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Reva O, Messina E, La Cono V, Crisafi F, Smedile F, La Spada G, Marturano L, Selivanova EA, Rohde M, Krupovic M, Yakimov MM. Functional diversity of nanohaloarchaea within xylan-degrading consortia. Front Microbiol 2023; 14:1182464. [PMID: 37323909 PMCID: PMC10266531 DOI: 10.3389/fmicb.2023.1182464] [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: 03/08/2023] [Accepted: 05/09/2023] [Indexed: 06/17/2023] Open
Abstract
Extremely halophilic representatives of the phylum Candidatus Nanohaloarchaeota (members of the DPANN superphyla) are obligately associated with extremely halophilic archaea of the phylum Halobacteriota (according to the GTDB taxonomy). Using culture-independent molecular techniques, their presence in various hypersaline ecosystems around the world has been confirmed over the past decade. However, the vast majority of nanohaloarchaea remain uncultivated, and thus their metabolic capabilities and ecophysiology are currently poorly understood. Using the (meta)genomic, transcriptomic, and DNA methylome platforms, the metabolism and functional prediction of the ecophysiology of two novel extremely halophilic symbiotic nanohaloarchaea (Ca. Nanohalococcus occultus and Ca. Nanohalovita haloferacivicina) stably cultivated in the laboratory as members of a xylose-degrading binary culture with a haloarchaeal host, Haloferax lucentense, was determined. Like all known DPANN superphylum nanoorganisms, these new sugar-fermenting nanohaloarchaea lack many fundamental biosynthetic repertoires, making them exclusively dependent on their respective host for survival. In addition, given the cultivability of the new nanohaloarchaea, we managed to discover many unique features in these new organisms that have never been observed in nano-sized archaea both within the phylum Ca. Nanohaloarchaeota and the entire superphylum DPANN. This includes the analysis of the expression of organism-specific non-coding regulatory (nc)RNAs (with an elucidation of their 2D-secondary structures) as well as profiling of DNA methylation. While some ncRNA molecules have been predicted with high confidence as RNAs of an archaeal signal recognition particle involved in delaying protein translation, others resemble the structure of ribosome-associated ncRNAs, although none belong to any known family. Moreover, the new nanohaloarchaea have very complex cellular defense mechanisms. In addition to the defense mechanism provided by the type II restriction-modification system, consisting of Dcm-like DNA methyltransferase and Mrr restriction endonuclease, Ca. Nanohalococcus encodes an active type I-D CRISPR/Cas system, containing 77 spacers divided into two loci. Despite their diminutive genomes and as part of their host interaction mechanism, the genomes of new nanohaloarchaea do encode giant surface proteins, and one of them (9,409 amino acids long) is the largest protein of any sequenced nanohaloarchaea and the largest protein ever discovered in cultivated archaea.
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Affiliation(s)
- Oleg Reva
- Department of Biochemistry, Genetics and Microbiology, Centre for Bioinformatics and Computational Biology, University of Pretoria, Pretoria, South Africa
| | | | - Violetta La Cono
- Extreme Microbiology, Biotechnology and Astrobiology Group, Institute of Polar Research, ISP-CNR, Messina, Italy
| | - Francesca Crisafi
- Extreme Microbiology, Biotechnology and Astrobiology Group, Institute of Polar Research, ISP-CNR, Messina, Italy
| | - Francesco Smedile
- Extreme Microbiology, Biotechnology and Astrobiology Group, Institute of Polar Research, ISP-CNR, Messina, Italy
| | - Gina La Spada
- Extreme Microbiology, Biotechnology and Astrobiology Group, Institute of Polar Research, ISP-CNR, Messina, Italy
| | - Laura Marturano
- Extreme Microbiology, Biotechnology and Astrobiology Group, Institute of Polar Research, ISP-CNR, Messina, Italy
| | - Elena A. Selivanova
- Institute for Cellular and Intracellular Symbiosis, Ural Branch, Russian Academy of Sciences, Orenburg, Russia
| | - Manfred Rohde
- Central Facility for Microbiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Mart Krupovic
- Archaeal Virology Unit, Institut Pasteur, Université Paris Cité, Paris, France
| | - Michail M. Yakimov
- Extreme Microbiology, Biotechnology and Astrobiology Group, Institute of Polar Research, ISP-CNR, Messina, Italy
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2
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Garcia PS, Gribaldo S, Borrel G. Diversity and Evolution of Methane-Related Pathways in Archaea. Annu Rev Microbiol 2022; 76:727-755. [PMID: 35759872 DOI: 10.1146/annurev-micro-041020-024935] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Methane is one of the most important greenhouse gases on Earth and holds an important place in the global carbon cycle. Archaea are the only organisms that use methanogenesis to produce energy and rely on the methyl-coenzyme M reductase (Mcr) complex. Over the last decade, new results have significantly reshaped our view of the diversity of methane-related pathways in the Archaea. Many new lineages that synthesize or use methane have been identified across the whole archaeal tree, leading to a greatly expanded diversity of substrates and mechanisms. In this review, we present the state of the art of these advances and how they challenge established scenarios of the origin and evolution of methanogenesis, and we discuss the potential trajectories that may have led to this strikingly wide range of metabolisms.Expected final online publication date for the Annual Review of Microbiology, Volume 76 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Pierre Simon Garcia
- Institut Pasteur, Université Paris Cité, UMR CNRS 6047, Evolutionary Biology of the Microbial Cell, Paris, France; ,
| | - Simonetta Gribaldo
- Institut Pasteur, Université Paris Cité, UMR CNRS 6047, Evolutionary Biology of the Microbial Cell, Paris, France; ,
| | - Guillaume Borrel
- Institut Pasteur, Université Paris Cité, UMR CNRS 6047, Evolutionary Biology of the Microbial Cell, Paris, France; ,
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3
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in 't Zandt MH, Frank J, Yilmaz P, Cremers G, Jetten MSM, Welte CU. Long-term enriched methanogenic communities from thermokarst lake sediments show species-specific responses to warming. FEMS MICROBES 2020; 1:xtaa008. [PMID: 37333957 PMCID: PMC10117432 DOI: 10.1093/femsmc/xtaa008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 10/14/2020] [Indexed: 04/05/2024] Open
Abstract
Thermokarst lakes are large potential greenhouse gas (GHG) sources in a changing Arctic. In a warming world, an increase in both organic matter availability and temperature is expected to boost methanogenesis and potentially alter the microbial community that controls GHG fluxes. These community shifts are, however, challenging to detect by resolution-limited 16S rRNA gene-based approaches. Here, we applied full metagenome sequencing on long-term thermokarst lake sediment enrichments on acetate and trimethylamine at 4°C and 10°C to unravel species-specific responses to the most likely Arctic climate change scenario. Substrate amendment was used to mimic the increased organic carbon availability upon permafrost thaw. By performing de novo assembly, we reconstructed five high-quality and five medium-quality metagenome-assembled genomes (MAGs) that represented 59% of the aligned metagenome reads. Seven bacterial MAGs belonged to anaerobic fermentative bacteria. Within the Archaea, the enrichment of methanogenic Methanosaetaceae/Methanotrichaceae under acetate amendment and Methanosarcinaceae under trimethylamine (TMA) amendment was not unexpected. Surprisingly, we observed temperature-specific methanogenic (sub)species responses with TMA amendment. These highlighted distinct and potentially functional climate-induced shifts could not be revealed with 16S rRNA gene-based analyses. Unraveling these temperature- and nutrient-controlled species-level responses is essential to better comprehend the mechanisms that underlie GHG production from Arctic lakes in a warming world.
