1887

Abstract

Bacteria from the genus are a major component of microbial assemblages at Hanford Site (a largely decommissioned nuclear production complex) in eastern Washington state, USA, and have been shown to change significantly in abundance in response to the subsurface intrusion of Columbia River water. Here we employed single-cell genomics techniques to shed light on the physiological niche of these micro-organisms. Analysis of four single amplified genomes (SAGs) from Hanford Site sediments revealed a chemoheterotrophic lifestyle, with the potential to exist under both aerobic and microaerophilic conditions via expression of both -type and -type cytochrome oxidases. These SAGs encoded a wide range of both intra- and extracellular carbohydrate-active enzymes, potentially enabling the degradation of recalcitrant substrates such as xylan and chitin, and the utilization of more labile sugars such as mannose and fucose. Coupled to these enzymes, a diversity of transporters and sugar-binding molecules were involved in the uptake of carbon from the extracellular local environment. The SAGs were enriched in TonB-dependent receptors, which play a key role in uptake of substrates resulting from degradation of recalcitrant carbon. Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-Cas mechanisms for resisting viral infections were identified in all SAGs. These data demonstrate the potential mechanisms utilized for persistence by heterotrophic micro-organisms in a carbon-limited aquifer, and hint at potential linkages between observed abundance shifts within the 300 Area (in the south-eastern corner of the site) subsurface and biogeochemical shifts associated with Columbia River water intrusion.

Funding
This study was supported by the:
  • US Department of Energy (DOE)
  • Office of Biological and Environmental Research (BER)
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2014-02-01
2021-07-29
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References

  1. An D.-S., Kim S.-G., Ten L. N., Cho C.-H. ( 2009). Pedobacter daechungensis sp. nov., from freshwater lake sediment in South Korea. Int J Syst Evol Microbiol 59:69–72 [View Article][PubMed]
    [Google Scholar]
  2. Anderson R. T., Vrionis H. A., Ortiz-Bernad I., Resch C. T., Long P. E., Dayvault R., Karp K., Marutzky S., Metzler D. R. & other authors ( 2003). Stimulating the in situ activity of Geobacter species to remove uranium from the groundwater of a uranium-contaminated aquifer. Appl Environ Microbiol 69:5884–5891 [View Article][PubMed]
    [Google Scholar]
  3. Ayuso S. V., Lopez-Archilla A. I., Montes C., Guerrero M. C. ( 2010). Microbial activities in a coastal, sandy aquifer system (Donana Natural Protected Area, SW Spain). Geomicrobiol J 27:409–423 [View Article]
    [Google Scholar]
  4. Aziz R. K., Bartels D., Best A. A., DeJongh M., Disz T., Edwards R. A., Formsma K., Gerdes S., Glass E. M. & other authors ( 2008). The rast Server: rapid annotations using subsystems technology. BMC Genomics 9:75 [View Article][PubMed]
    [Google Scholar]
  5. Bankevich A., Nurk S., Antipov D., Gurevich A. A., Dvorkin M., Kulikov A. S., Lesin V. M., Nikolenko S. I., Pham S. & other authors ( 2012). SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477 [View Article][PubMed]
    [Google Scholar]
  6. Bjornstad B., Horner J., Vermeul V., Lanigan D., Thorne P. ( 2009). Borehole completion and conceptual hydrogeologic model for the IFRC Well Field, 300 Area, Hanford Site. Richland, WA: Pacific Northwest National Laboratory; [View Article]
