New branches in the tree of life from geothermally active environments

MSU's Thermal Biology Institute (TBI) fall seminar series
October 19th, 2020

Transcript

1. New branches in the tree of life from geothermally active environments Research associate The University of Texas at Austin Marine Science Institute Baker Marine Microbial Ecology Lab Dr. Valerie De Anda valdeanda val_deanda valdeanda@utexas.edu MSU's Thermal Biology Institute (TBI) fall seminar series October 19th 2020
2. Content qMicrobial diversity and metagenomics qThe deep sea and the new branches of the tree of life qOverlooked archaeal phylum in geothermally active environments
3. Content qMicrobial diversity and metagenomics qThe deep sea and the new branches of the tree of life qOverlooked archaeal phylum in geothermally active environments
4. 1021 stars in the universe Flemming and Wuertz 2019 Nat Rev Copley, J. All at sea. Nature Microbiology by numbers. 2011 Nat Rev Microbiol @NatureRevMicro #microbiologybynumbers Microorganisms are the most abundant life form on our planet. More microbes in 5 g of soil than humans on Earth @NatureRevMicro #microbiologybynumbers 1030 microorganisms
5. 1021 stars in the universe @NatureRevMicro #microbiologybynumbers Microorganisms are the most abundant and diverse life form on our planet. @NatureRevMicro #microbiologybynumbers 1030 microorganisms Paradoxically, scientific understanding of how this “vast universe” of microbes catalyze biogeochemical reactions is not fully resolved because 99.99 % of Earth’s microbial taxa have not been described yet Flemming and Wuertz 2019 Nat Rev Copley, J. All at sea. Nature Microbiology by numbers. 2011 Nat Rev Microbiol
6. At best 0.1% of what is present in nature can be grown in the laboratory ≠ Cavicchioli et al., 2019 Nature Steen et al., 2019 ISME Lloyd et al., 2018 mBio Most microorganisms are unknown Uncultured majority a.k.a microbial dark matter Growth in the lab Natural community
7. Culturing Dick G 2019 BONCAT DNA-SIP Genome assembly Reconstruct metabolisms of all the microbes How do we investigate microbes in nature? Metagenomics Next generation physiology Hatzenpichler et al., 2020 Nat. Rev. Microbiol M etagenom ics Transcriptom ics Proteom ics
8. -1995 : H. influenzae becomes the first bacterium genome to be sequenced -2000: Genome sequence of model organism fruit fly -2003: Mouse becomes first mammal with sequenced genome -2005: Human Genome Project completion announced -2005: First NGS machine allowing sequencing DNA from environmental samples -2008 Human Microbiome -2015 Ocean Microbiome -2015: MAGs -2016: Updated tree of life https://unlockinglifescode.org/timeline Breakthrough moments Genomic Era -1995: .H influenzae becomes the first bacterium genome to be sequenced Metagenomics Metagenome reconstructed genomes
9. Hug et al. 2016 Nature Micro Updated tree of life Hubble space telescope
10. Solden et al., 2016 Curr. Opin. Microbiol. Updated tree of life uncultured isolates Hug et al. 2016 Nature Micro
11. Content qMicrobial diversity and metagenomics qThe deep sea and the new branches of the tree of life qOverlooked archaeal phylum in geothermally active environments
12. Marine sediments contain the largest pool of organic carbon on the planet Importance of marine sediments Jiao et al., 2010 Nat. Rev. Microbiol
13. Uncultured lineages in red Marine sediments are a biological black box Baker, De Anda et al., 2020 Nat. Microbiol
14. Baker et al., 2020 Marine sediments are a biological black box Jiao et al., 2010 Nat. Rev. Microbiol
15. Baker et al., 2020 Marine sediments are a biological black box Jiao et al., 2010 Nat. Rev. Microbiol
16. Baker Marine Microbial Ecology Lab bakermicrolab archaeal http://sites.utexas.edu/baker-lab/ Brenda Ortiz peika95
17. Exploring the deep sea The Guaymas Basin (GB) Sampling expedition 2018 Mar de Cortés México
18. Exploring the deep sea The Guaymas Basin (GB) Sampling expedition 2018
19. Exploring the deep sea The Guaymas Basin (GB) Sampling expedition 2018
20. https://youtu.be/NRZayrzpE00 Exploring the deep sea Dowmbrowski et al., 2018 Nat Comm
21. Exploring the deep sea Full video
22. ~ 4 TB sequencing data: 4 sites 16 samples (~300 Gb /sample) ~ 3000 MAGs + 551 MAGs Dowmbroski et al., 2018 Guaymas Project Baker Lab 2019 Exploring the deep sea 15 more sites in the process of being sequenced
