1
|
Oren A. Novel insights into the diversity of halophilic microorganisms and their functioning in hypersaline ecosystems. NPJ BIODIVERSITY 2024; 3:18. [PMID: 39242694 PMCID: PMC11332174 DOI: 10.1038/s44185-024-00050-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Accepted: 06/25/2024] [Indexed: 09/09/2024]
Abstract
Our understanding of the microbial diversity inhabiting hypersaline environments, here defined as containing >100-150 g/L salts, has greatly increased in the past five years. Halophiles are found in each of the three domains of life. Many novel types have been cultivated, and metagenomics and other cultivation-independent approaches have revealed the existence of many previously unrecognized lineages. Syntrophic interactions between different phylogenetic lineages have been discovered, such as the symbiosis between members of the archaeal class Halobacteria and the 'Candidatus Nanohalarchaeota'. Metagenomics techniques also have shed light on the biogeography of halophiles, especially of the genera Salinibacter (Bacteria) and Haloquadratum and Halorubrum (Archaea). Exploration of the microbiome of hypersaline lakes led to the discovery of novel types of metabolism previously unknown to occur at high salt concentrations. Studies of environments with high concentrations of chaotropic ions such as magnesium, calcium, and lithium have refined our understanding of the limits of life.
Collapse
Affiliation(s)
- Aharon Oren
- Department of Plant and Environmental Sciences, The Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, 9190401, Israel.
| |
Collapse
|
2
|
Lazar CS, Schmidt F, Elvert M, Heuer VB, Hinrichs KU, Teske AP. Microbial diversity gradients in the geothermal mud volcano underlying the hypersaline Urania Basin. Front Microbiol 2022; 13:1043414. [PMID: 36620052 PMCID: PMC9812581 DOI: 10.3389/fmicb.2022.1043414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 12/01/2022] [Indexed: 12/24/2022] Open
Abstract
Mud volcanoes transport deep fluidized sediment and their microbial communities and thus provide a window into the deep biosphere. However, mud volcanoes are commonly sampled at the surface and not probed at greater depths, with the consequence that their internal geochemistry and microbiology remain hidden from view. Urania Basin, a hypersaline seafloor basin in the Mediterranean, harbors a mud volcano that erupts fluidized mud into the brine. The vertical mud pipe was amenable to shipboard Niskin bottle and multicorer sampling and provided an opportunity to investigate the downward sequence of bacterial and archaeal communities of the Urania Basin brine, fluid mud layers and consolidated subsurface sediments using 16S rRNA gene sequencing. These microbial communities show characteristic, habitat-related trends as they change throughout the sample series, from extremely halophilic bacteria (KB1) and archaea (Halodesulfoarchaeum spp.) in the brine, toward moderately halophilic and thermophilic endospore-forming bacteria and uncultured archaeal lineages in the mud fluid, and finally ending in aromatics-oxidizing bacteria, uncultured spore formers, and heterotrophic subsurface archaea (Thermoplasmatales, Bathyarchaeota, and Lokiarcheota) in the deep subsurface sediment at the bottom of the mud volcano. Since these bacterial and archaeal lineages are mostly anaerobic heterotrophic fermenters, the microbial ecosystem in the brine and fluidized mud functions as a layered fermenter for the degradation of sedimentary biomass and hydrocarbons. By spreading spore-forming, thermophilic Firmicutes during eruptions, the Urania Basin mud volcano likely functions as a source of endospores that occur widely in cold seafloor sediments.
Collapse
Affiliation(s)
- Cassandre Sara Lazar
- Department of Biological Sciences, Université du Québec à Montréal, Montréal, QC, Canada
| | - Frauke Schmidt
- Organic Geochemistry Group, Department of Geosciences, MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Marcus Elvert
- Organic Geochemistry Group, Department of Geosciences, MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Verena B. Heuer
- Organic Geochemistry Group, Department of Geosciences, MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Kai-Uwe Hinrichs
- Organic Geochemistry Group, Department of Geosciences, MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Andreas P. Teske
- Department of Earth, Marine and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| |
Collapse
|
3
|
Wu JH, McGenity TJ, Rettberg P, Simões MF, Li WJ, Antunes A. The archaeal class Halobacteria and astrobiology: Knowledge gaps and research opportunities. Front Microbiol 2022; 13:1023625. [PMID: 36312929 PMCID: PMC9608585 DOI: 10.3389/fmicb.2022.1023625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 09/07/2022] [Indexed: 09/19/2023] Open
Abstract
Water bodies on Mars and the icy moons of the outer solar system are now recognized as likely being associated with high levels of salt. Therefore, the study of high salinity environments and their inhabitants has become increasingly relevant for Astrobiology. Members of the archaeal class Halobacteria are the most successful microbial group living in hypersaline conditions and are recognized as key model organisms for exposure experiments. Despite this, data for the class is uneven across taxa and widely dispersed across the literature, which has made it difficult to properly assess the potential for species of Halobacteria to survive under the polyextreme conditions found beyond Earth. Here we provide an overview of published data on astrobiology-linked exposure experiments performed with members of the Halobacteria, identifying clear knowledge gaps and research opportunities.
