Table 1.
Taxonomic survey for critical metabolic functions in all types of serpentinite-hosted environments, specifying the methodological approach including metagenome-assembled genomes (MAGs) and single-cell amplified genomes (SAGs).
| Metabolism | Taxon | Site | Method | References |
|---|---|---|---|---|
| Hydrogen oxidation | Bacteria_Pseudomonadota_Alphaproteobacteria1 | The Cedars (shallow waters) | MAGs | Suzuki et al. (2017) |
| Bacteria_Pseudomonadota_Gammaproteobacteria | The Cedars (shallow waters) | MAGs; 16S rRNA | Suzuki et al. (2013, 2017) | |
| Bacteria_Pseudomonadota_Gammaproteobacteria_Betaproteobacteriales (formerly Betaproteobacteria)2 | The Cedars (shallow waters) | MAGs | Suzuki et al. (2017) | |
| Bacteria_Pseudomonadota_Gammaproteobacteria_Burkholderiales_Burkholderiaceae_Hydrogenophaga3 | The Tablelands, Lost City (oxic/anoxic interface); Voltri; The Cedars (shallow waters); Prony Bay; Zambales | MAGs; 16S rRNA | Brazelton et al. (2012, 2017), Suzuki et al. (2013), Frouin et al. (2018), Woycheese et al. (2015) | |
| Bacteria_Pseudomonadota_Gammaproteobacteria_Burkholderiales_Burkholderiaceae_Serpentinimonas4 | Voltri; The Cedars (shallow waters/non-specified) | 16S rRNA; cultivation | Quéméneur et al. (2015), Suzuki et al. (2014, 2017), Brazelton et al. (2017), Bird et al. (2021) | |
| Bacteria_Pseudomonadota_Gammaproteobacteria_Burkholderiales_Burkholderiaceae_Serpentinimonas_S. raichei5 | The Cedars | Cultivation | Bird et al. (2021) | |
| Bacteria_Pseudomonadota_Gammaproteobacteria_Burkholderiales_Burkholderiaceae_Serpentinimonas_S. barnesii6 | The Cedars | Cultivation | Bird et al. (2021) | |
| Bacteria_Pseudomonadota_Gammaproteobacteria_Burkholderiales_Burkholderiaceae_Serpentinimonas_S. maccroryi7 | The Cedars | Cultivation | Bird et al. (2021) | |
| Bacteria_Pseudomonadota_Gammaproteobacteria_Burkholderiales_Burkholderiaceae_Cupriavidus_C. necator (formerly Ralstonia eutropha)8 | The Tablelands, Lost City (oxic/anoxic interface) | MAGs | Brazelton et al. (2012) | |
| Bacteria_Former class Deltaproteobacteria | The Cedars (shallow waters) | MAGs; 16S rRNA | Suzuki et al. (2013, 2017) | |
| Bacteria_Desulfobacterota_Desulfovibrionia_Desulfovibrionales9 | Voltri (deep subsurface) | MAGs | Brazelton et al. (2017) | |
| Bacteria_Desulfobacterota_Desulfovibrionia_Desulfovibrionales_Desulfonatronaceae_Desulfonatronum10 | Prony Bay | 16S rRNA | Postec et al. (2015), Mei et al. (2016) | |
| Bacteria_BacillotaB_Desulfotomaculia_Desulfotomaculales_ Desulfotomaculaceae_Desulfotomaculum_D. alkaliphilum11 | Lost City | 16S rRNA | Brazelton et al. (2006, 2010) | |
| Archaea_Methanobacteriota_Methanobacteria_Methanobacteriales_Methanobacteriaceae_Methanobacterium_Lineage type I | Voltri; Samail (surface waters); Prony Bay | MAGs, SAGs, 14C labelling | Quéméneur et al. (2015, 2021, 2023), Fones et al. (2021) | |