23. Woodcroft et al Nature 2018 Emerson et al., Nat Micro 2018 Tsagaraki et al., 2918 47 Novel phylum Genome resolve biogeochemical cycling Anantharaman, K. et al., 2016 Nature comm Permafrost Aquifers 214 samples 1529 MAGs 33 samples 2,516 MAGs So far, there has been no BIG sequencing efforts to understand the deep sea Big sequencing efforts Deep Sea ~ 4 TB sequencing data: 4 sites 16 samples (~300 Gb /sample) ~ 3000 MAGs + 551 MAGs Dowmbroski et al., 2018
24. Taylorbacteria Fusobacteria TM 6 (D ependentiae) Schekmanbacteria Nealson-/Staskaw icz-/W ilderm uthbacteria Azam-and Yanofsky-bacteria Omnitrophica Chlorobi Uhrbacteria Kuenenbacteria Sungbacteria Riflebacteria M oranbacteria loacim onetes Ryanbacteria Jorgensenbacteria Doudnabacteria io annonibacteria tribacteria oatesbacteria e ybacteria S Roizmanbacteria ambryskibacteria acteroidetes Marinimicrobia Dictyolomi erophobetes lusimicrobia Thermoto ae ctinobacteria Tenericutes loydbacteria Curtissbacteria dro enedentes hloro e i ipolaricaulota er eldbacteria iritim atiellaeota emmatimonadetes oykebacteria acebacteria minicenantes WO - and T 6 lassbacteria Adler- Kaiserbacteria na ibacteriae Firmicutes W S- ( remiobacteraeota) Delphibacteria S ner istetes Nomurabacteria Falkowbacteria Spirochaetes oribacteria b ssubacteria Woesebacteria erkelbacteria Kom eilibacteria uchananbacteria Co rotherm obacterota Shapirobacteria ottesbacteria indo bacteria azan entisphaerae roteobacteria Amesbacteria Rokubacteria arrison-and i ton-bacteria atescibacteria Kry tonia ortno bacteria errucom icrobia Cam bellbacteria Azambacteria isenbacteria Do kabacteria Nitrospinae Saccharibacteria alditrichaeota olfebacteria Fermentibacteria lackburnbacteria ere rinibacteria agasanikbacteria eck ithbacteria e iribacteria S echtbacteria lanctom cetes Fibrobacteres hlam diae Tagabacteria i ibacteria Chisholmbacteria Archaea ui cae Sumerlaeota cidobacteria allbacteria acksonbacteria C R aldiserica Yonathbacteria Nitrospirae W W Treescale This sequencing effort has resulted in: 13+ new bacteria phyla 6 new archaea phyla Guaymas sediments contain vast untapped diversity
25. Novel uncultured bacterial lineages in the tree of life Gong et al.
26. Novel uncultured branches of the tree of life Gong X, De Anda, Baker In Prep • 4 new previously unknown bacterial phyla • 2 characterized with 16S rRNA diversity studies • Understanding the metabolic and ecological potential of these novel uncultured groups
27. Carlton et al., Novel uncultured bacterial lineage in the tree of life: Zipacnabacteria
28. Novel uncultured branches of the tree of life Carlton, Vazquez, De Anda et al., In Prep •Novel bacterial phylum closely related to Chloroflexi and WPS-2 •Global distribution in anoxic aquatic sediments (marine and freshwater) •Multiple major metabolic groups within the phylum •Utilize sulfur compounds, nitrite, and arsenic compounds •Break down carbon macromolecules like cellulose Zipacna Mayan personification of Earth’s crust
29. Novel diversity in cultured representatives Langwig et al. In prep
30. Novel diversity in known cultured taxa Langwig M, De Anda et al., In Prep Protein-level comparison of nearly 2,000 Deltaproteobacteria reveals new ecological and biogeochemical roles
31. Carbon degradation in the deep sea De Anda et al., In prep
32. Genome resolved carbon cycling in the deep sea De Anda et al., In prep Genome-resolved carbon cycling in the deep-sea Deep sea genomic sequencing has been crucial to understand origin of cellular complexity Qr code
33. Content qMicrobial diversity and metagenomics qThe deep sea and the new branches of the tree of life q Overlooked archaeal phylum in geothermally active environments
34. Merino et al., 2019. Front. Microbiol Geothermally active environments “By studying extreme environments, we can explore the entire scale of diversity of life that exist on the planet” Hatzenpichler FEMS 2020
35. There are many novel taxa left to be explored Baker, De Anda et al., 2020 Nat. Microbiol Hua et al., 2018 Nat Comm Kozuba et al., 2013 ISME Novel taxa left to be found ? Jay et al., 2018 Seitz et al., 2019 ISME
36. Hot springs Deep sea sediments Hua et al. , 2018 Nat Comm Dombrowski et al , 2018 Nat Comm 62 °C MAGs from geothermally active environments De Anda et al. in review Nature Comm.