    [Google Scholar]
  7. Blanvillain S., Meyer D., Boulanger A., Lautier M., Guynet C., Denancé N., Vasse J., Lauber E., Arlat M. ( 2007). Plant carbohydrate scavenging through tonB-dependent receptors: a feature shared by phytopathogenic and aquatic bacteria. PLoS ONE 2:e224 [View Article][PubMed]
    [Google Scholar]
  8. Bordoli L., Kiefer F., Arnold K., Benkert P., Battey J., Schwede T. ( 2009). Protein structure homology modeling using swiss-model workspace. Nat Protoc 4:1–13 [View Article][PubMed]
    [Google Scholar]
  9. Buschmann S., Warkentin E., Xie H., Langer J. D., Ermler U., Michel H. ( 2010). The structure of cbb3 cytochrome oxidase provides insights into proton pumping. Science 329:327–330 [View Article][PubMed]
    [Google Scholar]
  10. Casamayor E. O., Schäfer H., Bañeras L., Pedrós-Alió C., Muyzer G. ( 2000). Identification of and spatio-temporal differences between microbial assemblages from two neighboring sulfurous lakes: comparison by microscopy and denaturing gradient gel electrophoresis. Appl Environ Microbiol 66:499–508 [View Article][PubMed]
    [Google Scholar]
  11. Chimento D. P., Kadner R. J., Wiener M. C. ( 2005). Comparative structural analysis of TonB-dependent outer membrane transporters: implications for the transport cycle. Proteins 59:240–251 [View Article][PubMed]
    [Google Scholar]
  12. Curtis D. S., Phillips A. R., Callister S. J., Conlan S., McCue L. A. ( 2013). spocs: software for predicting and visualizing orthology/paralogy relationships among genomes. Bioinformatics 29:2641–2642 [View Article][PubMed]
    [Google Scholar]
  13. Dean F. B., Hosono S., Fang L. H., Wu X. H., Faruqi A. F., Bray-Ward P., Sun Z. Y., Zong Q. L., Du Y. F. & other authors ( 2002). Comprehensive human genome amplification using multiple displacement amplification. Proc Natl Acad Sci U S A 99:5261–5266 [View Article][PubMed]
    [Google Scholar]
  14. Di Rienzi S. C., Sharon I., Wrighton K. C., Koren O., Hug L. A., Thomas B. C., Goodrich J. K., Bell J. T., Spector T. D. & other authors ( 2013). The human gut and subsurface harbor non-photosynthetic Cyanobacteria. eLife 2:e01102 [View Article][PubMed]
    [Google Scholar]
  15. Ducluzeau A.-L., Ouchane S., Nitschke W. ( 2008). The cbb3 oxidases are an ancient innovation of the domain bacteria. Mol Biol Evol 25:1158–1166 [View Article][PubMed]
    [Google Scholar]
  16. Freilich S., Kreimer A., Meilijson I., Gophna U., Sharan R., Ruppin E. ( 2010). The large-scale organization of the bacterial network of ecological co-occurrence interactions. Nucleic Acids Res 38:3857–3868 [View Article][PubMed]
    [Google Scholar]
  17. Fu H. A., Iuchi S., Lin E. C. C. ( 1991). The requirement of ArcA and Fnr for peak expression of the cyd operon in Escherichia coli under microaerobic conditions. Mol Gen Genet 226:209–213 [View Article][PubMed]
    [Google Scholar]
  18. Ginige M. P., Kaksonen A. H., Morris C., Shackelton M., Patterson B. M. ( 2013). Bacterial community and groundwater quality changes in an anaerobic aquifer during groundwater recharge with aerobic recycled water. FEMS Microbiol Ecol 85:553–567 [View Article][PubMed]
    [Google Scholar]
  19. Gordon N. S., Valenzuela A., Adams S. M., Ramsey P. W., Pollock J. L., Holben W. E., Gannon J. E. ( 2009). Pedobacter nyackensis sp. nov., Pedobacter alluvionis sp. nov. and Pedobacter borealis sp. nov., isolated from Montana flood-plain sediment and forest soil. Int J Syst Evol Microbiol 59:1720–1726 [View Article][PubMed]
