1
|
Chen JS, Hussain B, Tsai HC, Nagarajan V, Kumar RS, Lin IC, Hsu BM. Deciphering microbial communities and their unique metabolic repertoire across rock-soil-plant continuum in the Dayoukeng fumarolic geothermal field of the Tatun Volcano Group. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:7330-7344. [PMID: 38158533 DOI: 10.1007/s11356-023-31313-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 11/28/2023] [Indexed: 01/03/2024]
Abstract
High temperature and sulfur concentrations in geothermal sulfur fumaroles host unique microbial ecosystems with niche-specific metabolic diversity and physiological functions. In this study, the microbial communities and their functionalities associated with the Dayoukeng geothermal field and the rock-soil-plant continuum were investigated to underpin the microbial modulation at different distances from the fumaroles source. At the phylum level, Bacteroidota, Planctomycetota, Armatimonadota, and Patescibacteria were abundant in plant samples; Elusimicrobiota and Desulfobacterota were in the rock samples while Nitrospirota, Micrarchaeota, and Deinococcota were dominant in the soil samples. Acidophilic thermophiles were enriched in samples within close proximity to the fumaroles, primarily at a distance of 1 m. The sulfur and iron-oxidizing acidophilic bacterial genera such as Acidothiobacillus and Sulfobacillus were abundant in the rock samples. The thermoacidophilic archaeon Acidianus and acidophilic bacteria Acidiphilium were abundant in the soil samples. Additionally, Thermosporothrix and Acidothermus were found abundant in the plant samples. The results of the functional annotation indicated that dark sulfur oxidation, iron oxidation, and hydrogen oxidation pathways were abundant in the soil samples up to 1 m from the fumaroles, while methanogenic and fermentation pathways were more prevalent in the soil samples located 10 m from the fumaroles. Interestingly, the results of this study indicated a higher microbial richness and abundance of acidophilic communities in the soils and plants compared to the rocks of the DYK fumarolic geothermal field.
Collapse
Affiliation(s)
- Jung-Sheng Chen
- Department of Medical Research, E-Da Hospital, I-Shou University, Kaohsiung, Taiwan
| | - Bashir Hussain
- Department of Earth and Environmental Sciences, National Chung Cheng University, Minxiong, Chiayi County, Taiwan
- Department of Biomedical Sciences, National Chung Cheng University, Minxiong, Chiayi County, Taiwan
| | - Hsin-Chi Tsai
- Department of Psychiatry, School of Medicine, Tzu Chi University, Hualien, Taiwan
- Department of Psychiatry, Tzu-Chi General Hospital, Hualien, Taiwan
| | - Viji Nagarajan
- Department of Earth and Environmental Sciences, National Chung Cheng University, Minxiong, Chiayi County, Taiwan
| | - Rajendran Senthil Kumar
- Department of Earth and Environmental Sciences, National Chung Cheng University, Minxiong, Chiayi County, Taiwan
| | - I-Ching Lin
- Department of Family Medicine, Asia University Hospital, Taichung, Taiwan
- Department of Kinesiology, Health and Leisure, Chienkuo Technology University, Chenghua, Taiwan
| | - Bing-Mu Hsu
- Department of Earth and Environmental Sciences, National Chung Cheng University, Minxiong, Chiayi County, Taiwan.
| |
Collapse
|
2
|
Bulaev A, Kadnikov V, Elkina Y, Beletsky A, Melamud V, Ravin N, Mardanov A. Shifts in the Microbial Populations of Bioleach Reactors Are Determined by Carbon Sources and Temperature. BIOLOGY 2023; 12:1411. [PMID: 37998010 PMCID: PMC10669018 DOI: 10.3390/biology12111411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/06/2023] [Accepted: 11/06/2023] [Indexed: 11/25/2023]
Abstract
In the present study, the effect of additional carbon sources (carbon dioxide and molasses) on the bio-oxidation of a pyrite-arsenopyrite concentrate at temperatures of 40-50 °C was studied, and novel data regarding the patterns of the bio-oxidation of gold-bearing sulfide concentrates and the composition of the microbial populations performing these processes were obtained. At 40 °C, additional carbon sources did not affect the bio-oxidation efficiency. At the same time, the application of additional carbon dioxide improved the bio-oxidation performance at temperatures of 45 and 50 °C and made it possible to avoid the inhibition of bio-oxidation due to an increase in the temperature. Therefore, the use of additional carbon dioxide may be proposed to prevent the negative effect of an increase in temperature on the bio-oxidation of sulfide concentrates. 16S rRNA gene profiling revealed archaea of the family Thermoplasmataceae (Acidiplasma, Ferroplasma, Cuniculiplasma, and A-plasma group) and bacteria of the genera Leptospirillum, with Sulfobacillus and Acidithiobacillus among the dominant groups in the community. Temperature influenced the composition of the communities to a greater extent than the additional sources of carbon and the mode of operation of the bioreactor. Elevating the temperature from 40 °C to 50 °C resulted in increases in the shares of Acidiplasma and Sulfobacillus and decreases in the relative abundances of Ferroplasma, Leptospirillum, and Acidithiobacillus, while Cuniculiplasma and A-plasma were more abundant at 45 °C. A metagenomic analysis of the studied population made it possible to characterize novel archaea belonging to an uncultivated, poorly-studied group of Thermoplasmatales which potentially plays an important role in the bio-oxidation process. Based on an analysis of the complete genome, we propose describing the novel species and novel genus as "Candidatus Carboxiplasma ferriphilum" gen. nov., spec. nov.