Collapse
Affiliation(s)
- Jia-Hui Wu
- State Key Laboratory of Lunar and Planetary Sciences, Macau University of Science and Technology (MUST), Taipa, Macau SAR, China
- China National Space Administration (CNSA), Macau Center for Space Exploration and Science, Taipa, Macau SAR, China
| | - Terry J. McGenity
- School of Life Sciences, University of Essex, Colchester, United Kingdom
| | - Petra Rettberg
- German Aerospace Center (DLR), Institute of Aerospace Medicine, Köln, Germany
| | - Marta F. Simões
- State Key Laboratory of Lunar and Planetary Sciences, Macau University of Science and Technology (MUST), Taipa, Macau SAR, China
- China National Space Administration (CNSA), Macau Center for Space Exploration and Science, Taipa, Macau SAR, China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - André Antunes
- State Key Laboratory of Lunar and Planetary Sciences, Macau University of Science and Technology (MUST), Taipa, Macau SAR, China
- China National Space Administration (CNSA), Macau Center for Space Exploration and Science, Taipa, Macau SAR, China
| |
Collapse
|
4
|
Natranaeroarchaeum sulfidigenes gen. nov., sp. nov., carbohydrate-utilizing sulfur-respiring haloarchaeon from hypersaline soda lakes, a member of a new family Natronoarchaeaceae fam. nov. in the order Halobacteriales. Syst Appl Microbiol 2022; 45:126356. [DOI: 10.1016/j.syapm.2022.126356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 08/22/2022] [Accepted: 08/26/2022] [Indexed: 11/19/2022]
|
5
|
Sorokin DY, Merkel AY, Messina E, Tugui C, Pabst M, Golyshin PN, Yakimov MM. Anaerobic carboxydotrophy in sulfur-respiring haloarchaea from hypersaline lakes. THE ISME JOURNAL 2022; 16:1534-1546. [PMID: 35132120 PMCID: PMC9123189 DOI: 10.1038/s41396-022-01206-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 01/03/2022] [Accepted: 01/27/2022] [Indexed: 05/24/2023]
Abstract
Anaerobic carboxydotrophy is a widespread catabolic trait in bacteria, with two dominant pathways: hydrogenogenic and acetogenic. The marginal mode by direct oxidation to CO2 using an external e-acceptor has only a few examples. Use of sulfidic sediments from two types of hypersaline lakes in anaerobic enrichments with CO as an e-donor and elemental sulfur as an e-acceptor led to isolation of two pure cultures of anaerobic carboxydotrophs belonging to two genera of sulfur-reducing haloarchaea: Halanaeroarchaeum sp. HSR-CO from salt lakes and Halalkaliarchaeum sp. AArc-CO from soda lakes. Anaerobic growth of extremely halophilic archaea with CO was obligatory depended on the presence of elemental sulfur as the electron acceptor and yeast extract as the carbon source. CO served as a direct electron donor and H2 was not generated from CO when cells were incubated with or without sulfur. The genomes of the isolates encode a catalytic Ni,Fe-CODH subunit CooS (distantly related to bacterial homologs) and its Ni-incorporating chaperone CooC (related to methanogenic homologs) within a single genomic locus. Similar loci were also present in a genome of the type species of Halalkaliarchaeum closely related to AArc-CO, and the ability for anaerobic sulfur-dependent carboxydotrophy was confirmed for three different strains of this genus. Moreover, similar proteins are encoded in three of the four genomes of recently described carbohydrate-utilizing sulfur-reducing haloarchaea belonging to the genus Halapricum and in two yet undescribed haloarchaeal species. Overall, this work demonstrated for the first time the potential for anaerobic sulfur-dependent carboxydotrophy in extremely halophilic archaea.
Collapse
Affiliation(s)
- Dimitry Y Sorokin
- Winogradsky Institute of Microbiology, Federal Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia.
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands.
