Bibliography
Amend, J. P., and Shock, E. L., 2001. Energetics of overall metabolic reactions of thermophilic and hyperthermophilic Archaea
and Bacteria. FEMS Microbiology Reviews, 25, 175–243.
Beal, E. J., House, C. H., and Orphan, V. J., 2009. Manganeseand iron-dependent marine methane oxidation. Science,
325, 184–187.
Bernhard, A. E., and Bollmann, A., 2010. Estuarine nitrifiers: new
players, patterns and processes. Estuarine, Coastal and Shelf
Science, 88, 1–11.
Bini, E., 2010. Archaeal transformation of metals in the environment. FEMS Microbiology Ecology, 73, 1–16.
Bowers, K. J., and Wiegel, J., 2011. Temperature and pH optima of
extremely halophilic archaea: a mini-review. Extremophiles,
15, 119–128.
Brochier-Armanet, C., Forterre, P., and Gribaldo, S., 2011. Phylogeny and evolution of the Archaea: one hundred genomes later.
Current Opinion in Microbiology, 14, 274–281.
Cabello, P., Roldán, M. D., and Moreno-Vivián, C., 2004. Nitrate
reduction and the nitrogen cycle in archaea. Microbiology,
150, 3527–3546.
Conrad, R., 2009. The global methane cycle: recent advances in
understanding the microbial processes involved. Environmental
Microbiology Reports, 1, 285–292.
Erguder, T. H., Boon, N., Wittebolle, L., Marzorati, M., and
Verstraete, W., 2009. Environmental factors shaping the ecological niches of ammonia-oxidizing archaea. FEMS Microbiology
Reviews, 33, 855–869.
Francis, C. A., Roberts, K. J., Beman, J. M., Santoro, A. E., and
Oakley, B. B., 2005. Ubiquity and diversity of ammoniaoxidizing archaea in water columns and sediments of the ocean.
Proceedings of the National Academy of Sciences of the United
States of America, 102, 14683–14688.
Genomes Online database. www.genomesonline.org.
Hatzenpichler, R., 2012. Diversity, physiology, and niche differentiation of ammonia-oxidizing Archaea. Applied and Environmental Microbiology, 78, 7501–7510.
Knittel, K., and Boetius, A., 2009. Anaerobic oxidation of methane:
progress with an unknown process. Annual Review of Microbiology, 63, 311–334.
Lipp, J. S., Morono, Y., Inagaki, F., and Hinrichs, K.-U., 2008.
Significant contribution of Archaea to extant biomass in marine
subsurface sediments. Nature, 454, 991–994.
Liu, Y., and Whitman, W. B., 2008. Metabolic, phylogenetic, and
ecological diversity of the methanogenic Archaea. Annals of
the New York Academy of Sciences, 1125, 171–189.
Marraffini, L. A., and Sontheimer, E. J., 2010. CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea.
Nature Reviews Genetics, 11, 181–190.
Martens-Habbena, W., Berube, P. M., Urakawa, H., de la Torre,
J. R., and Stahl, D. A., 2009. Ammonia oxidation kinetics
determine niche separation of nitrifying Archaea and Bacteria.
Nature, 461, 976–979.
Milucka, J., Ferdelman, T. G., Polerecky, L., Franzke, D., Wegener,
G., Schmid, M., Lieberwirth, I., Wagner, M., Widdel, F., and
Kuypers, M. M. M., 2012. Zero-valent sulphur is a key intermediate in marine methane oxidation. Nature, 491, 541–546.
Moissl-Eichinger, C., and Huber, H., 2011. Archaeal symbionts and
parasites. Current Opinion in Microbiology, 14, 364–370.
Oelgeschläger, E., and Rother, M., 2008. Carbon monoxidedependent energy metabolism in anaerobic bacteria and archaea.
Archives of Microbiology, 190, 257–269.
Pester, M., Schleper, C., and Wagner, M., 2011. The
Thaumarchaeota: an emerging view of their phylogeny and
ecophysiology. Current Opinion in Microbiology, 14, 300–306.
Philippot, L., 2002. Denitrifying genes in bacterial and
archaeal genomes. Biochimica et Biophysica Acta, 1577,
355–376.
Pina, M., Bize, A., Forterre, P., and Prangishvili, D., 2011. The
archeoviruses. FEMS Microbiology Reviews, 35, 1035–1054.
Prosser, J. I., and Nicol, G. W., 2008. Relative contributions of
archaea and bacteria to aerobic ammonia oxidation in the
environment. Environmental Microbiology, 10, 2931–2941.
