisting microalgae species and bacteria in the presence level of fishy odor-causing Uroglena sp. in surface water. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:51312-51324. [PMID: 39107644 DOI: 10.1007/s11356-024-34592-0] [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: 05/21/2024] [Accepted: 07/29/2024] [Indexed: 09/06/2024]
Abstract
The study investigated the interplay of factors influencing the occurrence of Uroglena sp. blooms in surface water, particularly during the spring season. While Uroglena sp. typically demonstrates a propensity for blooming during the spring season, diminished population density was documented, underscoring the influence of pertinent environmental factors. To study the determinants, surface water samples collected for 3 years were analyzed for general water quality parameters, coexisting microalgae species, and total bacteria. Key determinants were found to include the ratio of dissolved nitrogen to dissolved phosphorus (DN: DP), temperature, bacterial density, the presence of Dinobryon sp. (golden algae) and Microcystis sp. (cyanobacteria). The findings indicate that factors such as DN:DP ratios and temperature variations intricately modulate Uroglena sp. bloom by affecting microbial dynamics, notably competitive interactions. The findings of this study offer further scientific insight into addressing seasonal occurrences of fishy odors in water reservoirs, with particular relevance to the spring season.
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Affiliation(s)
- Ramayandi
- Graduate School of Engineering, Gifu University, Gifu, 501-1193, Japan
| | - Nadya Diva Sagita
- Graduate School of Engineering, Gifu University, Gifu, 501-1193, Japan
| | - Fusheng Li
- Graduate School of Engineering, Gifu University, Gifu, 501-1193, Japan.
- River Basin Research Center, Gifu University, Gifu, 501-1193, Japan.
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2
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Antony R, Mongad D, Sanyal A, Dhotre D, Thamban M. Holed up, but thriving: Impact of multitrophic cryoconite communities on glacier elemental cycles. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 933:173187. [PMID: 38750762 DOI: 10.1016/j.scitotenv.2024.173187] [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: 12/11/2023] [Revised: 05/10/2024] [Accepted: 05/10/2024] [Indexed: 05/20/2024]
Abstract
Cryoconite holes (water and sediment-filled depressions), found on glacier surfaces worldwide, serve as reservoirs of microbes, carbon, trace elements, and nutrients, transferring these components downstream via glacier hydrological networks. Through targeted amplicon sequencing of carbon and nitrogen cycling genes, coupled with functional inference-based methods, we explore the functional diversity of these mini-ecosystems within Antarctica and the Himalayas. These regions showcase distinct environmental gradients and experience varying rates of environmental change influenced by global climatic shifts. Analysis revealed a diverse array of photosynthetic microorganisms, including Stramenopiles, Cyanobacteria, Rhizobiales, Burkholderiales, and photosynthetic purple sulfur Proteobacteria. Functional inference highlighted the high potential for carbohydrate, amino acid, and lipid metabolism in the Himalayan region, where organic carbon concentrations surpassed those in Antarctica by up to 2 orders of magnitude. Nitrogen cycling processes, including fixation, nitrification, and denitrification, are evident, with Antarctic cryoconite exhibiting a pronounced capacity for nitrogen fixation, potentially compensating for the limited nitrate concentrations in this region. Processes associated with the respiration of elemental sulfur and inorganic sulfur compounds such as sulfate, sulfite, thiosulfate, and sulfide suggest the presence of a complete sulfur cycle. The Himalayan region exhibits a higher potential for sulfur cycling, likely due to the abundant sulfate ions and sulfur-bearing minerals in this region. The capability for complete iron cycling through iron oxidation and reduction reactions was also predicted. Methanogenic archaea that produce methane during organic matter decomposition and methanotrophic bacteria that utilize methane as carbon and energy sources co-exist in the cryoconite, suggesting that these niches support the complete cycling of methane. Additionally, the presence of various microfauna suggests the existence of a complex food web. Collectively, these results indicate that cryoconite holes are self-sustaining ecosystems that drive elemental cycles on glaciers and potentially control carbon, nitrogen, sulfur, and iron exports downstream.
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Affiliation(s)
- Runa Antony
- National Centre for Polar and Ocean Research, Ministry of Earth Sciences, Vasco-da-Gama, India; GFZ German Research Centre for Geosciences, Potsdam, Germany.
| | - Dattatray Mongad
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
| | - Aritri Sanyal
- National Centre for Polar and Ocean Research, Ministry of Earth Sciences, Vasco-da-Gama, India
| | - Dhiraj Dhotre
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
| | - Meloth Thamban
- National Centre for Polar and Ocean Research, Ministry of Earth Sciences, Vasco-da-Gama, India
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3
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Phyu K, Zhi S, Liang J, Chang CC, Liu J, Cao Y, Wang H, Zhang K. Microalgal-bacterial consortia for the treatment of livestock wastewater: Removal of pollutants, interaction mechanisms, influencing factors, and prospects for application. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 349:123864. [PMID: 38554837 DOI: 10.1016/j.envpol.2024.123864] [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: 01/25/2024] [Revised: 03/06/2024] [Accepted: 03/23/2024] [Indexed: 04/02/2024]
Abstract
The livestock sector is responsible for a significant amount of wastewater globally. The microalgal-bacterial consortium (MBC) treatment has gained increasing attention as it is able to eliminate pollutants to yield value-added microalgal products. This review offers a critical discussion of the source of pollutants from livestock wastewater and the environmental impact of these pollutants. It also discusses the interactions between microalgae and bacteria in treatment systems and natural habitats in detail. The effects on MBC on the removal of various pollutants (conventional and emerging) are highlighted, focusing specifically on analysis of the removal mechanisms. Notably, the various influencing factors are classified into internal, external, and operating factors, and the mutual feedback relationships between them and the target (removal efficiency and biomass) have been thoroughly analysed. Finally, a wastewater recycling treatment model based on MBC is proposed for the construction of a green livestock farm, and the application value of various microalgal products has been analysed. The overall aim was to indicate that the use of MBC can provide cost-effective and eco-friendly approaches for the treatment of livestock wastewater, thereby advancing the path toward a promising microalgal-bacterial-based technology.
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Affiliation(s)
- KhinKhin Phyu
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, PR China.
| | - Suli Zhi
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, PR China; Key Laboratory of Low-Carbon Green Agriculture, North China, Ministry of Agriculture and Rural Affairs, Beijing 100193, PR China.
| | - Junfeng Liang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, PR China; Key Laboratory of Low-Carbon Green Agriculture, North China, Ministry of Agriculture and Rural Affairs, Beijing 100193, PR China.
| | - Chein-Chi Chang
- Washington D.C. Water and Sewer Authority, Ellicott City, MD, 21042, USA.
| | - Jiahua Liu
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, PR China.
| | - Yuang Cao
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, PR China.
| | - Han Wang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, PR China.
| | - Keqiang Zhang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, PR China; Key Laboratory of Low-Carbon Green Agriculture, North China, Ministry of Agriculture and Rural Affairs, Beijing 100193, PR China.
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4
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Yang Y, Wang Y, Wang Z, Yan H, Gong Y, Hu Y, Jiang Y, Wen S, Xu F, Wang B, Humphries F, Chen Y, Wang X, Yang S. ECSIT facilitates memory CD8 + T cell development by mediating fumarate synthesis during viral infection and tumorigenesis. Nat Cell Biol 2024; 26:450-463. [PMID: 38326554 DOI: 10.1038/s41556-024-01351-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 01/07/2024] [Indexed: 02/09/2024]
Abstract
Memory CD8+ T cells play a crucial role in infection and cancer and mount rapid responses to repeat antigen exposure. Although memory cell transcriptional programmes have been previously identified, the regulatory mechanisms that control the formation of CD8+ T cells have not been resolved. Here we report ECSIT as an essential mediator of memory CD8+ T cell differentiation. Ablation of ECSIT in T cells resulted in loss of fumarate synthesis and abrogated TCF-1 expression via demethylation of the TCF-1 promoter by the histone demethylase KDM5, thereby impairing memory CD8+ T cell development in a cell-intrinsic manner. In addition, ECSIT expression correlated positively with stem-like memory progenitor exhausted CD8+ T cells and the survival of patients with cancer. Our study demonstrates that ECSIT-mediated fumarate synthesis stimulates TCF-1 activity and memory CD8+ T cell development during viral infection and tumorigenesis and highlights the utility of therapeutic fumarate analogues and PD-L1 inhibition for tumour immunotherapy.
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Affiliation(s)
- Yongbing Yang
- Department of Immunology, State Key Laboratory of Reproductive Medicine, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Gusu School, the Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, National Vaccine Innovation Platform, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
- Department of Medical Laboratory, Affiliated Children's Hospital of Jiangnan University, Wuxi, China
| | - Yanan Wang
- Department of Immunology, State Key Laboratory of Reproductive Medicine, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Gusu School, the Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, National Vaccine Innovation Platform, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Zhongcheng Wang
- School of Pharmacy, Nanjing Medical University, Nanjing, China
| | - Huanyu Yan
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Yi Gong
- Department of Immunology, State Key Laboratory of Reproductive Medicine, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Gusu School, the Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, National Vaccine Innovation Platform, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Yingchao Hu
- Department of Immunology, State Key Laboratory of Reproductive Medicine, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Gusu School, the Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, National Vaccine Innovation Platform, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Yuying Jiang
- Department of Immunology, State Key Laboratory of Reproductive Medicine, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Gusu School, the Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, National Vaccine Innovation Platform, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Shuang Wen
- Department of Immunology, State Key Laboratory of Reproductive Medicine, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Gusu School, the Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, National Vaccine Innovation Platform, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Feifei Xu
- School of Pharmacy, Nanjing Medical University, Nanjing, China
| | - Bingwei Wang
- Department of Pharmacology, Nanjing University of Chinese Medicine, Nanjing, China
| | - Fiachra Humphries
- Division of Innate Immunity, Department of Medicine, UMass Chan Medical School, Worcester, MA, USA.
| | - Yun Chen
- School of Pharmacy, Nanjing Medical University, Nanjing, China.
| | - Xi Wang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China.
| | - Shuo Yang
- Department of Immunology, State Key Laboratory of Reproductive Medicine, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Gusu School, the Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, National Vaccine Innovation Platform, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China.
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5
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Venkatachalam S, Vipindas PV, Jabir T, Jain A, Krishnan KP. Metagenomic insights into novel microbial lineages with distinct ecological functions in the Arctic glacier foreland ecosystems. ENVIRONMENTAL RESEARCH 2024; 241:117726. [PMID: 37984782 DOI: 10.1016/j.envres.2023.117726] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 11/16/2023] [Accepted: 11/16/2023] [Indexed: 11/22/2023]
Abstract
Land-terminating glaciers are retreating globally, resulting in the expansion of the ice-free glacier forelands (GFs). These GFs act as a natural laboratory to study microbial community succession, soil formation, and ecosystem development. Here, we have employed gene-centric and genome-resolved metagenomic approaches to disseminate microbial diversity, community structure, and their associated biogeochemical processes involved in the carbon, nitrogen, and sulfur cycling across three GF ecosystems. Here, we present a compendium of draft Metagenome Assembled Genomes (MAGs) belonging to bacterial (n = 899) and archaeal (n = 4) domains. These MAGs were reconstructed using a total of 27 shotgun metagenomic datasets obtained from three different GFs, including Midtre Lovénbreen glacier (Svalbard), Russell glacier (Greenland), and Storglaciaren (Sweden). The taxonomic classification revealed that 98% of MAGs remained unclassified at species levels, suggesting the presence of novel microbial lineages. The abundance of metabolic genes associated with carbon, nitrogen, and sulfur cycling pathways varied between and within the samples collected across the three GF ecosystems. Our findings indicate that MAGs from different GFs share close phylogenetic relationships but exhibit significant differences in abundance, distribution patterns, and metabolic functions. This compendium of novel MAGs, encompassing autotrophic, phototrophic, and chemolithoautotrophic microbial groups reconstructed from GF ecosystems, represents a valuable resource for further studies.
