Zetaproteobacteria

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Zetaproteobacteria
Scientific classification
Domain: Bacteria
Phylum: Proteobacteria
Class: Zetaproteobacteria
Species
Mariprofundus ferrooxydans

The class Zetaproteobacteria is the sixth and most recently described class of the Proteobacteria.[1] Zetaproteobacteria can also refer to the group of organisms assigned to this class. The Zetaproteobacteria are represented by a single described species, Mariprofundus ferrooxydans,[2] which is an iron-oxidizing neutrophilic chemolithoautotroph originally isolated from Loihi Seamount in 1996 (post-eruption).[1][3] Molecular cloning techniques focusing on the small subunit ribosomal RNA gene have also been used to identify a more diverse majority of the Zetaproteobacteria that have as yet been unculturable.[4]

Regardless of culturing status, the Zetaproteobacteria show up worldwide in estuarine and marine habitats associated with opposing steep redox gradients of reduced (ferrous) iron and oxygen, either as a minor detectable component or as the dominant member of the microbial community.[5][6][7][8][9][10] Zetaproteobacteria have been most commonly found at deep-sea hydrothermal vents,[4] though recent discovery of members of this class in near-shore environments has led to the reevaluation of Zetaproteobacteria distribution and significance.[11]

Microbial mats encrusted with iron oxide on the flank of Loihi Seamount, Hawaii. Microbial communities in this type of habitat can harbor microbial communities dominated by the iron-oxidizing Zetaproteobacteria.

Significance[edit]

As potentially an entire class of marine iron oxidizers, the Zetaproteobacteria play a substantial role in biogeochemical cycling, both past and present. Ecologically, the Zetaproteobacteria play a major role in the engineering of their own environment through the use of the controlled deposition of mineralized iron oxides, also directly affecting the environment of other members of the microbial community.

Prevalence of the Zetaproteobacteria in near-shore metal (e.g. steel) coupon biocorrosion experiments highlights the impact of these marine iron oxidizers on expensive problems such as the rusting of ship hulls, metal pilings, and pipelines.[11][12]

Discovery[edit]

Mariprofundus ferrooxydans PV-1 twisted stalks TEM image. One example of Fe oxide morphotypes produced by the Zetaproteobacteria. Image by Clara Chan.

The Zetaproteobacteria were first discovered in 1991 by Craig Moyer, Fred Dobbs, and David Karl as a single rare clone in a mesophilic, or moderate temperature, hydrothermal vent field known as Pele's Vents at Loihi Seamount, Hawaii. This particular vent was dominated by sulfur-oxidizing Epsilonproteobacteria. With no close relatives known at the time, the clone was initially labeled as a Gammaproteobacteria.[13]

Subsequent isolation of two strains of M. ferrooxydans, PV-1 and JV-1,[3] along with the increasing realization that a phylogenetically distinct group of Proteobacteria (the Zetaproteobacteria) could be found globally as dominant members of bacterial communities led to the suggestion for the creation of this new class of the Proteobacteria.

Morphology[edit]

One of the most distinctive ways of identifying circumneutral iron oxidizing bacteria visually is by identifying the structure of the mineralized iron oxyhydroxide product created during iron oxidation.[3][14] Oxidized, or ferric iron is insoluble at circumneutral pH, thus the microbe must have a way of dealing with the mineralized "waste" product. It is thought that one method to accomplish this is to control the deposition of oxidized iron.[15][16] Some of the most common morphotypes include: amorphous particulate oxides, twisted or helical stalks (figure), sheaths, and y-shaped irregular filaments.

These morphologies exist both in freshwater and marine iron habitats, though common freshwater iron-oxidizing bacteria such as Gallionella sp. (twisted stalk) and Leptothrix ochracea (sheath) have only extremely rarely been found in the deep sea (not significant abundance). The only currently published morphotype that has been partially resolved is the twisted stalk, which is commonly formed by M. ferrooxydans. This bacteria is a gram negative kidney-bean-shaped cell that deposits iron oxides on the concave side of the cell, forming twisted stalks as it moves through its environment.[15][16]

Mariprofundus ferrooxydans PV-1 cell attached to twisted stalk TEM image. Image by Clara Chan.