| Aerobic methane oxidation | Archaea_Methanobacteriota_Methanobacteria_Methanobacteriales_Methanobacteriaceae_Methanobacterium_M. alkalithermotolerans strain DSM102889 | La Crouen | Cultivation | Mei et al. (2022) |
| Bacteria_Pseudomonadota_Gammaproteobacteria_Methylococcales_Methylococcaceae12 | Voltri (shallow subsurface mixing zone) | 16S rRNA, MAGs, 13C labelling | Brazelton et al. (2017) | |
| Bacteria_Pseudomonadota_Gammaproteobacteria_Methylococcales_Methylococcaceae_Methylococcus | Samail | 16S rRNA | Kraus et al. (2021) | |
| Bacteria_Pseudomonadota_Alphaproteobacteria_Rhizobiales_Beijerinckiaceae_Methylosinus | Voltri | 16S rRNA | Quéméneur et al. (2015) | |
| Methanogenesis/anaerobic methane oxidation | Archaea_Halobacteriota_Methanomicrobia_Methanomicrobiales | Santa Elena | 16S rRNA (MAGs) | Crespo-Medina et al. (2017) |
| Archaea_Methanobacteriota_Methanobacteria_Methanobacteriales | Santa Elena; Voltri | 16S rRNA (MAGs) | Crespo-Medina et al. (2017), Quéméneur et al. (2015) | |
| Archaea_Methanobacteriota_Methanobacteria_Methanobacteriales_Methanobacteriaceae13 | Voltri (deep subsurface) | 16S rRNA, MAGs, 13C labelling | Brazelton et al. (2017) | |
| Archaea_Methanobacteriota_Methanobacteria_Methanobacteriales_Methanobacteriaceae_Methanobacterium | Samail (subsurface); Voltri; Zambales | 16S rRNA; MAGs; SAGs; 13C labelling; 14C labelling | Kraus et al. (2021), Brazelton et al. (2017), Fones et al. (2021), Woycheese et al. (2015), Quéméneur et al. (2015) | |
| Archaea_Methanobacteriota_Methanobacteria_Methanobacteriales_Methanobacteriaceae_Methanobacterium_M. alcaliphilum strain DSM3387 | Del Puerto | 16S rRNA | Blank et al. (2009) | |
| Archaea_Methanobacteriota_Methanobacteria_Methanobacteriales_Methanobacteriaceae_Methanobacterium_M. alkalithermotolerans strain DSM102889 | La Crouen | Cultivation | Mei et al. (2022) | |
| Archaea_Halobacteriota_Methanosarcinia_Methanosarcinales | Santa Elena; Voltri | 16S rRNA (MAGs) | Crespo-Medina et al. (2017), Quéméneur et al. (2015), Suzuki et al. (2013) | |
| Archaea_Halobacteriota_Methanosarcinia_Methanosarcinales_LCMS phylotype14 | Lost City (Brazelton et al. (2006): High-temperature); Prony Bay (intertidal and submarine); Old City | 16S rRNA, MAGs; 13C labelling | Schrenk et al. (2004), Brazelton et al. (2006, 2011), Frouin et al. (2018), Lecoeuvre et al. (2021) | |
| Archaea_Halobacteriota_Methanosarcinia_Methanosarcinales_TCMS phylotype | The Cedars; Prony Bay (intertidal and submarine); Old City | 16S rRNA, MAGs | Suzuki et al. (2013), Frouin et al. (2018), Lecoeuvre et al. (2021) | |
| Archaea_Halobacteriota_Syntropharchaeia_ANME-1 | Lost City (low temperature); Santa Elena; Cabeço de Vide | 16S rRNA (MAGs) | Brazelton et al. (2006), Crespo-Medina et al. (2017), Tiago and Veríssimo (2013) | |
| Formate consumption | Bacteria_Pseudomonadota_Gammaproteobacteria_Methylococcales_Methylococcaceae12 | Voltri (shallow subsurface mixing zone) | MAGs | Brazelton et al. (2017) |