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Affiliation(s)
- Michiel H in 't Zandt
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
- Netherlands Earth System Science Centre, Utrecht University, Heidelberglaan 2, 3584 CS Utrecht, the Netherlands
| | - Jeroen Frank
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
- Soehngen Institute of Anaerobic Microbiology, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
| | - Polen Yilmaz
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
| | - Geert Cremers
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
| | - Mike S M Jetten
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
- Netherlands Earth System Science Centre, Utrecht University, Heidelberglaan 2, 3584 CS Utrecht, the Netherlands
- Soehngen Institute of Anaerobic Microbiology, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
| | - Cornelia U Welte
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
- Soehngen Institute of Anaerobic Microbiology, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
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4
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Wani SH, Kumar V, Khare T, Guddimalli R, Parveda M, Solymosi K, Suprasanna P, Kavi Kishor PB. Engineering salinity tolerance in plants: progress and prospects. PLANTA 2020; 251:76. [PMID: 32152761 DOI: 10.1007/s00425-020-03366-6] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 02/24/2020] [Indexed: 05/20/2023]
Abstract
There is a need to integrate conceptual framework based on the current understanding of salt stress responses with different approaches for manipulating and improving salt tolerance in crop plants. Soil salinity exerts significant constraints on global crop production, posing a serious challenge for plant breeders and biotechnologists. The classical transgenic approach for enhancing salinity tolerance in plants revolves by boosting endogenous defence mechanisms, often via a single-gene approach, and usually involves the enhanced synthesis of compatible osmolytes, antioxidants, polyamines, maintenance of hormone homeostasis, modification of transporters and/or regulatory proteins, including transcription factors and alternative splicing events. Occasionally, genetic manipulation of regulatory proteins or phytohormone levels confers salinity tolerance, but all these may cause undesired reduction in plant growth and/or yields. In this review, we present and evaluate novel and cutting-edge approaches for engineering salt tolerance in crop plants. First, we cover recent findings regarding the importance of regulatory proteins and transporters, and how they can be used to enhance salt tolerance in crop plants. We also evaluate the importance of halobiomes as a reservoir of genes that can be used for engineering salt tolerance in glycophytic crops. Additionally, the role of microRNAs as critical post-transcriptional regulators in plant adaptive responses to salt stress is reviewed and their use for engineering salt-tolerant crop plants is critically assessed. The potentials of alternative splicing mechanisms and targeted gene-editing technologies in understanding plant salt stress responses and developing salt-tolerant crop plants are also discussed.
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Affiliation(s)
- Shabir Hussain Wani
- Mountain Research Centre for Field Crops, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Khudwani, Anantnag, Jammu and Kashmir, 192 101, India.
| | - Vinay Kumar
- Department of Biotechnology, Modern College, Savitribai Phule Pune University, Ganeshkhind, Pune, 411 016, India
- Department of Environmental Science, Savitribai Phule Pune University, Ganeshkhind, Pune, 411 016, India
| | - Tushar Khare
- Department of Biotechnology, Modern College, Savitribai Phule Pune University, Ganeshkhind, Pune, 411 016, India
| | | | | | - Katalin Solymosi
- Department of Plant Anatomy, Institute of Biology, ELTE-Eötvös Loránd University, Budapest, 1053, Hungary
| | - Penna Suprasanna
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400 085, India
| | - P B Kavi Kishor
- Department of Biotechnology, Vignan's Foundation for Science Technology and Research, Vadlamudi, Guntur, 522 213, India
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5
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Guan Y, Ngugi DK, Vinu M, Blom J, Alam I, Guillot S, Ferry JG, Stingl U. Comparative Genomics of the Genus Methanohalophilus, Including a Newly Isolated Strain From Kebrit Deep in the Red Sea. Front Microbiol 2019; 10:839. [PMID: 31068917 PMCID: PMC6491703 DOI: 10.3389/fmicb.2019.00839] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 04/02/2019] [Indexed: 01/25/2023] Open
Abstract
Halophilic methanogens play an important role in the carbon cycle in hypersaline environments, but are under-represented in culture collections. In this study, we describe a novel Methanohalophilus strain that was isolated from the sulfide-rich brine-seawater interface of Kebrit Deep in the Red Sea. Based on physiological and phylogenomic features, strain RSK, which is the first methanogenic archaeon to be isolated from a deep hypersaline anoxic brine lake of the Red Sea, represents a novel species of this genus. In order to compare the genetic traits underpinning the adaptations of this genus in diverse hypersaline environments, we sequenced the genome of strain RSK and compared it with genomes of previously isolated and well characterized species in this genus (Methanohalophilus mahii, Methanohalophilus halophilus, Methanohalophilus portucalensis, and Methanohalophilus euhalobius). These analyses revealed a highly conserved genomic core of greater than 93% of annotated genes (1490 genes) containing pathways for methylotrophic methanogenesis, osmoprotection through salt-out strategy, and oxidative stress response, among others. Despite the high degree of genomic conservation, species-specific differences in sulfur and glycogen metabolisms, viral resistance, amino acid, and peptide uptake machineries were also evident. Thus, while Methanohalophilus species are found in diverse extreme environments, each genotype also possesses adaptive traits that are likely relevant in their respective hypersaline habitats.
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Affiliation(s)
- Yue Guan
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - David K. Ngugi
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Manikandan Vinu
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Jochen Blom
- Bioinformatik und Systembiologie, Justus-Liebig-Universität Giessen, Giessen, Germany
| | - Intikhab Alam
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Sylvain Guillot
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - James G. Ferry
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States
| | - Ulrich Stingl
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Department of Microbiology and Cell Science, UF/IFAS Fort Lauderdale Research and Education Center, University of Florida, Davie, FL, United States
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6
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Borton MA, Daly RA, O'Banion B, Hoyt DW, Marcus DN, Welch S, Hastings SS, Meulia T, Wolfe RA, Booker AE, Sharma S, Cole DR, Wunch K, Moore JD, Darrah TH, Wilkins MJ, Wrighton KC. Comparative genomics and physiology of the genus
Methanohalophilus
, a prevalent methanogen in hydraulically fractured shale. Environ Microbiol 2018; 20:4596-4611. [DOI: 10.1111/1462-2920.14467] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 10/30/2018] [Accepted: 10/31/2018] [Indexed: 11/28/2022]
Affiliation(s)
| | - Rebecca A. Daly
- Soil and Crop Sciences, Colorado State UniversityFort CollinsCOUSA
| | | | | | | | - Susan Welch
- School of Earth SciencesThe Ohio State UniversityColumbusOHUSA
| | | | - Tea Meulia
- Molecular and Cellular Imaging Center, The Ohio State University Wooster OH USA
| | - Richard A. Wolfe
- Soil and Crop Sciences, Colorado State UniversityFort CollinsCOUSA
| | - Anne E. Booker
- Depatment of MicrobiologyThe Ohio State UniversityColumbusOHUSA
| | - Shikha Sharma
- Department of Geology and Geography West Virginia University Morgantown WV USA
| | - David R. Cole
- School of Earth SciencesThe Ohio State UniversityColumbusOHUSA
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7
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Complete Genome Sequence of the Halophilic Methylotrophic Methanogen Archaeon Methanohalophilus portucalensis Strain FDF-1 T. GENOME ANNOUNCEMENTS 2018; 6:6/3/e01482-17. [PMID: 29348351 PMCID: PMC5773736 DOI: 10.1128/genomea.01482-17] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We report here the complete genome sequence (2.08 Mb) of Methanohalophilus portucalensis strain FDF-1T, a halophilic methylotrophic methanogen isolated from the sediment of a saltern in Figeria da Foz, Portugal. The average nucleotide identity and DNA-DNA hybridization analyses show that Methanohalophilus mahii, M. halophilus, and M. portucalensis are three different species within the Methanosarcinaceae family.