| | - Alexander Y Merkel
- Winogradsky Institute of Microbiology, Federal Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Enzo Messina
- IRBIM-CNR, Spianata S.Raineri 86, 98122, Messina, Italy
| | - Claudia Tugui
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Martin Pabst
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Peter N Golyshin
- School of Natural Sciences, Bangor University, Gwynedd, LL57 2UW, UK
| | | |
Collapse
|
6
|
Pavlović J, Bosch-Roig P, Rusková M, Planý M, Pangallo D, Sanmartín P. Long-amplicon MinION-based sequencing study in a salt-contaminated twelfth century granite-built chapel. Appl Microbiol Biotechnol 2022; 106:4297-4314. [PMID: 35596787 PMCID: PMC9200699 DOI: 10.1007/s00253-022-11961-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 04/14/2022] [Accepted: 05/02/2022] [Indexed: 11/30/2022]
Abstract
The irregular damp dark staining on the stonework of a salt-contaminated twelfth century granite-built chapel is thought to be related to a non-homogeneous distribution of salts and microbial communities. To enhance understanding of the role of microorganisms in the presence of salt and damp stains, we determined the salt content and identified the microbial ecosystem in several paving slabs and inner wall slabs (untreated and previously bio-desalinated) and in the exterior surrounding soil. Soluble salt analysis and culture-dependent approaches combined with archaeal and bacterial 16S rRNA and fungal ITS fragment as well as with the functional genes nirK, dsr, and soxB long-amplicon MinION-based sequencing were performed. State-of-the-art technology was used for microbial identification, providing information about the microbial diversity and phylogenetic groups present and enabling us to gain some insight into the biological cycles occurring in the community key genes involved in the different geomicrobiological cycles. A well-defined relationship between microbial data and soluble salts was identified, suggesting that poorly soluble salts (CaSO4) could fill the pores in the stone and lead to condensation and dissolution of highly soluble salts (Ca(NO3)2 and Mg(NO3)2) in the thin layer of water formed on the stonework. By contrast, no direct relationship between the damp staining and the salt content or related microbiota was established. Further analysis regarding organic matter and recalcitrant elements in the stonework should be carried out. KEY POINTS : • Poorly (CaSO4) and highly (Ca(NO3)2, Mg(NO3)2) soluble salts were detected • Halophilic and mineral weathering microorganisms reveal ecological impacts of salts • Microbial communities involved in nitrate and sulfate cycles were detected.
Collapse
Affiliation(s)
- Jelena Pavlović
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51, Bratislava, Slovakia
| | - Pilar Bosch-Roig
- Instituto Universitario de Restauración del Patrimonio, Universitat Politècnica de València, 46022, Valencia, Spain
| | - Magdalena Rusková
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51, Bratislava, Slovakia
| | - Matej Planý
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51, Bratislava, Slovakia
| | - Domenico Pangallo
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51, Bratislava, Slovakia
- Caravella, s.r.o., Tupolevova 2, 851 01, Bratislava, Slovakia
| | - Patricia Sanmartín
- Departamento de Edafoloxía e Química Agrícola, Facultade de Farmacia, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain.
- CRETUS, Universidade de Santiago de Compostela, Santiago de Compostela, Spain.
| |
Collapse
|
7
|
Zhou H, Zhao D, Zhang S, Xue Q, Zhang M, Yu H, Zhou J, Li M, Kumar S, Xiang H. Metagenomic insights into the environmental adaptation and metabolism of Candidatus Haloplasmatales, one archaeal order thriving in saline lakes. Environ Microbiol 2022; 24:2239-2258. [PMID: 35048500 DOI: 10.1111/1462-2920.15899] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 12/06/2021] [Indexed: 02/01/2023]
Abstract
The KTK 4A-related Thermoplasmata thrives in the sediment of saline lakes; however, systematic research on its taxonomy, environmental adaptation and metabolism is lacking. Here, we detected this abundant lineage in the sediment of five artificially separated ponds (salinity 7.0%-33.0%) within a Chinese soda-saline lake using culture-independent metagenomics and archaeal 16S rRNA gene amplicons. The phylogenies based on the 16S rRNA gene, and 122 archaeal ubiquitous single-copy proteins and genome-level identity analyses among the metagenome-assembled genomes demonstrate this lineage forming a novel order, Candidatus Haloplasmatales, comprising four genera affiliated with the identical family. Isoelectric point profiles of predicted proteomes suggest that most members adopt the energetically favourable 'salt-in' strategy. Functional prediction indicates the lithoheterotrophic nature with the versatile metabolic potentials for carbohydrate and organic acids as well as carbon monoxide and hydrogen utilization. Additionally, hydrogenase genes hdrABC-mvhADG are linked with incomplete reductive citrate cycle genes in the genomes, suggesting their functional connection. Comparison with the coupling of HdrABC-MvhADG and methanogenesis pathway provides new insights into the compatibility of laterally acquired methanogenesis with energy metabolism in the related order Methanomassiliicoccales. Globally, our research sheds light on the taxonomy, environmental adaptative mechanisms, metabolic potentials and evolutional significance of Ca. Haloplasmatales.