| Bacteria_Desulfobacterota_Desulfovibrionia_Desulfovibrionales9 | Voltri (deep subsurface) | MAGs | Brazelton et al. (2017) | |
| Bacteria_Ca. Lithacetigena15 | The Cedars, Hakuda Happo hot springs | MAGs | Nobu et al. (2022) | |
| Bacteria_Ca. Bipolaricaulota (OP1/MSBL6)17 | Lost City | MAGs | Brazelton et al. (2022) | |
| Archaea_Methanobacteriota_Methanobacteria_Methanobacteriales_Methanobacteriaceae_Methanobacterium_Lineage type II | Samail (subsurface) | MAGs, SAGs, 14C labelling | Fones et al. (2021) | |
| Acetate consumption | Bacteria_Desulfobacterota_Desulfovibrionia_Desulfovibrionales9 | Voltri (deep subsurface) | MAGs | Brazelton et al. (2017) |
| Archaea_Halobacteriota_Methanosarcinia_Methanosarcinales_LCMS phylotype14 | Lost City | MAGs | Brazelton et al. (2011) | |
| Glycine consumption | Bacteria_Ca. Lithacetigena15 | The Cedars, Hakuda Happo hot springs | MAGs | Nobu et al. (2022) |
| Calcium carbonate consumption | Bacteria_Pseudomonadota_Gammaproteobacteria_Burkholderiales_Burkholderiaceae_Serpentinimonas4 | The Cedars | Cultivation | Suzuki et al. (2014) |
| Bacteria_Pseudomonadota_Gammaproteobacteria_Burkholderiales_Burkholderiaceae_Serpentinimonas_S. raichei5 | The Cedars | Cultivation | Bird et al. (2021) | |
| Bacteria_Pseudomonadota_Gammaproteobacteria_Burkholderiales_Burkholderiaceae_Serpentinimonas_S. barnesii6 | The Cedars | Cultivation | Bird et al. (2021) | |
| Bacteria_Pseudomonadota_Gammaproteobacteria_Burkholderiales_Burkholderiaceae_Serpentinimonas_S. maccroryi7 | The Cedars | Cultivation | Bird et al. (2021) | |
| Bacteria_ NPL-UPA2 clade18 | The Cedars, Prony Bay, Lost City | MAGs | Suzuki et al. (2018), Brazelton et al. (2022) | |
| Bacteria_Ca. Bipolaricaulota (OP1/MSBL6)17 | Lost City | MAGs | Brazelton et al. (2022) | |
| CO oxidation | Bacteria_Pseudomonadota_Gammaproteobacteria_Burkholderiales_Burkholderiaceae_Hydrogenophaga3 | The Tablelands, Lost City (oxic/anoxic interface) | MAGs; 16S rRNA, 13C labelling | Brazelton et al. (2012), Morrill et al. (2014) |
| Bacteria_Pseudomonadota_Gammaproteobacteria_Burkholderiales_Burkholderiaceae_Cupriavidus_C. necator (formerly Ralstonia eutropha)8 | The Tablelands, Lost City (oxic/anoxic interface) | MAGs | Brazelton et al. (2012) | |
| Bacteria_Actinobacteriota_Ca. Hakubanella thermoalkaliphilus | Hakuda Happo hot springs | 16S rRNA, SAGs | Merino et al. (2020) | |
| Archaea_Hadesarchaea (formerly SAGMEG) | Prony Bay | 16S rRNA | Postec et al. (2015) | |
| Sulfide/sulfur oxidation | Bacteria_Pseudomonadota_Gammaproteobacteria_Betaproteobacteriales (formerly Betaproteobacteria)2 | Cabeço de Vide | 16sS rRNA (DGGE) | Tiago and Veríssimo (2013) |
| Bacteria_Pseudomonadota_Gammaproteobacteria_Thiomicrospirales_Thiomicrospiraceae_Hydrogenovibrio (formerly Thiomicrospira) | Lost City (low temperature) | 16S rRNA | Brazelton et al. (2006) | |