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8
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Lyu Z, Lu Y. Metabolic shift at the class level sheds light on adaptation of methanogens to oxidative environments. ISME JOURNAL 2017; 12:411-423. [PMID: 29135970 PMCID: PMC5776455 DOI: 10.1038/ismej.2017.173] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 07/31/2017] [Accepted: 08/09/2017] [Indexed: 11/09/2022]
Abstract
Methanogens have long been considered strictly anaerobic and oxygen-sensitive microorganisms, but their ability to survive oxygen stress has also been documented. Indeed, methanogens have been found in oxidative environments, and antioxidant genes have been detected in their genomes. How methanogens adapt to oxidative environments, however, remain poorly understood. Here, we systematically predicted and annotated antioxidant features from representative genomes across six well-established methanogen orders. Based on functional gene content involved in production of reactive oxygen species, Hierarchical Clustering analyses grouped methanogens into two distinct clusters, corresponding to the Class I and II methanogens, respectively. Comparative genomics suggested a systematic shift in metabolisms across the two classes, resulting in an enrichment of antioxidant features in the Class II. Moreover, meta-analysis of 16 S rRNA gene sequences obtained from EnvDB indicated that members of Class II were more frequently recovered from microaerophilic and even oxic environments than the Class I members. Phylogenomic analysis suggested that the Class I and II methanogens might have evolved before and around the Great Oxygenation Event, respectively. The enrichment of antioxidant features in the Class II methanogens may have played a key role in the adaption of this group to oxidative environments today and historically.
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Affiliation(s)
- Zhe Lyu
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, PR China.,Department of Microbiology, University of Georgia, Athens, GA, USA
| | - Yahai Lu
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, PR China.,College of Urban and Environmental Sciences, Peking University, Beijing, PR China
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9
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Site-specific His/Asp phosphoproteomic analysis of prokaryotes reveals putative targets for drug resistance. BMC Microbiol 2017; 17:123. [PMID: 28545444 PMCID: PMC5445275 DOI: 10.1186/s12866-017-1034-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 05/15/2017] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Phosphorylation of amino acid residues on proteins is an important and common post-translational modification in both eukaryotes and prokaryotes. Most research work has been focused on phosphorylation of serine, threonine or tyrosine residues, whereas phosphorylation of other amino acids are significantly less clear due to the controversy on their stability under standard bioanalytical conditions. RESULTS Here we applied a shotgun strategy to analyze the histidine and aspartate phosphorylations in different microbes. Our results collectively indicate that histidine and aspartate phosphorylations frequently occur also in proteins that are not part of the two-component systems. Noticeably, a number of the modified proteins are pathogenesis-related or essential for survival in host. These include the zinc ion periplasmic transporter ZnuA in Acinetobacter baumannii SK17, the multidrug and toxic compound extrusion (MATE) channel YeeO in Klebsiella pneumoniae NTUH-K2044, branched amino acid transporter AzlC in Vibrio vulnificus and the RNA-modifying pseudouridine synthase in Helicobacter pylori. CONCLUSIONS In summary, histidine and aspartate phosphorylation is likely to be ubiquitous and to take place in proteins of various functions. This work also sheds light into how these functionally important proteins and potential drug targets might be regulated at a post-translational level.
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Abstract
Ascomycete yeasts are metabolically diverse, with great potential for biotechnology. Here, we report the comparative genome analysis of 29 taxonomically and biotechnologically important yeasts, including 16 newly sequenced. We identify a genetic code change, CUG-Ala, in Pachysolen tannophilus in the clade sister to the known CUG-Ser clade. Our well-resolved yeast phylogeny shows that some traits, such as methylotrophy, are restricted to single clades, whereas others, such as l-rhamnose utilization, have patchy phylogenetic distributions. Gene clusters, with variable organization and distribution, encode many pathways of interest. Genomics can predict some biochemical traits precisely, but the genomic basis of others, such as xylose utilization, remains unresolved. Our data also provide insight into early evolution of ascomycetes. We document the loss of H3K9me2/3 heterochromatin, the origin of ascomycete mating-type switching, and panascomycete synteny at the MAT locus. These data and analyses will facilitate the engineering of efficient biosynthetic and degradative pathways and gateways for genomic manipulation.
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11
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Wu WL, Lai SJ, Yang JT, Chern J, Liang SY, Chou CC, Kuo CH, Lai MC, Wu SH. Phosphoproteomic analysis of Methanohalophilus portucalensis FDF1(T) identified the role of protein phosphorylation in methanogenesis and osmoregulation. Sci Rep 2016; 6:29013. [PMID: 27357474 PMCID: PMC4928046 DOI: 10.1038/srep29013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 06/10/2016] [Indexed: 02/02/2023] Open
Abstract
Methanogens have gained much attention for their metabolic product, methane, which could be an energy substitute but also contributes to the greenhouse effect. One factor that controls methane emission, reversible protein phosphorylation, is a crucial signaling switch, and phosphoproteomics has become a powerful tool for large-scale surveying. Here, we conducted the first phosphorylation-mediated regulation study in halophilic Methanohalophilus portucalensis FDF1(T), a model strain for studying stress response mechanisms in osmoadaptation. A shotgun approach and MS-based analysis identified 149 unique phosphoproteins. Among them, 26% participated in methanogenesis and osmolytes biosynthesis pathways. Of note, we uncovered that protein phosphorylation might be a crucial factor to modulate the pyrrolysine (Pyl) incorporation and Pyl-mediated methylotrophic methanogenesis. Furthermore, heterologous expression of glycine sarcosine N-methyltransferase (GSMT) mutant derivatives in the osmosensitive Escherichia coli MKH13 revealed that the nonphosphorylated T68A mutant resulted in increased salt tolerance. In contrast, mimic phosphorylated mutant T68D proved defective in both enzymatic activity and salinity tolerance for growth. Our study provides new insights into phosphorylation modification as a crucial role of both methanogenesis and osmoadaptation in methanoarchaea, promoting biogas production or reducing future methane emission in response to global warming and climate change.