Collapse
Affiliation(s)
- Heng Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Dahe Zhao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Shengjie Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Qiong Xue
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Manqi Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Haiying Yu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jian Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Ming Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Sumit Kumar
- Enzyme and Microbial Biochemistry Lab, Department of Chemistry, Indian Institute of Technology, Delhi, India
| | - Hua Xiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
8
|
Xue Q, Zhao D, Zhang S, Zhou H, Zuo Z, Zhou J, Li M, Xiang H. Highly integrated adaptive mechanisms in Spiribacter halalkaliphilus, a bacterium abundant in Chinese soda-saline lakes. Environ Microbiol 2021; 23:6463-6482. [PMID: 34587356 PMCID: PMC9292931 DOI: 10.1111/1462-2920.15794] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/23/2021] [Accepted: 09/27/2021] [Indexed: 11/29/2022]
Abstract
Soda-saline lakes are polyextreme environments inhabited by many haloalkaliphiles, including one of the most abundant Spiribacter species. However, its mechanisms of adaptation are not ecophysiologically characterized. Based on a large-scale cultivation strategy, we obtained a representative isolate of this Spiribacter species whose relative abundance was the highest (up to 15.63%) in a wide range of salinities in the soda-saline lakes in Inner Mongolia, China. This species is a chemoorganoheterotrophic haloalkaliphile. It has a small and streamlined genome and utilizes a wide variety of compatible solutes to resist osmotic pressure and multiple monovalent cation/proton antiporters for pH homeostasis. In addition to growth enhancement by light under microaerobic conditions, cell growth, organic substrate consumption and polyhydroxybutyrate biosynthesis were also improved by inorganic sulfide. Both quantitative RT-PCR and enzymatic assays verified that sulfide:quinone oxidoreductase was upregulated during this process. Metatranscriptomic analysis indicated that all genes related to environmental adaptation were transcribed in natural environments. Overall, this study has identified a novel abundant haloalkaliphile with multiple and highly integrated adaptive strategies and found that inorganic sulfide was able to improve the adaptation of a heterotroph to polyextreme environments.
Collapse
Affiliation(s)
- Qiong Xue
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dahe Zhao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Shengjie Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Heng Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhenqiang Zuo
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jian Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ming Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Hua Xiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| |
Collapse
|
9
|
Li J, Gao Y, Dong H, Sheng GP. Haloarchaea, excellent candidates for removing pollutants from hypersaline wastewater. Trends Biotechnol 2021; 40:226-239. [PMID: 34284891 DOI: 10.1016/j.tibtech.2021.06.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/23/2021] [Accepted: 06/23/2021] [Indexed: 11/25/2022]
Abstract
Hypersaline wastewater is difficult to treat due to the inhibition of salt stress on microbes' viability and metabolic capabilities. Haloarchaea, native microorganisms that thrive in hypersaline habitats, overcome this key obstacle naturally. This review provides a comprehensive overview of the metabolic versatility of Haloarchaea in hypersaline wastewater treatment, including carbon, nitrogen, phosphorus, sulfur, and heavy metal metabolism. It also analyzes factors affecting pollutant removal and addresses metabolic mechanisms. Additionally, haloarchaea microbial characteristics and strategies to cope with salt stress are highlighted. Finally, the biotechnological potential of biomolecules produced from haloarchaea is investigated. To get better insight into the potential of haloarchaea, a deeper investigation of basic metabolism and more in-depth studies of their genomics and applications in actual wastewater are also necessary.
Collapse
Affiliation(s)
- Jin Li
- School of Environmental Science and Engineering, Qingdao University, Qingdao 266071, China.
| | - Yuanyuan Gao
- School of Environmental Science and Engineering, Qingdao University, Qingdao 266071, China
| | - Huiyu Dong
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-environmental Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Guo-Ping Sheng
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China.
| |
Collapse
|
10
|
A standardized archaeal taxonomy for the Genome Taxonomy Database. Nat Microbiol 2021; 6:946-959. [PMID: 34155373 DOI: 10.1038/s41564-021-00918-8] [Citation(s) in RCA: 166] [Impact Index Per Article: 55.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 05/10/2021] [Indexed: 02/05/2023]
Abstract
The accrual of genomic data from both cultured and uncultured microorganisms provides new opportunities to develop systematic taxonomies based on evolutionary relationships. Previously, we established a bacterial taxonomy through the Genome Taxonomy Database. Here, we propose a standardized archaeal taxonomy that is derived from a 122-concatenated-protein phylogeny that resolves polyphyletic groups and normalizes ranks based on relative evolutionary divergence. The resulting archaeal taxonomy, which forms part of the Genome Taxonomy Database, is stable for a range of phylogenetic variables including marker gene selection, inference methods, corrections for rate heterogeneity and compositional bias, tree rooting scenarios and expansion of the genome database. Rank normalization is shown to robustly correct for substitution rates varying up to 30-fold using simulated datasets. Taxonomic curation follows the rules of the International Code of Nomenclature of Prokaryotes while taking into account proposals to formally recognize the rank of phylum and to use genome sequences as type material. This taxonomy is based on 2,392 archaeal genomes, 93.3% of which required one or more changes to their existing taxonomy, mainly owing to incomplete classification. We identify 16 archaeal phyla and reclassify 3 major monophyletic units from the former Euryarchaeota and one phylum that unites the Thaumarchaeota-Aigarchaeota-Crenarchaeota-Korarchaeota (TACK) superphylum into a single phylum.
