Shaw, D. G., and Day, R. H., 1994. Color- and form-dependent loss
of plastic micro-detritus from the North Pacific Ocean. Marine
Pollution Bulletin, 28, 39–45.
Shipley, F. S., and Kiesling, R. W. (eds.), 1994. The State of the Bay:
A Characterization of the Galveston Bay Ecosystem. Webster,
TX: Galveston Bay National Estuary Program. Publication,
GBNEP-44.
Skinner, L., 2012. A long view on climate sensitivity. Science,
337, 917–919.
Teal, J. M., Best, R., Caffrey, J., Hopkinson, C. S., McKee, K. L.,
Morris, J. T., Newman, S., and Orem, B., 2012. Mississippi
River freshwater diversions in Southern Louisiana: effects on
wetland vegetation, soils, and elevation. In Lewitus, A. J.,
Croom, M., Davison, T., Kidwell, D. M., Kleiss, B. A., Pahl,
J. W., and Swarzenski, C. M. (eds.), Final Report to the State
of Louisiana and U.S. Army Corps of Engineers through the
Louisiana Coastal Area Science and Technology Program,
Coordinated by the National Oceanic and Atmospheric Administration, Silver Spring, MD.
Cross-references
Anoxia, Hypoxia, and Dead Zones
Biochemical Oxygen Demand
Bulkheads
Clean Water Act
Climate Change
Dredging
Eutrophication
Extreme Events (Hurricanes)
Invasive Species
Marsh Sediment Toxicity
Nonpoint Source Pollution
Oil Pollution
Pathogens
Polycyclic Aromatic Hydrocarbons
Revetments
Storm Surges
Toxic Blooms
Trace Metals in Estuaries
Water Quality
Wetlands Reclamation
ARCHAEA
Antje Rusch
Department of Microbiology and Center for Ecology,
Southern Illinois University Carbondale, Carbondale,
IL, USA
Synonym
Archaebacteria
Definition
Archaea constitute one of the three domains of life,
as phylogenetically distinct from the domains
Bacteria and Eukarya (Woese and Fox, 1977; Woese
et al., 1990).
Etymology
Archaea (singular: archaeon) are derived from Greek
ἀrwaῖοB – ancient, primitive.
The term was coined to reflect the apparent antiquity of
traits in archaeal species and their aptness to inhabit
environments like those presumed for early Earth.
Phylogeny
On the phylogenetic tree of organisms, Archaea form one of
the three fundamental branches called domains (Woese
et al., 1990). Further branching within the archaeal domain
is largely based on ribosomal RNA sequences, but also
relies on evidence from comparative analysis of protein
sequences. Typical markers in archaeal phylogeny are
ribosomal proteins, histones, and components of the transcription system and the cell division apparatus (BrochierArmanet et al., 2011). In addition to the initially recognized
phyla Crenarchaeota and Euryarchaeota (Woese et al.,
1990), four candidate phyla have been proposed: Kor-,
Nano-, Thaum-, and Aigarchaeota (Brochier-Armanet
et al., 2011). Given the small number of 187 sequenced
archaeal genomes (Genomes OnLine Database; May
2013), archaeal phylogeny continues to be uncertain.
Physiology and metabolism
Archaea are single-celled organisms showing prokaryotic
structure, but differ from bacterial cells by the absence of
peptidoglycan from their cell wall and by the presence of
histones associated with their DNA. In contrast to the
phospholipid bilayer confining bacterial and eukaryotic
cells, archaeal cell membranes consist of a single layer
of isoprenoid diethers and tetraethers. Most archaeal
genomes contain clustered, regularly interspaced palindromic repeats (CRISPR) that confer adaptive immunity
against virus infections (Sorek et al., 2008; Marraffini
and Sontheimer, 2010).
No chlorophyll-like pigments or photosynthetic electron transport chains are known in Archaea. However,
some archaea possess bacteriorhodopsin, which functions
as light-driven proton pump across the cell membrane.
The reflux of protons can be exploited for ATP synthesis,
completing the conversion of light energy into chemical
energy for cellular metabolism.
Archaea show diverse forms of chemotrophic metabolism, including both the formation and the anaerobic
oxidation of methane, both oxidation and reduction of
CO, the aerobic oxidation of H 2 (knallgas reaction), most
of the oxidative and reductive processes in the N and
S cycle, and redox reactions of various metals and metalloids (Amend and Shock, 2001; Stolz et al., 2006;
Oelgeschläger and Rother, 2008; Conrad, 2009; Knittel
and Boetius, 2009; Bini, 2010).
In sulfur-based energy metabolism, oxidized and intermediate S compounds (sulfate, sulfite, thiosulfate, and
elemental sulfur) are reduced by H 2 or organic compounds, while reduced and intermediate S compounds
(sulfide, elemental sulfur, and thiosulfate) can be oxidized
ARCHAEA
35
of plastic micro-detritus from the North Pacific Ocean. Marine
Pollution Bulletin, 28, 39–45.