37. Brockarchaeota is a new lineage within TACK 37 conserved single copy protein-coding gene tree De Anda et al. in review Nature Comm. ?
38. A new archaeal phylum that has been overlooked in metagenomic databases 16S rRNA phylogenetic tree De Anda et al. in review Nature Comm. Only 3 sequences are derived from 16S rRNA studies, the rest are from metagenomic studies
39. A new archaeal phylum globally distributed in geothermally active environments De Anda et al. in review Nature Comm.
40. Methylotrophy related genes 37 conserved single copy protein-coding gene tree De Anda et al. in review Nature Comm.
41. Gaps of knowledge in ecological roles and taxa mediating them Methanol Methylamine Dimethylamine (DMA) Trimethylamine (TMA) CH3 NH2 CH3 NH2 CH3 CH3 CH3 OH C R Dimethylsulfide (DMS) CH3 S CH3 CH3 NH2 CH3 Important components of the global C, N, S Are derived from different sources such as phytoplankton, plants, and the decay of organic matter Abundant in the oceans, atmosphere and sediments Methylated compounds De Anda et al. in review Nature Comm.
42. Methanol DMA TMA MtaA MtaB MtaC MtbB MtbC MtbA CoM-S-S-CoB CoM-SH+HS-CoB Fdox Fdred 2H2 4H+ HdrB HdrC MvhG MvhA HdrA MvhD 1-2,5,8 1-2,5 FrhG FrhA F420 H2 F420 H2 2H+ 1-4 1-4 MttB MttA MttC HS-CoM CH3 S-CoM Biosynthesis F420 CH4 H2 MtrA MtrH CH3 -S-CoM H2 H2 H2 +HS-CoM +HS-CoM +HS-CoM 3 1-3,7 1-4,6 1-4 1-4 2-4,7 ATP ADP ATPase 1-4,6-8 1-2,6 FrhB 1-2,6 1-5,7 1-2,5,7 1-2,5-7 4 NiFe H+ H2 FdOX Fdred 2e- 8 ? ? 2e- ? PPi 2Pi H+ HppA 1-7 H+ H+ Unknown methylotrophic metabolism Absence of methylotrophic methanogenesis-genes Absence of aerobic methylotrophy-genes De Anda et al. in review Nature Comm.
43. Unknown methylotrophic metabolism Previously undescribed mechanism for anaerobic methylotropy De Anda et al. in review Nature Comm. Methanol TMA MtaA MtaB MtaC MttB MttA MttC Energy conservation Biosynthetic purpuses ? No methylotrophic members of the archaea domain have been described outside methanogenic groups
44. Proposed metabolic model De Anda et al. in review Nature Comm.
45. Proposed metabolic model De Anda et al. in review Nature Comm.
46. Utilization of extracellular organic carbon De Anda et al. in review Nature Comm.
47. Proposed metabolic model
48. Proposed ecological role of Brockarchaeota De Anda et al. in review Nature Comm.
49. Marine Science Institute Port Aransas Texas, USA Baker Marine Microbial Ecology Lab Understanding the physiologies of uncultured marine sediment microbes using high-throughput genomic techniques
50. Kiley Seitz Ian Rambo Maggie Langwig Valerie de Anda UC Berkeley Jill Banfield Lin-xing Chen Baker Lab Xianzhe Gong Wen-Jun Li Chen Jiang Zheng-Shuang Hua Thijs Ettema Roland Hatzenpichler‬ Andreas Teske