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Affiliation(s)
- Siddarthan Venkatachalam
- Arctic Ecology and Biogeochemistry Division, National Centre for Polar and Ocean Research, Ministry of Earth Sciences (Govt. of India), Vasco-da-Gama, Goa, India.
| | - Puthiya Veettil Vipindas
- Arctic Ecology and Biogeochemistry Division, National Centre for Polar and Ocean Research, Ministry of Earth Sciences (Govt. of India), Vasco-da-Gama, Goa, India
| | - Thajudeen Jabir
- Arctic Ecology and Biogeochemistry Division, National Centre for Polar and Ocean Research, Ministry of Earth Sciences (Govt. of India), Vasco-da-Gama, Goa, India
| | - Anand Jain
- Arctic Ecology and Biogeochemistry Division, National Centre for Polar and Ocean Research, Ministry of Earth Sciences (Govt. of India), Vasco-da-Gama, Goa, India
| | - Kottekkatu Padinchati Krishnan
- Arctic Ecology and Biogeochemistry Division, National Centre for Polar and Ocean Research, Ministry of Earth Sciences (Govt. of India), Vasco-da-Gama, Goa, India
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6
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Escuti C, Véliz R, Acosta M, Echeverría-Vega A, Araya G, Ayma D, Demergasso C. The dynamics of two iron-oxidizing Acidithiobacillus strains in industrial copper sulfide heap-leaching. Res Microbiol 2024; 175:104168. [PMID: 37995889 DOI: 10.1016/j.resmic.2023.104168] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 11/08/2023] [Accepted: 11/08/2023] [Indexed: 11/25/2023]
Abstract
Several species within the Acidithiobacillus (At.) genus can derive energy from oxidizing ferrous iron and sulfur. Two bacterial strains according to their 16S rRNA gene sequences closely related to At. ferridurans and At. ferrivorans were obtained from the industrial sulfide heap leaching process at Minera Escondida (SLH), named D2 and DM, respectively. We applied statistical and data mining analyses to the abundance of At. ferridurans D2 and At. ferrivorans DM taxa in the industrial process over 16 years of operation. In addition, we performed phylogenetic analysis and genome comparison of the type strains, as well as culturing approaches with representative isolates of At. ferridurans D2 and At. ferrivorans DM taxa to understand the differential phenotypic features. Throughout the 16 years, two main operational stages were identified based on the D2 and DM taxa predominance in solution samples. The better suitability of At. ferrivorans DM to grow in a wide range of temperature and in micro-oxic environments, and to oxidize S by reducing Fe(III) revealed through culturing approaches can, in a way, explain the taxa distribution in both operational stages. The isolate At. ferridurans D2 could be considered as a specialist in aerobic sulfur oxidation, while isolate At. ferrivorans DM is a specialist in iron oxidation. In addition, the results from ore samples occasionally obtained from the industrial heap suggest that At. ferridurans D2 abundance was more related to its abundance in the solution samples than At. ferrivorans DM was. This dynamic coincides with previously obtained results in in-lab cell-mineral attaching experiments with both strains. This information increases our knowledge the ecophysiology of Acidithiobacillus and of the importance of diverse physiological traits at industrial bioleaching scales.
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Affiliation(s)
- Camila Escuti
- Centro de Biotecnología, Universidad Católica del Norte, Av. Angamos 0610, Antofagasta, Chile
| | - Roberto Véliz
- Centro de Biotecnología, Universidad Católica del Norte, Av. Angamos 0610, Antofagasta, Chile
| | - Mauricio Acosta
- Centro de Biotecnología, Universidad Católica del Norte, Av. Angamos 0610, Antofagasta, Chile.
| | - Alex Echeverría-Vega
- Centro de Investigación en Estudios Avanzados del Maule (CIEAM), Universidad Católica del Maule, Av. San Miguel 3605, Talca, Chile
| | - Gonzalo Araya
- Département de Chimie Analytique, Université Claude Bernard Lyon1, 43, boulevard du 11 Novembre 1918, 69100 Villeurbanne, France
| | - Diego Ayma
- Departamento de Matemáticas, Facultad de Ciencias, Universidad Católica del Norte, Av. Angamos 0610, Antofagasta, Chile
| | - Cecilia Demergasso
- Centro de Biotecnología, Universidad Católica del Norte, Av. Angamos 0610, Antofagasta, Chile.
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7
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Prioretti L, D’Ermo G, Infossi P, Kpebe A, Lebrun R, Bauzan M, Lojou E, Guigliarelli B, Giudici-Orticoni MT, Guiral M. Carbon Fixation in the Chemolithoautotrophic Bacterium Aquifex aeolicus Involves Two Low-Potential Ferredoxins as Partners of the PFOR and OGOR Enzymes. Life (Basel) 2023; 13:life13030627. [PMID: 36983784 PMCID: PMC10052474 DOI: 10.3390/life13030627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/21/2023] [Accepted: 02/22/2023] [Indexed: 02/27/2023] Open
Abstract
Aquifex aeolicus is a microaerophilic hydrogen- and sulfur -oxidizing bacterium that assimilates CO2 via the reverse tricarboxylic acid cycle (rTCA). Key enzymes of this pathway are pyruvate:ferredoxin oxidoreductase (PFOR) and 2-oxoglutarate:ferredoxin oxidoreductase (OGOR), which are responsible, respectively, for the reductive carboxylation of acetyl-CoA to pyruvate and of succinyl-CoA to 2-oxoglutarate, two energetically unfavorable reactions that require a strong reduction potential. We have confirmed, by biochemistry and proteomics, that A. aeolicus possesses a pentameric version of these enzyme complexes ((αβγδε)2) and that they are highly abundant in the cell. In addition, we have purified and characterized, from the soluble fraction of A. aeolicus, two low redox potential and oxygen-stable [4Fe-4S] ferredoxins (Fd6 and Fd7, E0 = −440 and −460 mV, respectively) and shown that they can physically interact and exchange electrons with both PFOR and OGOR, suggesting that they could be the physiological electron donors of the system in vivo. Shotgun proteomics indicated that all the enzymes assumed to be involved in the rTCA cycle are produced in the A. aeolicus cells. A number of additional enzymes, previously suggested to be part of a putative partial Wood-Ljungdahl pathway used for the synthesis of serine and glycine from CO2 were identified by mass spectrometry, but their abundance in the cell seems to be much lower than that of the rTCA cycle. Their possible involvement in carbon assimilation is discussed.
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Affiliation(s)
- Laura Prioretti
- CNRS, Bioénergétique et Ingénierie des Protéines, Aix Marseille Université, IMM, 13009 Marseille, France
| | - Giulia D’Ermo
- CNRS, Bioénergétique et Ingénierie des Protéines, Aix Marseille Université, IMM, 13009 Marseille, France
| | - Pascale Infossi
- CNRS, Bioénergétique et Ingénierie des Protéines, Aix Marseille Université, IMM, 13009 Marseille, France
| | - Arlette Kpebe
- CNRS, Bioénergétique et Ingénierie des Protéines, Aix Marseille Université, IMM, 13009 Marseille, France
| | - Régine Lebrun
- CNRS, Aix Marseille Université, IMM, 13009 Marseille, France
| | - Marielle Bauzan
- CNRS, Aix Marseille Université, IMM, 13009 Marseille, France
| | - Elisabeth Lojou
- CNRS, Bioénergétique et Ingénierie des Protéines, Aix Marseille Université, IMM, 13009 Marseille, France
| | - Bruno Guigliarelli
- CNRS, Bioénergétique et Ingénierie des Protéines, Aix Marseille Université, IMM, 13009 Marseille, France
| | | | - Marianne Guiral
- CNRS, Bioénergétique et Ingénierie des Protéines, Aix Marseille Université, IMM, 13009 Marseille, France
- Correspondence:
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Rivera-Araya J, Heine T, Chávez R, Schlömann M, Levicán G. Transcriptomic analysis of chloride tolerance in Leptospirillum ferriphilum DSM 14647 adapted to NaCl. PLoS One 2022; 17:e0267316. [PMID: 35486621 PMCID: PMC9053815 DOI: 10.1371/journal.pone.0267316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 04/06/2022] [Indexed: 11/29/2022] Open
Abstract
Chloride ions are toxic for most acidophilic microorganisms. In this study, the chloride tolerance mechanisms in the acidophilic iron-oxidizing bacterium Leptospirillum ferriphilum DSM 14647 adapted to 180 mM NaCl were investigated by a transcriptomic approach. Results showed that 99 genes were differentially expressed in the adapted versus the non-adapted cultures, of which 69 and 30 were significantly up-regulated or down-regulated, respectively. Genes that were up-regulated include carbonic anhydrase, cytochrome c oxidase (ccoN) and sulfide:quinone reductase (sqr), likely involved in intracellular pH regulation. Towards the same end, the cation/proton antiporter CzcA (czcA) was down-regulated. Adapted cells showed a higher oxygen consumption rate (2.2 x 10−9 ppm O2 s-1cell-1) than non-adapted cells (1.2 x 10−9 ppm O2 s-1cell-1). Genes coding for the antioxidants flavohemoprotein and cytochrome c peroxidase were also up-regulated. Measurements of the intracellular reactive oxygen species (ROS) level revealed that adapted cells had a lower level than non-adapted cells, suggesting that detoxification of ROS could be an important strategy to withstand NaCl. In addition, data analysis revealed the up-regulation of genes for Fe-S cluster biosynthesis (iscR), metal reduction (merA) and activation of a cellular response mediated by diffusible signal factors (DSFs) and the second messenger c-di-GMP. Several genes related to the synthesis of lipopolysaccharide and peptidoglycan were consistently down-regulated. Unexpectedly, the genes ectB, ectC and ectD involved in the biosynthesis of the compatible solutes (hydroxy)ectoine were also down-regulated. In line with these findings, although hydroxyectoine reached 20 nmol mg-1 of wet biomass in non-adapted cells, it was not detected in L. ferriphilum adapted to NaCl, suggesting that this canonical osmotic stress response was dispensable for salt adaptation. Differentially expressed transcripts and experimental validations suggest that adaptation to chloride in acidophilic microorganisms involves a multifactorial response that is different from the response in other bacteria studied.
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Affiliation(s)
- Javier Rivera-Araya
- Biology Department, Faculty of Chemistry and Biology, University of Santiago of Chile (USACH), Santiago, Chile
| | - Thomas Heine
- Environmental Microbiology, Institute of Biosciences, TU Bergakademie Freiberg, Freiberg, Germany
| | - Renato Chávez
- Biology Department, Faculty of Chemistry and Biology, University of Santiago of Chile (USACH), Santiago, Chile
| | - Michael Schlömann
- Environmental Microbiology, Institute of Biosciences, TU Bergakademie Freiberg, Freiberg, Germany
| | - Gloria Levicán
- Biology Department, Faculty of Chemistry and Biology, University of Santiago of Chile (USACH), Santiago, Chile
- * E-mail:
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9
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Boase K, González C, Vergara E, Neira G, Holmes D, Watkin E. Prediction and Inferred Evolution of Acid Tolerance Genes in the Biotechnologically Important Acidihalobacter Genus. Front Microbiol 2022; 13:848410. [PMID: 35516430 PMCID: PMC9062700 DOI: 10.3389/fmicb.2022.848410] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 02/28/2022] [Indexed: 11/18/2022] Open
Abstract
Acidihalobacter is a genus of acidophilic, gram-negative bacteria known for its ability to oxidize pyrite minerals in the presence of elevated chloride ions, a capability rare in other iron-sulfur oxidizing acidophiles. Previous research involving Acidihalobacter spp. has focused on their applicability in saline biomining operations and their genetic arsenal that allows them to cope with chloride, metal and oxidative stress. However, an understanding of the molecular adaptations that enable Acidihalobacter spp. to thrive under both acid and chloride stress is needed to provide a more comprehensive understanding of how this genus can thrive in such extreme biomining conditions. Currently, four genomes of the Acidihalobacter genus have been sequenced: Acidihalobacter prosperus DSM 5130T, Acidihalobacter yilgarnensis DSM 105917T, Acidihalobacter aeolianus DSM 14174T, and Acidihalobacter ferrooxydans DSM 14175T. Phylogenetic analysis shows that the Acidihalobacter genus roots to the Chromatiales class consisting of mostly halophilic microorganisms. In this study, we aim to advance our knowledge of the genetic repertoire of the Acidihalobacter genus that has enabled it to cope with acidic stress. We provide evidence of gene gain events that are hypothesized to help the Acidihalobacter genus cope with acid stress. Potential acid tolerance mechanisms that were found in the Acidihalobacter genomes include multiple potassium transporters, chloride/proton antiporters, glutamate decarboxylase system, arginine decarboxylase system, urease system, slp genes, squalene synthesis, and hopanoid synthesis. Some of these genes are hypothesized to have entered the Acidihalobacter via vertical decent from an inferred non-acidophilic ancestor, however, horizontal gene transfer (HGT) from other acidophilic lineages is probably responsible for the introduction of many acid resistance genes.
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Affiliation(s)
- Katelyn Boase
- Curtin Medical School, Curtin University, Perth, WA, Australia
| | - Carolina González
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Santiago, Chile
| | - Eva Vergara
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Santiago, Chile
| | - Gonzalo Neira
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Santiago, Chile
| | - David Holmes
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Santiago, Chile
- Facultad de Medicina y Ciencias, Universidad San Sebastián, Santiago, Chile
- *Correspondence: David S. Holmes,
| | - Elizabeth Watkin
- Curtin Medical School, Curtin University, Perth, WA, Australia
- Elizabeth Watkin,
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10
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Santomartino R, Zea L, Cockell CS. The smallest space miners: principles of space biomining. Extremophiles 2022; 26:7. [PMID: 34993644 PMCID: PMC8739323 DOI: 10.1007/s00792-021-01253-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 12/09/2021] [Indexed: 12/03/2022]
Abstract
As we aim to expand human presence in space, we need to find viable approaches to achieve independence from terrestrial resources. Space biomining of the Moon, Mars and asteroids has been indicated as one of the promising approaches to achieve in-situ resource utilization by the main space agencies. Structural and expensive metals, essential mineral nutrients, water, oxygen and volatiles could be potentially extracted from extraterrestrial regolith and rocks using microbial-based biotechnologies. The use of bioleaching microorganisms could also be applied to space bioremediation, recycling of waste and to reinforce regenerative life support systems. However, the science around space biomining is still young. Relevant differences between terrestrial and extraterrestrial conditions exist, including the rock types and ores available for mining, and a direct application of established terrestrial biomining techniques may not be a possibility. It is, therefore, necessary to invest in terrestrial and space-based research of specific methods for space applications to learn the effects of space conditions on biomining and bioremediation, expand our knowledge on organotrophic and community-based bioleaching mechanisms, as well as on anaerobic biomining, and investigate the use of synthetic biology to overcome limitations posed by the space environments.