Collapse
|
11
|
Khan MA, Khan ST, Sequeira MC, Faheem SM, Rais N. Illumina sequencing of 16S rRNA genes reveals a unique microbial community in three anaerobic sludge digesters of Dubai. PLoS One 2021; 16:e0249023. [PMID: 33793629 PMCID: PMC8016227 DOI: 10.1371/journal.pone.0249023] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 03/09/2021] [Indexed: 01/12/2023] Open
Abstract
Understanding the microbial communities in anaerobic digesters, especially bacteria and archaea, is key to its better operation and regulation. Microbial communities in the anaerobic digesters of the Gulf region where climatic conditions and other factors may impact the incoming feed are not documented. Therefore, Archaeal and Bacterial communities of three full-scale anaerobic digesters, namely AD1, AD3, and AD5 of the Jebel Ali Sewage water Treatment Plant (JASTP) were analyzed by Illumina sequencing of 16S rRNA genes. Among bacteria, the most abundant genus was fermentative bacteria Acetobacteroides (Blvii28). Other predominant bacterial genera in the digesters included thermophilic bacteria (Fervidobacterium and Coprothermobacter) and halophilic bacteria like Haloterrigena and Sediminibacter. This can be correlated with the climatic condition in Dubai, where the bacteria in the incoming feed may be thermophilic or halophilic as much of the water used in the country is desalinated seawater. The predominant Archaea include mainly the members of the phyla Euryarchaeota and Crenarchaeota belonging to the genus Methanocorpusculum, Metallosphaera, Methanocella, and Methanococcus. The highest population of Methanocorpusculum (more than 50% of total Archaea), and other hydrogenotrophic archaea, is in agreement with the high population of bacterial genera Acetobacteroides (Blvii28) and Fervidobacterium, capable of fermenting organic substrates into acetate and H2. Coprothermobacter, which is known to improve protein degradation by establishing syntrophy with hydrogenotrophic archaea, is also one of the digesters’ dominant genera. The results suggest that the microbial community in three full-scale anaerobic digesters is different. To best of our knowledge this is the first detailed report from the UAE.
Collapse
Affiliation(s)
- Munawwar Ali Khan
- Department of Life and Environmental Sciences, College of Natural and Health Sciences, Zayed University, Dubai, United Arab Emirates
| | - Shams Tabrez Khan
- Department of Agricultural Microbiology, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
- * E-mail:
| | - Milred Cedric Sequeira
- School of Life Sciences, Manipal Academy of Higher Education, Academic City, Dubai, United Arab Emirates
| | - Sultan Mohammad Faheem
- School of Life Sciences, Manipal Academy of Higher Education, Academic City, Dubai, United Arab Emirates
| | - Naushad Rais
- School of Life Sciences, Manipal Academy of Higher Education, Academic City, Dubai, United Arab Emirates
| |
Collapse
|
12
|
Halo(natrono)archaea from hypersaline lakes can utilize sulfoxides other than DMSO as electron acceptors for anaerobic respiration. Extremophiles 2021; 25:173-180. [PMID: 33620581 DOI: 10.1007/s00792-021-01219-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 02/11/2021] [Indexed: 01/19/2023]
Abstract
Dimethylsulfoxide (DMSO) has long been known to support anaerobic respiration in a few species of basically aerobic extremely halophilic euryarchaea living in hypersaline lakes. Recently, it has also been shown to be utilized as an additional electron acceptor in basically anaerobic sulfur-reducing haloarchaea. Here we investigated whether haloarchaea would be capable of anaerobic respiration with other two sulfoxides, methionine sulfoxide (MSO) and tetramethylene sulfoxide (TMSO). For this, anaerobic enrichment cultures were inoculated with sediments from hypersaline salt and soda lakes in southwestern Siberia and southern Russia. Positive enrichments were obtained for both MSO and TMSO with yeast extract but not with formate or acetate as the electron donor. Two pure cultures obtained from salt lakes, either with MSO or TMSO, were obligate anaerobes closely related to sulfur-reducing Halanaeroarchaeum sulfurireducens, although the type strain of this genus was unable to utilize any sulfoxides. Two pure cultures isolated from soda lakes were facultatively anaerobic alkaliphilic haloarchaea using O2, sulfur and sulfoxides as the electron acceptors. One isolate was identical to the previously described sulfur-reducing Natrarchaeobaculum sulfurireducens, while another one, enriched at lower alkalinity, is forming a new species in the genus Halobiforma. Since all isolates enriched with either MSO or TMSO were able to respire all three sulfoxides including DMSO and the corresponding activities were cross-induced, it suggest that a single enzyme of the DMSO-reductase family with a broad substrate specificity is responsible for various sulfoxide-dependent respiration in haloarchaea.
