Archaea in Biogeochemical Cycles

Annu. Rev. Microbiol. 2013.67:437-457. Downloaded from www.annualreviews.org by University of Vienna - Main Library and Archive Services on 09/12/13. For personal use only. Archaea in Biogeochemical Cycles Pierre Offre, Anja Spang, and Christa Schleper Department of Genetics in Ecology, University of Vienna, A-1090 Wien, Austria; email: pierre.offre@univie.ac.at, anja.spang@univie.ac.at, christa.schleper@univie.ac.at Annu. Rev. Microbiol. 2013. 67:437–57 Keywords First published online as a Review in Advance on June 26, 2013 archaea, biogeochemical cycles, metabolism, carbon, nitrogen, sulfur The Annual Review of Microbiology is online at micro.annualreviews.org Abstract This article’s doi: 10.1146/annurev-micro-092412-155614 c 2013 by Annual Reviews. Copyright  All rights reserved Archaea constitute a considerable fraction of the microbial biomass on Earth. Like Bacteria they have evolved a variety of energy metabolisms using organic and/or inorganic electron donors and acceptors, and many of them are able to fix carbon from inorganic sources. Archaea thus play crucial roles in the Earth’s global geochemical cycles and influence greenhouse gas emissions. Methanogenesis and anaerobic methane oxidation are important steps in the carbon cycle; both are performed exclusively by anaerobic archaea. Oxidation of ammonia to nitrite is performed by Thaumarchaeota. They represent the only archaeal group that resides in large numbers in the global aerobic terrestrial and marine environments on Earth. Sulfur-dependent archaea are confined mostly to hot environments, but metal leaching by acidophiles and reduction of sulfate by anaerobic, nonthermophilic methane oxidizers have a potential impact on the environment. The metabolisms of a large number of archaea, in particular those dominating the subsurface, remain to be explored. 437 Contents Annu. Rev. Microbiol. 2013.67:437-457. Downloaded from www.annualreviews.org by University of Vienna - Main Library and Archive Services on 09/12/13. For personal use only. INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . THE DOMAIN ARCHAEA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ARCHAEAL METABOLISMS AND BIOGEOCHEMICAL CYCLES . . . . . . . . . . . . . Carbon Cycle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Nitrogen Cycle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sulfur Cycle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . CONCLUSIONS AND PERSPECTIVES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 438 438 440 440 445 447 450 INTRODUCTION All currently known life forms gain the free energy required to meet the energetic cost of maintenance, growth, and reproduction through enzymatically catalyzed redox reactions. Life exploits many pairs of electron donors and acceptors (redox pairs) for the generation of biochemical energy and the assimilation of nutrients, but single species use only a specific subset of those redox pairs. The survival of all living organisms thus depends on the constant supply of different combinations of electron donors and acceptors, which are present in limited amounts in the biosphere and therefore need to be constantly recycled. The cycling of these chemical substances emerges from geophysical processes and the combined metabolisms of all life forms (96). These self-organized nutrient cycles, which are increasingly influenced by human activities, can be represented as networks of processes, connecting different reservoirs of substances and defining biogeochemical cycles for various chemical elements and molecules. Owing to their versatile metabolisms, microorganisms drive most of the biological fluxes of the elements—particularly the six major building blocks of life, hydrogen, carbon, nitrogen, sulfur, oxygen, and phosphorus—and thus shape the biogeochemistry of our planet (32). For more than half a century, since Vladimir Vernadsky coined the term biogeochemistry in 1926, only Bacteria and Eukarya were considered to contribute significantly to global nutrient cycles. The Archaea, constituting the third fundamental domain of life, were not described until 50 years later (137). Until the early 1990s, they were perceived mainly as a group of microorganisms thriving in extreme habitats that have, except for the methanogens (130), little influence on global nutrient cycling. However, this view began to change when molecular biological techniques were introduced into microbial ecology. The discovery that archaea are found in oceanic plankton (23, 35) has triggered a huge number of follow-up studies showing that archaea represent an abundant and diverse group of microorganisms in the whole biosphere and suggesting that they have a significant impact on nutrient cycling. In addition to cultivation of novel archaeal strains, culture-independent techniques, in particular molecular biological, biochemical, and isotope-based methods, have since remained instrumental for recognizing and characterizing novel archaeal metabolisms and for estimating their environmental impact. Through these studies it has become increasingly evident that archaea are important players in both carbon and nitrogen cycling. In this review, the distribution of the Archaea in the biosphere and their role in extant biogeochemical cycles are discussed in light of recent discoveries. THE DOMAIN ARCHAEA Woese & Fox (137) and Woese et al. (138) provided the first evidence that Archaea constitute a third domain alongside Bacteria and Eukarya within the phylogenetic tree of life. This finding was 438 Offre · Spang · Schleper Crenarchaeota Geoarchaeota Thermoproteales/Sulfolobales/Desulfurococcales/Acidilobales/Fervidicoccales Geoarchaeota Hot Water Crenarchaeotic Group III Thaumarchaeota ALOHA group/Group 1.1c/psL12 group/Marine Benthic Group A Group 1.1a (and group 1.1a associated)/Group 1.1b Aigarchaeota (Hot Water Crenarchaeotic Group I) Miscellaneous Crenarchaeotal Groups Aigarchaeota and candidate lineages Annu. Rev. Microbiol. 2013.67:437-457. Downloaded from www.annualreviews.org by University of Vienna - Main Library and Archive Services on 09/12/13. For personal use only. Deep Sea Archaeal Group/Marine Benthic Group B Ancient Archaeal Group/Marine Hydrothermal Vent Group 2 Korarchaeota Korarchaeota Euryarchaeota Methanosarcinales/Methanocellales/Methanomicrobiales/ANME lineages 1–3/ Halobacteriales/Marine Group 4 Archaeoglobales Thermoplasmatales/Aciduliprofundum sp./Methanoplasmatales/Marine Group 2, 3, 5 Marine Benthic Group E/South African Goldmine Group/Miscellaneous + Deep Sea Euryarchaeota Group Nanosalinarum sp. Methanobacteriales Methanococcales Methanopyrales Thermococcales Micrarchaeum sp. Parvarcheum sp./Deep Sea Hydrothermal Vent Group 6 Nanoarchaeota Figure 1 Schematic representation of the phylogenetic diversity of archaea with the major lineages as referred to in the text. The multifurcations indicate that the placement of most lineages varies in different phylogenetic analyses. The tree is intended to give a general orientation to readers who are not familiar with archaea. Phyla in gray typeface have not been validated. overwhelmingly corroborated by genomic and biochemical data showing that all archaea share unique membranes and have cell walls that differ from those of bacteria (36). Furthermore, they use distinctive informational processing machineries (e.g., replication and transcription) considered to be derived from a common ancestor with Eukarya (36). Since their discovery as a separate domain, the number of known taxa within the Archaea has been expanded continuously. As of November 2, 2012, there were 116 archaeal genera representing 450 cultivated and validly described species (http://www.bacterio.cict.fr). However, most of the archaeal diversity, currently referenced in public databases, remains uncultivated (117) and is known only from 16S rRNA gene sequences obtained from molecular surveys (24). Many of these uncultivated archaea are only distantly related to their closest cultivated relatives and specify numerous lineages representing a wide range of taxonomic ranks, up to the phylum level. Cultivated and uncultivated archaeal lineages have been classified in a few high-rank taxa (Figure 1), and a short overview of currently proposed archaeal phyla is provided below. www.annualreviews.org • Archaea in Biogeochemical Cycles 439 MCG: Miscellaneous Crenarchaeotal Group Annu. Rev. Microbiol. 