Explorative Meta-Analysis of 417 Extant Archaeal Genomes to Predict Their Contribution to the Total Microbiome Functionality
Revealing the relationship between taxonomy and function in microbiomes is critical to discover their contribution to ecosystem functioning. However, while the relationship between taxonomic and functional diversity in bacteria and fungi is known, this is not the case for archaea. Here, we used a me...
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MDPI AG
2021-02-01
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| Series: | Microorganisms |
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| Online Access: | https://www.mdpi.com/2076-2607/9/2/381 |
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| author | Robert Starke Maysa Lima Parente Fernandes Daniel Kumazawa Morais Iñaki Odriozola Petr Baldrian Nico Jehmlich |
| author_facet | Robert Starke Maysa Lima Parente Fernandes Daniel Kumazawa Morais Iñaki Odriozola Petr Baldrian Nico Jehmlich |
| author_sort | Robert Starke |
| collection | DOAJ |
| description | Revealing the relationship between taxonomy and function in microbiomes is critical to discover their contribution to ecosystem functioning. However, while the relationship between taxonomic and functional diversity in bacteria and fungi is known, this is not the case for archaea. Here, we used a meta-analysis of 417 completely annotated extant and taxonomically unique archaeal genomes to predict the extent of microbiome functionality on Earth contained within archaeal genomes using accumulation curves of all known level 3 functions of KEGG Orthology. We found that intergenome redundancy as functions present in multiple genomes was inversely related to intragenome redundancy as multiple copies of a gene in one genome, implying the tradeoff between additional copies of functionally important genes or a higher number of different genes. A logarithmic model described the relationship between functional diversity and species richness better than both the unsaturated and the saturated model, which suggests a limited total number of archaeal functions in contrast to the sheer unlimited potential of bacteria and fungi. Using the global archaeal species richness estimate of 13,159, the logarithmic model predicted 4164.1 ± 2.9 KEGG level 3 functions. The non-parametric bootstrap estimate yielded a lower bound of 2994 ± 57 KEGG level 3 functions. Our approach not only highlighted similarities in functional redundancy but also the difference in functional potential of archaea compared to other domains of life. |
| first_indexed | 2024-03-09T00:53:58Z |
| format | Article |
| id | doaj.art-da01f72823a04f7aac359c92b13cf6cd |
| institution | Directory Open Access Journal |
| issn | 2076-2607 |
| language | English |
| last_indexed | 2024-03-09T00:53:58Z |
| publishDate | 2021-02-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Microorganisms |
| spelling | doaj.art-da01f72823a04f7aac359c92b13cf6cd2023-12-11T17:01:05ZengMDPI AGMicroorganisms2076-26072021-02-019238110.3390/microorganisms9020381Explorative Meta-Analysis of 417 Extant Archaeal Genomes to Predict Their Contribution to the Total Microbiome FunctionalityRobert Starke0Maysa Lima Parente Fernandes1Daniel Kumazawa Morais2Iñaki Odriozola3Petr Baldrian4Nico Jehmlich5Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, 142 00 Praha, Czech RepublicLaboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, 142 00 Praha, Czech RepublicLaboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, 142 00 Praha, Czech RepublicLaboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, 142 00 Praha, Czech RepublicLaboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, 142 00 Praha, Czech RepublicMolecular Systems Biology, Helmholtz-Center for Environmental Research, UFZ, 04318 Leipzig, GermanyRevealing the relationship between taxonomy and function in microbiomes is critical to discover their contribution to ecosystem functioning. However, while the relationship between taxonomic and functional diversity in bacteria and fungi is known, this is not the case for archaea. Here, we used a meta-analysis of 417 completely annotated extant and taxonomically unique archaeal genomes to predict the extent of microbiome functionality on Earth contained within archaeal genomes using accumulation curves of all known level 3 functions of KEGG Orthology. We found that intergenome redundancy as functions present in multiple genomes was inversely related to intragenome redundancy as multiple copies of a gene in one genome, implying the tradeoff between additional copies of functionally important genes or a higher number of different genes. A logarithmic model described the relationship between functional diversity and species richness better than both the unsaturated and the saturated model, which suggests a limited total number of archaeal functions in contrast to the sheer unlimited potential of bacteria and fungi. Using the global archaeal species richness estimate of 13,159, the logarithmic model predicted 4164.1 ± 2.9 KEGG level 3 functions. The non-parametric bootstrap estimate yielded a lower bound of 2994 ± 57 KEGG level 3 functions. Our approach not only highlighted similarities in functional redundancy but also the difference in functional potential of archaea compared to other domains of life.https://www.mdpi.com/2076-2607/9/2/381archaeafunctional diversitymicrobiome functionality |
| spellingShingle | Robert Starke Maysa Lima Parente Fernandes Daniel Kumazawa Morais Iñaki Odriozola Petr Baldrian Nico Jehmlich Explorative Meta-Analysis of 417 Extant Archaeal Genomes to Predict Their Contribution to the Total Microbiome Functionality Microorganisms archaea functional diversity microbiome functionality |
| title | Explorative Meta-Analysis of 417 Extant Archaeal Genomes to Predict Their Contribution to the Total Microbiome Functionality |
| title_full | Explorative Meta-Analysis of 417 Extant Archaeal Genomes to Predict Their Contribution to the Total Microbiome Functionality |
| title_fullStr | Explorative Meta-Analysis of 417 Extant Archaeal Genomes to Predict Their Contribution to the Total Microbiome Functionality |
| title_full_unstemmed | Explorative Meta-Analysis of 417 Extant Archaeal Genomes to Predict Their Contribution to the Total Microbiome Functionality |
| title_short | Explorative Meta-Analysis of 417 Extant Archaeal Genomes to Predict Their Contribution to the Total Microbiome Functionality |
| title_sort | explorative meta analysis of 417 extant archaeal genomes to predict their contribution to the total microbiome functionality |
| topic | archaea functional diversity microbiome functionality |
| url | https://www.mdpi.com/2076-2607/9/2/381 |
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