Skip to main content

Bacterial and archaeal profiling of hypersaline microbial mats and endoevaporites, under natural conditions and methanogenic microcosm experiments

Abstract

Bacterial and archaeal community structure of five microbial communities, developing at different salinities in Baja California Sur, Mexico, were characterized by 16S rRNA sequencing. The response of the microbial community to artificial changes in salinity–sulfate concentrations and to addition of trimethylamine was also evaluated in microcosm experiments. Ordination analyses of the microbial community structure showed that microbial composition was distinctive for each hypersaline site. Members of bacteria were dominated by Bacteroidetes and Proteobacteria phyla, while Halobacteria of the Euryarchaeota phylum was the most represented class of archaea for all the environmental samples. At a higher phylogenetic resolution, methanogenic communities were dominated by members of the Methanosarcinales, Methanobacteriales and Methanococcales orders. Incubation experiments showed that putative hydrogenotrophic methanogens of the Methanomicrobiales increased in abundance only under lowest salinity and sulfate concentrations. Trimethylamine addition effectively increased the abundance of methylotrophic members from the Methanosarcinales, but also increased the relative abundance of the Thermoplasmata class, suggesting the potential capability of these microorganisms to use trimethylamine in hypersaline environments. These results contribute to the knowledge of microbial diversity in hypersaline environments from Baja California Sur, Mexico, and expand upon the available information for uncultured methanogenic archaea in these ecosystems.

This is a preview of subscription content, access via your institution.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6

References

  1. Adam PS, Borrel G, Brochier-Armanet C, Gribaldo S (2017) The growing tree of Archaea: New perspectives on their diversity, evolution and ecology. ISME J 11:2407–2425

    Article  PubMed  Google Scholar 

  2. Altschul SF, Gish W, Miller W et al (1990) Basic local alignment search tool. J Mol Biol 215:403–410

    CAS  Article  PubMed  Google Scholar 

  3. Antón J, Peña A, Santos F et al (2008) Distribution, abundance and diversity of the extremely halophilic bacterium Salinibacter ruber. Saline Syst 4:1–10

    Article  CAS  Google Scholar 

  4. Bengtsson-Palme J, Hartmann M, Eriksson KM et al (2015) METAXA2: improved identification and taxonomic classification of small and large subunit rRNA in metagenomic data. Mol Ecol Resour 15:1403–1414

    CAS  Article  PubMed  Google Scholar 

  5. Boone DR, Whitman WB, Koga Y (2001) Order III. Methanosarcinales ord. nov. In: Boone DR, Castenholz RW (eds) Bergey´s manual of systematic bacteriology, 2nd edn. Springer, Berlin, pp 268–289

    Chapter  Google Scholar 

  6. Borrel G, McCann A, Deane J et al (2017) Genomics and metagenomics of trimethylamine-utilizing Archaea in the human gut microbiome. ISME J 11:2059–2074

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  7. Castelle CJ, Wrighton KC, Thomas BC et al (2015) Genomic expansion of domain Archaea highlights roles for organisms from new phyla in anaerobic carbon cycling. Curr Biol 25:690–701

    CAS  Article  PubMed  Google Scholar 

  8. Clarke KR, Warwick RM (2001) Ordination of samples by multi-dimensional scaling (MDS). In: Clarke KR and Warwick RM (eds) Change in marine communities: An approach to the statistical analysis and interpretation, 2nd edn. Plymouth, UK, pp 45–57

  9. Des Marais DJ (1990) Microbial mats and the early evolution of life. Trends Ecol Evol 5:140–144

    CAS  Article  PubMed  Google Scholar 

  10. Edgar RC (2013) UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods 10:996–998

    CAS  Article  PubMed  Google Scholar 

  11. Engelbrektson A, Kunin V, Wrighton KC et al (2010) Experimental factors affecting PCR-based estimates of microbial species richness and evenness. ISME J 4:642–647

    CAS  Article  PubMed  Google Scholar 

  12. Evans PN, Parks DH, Chadwick GL et al (2015) Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics. Science 350:434–438

    CAS  Article  PubMed  Google Scholar 

  13. Fernández-Gómez B, Richter M, Schüler M et al (2013) Ecology of marine Bacteroidetes: a comparative genomics approach. ISME J 7:1026–1037

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. García-Maldonado JQ, Bebout BM, Celis LB, López-Cortés A (2012) Phylogenetic diversity of methyl-coenzyme M reductase (mcrA) gene and methanogenesis from trimethylamine in hypersaline environments. Int Microbiol 15:33–41