2013.67:437-457. Downloaded from www.annualreviews.org by University of Vienna - Main Library and Archive Services on 09/12/13. For personal use only. DSAG: Deep Sea Archaeal Group Most cultivated archaea are assigned to two major archaeal phyla, Euryarchaeota and Crenarchaeota, that were originally defined by Woese et al. (138). Euryarchaeota include eight taxonomic classes (i.e., Methanopyri, Methanococci, Methanobacteria, Methanomicrobia, Archaeoglobi, Halobacteria, Thermococci, and Thermoplasmata) that include methanogens, methane-oxidizing archaea, denitrifiers, sulfate reducers, iron oxidizers, and organotrophs (61). Members of this phylum are globally distributed, and some lineages, often uncultivated ones, are abundant in marine waters, soils, and sediments (117, 128), whereas many of the long-known euryarchaeotes inhabit extreme environments and are therefore restricted to specific geographic areas. The hyperthermophilic, parasitic Nanoarchaeum equitans, initially suggested to represent a new candidate phylum (49), likely constitutes an additional fast-evolving lineage of the Euryarchaeota (14). Crenarchaeota contain only one taxonomic class (i.e., Thermoprotei ) and five taxonomic orders (i.e., Acidilobales, Desulfurococcales, Fervidicoccales, Sulfolobales, and Thermoproteales), two of which (Acidilobales and Fervidicoccales) were discovered only recently (100, 106). All crenarchaeotes have been found in hot environments such as acidic terrestrial hot springs and submarine hydrothermal vents, as well as smoldering refuse piles (61). Few organisms of the recently defined phylum Thaumarchaeota have been cultivated (124), all of which gain energy by ammonia oxidation. Organisms of this phylum are globally distributed and are found in high numbers in marine and freshwater environments, soils, and sediments and also occur in extreme environments including hot springs. On the basis of genomic data, additional archaeal phyla have recently been proposed. They include Korarchaeota (5, 29), Aigarchaeota (94), and Geoarchaeota (67). The affiliation of several deep-branching lineages such as the Miscellaneous Crenarchaeotal Group (MCG), Deep Sea Archaeal Group (DSAG), and Ancient Archaeal Group (AAG) is still unclear (43). Members of these new phyla have been found in the terrestrial and marine subsurface (128) but also in hot springs and deep-sea hydrothermal systems, and no representative has yet been obtained in pure culture. ARCHAEAL METABOLISMS AND BIOGEOCHEMICAL CYCLES Archaeal metabolisms sustain the production of the archaeomass and determine the biogeochemical impact of the Archaea. On the basis of cell counts and molecular studies, archaea account for more than 20% of all prokaryotes in ocean waters (56), about 1–5% in upper soil layers (6, 95), and probably represent the dominant group of microorganisms in marine subsurface sediments (76) and in most geothermal habitats. Their involvement in major geochemical cycles is discussed below. Carbon Cycle Archaea dominate the biogenic production of methane (CH4 ) but are also key to the oxidation of this important hydrocarbon. Archaeal organisms also play significant roles in the production and mineralization of organic matter. Carbon assimilation. Many cultivated representatives of the Crenarchaeota, Thaumarchaeota, and Euryarchaeota are capable of autotrophic growth (Supplemental Table 1; follow the Supplemental Material link from the Annual Reviews home page at http://www.annualreviews.org), as they assimilate carbon from oxidized inorganic compounds, i.e., carbon dioxide (CO2 ) or bicarbonate (HCO3 − ), reducing those substrates to form simple organic molecules (9) (Figure 2a). Investigation of the genome sequence of “Candidatus Caldiarchaeum subterraneum” (94) indicates 440 Offre · Spang · Schleper b Carbon cycle N2 Fermentation, anaerobic respiration Organic C N2 Anoxic N2O NO 3 4 Ammonia NH3 oxidation x amo Ann NO2– Nitrite oxidation NO3– on Organic N Aerobic respiration Fixation Oxic Anoxic N2O NO NO2– Oxic c Sulfur cycle Abiotic Metal sulfide H2S Ox ida tio n Sulfur oxidation Su lfit Sulfur reduction er ed uc tio n tio ida Ox fat e oxi reduc dat t ion ion/ n SO32– n ion ct io tat re du mu te Dis lfa Sul HS2– Su S2O32– Sulfur oxidation 5 S Th re ios du ulf ct at io e n Annu. Rev. Microbiol. 2013.67:437-457. Downloaded from www.annualreviews.org by University of Vienna - Main Library and Archive Services on 09/12/13. For personal use only. N fixation CO2 Mineralization ati A cetogen esis Nitrifier denitrification N2 nit r Small organics Methane oxidation ific CH4 2 N fixation is es en g o 1 an t h MethanoMe genesis Nitrogen cycle De a te lfa Su on cti u red SO42– Figure 2 Schematic representation of the involvement of archaea in (a) carbon, (b) nitrogen, and (c) sulfur cycles. Red arrows indicate metabolic steps found in archaea and bacteria; orange arrows indicate metabolic pathways present exclusively in archaea; and gray arrows indicate metabolisms known only from bacteria. Circled numbers can be defined as follows: 1, hydrogenotrophic methanogenesis is a lithotrophic process resulting from the reduction of CO2 with H2 as electron donor; 2, formatotrophic, acetotrophic, and methylotrophic methanogenesis are organotrophic processes supported by the degradation of formate, acetate, and methylated compounds, respectively; 3, nitrifier denitrification is thought to occur under low oxygen conditions; 4, N2 O might be a direct side product of the ammonia-oxidizing pathway; 5, S2 O3 2− is produced in several different ways including abiotic processes not presented here. that members of the Aigarchaeota might also be able to assimilate inorganic carbon. Three different metabolic pathways for autotrophic carbon fixation have been characterized in cultivated archaeal autotrophs, and these were reviewed recently (9). Many autotrophic members of the Archaea grow mixotrophically; i.e., they coassimilate small organic compounds under suitable conditions or switch between an autotrophic and a heterotrophic lifestyle (61). Whereas Thaumarchaeota as described thus far depend on inorganic www.annualreviews.org • Archaea in Biogeochemical Cycles 441 Annu. Rev. Microbiol. 2013.67:437-457. Downloaded from www.annualreviews.org by University of Vienna - Main Library and Archive Services on 09/12/13. For personal use only. Stable isotope probing (SIP): a substrate highly enriched in a stable isotope (e.g., 13 C) is given to an environmental sample to detect metabolically active organisms inside a complex microbial consortium ANME: anaerobic methanotroph Chemoorganotroph: organism that uses organic compounds as electron donors and energy sources carbon for assimilation, some lineages of Euryarchaeota and Crenarchaeota include several facultative autotrophic organisms but also obligate heterotrophs, such as the representatives of the Halobacteriales and Thermococcales (61). The determination of the growth mode of most archaea is based on in vitro experiments, which might not reflect the lifestyle of these organisms in their natural habitats and limits the current knowledge of those organisms that have been successfully cultivated. However, some environmental studies using natural radiocarbon content, stable isotope probing (SIP) techniques, or microautoradiography combined with catalyzed reporter deposition–fluorescence in situ hybridization (MICRO-CARD-FISH) have been performed to reveal the lifestyle of particular archaea in natural populations and microcosms. For example, the natural radiocarbon content of archaeal lipids indicates that Thaumarchaeota in ocean waters predominately grow autotrophically (50, 99, 140). Modeled estimates of archaeal biomass production in deep waters range from 0.7 to 0.8 Gt C/year, suggesting that Thaumarchaeota might contribute ∼1% of the annual primary production in the ocean (47, 50) and