Collapse
Affiliation(s)
- Aleksandr Bulaev
- Research Center of Biotechnology, The Russian Academy of Sciences, Leninsky Ave. 33 Bld. 2, 119071 Moscow, Russia; (V.K.); (Y.E.); (A.B.); (V.M.); (A.M.)
| | | | | | | | | | | | | |
Collapse
|
3
|
Marín-Paredes R, Bolívar-Torres HH, Coronel-Gaytán A, Martínez-Romero E, Servín-Garcidueñas LE. A Metagenome from a Steam Vent in Los Azufres Geothermal Field Shows an Abundance of Thermoplasmatales archaea and Bacteria from the Phyla Actinomycetota and Pseudomonadota. Curr Issues Mol Biol 2023; 45:5849-5864. [PMID: 37504286 PMCID: PMC10378326 DOI: 10.3390/cimb45070370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 07/09/2023] [Accepted: 07/10/2023] [Indexed: 07/29/2023] Open
Abstract
Los Azufres National Park is a geothermal field that has a wide number of thermal manifestations; nevertheless, the microbial communities in many of these environments remain unknown. In this study, a metagenome from a sediment sample from Los Azufres National Park was sequenced. In this metagenome, we found that the microbial diversity corresponds to bacteria (Actinomycetota, Pseudomonadota), archaea (Thermoplasmatales and Candidatus Micrarchaeota and Candidatus Parvarchaeota), eukarya (Cyanidiaceae), and viruses (Fussellovirus and Caudoviricetes). The functional annotation showed genes related to the carbon fixation pathway, sulfur metabolism, genes involved in heat and cold shock, and heavy-metal resistance. From the sediment, it was possible to recover two metagenome-assembled genomes from Ferrimicrobium and Cuniculiplasma. Our results showed that there are a large number of microorganisms in Los Azufres that deserve to be studied.
Collapse
Affiliation(s)
- Roberto Marín-Paredes
- Laboratorio de Microbiómica, Escuela Nacional de Estudios Superiores Unidad Morelia, Universidad Nacional Autónoma de México, Morelia 58341, Mexico
| | - Hermes H Bolívar-Torres
- Escuela de Ciencias Biológicas, Universidad Pedagógica y Tecnológica de Colombia, Tunja 150003, Colombia
| | - Alberto Coronel-Gaytán
- Laboratorio de Microbiómica, Escuela Nacional de Estudios Superiores Unidad Morelia, Universidad Nacional Autónoma de México, Morelia 58341, Mexico
| | | | - Luis E Servín-Garcidueñas
- Laboratorio de Microbiómica, Escuela Nacional de Estudios Superiores Unidad Morelia, Universidad Nacional Autónoma de México, Morelia 58341, Mexico
- Laboratorio Nacional de Análisis y Síntesis Ecológica, Escuela Nacional de Estudios Superiores Unidad Morelia, Morelia 58341, Mexico
| |
Collapse
|
4
|
Mohammadpour H, Cardin M, Carraro L, Fasolato L, Cardazzo B. Characterization of the archaeal community in foods: The neglected part of the food microbiota. Int J Food Microbiol 2023; 401:110275. [PMID: 37295268 DOI: 10.1016/j.ijfoodmicro.2023.110275] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 04/30/2023] [Accepted: 05/28/2023] [Indexed: 06/12/2023]
Abstract
Despite the large number of studies conducted on archaea associated with extreme environments, the archaeal community composition in food products is still poorly known. Here, we investigated a new insight into exploring the archaeal community in several food matrices, with a particular focus on determining whether living archaea were present. A total of 71 samples of milk, cheese and its derived brine, honey, hamburger, clam, and trout were analyzed by high-throughput 16S rRNA sequencing. Archaea were detected in all the samples, ranging from 0.62 % of microbial communities in trout to 37.71 % in brine. Methanogens dominated 47.28 % of the archaeal communities, except for brine, which was dominated by halophilic taxa affiliated with the genus Haloquadratum (52.45 %). Clams were found to be a food with high richness and diversity of archaea and were targeted for culturing living archaea under different incubation time and temperature conditions. A subset of 16 communities derived from culture-dependent and culture-independent communities were assessed. Among the homogenates and living archaeal communities, the predominant taxa were distributed in the genera Nitrosopumilus (47.61 %) and Halorussus (78.78 %), respectively. A comparison of the 28 total taxa obtained by culture-dependent and culture-independent methods enabled their categorization into different groups, including detectable (8 out of 28), cultivable (8 out of 28), and detectable-cultivable (12 out of 28) taxa. Furthermore, using the culture method, the majority (14 out of 20) of living taxa grew at lower temperatures of 22 and 4 °C during long-term incubation, and few taxa (2 out of 20) were found at 37 °C during the initial days of incubation. Our results demonstrated the distribution of archaea in all analyzed food matrices, which opens new perspectives to expand our knowledge on archaea in foods and their beneficial and detrimental effects.