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Affiliation(s)
- Wan-Ling Wu
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Shu-Jung Lai
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan
| | - Jhih-Tian Yang
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
- Ph.D program in Microbial Genomics, National Chung Hsing University and Academia Sinica, Taichung 40227, Taiwan
| | - Jeffy Chern
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Suh-Yuen Liang
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
- Core Facilities for Protein Structural Analysis, Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Chi-Chi Chou
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
- Core Facilities for Protein Structural Analysis, Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Chih-Horng Kuo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung 40227, Taiwan
| | - Mei-Chin Lai
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung 40227, Taiwan
| | - Shih-Hsiung Wu
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
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12
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Spring S, Bunk B, Spröer C, Schumann P, Rohde M, Tindall BJ, Klenk HP. Characterization of the first cultured representative of Verrucomicrobia subdivision 5 indicates the proposal of a novel phylum. ISME JOURNAL 2016; 10:2801-2816. [PMID: 27300277 PMCID: PMC5148204 DOI: 10.1038/ismej.2016.84] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 04/15/2016] [Accepted: 04/21/2016] [Indexed: 12/29/2022]
Abstract
The recently isolated strain L21-Fru-ABT represents moderately halophilic, obligately anaerobic and saccharolytic bacteria that thrive in the suboxic transition zones of hypersaline microbial mats. Phylogenetic analyses based on 16S rRNA genes, RpoB proteins and gene content indicated that strain L21-Fru-ABT represents a novel species and genus affiliated with a distinct phylum-level lineage originally designated Verrucomicrobia subdivision 5. A survey of environmental 16S rRNA gene sequences revealed that members of this newly recognized phylum are wide-spread and ecologically important in various anoxic environments ranging from hypersaline sediments to wastewater and the intestine of animals. Characteristic phenotypic traits of the novel strain included the formation of extracellular polymeric substances, a Gram-negative cell wall containing peptidoglycan and the absence of odd-numbered cellular fatty acids. Unusual metabolic features deduced from analysis of the genome sequence were the production of sucrose as osmoprotectant, an atypical glycolytic pathway lacking pyruvate kinase and the synthesis of isoprenoids via mevalonate. On the basis of the analyses of phenotypic, genomic and environmental data, it is proposed that strain L21-Fru-ABT and related bacteria are specifically adapted to the utilization of sulfated glycopolymers produced in microbial mats or biofilms.
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Affiliation(s)
- Stefan Spring
- Department Microorganisms, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Boyke Bunk
- Department Microbial Ecology and Diversity Research, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Cathrin Spröer
- Department Central Services, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Peter Schumann
- Department Central Services, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz-Centre of Infection Research, Braunschweig, Germany
| | - Brian J Tindall
- Department Microorganisms, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans-Peter Klenk
- Department Microorganisms, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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Crits-Christoph A, Gelsinger DR, Ma B, Wierzchos J, Ravel J, Davila A, Casero MC, DiRuggiero J. Functional interactions of archaea, bacteria and viruses in a hypersaline endolithic community. Environ Microbiol 2016; 18:2064-77. [DOI: 10.1111/1462-2920.13259] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 02/08/2016] [Indexed: 11/30/2022]
Affiliation(s)
| | | | - Bing Ma
- Institute for Genome Sciences, University of Maryland School of Medicine; Baltimore MD USA
| | - Jacek Wierzchos
- Department of Biochemistry and Microbial Ecology; Museo Nacional de Ciencias Naturales - Consejo Superior de Investigaciones Científicas; Madrid Spain
| | - Jacques Ravel
- Institute for Genome Sciences, University of Maryland School of Medicine; Baltimore MD USA
| | | | - M. Cristina Casero
- Department of Biochemistry and Microbial Ecology; Museo Nacional de Ciencias Naturales - Consejo Superior de Investigaciones Científicas; Madrid Spain
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Biofilm plasmids with a rhamnose operon are widely distributed determinants of the 'swim-or-stick' lifestyle in roseobacters. ISME JOURNAL 2016; 10:2498-513. [PMID: 26953602 PMCID: PMC5030684 DOI: 10.1038/ismej.2016.30] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 01/12/2016] [Accepted: 01/24/2016] [Indexed: 12/17/2022]
Abstract
Alphaproteobacteria of the metabolically versatile Roseobacter group (Rhodobacteraceae) are abundant in marine ecosystems and represent dominant primary colonizers of submerged surfaces. Motility and attachment are the prerequisite for the characteristic 'swim-or-stick' lifestyle of many representatives such as Phaeobacter inhibens DSM 17395. It has recently been shown that plasmid curing of its 65-kb RepA-I-type replicon with >20 genes for exopolysaccharide biosynthesis including a rhamnose operon results in nearly complete loss of motility and biofilm formation. The current study is based on the assumption that homologous biofilm plasmids are widely distributed. We analyzed 33 roseobacters that represent the phylogenetic diversity of this lineage and documented attachment as well as swimming motility for 60% of the strains. All strong biofilm formers were also motile, which is in agreement with the proposed mechanism of surface attachment. We established transposon mutants for the four genes of the rhamnose operon from P. inhibens and proved its crucial role in biofilm formation. In the Roseobacter group, two-thirds of the predicted biofilm plasmids represent the RepA-I type and their physiological role was experimentally validated via plasmid curing for four additional strains. Horizontal transfer of these replicons was documented by a comparison of the RepA-I phylogeny with the species tree. A gene content analysis of 35 RepA-I plasmids revealed a core set of genes, including the rhamnose operon and a specific ABC transporter for polysaccharide export. Taken together, our data show that RepA-I-type biofilm plasmids are essential for the sessile mode of life in the majority of cultivated roseobacters.
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Wei Y, Li B, Prakash D, Ferry JG, Elliott SJ, Stubbe J. A Ferredoxin Disulfide Reductase Delivers Electrons to the Methanosarcina barkeri Class III Ribonucleotide Reductase. Biochemistry 2015; 54:7019-28. [PMID: 26536144 PMCID: PMC4697749 DOI: 10.1021/acs.biochem.5b01092] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Two subtypes of class III anaerobic ribonucleotide reductases (RNRs) studied so far couple the reduction of ribonucleotides to the oxidation of formate, or the oxidation of NADPH via thioredoxin and thioredoxin reductase. Certain methanogenic archaea contain a phylogenetically distinct third subtype of class III RNR, with distinct active-site residues. Here we report the cloning and recombinant expression of the Methanosarcina barkeri class III RNR and show that the electrons required for ribonucleotide reduction can be delivered by a [4Fe-4S] protein ferredoxin disulfide reductase, and a conserved thioredoxin-like protein NrdH present in the RNR operon. The diversity of class III RNRs reflects the diversity of electron carriers used in anaerobic metabolism.
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Affiliation(s)
| | - Bin Li
- Department of Chemistry, Boston University , 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Divya Prakash
- Department of Biochemistry and Molecular Biology, Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - James G Ferry
- Department of Biochemistry and Molecular Biology, Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Sean J Elliott
- Department of Chemistry, Boston University , 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
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16
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A Three-Component Microbial Consortium from Deep-Sea Salt-Saturated Anoxic Lake Thetis Links Anaerobic Glycine Betaine Degradation with Methanogenesis. Microorganisms 2015; 3:500-17. [PMID: 27682102 PMCID: PMC5023251 DOI: 10.3390/microorganisms3030500] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 07/27/2015] [Accepted: 09/01/2015] [Indexed: 11/17/2022] Open
Abstract
Microbial communities inhabiting the deep-sea salt-saturated anoxic lakes of the Eastern Mediterranean operate under harsh physical-chemical conditions that are incompatible with the lifestyle of common marine microorganisms. Here, we investigated a stable three-component microbial consortium obtained from the brine of the recently discovered deep-sea salt-saturated Lake Thetis. The trophic network of this consortium, established at salinities up to 240, relies on fermentative decomposition of common osmoprotectant glycine betaine (GB). Similarly to known extreme halophilic anaerobic GB-degrading enrichments, the initial step of GB degradation starts with its reductive cleavage to trimethylamine and acetate, carried out by the fermenting member of the Thetis enrichment, Halobacteroides lacunaris TB21. In contrast to acetate, which cannot be easily oxidized in salt-saturated anoxic environments, trimethylamine represents an advantageous C₁-substrate for methylotrophic methanogenic member of the Thetis enrichment, Methanohalophilus sp. TA21. This second member of the consortium likely produces hydrogen via methylotrophic modification of reductive acetyl-CoA pathway because the initial anaerobic GB cleavage reaction requires the consumption of reducing equivalents. Ecophysiological role of the third member of the Thetis consortium, Halanaerobium sp. TB24, which lacks the capability of either GB or trimethylamine degradation, remains yet to be elucidated. As it is true for cultivated members of family Halanaerobiaceae, the isolate TB24 can obtain energy primarily by fermenting simple sugars and producing hydrogen as one of the end products. Hence, by consuming of TB21 and TA21 metabolites, Halanaerobium sp. TB24 can be an additional provider of reducing equivalents required for reductive degradation of GB. Description of the Thetis GB-degrading consortium indicated that anaerobic degradation of osmoregulatory molecules may play important role in the overall turnover of organic carbon in anoxic hypersaline biotopes.