could provide, at least in some instances, most of the reduced carbon for heterotrophic microorganisms in oxygen minimum zones (45). Similarly, evidence for autotrophic growth of at least some phylotypes of Thaumarchaeota has been provided in soil microcosms using SIP (105, 144). In contrast, representatives of the MCG and DSAG lineages, dominant groups of archaea in the ocean subsurface sediments (11, 68, 128), were shown to grow heterotrophically in ocean margin sediments (11). Dual SIP, i.e., a quantitative stable isotope probing approach, suggested that euryarchaeal anaerobic methanotroph (ANME) lineages are also autotrophs (59). Organic carbon mineralization. The catabolic degradation of organic substrates by chemoorganotrophs usually results in the production of CO2 as the main end product (Figure 2a). However, the absence of external electron acceptors (fermentative conditions) or a limitation in respiratory capacity is associated with the excretion of partially oxidized compounds, e.g., organic acids or alcohols, in addition to CO2 . Numerous archaeal organisms, including aerobes and anaerobes, can grow organotrophically (see below for a discussion of organotrophic methanogens and methane-oxidizing archaea). Those organisms that have been cultivated thus far are extremophiles, which belong to the Euryarchaeota and Crenarchaeota (Supplemental Table 1). A comprehensive description of the various organotrophic metabolisms supporting cultivated archaeal organisms can be found in Reference 61. On the basis of the genome sequence of uncultivated extremophilic archaea, representatives of the Korarchaeota, Geoarchaeota, Aigarchaeota, the provisional euryarchaeal class Nanohaloarchaea, and ARMAN lineages might also grow organotrophically (4, 29, 37, 67, 93, 94). Recent metagenomic studies suggest that euryarchaeal phototrophic organotrophs (Marine group II) could be ubiquitous in the global ocean (34, 51), but currently there is no proof that archaeal organisms present in moderate environments play a major role in organic carbon mineralization. Methanogenesis. Methane, a major greenhouse gas but also an important source of energy for humans, is the predominant hydrocarbon in Earth’s atmosphere. Methanogenic archaea are strict anaerobes that produce methane (CH4 ) as the major product of their energyconserving metabolism (Figure 2a). All methanogenic archaea characterized so far belong to the Euryarchaeota (Supplemental Table 1) and are distributed among five taxonomic classes, i.e., Methanopyri, Methanococci, Methanobacteria, Methanomicrobia, and Thermoplasmata (26, 79, 98). Several methanogenic pathways that rely on various substrates have been described (Figure 2a and Supplemental Table 1): CO2 reduction with hydrogen (hydrogenotrophic methanogens) or formate (formatotrophic methanogens) as electron donors; methanol reduction with hydrogen; fermentation of acetate (acetotrophic methanogens); and dismutation of methylated compounds 442 Offre · Spang · Schleper Annu. Rev. Microbiol. 2013.67:437-457. Downloaded from www.annualreviews.org by University of Vienna - Main Library and Archive Services on 09/12/13. For personal use only. (methylotrophic methanogens) such as methanol, methylamines, dimethylsulfide (DMS), or methanethiol (33, 79). Whereas most cultivated methanogens reduce CO2 with hydrogen, only members of Methanosarcinales have the ability to produce methane from the fermentation of acetate and the dismutation of methylated compounds. The recently discovered methanogenic Thermoplasmata reduce methanol with hydrogen (26, 98) and might also use methylamines as methanogenic substrate (104). Currently, none of these methanogenic metabolisms have been found in bacteria or eukaryotes. Although acetate fermentation is performed by only a few cultivated methanogens, this process could account for up to two-thirds of the methane released to the atmosphere by archaeal methanogenesis; the reduction of CO2 accounts for the rest of the archaeal contribution to atmospheric methane, with minor amounts of methane produced by the dismutation of methyl compounds (33). Methanogens have been isolated from various anoxic environments (20, 79) (e.g., rice paddies and peat bogs; freshwater, marine, and hypersaline sediments; hydrothermal vents; deepsubsurface habitats; the gastrointestinal tract of various animals) and are usually abundant where electron acceptors such as NO3 − , Fe3+ , and SO4 2− are in short supply. Hydrogenotrophic methanogens and acetogenic bacteria have similar requirements, including anoxic conditions, a source of H2 as electron donor, and a source of CO2 as electron acceptor (Figure 2a). But methanogenesis occurs preferentially at low H2 concentrations and at a pH lower than 7; it can also be performed at high temperatures (2, 65, 130). Interestingly, methanogenic archaea have also been found in oxic environments, i.e., various aerated soils (3, 102) and the oxygenated water column of an oligotrophic lake (40). The methanogens in aerated soils became active under wet anoxic conditions (3), and those in oxygenated lake waters were attached to photoautotrophs, which might enable anaerobic growth and supply of methanogenic substrates (40). Several other processes, such as the microbial decomposition of methylphosphonate (55, 88), could be responsible for methane production in oxygenated waters (60), and fungi (74) and plants (15) are possible sources of methane in aerated soils. The global significance of these alternative aerobic methanogenic pathways remains to be assessed. Archaeal methanogenesis produces about 1 Gt of methane every year (111, 130) and accounts for a significant fraction of the net annual emissions of methane to the atmosphere, with some estimates as high as 74% (79). Methanogenic archaea also produce methane that stays locked in underground reservoirs by taking part in the biodegradation of crude oil (52) and coal (126). Methane production by methanogenic archaea is suspected to rise considerably in arctic soils because of climate warming and is thus a major focus of current arctic research (82). Syntrophic partnerships: electron transfers between two organisms enabling growth on otherwise thermodynamically unfavorable reactions Methanogenic syntrophies. Methanogenic archaea engage in various syntrophic partnerships (121) that involve the transfer of electrons from a fermentative organism to the methanogen via a carrier molecule, such as H2 or acetate. The methanogens use the carrier molecule as electron donor for energy conservation, and the fermentative organism gains energy from the redox reaction that produces the electron carrier only if the methanogens oxidize the carrier molecule, keeping the carrier at a low concentration. Methanogens might also receive electrons directly (121) via conductive pili or nanowires (112) or across conductive iron-oxide minerals (58). Syntrophic interactions enable methanogenesis when methanogenic substrates are limiting, and their establishment can also lead to increased methane production rates (58, 120). The global biogeochemical impact of syntrophic interactions involving methanogenic Euryarchaeota is considerable as they enable the complete degradation of complex organic molecules to carbon dioxide and methane in methanogenic habitats (121). Acetotrophic methanogens can also produce hydrogen and support the hydrogen-dependent dechlorination of xenobiotic compounds by dehalorespiring www.annualreviews.org • Archaea in Biogeochemical Cycles 443 microorganisms (46), further broadening the biogeochemical significance of interactions involving methanogenic archaea. Annu. Rev. Microbiol. 