    PubMed  Google Scholar 

  15. García-Maldonado JQ, Bebout BM, Everroad RC, López-Cortés A (2015) Evidence of novel phylogenetic lineages of methanogenic Archaea from hypersaline microbial mats. Microb Ecol 69:106–117

    Article  CAS  PubMed  Google Scholar 

  16. Han R, Zhang X, Liu J, Long Q, Chen L, Lui D, Zhu D (2017) Microbial community structure and diversity within hypersaline Keke Salt Lake environments. Can J Microbiol 63:895–908

    CAS  Article  PubMed  Google Scholar 

  17. Harris JK, Caporaso JG, Walker JJ et al (2013) Phylogenetic stratigraphy in the Guerrero Negro hypersaline microbial mat. ISME J 7:50–60

    Article  CAS  PubMed  Google Scholar 

  18. Jahnke LL, Orphan VJ, Embaye T et al (2008) Lipid biomarker and phylogenetic analyses to reveal archaeal biodiversity and distribution in hypersaline microbial mat and underlying sediment. Geobiology 6:394–410

    CAS  Article  PubMed  Google Scholar 

  19. Kelley C, Poole J, Tazaz AM et al (2012) Substrate limitation for methanogenesis in hypersaline environments. Astrobiology 12:89–97

    CAS  Article  PubMed  Google Scholar 

  20. Kelley C, Nicholson BE, Beaudoin CS et al (2014) Trimethylamine and organic matter additions reverse substrate limitation effects on the δ13C values of methane produced in hypersaline microbial mats. Appl Environ Microbiol 80:7316–7323

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Kelley CA, Chanton JP, Bebout BM (2015) Rates and pathways of methanogenesis in hypersaline environments as determined by 13C-labeling. Biogeochemistry 126:329–341

    CAS  Article  Google Scholar 

  22. King GM (1988) Methanogenesis from methylated amines in a hypersaline algal mat. Appl Environ Microbiol 54:130–136

    CAS  PubMed  PubMed Central  Google Scholar 

  23. Knoll AH (1985) The distribution and evolution of microbial life in the late Proterozoic era. Ann Rev Microbiol 39:391–417

    CAS  Article  Google Scholar 

  24. Lazar CS, Parkes RJ, Cragg BA et al (2011) Methanogenic diversity and activity in hypersaline sediments of the centre of the Napoli mud volcano, Eastern Mediterranean Sea. Environ Microbiol 13:2078–2091

    CAS  Article  PubMed  Google Scholar 

  25. Ley RE, Harris JK, Wilcox J et al (2006) Unexpected diversity and complexity of the Guerrero Negro hypersaline microbial mat. Appl Environ Microbiol 72:3685–3695

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  26. Li W, Godzik A (2006) CD-HIT: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22:1658–1659

    CAS  Article  PubMed  Google Scholar 

  27. Ludwig W, Strunk O, Westram R et al (2004) ARB: a software environment for sequence data. Nucleic Acids Res 32:1363–1371

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  28. Lydvo S (2015) Investigation of the putative iron reducing capabilities of Lokiarchaeota. Dissertation, University of Bergen

  29. Mcgenity TJ (2010) Methanogens and methanogenesis in hypersaline environments. In: Timmis KN (ed) Handbook of hydrocarbon and lipid microbiology, 1st edn. Springer, Berlin, pp 665–680

    Chapter  Google Scholar 

  30. McMurdie PJ, Holmes S (2013) Phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS One 8:e61217

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  31. McMurdie PJ, Holmes S (2014) Waste not, want not: why rarefying microbiome data is inadmissible. PLoS Comput Biol 10:e1003531

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Najjari A, Elshahed MS, Cherif A, Youssef NH (2015) Patterns and determinants of halophilic Archaea (Class Halobacteria) diversity in tunisian endorheic salt lakes and sebkhet systems. Appl Environ Microbiol 81:4432–4441

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  33. Narasingarao P, Podell S, Ugalde JA et al (2012) De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities. ISME J 6:81–93

    CAS  Article  PubMed  Google Scholar 

  34. Ondov BD, Bergman NH, Phillippy AM (2011) Interactive metagenomic visualization in a Web browser. BMC Bioinform 12:385

    Article  Google Scholar 

  35. Oremland RS, Polcin S (1982) Methanogenesis and sulfate reduction: competitive and noncompetitive substrates in estuarine sediments. Appl Environ Microbiol 44:1270–1276