Sorek, R., Kunin, V., and Hugenholtz, P., 2008. CRISPR –
a widespread system that provides acquired resistance against
phages in bacteria and archaea. Nature Reviews Microbiology,
6, 181–186.
Stahl, D. A., and de la Torre, J. R., 2012. Physiology and diversity of
ammonia-oxidizing Archaea. Annual Review of Microbiology,
66, 83–101.
Stolz, J. A., Basu, P., Santini, J. M., and Oremland, R. S., 2006.
Arsenic and selenium in microbial metabolism. Annual Review
of Microbiology, 60, 107–130.
Takai, K., and Nakamura, K., 2011. Archaeal diversity and community development in deep-sea hydrothermal vents. Current
Opinion in Microbiology, 14, 282–291.
Torres-Alvarado, M. R., Fernández, F. J., Ramírez Vives, F., and
Varona-Cordero, F., 2013. Dynamics of the methanogenic
Archaea in tropical estuarine sediments. Archaea, 0, 582646.
Valentine, D. L., 2007. Adaptations to energy stress dictate the ecology and evolution of the Archaea. Nature Reviews Microbiology,
5, 316–323.
Woese, C. R., and Fox, G. E., 1977. Phylogenetic structure of the
prokaryotic domain: the primary kingdoms. Proceedings of the
National Academy of Sciences of the United States of America,
74, 5088–5090.
Woese, C. R., Kandler, O., and Wheelis, M. L., 1990. Towards
a natural system of organisms: proposal for the domains
Archaea, Bacteria, and Eukarya. Proceedings of the National
Academy of Sciences of the United States of America,
87, 4576–4579.
Wrede, C., Dreier, A., Kokoschka, S., and Hoppert, M., 2012.
Archaea in symbioses. Archaea, 0, 596846.
Zumft, W. G., 1997. Cell biology and molecular basis of denitrification. Microbiology and Molecular Biology Reviews, 61,
533–616.
Cross-references
Nitrate Reduction
Nitrification
Symbiosis
ARTIFICIAL REEF
Stephen A. Bortone
Osprey Aquatic Sciences, Inc., Tampa, FL, USA
Synonyms
Artificial habitats; Artificial reef structures; Man-made
habitats; Man-made reefs
Definition
“An artificial reef is one or more objects of natural
or human origin deployed purposefully on the seafloor
ARTIFICIAL REEF
37
Amend, J. P., and Shock, E. L., 2001. Energetics of overall metabolic reactions of thermophilic and hyperthermophilic Archaea
and Bacteria. FEMS Microbiology Reviews, 25, 175–243.
Beal, E. J., House, C. H., and Orphan, V. J., 2009. Manganeseand iron-dependent marine methane oxidation. Science,
325, 184–187.
Bernhard, A. E., and Bollmann, A., 2010. Estuarine nitrifiers: new
players, patterns and processes. Estuarine, Coastal and Shelf
Science, 88, 1–11.
Bini, E., 2010. Archaeal transformation of metals in the environment. FEMS Microbiology Ecology, 73, 1–16.
Bowers, K. J., and Wiegel, J., 2011. Temperature and pH optima of
extremely halophilic archaea: a mini-review. Extremophiles,
15, 119–128.
Brochier-Armanet, C., Forterre, P., and Gribaldo, S., 2011. Phylogeny and evolution of the Archaea: one hundred genomes later.
Current Opinion in Microbiology, 14, 274–281.
Cabello, P., Roldán, M. D., and Moreno-Vivián, C., 2004. Nitrate
reduction and the nitrogen cycle in archaea. Microbiology,
150, 3527–3546.
Conrad, R., 2009. The global methane cycle: recent advances in
understanding the microbial processes involved. Environmental
Microbiology Reports, 1, 285–292.
Erguder, T. H., Boon, N., Wittebolle, L., Marzorati, M., and
Verstraete, W., 2009. Environmental factors shaping the ecological niches of ammonia-oxidizing archaea. FEMS Microbiology
Reviews, 33, 855–869.
Francis, C. A., Roberts, K. J., Beman, J. M., Santoro, A. E., and
Oakley, B. B., 2005. Ubiquity and diversity of ammoniaoxidizing archaea in water columns and sediments of the ocean.
Proceedings of the National Academy of Sciences of the United
States of America, 102, 14683–14688.
Genomes Online database. www.genomesonline.org.
Hatzenpichler, R., 2012. Diversity, physiology, and niche differentiation of ammonia-oxidizing Archaea. Applied and Environmental Microbiology, 78, 7501–7510.
Knittel, K., and Boetius, A., 2009. Anaerobic oxidation of methane:
progress with an unknown process. Annual Review of Microbiology, 63, 311–334.