| Bacteria_Pseudomonadota_Alphaproteobacteria_Rhodobacterales_Rhodobacteraceae | Ney Springs | MAGs, Cultivation | Trutschel et al. (2022) | |
| Bacteria_Pseudomonadota_Gammaproteobacteria_Pseudomonadales_Halomonadaceae_Halomonas | Ney Springs | MAGs, Cultivation | Trutschel et al. (2022) | |
| Sulfate reduction | Bacteria_BacillotaA_Clostridia16 | Cabeço de Vide; The Cedars (deep subsurface) | 16S rRNA (DGGE) | Tiago and Veríssimo (2013), Suzuki et al. (2013) |
| Bacteria_BacillotaB_Desulfotomaculia_Desulfotomaculales_ Desulfotomaculaceae_Desulfotomaculum_D. alkaliphilum11 | Lost City | 16S rRNA | Brazelton et al. (2006, 2010) | |
| Bacteria_BacillotaD_Dethiobacteria_Dethiobacterales_Dethiobacteraceae_Dethiobacter | The Tablelands, The Cedars, Cabeço de Vide, Prony Bay, Zambales | Brazelton et al. (2012), Suzuki et al. (2013), Tiago and Veríssimo (2013), Postec et al. (2015), Woycheese et al. (2015), Crespo-Medina et al. (2017), Trutschel et al. (2022), Twing et al. (2017) | ||
| Bacteria_Desulfobacterota_Desulfovibrionia_Desulfovibrionales9 | Voltri | MAGs | Brazelton et al. (2017) | |
| Bacteria_Desulfobacterota_Desulfovibrionia_Desulfovibrionales_Desulfonatronaceae_Desulfonatronum10 | Prony Bay | 16S rRNA | Postec et al. (2015), Mei et al. (2016) | |
| Bacteria_Nitrospirota_Thermodesulfovibrionia_Thermodesulfovibrionales_Thermodesulfovibrionaceae | Samail (subsurface fluids) | 16S rRNA | Rempfert et al. (2017) | |
| Nitrogen fixation | Bacteria_Pseudomonadota_Alphaproteobacteria_Azospirillales_Azospirillaceae_Azospirillum | Voltri | 16S rRNA | Quéméneur et al. (2015) |
| Archaea_Methanobacteriota_Methanobacteria_Methanobacteriales_Methanobacteriaceae13 | Voltri (deep subsurface) | 16S rRNA, MAGs | Brazelton et al. (2017) | |
| Archaea_Halobacteriota_Methanosarcinia_Methanosarcinales_LCMS phylotype14 | Lost City | MAGs | Brazelton et al. (2011) | |
| Phosphonate catabolism | Bacteria_Proteobacteria_Alphaproteobacteria1 | Prony Bay, Lost City | MAGs | Frouin et al. (2022) |
| Bacteria_Proteobacteria_Gammaproteobacteria_Betaproteobacteriales (formerly Betaproteobacteria)2 | Coast Range, Voltri, Santa Elena, Cabeço de Vide | MAGs | Frouin et al. (2022) | |
| Bacteria_ BacillotaA _Clostridia16 | Prony Bay, Lost City | MAGs | Frouin et al. (2022) | |
| Acetogenesis | Bacteria_Chloroflexota (formerly Chloroflexi) | The Cedars (deep subsurface); Prony Bay (submarine) | MAGs; 16S rRNA | Suzuki et al. (2013, 2017), Frouin et al. (2018) |
| Bacteria_ NPL-UPA2 clade18 | The Cedars; Prony Bay | 16S rRNA; MAGs | Postec et al. (2015), Mei et al. (2016), Suzuki et al. (2018) | |
| Bacteria_BacillotaD_Dethiobacteria_Dethiobacterales_Dethiobacteraceae_Dethiobacter_D. alkaliphilus | The Cedars; Prony Bay; Cabeço de Vide | 16S rRNA | Postec et al. (2015), Mei et al. (2016), Suzuki et al. (2013), Tiago and Veríssimo (2013) | |