    CAS  PubMed  PubMed Central  Google Scholar 

  36. Oren A (2011) Thermodynamic limits to microbial life at high salt concentrations. Environ Microbiol 13:1908–1923

    CAS  Article  PubMed  Google Scholar 

  37. Oren A (2013) Salinibacter: an extremely halophilic bacterium with archaeal properties. FEMS Microbiol Lett 342:1–9

    CAS  Article  PubMed  Google Scholar 

  38. Orphan VJ, Jahnke LL, Embaye T et al (2008) Characterization and spatial distribution of methanogens and methanogenic biosignatures in hypersaline microbial mats of Baja California. Geobiology 6:376–393

    CAS  Article  PubMed  Google Scholar 

  39. Ortiz-Alvarez R, Casamayor EO (2016) High occurrence of Pacearchaeota and Woesearchaeota (Archaea superphylum DPANN) in the surface waters of oligotrophic high-altitude lakes. Environ Microbiol Rep 8:210–217

    CAS  Article  PubMed  Google Scholar 

  40. Paul K, Nonoh JO, Mikulski L, Brune A (2012) “Methanoplasmatales” Thermoplasmatales-related Archaea in termite guts and other environments, are the seventh order of methanogens. Appl Environ Microbiol 78:8245–8253

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  41. Podell S, Ugalde JA, Narasingarao P et al (2013) Assembly-driven community genomics of a hypersaline microbial ecosystem. PLoS One 8:e61692

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  42. Poulsen M, Schwab C, Borg Jensen B et al (2013) Methylotrophic methanogenic Thermoplasmata implicated in reduced methane emissions from bovine rumen. Nat Commun 4:1428

    Article  CAS  PubMed  Google Scholar 

  43. Pruesse E, Quast C, Knittel K et al (2007) SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 35:7188–7196

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  44. Reeburgh W (2007) Oceanic methane biogeochemistry. Chem Rev 107:486–513

    CAS  Article  PubMed  Google Scholar 

  45. Rinke C, Schwientek P, Sczyrba A et al (2013) Insights into the phylogeny and coding potential of microbial dark matter. Nature 499:431–437

    CAS  Article  PubMed  Google Scholar 

  46. Robertson CE, Spear JR, Harris JK, Pace NR (2009) Diversity and stratification of archaea in a hypersaline microbial mat. Appl Environ Microbiol 75:1801–1810

    CAS  Article  PubMed  Google Scholar 

  47. Rognes T, Flouri T, Nichols B, Quince C, Mahé F (2016) VSEARCH: a versatile open source tool for metagenomics. PeerJ 4:e2584. https://doi.org/10.7717/peerj.2584

    Article  PubMed  PubMed Central  Google Scholar 

  48. Sahl JW, Pace NR, Spear JR (2008) Comparative molecular analysis of endoevaporitic microbial communities. Appl Environ Microbiol 74:6444–6446

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  49. Smith JM, Green SJ, Kelley C et al (2008) Shifts in methanogen community structure and function associated with long-term manipulation of sulfate and salinity in a hypersaline microbial mat. Environ Microbiol 10:386–394

    CAS  Article  PubMed  Google Scholar 

  50. Sørensen KB, Canfield DE, Teske AP, Oren A (2005) Community composition of a hypersaline endoevaporitic microbial mat community composition of a hypersaline endoevaporitic microbial mat. Appl Environ Microbiol 71:7352–7365

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Sorokin DY, Makarova KS, Abbas B et al (2017) Discovery of extremely halophilic, methyl-reducing Euryarchaea provides insights into the evolutionary origin of methanogenesis. Nat Microbiol 2:1–11

    Article  CAS  Google Scholar 

  52. Sousa FL, Neukirchen S, Allen JF et al (2016) Lokiarchaeon is hydrogen dependent. Nat Microbiol 1:14–16

    Article  CAS  Google Scholar 

  53. Spang A, Ettema TJG (2017) Archaeal evolution: the methanogenic roots of Archaea. Nat Microbiol 2:1–2

    Article  CAS  Google Scholar 

  54. Spang A, Saw JH, Jørgensen SL et al (2015) Complex archaea that bridge the gap between prokaryotes and eukaryotes. Nature 521:173–179

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  55. Spear JR, Ley RE, Berger AB, Pace NR (2003) Complexity in natural microbial ecosystems: the Guerrero Negro experience. Biol Bull 204:168–173

    CAS  Article  PubMed  Google Scholar 

  56. Vanwonterghem I, Evans PN, Parks DH et al (2016) Methylotrophic methanogenesis discovered in the archaeal phylum Verstraetearchaeota. Nat Microbiol. https://doi.org/10.1038/nmicrobiol.2016.170

    Article  PubMed  Google Scholar 

  57. Ventosa A, de la Haba RR, Sánchez-Porro C, Papke RT (2015) Microbial diversity of hypersaline environments: a metagenomic approach. Curr Opin Microbiol 25:80–87