    [Google Scholar]
  20. Grissa I., Vergnaud G., Pourcel C. ( 2007). CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res 35:Web Server issueW52–W57[PubMed] [CrossRef]
    [Google Scholar]
  21. Hemme C. L., Deng Y., Gentry T. J., Fields M. W., Wu L., Barua S., Barry K., Tringe S. G., Watson D. B. & other authors ( 2010). Metagenomic insights into evolution of a heavy metal-contaminated groundwater microbial community. ISME J 4:660–672 [View Article][PubMed]
    [Google Scholar]
  22. Hoang V.-A., Kim Y.-J., Nguyen N. L., Min J.-W., Yang D.-C. ( 2013). Pedobacter ginsengiterrae sp. nov., isolated from soil of a ginseng field. Int J Syst Evol Microbiol 63:1273–1279 [View Article][PubMed]
    [Google Scholar]
  23. Islam F. S., Gault A. G., Boothman C., Polya D. A., Charnock J. M., Chatterjee D., Lloyd J. R. ( 2004). Role of metal-reducing bacteria in arsenic release from Bengal delta sediments. Nature 430:68–71 [View Article][PubMed]
    [Google Scholar]
  24. Jeon Y., Kim J. M., Park J. H., Lee S. H., Seong C.-N., Lee S.-S., Jeon C. O. ( 2009). Pedobacter oryzae sp. nov., isolated from rice paddy soil. Int J Syst Evol Microbiol 59:2491–2495 [View Article][PubMed]
    [Google Scholar]
  25. Jung Y.-T., Lee S.-Y., Choi W.-C., Oh T.-K., Yoon J.-H. ( 2012). Pedobacter boryungensis sp. nov., isolated from soil. Int J Syst Evol Microbiol 62:13–17 [View Article][PubMed]
    [Google Scholar]
  26. Kolker E., Picone A. F., Galperin M. Y., Romine M. F., Higdon R., Makarova K. S., Kolker N., Anderson G. A., Qiu X. & other authors ( 2005). Global profiling of Shewanella oneidensis MR-1: expression of hypothetical genes and improved functional annotations. Proc Natl Acad Sci U S A 102:2099–2104 [View Article][PubMed]
    [Google Scholar]
  27. Kwon S.-W., Son J.-A., Kim S.-J., Kim Y.-S., Park I.-C., Bok J.-I., Weon H.-Y. ( 2011). Pedobacter rhizosphaerae sp. nov. and Pedobacter soli sp. nov., isolated from rhizosphere soil of Chinese cabbage (Brassica campestris). Int J Syst Evol Microbiol 61:2874–2879 [View Article][PubMed]
    [Google Scholar]
  28. Lane D. J. ( 1991). 16S/23S rRNA sequencing. Nucleic Acid Techniques in Bacterial Systematics115–175 Stackebrandt E., Goodfellow M. Chichester: Wiley;
    [Google Scholar]
  29. Lin X., Kennedy D., Peacock A., McKinley J., Resch C. T., Fredrickson J., Konopka A. ( 2012a). Distribution of microbial biomass and potential for anaerobic respiration in Hanford Site 300 Area subsurface sediment. Appl Environ Microbiol 78:759–767 [View Article][PubMed]
    [Google Scholar]
  30. Lin X., McKinley J., Resch C. T., Kaluzny R., Lauber C. L., Fredrickson J., Knight R., Konopka A. ( 2012b). Spatial and temporal dynamics of the microbial community in the Hanford unconfined aquifer. ISME J 6:1665–1676 [View Article][PubMed]
    [Google Scholar]
  31. Luo X., Wang Z., Dai J., Zhang L., Li J., Tang Y., Wang Y., Fang C. ( 2010). Pedobacter glucosidilyticus sp. nov., isolated from dry riverbed soil. Int J Syst Evol Microbiol 60:229–233 [View Article][PubMed]
    [Google Scholar]
  32. Makarova K. S., Haft D. H., Barrangou R., Brouns S. J. J., Charpentier E., Horvath P., Moineau S., Mojica F. J. M., Wolf Y. I. & other authors ( 2011). Evolution and classification of the CRISPR-Cas systems. Nat Rev Microbiol 9:467–477 [View Article][PubMed]