Collapse
Affiliation(s)
- Hooriyeh Mohammadpour
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale Universit'a 16, 35020 Legnaro, Pd, Italy
| | - Marco Cardin
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale Universit'a 16, 35020 Legnaro, Pd, Italy
| | - Lisa Carraro
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale Universit'a 16, 35020 Legnaro, Pd, Italy
| | - Luca Fasolato
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale Universit'a 16, 35020 Legnaro, Pd, Italy.
| | - Barbara Cardazzo
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale Universit'a 16, 35020 Legnaro, Pd, Italy
| |
Collapse
|
5
|
García-Maldonado JQ, Latisnere-Barragán H, Escobar-Zepeda A, Cadena S, Ramírez-Arenas PJ, Vázquez-Juárez R, Rojas-Contreras M, López-Cortés A. Revisiting Microbial Diversity in Hypersaline Microbial Mats from Guerrero Negro for a Better Understanding of Methanogenic Archaeal Communities. Microorganisms 2023; 11:microorganisms11030812. [PMID: 36985385 PMCID: PMC10059902 DOI: 10.3390/microorganisms11030812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/21/2023] [Accepted: 02/23/2023] [Indexed: 03/30/2023] Open
Abstract
Knowledge regarding the diversity of methanogenic archaeal communities in hypersaline environments is limited because of the lack of efficient cultivation efforts as well as their low abundance and metabolic activities. In this study, we explored the microbial communities in hypersaline microbial mats. Bioinformatic analyses showed significant differences among the archaeal community structures for each studied site. Taxonomic assignment based on 16S rRNA and methyl coenzyme-M reductase (mcrA) gene sequences, as well as metagenomic analysis, corroborated the presence of Methanosarcinales. Furthermore, this study also provided evidence for the presence of Methanobacteriales, Methanomicrobiales, Methanomassiliicoccales, Candidatus Methanofastidiosales, Methanocellales, Methanococcales and Methanopyrales, although some of these were found in extremely low relative abundances. Several mcrA environmental sequences were significantly different from those previously reported and did not match with any known methanogenic archaea, suggesting the presence of specific environmental clusters of methanogenic archaea in Guerrero Negro. Based on functional inference and the detection of specific genes in the metagenome, we hypothesised that all four methanogenic pathways were able to occur in these environments. This study allowed the detection of extremely low-abundance methanogenic archaea, which were highly diverse and with unknown physiology, evidencing the presence of all methanogenic metabolic pathways rather than the sheer existence of exclusively methylotrophic methanogenic archaea in hypersaline environments.
Collapse
Affiliation(s)
- José Q García-Maldonado
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Mérida, Mérida 97310, Yucatán, Mexico
| | - Hever Latisnere-Barragán
- Centro de Investigaciones Biológicas del Noroeste (CIBNOR), La Paz 23205, Baja California Sur, Mexico
| | | | - Santiago Cadena
- Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Morelos, Mexico
| | - Patricia J Ramírez-Arenas
- Centro de Investigaciones Biológicas del Noroeste (CIBNOR), La Paz 23205, Baja California Sur, Mexico
| | - Ricardo Vázquez-Juárez
- Centro de Investigaciones Biológicas del Noroeste (CIBNOR), La Paz 23205, Baja California Sur, Mexico
| | - Maurilia Rojas-Contreras
- Departamento de Agronomía, Universidad Autónoma de Baja California Sur, La Paz 23080, Baja California Sur, Mexico
| | - Alejandro López-Cortés
- Centro de Investigaciones Biológicas del Noroeste (CIBNOR), La Paz 23205, Baja California Sur, Mexico
| |
Collapse
|
6
|
Microbial Diversity of a Disused Copper Mine Site (Parys Mountain, UK), Dominated by Intensive Eukaryotic Filamentous Growth. Microorganisms 2022; 10:microorganisms10091694. [PMID: 36144296 PMCID: PMC9504087 DOI: 10.3390/microorganisms10091694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/06/2022] [Accepted: 08/10/2022] [Indexed: 11/17/2022] Open
Abstract
The Parys Mountain copper mine (Wales, UK) contains a wide range of discrete environmental microniches with various physicochemical conditions that shape microbial community composition. Our aim was to assess the microbial community in the sediments and overlying water column in an acidic mine drainage (AMD) site containing abundant filamentous biogenic growth via application of a combination of chemical analysis and taxonomic profiling using 16S rRNA gene amplicon sequencing. Our results were then compared to previously studied sites at Parys Mt. Overall, the sediment microbiome showed a dominance of bacteria over archaea, particularly those belonging to Proteobacteria (genera Acidiphilium and Acidisphaera), Acidobacteriota (subgroup 1), Chloroflexota (AD3 cluster), Nitrospirota (Leptospirillum) and the uncultured Planctomycetota/CPIa-3 termite group. Archaea were only present in the sediment in small quantities, being represented by the Terrestrial Miscellaneous Euryarchaeota Group (TMEG), Thermoplasmatales and Ca. Micrarchaeota (Ca. Micracaldota). Bacteria, mostly of the genera Acidiphilium and Leptospirillum, also dominated within the filamentous streamers while archaea were largely absent. This study found pH and dissolved solutes to be the most important parameters correlating with relative proportions of bacteria to archaea in an AMD environment and revealed the abundance patterns of native acidophilic prokaryotes inhabiting Parys Mt sites and their niche specificities.