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Affiliation(s)
- Rosa Santomartino
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, EH9 3FD, UK.
| | - Luis Zea
- BioServe Space Technologies, University of Colorado Boulder, Boulder, CO, USA
| | - Charles S Cockell
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, EH9 3FD, UK
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11
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Huang Y, Li XT, Jiang Z, Liang ZL, Wang P, Liu ZH, Li LZ, Yin HQ, Jia Y, Huang ZS, Liu SJ, Jiang CY. Key Factors Governing Microbial Community in Extremely Acidic Mine Drainage (pH <3). Front Microbiol 2021; 12:761579. [PMID: 34917049 PMCID: PMC8670003 DOI: 10.3389/fmicb.2021.761579] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 10/28/2021] [Indexed: 12/05/2022] Open
Abstract
The microbial community of acid mine drainage (AMD) fascinates researchers by their adaption and roles in shaping the environment. Molecular surveys have recently helped to enhance the understanding of the distribution, adaption strategy, and ecological function of microbial communities in extreme AMD environments. However, the interactions between the environment and microbial community of extremely acidic AMD (pH <3) from different mining areas kept unanswered questions. Here, we measured physicochemical parameters and profiled the microbial community of AMD collected from four mining areas with different mineral types to provide a better understanding of biogeochemical processes within the extremely acidic water environment. The prominent physicochemical differences across the four mining areas were in SO42−, metal ions, and temperature, and distinct microbial diversity and community assemblages were also discovered in these areas. Mg2+ and SO42− were the predominant factors determining the microbial structure and prevalence of dominant taxa in AMD. Leptospirillum, Ferroplasma, and Acidithiobacillus were abundant but showed different occurrence patterns in AMD from different mining areas. More diverse communities and functional redundancy were identified in AMD of polymetallic mining areas compared with AMD of copper mining areas. Functional prediction revealed iron, sulfur, nitrogen, and carbon metabolisms driven by microorganisms were significantly correlated with Mg2+ and SO42−, Ca2+, temperature, and Fe2+, which distinguish microbial communities of copper mine AMD from that of polymetallic mine AMD. In summary, microbial diversity, composition, and metabolic potential were mainly shaped by Mg2+ and SO42− concentrations of AMD, suggesting that the substrate concentrations may contribute to the distinct microbiological profiles of AMD from different mining areas. These findings highlight the microbial community structure in extremely acidic AMD forming by types of minerals and the interactions of physicochemical parameters and microbiology, providing more clues of the microbial ecological function and adaptation mechanisms in the extremely acidic environment.
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Affiliation(s)
- Ye Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,School of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Xiu-Tong Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,School of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Zhen Jiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,School of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Zong-Lin Liang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,School of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Pei Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,School of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Zheng-Hua Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Liang-Zhi Li
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Hua-Qun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Yan Jia
- National Engineering Laboratory for Hydrometallurgical Cleaner Production Technology, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, China
| | - Zhong-Sheng Huang
- Zijin Mining Group Company Limited, Fujian, China.,School of Metallurgy and Environment, Central South University, Changsha, China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,School of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Cheng-Ying Jiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,School of Life Science, University of Chinese Academy of Sciences, Beijing, China
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12
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Moazzam P, Boroumand Y, Rabiei P, Baghbaderani SS, Mokarian P, Mohagheghian F, Mohammed LJ, Razmjou A. Lithium bioleaching: An emerging approach for the recovery of Li from spent lithium ion batteries. CHEMOSPHERE 2021; 277:130196. [PMID: 33784558 DOI: 10.1016/j.chemosphere.2021.130196] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 02/08/2021] [Accepted: 03/03/2021] [Indexed: 06/12/2023]
Abstract
The rapidly growing demand for lithium has resulted in a sharp increase in its price. This is due to the ubiquitous use of lithium-ion batteries (LIBs) in large-scale energy and transportation sectors as well as portable devices. Recycling of the LIBs for being the supply of critical metals hence becomes environmentally and economically viable. The presently used approaches for the recovery of spent LIBs like pyrometallurgical process can effectively recover nickel, cobalt, and copper, while lithium is usually lost in slag. Bioleaching process as an alternative method of extraction and recovery of valuable metals from the primary and secondary resources has been attracting a large pool of attraction. This method can provide higher recovery yield even for low concentration of metals which makes it viable among conventional methods. The bioleaching process can work with lower operating cost and consumed water and energy along with a simple condition, which produces less hazardous by-products ultimately. Here, we comprehensively review the biological and chemical mechanisms of the bioleaching process with a conclusive discussion to help how to extend the use of bioleaching for lithium extraction and recovery from the spent LIBs with a focus on recovery yields improvement. We elaborate on the three main types of the reported bioleaching with considering effective parameters including temperature, initial pH, pulp density, aeration, and medium and cell nutrients to sustain microorganism activity. Finally, practical challenges and future opportunities of lithium are discussed to inspire future research trends and pilot studies to realize the full potential of lithium recovery using sustainable bioleaching processes to extend a clean energy future.
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Affiliation(s)
- Parisa Moazzam
- School of Chemistry, University of New South Wales, Sydney, 2052, Australia
| | - Yasaman Boroumand
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, 81746-73441, Iran
| | - Parisa Rabiei
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, 81746-73441, Iran
| | - Sorour Salehi Baghbaderani
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, 81746-73441, Iran
| | - Parastou Mokarian
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, 81746-73441, Iran
| | - Fereshteh Mohagheghian
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, 81746-73441, Iran
| | - Layth Jasim Mohammed
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, 81746-73441, Iran
| | - Amir Razmjou
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, 81746-73441, Iran; Centre for Technology in Water and Wastewater, University of Technology Sydney, New South Wales, Australia; UNESCO Centre for Membrane Science and Technology, School of Chemical Engineering, University of New South Wales, Sydney, 2052, Australia.
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13
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Schmitz RA, Peeters SH, Versantvoort W, Picone N, Pol A, Jetten MSM, Op den Camp HJM. Verrucomicrobial methanotrophs: ecophysiology of metabolically versatile acidophiles. FEMS Microbiol Rev 2021; 45:6125968. [PMID: 33524112 PMCID: PMC8498564 DOI: 10.1093/femsre/fuab007] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 01/15/2021] [Indexed: 12/26/2022] Open
Abstract
Methanotrophs are an important group of microorganisms that counteract methane emissions to the atmosphere. Methane-oxidising bacteria of the Alpha- and Gammaproteobacteria have been studied for over a century, while methanotrophs of the phylum Verrucomicrobia are a more recent discovery. Verrucomicrobial methanotrophs are extremophiles that live in very acidic geothermal ecosystems. Currently, more than a dozen strains have been isolated, belonging to the genera Methylacidiphilum and Methylacidimicrobium. Initially, these methanotrophs were thought to be metabolically confined. However, genomic analyses and physiological and biochemical experiments over the past years revealed that verrucomicrobial methanotrophs, as well as proteobacterial methanotrophs, are much more metabolically versatile than previously assumed. Several inorganic gases and other molecules present in acidic geothermal ecosystems can be utilised, such as methane, hydrogen gas, carbon dioxide, ammonium, nitrogen gas and perhaps also hydrogen sulfide. Verrucomicrobial methanotrophs could therefore represent key players in multiple volcanic nutrient cycles and in the mitigation of greenhouse gas emissions from geothermal ecosystems. Here, we summarise the current knowledge on verrucomicrobial methanotrophs with respect to their metabolic versatility and discuss the factors that determine their diversity in their natural environment. In addition, key metabolic, morphological and ecological characteristics of verrucomicrobial and proteobacterial methanotrophs are reviewed.
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Affiliation(s)
- Rob A Schmitz
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Stijn H Peeters
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Wouter Versantvoort
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Nunzia Picone
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Arjan Pol
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Mike S M Jetten
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Huub J M Op den Camp
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
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14
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Abstract
Manganese is among Earth’s most abundant elements. Its oxidation had long been theorized1, yet undemonstrated2–4, to fuel chemolithoautotrophic microbial growth. Here, an enrichment culture exhibiting Mn(II)-oxidation-dependent, exponential growth was refined to a two species co-culture. Oxidation required viable bacteria at permissive temperatures, resulting in the generation of small Mn oxide nodules to which the cells associated. The majority member of the culture, ‘Candidatus Manganitrophus noduliformans’, affiliates within phylum Nitrospirae (Nitrospirota) but is distantly related to known Nitrospira and Leptospirillum species. The minority member has been isolated, but does not oxidise Mn(II) alone. Stable isotope probing revealed Mn(II)-oxidation-dependent, 13CO2-fixation into cellular biomass. Transcriptomics reveals candidate pathways for coupling extracellular manganese oxidation to aerobic energy conservation and to autotrophic CO2-fixation. These findings expand the known diversity of inorganic metabolisms supporting life, while completing a biogeochemical energy cycle for manganese5,6, one that may interface with other major global elemental cycles.
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15
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González D, Álamos P, Rivero M, Orellana O, Norambuena J, Chávez R, Levicán G. Deciphering the Role of Multiple Thioredoxin Fold Proteins of Leptospirillum sp. in Oxidative Stress Tolerance. Int J Mol Sci 2020; 21:E1880. [PMID: 32164170 PMCID: PMC7084401 DOI: 10.3390/ijms21051880] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 03/04/2020] [Accepted: 03/05/2020] [Indexed: 12/22/2022] Open
Abstract
Thioredoxin fold proteins (TFPs) form a family of diverse proteins involved in thiol/disulfide exchange in cells from all domains of life. Leptospirillum spp. are bioleaching bacteria naturally exposed to extreme conditions like acidic pH and high concentrations of metals that can contribute to the generation of reactive oxygen species (ROS) and consequently the induction of thiol oxidative damage. Bioinformatic studies have predicted 13 genes that encode for TFP proteins in Leptospirillum spp. We analyzed the participation of individual tfp genes from Leptospirillum sp. CF-1 in the response to oxidative conditions. Genomic context analysis predicted the involvement of these genes in the general thiol-reducing system, cofactor biosynthesis, carbon fixation, cytochrome c biogenesis, signal transduction, and pilus and fimbria assembly. All tfp genes identified were transcriptionally active, although they responded differentially to ferric sulfate and diamide stress. Some of these genes confer oxidative protection to a thioredoxin-deficient Escherichia coli strain by restoring the wild-type phenotype under oxidative stress conditions. These findings contribute to our understanding of the diversity and complexity of thiol/disulfide systems, and of adaptations that emerge in acidophilic microorganisms that allow them to thrive in highly oxidative environments. These findings also give new insights into the physiology of these microorganisms during industrial bioleaching operations.
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Affiliation(s)
- Daniela González
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Avenida Libertador Bernardo O’Higgins 3363, Estación Central Santiago 917022, Chile; (D.G.); (P.Á.); (M.R.); (J.N.); (R.C.)
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago 8380453, Chile;
| | - Pamela Álamos
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Avenida Libertador Bernardo O’Higgins 3363, Estación Central Santiago 917022, Chile; (D.G.); (P.Á.); (M.R.); (J.N.); (R.C.)
| | - Matías Rivero
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Avenida Libertador Bernardo O’Higgins 3363, Estación Central Santiago 917022, Chile; (D.G.); (P.Á.); (M.R.); (J.N.); (R.C.)
| | - Omar Orellana
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago 8380453, Chile;
| | - Javiera Norambuena
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Avenida Libertador Bernardo O’Higgins 3363, Estación Central Santiago 917022, Chile; (D.G.); (P.Á.); (M.R.); (J.N.); (R.C.)
| | - Renato Chávez
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Avenida Libertador Bernardo O’Higgins 3363, Estación Central Santiago 917022, Chile; (D.G.); (P.Á.); (M.R.); (J.N.); (R.C.)
| | - Gloria Levicán
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Avenida Libertador Bernardo O’Higgins 3363, Estación Central Santiago 917022, Chile; (D.G.); (P.Á.); (M.R.); (J.N.); (R.C.)