    [Google Scholar]
  33. Margesin R., Zhang D.-C. ( 2013). Pedobacter ruber sp. nov., a psychrophilic bacterium isolated from soil. Int J Syst Evol Microbiol 63:339–344 [View Article][PubMed]
    [Google Scholar]
  34. Margesin R., Spröer C., Schumann P., Schinner F. ( 2003). Pedobacter cryoconitis sp. nov., a facultative psychrophile from alpine glacier cryoconite. Int J Syst Evol Microbiol 53:1291–1296 [View Article][PubMed]
    [Google Scholar]
  35. Maymó-Gatell X., Chien Y., Gossett J. M., Zinder S. H. ( 1997). Isolation of a bacterium that reductively dechlorinates tetrachloroethene to ethene. Science 276:1568–1571 [View Article][PubMed]
    [Google Scholar]
  36. Morris R. L., Schmidt T. M. ( 2013). Shallow breathing: bacterial life at low O2. . Nat Rev Microbiol 11:205–212 [View Article][PubMed]
    [Google Scholar]
  37. Muurholm S., Cousin S., Päuker O., Brambilla E., Stackebrandt E. ( 2007). Pedobacter duraquae sp. nov., Pedobacter westerhofensis sp. nov., Pedobacter metabolipauper sp. nov., Pedobacter hartonius sp. nov. and Pedobacter steynii sp. nov., isolated from a hard-water rivulet. Int J Syst Evol Microbiol 57:2221–2227 [View Article][PubMed]
    [Google Scholar]
  38. Neugebauer H., Herrmann C., Kammer W., Schwarz G., Nordheim A., Braun V. ( 2005). ExbBD-dependent transport of maltodextrins through the novel MalA protein across the outer membrane of Caulobacter crescentus . J Bacteriol 187:8300–8311 [View Article][PubMed]
    [Google Scholar]
  39. Nguyen H. D., Cao B., Mishra B., Boyanov M. I., Kemner K. M., Fredrickson J. K., Beyenal H. ( 2012). Microscale geochemical gradients in Hanford 300 Area sediment biofilms and influence of uranium. Water Res 46:227–234 [View Article][PubMed]
    [Google Scholar]
  40. Oh H.-W., Kim B.-C., Park D.-S., Jeong W.-J., Kim H., Lee K. H., Kim S. U. ( 2013). Pedobacter luteus sp. nov., isolated from soil. Int J Syst Evol Microbiol 63:1304–1310 [View Article][PubMed]
    [Google Scholar]
  41. Patel R. K., Jain M. ( 2012). NGS QC Toolkit: a toolkit for quality control of next generation sequencing data. PLoS ONE 7:e30619 [View Article][PubMed]
    [Google Scholar]
  42. Pereira M. M., Refojo P. N., Hreggvidsson G. O., Hjorleifsdottir S., Teixeira M. ( 2007). The alternative complex III from Rhodothermus marinus – a prototype of a new family of quinol:electron acceptor oxidoreductases. FEBS Lett 581:4831–4835 [View Article][PubMed]
    [Google Scholar]
  43. Peretyazhko T. S., Zachara J. M., Kukkadapu R. K., Heald S. M., Kutnyakov I. V., Resch C. T., Arey B. W., Wang C. M., Kovarik L. & other authors ( 2012). Pertechnetate (TcO4 ) reduction by reactive ferrous iron forms in naturally anoxic, redox transition zone sediments from the Hanford Site, USA. Geochim Cosmochim Acta 92:48–66 [View Article]
    [Google Scholar]
  44. Pinhassi J., Zweifel U. L., Hagström A. ( 1997). Dominant marine bacterioplankton species found among colony-forming bacteria. Appl Environ Microbiol 63:3359–3366[PubMed]
    [Google Scholar]
  45. Postle K., Kadner R. J. ( 2003). Touch and go: tying TonB to transport. Mol Microbiol 49:869–882 [View Article][PubMed]
    [Google Scholar]
  46. Preisig O., Zufferey R., Thöny-Meyer L., Appleby C. A., Hennecke H. ( 1996). A high-affinity cbb3 -type cytochrome oxidase terminates the symbiosis-specific respiratory chain of Bradyrhizobium japonicum . J Bacteriol 178:1532–1538[PubMed]
    [Google Scholar]