2013.67:437-457. Downloaded from www.annualreviews.org by University of Vienna - Main Library and Archive Services on 09/12/13. For personal use only. AOM: anaerobic oxidation of methane 444 Methane oxidation. Methanogenic archaea are a major source of CH4 emissions, but some of their closest relatives in turn play a critical role in controlling these emissions by oxidizing CH4 back to CO2 (Figure 2a). Methane-oxidizing archaea, also called methanotrophic archaea, are strict anaerobes that gain energy by coupling the oxidation of methane to the reduction of sulfate (SO4 2− ) (129, 131). These organisms belong to the Euryarchaeota and all are representatives of a single taxonomic class, the Methanomicrobia, along with various methanogenic archaea. The 16S rRNA gene sequences of the euryarchaeal ANMEs determine three sequence clusters, namely ANME-1, ANME-2, and ANME-3 (Supplemental Table 1), which are distantly related to each other (16S sequence similarity of 75–92%) and do not form a monophyletic lineage (63). Representatives of the ANME lineages have not been obtained in pure culture; therefore, their taxonomy has not been formally established. These archaea often, but not always, form microbial consortia with sulfate-reducing Deltaproteobacteria (reviewed in 63), which led to the suggestion that the sulfate-dependent anaerobic oxidation of methane (AOM) is a syntrophic process. The very low energy yield of this metabolism, however, led researchers to question the viability of these putative syntrophies (129, 131), and a recent breakthrough study (89) showed that ANME-2 organisms alone perform AOM coupled to dissimilatory sulfate reduction (see Sulfidogenesis, below). No other organism, bacterial or eukaryotic, is known to perform a similar process. The environmental distribution of ANME organisms has been reviewed extensively by Knittel & Boetius (63), and a short account of their report is presented here. Methanotrophic archaea thrive in anoxic environments where both methane and sulfate are present, which often occurs in marine benthic systems. Accordingly, ANME organisms are widely distributed in methane seep ecosystems as well as in marine sediments, where their habitat is restricted to the sulfatemethane transition zone. The abundance of methanotrophic archaea often mirrors the rates of anaerobic methane oxidation measured in those habitats; i.e., dense populations (up to densities greater than 1010 cells cm−3 ) are found at methane seeps, hotspots of AOM, and small populations (<106 cells cm−3 ) occur in marine sediments, where process rates are lower. Methane-oxidizing archaea have also been detected in anoxic water columns, hydrothermal vents, soils, aquifers, and freshwater habitats, the physicochemical settings of which differ widely, further indicating that archaeal methanotrophs are physiologically diverse. The habitat ranges of the ANME-1, ANME2, and ANME-3 lineages are not identical. ANME-1 and ANME-2 are globally distributed and present in similar environments, but one of these two groups usually dominates at a specific geographic location. ANME-3 organisms are essentially present at submarine mud volcanoes sites. The physiological and metabolic bases of these differences, if any, are not clear. Iron (as ferrihydrite) and manganese (as birnessite) are alternative electron acceptors suitable for AOM, and there is evidence that these processes may occur in marine sediments where SO4 2− dependent AOM may also take place (7). The potential rate of SO4 2− -driven AOM was reported to be 4 and 10 times as fast as birnessite- and ferrihydrite-dependent AOM in Eel River Basin sediments, respectively, but the global co-occurrence of these processes, their relative contribution to in situ rates of AOM, and the identity of the microorganisms responsible for the ironand manganese-dependent processes remain to be determined. AOM can also be coupled in a fundamentally different biochemical pathway to the denitrification from nitrite (NO2 − ), a process occurring in freshwater habitats (31, 145) and performed by recently discovered bacteria belonging to the NC10 candidate division (30), but there is no indication that NO2 − - and SO4 2− -driven AOM can occur in the same environment (see, e.g., 25). Offre · Spang · Schleper Annu. Rev. Microbiol. 2013.67:437-457. Downloaded from www.annualreviews.org by University of Vienna - Main Library and Archive Services on 09/12/13. For personal use only. AOM exerts a strong control over ocean CH4 emissions, which account for only 2% of the CH4 released to the atmosphere. Global estimates of the rate of AOM in oceanic environments suggest that a large fraction (>50%) of the gross annual production of CH4 in marine systems is consumed by anaerobic methanotrophs before CH4 is even released to ocean waters (111). The AOM in marine sediments has been attributed to the CH4 -oxidizing activity of ANME archaea, but other microorganisms may be involved (7) and their identity and contribution to the global CH4 budget need to be determined. There are, however, some uncertainties about the ability of ANME archaea to respond to a potential increase in ocean methane production, which could result from an accelerated melting of the massive reservoir of methane hydrates present in the seabed (13). Carbonate precipitation. Anaerobic methanotrophic archaea promote the precipitation of carbonates from the inorganic carbon dissolved in the sediment pore water by locally increasing the alkalinity and inorganic carbon concentration of the water (16, 134). Because carbonates are relatively stable in sediments, their formation results in the long-term storage of carbon in the lithosphere. The carbon of carbonate rocks is re-emitted to the atmosphere only slowly over geological timescales through volcanism associated with tectonic plate subductions, which is part of the long-term carbon cycle (10). Anaerobic methane-oxidizing archaea buffer the global climatic impact of marine CH4 production not only by oxidizing CH4 to CO2 but also by transferring to the lithosphere some of the carbon cycled on a short timescale by living organisms. Nitrogen Cycle Archaea are central to the oxidation of ammonia (NH3 ) to nitrite (NO2 − ) but are also involved in the fixation of dinitrogen (N2 ) gas and denitrification process. The mineralization of organic nitrogen compounds by archaeal organotrophs is not discussed. Nitrogen fixation. Most organisms, including the great majority of archaea, assimilate nitrogen either from inorganic nitrogen sources, such as NH3 and nitrate (NO3 − ), or from nitrogencontaining organic compounds (17). These organic and inorganic nitrogen sources, however, are in short supply within the biosphere, and the maintenance of most life forms is dependent on processes that continuously produce suitable nitrogen compounds from the large reservoir of N2 in the atmosphere. The atmospheric nitrogen enters the food chain essentially via a biogeochemical process called nitrogen fixation, which consists of the reduction of N2 to NH3 (Figure 2b). This process is performed naturally by a number of bacterial and archaeal microorganisms, but the industrial fixation of nitrogen through the Haber-Bosch process produces similarly large quantities of ammonia used as fertilizers in agriculture, which is currently strongly disturbing the nitrogen cycle (19, 41). The ability to fix N2 gas, or diazotrophy, is a widespread feature of methanogenic archaea and is also present in anaerobic methane-oxidizing euryarchaea (Supplemental Table 1), but is expressed only in the absence of other nitrogen sources as for bacterial nitrogen fixers (17, 22, 72). Diazotrophic methanogens belong to three major taxonomic classes, i.e., Methanobacteria, Methanococci, and Methanomicrobia (Supplemental Table 1), and have been isolated from various environments (17, 72, 87), suggesting a widespread occurrence in anoxic habitats (Figure 2b). Diazotrophic methanotrophs belong to the ANME-2 lineage (22, 101) and are known only from methane seep sediments. Cultivation experiments have shown that methanotrophic diazotrophs not only fix but also share nitrogen with bacterial partners in AOM consortia (22). The prevalence of in situ diazotrophic growth by methanogenic and methanotrophic archaea, however, is www.annualreviews.org • Archaea in Biogeochemical Cycles 445 uncertain, and the importance of archaeal nitrogen fixation in providing reduced nitrogen for anaerobic microbial communities remains to be assessed. Lithoautotrophic: describes an organism that uses inorganic compounds as energy sources and fixes carbon from inorganic compounds Annu. Rev. Microbiol. 