| Bacteria_Ca. Bipolaricaulota (OP1/MSBL6)17 | Samail (subsurface fluids) | MAGs | Colman et al. (2022) | |
| Fermentation | Bacteria_ BacillotaA _Clostridia | The Tablelands, Lost City | MAGs | Brazelton et al. (2012) |
| Bacteria_ BacillotaA _Clostridia_Thermoanaerobacterales_Candidate Division OD1 | The Cedars (deep subsurface); Voltri | 16S rRNA, MAGs, 13C labelling | Suzuki et al. (2013, 2017), Brazelton et al. (2017) | |
| Bacteria_ BacillotaA _Clostridia_Lachnospirales_Vallitaleaceae_Vallitalea_V. pronyensis | Prony Bay | Cultivation | Ben Aissa et al. (2014), Mei et al. (2014) | |
| Bacteria_ BacillotaA _Clostridia_Peptostreptococcales_Natronincolaceae_Alkaliphilus_A. hydrothermalis | Prony Bay | Cultivation | Ben Aissa et al. (2015) | |
| Bacteria_ BacillotaA _Clostridia_Peptostreptococcales_Natronincolaceae_Alkaliphilus_A. serpentinus | Prony Bay | Cultivation | Postec et al. (2021) | |
| Bacteria_ BacillotaA _Clostridia_Peptostreptococcales_Natronincolaceae_Alkaliphilus_A. pronyensis | Prony Bay | Cultivation | Postec et al. (2021) | |
| Bacteria_ BacillotaA _Clostridia_Peptostreptococcales_Natronincolaceae_Serpentinicella_S. alkaliphila | Prony Bay | Cultivation | Mei et al. (2016) | |
| Bacteria_ BacillotaA _Clostridia_Peptostreptococcales_Peptostreptococcaceae_Acetoanaerobium_A. pronyense | Prony Bay | Cultivation | Bes et al. (2015) | |
| Bacteria_Bacteroidetes_Bacteroidia_Bacteroidales_ML635J-40 | Voltri | 16S rRNA, MAGs, 13C labelling | Brazelton et al. (2017) | |
| Bacteria_BacillotaA_Clostridia_Peptostreptococcales_Peptostreptococcaceae | Ney Springs | MAGs, 16S rRNA | Trutschel et al. (2022) | |
| Bacteria_BacillotaA_Clostridia_Peptostreptococcales_Tindalliaceae_Tindallia | Ney Springs | MAGs, 16S rRNA | Trutschel et al. (2022) | |
| Bacteria_BacillotaB_Desulfotomaculia_Desulfotomaculales_ Desulfotomaculaceae_Desulfotomaculum | The Tablelands, Lost City | MAGs | Brazelton et al. (2012) | |
| Bacteria_Bacilli_Bacillota_Erysipelotrichales_Erysipelotrichaceae | The Tablelands | MAGs | Brazelton et al. (2012) | |
| Iron reduction | Bacteria_ BacillotaA _Clostridia_Peptostreptococcales_Natronincolaceae_Alkaliphilus | Troodos | Cultivation | Rizoulis et al. (2016) |
| Bacteria_Bacillota_Bacilli_Paenibacillales_Paenibacillaceae_Paenibacillus | The Cedars | Cultivation | Rowe et al. (2017) | |
| Photosynthesis | Bacteria_Cyanobacteria_Cyanobacteriia_Leptolyngbyales_Leptolyngbyaceae_Leptolyngbya | Voltri (surface); Del Puerto | 16S rRNA | Kamran et al. (2020), Blank et al. (2009) |
| Bacteria_Cyanobacteria_Cyanobacteriia_Synechococcales_Synechococcaceae_Synechococcus | Prony Bay | 16S rRNA | Mei et al. (2016) |
Taxa appearing in several metabolic groups on the same taxonomic level are assigned with superscript numbers. The taxonomy is based on the Genome Taxonomy Database (GTDB Release 214).