Collapse
|
7
|
Krause S, Gfrerer S, von Kügelgen A, Reuse C, Dombrowski N, Villanueva L, Bunk B, Spröer C, Neu TR, Kuhlicke U, Schmidt-Hohagen K, Hiller K, Bharat TAM, Rachel R, Spang A, Gescher J. The importance of biofilm formation for cultivation of a Micrarchaeon and its interactions with its Thermoplasmatales host. Nat Commun 2022; 13:1735. [PMID: 35365607 PMCID: PMC8975820 DOI: 10.1038/s41467-022-29263-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 02/28/2022] [Indexed: 01/05/2023] Open
Abstract
Micrarchaeota is a distinctive lineage assigned to the DPANN archaea, which includes poorly characterised microorganisms with reduced genomes that likely depend on interactions with hosts for growth and survival. Here, we report the enrichment of a stable co-culture of a member of the Micrarchaeota (Ca. Micrarchaeum harzensis) together with its Thermoplasmatales host (Ca. Scheffleriplasma hospitalis), as well as the isolation of the latter. We show that symbiont-host interactions depend on biofilm formation as evidenced by growth experiments, comparative transcriptomic analyses and electron microscopy. In addition, genomic, metabolomic, extracellular polymeric substances and lipid content analyses indicate that the Micrarchaeon symbiont relies on the acquisition of metabolites from its host. Our study of the cell biology and physiology of a Micrarchaeon and its host adds to our limited knowledge of archaeal symbioses. The Micrarchaeota lineage includes poorly characterized archaea with reduced genomes that likely depend on host interactions for survival. Here, the authors report a stable co-culture of a member of the Micrarchaeota and its host, and use multi-omic and physiological analyses to shed light on this symbiosis.
Collapse
Affiliation(s)
- Susanne Krause
- Department of Applied Biology, Karlsruhe, Institute of Technology (KIT), Karlsruhe, Germany
| | - Sabrina Gfrerer
- Department of Applied Biology, Karlsruhe, Institute of Technology (KIT), Karlsruhe, Germany.,Institute for Biological Interfaces, Karlsruhe, Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
| | - Andriko von Kügelgen
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, United Kingdom
| | - Carsten Reuse
- Bioinformatics & Biochemistry, Technische Universität Braunschweig, Braunschweig, Germany.,Braunschweig Integrated Centre for Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Nina Dombrowski
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, Den Burg, The Netherlands
| | - Laura Villanueva
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, Den Burg, The Netherlands.,Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, The Netherlands
| | - Boyke Bunk
- Leibniz Institute DSMZ, Braunschweig, Germany
| | | | - Thomas R Neu
- Helmholtz-Centre for Environmental, Research UFZ, Magdeburg, Germany
| | - Ute Kuhlicke
- Helmholtz-Centre for Environmental, Research UFZ, Magdeburg, Germany
| | - Kerstin Schmidt-Hohagen
- Bioinformatics & Biochemistry, Technische Universität Braunschweig, Braunschweig, Germany.,Braunschweig Integrated Centre for Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Karsten Hiller
- Bioinformatics & Biochemistry, Technische Universität Braunschweig, Braunschweig, Germany.,Braunschweig Integrated Centre for Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Tanmay A M Bharat
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, United Kingdom.,Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, United Kingdom
| | - Reinhard Rachel
- Center for Electron Microscopy, University of Regensburg, Regensburg, Germany
| | - Anja Spang
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, Den Burg, The Netherlands.,Department of Cell- and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Johannes Gescher
- Department of Applied Biology, Karlsruhe, Institute of Technology (KIT), Karlsruhe, Germany. .,Institute for Biological Interfaces, Karlsruhe, Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany. .,Institute of Technical Microbiology, Technical University of Hamburg, Hamburg, Germany.
| |
Collapse
|
8
|
Kochetkova TV, Podosokorskaya OA, Elcheninov AG, Kublanov IV. Diversity of Thermophilic Prokaryotes Inhabiting Russian Natural Hot Springs. Microbiology (Reading) 2022. [DOI: 10.1134/s0026261722010064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
|
9
|
Winkler D, Gfrerer S, Gescher J. Biochemical Characterization of Recombinant Isocitrate Dehydrogenase and Its Putative Role in the Physiology of an Acidophilic Micrarchaeon. Microorganisms 2021; 9:2318. [PMID: 34835444 PMCID: PMC8623467 DOI: 10.3390/microorganisms9112318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/20/2021] [Accepted: 11/04/2021] [Indexed: 11/17/2022] Open
Abstract
Despite several discoveries in recent years, the physiology of acidophilic Micrarchaeota, such as "Candidatus Micrarchaeum harzensis A_DKE", remains largely enigmatic, as they highly express numerous genes encoding hypothetical proteins. Due to a lacking genetic system, it is difficult to elucidate the biological function of the corresponding proteins and heterologous expression is required. In order to prove the viability of this approach, A_DKE's isocitrate dehydrogenase (MhIDH) was recombinantly produced in Escherichia coli and purified to electrophoretic homogeneity for biochemical characterization. MhIDH showed optimal activity around pH 8 and appeared to be specific for NADP+ yet promiscuous regarding divalent cations as cofactors. Kinetic studies showed KM-values of 53.03 ± 5.63 µM and 1.94 ± 0.12 mM and kcat-values of 38.48 ± 1.62 and 43.99 ± 1.46 s-1 resulting in kcat/KM-values of 725 ± 107.62 and 22.69 ± 2.15 mM-1 s-1 for DL-isocitrate and NADP+, respectively. MhIDH's exceptionally low affinity for NADP+, potentially limiting its reaction rate, can likely be attributed to the presence of a proline residue in the NADP+ binding pocket, which might cause a decrease in hydrogen bonding of the cofactor and a distortion of local secondary structure.