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16
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Wu C, Jiang M, Hsieh L, Cai Y, Shen Y, Wang H, Lin Q, Shen C, Hu B, Lou L. Feasibility of bioleaching of heavy metals from sediment with indigenous bacteria using agricultural sulfur soil conditioners. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 703:134812. [PMID: 31734500 DOI: 10.1016/j.scitotenv.2019.134812] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 09/30/2019] [Accepted: 10/02/2019] [Indexed: 06/10/2023]
Abstract
Sediment bioleaching using a sulfur substrate is a promising approach to the removal of heavy metals. Compared with commercial sulfur powder used as the sulfur substrate, agricultural sulfur soil conditioners may reduce secondary pollution and facilitate the reuse of sediment. This study explored the bioleaching effect of three agricultural sulfur soil conditioners, including sulfur-coated urea, bentonite sulfur, and bio-sulfur, and the bioleaching potential of the indigenous sediment bacteria. The results showed that the sulfur-coated urea had a comparable bioleaching effect with sulfur powder (Ni 35.35%, Cu 74.27%, Zn 69.92%) and the highest maximum bioleaching rate because of the additional nitrogen. The bentonite sulfur leached the least but increased the proportion of the residual state due to its adsorption of heavy metal. Similar changes to the microbial flora structure and bioleaching mechanism were found with the use of sulfur powder, sulfur-coated urea, and bentonite sulfur as the bioleaching substrate. There was no significant difference between the indigenous bacteria and the sludge-enriched bacteria in the bioleaching effect except for bio-sulfur, which only performed well with the sludge-enriched bacteria. In the absence of inoculum, the bio-sulfur hindered the bioleaching process due to high levels of organic matter. This study provides insights into the practical application of bioleaching heavy metal removal technology from the perspective of sulfur substrate selection.
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Affiliation(s)
- Chuncheng Wu
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310029, People's Republic of China.
| | - Mengying Jiang
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310029, People's Republic of China
| | - Lichun Hsieh
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310029, People's Republic of China
| | - Yuchen Cai
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310029, People's Republic of China
| | - Yutao Shen
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310029, People's Republic of China
| | - Haizhen Wang
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310029, People's Republic of China.
| | - Qi Lin
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310029, People's Republic of China.
| | - Chaofeng Shen
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310029, People's Republic of China.
| | - Baolan Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310029, People's Republic of China.
| | - Liping Lou
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310029, People's Republic of China; Key Laboratory of Water Pollution Control and Environmental Safety of Zhejiang Province 310020, People's Republic of China.
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17
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Yang L, Zhao D, Yang J, Wang W, Chen P, Zhang S, Yan L. Acidithiobacillus thiooxidans and its potential application. Appl Microbiol Biotechnol 2019; 103:7819-7833. [PMID: 31463545 DOI: 10.1007/s00253-019-10098-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 08/12/2019] [Accepted: 08/21/2019] [Indexed: 11/26/2022]
Abstract
Acidithiobacillus thiooxidans (A. thiooxidans) is a widespread, mesophilic, obligately aerobic, extremely acidophilic, rod-shaped, and chemolithoautotrophic gram-negative gammaproteobacterium. It can obtain energy and electrons from the oxidation of reducible sulfur, and it can fix carbon dioxide and assimilate nitrate, nitrite, and ammonium to satisfy carbon and nitrogen requirement. This bacterium exists as different genomovars and its genome size range from 3.02 to 3.97 Mb. Here, we highlight the recent advances in the understanding of the general biological features of A. thiooxidans, as well as the genetic diversity and the sulfur oxidation pathway system. Additionally, the potential applications of A. thiooxidans were summarized including the recycling of metals from metal-bearing ores, electric wastes, and sludge, the improvement of alkali-salinity soils, and the removal of sulfur from sulfur-containing solids and gases.
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Affiliation(s)
- Lei Yang
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, 163319, People's Republic of China
| | - Dan Zhao
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, 163319, People's Republic of China
| | - Jian Yang
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, 163319, People's Republic of China
| | - Weidong Wang
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, 163319, People's Republic of China
| | - Peng Chen
- School of Pharmacy, Lanzhou University, Donggang West Road No. 199, Lanzhou, 730020, People's Republic of China
| | - Shuang Zhang
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, 163319, People's Republic of China.
| | - Lei Yan
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, 163319, People's Republic of China.
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18
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Esparza M, Jedlicki E, González C, Dopson M, Holmes DS. Effect of CO 2 Concentration on Uptake and Assimilation of Inorganic Carbon in the Extreme Acidophile Acidithiobacillus ferrooxidans. Front Microbiol 2019; 10:603. [PMID: 31019493 PMCID: PMC6458275 DOI: 10.3389/fmicb.2019.00603] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 03/11/2019] [Indexed: 02/01/2023] Open
Abstract
This study was motivated by surprising gaps in the current knowledge of microbial inorganic carbon (Ci) uptake and assimilation at acidic pH values (pH < 3). Particularly striking is the limited understanding of the differences between Ci uptake mechanisms in acidic versus circumneutral environments where the Ci predominantly occurs either as a dissolved gas (CO2) or as bicarbonate (HCO3 -), respectively. In order to gain initial traction on the problem, the relative abundance of transcripts encoding proteins involved in Ci uptake and assimilation was studied in the autotrophic, polyextreme acidophile Acidithiobacillus ferrooxidans whose optimum pH for growth is 2.5 using ferrous iron as an energy source, although they are able to grow at pH 5 when using sulfur as an energy source. The relative abundance of transcripts of five operons (cbb1-5) and one gene cluster (can-sulP) was monitored by RT-qPCR and, in selected cases, at the protein level by Western blotting, when cells were grown under different regimens of CO2 concentration in elemental sulfur. Of particular note was the absence of a classical bicarbonate uptake system in A. ferrooxidans. However, bioinformatic approaches predict that sulP, previously annotated as a sulfate transporter, is a novel type of bicarbonate transporter. A conceptual model of CO2 fixation was constructed from combined bioinformatic and experimental approaches that suggests strategies for providing ecological flexibility under changing concentrations of CO2 and provides a portal to elucidating Ci uptake and regulation in acidic conditions. The results could advance the understanding of industrial bioleaching processes to recover metals such as copper at acidic pH. In addition, they may also shed light on how chemolithoautotrophic acidophiles influence the nutrient and energy balance in naturally occurring low pH environments.
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Affiliation(s)
- Mario Esparza
- Laboratorio de Biominería, Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
| | - Eugenia Jedlicki
- Center for Bioinformatics and Genome Biology, Fundación Ciencia & Vida, Santiago, Chile
| | - Carolina González
- Center for Bioinformatics and Genome Biology, Fundación Ciencia & Vida, Santiago, Chile
| | - Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - David S. Holmes
- Center for Bioinformatics and Genome Biology, Fundación Ciencia & Vida, Santiago, Chile
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
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19
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Wilkins LGE, Ettinger CL, Jospin G, Eisen JA. Metagenome-assembled genomes provide new insight into the microbial diversity of two thermal pools in Kamchatka, Russia. Sci Rep 2019; 9:3059. [PMID: 30816235 PMCID: PMC6395817 DOI: 10.1038/s41598-019-39576-6] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 01/17/2019] [Indexed: 12/21/2022] Open
Abstract
Culture-independent methods have contributed substantially to our understanding of global microbial diversity. Recently developed algorithms to construct whole genomes from environmental samples have further refined, corrected and revolutionized understanding of the tree of life. Here, we assembled draft metagenome-assembled genomes (MAGs) from environmental DNA extracted from two hot springs within an active volcanic ecosystem on the Kamchatka peninsula, Russia. This hydrothermal system has been intensively studied previously with regard to geochemistry, chemoautotrophy, microbial isolation, and microbial diversity. We assembled genomes of bacteria and archaea using DNA that had previously been characterized via 16S rRNA gene clone libraries. We recovered 36 MAGs, 29 of medium to high quality, and inferred their placement in a phylogenetic tree consisting of 3,240 publicly available microbial genomes. We highlight MAGs that were taxonomically assigned to groups previously underrepresented in available genome data. This includes several archaea (Korarchaeota, Bathyarchaeota and Aciduliprofundum) and one potentially new species within the bacterial genus Sulfurihydrogenibium. Putative functions in both pools were compared and are discussed in the context of their diverging geochemistry. This study adds comprehensive information about phylogenetic diversity and functional potential within two hot springs in the caldera of Kamchatka.
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Affiliation(s)
- Laetitia G E Wilkins
- Department of Environmental Sciences, Policy & Management, University of California, Berkeley, CA, 94720, USA. .,Genome Center, University of California, Davis, CA, 95616, USA.
| | | | | | - Jonathan A Eisen
- Genome Center, University of California, Davis, CA, 95616, USA.,Department of Evolution and Ecology, University of California, Davis, CA, 95616, USA.,Department of Medical Microbiology and Immunology, University of California, Davis, CA, 95616, USA
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20
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Khaleque HN, González C, Shafique R, Kaksonen AH, Holmes DS, Watkin ELJ. Uncovering the Mechanisms of Halotolerance in the Extremely Acidophilic Members of the Acidihalobacter Genus Through Comparative Genome Analysis. Front Microbiol 2019; 10:155. [PMID: 30853944 PMCID: PMC6396713 DOI: 10.3389/fmicb.2019.00155] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 01/22/2019] [Indexed: 12/21/2022] Open
Abstract
There are few naturally occurring environments where both acid and salinity stress exist together, consequently, there has been little evolutionary pressure for microorganisms to develop systems that enable them to deal with both stresses simultaneously. Members of the genus Acidihalobacter are iron- and sulfur-oxidizing, halotolerant acidophiles that have developed the ability to tolerate acid and saline stress and, therefore, have the potential to bioleach ores with brackish or saline process waters under acidic conditions. The genus consists of four members, A. prosperus DSM 5130T, A. prosperus DSM 14174, A. prosperus F5 and "A. ferrooxidans" DSM 14175. An in depth genome comparison was undertaken in order to provide a more comprehensive description of the mechanisms of halotolerance used by the different members of this genus. Pangenome analysis identified 29, 3 and 9 protein families related to halotolerance in the core, dispensable and unique genomes, respectively. The genes for halotolerance showed Ka/Ks ratios between 0 and 0.2, confirming that they are conserved and stabilized. All the Acidihalobacter genomes contained similar genes for the synthesis and transport of ectoine, which was recently found to be the dominant osmoprotectant in A. prosperus DSM 14174 and A. prosperus DSM 5130T. Similarities also existed in genes encoding low affinity potassium pumps, however, A. prosperus DSM 14174 was also found to contain genes encoding high affinity potassium pumps. Furthermore, only A. prosperus DSM 5130T and "A. ferrooxidans" DSM 14175 contained genes allowing the uptake of taurine as an osmoprotectant. Variations were also seen in genes encoding proteins involved in the synthesis and/or transport of periplasmic glucans, sucrose, proline, and glycine betaine. This suggests that versatility exists in the Acidihalobacter genus in terms of the mechanisms they can use for halotolerance. This information is useful for developing hypotheses for the search for life on exoplanets and moons.
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Affiliation(s)
- Himel N. Khaleque
- School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University, Perth, WA, Australia
- CSIRO Land and Water, Floreat, WA, Australia
| | - Carolina González
- Center for Bioinformatics and Genome Biology, Science for Life Foundation, Santiago, Chile
| | | | | | - David S. Holmes
- Center for Bioinformatics and Genome Biology, Science for Life Foundation, Santiago, Chile
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
| | - Elizabeth L. J. Watkin
- School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University, Perth, WA, Australia
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21
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Zhang X, Liu Z, Wei G, Yang F, Liu X. In Silico Genome-Wide Analysis Reveals the Potential Links Between Core Genome of Acidithiobacillus thiooxidans and Its Autotrophic Lifestyle. Front Microbiol 2018; 9:1255. [PMID: 29937764 PMCID: PMC6002666 DOI: 10.3389/fmicb.2018.01255] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 05/24/2018] [Indexed: 12/27/2022] Open
Abstract
The coinage “pan-genome” was first introduced dating back to 2005, and was used to elaborate the entire gene repertoire of any given species. Core genome consists of genes shared by all bacterial strains studied and is considered to encode essential functions associated with species’ basic biology and phenotypes, yet its relatedness with bacterial lifestyle of the species remains elusive. We performed the pan-genome analysis of sulfur-oxidizing acidophile Acidithiobacillus thiooxidans as a case study to highlight species’ core genome and its relevance with autotrophic lifestyle of bacterial species. The mathematical modeling based on bacterial genomes of A. thiooxidans species, including a novel strain ZBY isolated from Zambian copper mine plus eight other recognized strains, was attempted to extrapolate the expansion of its pan-genome, suggesting that A. thiooxidans pan-genome is closed. Further investigation revealed a common set of genes, many of which were assigned to metabolic profiles, notably with respect to energy metabolism, amino acid metabolism, and carbohydrate metabolism. The predicted metabolic profiles of A. thiooxidans were characterized by the fixation of inorganic carbon, assimilation of nitrogen compounds, and aerobic oxidation of various sulfur species. Notably, several hydrogenase (H2ase)-like genes dispersed in core genome might represent the novel classes due to the potential functional disparities, despite being closely related homologous genes that code for H2ase. Overall, the findings shed light on the distinguishing features of A. thiooxidans genomes on a global scale, and extend the understanding of its conserved core genome pertaining to autotrophic lifestyle.