Collapse
|
13
|
Sorokin DY, Messina E, Smedile F, La Cono V, Hallsworth JE, Yakimov MM. Carbohydrate‐dependent sulfur respiration in halo(alkali)philic archaea. Environ Microbiol 2021; 23:3789-3808. [DOI: 10.1111/1462-2920.15421] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/03/2021] [Accepted: 02/01/2021] [Indexed: 12/16/2022]
Affiliation(s)
- Dimitry Y. Sorokin
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology Russian Academy of Sciences Moscow Russia
- Department of Biotechnology Delft University of Technology Delft The Netherlands
| | - Enzo Messina
- Institute of Biological Resources and Marine Biotechnology, IRBIM‐CNR Messina Italy
| | - Francesco Smedile
- Institute of Biological Resources and Marine Biotechnology, IRBIM‐CNR Messina Italy
| | - Violetta La Cono
- Institute of Biological Resources and Marine Biotechnology, IRBIM‐CNR Messina Italy
| | - John E. Hallsworth
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast Belfast, Northern Ireland BT9 5DL UK
| | - Michail M. Yakimov
- Institute of Biological Resources and Marine Biotechnology, IRBIM‐CNR Messina Italy
| |
Collapse
|
14
|
Zavarzina DG, Zhilina TN, Kostrikina NA, Toshchakov SV, Kublanov IV. Isachenkonia alkalipeptolytica gen. nov. sp. nov., a new anaerobic, alkaliphilic proteolytic bacterium capable of reducing Fe(III) and sulfur. Int J Syst Evol Microbiol 2020; 70:4730-4738. [PMID: 32697189 DOI: 10.1099/ijsem.0.004341] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An obligately alkaliphilic, anaerobic, proteolytic bacterium was isolated from a sample of Tanatar III soda lake sediment (Altai region, Russia) and designated as strain Z-1701T. Cells of strain Z-1701T were short, straight, motile Gram-stain-positive rods. Growth of Z-1701T obligately depended on the presence of sodium carbonate. Strain Z-1701T could utilize various peptides mixtures, such as beef and yeast extracts, peptone, soytone, trypticase and tryptone, as well as such proteins as albumin, gelatin and sodium caseinate. It was able to grow oligotrophically with 0.02 g l-1 yeast extract as the sole energy and carbon source. Carbohydrates did not support the growth of strain Z-1701T. The main products released during the growth of strain Z-1701T on tryptone were formate, acetate and ammonium. Strain Z-1701T was able to reduce ferrihydrite, Fe(III)-EDTA, anthraquinone-2,6-disulfonate and elemental sulfur, using proteinaceous substrates as electron donors. In all cases the presence of the electron acceptor in the medium stimulated growth. The main cellular fatty acids were iso-C15 : 0, iso-C15 : 0 aldehyde, iso-C15 : 1 ω6, C16 : 0, iso-C17 : 0 aldehyde, C16 : 0 aldehyde and C14 : 0. The DNA G+C content of the isolate was 43.9 mol%. Phylogenetic analysis based on the concatenated alignment of 120 protein-marker sequences revealed that strain Z-1701T falls into a cluster with the genus Tindallia, family Clostridiaceae. 16S rRNA gene sequence identity between strain Z-1701T and Tindallia species were 88.3-89.75 %. On the basis of its phenotypic characteristics and phylogenetic position, the novel isolate is considered to be a representative of a novel genus and species for which the name Isachenkonia alkalipeptolytica gen. nov., sp. nov. is proposed, with Z-1701T (=JCM 32929Т=DSM 109060Т=VKM B-3261Т) as its type strain.
Collapse
Affiliation(s)
- Daria G Zavarzina
- Winogradsky Institute of Microbiology of Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, 60-let Oktyabrya prospect 7/2, 117312, Moscow, Russia
| | - Tatyana N Zhilina
- Winogradsky Institute of Microbiology of Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, 60-let Oktyabrya prospect 7/2, 117312, Moscow, Russia
| | - Nadegda A Kostrikina
- Winogradsky Institute of Microbiology of Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, 60-let Oktyabrya prospect 7/2, 117312, Moscow, Russia
| | - Stepan V Toshchakov
- Winogradsky Institute of Microbiology of Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, 60-let Oktyabrya prospect 7/2, 117312, Moscow, Russia
| | - Ilya V Kublanov
- Winogradsky Institute of Microbiology of Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, 60-let Oktyabrya prospect 7/2, 117312, Moscow, Russia
| |
Collapse
|
15
|
Sorokin DY, Merkel AY, Messina E, Yakimov MM, Itoh T, Mesbah NM, Wiegel J, Oren A. Reclassification of the genus Natronolimnobius: proposal of two new genera, Natronolimnohabitans gen. nov. to accommodate Natronolimnobius innermongolicus and Natrarchaeobaculum gen. nov. to accommodate Natronolimnobius aegyptiacus and Natronolimnobius sulfurireducens. Int J Syst Evol Microbiol 2020; 70:3399-3405. [DOI: 10.1099/ijsem.0.004186] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The genus
Natronolimnobius
, currently including four species, is a member of the order
Natrialbales
, class Halobacteria, and consists of obligately alkaliphilic and extremely halophilic members found exclusively in highly alkaline hypersaline soda lakes. The species were classified into this genus mostly based on phylogenetic analysis of the 16S rRNA gene. However, a more advanced phylogenomic reconstruction based on 122 conserved single-copy archaeal protein markers clearly indicates a polyphyletic origin of the species included into this genus, thus warranting its reclassification into three separate genera. We therefore propose to transfer Nlb. innermongolicus (type strain N-1311) to a new genus Natronolimnohabitans as Nlh. innermongolicus comb. nov. and to transfer Nlb. aegyptiacus (type strain JW/NM-HA 15) and Nlb. sulfurireducens (type strain AArc1) to a new genus Natrarchaeobaculum as Nbl. aegyptiacum comb. nov. and Nbl. sulfurireducens comb. nov. The phylogenomic differentiation of these four species is also supported by the ANI/AAI distances and unique phenotypes. The most important physiological differences includes a previously unreported ability for cellulose and xylan utilization in Nlb. baerhuensis, thermophily in Nbl. aegyptiacus and anaerobic sulfur respiration in Nbl. sulfurireducens. We further present an emended description of
Natronolimnobius baerhuensis
.