Collapse
Affiliation(s)
- Dennis Winkler
- Department of Applied Biology, Institute for Applied Biosciences, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 2, 76131 Karlsruhe, Germany; (D.W.); (S.G.)
| | - Sabrina Gfrerer
- Department of Applied Biology, Institute for Applied Biosciences, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 2, 76131 Karlsruhe, Germany; (D.W.); (S.G.)
| | - Johannes Gescher
- Department of Applied Biology, Institute for Applied Biosciences, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 2, 76131 Karlsruhe, Germany; (D.W.); (S.G.)
- Institute for Biological Interfaces, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
- Institute of Technical Microbiology, Department of Process and Chemical Engineering, Technical University of Hamburg, Kasernenstr. 12, 21073 Hamburg, Germany
| |
Collapse
|
10
|
Owusu-Agyeman I, Plaza E, Cetecioglu Z. A pilot-scale study of granule-based anaerobic reactors for biogas recovery from municipal wastewater under sub-mesophilic conditions. BIORESOURCE TECHNOLOGY 2021; 337:125431. [PMID: 34198242 DOI: 10.1016/j.biortech.2021.125431] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 06/11/2021] [Accepted: 06/16/2021] [Indexed: 06/13/2023]
Abstract
The influence of hydraulic retention time (HRT of 3-5 h) and temperature (20-25 °C) on performance and microbial dynamics of two pilot-scale upflow anaerobic sludge blanket (UASB) reactors with different granule size distribution (UASB1 = 3-4 mm and UASB2 = 1-2 mm) were investigated for 217 days. Increasing the HRT to 5 h even at a lower temperature of 20 °C enhanced COD removal and biogas production with average of 59 ± 16% (up to 85%) and 73 ± 9 L/(m3·d) (up to 102 L/(m3·d)) for UASB1; 63 ± 16% (up to 85%) and 75 ± 9 L/(m3·d) (up to 90 L/(m3·d)) for UASB2, respectively. This is explained by sufficient contact time between microorganisms and substrate. Acetoclastic methanogenic activity was higher in UASB1 because Methanosaetaceae (produces methane from acetate) dominated (64 ± 4%). However, Methanoregulaceae (29 ± 3%) and Methanomicrobiales_unassigned (20 ± 6%) which produce methane from H2/CO2 and formate were significant in UASB2. The extent of change in the microbial dynamics with HRT and temperature was more obvious in the smaller granule reactor.
Collapse
Affiliation(s)
- Isaac Owusu-Agyeman
- Department of Chemical Engineering, KTH Royal Institute of Technology, SE-100 44, Stockholm, Sweden.
| | - Elzbieta Plaza
- Department of Sustainable Development, Environmental Science and Engineering, KTH Royal Institute of Technology, SE-100 44, Stockholm, Sweden
| | - Zeynep Cetecioglu
- Department of Chemical Engineering, KTH Royal Institute of Technology, SE-100 44, Stockholm, Sweden
| |
Collapse
|
11
|
Martin-Pozas T, Sanchez-Moral S, Cuezva S, Jurado V, Saiz-Jimenez C, Perez-Lopez R, Carrey R, Otero N, Giesemann A, Well R, Calaforra JM, Fernandez-Cortes A. Biologically mediated release of endogenous N 2O and NO 2 gases in a hydrothermal, hypoxic subterranean environment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 747:141218. [PMID: 32777502 DOI: 10.1016/j.scitotenv.2020.141218] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 07/17/2020] [Accepted: 07/22/2020] [Indexed: 06/11/2023]
Abstract
The migration of geogenic gases in continental areas with geothermal activity and active faults is an important process releasing greenhouse gases (GHG) to the lower troposphere. In this respect, caves in hypogenic environments are natural laboratories to study the compositional evolution of deep-endogenous fluids through the Critical Zone. Vapour Cave (Alhama, Murcia, Spain) is a hypogenic cave formed by the upwelling of hydrothermal CO2-rich fluids. Anomalous concentrations of N2O and NO2 were registered in the cave's subterranean atmosphere, averaging ten and five times the typical atmospheric backgrounds, respectively. We characterised the thermal conditions, gaseous compositions, sediments, and microbial communities at different depths in the cave. We did so to understand the relation between N-cycling microbial groups and the production and transformation of nitrogenous gases, as well as their coupled evolution with CO2 and CH4 during their migration through the Critical Zone to the lower troposphere. Our results showed an evident vertical stratification of selected microbial groups (Archaea and Bacteria) depending on the environmental parameters, including O2, temperature, and GHG concentration. Both the N2O isotope ratios and the predicted ecological functions of bacterial and archaeal communities suggest that N2O and NO2 emissions mainly depend on the nitrification by ammonia-oxidising microorganisms. Denitrification and abiotic reactions of the reactive intermediates NH2OH, NO, and NO2- are also plausible according to the results of the phylogenetic analyses of the microbial communities. Nitrite-dependent anaerobic methane oxidation by denitrifying methanotrophs of the NC10 phylum was also identified as a post-genetic process during migration of this gas to the surface. To the best of our knowledge, our report provides, for the first time, evidence of a niche densely populated by Micrarchaeia, which represents more than 50% of the total archaeal abundance. This raises many questions on the metabolic behaviour of this and other archaeal phyla.