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Affiliation(s)
- Xian Zhang
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha, China
| | - Zhenghua Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Guanyun Wei
- College of Life Science, Nanjing Normal University, Nanjing, China
| | - Fei Yang
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha, China
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
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22
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A thiotrophic microbial community in an acidic brine lake in Northern Chile. Antonie van Leeuwenhoek 2018; 111:1403-1419. [PMID: 29748902 DOI: 10.1007/s10482-018-1087-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 04/12/2018] [Indexed: 10/16/2022]
Abstract
The endorheic basins of the Northern Chilean Altiplano contain saline lakes and salt flats. Two of the salt flats, Gorbea and Ignorado, have high acidic brines. The causes of the local acidity have been attributed to the occurrence of volcanic native sulfur, the release of sulfuric acid by oxidation, and the low buffering capacity of the rocks in the area. Understanding the microbial community composition and available energy in this pristine ecosystem is relevant in determining the origin of the acidity and in supporting the rationale of conservation policies. Besides, a comparison between similar systems in Australia highlights key microbial components and specific ones associated with geological settings and environmental conditions. Sediment and water samples from the Salar de Gorbea were collected, physicochemical parameters measured and geochemical and molecular biological analyses performed. A low diversity microbial community was observed in brines and sediments dominated by Actinobacteria, Algae, Firmicutes and Proteobacteria. Most of the constituent genera have been reported to be either sulfur oxidizing microorganisms or ones having the potential for sulfur oxidation given available genomic data and information drawn from the literature on cultured relatives. In addition, a link between sulfur oxidation and carbon fixation was observed. In contrast, to acid mine drainage communities, Gorbea microbial diversity is mainly supported by chemolithoheterotrophic, facultative chemolithoautotrophic and oligotrophic sulfur oxidizing populations indicating that microbial activity should also be considered as a causative agent of local acidity.
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23
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Panda S, Akcil A, Mishra S, Erust C. A novel bioreactor system for simultaneous mutli-metal leaching from industrial pyrite ash: Effect of agitation and sulphur dosage. JOURNAL OF HAZARDOUS MATERIALS 2018; 342:454-463. [PMID: 28881272 DOI: 10.1016/j.jhazmat.2017.08.038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 07/31/2017] [Accepted: 08/14/2017] [Indexed: 06/07/2023]
Abstract
Simultaneous multi-metal leaching from industrial pyrite ash is reported for the first time using a novel bioreactor system that allows natural diffusion of atmospheric O2 and CO2 along with the required temperature maintenance. The waste containing economically important metals (Cu, Co, Zn & As) was leached using an adapted consortium of meso-acidophilic Fe2+ and S oxidising bacteria. The unique property of the sample supported adequate growth and activity of the acidophiles, thereby, driving the (bio) chemical reactions. Oxido-reductive potentials were seen to improve with time and the system's pH lowered as a result of active S oxidation. Increase in sulphur dosage (>1g/L) and agitation speed (>150rpm) did not bear any significant effect on metal dissolution. The consortium was able to leach 94.01% Cu (11.75% dissolution/d), 98.54% Co (12.3% dissolution/d), 75.95% Zn (9.49% dissolution/d) and 60.80% As (7.6% dissolution/d) at 150rpm, 1g/L sulphur, 30°C in 8days.
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Affiliation(s)
- Sandeep Panda
- Mineral-Metal Recovery and Recycling (MMR&R) Research Group, Mineral Processing Division, Department of Mining Engineering, Suleyman Demirel University, TR32260 Isparta, Turkey
| | - Ata Akcil
- Mineral-Metal Recovery and Recycling (MMR&R) Research Group, Mineral Processing Division, Department of Mining Engineering, Suleyman Demirel University, TR32260 Isparta, Turkey.
| | - Srabani Mishra
- Mineral-Metal Recovery and Recycling (MMR&R) Research Group, Mineral Processing Division, Department of Mining Engineering, Suleyman Demirel University, TR32260 Isparta, Turkey; Academy of Scientific and Innovation Research, CSIR - Institute of Minerals & Materials Technology (AcSIR), Bhubaneswar, 751013, India
| | - Ceren Erust
- Mineral-Metal Recovery and Recycling (MMR&R) Research Group, Mineral Processing Division, Department of Mining Engineering, Suleyman Demirel University, TR32260 Isparta, Turkey
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24
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Buchanan BB, Sirevåg R, Fuchs G, Ivanovsky RN, Igarashi Y, Ishii M, Tabita FR, Berg IA. The Arnon-Buchanan cycle: a retrospective, 1966-2016. PHOTOSYNTHESIS RESEARCH 2017; 134:117-131. [PMID: 29019085 DOI: 10.1007/s11120-017-0429-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 08/03/2017] [Indexed: 06/07/2023]
Abstract
For the first decade following its description in 1954, the Calvin-Benson cycle was considered the sole pathway of autotrophic CO2 assimilation. In the early 1960s, experiments with fermentative bacteria uncovered reactions that challenged this concept. Ferredoxin was found to donate electrons directly for the reductive fixation of CO2 into alpha-keto acids via reactions considered irreversible. Thus, pyruvate and alpha-ketoglutarate could be synthesized from CO2, reduced ferredoxin and acetyl-CoA or succinyl-CoA, respectively. This work opened the door to the discovery that reduced ferredoxin could drive the Krebs citric acid cycle in reverse, converting the pathway from its historical role in carbohydrate breakdown to one fixing CO2. Originally uncovered in photosynthetic green sulfur bacteria, the Arnon-Buchanan cycle has since been divorced from light and shown to function in a variety of anaerobic chemoautotrophs. In this retrospective, colleagues who worked on the cycle at its inception in 1966 and those presently working in the field trace its development from a controversial reception to its present-day inclusion in textbooks. This pathway is now well established in major groups of chemoautotrophic bacteria, instead of the Calvin-Benson cycle, and is increasingly referred to as the Arnon-Buchanan cycle. In this retrospective, separate sections have been written by the authors indicated. Bob Buchanan wrote the abstract and the concluding comments.
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Affiliation(s)
- Bob B Buchanan
- Department of Plant & Microbial Biology, University of California, 111 Koshland Hall, Berkeley, CA, 94720, USA.
| | - Reidun Sirevåg
- Department of Biosciences, University of Oslo, Blindern, Box 1066, 0316, Oslo, Norway
| | - Georg Fuchs
- Mikrobiologie, Fakultät für Biologie, Albert-Ludwigs-Universität Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany
| | - Ruslan N Ivanovsky
- Department of Microbiology, M.V. Lomonosov Moscow State University, 1/12 Lenin's Hills, Moscow, Russia, 119991
| | - Yasuo Igarashi
- Southwest University, Chongqing, 2 Tiansheng Rd, Beibei Qu, Chongqing Shi, 400700, China
| | - Masaharu Ishii
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - F Robert Tabita
- Department of Microbiology, The Ohio State University, 484 West 12th Avenue, Columbus, OH, 43210, USA
| | - Ivan A Berg
- Institute for Molecular Microbiology and Biotechnology, University of Münster, Corrensstr. 3, 48149, Münster, Germany
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25
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Zhang X, Liu X, Liang Y, Xiao Y, Ma L, Guo X, Miao B, Liu H, Peng D, Huang W, Yin H. Comparative Genomics Unravels the Functional Roles of Co-occurring Acidophilic Bacteria in Bioleaching Heaps. Front Microbiol 2017; 8:790. [PMID: 28529505 PMCID: PMC5418355 DOI: 10.3389/fmicb.2017.00790] [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: 02/11/2017] [Accepted: 04/18/2017] [Indexed: 12/27/2022] Open
Abstract
The spatial-temporal distribution of populations in various econiches is thought to be potentially related to individual differences in the utilization of nutrients or other resources, but their functional roles in the microbial communities remain elusive. We compared differentiation in gene repertoire and metabolic profiles, with a focus on the potential functional traits of three commonly recognized members (Acidithiobacillus caldus, Leptospirillum ferriphilum, and Sulfobacillus thermosulfidooxidans) in bioleaching heaps. Comparative genomics revealed that intra-species divergence might be driven by horizontal gene transfer. These co-occurring bacteria shared a few homologous genes, which significantly suggested the genomic differences between these organisms. Notably, relatively more genes assigned to the Clusters of Orthologous Groups category [G] (carbohydrate transport and metabolism) were identified in Sulfobacillus thermosulfidooxidans compared to the two other species, which probably indicated their mixotrophic capabilities that assimilate both organic and inorganic forms of carbon. Further inspection revealed distinctive metabolic capabilities involving carbon assimilation, nitrogen uptake, and iron-sulfur cycling, providing robust evidence for functional differences with respect to nutrient utilization. Therefore, we proposed that the mutual compensation of functionalities among these co-occurring organisms might provide a selective advantage for efficiently utilizing the limited resources in their habitats. Furthermore, it might be favorable to chemoautotrophs' lifestyles to form mutualistic interactions with these heterotrophic and/or mixotrophic acidophiles, whereby the latter could degrade organic compounds to effectively detoxify the environments. Collectively, the findings shed light on the genetic traits and potential metabolic activities of these organisms, and enable us to make some inferences about genomic and functional differences that might allow them to co-exist.
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Affiliation(s)
- Xian Zhang
- School of Minerals Processing and Bioengineering, Central South UniversityChangsha, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South UniversityChangsha, China
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South UniversityChangsha, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South UniversityChangsha, China
| | - Yili Liang
- School of Minerals Processing and Bioengineering, Central South UniversityChangsha, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South UniversityChangsha, China
| | - Yunhua Xiao
- School of Minerals Processing and Bioengineering, Central South UniversityChangsha, China
| | - Liyuan Ma
- School of Minerals Processing and Bioengineering, Central South UniversityChangsha, China
| | - Xue Guo
- School of Minerals Processing and Bioengineering, Central South UniversityChangsha, China
| | - Bo Miao
- School of Minerals Processing and Bioengineering, Central South UniversityChangsha, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South UniversityChangsha, China
| | - Hongwei Liu
- School of Minerals Processing and Bioengineering, Central South UniversityChangsha, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South UniversityChangsha, China
| | - Deliang Peng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural SciencesBeijing, China
| | - Wenkun Huang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural SciencesBeijing, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South UniversityChangsha, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South UniversityChangsha, China
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26
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Zhang X, Liu X, He Q, Dong W, Zhang X, Fan F, Peng D, Huang W, Yin H. Gene Turnover Contributes to the Evolutionary Adaptation of Acidithiobacillus caldus: Insights from Comparative Genomics. Front Microbiol 2016; 7:1960. [PMID: 27999570 PMCID: PMC5138436 DOI: 10.3389/fmicb.2016.01960] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 11/22/2016] [Indexed: 12/20/2022] Open
Abstract
Acidithiobacillus caldus is an extremely acidophilic sulfur-oxidizer with specialized characteristics, such as tolerance to low pH and heavy metal resistance. To gain novel insights into its genetic complexity, we chosen six A. caldus strains for comparative survey. All strains analyzed in this study differ in geographic origins as well as in ecological preferences. Based on phylogenomic analysis, we clustered the six A. caldus strains isolated from various ecological niches into two groups: group 1 strains with smaller genomes and group 2 strains with larger genomes. We found no obvious intraspecific divergence with respect to predicted genes that are related to central metabolism and stress management strategies between these two groups. Although numerous highly homogeneous genes were observed, high genetic diversity was also detected. Preliminary inspection provided a first glimpse of the potential correlation between intraspecific diversity at the genome level and environmental variation, especially geochemical conditions. Evolutionary genetic analyses further showed evidence that the difference in environmental conditions might be a crucial factor to drive the divergent evolution of A. caldus species. We identified a diverse pool of mobile genetic elements including insertion sequences and genomic islands, which suggests a high frequency of genetic exchange in these harsh habitats. Comprehensive analysis revealed that gene gains and losses were both dominant evolutionary forces that directed the genomic diversification of A. caldus species. For instance, horizontal gene transfer and gene duplication events in group 2 strains might contribute to an increase in microbial DNA content and novel functions. Moreover, genomes undergo extensive changes in group 1 strains such as removal of potential non-functional DNA, which results in the formation of compact and streamlined genomes. Taken together, the findings presented herein show highly frequent gene turnover of A. caldus species that inhabit extremely acidic environments, and shed new light on the contribution of gene turnover to the evolutionary adaptation of acidophiles.
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Affiliation(s)
- Xian Zhang
- School of Minerals Processing and Bioengineering, Central South UniversityChangsha, China; Key Laboratory of Biometallurgy of Ministry of Education, Central South UniversityChangsha, China
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South UniversityChangsha, China; Key Laboratory of Biometallurgy of Ministry of Education, Central South UniversityChangsha, China
| | - Qiang He
- Department of Civil and Environmental Engineering, the University of Tennessee, Knoxville TN, USA
| | - Weiling Dong
- School of Minerals Processing and Bioengineering, Central South University Changsha, China
| | - Xiaoxia Zhang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences Beijing, China
| | - Fenliang Fan
- Key Laboratory of Plant Nutrition and Fertilizer, Chinese Academy of Agricultural Sciences Beijing, China
| | - Deliang Peng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences Beijing, China
| | - Wenkun Huang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences Beijing, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South UniversityChangsha, China; Key Laboratory of Biometallurgy of Ministry of Education, Central South UniversityChangsha, China
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27
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Experiences and Future Challenges of Bioleaching Research in South Korea. MINERALS 2016. [DOI: 10.3390/min6040128] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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28
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Zhang X, Liu X, Liang Y, Fan F, Zhang X, Yin H. Metabolic diversity and adaptive mechanisms of iron- and/or sulfur-oxidizing autotrophic acidophiles in extremely acidic environments. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:738-751. [PMID: 27337207 DOI: 10.1111/1758-2229.12435] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 05/30/2016] [Indexed: 06/06/2023]
Abstract
Many studies have investigated the mechanisms underlying the survival and growth of certain organisms in extremely acidic environments known to be harmful to most prokaryotes and eukaryotes. Acidithiobacillus and Leptospirillum spp. are dominant bioleaching bacteria widely used in bioleaching systems, which are characterized by extremely acidic environments. To survive and grow in such settings, these acidophiles utilize shared molecular mechanisms that allow life in extreme conditions. In this review, we have summarized the results of published genomic analyses, which underscore the ability of iron- and/or sulfur-oxidizing autotrophic acidophiles belonging to the genera Acidithiobacillus and Leptospirillum to adapt to acidic environmental conditions. Several lines of evidence point at the metabolic diversity and multiplicity of pathways involved in the survival of these organisms. The ability to thrive in adverse environments requires versatile activation of structural and functional adaptive responses, including bacterial adhesion, motility, and resistance to heavy metals. We have highlighted recent developments centered on the key survival mechanisms employed by dominant extremophiles, and have laid the foundation for future studies focused on the ability of acidophiles to thrive in extremely acidic environments.