Collapse
Affiliation(s)
- Dimitry Y. Sorokin
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia
- Department of Biotechnology, TU Delft, The Netherlands
| | - Alexander Y. Merkel
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | | | | | - Takashi Itoh
- Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki, Japan
| | - Noha M. Mesbah
- Faculty of Pharmacy, Suez Canal University, Ismailia, Egypt
| | - Juergen Wiegel
- Department of Microbiology, University of Georgia, Athens, GA, USA
| | - Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| |
Collapse
|
16
|
Sorokin DY, Yakimov M, Messina E, Merkel AY, Bale NJ, Sinninghe Damsté JS. Natronolimnobius sulfurireducens sp. nov. and Halalkaliarchaeum desulfuricum gen. nov., sp. nov., the first sulfur-respiring alkaliphilic haloarchaea from hypersaline alkaline lakes. Int J Syst Evol Microbiol 2019; 69:2662-2673. [DOI: 10.1099/ijsem.0.003506] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Dimitry Y. Sorokin
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia
- Department of Biotechnology, TU Delft, CD Delft, The Netherlands
| | | | - Enzo Messina
- IAMC-CNR, Spianata S.Raineri 86, 98122 Messina, Italy
| | - Alexander Y. Merkel
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia
- Faculty of Geosciences, Department of Earth Sciences, Utrecht University, Utrecht, The Netherlands
| | - Nicole J. Bale
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Utrecht University, PO Box 59, 1790 AB Den Burg, Texel, The Netherlands
| | - Jaap S. Sinninghe Damsté
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Utrecht University, PO Box 59, 1790 AB Den Burg, Texel, The Netherlands
| |
Collapse
|
17
|
Vavourakis CD, Mehrshad M, Balkema C, van Hall R, Andrei AŞ, Ghai R, Sorokin DY, Muyzer G. Metagenomes and metatranscriptomes shed new light on the microbial-mediated sulfur cycle in a Siberian soda lake. BMC Biol 2019; 17:69. [PMID: 31438955 PMCID: PMC6704655 DOI: 10.1186/s12915-019-0688-7] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 08/09/2019] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND The planetary sulfur cycle is a complex web of chemical reactions that can be microbial-mediated or can occur spontaneously in the environment, depending on the temperature and pH. Inorganic sulfur compounds can serve as energy sources for specialized prokaryotes and are important substrates for microbial growth in general. Here, we investigate dissimilatory sulfur cycling in the brine and sediments of a southwestern Siberian soda lake characterized by an extremely high pH and salinity, combining meta-omics analyses of its uniquely adapted highly diverse prokaryote communities with biogeochemical profiling to identify key microbial players and expand our understanding of sulfur cycling under haloalkaline conditions. RESULTS Peak microbial activity was found in the top 4 cm of the sediments, a layer with a steep drop in oxygen concentration and redox potential. The majority of sulfur was present as sulfate or iron sulfide. Thiosulfate was readily oxidized by microbes in the presence of oxygen, but oxidation was partially inhibited by light. We obtained 1032 metagenome-assembled genomes, including novel population genomes of characterized colorless sulfur-oxidizing bacteria (SOB), anoxygenic purple sulfur bacteria, heterotrophic SOB, and highly active lithoautotrophic sulfate reducers. Surprisingly, we discovered the potential for nitrogen fixation in a new genus of colorless SOB, carbon fixation in a new species of phototrophic Gemmatimonadetes, and elemental sulfur/sulfite reduction in the "Candidatus Woesearchaeota." Polysulfide/thiosulfate and tetrathionate reductases were actively transcribed by various (facultative) anaerobes. CONCLUSIONS The recovery of over 200 genomes that encoded enzymes capable of catalyzing key reactions in the inorganic sulfur cycle indicates complete cycling between sulfate and sulfide at moderately hypersaline and extreme alkaline conditions. Our results suggest that more taxonomic groups are involved in sulfur dissimilation than previously assumed.