Collapse
Affiliation(s)
- Tamara Martin-Pozas
- Department of Geology, National Museum of Natural Sciences (MNCN-CSIC), 28006 Madrid, Spain.
| | - Sergio Sanchez-Moral
- Department of Geology, National Museum of Natural Sciences (MNCN-CSIC), 28006 Madrid, Spain.
| | - Soledad Cuezva
- Plants and Ecosystems, Department of Biology, University of Antwerp, 2610 Wilrijk, Belgium.
| | - Valme Jurado
- Department of Agrochemistry, Environmental Microbiology and Soil Conservation, Institute of Natural Resources and Agricultural Biology (IRNAS-CSIC), 41012 Seville, Spain.
| | - Cesareo Saiz-Jimenez
- Department of Agrochemistry, Environmental Microbiology and Soil Conservation, Institute of Natural Resources and Agricultural Biology (IRNAS-CSIC), 41012 Seville, Spain.
| | - Raul Perez-Lopez
- Geological Hazard Division, Geological Survey of Spain (IGME), 28003 Madrid, Spain.
| | - Raul Carrey
- Grup MAiMA, SGR Mineralogia Aplicada, Geoquímica i Geomicrobiologia, Departament de Mineralogia, Petrologia i Geologia Aplicada, Facultat de Ciències de la Terra, Universitat de Barcelona (UB), 08028 Barcelona, Spain; Institut de Recerca de l'Aigua (IdRA), UB, 08001 Barcelona, Spain.
| | - Neus Otero
- Grup MAiMA, SGR Mineralogia Aplicada, Geoquímica i Geomicrobiologia, Departament de Mineralogia, Petrologia i Geologia Aplicada, Facultat de Ciències de la Terra, Universitat de Barcelona (UB), 08028 Barcelona, Spain; Institut de Recerca de l'Aigua (IdRA), UB, 08001 Barcelona, Spain.
| | - Anette Giesemann
- Thünen Institute of Climate-Smart Agriculture, Federal Research Institute for Rural Areas, Forestry and Fisheries, 38116 Braunschweig, Germany.
| | - Reinhard Well
- Thünen Institute of Climate-Smart Agriculture, Federal Research Institute for Rural Areas, Forestry and Fisheries, 38116 Braunschweig, Germany.
| | - Jose M Calaforra
- Department of Biology and Geology, University of Almeria, 04120 Almeria, Spain.
| | | |
Collapse
|
12
|
Distaso MA, Bargiela R, Brailsford FL, Williams GB, Wright S, Lunev EA, Toshchakov SV, Yakimov MM, Jones DL, Golyshin PN, Golyshina OV. High Representation of Archaea Across All Depths in Oxic and Low-pH Sediment Layers Underlying an Acidic Stream. Front Microbiol 2020; 11:576520. [PMID: 33329440 PMCID: PMC7716880 DOI: 10.3389/fmicb.2020.576520] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 10/23/2020] [Indexed: 12/26/2022] Open
Abstract
Parys Mountain or Mynydd Parys (Isle of Anglesey, United Kingdom) is a mine-impacted environment, which accommodates a variety of acidophilic organisms. Our previous research of water and sediments from one of the surface acidic streams showed a high proportion of archaea in the total microbial community. To understand the spatial distribution of archaea, we sampled cores (0-20 cm) of sediment and conducted chemical analyses and taxonomic profiling of microbiomes using 16S rRNA gene amplicon sequencing in different core layers. The taxonomic affiliation of sequencing reads indicated that archaea represented between 6.2 and 54% of the microbial community at all sediment depths. Majority of archaea were associated with the order Thermoplasmatales, with the most abundant group of sequences being clustered closely with the phylotype B_DKE, followed by "E-plasma," "A-plasma," other yet uncultured Thermoplasmatales with Ferroplasma and Cuniculiplasma spp. represented in minor proportions. Thermoplasmatales were found at all depths and in the whole range of chemical conditions with their abundance correlating with sediment Fe, As, Cr, and Mn contents. The bacterial microbiome component was largely composed in all layers of sediment by members of the phyla Proteobacteria, Actinobacteria, Nitrospirae, Firmicutes, uncultured Chloroflexi (AD3 group), and Acidobacteria. This study has revealed a high abundance of Thermoplasmatales in acid mine drainage-affected sediment layers and pointed at these organisms being the main contributors to carbon, and probably to iron and sulfur cycles in this ecosystem.