2013.67:437-457. Downloaded from www.annualreviews.org by University of Vienna - Main Library and Archive Services on 09/12/13. For personal use only. AOA: ammonia-oxidizing archaea 446 Nitrification. Not only is ammonia taken up by most organisms and immobilized in their biomass, it is also oxidized to NO3 − in oxic environments via the nitrification process (Figure 2b), which consists of two steps, i.e., the oxidation of NH3 to NO2 − and its further conversion to NO3 − . Each step is catalyzed by different guilds of microorganisms, namely the ammonia and nitrite oxidizers, respectively. Until recently, it was assumed that only lithotrophic bacteria (66) and, to a limited extent, heterotrophic microorganisms (125) are involved in nitrification. The discovery that lithoautotrophic archaea thriving in oxic and moderate habitats have the capacity to oxidize NH3 to NO2 − (64, 133) was unexpected, and their high numbers in marine and freshwaters, soils and surface sediments, and thermally heated environments suggest a prominent role in global nitrogen cycling (73, 118, 139). A handful of ammonia-oxidizing archaea (AOA), all belonging to Thaumarchaeota (Supplemental Table 1), have been obtained in pure culture or enrichments. They stem from marine and continental habitats and are assigned to four different thaumarchaeal lineages: group 1.1a, group 1.1a associated, group 1.1b, and ThAOA/HWCG III (for a recent review, see 124). Physiological studies have recently shown that the ammonia-oxidizing soil thaumarchaeon “Candidatus Nitrososphaera viennensis” (132) is able to grow on urea as an alternative source of NH3 (Supplemental Table 1), and there is evidence suggesting that urea is an important substrate for archaeal ammonia oxidation in polar waters (1). Furthermore, analysis of the “Candidatus Nitrososphaera gargensis” genome indicated that cyanate (OCN− ) might be used as substrate for archaeal ammonia oxidation (123) (Supplemental Table 1). However, thaumarchaeal relatives of cultivated AOA might not always grow by oxidizing NH3 (91) or they might use different electron acceptors (54, 128). The relative contribution of archaeal and bacterial ammonia oxidizers to the NH3 oxidation process is uncertain, and their respective ecological niches have been discussed (107). Cultivated AOA are characterized by a low tolerance to high NH3 concentrations, and the highest growth inhibitory concentration reported for an AOA, i.e., 20 mM NH4 + (pH 7.5) for “Ca. N. viennensis” (132), is similar to the lowest inhibitory concentration reported for an ammonia-oxidizing bacterium (AOB), i.e., 21.4 mM NH4 + for the JL21 strain (127). However, according to very few studies, AOA also have lower substrate threshold and half-saturation constant (Km ) for ammonium uptake than AOB (85, 107). Together these data suggest that AOA outcompete AOB at low substrate concentrations, such as those in ocean waters, where AOA might be responsible for most of the ammonia oxidation (85). Microcosm experiments indicate that AOA can also play a major role in soil NH3 oxidation (42, 97), even in fertilized soils (116, 135), which could be explained by an uneven distribution of fertilizer in the soil pore space, defining a mosaic of high- and low-ammonia niches. Other studies have also indicated that archaeal ammonia oxidation in soils might be fueled by the mineralization of organic nitrogen compounds (75), suggesting interactions with ammonifying microorganisms. Furthermore, AOA seem to be responsible for most of the ammonia oxidation in some acidic soils (42, 81, 143), and the first acidophilic ammonia oxidizer, the thaumarchaeon “Candidatus Nitrosotalea devanaterra,” was cultivated only recently (71). Ammonia oxidation is the rate-limiting step of the nitrification process and supports the oxidation of NO2 − to NO3 − (Figure 2b) by nitrite-oxidizing bacteria (NOB), but the nature of the interactions between AOA and NOB is still unclear. In the marine environment, especially in oxygen minimum zones, AOA might also support the anaerobic oxidation of NH4 + with NO2 − (anammox) (Figure 2b) by supplying nitrite and consuming oxygen (69, 141). Nitrification has a global impact on the form of inorganic nitrogen (NH3 or NO3 − ) available in ecosystems. The assimilation of NO3 − has a higher energetic cost than that of NH3 because Offre · Spang · Schleper Annu. Rev. Microbiol. 2013.67:437-457. Downloaded from www.annualreviews.org by University of Vienna - Main Library and Archive Services on 09/12/13. For personal use only. NO3 − is first reduced to NH3 before assimilation. Nevertheless, NO3 − is a primary nitrogen source for many phototrophs such as phytoplankton and crops. In soils, nitrification is also responsible for losses of nitrogen (including nitrogen fertilizers), as NO2 − and NO3 − are easily leached to groundwater. High nitrification activity supported by heavy fertilization of agricultural soils may then cause groundwater pollution and ecosystem eutrophication at groundwater resurgence points. Denitrification. The existence of processes regenerating atmospheric N2 gas from oxidized inorganic nitrogen compounds, i.e., NO2 − and NO3 − , is essential for the long-term survival of continental ecosystems, as all earth nitrogen would otherwise accumulate in the ocean due to ongoing nitrification activity. Dinitrogen production occurs mainly via two processes (Figure 2b), namely denitrification (17, 146) and the anaerobic oxidation of NH4 + with NO2 − (anammox) (57). The relative contribution of these two processes on a global scale remains unclear. The anammox is performed solely by bacteria and is not further discussed. Denitrification is a form of anaerobic respiration that uses NO3 − or NO2 − as electron acceptor and results in the sequential formation of gaseous nitrogen compounds, i.e., nitric oxide (NO), nitrous oxide (N2 O), and/or N2 . The process does not always produce N2 as final product, which can lead to the release of significant amounts of NO, a major ozone-depleting substance, and N2 O, a potent greenhouse gas and source of NO (109). Denitrification occurs in many environments including soils, oceans, and freshwaters and is usually performed by facultative anaerobes growing under microaerophilic or anoxic conditions (146). Denitrifiers include various bacteria, some archaea, and even eukaryotes (17, 146). Only a few cultivated archaea are capable of denitrification (Supplemental Table 1). The prevalence of this metabolism in the archaeal domain and the biogeochemical significance of archaeal denitrification have been little investigated. All denitrifying archaea characterized thus far are either organotrophic halophiles or lithoautotrophic (facultative or obligate) hyperthermophiles using NO3 − as electron acceptor (12, 44, 83, 136). The exception is Pyrobaculum aerophilum, which accepts both NO3 − and NO2 − (136). Archaeal denitrifiers produce various mixtures of NO2 − , NO, N2 O, and N2 , and Pyrolobus fumarii releases NH4 + in a biochemically unrelated process called nitrate ammonification (12). A metagenomic analysis suggested that the uncultivated archaeon “Ca. C. subterraneum” might also be able to use NO3 − as electron acceptor (94). The ammonia-oxidizing thaumarchaeon “Candidatus Nitrosopumilus maritimus” and thaumarchaeal enrichment cultures obtained from pelagic waters were shown to produce N2 O (80, 115) (Supplemental Table 1), and the comparison of the isotopic signature of the N2 O emitted by cultures and ocean waters indicated that AOA could account for most of the oceanic production of this greenhouse gas (115), which represents up to 30% of the worldwide emissions of N2 O to the atmosphere. Whether this finding represents a form of nitrifier denitrification as performed by AOB (119) remains unclear, and the biochemical basis of this process has not been determined. Hyperthermophiles: organisms with optimal growth temperature at or above 80◦ C Sulfur Cycle Archaea influence the cycling of sulfur through a variety of processes, which result in the production or the oxidation of sulfidic compounds. Sulfidogenesis. Sulfidogenesis describes the production of hydrogen sulfide (H2 S), a by-product of the metabolism of various facultative and obligate anaerobes, including many archaea. Hydrogen sulfide is also a component of volcanic exhalations, particularly in hydrothermal fields and submarine vents (62). Although sulfidogenesis is a major biogeochemical process, H2 S is a reactive molecule and therefore does not always accumulate in environments where it is produced. It can react with metal ions to form metal sulfides; be oxidized in air, resulting in sulfur deposition; or www.annualreviews.org • Archaea in Biogeochemical Cycles 447 Annu. Rev. Microbiol. 