Iron oxidation morphotypes can be preserved and have been detected in ancient hydrothermal deposits.[17]

Ecology[edit]

Phylogenetic tree showing the phylogenetic placement of the Zetaproteobacteria (orange branches) within the Proteobacteria. Asterisks highlight the Zetaproteobacteria cultured isolates.

Biodiversity[edit]

An operational taxonomic unit, or an OTU, allows a microbiologist to define a bacterial taxa using defined similarity bins based on a gene of interest. In microbial ecology, the small subunit ribosomal RNA gene is generally used at a cut off of 97% similarity to define an OTU. In the most basic sense, the OTU represents a bacterial species.

For the Zetaproteobacteria, 28 OTUs have been defined.[4] Of interest were the two globally distributed OTUs that dominated the phylogenetic tree, two OTUs that seemed to originate in the deep subsurface,[10] and several endemic OTUs, along with the relatively limited detection of the isolated Zetaproteobacteria representative.

Habitats[edit]

Ecological Niche[edit]

All of the habitats where Zetaproteobacteria have been found have (at least) one thing in common: they all provide an interface of steep redox gradients of oxygen and iron.[32]

Reduced hydrothermal fluids, for instance, exiting from vents in the deep-sea carry with them high concentrations of ferrous iron and other reduced chemical species, creating a gradient upward through a microbial mat of high to low ferrous iron. Similarly, oxygen from the overlying seawater diffuses into the microbial mat resulting in a downward gradient of high to low oxygen. Zetaproteobacteria are thought to live at the interface, where there is enough oxygen for use as an electron acceptor without there being too much oxygen for the organism to compete with the increased rate of chemical oxidation, and where there is enough ferrous iron for growth.[14][32]

Iron oxidation is not always energetically favorable. Reference[33] discusses favorable conditions for iron oxidation in habitats that otherwise may have been thought to be dominated by the more energy yielding metabolisms of hydrogen or sulfur oxidation.

Note: Iron is not the only reduced chemical species accociated with these redox gradient environments. It is likely that Zetaproteobacteria are not all iron oxidizers.

Metabolism[edit]

Iron oxidation pathways in both freshwater acidophilic and circumneutral iron oxidation habitats such as acid mine drainage or groundwater iron seeps, respectively, though not complete, are better understood than marine circumneutral iron oxidation.

The genome for the only described cultured representative of the Zetaproteobacteria was recently published, and while no definitive iron oxidation genes were identified, the gene neighborhood of a molybdopterin oxidoreductase protein was identified as a place to start looking at candidate iron oxidation pathway genes.[34] Though M. ferrooxydans was isolated as an autotroph, able to fix carbon dioxide, the genome of PV-1 revealed an ability to grow mixotrophically on fructose or mannose.

It is difficult at this point to speculate on the metabolism of the entire class with the limited sample size.

See also[edit]

References[edit]