Lipp, J. S., Morono, Y., Inagaki, F., and Hinrichs, K.-U., 2008.
Significant contribution of Archaea to extant biomass in marine
subsurface sediments. Nature, 454, 991–994.
Liu, Y., and Whitman, W. B., 2008. Metabolic, phylogenetic, and
ecological diversity of the methanogenic Archaea. Annals of
the New York Academy of Sciences, 1125, 171–189.
Marraffini, L. A., and Sontheimer, E. J., 2010. CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea.
Nature Reviews Genetics, 11, 181–190.
Martens-Habbena, W., Berube, P. M., Urakawa, H., de la Torre,
J. R., and Stahl, D. A., 2009. Ammonia oxidation kinetics
determine niche separation of nitrifying Archaea and Bacteria.
Nature, 461, 976–979.
Milucka, J., Ferdelman, T. G., Polerecky, L., Franzke, D., Wegener,
G., Schmid, M., Lieberwirth, I., Wagner, M., Widdel, F., and
Kuypers, M. M. M., 2012. Zero-valent sulphur is a key intermediate in marine methane oxidation. Nature, 491, 541–546.
Moissl-Eichinger, C., and Huber, H., 2011. Archaeal symbionts and
parasites. Current Opinion in Microbiology, 14, 364–370.
Oelgeschläger, E., and Rother, M., 2008. Carbon monoxidedependent energy metabolism in anaerobic bacteria and archaea.
Archives of Microbiology, 190, 257–269.
Pester, M., Schleper, C., and Wagner, M., 2011. The
Thaumarchaeota: an emerging view of their phylogeny and
ecophysiology. Current Opinion in Microbiology, 14, 300–306.
Philippot, L., 2002. Denitrifying genes in bacterial and
archaeal genomes. Biochimica et Biophysica Acta, 1577,
355–376.
Pina, M., Bize, A., Forterre, P., and Prangishvili, D., 2011. The
archeoviruses. FEMS Microbiology Reviews, 35, 1035–1054.
Prosser, J. I., and Nicol, G. W., 2008. Relative contributions of
archaea and bacteria to aerobic ammonia oxidation in the
environment. Environmental Microbiology, 10, 2931–2941.
Sorek, R., Kunin, V., and Hugenholtz, P., 2008. CRISPR –
a widespread system that provides acquired resistance against
phages in bacteria and archaea. Nature Reviews Microbiology,
6, 181–186.
Stahl, D. A., and de la Torre, J. R., 2012. Physiology and diversity of
ammonia-oxidizing Archaea. Annual Review of Microbiology,
66, 83–101.
Stolz, J. A., Basu, P., Santini, J. M., and Oremland, R. S., 2006.
Arsenic and selenium in microbial metabolism. Annual Review
of Microbiology, 60, 107–130.
Takai, K., and Nakamura, K., 2011. Archaeal diversity and community development in deep-sea hydrothermal vents. Current
Opinion in Microbiology, 14, 282–291.
Torres-Alvarado, M. R., Fernández, F. J., Ramírez Vives, F., and
Varona-Cordero, F., 2013. Dynamics of the methanogenic
Archaea in tropical estuarine sediments. Archaea, 0, 582646.
Valentine, D. L., 2007. Adaptations to energy stress dictate the ecology and evolution of the Archaea. Nature Reviews Microbiology,
5, 316–323.
Woese, C. R., and Fox, G. E., 1977. Phylogenetic structure of the
prokaryotic domain: the primary kingdoms. Proceedings of the
National Academy of Sciences of the United States of America,
74, 5088–5090.
Woese, C. R., Kandler, O., and Wheelis, M. L., 1990. Towards
a natural system of organisms: proposal for the domains
Archaea, Bacteria, and Eukarya. Proceedings of the National
Academy of Sciences of the United States of America,
87, 4576–4579.
Wrede, C., Dreier, A., Kokoschka, S., and Hoppert, M., 2012.
Archaea in symbioses. Archaea, 0, 596846.
Zumft, W. G., 1997. Cell biology and molecular basis of denitrification. Microbiology and Molecular Biology Reviews, 61,
533–616.
Cross-references
Nitrate Reduction
Nitrification
Symbiosis
ARTIFICIAL REEF
Stephen A. Bortone
Osprey Aquatic Sciences, Inc., Tampa, FL, USA
Synonyms
Artificial habitats; Artificial reef structures; Man-made
habitats; Man-made reefs
Definition
“An artificial reef is one or more objects of natural
or human origin deployed purposefully on the seafloor
ARTIFICIAL REEF
37