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Affiliation(s)
- Xian Zhang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Yili Liang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Fenliang Fan
- Key Laboratory of Plant Nutrition and Fertilizer, Beijing, China
| | - Xiaoxia Zhang
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Beijing, China
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
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29
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Zhang X, She S, Dong W, Niu J, Xiao Y, Liang Y, Liu X, Zhang X, Fan F, Yin H. Comparative genomics unravels metabolic differences at the species and/or strain level and extremely acidic environmental adaptation of ten bacteria belonging to the genus Acidithiobacillus. Syst Appl Microbiol 2016; 39:493-502. [PMID: 27712915 DOI: 10.1016/j.syapm.2016.08.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 07/22/2016] [Accepted: 08/11/2016] [Indexed: 01/17/2023]
Abstract
Members of the Acidithiobacillus genus are widely found in extreme environments characterized by low pH and high concentrations of toxic substances, thus it is necessary to identify the cellular mechanisms needed to cope with these harsh conditions. Pan-genome analysis of ten bacteria belonging to the genus Acidithiobacillus suggested the existence of core genome, most of which were assigned to the metabolism-associated genes. Additionally, the unique genes of Acidithiobacillus ferrooxidans were much less than those of other species. A large proportion of Acidithiobacillus ferrivorans-specific genes were mapped especially to metabolism-related genes, indicating that diverse metabolic pathways might confer an advantage for adaptation to local environmental conditions. Analyses of functional metabolisms revealed the differences of carbon metabolism, nitrogen metabolism, and sulfur metabolism at the species and/or strain level. The findings also showed that Acidithiobacillus spp. harbored specific adaptive mechanisms for thriving under extreme environments. The genus Acidithiobacillus had the genetic potential to resist and metabolize toxic substances such as heavy metals and organic solvents. Comparison across species and/or strains of Acidithiobacillus populations provided a deeper appreciation of metabolic differences and environmental adaptation, as well as highlighting the importance of cellular mechanisms that maintain the basal physiological functions under complex acidic environmental conditions.
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Affiliation(s)
- Xian Zhang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China; Key Laboratory of Biometallurgy, Ministry of Education, Central South University, Changsha, China.
| | - Siyuan She
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China; Key Laboratory of Biometallurgy, Ministry of Education, Central South University, Changsha, China.
| | - Weiling Dong
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China; Key Laboratory of Biometallurgy, Ministry of Education, Central South University, Changsha, China.
| | - Jiaojiao Niu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China; Key Laboratory of Biometallurgy, Ministry of Education, Central South University, Changsha, China.
| | - Yunhua Xiao
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China; Key Laboratory of Biometallurgy, Ministry of Education, Central South University, Changsha, China.
| | - Yili Liang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China; Key Laboratory of Biometallurgy, Ministry of Education, Central South University, Changsha, China.
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China; Key Laboratory of Biometallurgy, Ministry of Education, Central South University, Changsha, China.
| | - Xiaoxia Zhang
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Beijing, China; Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Fenliang Fan
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China; Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture, Beijing, China.
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China; Key Laboratory of Biometallurgy, Ministry of Education, Central South University, Changsha, China.
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30
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Merino MP, Andrews BA, Parada P, Asenjo JA. Characterization of Ferroplasma acidiphilum growing in pure and mixed culture with Leptospirillum ferriphilum. Biotechnol Prog 2016; 32:1390-1396. [PMID: 27535541 DOI: 10.1002/btpr.2340] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 05/27/2016] [Indexed: 11/07/2022]
Abstract
Biomining is defined as biotechnology for metal recovery from minerals, and is promoted by the concerted effort of a consortium of acidophile prokaryotes, comprised of members of the Bacteria and Archaea domains. Ferroplasma acidiphilum and Leptospirillum ferriphilum are the dominant species in extremely acid environments and have great use in bioleaching applications; however, the role of each species in this consortia is still a subject of research. The hypothesis of this work is that F. acidiphilum uses the organic matter secreted by L. ferriphilum for growth, maintaining low levels of organic compounds in the culture medium, preventing their toxic effects on L. ferriphilum. To test this hypothesis, a characterization of Ferroplasma acidiphilum strain BRL-115 was made with the objective of determining its optimal growth conditions. Subsequently, under the optimal conditions, L. ferriphilum and F. acidiphilum were tested growing in each other's supernatant, in order to define if there was exchange of metabolites between the species. With these results, a mixed culture in batch cyclic operation was performed to obtain main specific growth rates, which were used to evaluate a mixed metabolic model previously developed by our group. It was observed that F. acidiphilum, strain BRL-115 is a chemomixotrophic organism, and its growth is maximized with yeast extract at a concentration of 0.04% wt/vol. From the experiments of L. ferriphilum growing on F. acidiphilum supernatant and vice versa, it was observed that in both cases cell growth is favorably affected by the presence of the filtered medium of the other microorganism, proving a synergistic interaction between these species. Specific growth rates were obtained in cyclic batch operation of the mixed culture and were used as input data for a Flux Balance Analysis of the mixed metabolic model, obtaining a reasonable behavior of the metabolic fluxes and the system as a whole, therefore consolidating the model previously developed. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:1390-1396, 2016.
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Affiliation(s)
- M P Merino
- Centre for Biotechnology and Bioengineering, CeBiB, Dept. of Chemical Engineering and Biotechnology, University of Chile, Beauchef 851, Santiago, Chile
| | - B A Andrews
- Centre for Biotechnology and Bioengineering, CeBiB, Dept. of Chemical Engineering and Biotechnology, University of Chile, Beauchef 851, Santiago, Chile
| | - P Parada
- Biosigma S.A, Carretera Gral. San Martín 16500, Loteo Industrial Los Libertadores, Lote 106, Colina, Chile
| | - J A Asenjo
- Centre for Biotechnology and Bioengineering, CeBiB, Dept. of Chemical Engineering and Biotechnology, University of Chile, Beauchef 851, Santiago, Chile
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Comparative Genomics of the Extreme Acidophile Acidithiobacillus thiooxidans Reveals Intraspecific Divergence and Niche Adaptation. Int J Mol Sci 2016; 17:ijms17081355. [PMID: 27548157 PMCID: PMC5000751 DOI: 10.3390/ijms17081355] [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: 07/03/2016] [Revised: 08/05/2016] [Accepted: 08/11/2016] [Indexed: 11/17/2022] Open
Abstract
Acidithiobacillus thiooxidans known for its ubiquity in diverse acidic and sulfur-bearing environments worldwide was used as the research subject in this study. To explore the genomic fluidity and intraspecific diversity of Acidithiobacillus thiooxidans (A. thiooxidans) species, comparative genomics based on nine draft genomes was performed. Phylogenomic scrutiny provided first insights into the multiple groupings of these strains, suggesting that genetic diversity might be potentially correlated with their geographic distribution as well as geochemical conditions. While these strains shared a large number of common genes, they displayed differences in gene content. Functional assignment indicated that the core genome was essential for microbial basic activities such as energy acquisition and uptake of nutrients, whereas the accessory genome was thought to be involved in niche adaptation. Comprehensive analysis of their predicted central metabolism revealed that few differences were observed among these strains. Further analyses showed evidences of relevance between environmental conditions and genomic diversification. Furthermore, a diverse pool of mobile genetic elements including insertion sequences and genomic islands in all A. thiooxidans strains probably demonstrated the frequent genetic flow (such as lateral gene transfer) in the extremely acidic environments. From another perspective, these elements might endow A. thiooxidans species with capacities to withstand the chemical constraints of their natural habitats. Taken together, our findings bring some valuable data to better understand the genomic diversity and econiche adaptation within A. thiooxidans strains.
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Cárdenas JP, Quatrini R, Holmes DS. Genomic and metagenomic challenges and opportunities for bioleaching: a mini-review. Res Microbiol 2016; 167:529-38. [PMID: 27394987 DOI: 10.1016/j.resmic.2016.06.007] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 06/28/2016] [Accepted: 06/29/2016] [Indexed: 12/19/2022]
Abstract
High-throughput genomic technologies are accelerating progress in understanding the diversity of microbial life in many environments. Here we highlight advances in genomics and metagenomics of microorganisms from bioleaching heaps and related acidic mining environments. Bioleaching heaps used for copper recovery provide significant opportunities to study the processes and mechanisms underlying microbial successions and the influence of community composition on ecosystem functioning. Obtaining quantitative and process-level knowledge of these dynamics is pivotal for understanding how microorganisms contribute to the solubilization of copper for industrial recovery. Advances in DNA sequencing technology provide unprecedented opportunities to obtain information about the genomes of bioleaching microorganisms, allowing predictive models of metabolic potential and ecosystem-level interactions to be constructed. These approaches are enabling predictive phenotyping of organisms many of which are recalcitrant to genetic approaches or are unculturable. This mini-review describes current bioleaching genomic and metagenomic projects and addresses the use of genome information to: (i) build metabolic models; (ii) predict microbial interactions; (iii) estimate genetic diversity; and (iv) study microbial evolution. Key challenges and perspectives of bioleaching genomics/metagenomics are addressed.
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Affiliation(s)
| | | | - David S Holmes
- Fundación Ciencia & Vida, Santiago, Chile; Facultad de Ciencias Biologicas, Universidad Andres Bello, Santiago, Chile.
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Zhang X, Niu J, Liang Y, Liu X, Yin H. Metagenome-scale analysis yields insights into the structure and function of microbial communities in a copper bioleaching heap. BMC Genet 2016; 17:21. [PMID: 26781463 PMCID: PMC4717592 DOI: 10.1186/s12863-016-0330-4] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 01/13/2016] [Indexed: 01/18/2023] Open
Abstract
Background Metagenomics allows us to acquire the potential resources from both cultivatable and uncultivable microorganisms in the environment. Here, shotgun metagenome sequencing was used to investigate microbial communities from the surface layer of low grade copper tailings that were industrially bioleached at the Dexing Copper Mine, China. A bioinformatics analysis was further performed to elucidate structural and functional properties of the microbial communities in a copper bioleaching heap. Results Taxonomic analysis revealed unexpectedly high microbial biodiversity of this extremely acidic environment, as most sequences were phylogenetically assigned to Proteobacteria, while Euryarchaeota-related sequences occupied little proportion in this system, assuming that Archaea probably played little role in the bioleaching systems. At the genus level, the microbial community in mineral surface-layer was dominated by the sulfur- and iron-oxidizing acidophiles such as Acidithiobacillus-like populations, most of which were A. ferrivorans-like and A. ferrooxidans-like groups. In addition, Caudovirales were the dominant viral type observed in this extremely environment. Functional analysis illustrated that the principal participants related to the key metabolic pathways (carbon fixation, nitrogen metabolism, Fe(II) oxidation and sulfur metabolism) were mainly identified to be Acidithiobacillus-like, Thiobacillus-like and Leptospirillum-like microorganisms, indicating their vital roles. Also, microbial community harbored certain adaptive mechanisms (heavy metal resistance, low pH adaption, organic solvents tolerance and detoxification of hydroxyl radicals) as they performed their functions in the bioleaching system. Conclusion Our study provides several valuable datasets for understanding the microbial community composition and function in the surface-layer of copper bioleaching heap. Electronic supplementary material The online version of this article (doi:10.1186/s12863-016-0330-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xian Zhang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China. .,Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China.
| | - Jiaojiao Niu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China. .,Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China.
| | - Yili Liang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China. .,Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China.
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China. .,Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China.
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China. .,Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China.