Shipley, F. S., and Kiesling, R. W. (eds.), 1994. The State of the Bay:
A Characterization of the Galveston Bay Ecosystem. Webster,
TX: Galveston Bay National Estuary Program. Publication,
GBNEP-44.
Skinner, L., 2012. A long view on climate sensitivity. Science,
337, 917–919.
Teal, J. M., Best, R., Caffrey, J., Hopkinson, C. S., McKee, K. L.,
Morris, J. T., Newman, S., and Orem, B., 2012. Mississippi
River freshwater diversions in Southern Louisiana: effects on
wetland vegetation, soils, and elevation. In Lewitus, A. J.,
Croom, M., Davison, T., Kidwell, D. M., Kleiss, B. A., Pahl,
J. W., and Swarzenski, C. M. (eds.), Final Report to the State
of Louisiana and U.S. Army Corps of Engineers through the
Louisiana Coastal Area Science and Technology Program,
Coordinated by the National Oceanic and Atmospheric Administration, Silver Spring, MD.
Cross-references
Anoxia, Hypoxia, and Dead Zones
Biochemical Oxygen Demand
Bulkheads
Clean Water Act
Climate Change
Dredging
Eutrophication
Extreme Events (Hurricanes)
Invasive Species
Marsh Sediment Toxicity
Nonpoint Source Pollution
Oil Pollution
Pathogens
Polycyclic Aromatic Hydrocarbons
Revetments
Storm Surges
Toxic Blooms
Trace Metals in Estuaries
Water Quality
Wetlands Reclamation
ARCHAEA
Antje Rusch
Department of Microbiology and Center for Ecology,
Southern Illinois University Carbondale, Carbondale,
IL, USA
Synonym
Archaebacteria
Definition
Archaea constitute one of the three domains of life,
as phylogenetically distinct from the domains
Bacteria and Eukarya (Woese and Fox, 1977; Woese
et al., 1990).
Etymology
Archaea (singular: archaeon) are derived from Greek
ἀrwaῖοB – ancient, primitive.
The term was coined to reflect the apparent antiquity of
traits in archaeal species and their aptness to inhabit
environments like those presumed for early Earth.
Phylogeny
On the phylogenetic tree of organisms, Archaea form one of
the three fundamental branches called domains (Woese
et al., 1990). Further branching within the archaeal domain
is largely based on ribosomal RNA sequences, but also
relies on evidence from comparative analysis of protein
sequences. Typical markers in archaeal phylogeny are
ribosomal proteins, histones, and components of the transcription system and the cell division apparatus (BrochierArmanet et al., 2011). In addition to the initially recognized
phyla Crenarchaeota and Euryarchaeota (Woese et al.,
1990), four candidate phyla have been proposed: Kor-,
Nano-, Thaum-, and Aigarchaeota (Brochier-Armanet
et al., 2011). Given the small number of 187 sequenced
archaeal genomes (Genomes OnLine Database; May
2013), archaeal phylogeny continues to be uncertain.
Physiology and metabolism
Archaea are single-celled organisms showing prokaryotic
structure, but differ from bacterial cells by the absence of
peptidoglycan from their cell wall and by the presence of
histones associated with their DNA. In contrast to the
phospholipid bilayer confining bacterial and eukaryotic
cells, archaeal cell membranes consist of a single layer
of isoprenoid diethers and tetraethers. Most archaeal
genomes contain clustered, regularly interspaced palindromic repeats (CRISPR) that confer adaptive immunity
against virus infections (Sorek et al., 2008; Marraffini
and Sontheimer, 2010).
No chlorophyll-like pigments or photosynthetic electron transport chains are known in Archaea. However,
some archaea possess bacteriorhodopsin, which functions
as light-driven proton pump across the cell membrane.
The reflux of protons can be exploited for ATP synthesis,
completing the conversion of light energy into chemical
energy for cellular metabolism.
Archaea show diverse forms of chemotrophic metabolism, including both the formation and the anaerobic
oxidation of methane, both oxidation and reduction of
CO, the aerobic oxidation of H 2 (knallgas reaction), most
of the oxidative and reductive processes in the N and
S cycle, and redox reactions of various metals and metalloids (Amend and Shock, 2001; Stolz et al., 2006;
Oelgeschläger and Rother, 2008; Conrad, 2009; Knittel
and Boetius, 2009; Bini, 2010).
In sulfur-based energy metabolism, oxidized and intermediate S compounds (sulfate, sulfite, thiosulfate, and
elemental sulfur) are reduced by H 2 or organic compounds, while reduced and intermediate S compounds
(sulfide, elemental sulfur, and thiosulfate) can be oxidized
ARCHAEA
35