2013.67:437-457. Downloaded from www.annualreviews.org by University of Vienna - Main Library and Archive Services on 09/12/13. For personal use only. be used as electron donor by various microorganisms (see Sulfide Oxidation, below). Cultivated archaeal sulfidogens belong to Euryarchaeota and Crenarchaeota (Supplemental Table 1), and there is no indication that members of other archaeal phyla release H2 S as a main product of their metabolism. Archaeal sulfidogens produce H2 S essentially by the dissimilatory reduction of elemental sulfur (S0 most often present as S8 ), sulfite (SO3 2− ), thiosulfate (S2 O3 2− ), or sulfate (SO4 2− ). The ability to use elemental sulfur as electron acceptor (Figure 2c) is widespread, though not universal, in cultivated representatives of the hyperthermophilic Crenarchaeota as well as in those of Thermococci and Thermoplasmata (Euryarchaeota) (62, 78, 113). Elemental sulfur may be either respired with H2 or organic compounds as electron donors, as performed by various members of Crenarchaeota and Thermoplasmata, or used as electron sinks in fermentation processes carried out by many Thermococci and some representatives of Desulfurococcales (Supplemental Table 1). Some methanogenic archaea, e.g., Methanopyrus and Methanobacterium, produce significant quantities of H2 S when grown with elemental sulfur but do not conserve energy from the reaction (77, 78). All sulfur-reducing archaea, with the exception of H2 S-producing mesophilic methanogens, are (hyper)thermophiles thriving in geothermal environments, high-temperature oil reservoirs (38, 84), and coal beds (126), and they are even associated with deep-sea animals (48). Several bacteria are able to reduce elemental sulfur to H2 S, including members of the Deltaproteobacteria and Epsilonproteobacteria, which are present, for example, in marine and freshwater sediments, continental hot springs, deep-sea hydrothermal vents, and subsurface environments (18, 92). Archaeal and bacterial sulfur reducers therefore can inhabit similar environments, although archaea prevail at higher temperature, lower pH, and in more reducing conditions. The global rate of elemental sulfur reduction to H2 S and the relative contribution of archaeal and bacterial organisms to this process have not been assessed, and the impact of sulfur-reducing archaea on the functioning of microbial communities remains largely unknown. Cultivated archaea able to perform the dissimilatory reduction of SO4 2− to H2 S (Figure 2c) belong to only three genera: Archaeoglobus (Euryarchaeota), Caldivirga (Crenarchaeota), and Thermocladium (Crenarchaeota) (Supplemental Table 1). Archaeoglobus spp. use H2 as electron donors and, in some instances, simple organic acids, while Caldivirga spp. and Thermocladium spp. use complex organic substrates (62, 78). Thiosulfate (S2 O3 2− ) can also be used as electron acceptor by members of all three genera and SO3 2− by Archaeoglobus spp. (Figure 2c and Supplemental Table 1). A few additional genera belonging to Archaeoglobi, Desulfurococcales, and Thermoproteales can also respire SO3 2− and/or S2 O3 2− (Supplemental Table 1). Whereas all these organisms are hyperthermophiles, bacterial sulfate reducers form an abundant and diverse group of microorganisms that occurs in a broad range of anoxic habitats and may account for most of the global biogenic H2 S production (92). Nevertheless, Archaeoglobus spp. thrive in high-temperature oil reservoirs (8, 38), where they may contribute to crude oil souring, which has detrimental impacts on the cost and safety of oil exploitation and its market value. A new perspective on the contribution of archaeal organisms to dissimilatory sulfate reduction and sulfidogenesis has emerged from research showing that ANME-2 archaea (see Methane Oxidation, above) use sulfate as electron acceptor, reducing it to zero valent sulfur, possibly in the form of disulfide (HS2 − ) (Figure 2c and Supplemental Table 1), a completely new process in the sulfur cycle (89). The authors suggest that bisulfide (HS− , i.e., dissociated H2 S) is produced from the dismutation of HS2 − (Figure 2c), also a new process, performed by Deltaproteobacteria often growing in consortia with ANME archaea, and that bisulfide could also be produced, to some extent, directly by the archaeal methanotroph. These processes, if proven to be general features of ANME archaea, including ANME-1 and ANME-3 lineages, and associated Deltaproteobacteria, imply that archaea could have a significant role in the dissimilatory reduction of sulfate and in the biogenesis of sedimentary metal sulfides, and will also force a revision of our view of carbon 448 Offre · Spang · Schleper Annu. Rev. Microbiol. 2013.67:437-457. Downloaded from www.annualreviews.org by University of Vienna - Main Library and Archive Services on 09/12/13. For personal use only. and sulfur cycling in marine sediments. Although the final products of sulfate reduction in deep marine sediments are metal sulfides, essentially pyrite (FeS2 ), the production of H2 S/HS− from AOM at methane seeps occurs in near-surface sediments and supports entire ecosystems, including macrofauna, that are based on the lithoautotrophic oxidation of H2 S (53). Dimethylsulfide (DMS), a volatile organic sulfide (thioether), is another important intermediate in the sulfur cycle. DMS is biogenically produced and released in significant amounts to the atmosphere from aquatic environments. Processes controlling the production of DMS in marine surface waters have received special attention owing to the potential effect of DMS on cloud formation and global climate (21, 70, 108). Various archaeal organisms have the ability to produce but also oxidize DMS (for DMS oxidation, see Methanogenesis, above). All DMS-producing archaea belong to the Euryarchaeota (Supplemental Table 1), including representatives of Halobacteria (78, 90) and possibly members of the uncultivated Marine group II (86). Halobacteria produce DMS via the dissimilatory reduction of dimethylsulfoxide (DMSO) as a form of anaerobic respiration (78, 90), and representatives of Marine group II, widespread in ocean waters, might have a similar ability (86). DMSO is abundant in aquatic environments and could act as an important precursor to the production of DMS (70), but the significance of archaeal DMSO reduction remains to be clarified. Sulfide oxidation. A number of acidophilic archaea (and bacteria) are able to oxidize sulfide minerals (Figure 2c) such as pyrite (FeS2 ), marcasite (FeS2 ), and chalcopyrite (CuFeS2 ) (28, 39, 110). The oxidation of these metal sulfides can result from the direct enzymatic attack of the mineral surface (110), in which case the sulfide compound constitutes the source of electrons and energy of the oxidizing microorganism. However, microorganisms can oxidize metal sulfides indirectly via the production of an oxidant, i.e., Fe3+ , which is generated from the biooxidation of Fe2+ ions dissolved in the water surrounding the mineral particle (110). Archaeal organisms able to oxidize sulfide minerals belong to Sulfolobales (Crenarchaeota) and Thermoplasmatales (Euryarchaeota) (Supplemental Table 1). These organisms and their bacterial counterparts have been found in geothermal environments and mining areas and are thought to pervade in sulfide ore deposits (39, 110). Crenarchaeotes often have the ability to oxidize elemental sulfur (Figure 2c and Supplemental Table 1), like many bacterial sulfide oxidizers, but grow only at high (>65◦ C) temperatures, whereas Thermoplasmatales (euryarchaeotes) include mesophiles that can withstand extreme acidity (pH 0). The exposure of sulfide minerals to moisture and air at mining sites results in increased rates of metal sulfide bio-oxidation, which lead to the production of significant amounts of sulfuric acid, causing serious environmental pollution in the form of acid mine drainage. The relative contributions of bacterial and archaeal organisms to metal sulfide oxidation are unclear, but archaeal organisms can dominate acid mine drainage communities and have an important role in pyrite oxidation (27). Furthermore, bioreactor experiments have shown that archaeal organisms can be more efficient than bacteria in solubilizing sulfide minerals (110, 114), which points to the importance of archaeal organisms for the biomining industry. Although H2 S often reacts with metal ions to form insoluble metal sulfides, H2 S can accumulate in significant amounts in a number of environments (e.g., Black Sea, meromictic lakes, swamps, solfataras). Despite its toxicity toward most living organisms, H2 S supports the growth of many bacteria and few hyperthermophilic archaea (Figure 2c) by serving as electron donor and energy source. Archaeal H2 S oxidizers (Supplemental Table 1) are poorly characterized and include representatives of only two genera: Acidianus (103) and Ferroglobus (44). Growth on H2 S occurs anaerobically with Fe3+ and NO3 − as electron acceptors. Some Acidianus strains are also able to grow on carbon disulfide (CS2 ), a component of volcanic exhalations, by enzymatically converting CS2 to H2 S (122). In contrast, diverse H2 S-oxidizing bacteria are known, including phototrophs, www.annualreviews.org • Archaea in Biogeochemical Cycles 449 chemotrophs, aerobes, anaerobes, autotrophs, and heterotrophs, which are thought to play a significant role in the formation of biogenic sulfur deposits (28). CONCLUSIONS AND PERSPECTIVES Annu. Rev. Microbiol. 2013.67:437-457. Downloaded from www.annualreviews.org by University of Vienna - Main Library and Archive Services on 09/12/13. For personal use only. Archaea have taken center stage in modern ecology and biogeochemistry research, although they were long seen as an assemblage of extremophilic organisms without a major role in the Earth system. Archaea are now recognized to have important roles in global biogeochemical cycles while being diverse and truly ubiquitous in the biosphere. At least two metabolisms essential for global nutrient cyclings are carried out exclusively by archaea: methanogenesis and sulfatedependent anaerobic methane oxidation. The third archaeal metabolism of global importance is aerobic ammonia oxidation. Although both archaea and bacteria contribute to this process and their metabolic and ecological differences need to be clarified, the wide distribution of ammoniaoxidizing archaea in virtually all investigated aerobic habitats indicates a prominent role for these organisms. A full appreciation of the contribution of Archaea to Earth’s biogeochemistry still lies far ahead, and a minimum of two fundamental issues need to be addressed: the inventory of all biogeochemical processes carried out by archaeal organisms and the quantification of archaeal biomass, production, and nutrient cycling activities in natural environments. Characterization of the physiology and metabolism of uncultivated archaea is likely to identify new players of known biogeochemical processes but might also reveal novel nutrient cycling activities. Besides metagenomic studies and single-cell genomics, distribution patterns of microbial groups across physicochemical gradients have been used to raise hypotheses about biogeochemical reactions performed by currently uncultivated archaeal lineages (54). This approach led, for example, to the suggestion that representatives of DSAG could be heterotrophs using ferric iron (Fe3+ ) as electron acceptor (11, 54). Such hypotheses, however, need to be experimentally tested in order to ascertain the biogeochemical function of these organisms. Furthermore, the full appreciation of the biogeochemical impact of an organism can only be achieved by taking into account the whole set of its metabolic pathways. For example, the recent discovery of a pathway for methylphosphonate biosynthesis in “Ca. Nitrosopumilus maritimus” (88) illustrated that this ammonia-oxidizing thaumarchaeon is not only involved in the nitrogen cycle but also takes part in the redox cycling of phosphorus, a poorly characterized component of the global phosphorus cycle. A better understanding of the biogeochemical function of the Archaea will also emerge from progress in our ability to predict and measure biogeochemical fluxes resulting from the metabolic activities of archaeal organisms in their natural environment. This requires tackling the intricate nature of microbial communities to decipher archaeal signatures within a multitude of overlapping processes. Two opposite and complementary paths, i.e., systems ecology and synthetic ecology, also called top-down and bottom-up approaches, respectively, are currently being developed to characterize microbial metabolism on a community-wide scale (142). SUMMARY POINTS 1. Archaea have evolved a number of energy metabolisms using inorganic and organic electron donors and acceptors. 2. Like bacteria, archaea play crucial roles in biogeochemical cycles, particularly the carbon and nitrogen cycles. 3. Methanogenesis and anaerobic methane oxidation are two processes of global importance that are performed exclusively by archaea. 450 Offre · Spang · Schleper 4. Ammonia oxidation, the first step of nitrification, is performed by aerobic Thaumarchaeota, as well as by some bacterial lineages. 5. Thaumarchaeota represent one of the largest populations in oceanic plankton; they also occur in high numbers in terrestrial environments. 6. Sulfate reduction to disulfide as performed by ANME organisms may have a large impact on ocean seafloor sulfur cycling. Annu. Rev. Microbiol. 2013.67:437-457. Downloaded from www.annualreviews.org by University of Vienna - Main Library and Archive Services on 09/12/13. For personal use only. 7. Leaching of metal sulfide by extreme acidophilic archaea in acidic coal mines contributes to the formation of acid mine drainage but may also help recover commercially important metals from sulfide ores. 8. Molecular techniques in addition to classical physiological characterization of isolated strains are indispensable for estimating the role of archaea in geochemical cycles. DISCLOSURE STATEMENT The authors are not aware of any affiliations, memberships, funding, or financial holdings that might be perceived as affecting the objectivity of this review. ACKNOWLEDGMENTS We would like to thank Tim Urich and Jim Prosser for critically reading the manuscript. During the preparation of this review, P.O. was supported by a research grant (09-EuroEEFG-FP-034) from the European Science Foundation. LITERATURE CITED 1. Alonso-Sáez L, Waller AS, Mende DR, Bakker K, Farnelid H, et al. 2012. Role for urea in nitrification by polar marine Archaea. Proc. Natl. Acad. Sci. USA 109:17989–94 2. 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Microbiol. 2013. 