  47. Punta M., Coggill P. C., Eberhardt R. Y., Mistry J., Tate J., Boursnell C., Pang N., Forslund K., Ceric G. & other authors ( 2012). The Pfam protein families database. Nucleic Acids Res 40:Database issueD290–D301 [View Article][PubMed]
    [Google Scholar]
  48. Puustinen A., Finel M., Haltia T., Gennis R. B., Wikström M. ( 1991). Properties of the two terminal oxidases of Escherichia coli . Biochemistry 30:3936–3942 [View Article][PubMed]
    [Google Scholar]
  49. Raes J., Korbel J. O., Lercher M. J., von Mering C., Bork P. ( 2007). Prediction of effective genome size in metagenomic samples. Genome Biol 8:R10 [View Article][PubMed]
    [Google Scholar]
  50. Raghunathan A., Ferguson H. R. Jr, Bornarth C. J., Song W. M., Driscoll M., Lasken R. S. ( 2005). Genomic DNA amplification from a single bacterium. Appl Environ Microbiol 71:3342–3347 [View Article][PubMed]
    [Google Scholar]
  51. Refojo P. N., Teixeira M., Pereira M. M. ( 2010). The alternative complex III of Rhodothermus marinus and its structural and functional association with caa3 oxygen reductase. Biochim Biophys Acta 1797:1477–1482 [View Article][PubMed]
    [Google Scholar]
  52. Rice C. W., Hempfling W. P. ( 1978). Oxygen-limited continuous culture and respiratory energy conservation in Escherichia coli . J Bacteriol 134:115–124[PubMed]
    [Google Scholar]
  53. Roh S. W., Quan Z.-X., Nam Y.-D., Chang H.-W., Kim K.-H., Kim M.-K., Im W.-T., Jin L., Kim S.-H. & other authors ( 2008). Pedobacter agri sp. nov., from soil. Int J Syst Evol Microbiol 58:1640–1643 [View Article][PubMed]
    [Google Scholar]
  54. Schwede T., Kopp J., Guex N., Peitsch M. C. ( 2003). swiss-model: an automated protein homology-modeling server. Nucleic Acids Res 31:3381–3385 [View Article][PubMed]
    [Google Scholar]
  55. Shulami S., Zaide G., Zolotnitsky G., Langut Y., Feld G., Sonenshein A. L., Shoham Y. ( 2007). A two-component system regulates the expression of an ABC transporter for xylo-oligosaccharides in Geobacillus stearothermophilus . Appl Environ Microbiol 73:874–884 [View Article][PubMed]
    [Google Scholar]
  56. Sieracki M., Poulton N., Crosbie N. ( 2005). Automated isolation techniques for microalgae. Chapter 7, 101-116. Algal Culturing Techniques Anderson R. New York: Elsevier Academic;
    [Google Scholar]
  57. Stepanauskas R. ( 2012). Single cell genomics: an individual look at microbes. Curr Opin Microbiol 15:613–620 [View Article][PubMed]
    [Google Scholar]
  58. Stepanauskas R., Sieracki M. E. ( 2007). Matching phylogeny and metabolism in the uncultured marine bacteria, one cell at a time. Proc Natl Acad Sci U S A 104:9052–9057 [View Article][PubMed]
    [Google Scholar]
  59. Steyn P. L., Segers P., Vancanneyt M., Sandra P., Kersters K., Joubert J. J. ( 1998). Classification of heparinolytic bacteria into a new genus, Pedobacter, comprising four species: Pedobacter heparinus comb. nov., Pedobacter piscium comb. nov., Pedobacter africanus sp. nov. and Pedobacter saltans sp. nov. Proposal of the family Sphingobacteriaceae fam. nov.. Int J Syst Bacteriol 48:165–177 [View Article][PubMed]
    [Google Scholar]
  60. Swan B. K., Martinez-Garcia M., Preston C. M., Sczyrba A., Woyke T., Lamy D., Reinthaler T., Poulton N. J., Masland E. D. P. & other authors ( 2011). Potential for chemolithoautotrophy among ubiquitous bacteria lineages in the dark ocean. Science 333:1296–1300 [View Article][PubMed]
    [Google Scholar]
