Environmental Science and Pollution Research

, Volume 22, Issue 18, pp 13613–13624 | Cite as

Endolithic microbial communities in carbonate precipitates from serpentinite-hosted hyperalkaline springs of the Voltri Massif (Ligurian Alps, Northern Italy)

  • Marianne QuéméneurEmail author
  • Alexandra Palvadeau
  • Anne Postec
  • Christophe Monnin
  • Valérie Chavagnac
  • Bernard Ollivier
  • Gaël Erauso
Microbial Ecology of the Continental and Coastal Environments


The Voltri Massif is an ophiolitic complex located in the Ligurian Alps close to the city of Genova (Northern Italy) where several springs discharge high pH (up to 11.7), low salinity waters produced by the active serpentinization of the ultramafic basement. Mixing of these hyperalkaline waters with the river waters along with the uptake of atmospheric carbon dioxide forms brownish carbonate precipitates covering the bedrock at the springs. Diverse archaeal and bacterial communities were detected in these carbonate precipitates using 454 pyrosequencing analyses of 16S ribosomal RNA (rRNA) genes. Archaeal communities were dominated by members of potential methane-producing and/or methane-oxidizing Methanobacteriales and Methanosarcinales (Euryarchaeota) together with ammonia-oxidizing Nitrososphaerales (Thaumarchaeota) similar to those found in other serpentinization-driven submarine and terrestrial ecosystems. Bacterial communities consisted of members of the Proteobacteria, Actinobacteria, Planctomycetes, Bacteroidetes, Chloroflexi, and Verrucomicrobia phyla, altogether accounting for 92.2 % of total retrieved bacterial 16S rRNA gene sequences. Amongst Bacteria, potential chemolithotrophy was mainly associated with Alpha- and Betaproteobacteria classes, including nitrogen-fixing, methane-oxidizing or hydrogen-oxidizing representatives of the genera Azospirillum, Methylosinus, and Hydrogenophaga/Serpentinomonas’, respectively. Besides, potential chemoorganotrophy was attributed mainly to representatives of Actinobacteria and Planctomycetales phyla. The reported 16S rRNA gene data strongly suggested that hydrogen, methane, and nitrogen-based chemolithotrophy can sustain growth of the microbial communities inhabiting the carbonate precipitates in the hyperalkaline springs of the Voltri Massif, similarly to what was previously observed in other serpentinite-hosted ecosystems.


Microbial diversity Serpentinization Carbonates Liguria Alkaliphilic Extreme environment Pyrosequencing 



This project was financially supported by the French national programs EC2CO-Biohefect/Ecodyn/Dril/MicrobiEn (MicroProny), the French Institute of Research for Development (IRD) and CESSUR of the Institut des Sciences de la Terre et de l'Univers (CNRS-INSU).

Supplementary material

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Table S1 (DOC 53 kb)
11356_2015_4113_MOESM2_ESM.doc (72 kb)
Table S2 (DOC 72 kb)
11356_2015_4113_MOESM3_ESM.doc (68 kb)
Table S3 (DOC 68 kb)