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17
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Garushyants SK, Kazanov MD, Gelfand MS. Horizontal gene transfer and genome evolution in Methanosarcina. BMC Evol Biol 2015; 15:102. [PMID: 26044078 PMCID: PMC4455057 DOI: 10.1186/s12862-015-0393-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 05/29/2015] [Indexed: 12/29/2022] Open
Abstract
Background Genomes of Methanosarcina spp. are among the largest archaeal genomes. One suggested reason for that is massive horizontal gene transfer (HGT) from bacteria. Genes of bacterial origin may be involved in the central metabolism and solute transport, in particular sugar synthesis, sulfur metabolism, phosphate metabolism, DNA repair, transport of small molecules etc. Horizontally transferred (HT) genes are considered to play the key role in the ability of Methanosarcina spp. to inhabit diverse environments. At the moment, genomes of three Methanosarcina spp. have been sequenced, and while these genomes vary in length and number of protein-coding genes, they all have been shown to accumulate HT genes. However, previous estimates had been made when fewer archaeal genomes were known. Moreover, several Methanosarcinaceae genomes from other genera have been sequenced recently. Here, we revise the census of genes of bacterial origin in Methanosarcinaceae. Results About 5 % of Methanosarcina genes have been shown to be horizontally transferred from various bacterial groups to the last common ancestor either of Methanosarcinaceae, or Methanosarcina, or later in the evolution. Simulation of the composition of the NCBI protein non-redundant database for different years demonstrates that the estimates of the HGT rate have decreased drastically since 2002, the year of publication of the first Methanosarcina genome. The phylogenetic distribution of HT gene donors is non-uniform. Most HT genes were transferred from Firmicutes and Proteobacteria, while no HGT events from Actinobacteria to the common ancestor of Methanosarcinaceae were found. About 50 % of HT genes are involved in metabolism. Horizontal transfer of transcription factors is not common, while 46 % of horizontally transferred genes have demonstrated differential expression in a variety of conditions. HGT of complete operons is relatively infrequent and half of HT genes do not belong to operons. Conclusions While genes of bacterial origin are still more frequent in Methanosarcinaceae than in other Archaea, most HGT events described earlier as Methanosarcina-specific seem to have occurred before the divergence of Methanosarcinaceae. Genes horizontally transferred from bacteria to archaea neither tend to be transferred with their regulators, nor in long operons. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0393-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sofya K Garushyants
- A.A. Kharkevich Institute for Information Transmission Problems, RAS, Bolshoi Karetny per. 19, build.1, Moscow, 127051, Russia.
| | - Marat D Kazanov
- A.A. Kharkevich Institute for Information Transmission Problems, RAS, Bolshoi Karetny per. 19, build.1, Moscow, 127051, Russia.
| | - Mikhail S Gelfand
- A.A. Kharkevich Institute for Information Transmission Problems, RAS, Bolshoi Karetny per. 19, build.1, Moscow, 127051, Russia. .,Faculty of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, Vorobievy Gory 1-73, Moscow, 119991, Russia.
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18
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Spring S, Scheuner C, Göker M, Klenk HP. A taxonomic framework for emerging groups of ecologically important marine gammaproteobacteria based on the reconstruction of evolutionary relationships using genome-scale data. Front Microbiol 2015; 6:281. [PMID: 25914684 PMCID: PMC4391266 DOI: 10.3389/fmicb.2015.00281] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Accepted: 03/21/2015] [Indexed: 11/13/2022] Open
Abstract
In recent years a large number of isolates were obtained from saline environments that are phylogenetically related to distinct clades of oligotrophic marine gammaproteobacteria, which were originally identified in seawater samples using cultivation independent methods and are characterized by high seasonal abundances in coastal environments. To date a sound taxonomic framework for the classification of these ecologically important isolates and related species in accordance with their evolutionary relationships is missing. In this study we demonstrate that a reliable allocation of members of the oligotrophic marine gammaproteobacteria (OMG) group and related species to higher taxonomic ranks is possible by phylogenetic analyses of whole proteomes but also of the RNA polymerase beta subunit, whereas phylogenetic reconstructions based on 16S rRNA genes alone resulted in unstable tree topologies with only insignificant bootstrap support. The identified clades could be correlated with distinct phenotypic traits illustrating an adaptation to common environmental factors in their evolutionary history. Genome wide gene-content analyses revealed the existence of two distinct ecological guilds within the analyzed lineage of marine gammaproteobacteria which can be distinguished by their trophic strategies. Based on our results a novel order within the class Gammaproteobacteria is proposed, which is designated Cellvibrionales ord. nov. and comprises the five novel families Cellvibrionaceae fam. nov., Halieaceae fam. nov., Microbulbiferaceae fam. nov., Porticoccaceae fam. nov., and Spongiibacteraceae fam. nov.