  1. ^ a b c Emerson, D.; Rentz, J. A.; Lilburn, T. G.; Davis, R. E.; Aldrich, H.; Chan, C.; Moyer, C. L. (2007). "A Novel Lineage of Proteobacteria Involved in Formation of Marine Fe-Oxidizing Microbial Mat Communities". In Reysenbach, Anna-Louise. PLoS ONE 2 (8): e667. Bibcode:2007PLoSO...2..667E. doi:10.1371/journal.pone.0000667. PMC 1930151. PMID 17668050.  edit
  2. ^ mariprofundus entry in LPSN [Euzéby, J.P. (1997). "List of Bacterial Names with Standing in Nomenclature: a folder available on the Internet". Int J Syst Bacteriol 47 (2): 590–2. doi:10.1099/00207713-47-2-590. ISSN 0020-7713. PMID 9103655. ]
  3. ^ a b c Emerson, D.; Moyer, C. L. (2002). "Neutrophilic Fe-oxidizing bacteria are abundant at the Loihi Seamount hydrothermal vents and play a major role in Fe oxide deposition". Applied and environmental microbiology 68 (6): 3085–3093. doi:10.1128/AEM.68.6.3085-3093.2002. PMC 123976. PMID 12039770.  edit
  4. ^ a b c d McAllister, S. M.; Davis, R. E.; McBeth, J. M.; Tebo, B. M.; Emerson, D.; Moyer, C. L. (2011). "Biodiversity and Emerging Biogeography of the Neutrophilic Iron-Oxidizing Zetaproteobacteria". Applied and Environmental Microbiology 77 (15): 5445–5457. doi:10.1128/AEM.00533-11. PMC 3147450. PMID 21666021.  edit
  5. ^ a b Schauer, R.; Røy, H.; Augustin, N.; Gennerich, H. H.; Peters, M.; Wenzhoefer, F.; Amann, R.; Meyerdierks, A. (2011). "Bacterial sulfur cycling shapes microbial communities in surface sediments of an ultramafic hydrothermal vent field". Environmental Microbiology 13 (10): 2633–2648. doi:10.1111/j.1462-2920.2011.02530.x. PMID 21895907.  edit
  6. ^ a b Hodges, T. W.; Olson, J. B. (2008). "Molecular Comparison of Bacterial Communities within Iron-Containing Flocculent Mats Associated with Submarine Volcanoes along the Kermadec Arc". Applied and Environmental Microbiology 75 (6): 1650–1657. doi:10.1128/AEM.01835-08. PMC 2655482. PMID 19114513.  edit
  7. ^ a b Davis, R. E.; Stakes, D. S.; Wheat, C. G.; Moyer, C. L. (2009). "Bacterial Variability within an Iron-Silica-Manganese-rich Hydrothermal Mound Located Off-axis at the Cleft Segment, Juan de Fuca Ridge". Geomicrobiology Journal 26 (8): 570. doi:10.1080/01490450902889080.  edit
  8. ^ a b Forget, N. L.; Murdock, S. A.; Juniper, S. K. (2010). "Bacterial diversity in Fe-rich hydrothermal sediments at two South Tonga Arc submarine volcanoes". Geobiology 8 (5): 417–432. doi:10.1111/j.1472-4669.2010.00247.x. PMID 20533949.  edit
  9. ^ a b Handley, K. M.; Boothman, C.; Mills, R. A.; Pancost, R. D.; Lloyd, J. R. (2010). "Functional diversity of bacteria in a ferruginous hydrothermal sediment". The ISME Journal 4 (9): 1193–1205. doi:10.1038/ismej.2010.38. PMID 20410934.  edit
  10. ^ a b c Kato, S.; Yanagawa, K.; Sunamura, M.; Takano, Y.; Ishibashi, J. I.; Kakegawa, T.; Utsumi, M.; Yamanaka, T.; Toki, T.; Noguchi, T.; Kobayashi, K.; Moroi, A.; Kimura, H.; Kawarabayasi, Y.; Marumo, K.; Urabe, T.; Yamagishi, A. (2009). "Abundance ofZetaproteobacteriawithin crustal fluids in back-arc hydrothermal fields of the Southern Mariana Trough". Environmental Microbiology 11 (12): 3210–3222. doi:10.1111/j.1462-2920.2009.02031.x. PMID 19691504.  edit
  11. ^ a b c d McBeth, J. M.; Little, B. J.; Ray, R. I.; Farrar, K. M.; Emerson, D. (2010). "Neutrophilic Iron-Oxidizing "Zetaproteobacteria" and Mild Steel Corrosion in Nearshore Marine Environments". Applied and Environmental Microbiology 77 (4): 1405–1412. doi:10.1128/AEM.02095-10. PMC 3067224. PMID 21131509.  edit