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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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35
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Azizur Rahman M. Development of bioleaching: proteomics and genomics approach in metals extraction process. AIMS Microbiol 2016. [DOI: 10.3934/microbiol.2016.3.332] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Bordron P, Latorre M, Cortés MP, González M, Thiele S, Siegel A, Maass A, Eveillard D. Putative bacterial interactions from metagenomic knowledge with an integrative systems ecology approach. Microbiologyopen 2015; 5:106-17. [PMID: 26677108 PMCID: PMC4767419 DOI: 10.1002/mbo3.315] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 10/12/2015] [Accepted: 10/19/2015] [Indexed: 12/25/2022] Open
Abstract
Following the trend of studies that investigate microbial ecosystems using different metagenomic techniques, we propose a new integrative systems ecology approach that aims to decipher functional roles within a consortium through the integration of genomic and metabolic knowledge at genome scale. For the sake of application, using public genomes of five bacterial strains involved in copper bioleaching: Acidiphilium cryptum, Acidithiobacillus ferrooxidans, Acidithiobacillus thiooxidans, Leptospirillum ferriphilum, and Sulfobacillus thermosulfidooxidans, we first reconstructed a global metabolic network. Next, using a parsimony assumption, we deciphered sets of genes, called Sets from Genome Segments (SGS), that (1) are close on their respective genomes, (2) take an active part in metabolic pathways and (3) whose associated metabolic reactions are also closely connected within metabolic networks. Overall, this SGS paradigm depicts genomic functional units that emphasize respective roles of bacterial strains to catalyze metabolic pathways and environmental processes. Our analysis suggested that only few functional metabolic genes are horizontally transferred within the consortium and that no single bacterial strain can accomplish by itself the whole copper bioleaching. The use of SGS pinpoints a functional compartmentalization among the investigated species and exhibits putative bacterial interactions necessary for promoting these pathways.
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Affiliation(s)
- Philippe Bordron
- Mathomics, Center for Mathematical Modeling, Universidad de Chile, Santiago, Chile.,Center for Genome Regulation (Fondap 15090007), Universidad de Chile, Santiago, Chile
| | - Mauricio Latorre
- Mathomics, Center for Mathematical Modeling, Universidad de Chile, Santiago, Chile.,Center for Genome Regulation (Fondap 15090007), Universidad de Chile, Santiago, Chile.,Laboratorio de Bioinformática y Expresión Génica, INTA, Universidad de Chile, Santiago, Chile
| | - Maria-Paz Cortés
- Mathomics, Center for Mathematical Modeling, Universidad de Chile, Santiago, Chile.,Center for Genome Regulation (Fondap 15090007), Universidad de Chile, Santiago, Chile
| | - Mauricio González
- Center for Genome Regulation (Fondap 15090007), Universidad de Chile, Santiago, Chile.,Laboratorio de Bioinformática y Expresión Génica, INTA, Universidad de Chile, Santiago, Chile
| | - Sven Thiele
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Anne Siegel
- IRISA, UMR 6074, CNRS, Rennes, France.,INRIA, Dyliss Team, Centre Rennes-Bretagne-Atlantique, Rennes, France
| | - Alejandro Maass
- Mathomics, Center for Mathematical Modeling, Universidad de Chile, Santiago, Chile.,Center for Genome Regulation (Fondap 15090007), Universidad de Chile, Santiago, Chile.,Department of Mathematical Engineering, Universidad de Chile, Santiago, Chile
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Yan L, Zhang S, Liu H, Wang W, Chen P, Li H. Optimization of magnetosome production by Acidithiobacillus ferrooxidans using desirability function approach. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2015; 59:731-739. [PMID: 26652427 DOI: 10.1016/j.msec.2015.10.060] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 09/24/2015] [Accepted: 10/20/2015] [Indexed: 10/22/2022]
Abstract
Present study aimed to resolve the conflict between cell growth and magnetosome formation of Acidithiobacillus ferrooxidans (A. ferrooxidans) in batch experiments by applying response surface methodology (RSM) integrated a desirability function approach. The effects of several operating parameters on cell growth (OD600) and magnetosome production (Cmag) were evaluated. The maximum overall desirability (D) of 0.923 was achieved at iron concentration of 125.07mM, shake speed of 122.37rpm and nitrogen concentration of 2.40g/L. Correspondingly, the OD600 and Cmag were 0.522 and 1.196, respectively. The confirmation experiment confirmed that the optimum OD600 and Cmag obtained were in good agreement with the predicted values. The inductively coupled plasma atomic emission spectrometer (ICP-AES) and transmission electron microscopy (TEM) analyses revealed that the production of magnetosomes could be improved via optimization. X-ray diffraction (XRD) showed the magnetosomes are magnetite. Results indicated that RSM with a desirability function was a useful technique to get the maximum OD600 and Cmag simultaneously.
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Affiliation(s)
- Lei Yan
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing 163319, PR China.
| | - Shuang Zhang
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing 163319, PR China
| | - Hetao Liu
- School of Basic Medical Sciences, Ningxia Medical University, Yinchuan 750004, PR China
| | - Weidong Wang
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing 163319, PR China
| | - Peng Chen
- School of Pharmacy, Lanzhou University, Lanzhou 730000, PR China
| | - Hongyu Li
- School of Pharmacy, Lanzhou University, Lanzhou 730000, PR China
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38
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Martinez P, Vera M, Bobadilla-Fazzini RA. Omics on bioleaching: current and future impacts. Appl Microbiol Biotechnol 2015; 99:8337-50. [PMID: 26278538 PMCID: PMC4768214 DOI: 10.1007/s00253-015-6903-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 07/27/2015] [Accepted: 07/30/2015] [Indexed: 11/28/2022]
Abstract
Bioleaching corresponds to the microbial-catalyzed process of conversion of insoluble metals into soluble forms. As an applied biotechnology globally used, it represents an extremely interesting field of research where omics techniques can be applied in terms of knowledge development, but moreover in terms of process design, control, and optimization. In this mini-review, the current state of genomics, proteomics, and metabolomics of bioleaching and the major impacts of these analytical methods at industrial scale are highlighted. In summary, genomics has been essential in the determination of the biodiversity of leaching processes and for development of conceptual and functional metabolic models. Proteomic impacts are mostly related to microbe-mineral interaction analysis, including copper resistance and biofilm formation. Early steps of metabolomics in the field of bioleaching have shown a significant potential for the use of metabolites as industrial biomarkers. Development directions are given in order to enhance the future impacts of the omics in biohydrometallurgy.
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Affiliation(s)
- Patricio Martinez
- BioSigma 'S.A.', Parque Industrial Los Libertadores, Lote 106, Colina, Chile
| | - Mario Vera
- Biofilm Centre, Aquatische Biotechnologie, Universität Duisburg-Essen, Universitätstraße 5, 45141, Essen, Germany
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Orcutt BN, Sylvan JB, Rogers DR, Delaney J, Lee RW, Girguis PR. Carbon fixation by basalt-hosted microbial communities. Front Microbiol 2015; 6:904. [PMID: 26441854 PMCID: PMC4561358 DOI: 10.3389/fmicb.2015.00904] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 08/19/2015] [Indexed: 11/13/2022] Open
Abstract
Oceanic crust is a massive potential habitat for microbial life on Earth, yet our understanding of this ecosystem is limited due to difficulty in access. In particular, measurements of rates of microbial activity are sparse. We used stable carbon isotope incubations of crustal samples, coupled with functional gene analyses, to examine the potential for carbon fixation on oceanic crust. Both seafloor-exposed and subseafloor basalts were recovered from different mid-ocean ridge and hot spot environments (i.e., the Juan de Fuca Ridge, the Mid-Atlantic Ridge, and the Loihi Seamount) and incubated with (13)C-labeled bicarbonate. Seafloor-exposed basalts revealed incorporation of (13)C-label into organic matter over time, though the degree of incorporation was heterogeneous. The incorporation of (13)C into biomass was inconclusive in subseafloor basalts. Translating these measurements into potential rates of carbon fixation indicated that 0.1-10 nmol C g(-1) rock d(-1) could be fixed by seafloor-exposed rocks. When scaled to the global production of oceanic crust, this suggests carbon fixation rates of 10(9)-10(12) g C year(-1), which matches earlier predictions based on thermodynamic calculations. Functional gene analyses indicate that the Calvin cycle is likely the dominant biochemical mechanism for carbon fixation in basalt-hosted biofilms, although the reductive acetyl-CoA pathway and reverse TCA cycle likely play some role in net carbon fixation. These results provide empirical evidence for autotrophy in oceanic crust, suggesting that basalt-hosted autotrophy could be a significant contributor of organic matter in this remote and vast environment.
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Affiliation(s)
- Beth N. Orcutt
- Bigelow Laboratory for Ocean SciencesEast Boothbay, ME, USA
- University of Southern CaliforniaLos Angeles, CA, USA
| | | | - Daniel R. Rogers
- Biological Laboratories, Harvard UniversityCambridge, MA, USA
- Stonehill CollegeNorth Easton, MA, USA
| | | | - Raymond W. Lee
- School of Biological Sciences, Washington State UniversityPullman, WA, USA
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40
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Hua ZS, Han YJ, Chen LX, Liu J, Hu M, Li SJ, Kuang JL, Chain PSG, Huang LN, Shu WS. Ecological roles of dominant and rare prokaryotes in acid mine drainage revealed by metagenomics and metatranscriptomics. THE ISME JOURNAL 2015; 9:1280-94. [PMID: 25361395 PMCID: PMC4438317 DOI: 10.1038/ismej.2014.212] [Citation(s) in RCA: 157] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Revised: 07/21/2014] [Accepted: 09/21/2014] [Indexed: 12/22/2022]
Abstract
High-throughput sequencing is expanding our knowledge of microbial diversity in the environment. Still, understanding the metabolic potentials and ecological roles of rare and uncultured microbes in natural communities remains a major challenge. To this end, we applied a 'divide and conquer' strategy that partitioned a massive metagenomic data set (>100 Gbp) into subsets based on K-mer frequency in sequence assembly to a low-diversity acid mine drainage (AMD) microbial community and, by integrating with an additional metatranscriptomic assembly, successfully obtained 11 draft genomes most of which represent yet uncultured and/or rare taxa (relative abundance <1%). We report the first genome of a naturally occurring Ferrovum population (relative abundance >90%) and its metabolic potentials and gene expression profile, providing initial molecular insights into the ecological role of these lesser known, but potentially important, microorganisms in the AMD environment. Gene transcriptional analysis of the active taxa revealed major metabolic capabilities executed in situ, including carbon- and nitrogen-related metabolisms associated with syntrophic interactions, iron and sulfur oxidation, which are key in energy conservation and AMD generation, and the mechanisms of adaptation and response to the environmental stresses (heavy metals, low pH and oxidative stress). Remarkably, nitrogen fixation and sulfur oxidation were performed by the rare taxa, indicating their critical roles in the overall functioning and assembly of the AMD community. Our study demonstrates the potential of the 'divide and conquer' strategy in high-throughput sequencing data assembly for genome reconstruction and functional partitioning analysis of both dominant and rare species in natural microbial assemblages.
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Affiliation(s)
- Zheng-Shuang Hua
- State Key Laboratory of Biocontrol, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, College of Ecology and Evolution, Sun Yat-sen University, Guangzhou, PR China
| | - Yu-Jiao Han
- State Key Laboratory of Biocontrol, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, College of Ecology and Evolution, Sun Yat-sen University, Guangzhou, PR China
| | - Lin-Xing Chen
- State Key Laboratory of Biocontrol, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, College of Ecology and Evolution, Sun Yat-sen University, Guangzhou, PR China
| | - Jun Liu
- State Key Laboratory of Biocontrol, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, College of Ecology and Evolution, Sun Yat-sen University, Guangzhou, PR China
| | - Min Hu
- State Key Laboratory of Biocontrol, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, College of Ecology and Evolution, Sun Yat-sen University, Guangzhou, PR China
| | - Sheng-Jin Li
- State Key Laboratory of Biocontrol, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, College of Ecology and Evolution, Sun Yat-sen University, Guangzhou, PR China
| | - Jia-Liang Kuang
- State Key Laboratory of Biocontrol, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, College of Ecology and Evolution, Sun Yat-sen University, Guangzhou, PR China
| | - Patrick SG Chain
- Metagenomics Applications Team, Genome Science Group, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Li-Nan Huang
- State Key Laboratory of Biocontrol, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, College of Ecology and Evolution, Sun Yat-sen University, Guangzhou, PR China
| | - Wen-Sheng Shu
- State Key Laboratory of Biocontrol, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, College of Ecology and Evolution, Sun Yat-sen University, Guangzhou, PR China
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Méndez-García C, Peláez AI, Mesa V, Sánchez J, Golyshina OV, Ferrer M. Microbial diversity and metabolic networks in acid mine drainage habitats. Front Microbiol 2015; 6:475. [PMID: 26074887 PMCID: PMC4448039 DOI: 10.3389/fmicb.2015.00475] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 04/29/2015] [Indexed: 11/13/2022] Open
Abstract
Acid mine drainage (AMD) emplacements are low-complexity natural systems. Low-pH conditions appear to be the main factor underlying the limited diversity of the microbial populations thriving in these environments, although temperature, ionic composition, total organic carbon, and dissolved oxygen are also considered to significantly influence their microbial life. This natural reduction in diversity driven by extreme conditions was reflected in several studies on the microbial populations inhabiting the various micro-environments present in such ecosystems. Early studies based on the physiology of the autochthonous microbiota and the growing success of omics-based methodologies have enabled a better understanding of microbial ecology and function in low-pH mine outflows; however, complementary omics-derived data should be included to completely describe their microbial ecology. Furthermore, recent updates on the distribution of eukaryotes and archaea recovered through sterile filtering (herein referred to as filterable fraction) in these environments demand their inclusion in the microbial characterization of AMD systems. In this review, we present a complete overview of the bacterial, archaeal (including filterable fraction), and eukaryotic diversity in these ecosystems, and include a thorough depiction of the metabolism and element cycling in AMD habitats. We also review different metabolic network structures at the organismal level, which is necessary to disentangle the role of each member of the AMD communities described thus far.