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Affiliation(s)
- Stefan Spring
- Department Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures Braunschweig, Germany
| | - Carmen Scheuner
- Department Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures Braunschweig, Germany
| | - Markus Göker
- Department Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures Braunschweig, Germany
| | - Hans-Peter Klenk
- Department Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures Braunschweig, Germany ; School of Biology, Newcastle University Newcastle upon Tyne, UK
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19
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Scheuner C, Tindall BJ, Lu M, Nolan M, Lapidus A, Cheng JF, Goodwin L, Pitluck S, Huntemann M, Liolios K, Pagani I, Mavromatis K, Ivanova N, Pati A, Chen A, Palaniappan K, Jeffries CD, Hauser L, Land M, Mwirichia R, Rohde M, Abt B, Detter JC, Woyke T, Eisen JA, Markowitz V, Hugenholtz P, Göker M, Kyrpides NC, Klenk HP. Complete genome sequence of Planctomyces brasiliensis type strain (DSM 5305(T)), phylogenomic analysis and reclassification of Planctomycetes including the descriptions of Gimesia gen. nov., Planctopirus gen. nov. and Rubinisphaera gen. nov. and emended descriptions of the order Planctomycetales and the family Planctomycetaceae. Stand Genomic Sci 2014; 9:10. [PMID: 25780503 PMCID: PMC4334474 DOI: 10.1186/1944-3277-9-10] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 06/16/2014] [Indexed: 12/21/2022] Open
Abstract
Planctomyces brasiliensis Schlesner 1990 belongs to the order Planctomycetales, which differs from other bacterial taxa by several distinctive features such as internal cell compartmentalization, multiplication by forming buds directly from the spherical, ovoid or pear-shaped mother cell and a cell wall consisting of a proteinaceous layer rather than a peptidoglycan layer. The first strains of P. brasiliensis, including the type strain IFAM 1448(T), were isolated from a water sample of Lagoa Vermelha, a salt pit near Rio de Janeiro, Brasil. This is the second completed genome sequence of a type strain of the genus Planctomyces to be published and the sixth type strain genome sequence from the family Planctomycetaceae. The 6,006,602 bp long genome with its 4,811 protein-coding and 54 RNA genes is a part of the G enomic E ncyclopedia of Bacteria and Archaea project. Phylogenomic analyses indicate that the classification within the Planctomycetaceae is partially in conflict with its evolutionary history, as the positioning of Schlesneria renders the genus Planctomyces paraphyletic. A re-analysis of published fatty-acid measurements also does not support the current arrangement of the two genera. A quantitative comparison of phylogenetic and phenotypic aspects indicates that the three Planctomyces species with type strains available in public culture collections should be placed in separate genera. Thus the genera Gimesia, Planctopirus and Rubinisphaera are proposed to accommodate P. maris, P. limnophilus and P. brasiliensis, respectively. Pronounced differences between the reported G + C content of Gemmata obscuriglobus, Singulisphaera acidiphila and Zavarzinella formosa and G + C content calculated from their genome sequences call for emendation of their species descriptions. In addition to other features, the range of G + C values reported for the genera within the Planctomycetaceae indicates that the descriptions of the family and the order should be emended.
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Affiliation(s)
- Carmen Scheuner
- DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Brian J Tindall
- DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Megan Lu
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Matt Nolan
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Alla Lapidus
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Jan-Fang Cheng
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Lynne Goodwin
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Sam Pitluck
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | | | - Ioanna Pagani
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | | | - Amrita Pati
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Amy Chen
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Krishna Palaniappan
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Cynthia D Jeffries
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Loren Hauser
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Miriam Land
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Romano Mwirichia
- Jomo Kenyatta University of Agriculture and Technology, Juja, Kenya
| | - Manfred Rohde
- HZI – Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Birte Abt
- DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - John C Detter
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Jonathan A Eisen
- DOE Joint Genome Institute, Walnut Creek, California, USA
- University of California Davis Genome Center, Davis, California, USA
| | - Victor Markowitz
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Philip Hugenholtz
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Markus Göker
- DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Nikos C Kyrpides
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hans-Peter Klenk
- DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
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20
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Meier-Kolthoff JP, Hahnke RL, Petersen J, Scheuner C, Michael V, Fiebig A, Rohde C, Rohde M, Fartmann B, Goodwin LA, Chertkov O, Reddy TBK, Pati A, Ivanova NN, Markowitz V, Kyrpides NC, Woyke T, Göker M, Klenk HP. Complete genome sequence of DSM 30083(T), the type strain (U5/41(T)) of Escherichia coli, and a proposal for delineating subspecies in microbial taxonomy. Stand Genomic Sci 2014; 9:2. [PMID: 25780495 PMCID: PMC4334874 DOI: 10.1186/1944-3277-9-2] [Citation(s) in RCA: 364] [Impact Index Per Article: 36.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 06/16/2014] [Indexed: 12/02/2022] Open
Abstract
Although Escherichia coli is the most widely studied bacterial model organism and often considered to be the model bacterium per se, its type strain was until now forgotten from microbial genomics. As a part of the G enomic E ncyclopedia of B acteria and A rchaea project, we here describe the features of E. coli DSM 30083(T) together with its genome sequence and annotation as well as novel aspects of its phenotype. The 5,038,133 bp containing genome sequence includes 4,762 protein-coding genes and 175 RNA genes as well as a single plasmid. Affiliation of a set of 250 genome-sequenced E. coli strains, Shigella and outgroup strains to the type strain of E. coli was investigated using digital DNA:DNA-hybridization (dDDH) similarities and differences in genomic G+C content. As in the majority of previous studies, results show Shigella spp. embedded within E. coli and in most cases forming a single subgroup of it. Phylogenomic trees also recover the proposed E. coli phylotypes as monophyla with minor exceptions and place DSM 30083(T) in phylotype B2 with E. coli S88 as its closest neighbor. The widely used lab strain K-12 is not only genomically but also physiologically strongly different from the type strain. The phylotypes do not express a uniform level of character divergence as measured using dDDH, however, thus an alternative arrangement is proposed and discussed in the context of bacterial subspecies. Analyses of the genome sequences of a large number of E. coli strains and of strains from > 100 other bacterial genera indicate a value of 79-80% dDDH as the most promising threshold for delineating subspecies, which in turn suggests the presence of five subspecies within E. coli.
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Affiliation(s)
- Jan P Meier-Kolthoff
- />Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Richard L Hahnke
- />Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Jörn Petersen
- />Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Carmen Scheuner
- />Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Victoria Michael
- />Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Anne Fiebig
- />Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Christine Rohde
- />Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Manfred Rohde
- />Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany
| | | | | | | | - TBK Reddy
- />DOE Joint Genome Institute, Walnut Creek, Ca USA
| | - Amrita Pati
- />DOE Joint Genome Institute, Walnut Creek, Ca USA
| | | | | | - Nikos C Kyrpides
- />DOE Joint Genome Institute, Walnut Creek, Ca USA
- />Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Tanja Woyke
- />DOE Joint Genome Institute, Walnut Creek, Ca USA
| | - Markus Göker
- />Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Hans-Peter Klenk
- />Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
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21
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Breider S, Scheuner C, Schumann P, Fiebig A, Petersen J, Pradella S, Klenk HP, Brinkhoff T, Göker M. Genome-scale data suggest reclassifications in the Leisingera-Phaeobacter cluster including proposals for Sedimentitalea gen. nov. and Pseudophaeobacter gen. nov. Front Microbiol 2014; 5:416. [PMID: 25157246 PMCID: PMC4127530 DOI: 10.3389/fmicb.2014.00416] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 07/22/2014] [Indexed: 11/13/2022] Open
Abstract
Earlier phylogenetic analyses of the marine Rhodobacteraceae (class Alphaproteobacteria) genera Leisingera and Phaeobacter indicated that neither genus might be monophyletic. We here used phylogenetic reconstruction from genome-scale data, MALDI-TOF mass-spectrometry analysis and a re-assessment of the phenotypic data from the literature to settle this matter, aiming at a reclassification of the two genera. Neither Phaeobacter nor Leisingera formed a clade in any of the phylogenetic analyses conducted. Rather, smaller monophyletic assemblages emerged, which were phenotypically more homogeneous, too. We thus propose the reclassification of Leisingera nanhaiensis as the type species of a new genus as Sedimentitalea nanhaiensis gen. nov., comb. nov., the reclassification of Phaeobacter arcticus and Phaeobacter leonis as Pseudophaeobacter arcticus gen. nov., comb. nov. and Pseudophaeobacter leonis comb. nov., and the reclassification of Phaeobacter aquaemixtae, Phaeobacter caeruleus, and Phaeobacter daeponensis as Leisingera aquaemixtae comb. nov., Leisingera caerulea comb. nov., and Leisingera daeponensis comb. nov. The genera Phaeobacter and Leisingera are accordingly emended.