Collapse
Affiliation(s)
- Marco A. Distaso
- School of Natural Sciences, Bangor University, Bangor, United Kingdom
- Centre for Environmental Biotechnology, Bangor University, Bangor, United Kingdom
| | - Rafael Bargiela
- School of Natural Sciences, Bangor University, Bangor, United Kingdom
| | - Francesca L. Brailsford
- School of Natural Sciences, Bangor University, Bangor, United Kingdom
- Centre for Environmental Biotechnology, Bangor University, Bangor, United Kingdom
- School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
| | - Gwion B. Williams
- School of Natural Sciences, Bangor University, Bangor, United Kingdom
- Centre for Environmental Biotechnology, Bangor University, Bangor, United Kingdom
| | - Samuel Wright
- School of Natural Sciences, Bangor University, Bangor, United Kingdom
- Centre for Environmental Biotechnology, Bangor University, Bangor, United Kingdom
| | - Evgenii A. Lunev
- Institute of Living Systems, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | | | - Michail M. Yakimov
- Institute for Biological Resources and Marine Biotechnology, CNR, Messina, Italy
| | - David L. Jones
- School of Natural Sciences, Bangor University, Bangor, United Kingdom
- Centre for Environmental Biotechnology, Bangor University, Bangor, United Kingdom
- School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
| | - Peter N. Golyshin
- School of Natural Sciences, Bangor University, Bangor, United Kingdom
- Centre for Environmental Biotechnology, Bangor University, Bangor, United Kingdom
| | - Olga V. Golyshina
- School of Natural Sciences, Bangor University, Bangor, United Kingdom
- Centre for Environmental Biotechnology, Bangor University, Bangor, United Kingdom
| |
Collapse
|
13
|
Metabolic Diversity and Evolutionary History of the Archaeal Phylum " Candidatus Micrarchaeota" Uncovered from a Freshwater Lake Metagenome. Appl Environ Microbiol 2020; 86:AEM.02199-20. [PMID: 32978130 DOI: 10.1128/aem.02199-20] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 09/18/2020] [Indexed: 12/19/2022] Open
Abstract
Acidophilic archaea of the archaeal Richmond Mine acidophilic nanoorganisms (ARMAN) group from the uncultured candidate phylum "Candidatus Micrarchaeota" have small genomes and cell sizes and are known to be metabolically dependent and physically associated with their Thermoplasmatales hosts. However, phylogenetically diverse "Ca Micrarchaeota" are widely distributed in various nonacidic environments, and it remains uncertain because of the lack of complete genomes whether they are also devoted to a partner-dependent lifestyle. Here, we obtained nine metagenome-assembled genomes of "Ca Micrarchaeota" from the sediments of a meromictic freshwater lake, including a complete, closed 1.2 Mbp genome of "Ca Micrarchaeota" Sv326, an archaeon phylogenetically distant from the ARMAN lineage. Genome analysis revealed that, contrary to ARMAN "Ca Micrarchaeota," the Sv326 archaeon has complete glycolytic pathways and ATP generation mechanisms in substrate phosphorylation reactions, the capacities to utilize some sugars and amino acids as substrates, and pathways for de novo nucleotide biosynthesis but lacked an aerobic respiratory chain. We suppose that Sv326 is a free-living scavenger rather than an obligate parasite/symbiont. Comparative analysis of "Ca Micrarchaeota" genomes representing different order-level divisions indicated that evolution of the "Ca Micrarchaeota" from a free-living "Candidatus Diapherotrites"-like ancestor involved losses of important metabolic pathways in different lineages and gains of specific functions in the course of adaptation to a partner-dependent lifestyle and specific environmental conditions. The ARMAN group represents the most pronounced case of genome reduction and gene loss, while the Sv326 lineage appeared to be rather close to the ancestral state of the "Ca Micrarchaeota" in terms of metabolic potential.IMPORTANCE The recently described superphylum DPANN includes several phyla of uncultivated archaea with small cell sizes, reduced genomes, and limited metabolic capabilities. One of these phyla, "Ca Micrarchaeota," comprises an enigmatic group of archaea found in acid mine drainage environments, the archaeal Richmond Mine acidophilic nanoorganisms (ARMAN) group. Analysis of their reduced genomes revealed the absence of key metabolic pathways consistent with their partner-associated lifestyle, and physical associations of ARMAN cells with their hosts were documented. However, "Ca Micrarchaeota" include several lineages besides the ARMAN group found in nonacidic environments, and none of them have been characterized. Here, we report a complete genome of "Ca Micrarchaeota" from a non-ARMAN lineage. Analysis of this genome revealed the presence of metabolic capacities lost in ARMAN genomes that could enable a free-living lifestyle. These results expand our understanding of genetic diversity, lifestyle, and evolution of "Ca Micrarchaeota."