67: 437-57 doi: 10.1146/annurev-micro-092412-155614 Archaea in Biogeochemical Cycles Offre, Spang, and Schleper Supplemental Table 1: Electron donors, acceptors, metabolic products, and mode of carbon assimilation of archaeal organisms involved in carbon, nitrogen, and sulfur cycling Processes Electron donor Electron acceptor Products Carbon assimilation Archaea involved Environment Heterotrophy Euryarchaeota: Thermoplasmata, including Marine group II, Halobacteria; Nanohaloarchaea Crenarchaeota: Sulfolobales and few Desulfurococcales and Thermoproteales; Geoarchaeota, evtl. Aigarchaeota Geothermal, alkaline, hypersaline environments; subsurface and marine environments Heterotrophy Euryarchaeota: Archaeoglobi, Thermococci, Thermoplasmata, Halobacteria; Crenarchaeota: Desulfurococcales, Thermoproteales, Acidilobales, Fervidicoccales; Korarchaeota; evtl. Aigarchaeota Geothermal, alkaline, hypersaline environments; subsurface and marine environments Euryarchaeota: Methanopyri + Methanobacteria + Methanococci + Methanomicrobiales + Methanocellales + some representatives of Methanosarcinales Various anoxic environments including geothermal, alkaline, hypersaline environments, but also some oxic environments such as aerated upland soils and oxic lake waters C‐cycle CO2 + H2O Organics O2 Organics NO3 , NO2 , SO4 , S8, + H , organics and others Organic carbon mineralization ‐ ‐ 2‐ CO2 + / ‐ partially oxdized organics (+ ‐ reduced e acceptor) H2 CO2 CH4 + H2O Autotrophy or heterotrophy depending on the organism H2 CH3OH CH4 + H2O Mixotrophy or heterotrophy (unconfirmed) Euryarchaeota: Methanoplasmatales + Methanosphaera spp. + Methanomicrococcus blatticola Digestive tract of insects, cow rumen, human gut H2 CH3NH2 or (CH3)2NH or (CH3)3N CH4 + NH3 Mixotrophy or heterotrophy (unconfirmed) Euryarchaeota: Methanoplasmatales (?) + Methanomicroccus blatticola Digestive tract of insects Euryarchaeota: some representatives of the Methanobacteria, Methanococci, Methanomicrobiales, Methanocellales Various anoxic environments including geothermal, alkaline, and hypersaline environments Euryarchaeota: Methanothermobacter thermoautotrophicus + Methanosarcina barkeri Sewage sludge, freshwater lake mud, and possibly cattle rumen Hydrogenotrophic methanogenesis Formatotrophic methanogenesis HCOO + H Carboxydotrophic methanogenesis CO (H2 produced as intermediate for CO2 reduction) − + CO2 CO2 CH4 + CO2 + 2H2O CH4 + CO2 Autotrophy or heterotrophy depending on the organism Autotrophy or mixotrophy depending on the organism and growth conditions Acetotrophic methanogenesis CH3COO + H Methylotrophic methanogenesis R‐CH3 (R= ‐SH, ‐OH, ‐ NH2, ‐NHCH3, N(CH3)2, + ‐N(CH3)3 ), (CH3)2S ‐ + CH3 group of CH3COO CH3 group of R‐CH3 2‐ SO4 CH4 ‐ CH4 + CO2 Heterotrophy Euryarchaeota: Methanosarcinales Freshwater sediments, rice field soils, termite hindgut, anaerobic digestors, but also some oxic environments such as aerated upland soils and oxic lake waters CH4 + CO2 + RH Heterotrophy Euryarchaeota: Methanosarcinales + Methanoplasmatales (?) Sulfate‐rich sediments, some rumen environments, termite hindgut Mixotrophy (unconfirmed) Euryarchaeota: Methanomicrobia (ANME‐2 lineage) Methane seep ecosystems, sulfate‐ methane transition zones in marine sediments, hydrothermal vents, freshwater sediments, marine water column, deep subsurface Autotrophy (ANME‐1) Euryarchaeota: Methanomicrobia (ANME‐1 and ANME‐3 lineages) Methane seep ecosystems, sulfate‐ methane transition zones in marine sediments, hydrothermal vents, marine water column, deep subsurface Euryarchaeota: representatives of the Methanobacteria, Methanococci, and Methanomicrobia including members of the ANME‐2 lineage Marine and freshwater sediments, geothermally heated sediments, hydrothermal vents, deep subsurface aquifer, and sewage sludge Thaumarchaeota: members of group 1.1a, 1.1b, ThAOA and Nitrosotalea cluster Most oxic environments on Earth, particularly abundant below the euphotic zone in the ocean (>20% of prokaryotes), in oxic sediment layers and soils including acidic soils; also present in continental hot springs Autotrophy or mixotrophy Thaumarchaeota: some members of group 1.1a and 1.1b Most oxic environments on Earth, particularly abundant below the euphotic zone in the ocean (>20% of prokaryotes), in oxic sediment layers and soils including acidic soils; also present in continental thermal springs Autotrophy or mixotrophy (?) Thaumarchaeota: "Candidatus Nitrososphaera gargensis" Garga spring, Kamchatka, Russia ‐ CO2 + HS2 Anaerobic methane oxidation (AOM) CH4 ? CO2 + ? N‐cycle N‐Fixation Methanogenic substrates and CH4; electron carrier: reduced ferredoxin NH3 N2 ‐ O2 NH3 NO2 + H + Autotrophy or mixotrophy Ammonia oxidation (NH2)2CO ‐ OCN (?) Denitrification ‐ + ‐ + O2 NO2 + H O2 NO2 + H (?) ‐ 3 H2 NO H2 NO3 ‐ ‐ 2 NO + NO Autotrophy Euryarchaeota: Ferroglobus placidus Submarine hydrothermal systems N2 Autotrophy Crenarchaeota: Pyrobaculum aerophilum Hot marine water holes 2 Nitrifier denitrification (?) ‐ H2 NO3 Organics NO3 Organics NO3 H2 / organics NO2 NH3 (?) NO2 (?) H2 + NH4 Autotrophy Crenarchaeota: Pyrolobus fumarii Hydrothermally heated black smokers CO2 + N2 and / or N2O Heterotrophy Euryarchaeota: Halobacteria Anoxic niches of hypersaline environments CO2 + N2 Heterotrophy Crenarchaeota: Pyrobaculum aerophilum Hot marine water holes Auto‐/ heterotrophy Crenarchaeota: Pyrobaculum aerophilum Hot marine water holes N2O Autotrophy or mixotrophy Thaumarchaeota: representatives of the group 1.1a and 1.1b Marine waters and soils S8 H2S Autotrophy Crenarchaeota: several representatives of Sulfolobales, Desulfurococcales, Thermoproteales Continental and submarine geothermal environments: solfatara, shallow and deep sea vents Organics S8 H2S + CO2 + / ‐ organics depending ‐ on the e donor Heterotrophy Crenarchaeota: several representatives of Desulfurococcales, Thermoproteales, and Acidilobales; Euryarchaeota: Thermococci + DHVE2 lineage + some representatives of Thermoplasmatales and Halobacteriales Continental and submarine geothermal environments: solfatara, shallow and deep sea vents, smoldering coal refuse pile, sulfide‐ and sulfur‐rich spring, hypersaline environments H2 SO4 Autotrophy Euryarchaeota: Archaeoglobus spp. Hydrothermal vents, high‐temperature oil reservoirs Organics SO4 Heterotrophy Crenarchaeota: Caldivirga spp. + Thermocladium spp.; Euryarchaeota: Archaeoglobus spp. Hydrothermal vents, high‐temperature oil reservoirs, acidic hot springs H2 S2O3 Autotrophy Crenarchaeota: Pyrodictium spp. + Pyrobaculum spp.; Euryarchaeota: Archaeoglobus spp. + Ferroglobus placidus Geothermal environments, deep sea vents, high‐temperature oil reservoirs Organics S2O3 Heterotrophy Crenarchaeota: several representatives of Desulfurococcales and Thermoproteales; Euryarchaeota: Archaeoglobus spp. Geothermal environments, deep sea vents, hot springs, high‐temperature oil reservoirs H2 SO3 Crenarchaeota: Pyrobaculum spp. Geothermal environments Organics SO3 Crenarchaeota: Pyrobaculum spp. + Pyrodictium spp.; Euryarchaeota: Archaeoglobus spp. Geothermal environments ‐ ‐ ‐ ‐ N2 / CO2 + N2 S‐cycle Sulfidogenesis 2‐ 2‐ 2‐ 2‐ 2‐ 2‐ H2S H2S + CO2 + / ‐ organics depending ‐ on the e donor H2S H2S + CO2 + / ‐ organics depending ‐ on the e donor H2S H2S + CO2 + / ‐ organics depending ‐ on the e donor Autotrophy Heterotrophy 3 ‐ 2‐ CH4 SO4 CO2 + HS2 Organics (CH3)2SO (CH3)2S + CO2 FeS2, FeAsS, CuFeS2 orNiS O2 SO4 + H + metal ion(s) Fe O2 Fe (Fe oxidizes FeS2 2+ 2‐ releasing Fe + SO4 + +H ) Sulfide and sulfur oxidation S8 O2 SO4 + H H2S NO3 H2S S8 or Fe CS2 O2 2‐ ‐ + ‐ unclear 2‐ Hypersaline environments and possibly ocean waters Crenarchaeota: Acidianus spp., Metallosphaera spp., Sulfolobus spp., Sulfurococcus spp. Geothermal environments (solfatara), smoldering coal refuse piles and slag heaps, sulfide ores, deep subsurface Euryarchaeota: Ferroplasma and Acidiplasma; Crenarchaeota: Acidianus spp., Metallosphaera spp., Sulfolobus spp., Sulfurococcus spp. Geothermal environments (solfatara), smoldering coal refuse piles and slag heaps, acid mine drainage systems, sulfide ores, deep subsurface Autotrophy Crenarchaeota: several representatives of Sulfolobales Geothermal environments (solfatara), smoldering coal refuse piles and slag heaps Autotrophy Euryarchaeota: Ferroglobus placidus Submarine hydrothermal system Crenarchaeota: Acidianus sulfidivorans Geothermal environments (solfatara) Crenarchaeota: Acidianus sp. A1‐3 Geothermal environment (solfatara) Heterotrophy Autotrophy 3+ S8 + NO2 + NO 3+ Euryarchaeota: some representatives of Halobacteria and possibly Marine group II Autotrophy + 2‐ 3+ 2+ Euryarchaeota: Methanomicrobia (ANME‐2 lineage) Methane seep ecosystems, sulfate‐ methane transition zones in marine sediments, hydrothermal vents, freshwater sediments, marine water column, deep subsurface SO4 + H + Autotrophy or mixotrophy Autotrophy or mixotrophy (unconfirmed) Autotrophy The table was compiled from Kletzin (2007a,b), Liu & Whitman (2008), Chaban et al. (2006), and other references cited in the main text 4