  12. ^ a b Dang, H.; Chen, R.; Wang, L.; Shao, S.; Dai, L.; Ye, Y.; Guo, L.; Huang, G.; Klotz, M. G. (2011). "Molecular characterization of putative biocorroding microbiota with a novel niche detection of Epsilon- and Zetaproteobacteria in Pacific Ocean coastal seawaters". Environmental Microbiology 13 (11): 3059–3074. doi:10.1111/j.1462-2920.2011.02583.x. PMID 21951343.  edit
  13. ^ Moyer, C. L.; Dobbs, F. C.; Karl, D. M. (1995). "Phylogenetic diversity of the bacterial community from a microbial mat at an active, hydrothermal vent system, Loihi Seamount, Hawaii". Applied and environmental microbiology 61 (4): 1555–1562. PMC 167411. PMID 7538279.  edit
  14. ^ a b Emerson, D.; Fleming, E. J.; McBeth, J. M. (2010). "Iron-Oxidizing Bacteria: An Environmental and Genomic Perspective". Annual Review of Microbiology 64: 561–583. doi:10.1146/annurev.micro.112408.134208. PMID 20565252.  edit
  15. ^ a b Chan, C. S.; Fakra, S. C.; Emerson, D.; Fleming, E. J.; Edwards, K. J. (2010). "Lithotrophic iron-oxidizing bacteria produce organic stalks to control mineral growth: Implications for biosignature formation". The ISME Journal 5 (4): 717–727. doi:10.1038/ismej.2010.173. PMC 3105749. PMID 21107443.  edit
  16. ^ a b Comolli, L. R.; Luef, B.; Chan, C. S. (2011). "High-resolution 2D and 3D cryo-TEM reveals structural adaptations of two stalk-forming bacteria to an Fe-oxidizing lifestyle". Environmental Microbiology 13 (11): 2915–2929. doi:10.1111/j.1462-2920.2011.02567.x. PMID 21895918.  edit
  17. ^ Juniper, S. Kim; Yves Fouquet (1988). "Filamentous iron-silica deposits from modern and ancient hydrothermal sites". Canadian Mineralogist 26: 859–869. 
  18. ^ Rassa, A. C.; McAllister, S. M.; Safran, S. A.; Moyer, C. L. (2009). "Zeta-ProteobacteriaDominate the Colonization and Formation of Microbial Mats in Low-Temperature Hydrothermal Vents at Loihi Seamount, Hawaii". Geomicrobiology Journal 26 (8): 623. doi:10.1080/01490450903263350.  edit
  19. ^ Emerson, D.; Moyer, C. (2010). "Microbiology of Seamounts: Common Patterns Observed in Community Structure". Oceanography 23: 148. doi:10.5670/oceanog.2010.67.  edit
  20. ^ Sudek, L. A.; Templeton, A. S.; Tebo, B. M.; Staudigel, H. (2009). "Microbial Ecology of Fe (hydr)oxide Mats and Basaltic Rock from Vailulu'u Seamount, American Samoa". Geomicrobiology Journal 26 (8): 581. doi:10.1080/01490450903263400.  edit
  21. ^ Edwards, K. J.; Glazer, B. T.; Rouxel, O. J.; Bach, W.; Emerson, D.; Davis, R. E.; Toner, B. M.; Chan, C. S.; Tebo, B. M.; Staudigel, H.; Moyer, C. L. (2011). "Ultra-diffuse hydrothermal venting supports Fe-oxidizing bacteria and massive umber deposition at 5000 m off Hawaii". The ISME Journal 5 (11): 1748–1758. doi:10.1038/ismej.2011.48. PMC 3197161. PMID 21544100.  edit
  22. ^ Kato, S.; Kobayashi, C.; Kakegawa, T.; Yamagishi, A. (2009). "Microbial communities in iron-silica-rich microbial mats at deep-sea hydrothermal fields of the Southern Mariana Trough". Environmental Microbiology 11 (8): 2094–2111. doi:10.1111/j.1462-2920.2009.01930.x. PMID 19397679.  edit
  23. ^ Davis, R. E.; Moyer, C. L. (2008). "Extreme spatial and temporal variability of hydrothermal microbial mat communities along the Mariana Island Arc and southern Mariana back-arc system". Journal of Geophysical Research 113. doi:10.1029/2007JB005413.  edit