    CAS  Article  PubMed  Google Scholar 

  58. Vogt JC, Abed RMM, Albach DC, Palinska KA (2017) Bacterial and archaeal diversity in hypersaline cyanobacterial mats along a transect in the intertidal flats of the Sultanate of Oman. Microb Ecol 2:1–17

    Google Scholar 

  59. Whitman WB, Bowen TL, Boone DR (2006) The methanogenic bacteria. In: Dworkin M, Falkow S, Rosenberg E, Schleifer KH, Stackebrandt E (eds) The prokaryotes, 4th edn. Springer, Berlin, pp 165–207

    Chapter  Google Scholar 

  60. Wong HL, Ahmed-cox A, Burns BP (2016) Molecular ecology of hypersaline microbial mats: current insights and new directions. Microorganisms 6:2–15

    Google Scholar 

  61. Wong HL, Visscher PT, White RA III, Smith DL, Patterson MM, Burns BP (2017) Dynamics of archaea at fine spatial scales in Shark Bay mat microbiomes. Sci Rep 7:46160

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  62. Youssef NH, Rinke C, Stepanauskas R et al (2015) Insights into the metabolism, lifestyle and putative evolutionary history of the novel archaeal phylum “Diapherotrites”. ISME J 9:447–460

    CAS  Article  PubMed  Google Scholar 

  63. Zhuang G, Elling FJ, Nigro LM et al (2016) Multiple evidence for methylotrophic methanogenesis as the dominant methanogenic pathway in hypersaline sediments from the Orca Basin, Gulf of Mexico. Geochim Cosmochim Acta 187:1–20

    CAS  Article  Google Scholar 

Download references

Acknowledgements

This project was supported by CONACYT grant 105969-Z (2008–2014) to ALC and by grants to BMB by NASA’s Exobiology program. We are grateful with Exportadora de Sal, S.A. for access to the Guerrero Negro field site. We thank to Adrian Mungia for technical assistance in the library prep and 454 pyrosequencing. We thank ‘Unidad de Secuenciación Masiva y Bioinformática’ at the ‘Laboratorio Nacional de Apoyo Tecnológico a las Ciencias Genómicas’, CONACyT #260481, Instituto de Biotecnología/UNAM for computational resources used for the bioinformatics analyses. We are thankful to Santiago Cadena Rodríguez for lab assistance and for his contributions on the interpretations of the results. We are very appreciative of many helpful discussions with Cheryl Kelley and for the field assistance of Angela M. Detweiler.

Author information

Affiliations

Authors

Corresponding authors

Correspondence to José Q. García-Maldonado or Alejandro López-Cortés.

Additional information

Communicated by A. Oren.

Electronic supplementary material

Below is the link to the electronic supplementary material.

792_2018_1047_MOESM1_ESM.png

Supplementary Figure S1. Composition of the methanogenic archaeal community in relative abundance at genus level. The environmental samples from natural hypersaline microbial mats and endovaporitic communities from Laguna San Ignacio (LSI) and Exportadora de Sal S.A. de C.V. (ESSA) in Guerrero Negro, are intercalated with the samples from the microcosms experiments with a decreased salinity–sulfate concentrations (LOW suffix) or trimethylamine additions (TMA suffix). Notably, sample ESSA-A9-LOW was completely absent from methanogenic archaea. Sample LSI-S3-TMA was discarded because of low sequencing yield. (PNG 232 kb)

792_2018_1047_MOESM2_ESM.html

Supplementary Material S2. Interactive abundance charts showing the relative abundance of bacteria at the genus level. A different Krona chart is displayed separately for the environmental samples from natural hypersaline microbial mats and endovaporitic communities from Laguna San Ignacio (LSI) and Exportadora de Sal S.A. de C.V. (ESSA) in Guerrero Negro, and for the samples in microcosm experiments incubated 23 days in a low salinity (LOW suffix) or trimethylamine (TMA suffix). Sample LSI-S3-TMA was discarded because of low sequencing yield. (HTML 434 kb)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

García-Maldonado, J.Q., Escobar-Zepeda, A., Raggi, L. et al. Bacterial and archaeal profiling of hypersaline microbial mats and endoevaporites, under natural conditions and methanogenic microcosm experiments. Extremophiles 22, 903–916 (2018). https://doi.org/10.1007/s00792-018-1047-2

Download citation

Keywords

  • Hypersaline microbial mats
  • Microbial diversity
  • Methanogenesis
  • Microcosm incubations
  • 454 pyrosequencing