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Affiliation(s)
| | - Ana I. Peláez
- Department of Functional Biology-IUBA, Universidad de OviedoOviedo, Spain
| | - Victoria Mesa
- Department of Functional Biology-IUBA, Universidad de OviedoOviedo, Spain
| | - Jesús Sánchez
- Department of Functional Biology-IUBA, Universidad de OviedoOviedo, Spain
| | | | - Manuel Ferrer
- Department of Applied Biocatalysis, Consejo Superior de Investigaciones Científicas, Institute of CatalysisMadrid, Spain
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Merino MP, Andrews BA, Asenjo JA. Stoichiometric model and flux balance analysis for a mixed culture of Leptospirillum ferriphilum and Ferroplasma acidiphilum. Biotechnol Prog 2014; 31:307-15. [PMID: 25504621 DOI: 10.1002/btpr.2028] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 11/20/2014] [Indexed: 11/08/2022]
Abstract
The oxidation process of sulfide minerals in natural environments is achieved by microbial communities from the Archaea and Bacteria domains. A metabolic reconstruction of two dominant species, Leptospirillum ferriphilum and Ferroplasma acidiphilum, which are always found together as a mixed culture in this natural environments, was made. The metabolic model, composed of 152 internal reactions and 29 transport reactions, describes the main interactions between these species, assuming that both use ferrous iron as energy source, and F. acidiphilum takes advantage of the organic compounds secreted by L. ferriphilum for chemomixotrophic growth. A first metabolic model for a mixed culture used in bacterial leaching is proposed in this article, which pretends to represent the characteristics of the mixed culture in a simplified manner. It was evaluated with experimental data through flux balance analysis (FBA) using as objective function the maximization of biomass. The growth yields on ferrous iron obtained for each microorganism are consistent with experimental data, and the flux distribution obtained allows understanding of the metabolic capabilities of both microorganisms growing together in a bioleaching process. The model was used to simulate the growth of F. acidiphilum on different substrates, to determine in silico which compounds maximize cell growth, and which are essential. Knockout simulations were carried out for L. ferriphilum and F. acidiphilum metabolic models, predicting key enzymes of central metabolism. The results of this analysis are consistent with experimental data from literature, showing a robust behavior of the metabolic model.
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Affiliation(s)
- M P Merino
- Dept. of Chemical Engineering and Biotechnology, Centre for Biotechnology and Bioengineering, CeBiB, University of Chile, Beauchef, 850, Santiago, Chile
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Draft Genome Sequence of the Iron-Oxidizing Acidophile Leptospirillum ferriphilum Type Strain DSM 14647. GENOME ANNOUNCEMENTS 2014; 2:2/6/e01153-14. [PMID: 25377718 PMCID: PMC4223469 DOI: 10.1128/genomea.01153-14] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The genomic features of the Leptospirillum ferriphilum type strain DSM 14647 are described here. An analysis of the predicted genes enriches our knowledge of the molecular basis of iron oxidation, improves our understanding of its role in industrial bioleaching, and suggests how it is adapted to live at extremely low pH.
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Travisany D, Cortés MP, Latorre M, Di Genova A, Budinich M, Bobadilla-Fazzini RA, Parada P, González M, Maass A. A new genome of Acidithiobacillus thiooxidans provides insights into adaptation to a bioleaching environment. Res Microbiol 2014; 165:743-52. [PMID: 25148779 DOI: 10.1016/j.resmic.2014.08.004] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 08/07/2014] [Accepted: 08/08/2014] [Indexed: 11/25/2022]
Abstract
Acidithiobacillus thiooxidans is a sulfur oxidizing acidophilic bacterium found in many sulfur-rich environments. It is particularly interesting due to its role in bioleaching of sulphide minerals. In this work, we report the genome sequence of At. thiooxidans Licanantay, the first strain from a copper mine to be sequenced and currently used in bioleaching industrial processes. Through comparative genomic analysis with two other At. thiooxidans non-metal mining strains (ATCC 19377 and A01) we determined that these strains share a large core genome of 2109 coding sequences and a high average nucleotide identity over 98%. Nevertheless, the presence of 841 strain-specific genes (absent in other At. thiooxidans strains) suggests a particular adaptation of Licanantay to its specific biomining environment. Among this group, we highlight genes encoding for proteins involved in heavy metal tolerance, mineral cell attachment and cysteine biosynthesis. Several of these genes were located near genetic motility genes (e.g. transposases and integrases) in genomic regions of over 10 kbp absent in the other strains, suggesting the presence of genomic islands in the Licanantay genome probably produced by horizontal gene transfer in mining environments.
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Affiliation(s)
- 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
| | - 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
| | - Mauricio Latorre
- 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
| | - Alex Di Genova
- 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
| | | | - Pilar Parada
- BioSigma S.A., Loteo Los Libertadores, Lote 106, Colina, Chile
| | - Mauricio González
- 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
| | - 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; Department of Mathematical Engineering, Universidad de Chile, Beauchef 851, 5th Floor, Santiago, Chile.
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Biotechnological applications derived from microorganisms of the Atacama Desert. BIOMED RESEARCH INTERNATIONAL 2014; 2014:909312. [PMID: 25147824 PMCID: PMC4132489 DOI: 10.1155/2014/909312] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Revised: 06/29/2014] [Accepted: 07/07/2014] [Indexed: 01/18/2023]
Abstract
The Atacama Desert in Chile is well known for being the driest and oldest desert on Earth. For these same reasons, it is also considered a good analog model of the planet Mars. Only a few decades ago, it was thought that this was a sterile place, but in the past years fascinating adaptations have been reported in the members of the three domains of life: low water availability, high UV radiation, high salinity, and other environmental stresses. However, the biotechnological applications derived from the basic understanding and characterization of these species, with the notable exception of copper bioleaching, are still in its infancy, thus offering an immense potential for future development.
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Genomic insights into the uncultured genus 'Candidatus Magnetobacterium' in the phylum Nitrospirae. ISME JOURNAL 2014; 8:2463-77. [PMID: 24914800 DOI: 10.1038/ismej.2014.94] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2014] [Revised: 04/27/2014] [Accepted: 05/08/2014] [Indexed: 11/09/2022]
Abstract
Magnetotactic bacteria (MTB) of the genus 'Candidatus Magnetobacterium' in phylum Nitrospirae are of great interest because of the formation of hundreds of bullet-shaped magnetite magnetosomes in multiple bundles of chains per cell. These bacteria are worldwide distributed in aquatic environments and have important roles in the biogeochemical cycles of iron and sulfur. However, except for a few short genomic fragments, no genome data are available for this ecologically important genus, and little is known about their metabolic capacity owing to the lack of pure cultures. Here we report the first draft genome sequence of 3.42 Mb from an uncultivated strain tentatively named 'Ca. Magnetobacterium casensis' isolated from Lake Miyun, China. The genome sequence indicates an autotrophic lifestyle using the Wood-Ljungdahl pathway for CO2 fixation, which has not been described in any previously known MTB or Nitrospirae organisms. Pathways involved in the denitrification, sulfur oxidation and sulfate reduction have been predicted, indicating its considerable capacity for adaptation to variable geochemical conditions and roles in local biogeochemical cycles. Moreover, we have identified a complete magnetosome gene island containing mam, mad and a set of novel genes (named as man genes) putatively responsible for the formation of bullet-shaped magnetite magnetosomes and the arrangement of multiple magnetosome chains. This first comprehensive genomic analysis sheds light on the physiology, ecology and biomineralization of the poorly understood 'Ca. Magnetobacterium' genus.
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Dai Z, Guo X, Yin H, Liang Y, Cong J, Liu X. Identification of nitrogen-fixing genes and gene clusters from metagenomic library of acid mine drainage. PLoS One 2014; 9:e87976. [PMID: 24498417 PMCID: PMC3912193 DOI: 10.1371/journal.pone.0087976] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Accepted: 01/02/2014] [Indexed: 11/19/2022] Open
Abstract
Biological nitrogen fixation is an essential function of acid mine drainage (AMD) microbial communities. However, most acidophiles in AMD environments are uncultured microorganisms and little is known about the diversity of nitrogen-fixing genes and structure of nif gene cluster in AMD microbial communities. In this study, we used metagenomic sequencing to isolate nif genes in the AMD microbial community from Dexing Copper Mine, China. Meanwhile, a metagenome microarray containing 7,776 large-insertion fosmids was constructed to screen novel nif gene clusters. Metagenomic analyses revealed that 742 sequences were identified as nif genes including structural subunit genes nifH, nifD, nifK and various additional genes. The AMD community is massively dominated by the genus Acidithiobacillus. However, the phylogenetic diversity of nitrogen-fixing microorganisms is much higher than previously thought in the AMD community. Furthermore, a 32.5-kb genomic sequence harboring nif, fix and associated genes was screened by metagenome microarray. Comparative genome analysis indicated that most nif genes in this cluster are most similar to those of Herbaspirillum seropedicae, but the organization of the nif gene cluster had significant differences from H. seropedicae. Sequence analysis and reverse transcription PCR also suggested that distinct transcription units of nif genes exist in this gene cluster. nifQ gene falls into the same transcription unit with fixABCX genes, which have not been reported in other diazotrophs before. All of these results indicated that more novel diazotrophs survive in the AMD community.
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Affiliation(s)
- Zhimin Dai
- School of Minerals Processing and Bioengineering, Central South University, Changsha, P. R. China
| | - Xue Guo
- School of Minerals Processing and Bioengineering, Central South University, Changsha, P. R. China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, P. R. China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, P. R. China
| | - Yili Liang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, P. R. China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, P. R. China
| | - Jing Cong
- School of Minerals Processing and Bioengineering, Central South University, Changsha, P. R. China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, P. R. China
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, P. R. China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, P. R. China
- * E-mail:
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Tourova TP, Kovaleva OL, Gorlenko VM, Ivanovsky RN. Use of genes of carbon metabolism enzymes as molecular markers of Chlorobi phylum representatives. Microbiology (Reading) 2014. [DOI: 10.1134/s0026261714010159] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Heterodisulfide Reductase from Acidithiobacilli is a Key Component Involved in Metabolism of Reduced Inorganic Sulfur Compounds. ACTA ACUST UNITED AC 2013. [DOI: 10.4028/www.scientific.net/amr.825.194] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Heterodisulfide reductase (Hdr), is an iron-sulfur protein which in anaerobic methanogenic archaea catalyzes the reduction of the disulphide bond between coenzyme M and coenzyme B and is coupled to methane formation. In aerobic acidophilic chemolithotrophic bacteria (e.g., biomining bacteria) the function of this enzyme is unclear. Inspection of the genomic sequences of Acidithiobacillus ferrooxidans DSM 16786 and Acidithiobacillus thiooxidans DSM 17318 and reverse transcriptase-PCR results revealed a cluster of six co-transcribed genes, hdrC1, hdrB1, hdrA, orf1, hdrC2 and hdrB2, encoding proteins with high similarity to catalytic Hdr subunits. Additionally, microarray expression profiling and quantitative RT-PCR experiments demonstrated that the hdr genes of A.ferrooxidans and A. thiooxidans were highly expressed when bacteria are grown in the presence of sulfur and tetrathionate. Moreover, hdr genes in A. ferrooxidans were greatly up-regulated when this microorganism was grown in sulfur compared to ferrous medium. These results strongly support a role for Hdr in oxidative metabolism of reduced sulfur compounds in aerobic chemolithotrophic bacteria.
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Marakushev SA, Belonogova OV. The divergence and natural selection of autocatalytic primordial metabolic systems. ORIGINS LIFE EVOL B 2013; 43:263-81. [PMID: 23860777 DOI: 10.1007/s11084-013-9340-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Accepted: 06/28/2013] [Indexed: 11/24/2022]
Abstract
The diversity of the central metabolism of modern organisms is caused by the existence of a few metabolic modules, combination of which produces multiple metabolic pathways. This paper analyzes biomimetically reconstructed coupled autocatalytic cycles as the basis of ancestral metabolic systems. The mechanism for natural selection and evolution in autocatalytic chemical systems may be affected by natural homeostatic parameters such as ambient chemical potentials, temperature, and pressure. Competition between separate parts of an autocatalytic network with positive-plus-negative feedback resulted in the formation of primordial autotrophic, mixotrophic, and heterotrophic metabolic systems. This work examined the last common ancestor of a set of coupled metabolic cycles in a population of protocells. Physical-chemical properties of these cycles determined the main principles of natural selection for the ancestral Bacteria and Archaea taxa.
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Affiliation(s)
- Sergey A Marakushev
- Institute of Problem of Chemical Physics, Russian Academy of Sciences, 142432, Chernogolovka, Moscow Region, Russia.
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