Collapse
|
14
|
Podosokorskaya OA, Kochetkova TV, Novikov AA, Toshchakov SV, Elcheninov AG, Kublanov IV. Tenuifilum thalassicum gen. nov., sp. nov., a novel moderate thermophilic anaerobic bacterium from a Kunashir Island shallow hot spring representing a new family Tenuifilaceae fam. nov. in the class Bacteroidia. Syst Appl Microbiol 2020; 43:126126. [DOI: 10.1016/j.syapm.2020.126126] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 07/15/2020] [Accepted: 07/16/2020] [Indexed: 01/23/2023]
|
15
|
Bargiela R, Lanthaler K, Potter CM, Ferrer M, Yakunin AF, Paizs B, Golyshin PN, Golyshina OV. Proteome Cold-Shock Response in the Extremely Acidophilic Archaeon, Cuniculiplasma divulgatum. Microorganisms 2020; 8:E759. [PMID: 32438588 PMCID: PMC7285479 DOI: 10.3390/microorganisms8050759] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 05/13/2020] [Accepted: 05/15/2020] [Indexed: 11/16/2022] Open
Abstract
The archaeon Cuniculiplasma divulgatum is ubiquitous in acidic environments with low-to-moderate temperatures. However, molecular mechanisms underlying its ability to thrive at lower temperatures remain unexplored. Using mass spectrometry (MS)-based proteomics, we analysed the effect of short-term (3 h) exposure to cold. The C. divulgatum genome encodes 2016 protein-coding genes, from which 819 proteins were identified in the cells grown under optimal conditions. In line with the peptidolytic lifestyle of C. divulgatum, its intracellular proteome revealed the abundance of proteases, ABC transporters and cytochrome C oxidase. From 747 quantifiable polypeptides, the levels of 582 proteins showed no change after the cold shock, whereas 104 proteins were upregulated suggesting that they might be contributing to cold adaptation. The highest increase in expression appeared in low-abundance (0.001-0.005 fmol%) proteins for polypeptides' hydrolysis (metal-dependent hydrolase), oxidation of amino acids (FAD-dependent oxidoreductase), pyrimidine biosynthesis (aspartate carbamoyltransferase regulatory chain proteins), citrate cycle (2-oxoacid ferredoxin oxidoreductase) and ATP production (V type ATP synthase). Importantly, the cold shock induced a substantial increase (6% and 9%) in expression of the most-abundant proteins, thermosome beta subunit and glutamate dehydrogenase. This study has outlined potential mechanisms of environmental fitness of Cuniculiplasma spp. allowing them to colonise acidic settings at low/moderate temperatures.
Collapse
Affiliation(s)
- Rafael Bargiela
- School of Natural Sciences, Bangor University, Deiniol Rd, Bangor LL57 2UW, UK; (R.B.); (K.L.); (C.M.P.); (A.F.Y.); (B.P.); (P.N.G.)
| | - Karin Lanthaler
- School of Natural Sciences, Bangor University, Deiniol Rd, Bangor LL57 2UW, UK; (R.B.); (K.L.); (C.M.P.); (A.F.Y.); (B.P.); (P.N.G.)
- Centre for Environmental Biotechnology, Bangor University, Deiniol Rd, Bangor LL57 2UW, UK
| | - Colin M. Potter
- School of Natural Sciences, Bangor University, Deiniol Rd, Bangor LL57 2UW, UK; (R.B.); (K.L.); (C.M.P.); (A.F.Y.); (B.P.); (P.N.G.)
- Centre for Environmental Biotechnology, Bangor University, Deiniol Rd, Bangor LL57 2UW, UK
| | - Manuel Ferrer
- Systems Biotechnology Group, Department of Applied Biocatalysis, CSIC—Institute of Catalysis, Marie Curie 2, 28049 Madrid, Spain;
| | - Alexander F. Yakunin
- School of Natural Sciences, Bangor University, Deiniol Rd, Bangor LL57 2UW, UK; (R.B.); (K.L.); (C.M.P.); (A.F.Y.); (B.P.); (P.N.G.)
- Centre for Environmental Biotechnology, Bangor University, Deiniol Rd, Bangor LL57 2UW, UK
| | - Bela Paizs
- School of Natural Sciences, Bangor University, Deiniol Rd, Bangor LL57 2UW, UK; (R.B.); (K.L.); (C.M.P.); (A.F.Y.); (B.P.); (P.N.G.)
- Centre for Environmental Biotechnology, Bangor University, Deiniol Rd, Bangor LL57 2UW, UK
| | - Peter N. Golyshin
- School of Natural Sciences, Bangor University, Deiniol Rd, Bangor LL57 2UW, UK; (R.B.); (K.L.); (C.M.P.); (A.F.Y.); (B.P.); (P.N.G.)
- Centre for Environmental Biotechnology, Bangor University, Deiniol Rd, Bangor LL57 2UW, UK
| | - Olga V. Golyshina
- School of Natural Sciences, Bangor University, Deiniol Rd, Bangor LL57 2UW, UK; (R.B.); (K.L.); (C.M.P.); (A.F.Y.); (B.P.); (P.N.G.)
- Centre for Environmental Biotechnology, Bangor University, Deiniol Rd, Bangor LL57 2UW, UK
| |
Collapse
|