  61. Um W., Zachara J. M., Liu C., Moore D. A., Rod K. A. ( 2010). Resupply mechanism to a contaminated aquifer: a laboratory study of U(VI) desorption from capillary fringe sediments. Geochim Cosmochim Acta 74:5155–5170 [View Article]
    [Google Scholar]
  62. Wilkins M. J., Wrighton K. C., Nicora C. D., Williams K. H., McCue L. A., Handley K. M., Miller C. S., Giloteaux L., Montgomery A. P. & other authors ( 2013). Fluctuations in species-level protein expression occur during element and nutrient cycling in the subsurface. PLoS ONE 8:e57819 [View Article][PubMed]
    [Google Scholar]
  63. Williams K. H., Long P. E., Davis J. A., Wilkins M. J., N’Guessan A. L., Steefel C. I., Yang L., Newcomer D. R., Spane F. A. & other authors ( 2011). Acetate availability and its influence on sustainable bioremediation of uranium-contaminated groundwater. Geomicrobiol J 28:519–539 [View Article]
    [Google Scholar]
  64. Woyke T., Xie G., Copeland A., González J. M., Han C., Kiss H., Saw J. H., Senin P., Yang C. & other authors ( 2009). Assembling the marine metagenome, one cell at a time. PLoS ONE 4:e5299 [View Article][PubMed]
    [Google Scholar]
  65. Woyke T., Sczyrba A., Lee J., Rinke C., Tighe D., Clingenpeel S., Malmstrom R., Stepanauskas R., Cheng J.-F. ( 2011). Decontamination of MDA reagents for single cell whole genome amplification. PLoS ONE 6:e26161 [View Article][PubMed]
    [Google Scholar]
  66. Wrighton K. C., Thomas B. C., Sharon I., Miller C. S., Castelle C. J., VerBerkmoes N. C., Wilkins M. J., Hettich R. L., Lipton M. S. & other authors ( 2012). Fermentation, hydrogen, and sulfur metabolism in multiple uncultivated bacterial phyla. Science 337:1661–1665 [View Article][PubMed]
    [Google Scholar]
  67. Yu N. Y., Wagner J. R., Laird M. R., Melli G., Rey S., Lo R., Dao P., Sahinalp S. C., Ester M. & other authors ( 2010). PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes. Bioinformatics 26:1608–1615 [View Article][PubMed]
    [Google Scholar]
  68. Zachara J. M., Long P. E., Bargar J., Davis J. A., Fox P., Fredrickson J. K., Freshley M. D., Konopka A. E., Liu C. & other authors ( 2013). Persistence of uranium groundwater plumes: contrasting mechanisms at two DOE sites in the groundwater–river interaction zone. J Contam Hydrol 147:45–72 [View Article][PubMed]
    [Google Scholar]
  69. Zhang K., Martiny A. C., Reppas N. B., Barry K. W., Malek J., Chisholm S. W., Church G. M. ( 2006). Sequencing genomes from single cells by polymerase cloning. Nat Biotechnol 24:680–686 [View Article][PubMed]
    [Google Scholar]
  70. Zhang D.-C., Schinner F., Margesin R. ( 2010). Pedobacter bauzanensis sp. nov., isolated from soil. Int J Syst Evol Microbiol 60:2592–2595 [View Article][PubMed]
    [Google Scholar]
  71. Zhou Y., Kellermann C., Griebler C. ( 2012a). Spatio-temporal patterns of microbial communities in a hydrologically dynamic pristine aquifer. FEMS Microbiol Ecol 81:230–242 [View Article][PubMed]
    [Google Scholar]
  72. Zhou Z., Jiang F., Wang S., Peng F., Dai J., Li W., Fang C. ( 2012b). Pedobacter arcticus sp. nov., a facultative psychrophile isolated from Arctic soil, and emended descriptions of the genus Pedobacter, Pedobacter heparinus, Pedobacter daechungensis, Pedobacter terricola, Pedobacter glucosidilyticus and Pedobacter lentus . Int J Syst Evol Microbiol 62:1963–1969 [View Article][PubMed]
    [Google Scholar]
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