  1. Albuquerque L, Simões C, Nobre MF, Pino NM, Battista JR, Silva MT, Rainey FA, da Costa MS (2005) Truepera radiovictrix gen. nov., sp. nov., a new radiation resistant species and the proposal of Trueperaceae fam. nov. FEMS Microbiol Lett 247(2):161–169Google Scholar
  2. Blank JG, Green SJ, Blake D, Valley JW, Kita NT, Treiman A, Dobson PF (2009) An alkaline spring system within the Del Puerto Ophiolite (California, USA): a Mars analog site. Planet Space Sci 57(5):533–540CrossRefGoogle Scholar
  3. Boschetti T, Etiope G, Toscani L (2013) Abiotic methane in the hyperalkaline springs of Genova, Italy. Proc Earth Planet Sci 7:248–251CrossRefGoogle Scholar
  4. Boulart C, Chavagnac V, Monnin C, Delacour A, Ceuleneer G, Hoareau G (2013) Differences in gas venting from ultramafic-hosted warm springs: the example of Oman and Voltri ophiolites. Ofioliti 38(2):142–156Google Scholar
  5. Brazelton WJ, Schrenk MO, Kelley DS, Baross JA (2006) Methane-and sulfur-metabolizing microbial communities dominate the Lost City hydrothermal field ecosystem. Appl Environ Microbiol 72(9):6257–6270CrossRefGoogle Scholar
  6. Brazelton WJ, Mehta MP, Kelley DS, Baross JA (2011) Physiological differentiation within a single-species biofilm fueled by serpentinization. MBio 2(4)Google Scholar
  7. Brazelton WJ, Morrill PL, Szponar N, Schrenk MO (2013) Bacterial communities associated with subsurface geochemical processes in continental serpentinite springs. Appl Environ Microbiol 79(13):3906–3916CrossRefGoogle Scholar
  8. Caporaso JG, Kuczynski J, Stombaugh J et al (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7(5):335–336CrossRefGoogle Scholar
  9. Chao A (1984) Nonparametric estimation of the number of classes in a population. Scand J Stat 11:265–270Google Scholar
  10. Chavagnac V, Ceuleneer G, Monnin C, Lansac B, Hoareau G, Boulart C (2013a) Mineralogical assemblages forming at hyperalkaline warm springs hosted on ultramafic rocks: a case study of Oman and Ligurian ophiolites. Geochem Geophys Geosyst 14(7):2474–2495CrossRefGoogle Scholar
  11. Chavagnac V, Monnin C, Ceuleneer G, Boulart C, Hoareau G (2013b) Characterization of hyperalkaline fluids produced by low-temperature serpentinization of mantle peridotites in the Oman and Ligurian ophiolites. Geochem Geophys Geosyst 14(7):2496–2522CrossRefGoogle Scholar
  12. Chistoserdova L, Jenkins C, Kalyuzhnaya MG et al (2004) The enigmatic planctomycetes may hold a key to the origins of methanogenesis and methylotrophy. Mol Biol Evol 21(7):1234–1241CrossRefGoogle Scholar
  13. Cipolli F, Gambardella B, Marini L, Ottonello G, Vetuschi Zuccolini M (2004) Geochemistry of high-pH waters from serpentinites of the Gruppo di Voltri (Genova, Italy) and reaction path modeling of CO2 sequestration in serpentinite aquifers. Appl Geochem 19(5):787–802CrossRefGoogle Scholar
  14. Couradeau E, Benzerara K, Moreira D, Gerard E, Kaźmierczak J, Tavera R, López-García P (2011) Prokaryotic and eukaryotic community structure in field and cultured microbialites from the alkaline Lake Alchichica (Mexico). PLoS One 6(12):e28767CrossRefGoogle Scholar
  15. Curtis AC, Wheat CG, Fryer P, Moyer CL (2013) Mariana Forearc serpentinite mud volcanoes harbor novel communities of extremophilic archaea. Geomicrobiol J 30(5):430–441CrossRefGoogle Scholar
  16. Daae FL, Økland I, Dahle H, Jørgensen SL, Thorseth IH, Pedersen RB (2013) Microbial life associated with low temperature alteration of ultramafic rocks in the Leka ophiolite complex. Geobiology 11(4):318–339CrossRefGoogle Scholar
  17. de Menezes AB, McDonald JE, Allison HE, McCarthy AJ (2012) Importance of Micromonospora spp. as colonizers of cellulose in freshwater lakes as demonstrated by quantitative reverse transcriptase PCR of 16S rRNA. Appl Environ Microbiol 78(9):3495–3499CrossRefGoogle Scholar
  18. Dowd SE, Callaway TR, Wolcott RD, Sun Y, McKeehan T, Hagevoort RG, Edrington TS (2008) Evaluation of the bacterial diversity in the feces of cattle using 16S rDNA bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP). BMC Microbiol 8(1):125CrossRefGoogle Scholar
  19. Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32(5):1792–1797CrossRefGoogle Scholar
  20. Edgar RC (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26(19):2460–2461CrossRefGoogle Scholar
  21. Felsenstein J (1985) Confidence-limits on phylogenies: an approach using the bootstrap. Evolution 39(4):783–791CrossRefGoogle Scholar
  22. Good IJ (1953) The population frequencies of species and the estimation of population parameters. Biometrika 40(3–4):237–264CrossRefGoogle Scholar
  23. Kelley DS, Karson JA, Früh-Green GL et al (2005) A serpentinite-hosted ecosystem: the Lost City hydrothermal field. Science 307(5714):1428–1434CrossRefGoogle Scholar
  24. Mei N, Zergane N, Postec A, Erauso G, Ollier A, Payri C, Pelletier B, Fardeau ML, Ollivier B, Quéméneur M (2014) Fermentative hydrogen production by a new alkaliphilic Clostridium sp. (strain PROH2) isolated from a shallow submarine hydrothermal chimney in Prony Bay, New Caledonia. Int J Hydrogen Energy 39:19465–19473CrossRefGoogle Scholar