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Affiliation(s)
- Sven Breider
- Department of Biology of Geological Processes - Aquatic Microbial Ecology, Institute for Chemistry and Biology of the Marine Environment (ICBM), University of OldenburgOldenburg, Germany
| | - Carmen Scheuner
- Department of Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell CulturesBraunschweig, Germany
| | - Peter Schumann
- Department of Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell CulturesBraunschweig, Germany
| | - Anne Fiebig
- Department of Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell CulturesBraunschweig, Germany
| | - Jörn Petersen
- Department of Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell CulturesBraunschweig, Germany
| | - Silke Pradella
- Department of Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell CulturesBraunschweig, Germany
| | - Hans-Peter Klenk
- Department of Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell CulturesBraunschweig, Germany
| | - Thorsten Brinkhoff
- Department of Biology of Geological Processes - Aquatic Microbial Ecology, Institute for Chemistry and Biology of the Marine Environment (ICBM), University of OldenburgOldenburg, Germany
| | - Markus Göker
- Department of Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell CulturesBraunschweig, Germany
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22
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Taxonomy of halophilic Archaea: current status and future challenges. Extremophiles 2014; 18:825-34. [DOI: 10.1007/s00792-014-0654-9] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Accepted: 05/09/2014] [Indexed: 10/24/2022]
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23
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Frank O, Pradella S, Rohde M, Scheuner C, Klenk HP, Göker M, Petersen J. Complete genome sequence of the Phaeobacter gallaeciensis type strain CIP 105210(T) (= DSM 26640(T) = BS107(T)). Stand Genomic Sci 2014; 9:914-32. [PMID: 25197473 PMCID: PMC4148982 DOI: 10.4056/sigs.5179110] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Phaeobacter gallaeciensis CIP 105210(T) (= DSM 26640(T) = BS107(T)) is the type strain of the species Phaeobacter gallaeciensis. The genus Phaeobacter belongs to the marine Roseobacter group (Rhodobacteraceae, Alphaproteobacteria). Phaeobacter species are effective colonizers of marine surfaces, including frequent associations with eukaryotes. Strain BS107(T) was isolated from a rearing of the scallop Pecten maximus. Here we describe the features of this organism, together with the complete genome sequence, comprising eight circular replicons with a total of 4,448 genes. In addition to a high number of extrachromosomal replicons, the genome contains six genomic island and three putative prophage regions, as well as a hybrid between a plasmid and a circular phage. Phylogenomic analyses confirm previous results, which indicated that the originally reported P. gallaeciensis type-strain deposit DSM 17395 belongs to P. inhibens and that CIP 105210(T) (= DSM 26640(T)) is the sole genome-sequenced representative of P. gallaeciensis.
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Affiliation(s)
- Oliver Frank
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Silke Pradella
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Manfred Rohde
- Helmholtz-Centre for Infection Research, Braunschweig, Germany
| | - Carmen Scheuner
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans-Peter Klenk
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Markus Göker
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Jörn Petersen
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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Murali Mohan A, Hartsock A, Hammack RW, Vidic RD, Gregory KB. Microbial communities in flowback water impoundments from hydraulic fracturing for recovery of shale gas. FEMS Microbiol Ecol 2013; 86:567-80. [DOI: 10.1111/1574-6941.12183] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Revised: 07/02/2013] [Accepted: 07/16/2013] [Indexed: 11/29/2022] Open
Affiliation(s)
- Arvind Murali Mohan
- National Energy Technology Laboratory; Pittsburgh PA USA
- Department of Civil and Environmental Engineering; Carnegie Mellon University; Pittsburgh PA USA
| | | | | | - Radisav D. Vidic
- National Energy Technology Laboratory; Pittsburgh PA USA
- Department of Civil and Environmental Engineering; University of Pittsburgh; Pittsburgh PA USA
| | - Kelvin B. Gregory
- National Energy Technology Laboratory; Pittsburgh PA USA
- Department of Civil and Environmental Engineering; Carnegie Mellon University; Pittsburgh PA USA
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MrpA functions in energy conversion during acetate-dependent growth of Methanosarcina acetivorans. J Bacteriol 2013; 195:3987-94. [PMID: 23836862 DOI: 10.1128/jb.00581-13] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The role of the multisubunit sodium/proton antiporter (Mrp) of Methanosarcina acetivorans was investigated with a mutant deleted for the gene encoding the MrpA subunit. Antiporter activity was 5-fold greater in acetate-grown versus methanol-grown wild-type cells, consistent with the previously published relative levels of mrp transcript. The rate, final optical density, and dry weight/methane ratio decreased for the mutant versus wild type when cultured with a growth-limiting concentration of acetate. All growth parameters of the mutant or wild type were identical when grown with methanol in medium containing a growth-limiting Na(+) concentration of 1.04 M. The lag phase, growth rate, and final optical density for growth of the mutant were suboptimal compared to the wild type when cultured with acetate in medium containing either 0.54 or 1.04 M Na(+). The addition of 25 mM NaCl to resting cell suspensions stimulated ATP synthesis driven by a potassium diffusion potential. ATP synthesis was greater in wild-type than mutant cells grown with acetate, a trend that held for methanol-grown cells, albeit less pronounced. Both sodium and proton ionophores reduced ATP synthesis in the wild type grown with either substrate. The results indicated that the Mrp complex is essential for efficient ATP synthesis and optimal growth at the low concentrations of acetate encountered in the environment.
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Morris BEL, Herbst FA, Bastida F, Seifert J, von Bergen M, Richnow HH, Suflita JM. Microbial interactions during residual oil and n-fatty acid metabolism by a methanogenic consortium. ENVIRONMENTAL MICROBIOLOGY REPORTS 2012; 4:297-306. [PMID: 23760793 DOI: 10.1111/j.1758-2229.2012.00333.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Carbon flow in a model methanogenic consortium capable of hydrocarbon degradation was investigated using a combination of stable isotope fractionation, protein-based stable isotope probing, and metaproteomics. Overall δ(13) C enrichment for methane and CO2 in the presence and absence of oil suggests that complex microbial interactions occur during methanogenic hydrocarbon mineralization. Specifically, the Δδ(13) C of CO2 was statistically identical in all incubations irrespective of oil presence, but the Δδ(13) C for methane was greater in the presence of oil compared with fatty acids alone. In addition, carbon from uniformly ((13) C) labelled n-fatty acids was distributed evenly among consortium members in the presence of oil, but used by relatively few community members when provided alone. In all incubations, aceticlastic and hydrogenotrophic methanogens were labelled to an equal extent, suggesting that no pathway is overwhelmingly dominant during methane production by the model consortium. Protein-based stable isotope probing identified key enzymes responsible for methanogenesis from CO2 and acetate labelled with 78.0 ± 4.4% and 73.3 ± 1.0% (13) C respectively. Results suggest that acetate was used directly by methanogens in the presence of n-fatty acids alone, and that methanogenesis from CO2 was a secondary process. Proteins capable of catalysing hydrocarbon activation by addition to fumarate were not found. Collectively, this study demonstrates that significant microbial cooperation is required to recover hydrocarbons as methane.