Collapse
Affiliation(s)
- Charlotte D Vavourakis
- Microbial Systems Ecology, Department of Freshwater and Marine Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, P.O. Box 94240, 1090 GE, Amsterdam, the Netherlands
| | - Maliheh Mehrshad
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice, Czech Republic
| | - Cherel Balkema
- Microbial Systems Ecology, Department of Freshwater and Marine Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, P.O. Box 94240, 1090 GE, Amsterdam, the Netherlands
| | - Rutger van Hall
- Department of Ecosystem & Landscape Dynamics, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, the Netherlands
| | - Adrian-Ştefan Andrei
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice, Czech Republic
| | - Rohit Ghai
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice, Czech Republic
| | - Dimitry Y Sorokin
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russian Federation
- Department of Biotechnology, Environmental Biotechnology, Delft University of Technology, Delft, the Netherlands
| | - Gerard Muyzer
- Microbial Systems Ecology, Department of Freshwater and Marine Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, P.O. Box 94240, 1090 GE, Amsterdam, the Netherlands.
| |
Collapse
|
18
|
Bale NJ, Sorokin DY, Hopmans EC, Koenen M, Rijpstra WIC, Villanueva L, Wienk H, Sinninghe Damsté JS. New Insights Into the Polar Lipid Composition of Extremely Halo(alkali)philic Euryarchaea From Hypersaline Lakes. Front Microbiol 2019; 10:377. [PMID: 30930858 PMCID: PMC6423904 DOI: 10.3389/fmicb.2019.00377] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 02/13/2019] [Indexed: 12/14/2022] Open
Abstract
We analyzed the polar membrane lipids of 13 strains of halo(alkali)philic euryarchaea from hypersaline lakes. Nine belong to the class Halobacteria, representing two functional groups: aerobic polysaccharide utilizers and sulfur-respiring anaerobes. The other four strains represent halo(alkali)philic methanogens from the class Methanomicrobia and a recently discovered class Methanonatronarchaeia. A wide range of polar lipids were detected across the 13 strains including dialkyl glycerol diethers (archaeols), membrane-spanning glycerol tetraethers and diether-based cardiolipins. The archaeols contained a range of core lipid structures, including combinations of C20 and C25 isoprenoidal alkyl chains, unsaturations, and hydroxy moieties. Several diether lipids were novel, including: (a) a phosphatidylglycerolhexose (PG-Gly) headgroup, (b) a N,N,N-trimethyl aminopentanetetrol (APT)-like lipid with a methoxy group in place of a hydroxy group on the pentanetetrol, (c) a series of polar lipids with a headgroup with elemental composition of either C12H25NO13S or C12H25NO16S2, and (d) novel cardiolipins containing a putative phosphatidylglycerolphosphate glycerophosphate (PGPGP) polar moiety. We found that the lipid distribution of the 13 strains could be generally separated into two groups, the methanogens (group) and the Halobacteria (class) based on the presence of specific core lipids. Within the methanogens, adaption to a high or more moderate salt concentration resulted in different ratios of glycerol dialkyl glycerol tetraethers (GDGTs) to archaeol. The methanogen Methanosalsum natronophilum AME2T had the most complex diether lipid composition of any of the 13 strains, including hydroxy archaeol and macrocyclic archaeol which we surmise is an order-specific membrane adaption. The zwitterionic headgroups APT and APT-Me were detected only in the Methanomicrobiales member Methanocalculus alkaliphilus AMF2T which also contained the highest level of unsaturated lipids. Only alkaliphilic members of the Natrialbales order contained PGPGP cardiolipins and the PG-Gly headgroup. The four analyzed neutrophilic members of the Halobacteria were characterized by the presence of sulfur-containing headgroups and glycolipids. The presence of cardiolipins with one or more i-C25 alkyl chains, generally termed extended archaeol (EXT-AR), in one of the Methanonatronarchaeia strains was unexpected as only one other order of methanogenic archaea has been reported to produce EXT-AR. We examined this further by looking into the genomic potential of various archaea to produce EXT-AR.
Collapse
Affiliation(s)
- Nicole J. Bale
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Institute for Sea Research, Utrecht University, Texel, Netherlands
| | - Dimitry Y. Sorokin
- Research Centre of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
- Department of Biotechnology, Faculty of Applied Sciences, Delft University of Technology, Delft, Netherlands
| | - Ellen C. Hopmans
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Institute for Sea Research, Utrecht University, Texel, Netherlands
| | - Michel Koenen
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Institute for Sea Research, Utrecht University, Texel, Netherlands
| | - W. Irene C. Rijpstra
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Institute for Sea Research, Utrecht University, Texel, Netherlands
| | - Laura Villanueva
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Institute for Sea Research, Utrecht University, Texel, Netherlands
| | - Hans Wienk
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | - Jaap S. Sinninghe Damsté
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Institute for Sea Research, Utrecht University, Texel, Netherlands
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, Netherlands
| |
Collapse
|