  24. ^ Meyer-Dombard, D. A. R.; Amend, J. P.; Osburn, M. R. (2012). "Microbial diversity and potential for arsenic and iron biogeochemical cycling at an arsenic rich, shallow-sea hydrothermal vent (Tutum Bay, Papua New Guinea)". Chemical Geology. doi:10.1016/j.chemgeo.2012.02.024.  edit
  25. ^ Li, J.; Zhou, H.; Peng, X.; Wu, Z.; Chen, S.; Fang, J. (2012). "Microbial diversity and biomineralization in low-temperature hydrothermal iron-silica-rich precipitates of the Lau Basin hydrothermal field". FEMS Microbiology Ecology 81 (1): 205–216. doi:10.1111/j.1574-6941.2012.01367.x. PMID 22443540.  edit
  26. ^ Sylvan, J. B.; Toner, B. M.; Edwards, K. J. (2012). "Life and Death of Deep-Sea Vents: Bacterial Diversity and Ecosystem Succession on Inactive Hydrothermal Sulfides". MBio 3 (1): e00279–e00211. doi:10.1128/mBio.00279-11. PMC 3262234. PMID 22275502.  edit
  27. ^ Dhillon, A.; Teske, A.; Dillon, J.; Stahl, D. A.; Sogin, M. L. (2003). "Molecular characterization of sulfate-reducing bacteria in the Guaymas Basin". Applied and environmental microbiology 69 (5): 2765–2772. doi:10.1128/AEM.69.5.2765-2772.2003. PMC 154542. PMID 12732547.  edit
  28. ^ Eder, W.; Jahnke, L. L.; Schmidt, M.; Huber, R. (2001). "Microbial Diversity of the Brine-Seawater Interface of the Kebrit Deep, Red Sea, Studied via 16S rRNA Gene Sequences and Cultivation Methods". Applied and Environmental Microbiology 67 (7): 3077–3085. doi:10.1128/AEM.67.7.3077-3085.2001. PMC 92984. PMID 11425725.  edit
  29. ^ Moreau, J. W.; Zierenberg, R. A.; Banfield, J. F. (2010). "Diversity of Dissimilatory Sulfite Reductase Genes (dsrAB) in a Salt Marsh Impacted by Long-Term Acid Mine Drainage". Applied and Environmental Microbiology 76 (14): 4819–4828. doi:10.1128/AEM.03006-09. PMC 2901737. PMID 20472728.  edit
  30. ^ Zbinden, M.; Cambon-Bonavita, M. A. (2003). "Occurrence of Deferribacterales and Entomoplasmatales in the deep-sea Alvinocarid shrimp Rimicaris exoculata gut". FEMS Microbiology Ecology 46 (1): 23–30. doi:10.1016/S0168-6496(03)00176-4. PMID 19719579.  edit
  31. ^ Bowman, J. P.; McCuaig, R. D. (2003). "Biodiversity, community structural shifts, and biogeography of prokaryotes within Antarctic continental shelf sediment". Applied and environmental microbiology 69 (5): 2463–2483. doi:10.1128/AEM.69.5.2463-2483.2003. PMC 154503. PMID 12732511.  edit
  32. ^ a b Glazer, B. T.; Rouxel, O. J. (2009). "Redox Speciation and Distribution within Diverse Iron-dominated Microbial Habitats at Loihi Seamount". Geomicrobiology Journal 26 (8): 606. doi:10.1080/01490450903263392.  edit
  33. ^ Kato, S.; Nakamura, K.; Toki, T.; Ishibashi, J. I.; Tsunogai, U.; Hirota, A.; Ohkuma, M.; Yamagishi, A. (2012). "Iron-Based Microbial Ecosystem on and Below the Seafloor: A Case Study of Hydrothermal Fields of the Southern Mariana Trough". Frontiers in Microbiology 3. doi:10.3389/fmicb.2012.00089.  edit
  34. ^ Singer, E.; Emerson, D.; Webb, E. A.; Barco, R. A.; Kuenen, J. G.; Nelson, W. C.; Chan, C. S.; Comolli, L. R.; Ferriera, S.; Johnson, J.; Heidelberg, J. F.; Edwards, K. J. (2011). "Mariprofundus ferrooxydans PV-1 the First Genome of a Marine Fe(II) Oxidizing Zetaproteobacterium". In Khodursky, Arkady B. PLoS ONE 6 (9): e25386. doi:10.1371/journal.pone.0025386. PMC 3179512. PMID 21966516.  edit