  25. Monnin C, Chavagnac V, Boulart C, Payri C, Ménez B, Gérard M, Gérard E, Quéméneur M, Erauso G, Postec A, Dombrowski L, Pelletier B (2014) Fluid chemistry of the low temperature hyperalkaline hydrothermal system of the Prony Bay (New Caledonia). Biogeosciences 11:5687–5706CrossRefGoogle Scholar
  26. Proskurowski G, Lilley MD, Seewald JS, Früh-Green GL, Olson EJ, Lupton JE, Sylva SP, Kelley DS (2008) Abiogenic hydrocarbon production at Lost City hydrothermal field. Science 319(5863):604–607CrossRefGoogle Scholar
  27. Quéméneur M, Bes M, Postec A, Mei N, Hamelin J, Monnin C, Chavagnac V, Payri C, Pelletier B, Guentas-Dombrowsky L, Gérard M, Pisapia C, Gérard E, Ménez B, Ollivier B, Erauso G (2014) Spatial distribution of microbial communities in the shallow submarine alkaline hydrothermal field of the Prony Bay, New Caledonia. Environ Microbiol Rep 6(6):665–674CrossRefGoogle Scholar
  28. Russell MJ, Hall AJ, Martin W (2010) Serpentinization as a source of energy at the origin of life. Geobiology 8(5):355–371CrossRefGoogle Scholar
  29. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425Google Scholar
  30. Shannon CE, Weaver W (1949) The mathematical theory of communication. Urbana, IL: University of Illinois Press.Google Scholar
  31. Simpson EH (1949) Measurement of diversity, Nature, 163, 688.Google Scholar
  32. Schrenk MO, Brazelton WJ, Lang SQ (2013) Serpentinization, carbon, and deep life. Rev Mineral Geochem 75:575–606CrossRefGoogle Scholar
  33. Schulte M, Blake D, Hoehler T, McCollom T (2006) Serpentinization and its implications for life on the early Earth and Mars. Astrobiology 6(2):364–376CrossRefGoogle Scholar
  34. Schwarzenbach EM, Lang SQ, Früh-Green GL, Lilley MD, Bernasconi SM, Méhay S (2013) Sources and cycling of carbon in continental, serpentinite-hosted alkaline springs in the Voltri Massif, Italy. Lithos 177:226–244CrossRefGoogle Scholar
  35. Sleep NH, Meibom A, Fridriksson T, Coleman RG, Bird DK (2004) H2-rich fluids from serpentinization: geochemical and biotic implications. Proc Natl Acad Sci 101(35):12818–12823CrossRefGoogle Scholar
  36. Spang A, Poehlein A, Offre P et al (2012) The genome of the ammonia-oxidizing Candidatus Nitrososphaera gargensis: insights into metabolic versatility and environmental adaptations. Environ Microbiol 14(12):3122–3145CrossRefGoogle Scholar
  37. Suzuki S, Ishii S, Wu A, Cheung A, Tenney A, Wanger G, Kuenen JG, Nealson KH (2013) Microbial diversity in The Cedars, an ultrabasic, ultrareducing, and low salinity serpentinizing ecosystem. Proc Natl Acad Sci 110(38):15336–15341CrossRefGoogle Scholar
  38. Suzuki S, Kuenen JG, Schipper K et al (2014) Physiological and genomic features of highly alkaliphilic hydrogen-utilizing Betaproteobacteria from a continental serpentinizing site. Nat Commun 5Google Scholar
  39. Tamura K, Nei M, Kumar S (2004) Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc Natl Acad Sci 101:11030–11035CrossRefGoogle Scholar
  40. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30(12):2725–2729CrossRefGoogle Scholar
  41. Tiago I, Verissimo A (2013) Microbial and functional diversity of a subterrestrial high pH groundwater associated to serpentinization. Environ Microbiol 15(6):1687–1706CrossRefGoogle Scholar
  42. Tiago I, Chung AP, Verissimo A (2004) Bacterial diversity in a nonsaline alkaline environment: heterotrophic aerobic populations. Appl Environ Microbiol 70(12):7378–7387CrossRefGoogle Scholar
  43. Tiago I, Morais PV, da Costa MS, Veríssimo A (2006) Microcella alkaliphila sp. nov, a novel member of the family Microbacteriaceae isolated from a non-saline alkaline groundwater, and emended description of the genus Microcella. Int J Syst Evol Microbiol 56(10):2313–2316CrossRefGoogle Scholar
  44. Wang Q, Garrity GM, Tiedje JM, Cole JR (2007) Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. App Environ Microbiol 73(16):5261–5267.Google Scholar
  45. Willems A, Busse J, Goor M et al (1989) Hydrogenophaga, a new genus of hydrogen-oxidizing bacteria that includes Hydrogenophaga flava comb. nov. (formerly Pseudomonas flava), Hydrogenophaga palleronii (formerly Pseudomonas palleronii), Hydrogenophaga pseudoflava (formerly Pseudomonas pseudoflava and "Pseudomonas carboxydoflava"), and Hydrogenophaga taeniospiralis (formerly Pseudomonas taeniospiralis). Int J Syst Bacteriol 39(3):319–333CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2015

Authors and Affiliations

  • Marianne Quéméneur
    • 1
    Email author
  • Alexandra Palvadeau
    • 1
  • Anne Postec
    • 1
  • Christophe Monnin
    • 2
  • Valérie Chavagnac
    • 2
  • Bernard Ollivier
    • 1
  • Gaël Erauso
    • 1
  1. 1.Aix-Marseille Université, CNRS/INSUUniversité de Toulon, IRD, Mediterranean Institute of Oceanography (MIO)MarseilleFrance
  2. 2.GET (Géosciences Environnement Toulouse) UMR5563, Observatoire Midi-Pyrénées, Université de Toulouse, CNRS, IRDToulouseFrance

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