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Affiliation(s)
- Brandon E L Morris
- Department of Botany & Microbiology, Institute for Energy & the Environment, The University of Oklahoma, 770 Van Vleet Oval, Norman, OK 73019, USADepartments of Isotope Biogeochemistry Proteomics Metabolomics, Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15, D-04318 Leipzig, Germany Department of Soil and Water Conservation, CEBAS-CSIC, Campus Universitario de Espinardo, 30100, Espinardo, Murcia, Spain
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Zhu J, Zheng H, Ai G, Zhang G, Liu D, Liu X, Dong X. The genome characteristics and predicted function of methyl-group oxidation pathway in the obligate aceticlastic methanogens, Methanosaeta spp. PLoS One 2012; 7:e36756. [PMID: 22590603 PMCID: PMC3349665 DOI: 10.1371/journal.pone.0036756] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Accepted: 04/11/2012] [Indexed: 11/19/2022] Open
Abstract
In this work, we report the complete genome sequence of an obligate aceticlastic methanogen, Methanosaeta harundinacea 6Ac. Genome comparison indicated that the three cultured Methanosaeta spp., M. thermophila, M. concilii and M. harundinacea 6Ac, each carry an entire suite of genes encoding the proteins involved in the methyl-group oxidation pathway, a pathway whose function is not well documented in the obligately aceticlastic methanogens. Phylogenetic analysis showed that the methyl-group oxidation-involving proteins, Fwd, Mtd, Mch, and Mer from Methanosaeta strains cluster with the methylotrophic methanogens, and were not closely related to those from the hydrogenotrophic methanogens. Quantitative PCR detected the expression of all genes for this pathway, albeit ten times lower than the genes for aceticlastic methanogenesis in strain 6Ac. Western blots also revealed the expression of fwd and mch, genes involved in methyl-group oxidation. Moreover, (13)C-labeling experiments suggested that the Methanosaeta strains might use the pathway as a methyl oxidation shunt during the aceticlastic metabolism. Because the mch mutants of Methanosarcina barkeri or M. acetivorans failed to grow on acetate, we suggest that Methanosaeta may use methyl-group oxidation pathway to generate reducing equivalents, possibly for biomass synthesis. An fpo operon, which encodes an electron transport complex for the reduction of CoM-CoB heterodisulfide, was found in the three genomes of the Methanosaeta strains. However, an incomplete protein complex lacking the FpoF subunit was predicted, as the gene for this protein was absent. Thus, F(420)H(2) was predicted not to serve as the electron donor. In addition, two gene clusters encoding the two types of heterodisulfide reductase (Hdr), hdrABC, and hdrED, respectively, were found in the three Methanosaeta genomes. Quantitative PCR determined that the expression of hdrED was about ten times higher than hdrABC, suggesting that hdrED plays a major role in aceticlastic methanogenesis.
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Affiliation(s)
- Jinxing Zhu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, People’s Republic of China
- Graduate School, Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Huajun Zheng
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, People’s Republic of China
| | - Guomin Ai
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Guishan Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Di Liu
- Information center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Xiaoli Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Xiuzhu Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, People’s Republic of China
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Characterization and regulation of the osmolyte betaine synthesizing enzymes GSMT and SDMT from halophilic methanogen Methanohalophilus portucalensis. PLoS One 2011; 6:e25090. [PMID: 21949863 PMCID: PMC3176816 DOI: 10.1371/journal.pone.0025090] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2011] [Accepted: 08/26/2011] [Indexed: 11/20/2022] Open
Abstract
The halophilic methanoarchaeon Methanohalophilus portucalensis can synthesize the osmolyte betaine de novo in response to extracellular salt stress. Betaine is generated by the stepwise methylation of glycine to form sarcosine, N, N-dimethylglycine and betaine by using S-adenosyl-L-methionine (AdoMet) as the methyl donor. The complete gene cluster of Mpgsmt-sdmt was cloned from Southern hybridization and heterologous expressed in E. coli respectively. The recombinant MpGSMT and MpSDMT both retained their in vivo functional activities in E. coli BL21(DE3)RIL to synthesize and accumulate betaine and conferred elevated survival ability in betaine transport deficient mutant E. coli MKH13 under high salt stress. The dramatic activating effects of sodium and potassium ions on the in vitro methyltransferase activities of MpGSMT, but not MpSDMT or bacterial GSMT and SDMT, revealed that GSMT from halophilic methanoarchaeon possesses novel regulate mechanism in betaine biosynthesis pathway. The circular dichroism spectra showed the fluctuated peaks at 206 nm were detected in the MpGSMT under various concentrations of potassium or sodium ions. This fluctuated difference may cause by a change in the β-turn structure located at the conserved glycine- and sarcosine-binding residue Arg167 of MpGSMT. The analytical ultracentrifugation analysis indicated that the monomer MpGSMT switched to dimeric form increased from 7.6% to 70% with KCl concentration increased from 0 to 2.0 M. The level of potassium and sodium ions may modulate the substrate binding activity of MpGSMT through the conformational change. Additionally, MpGSMT showed a strong end product, betaine, inhibitory effect and was more sensitive to the inhibitor AdoHcy. The above results indicated that the first enzymatic step involved in synthesizing the osmolyte betaine in halophilic archaea, namely, GSMT, may also play a major role in coupling the salt-in and compatible solute (osmolyte) osmoadaptative strategies in halophilic methanogens for adapting to high salt environments.
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Göker M, Scheuner C, Klenk HP, Stielow JB, Menzel W. Codivergence of mycoviruses with their hosts. PLoS One 2011; 6:e22252. [PMID: 21829452 PMCID: PMC3146478 DOI: 10.1371/journal.pone.0022252] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2011] [Accepted: 06/17/2011] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND The associations between pathogens and their hosts are complex and can result from any combination of evolutionary events such as codivergence, switching, and duplication of the pathogen. Mycoviruses are RNA viruses which infect fungi and for which natural vectors are so far unknown. Thus, lateral transfer might be improbable and codivergence their dominant mode of evolution. Accordingly, mycoviruses are a suitable target for statistical tests of virus-host codivergence, but inference of mycovirus phylogenies might be difficult because of low sequence similarity even within families. METHODOLOGY We analyzed here the evolutionary dynamics of all mycovirus families by comparing virus and host phylogenies. Additionally, we assessed the sensitivity of the co-phylogenetic tests to the settings for inferring virus trees from their genome sequences and approximate, taxonomy-based host trees. CONCLUSIONS While sequence alignment filtering modes affected branch support, the overall results of the co-phylogenetic tests were significantly influenced only by the number of viruses sampled per family. The trees of the two largest families, Partitiviridae and Totiviridae, were significantly more similar to those of their hosts than expected by chance, and most individual host-virus links had a significant positive impact on the global fit, indicating that codivergence is the dominant mode of virus diversification. However, in this regard mycoviruses did not differ from closely related viruses sampled from non-fungus hosts. The remaining virus families were either dominated by other evolutionary modes or lacked an apparent overall pattern. As this negative result might be caused by insufficient taxon sampling, the most parsimonious hypothesis still is that host-parasite evolution is basically the same in all mycovirus families. This is the first study of mycovirus-host codivergence, and the results shed light not only on how mycovirus biology affects their co-phylogenetic relationships, but also on their presumable host range itself.
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Affiliation(s)
- Markus Göker
- DSMZ-German Collection for Microorganisms and Cell Cultures, Braunschweig, Germany.
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