Download Anaerobic bacteria in the sediment oxidaze methane present in the

Biogeochemical processes and global change coursework
Lara Beth Ainley
Miguel Simões Baptista
Buga Berković
student no. 37492
student no. 37574
student no. 37483
Cold seeps - summary
EMBC
May 2009
Faro
Biogeochemical processes and global change coursework
Cold seeps: geochemistry, chemosynthesis and microbial consortium
SUMMARY
Large quantities of methane lie beneath the seafloor dissolved in pore fluids, crystallized in solid phase
gas hydrates, or as a free gas. Little of this methane reaches the oxic water column, given that most of it is
oxidized to CO2 by microbes that inhabit anoxic marine sediments. Cold seeps are the areas of the seafloor where
hydrogen rich fluids leach from the sediment. Methane is the primary seepage fluid characterising cold seeps, but
often hydrogen sulphides and hydrocarbons are also present. Generally, light independent extremophiles,
chemotrophs, archaea and bacteria dominate the biological assemblage of cold seep environments. Cold seeps
are usually found at both geologically active and passive plate margins where the interstitial waters of the
sediment are enriched with methane that is forced upwards and out of the sediment due to pressure gradients.
There are a number of processes responsible for the formation of methane in cold seep sediments.
Methane can form by the decomposition and thermogenic degradation of organic matter. Geologically, methane
hydrates form due to mineral dehydration and gas migration. Overpressuring of the sediment causes these
hydrates to migrate along geological fault lines. Finally, Anaerobic Methane Oxidation (AOM) is an important
biochemical process responsible for the formation of methane in the sediment. Also a form of methanogenesis,
AOM is mediated by the respiration of anaerobic microbial organisms. This process occurs in anoxic sediments
where the methane is oxidised by a syntrophic consortium of anaerobic methanotrophics, typically Archaea, and
often occurs in conjunction with sulphate reduction by symbiotic bacteria. AOM and sulphate reduction lead to the
formation of authigenic carbonates and hydrogen sulphide in the sediments.
Processes of chemosynthesis related to cold seeps are due to the bacterial assemblages in these
habitats. Besides free living bacteria, which can form extensive mats, there can be found animals having symbiotic
bacteria that oxidise sulphur compounds. Such chemotrophic bacteria found in the symbiosis with marine
invertebrates, need reduced inorganic compounds and oxygen. In the case of cold seeps, reduced compounds
can be both sulphide and methane. But the oxygen can usually only be found in narrow boundary zone between
oxic and anoxic environments, due to the rapid oxidation. Hosts of chemoautotrophic bacteria, in this case clams
and worms, serve to gap that boundary to provide everything necessary to their symbiotic bacteria. Anaerobic
bacteria are found where they can oxidise the methane present in the sediment. Simultaneously sulfate rich water
diffuses into the surrounding sediments and is also used by the same group of the bacteria along with the
methane. As methane and sulfate are processed, large amounts of hydrogen sulfide and carbon dioxide are
produced. Hydrogen sulfide is then used along with the oxygen from the water by the symbiotic bacteria. Clams
found in the area differ from other clams found in the oceans, because they have to take up the oxygen and
carbon dioxide through the gills and sulfide through the foot, which is in the sediment, to meet the needs of their
symbiotic bacteria.
Although a growing amount of research is focusing on the microbial presence around cold seeps, still
many questions remain unanswered regarding the biochemical pathways, microbes involved and the physiological
interactions regulating AOM. Recent genetic studies supported the existence of several archaeal groups involved
in AOM. The existence of distinct compounds found in lipid biomarkers and the diversity of archaeal 16S rRN
genes found in methane seep sediments both indicate the presence of several groups of putative methaneoxidizing Archaea, including ANME-1 and ANME-2. Furthermore, the existence of microbial consortia coupling
AOM with sulfate reduction has been confirmed upon the observation of archaeal group ANME-2 as being
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Biogeochemical processes and global change coursework
Cold seeps - summary
physically associated with Desulfosarcina spp, a sulfate-reducing bacteria. In each microbial aggregate, a central
core of ANME-2 is surrounded by a shell of its sulfate-reducing partner. In the reported case, ANME-2 bacteria is
believed to mediate “reverse methanogenesis” and Desulfosarcina spp is assumed to couple the oxidation of
incompletely oxidized byproducts of AOM (e.g. H2, acetate or formate) to the reduction of sulfate. Also, it has been
found that in some regions over 90% of the archaeal and sulfate-reducing bacterial biomass are caused by the
above mentioned consortia, indicating that this type of association dominates the anaerobic methanotrophication
activity at methane cold seeps. Still, circumstantial evidence indicates the possibility of additional methaneoxidizing archaeal types. Both ANME-2 and ANME-1 archaea also appear to exist aggregated with bacterial
partners other than Desulfosarcina and as monospecific aggregates in some circumstances, both enforcing the
belief that they are actively involved in AOM. ANME-1 however, more frequently occur as monospecific mats or
single filaments and appear to be less dependent on the activities of a closely associated bacterial partner. ANME1 and ANME-2 archaea play a crucial role in the establishment and success of methane-seep communities
through the conversion of methane into more readily accessible carbon and energy substrates.
Other studies used fluorescence in situ hybridization (FISH) and detected sulphide-oxidizing Beggiatoa
that generally occur as thick mats. These archaea, however, were also found coupled with delta-proteobacteria
(Desulfosarcina and Desulfococcus) that surrounded a cluster of Beggiatoa. These consortia where highly
abundant in surface sediments at sulphide concentrations < 10mM, and are believed to mediate the anaerobic
oxidation of methane. This process is supposed to be a reversal of methane formation that involves methanogens
and a sulphate reducing partner. These consortia should occur as a result of the benefits of a highly efficient
transfer of intermediates by molecular diffusion.
REFERENCES
Boetius, A., Ravenschlag, K., Schubert, C.J., Rickert, D., Widdel, F., Gieseke, A., Amann, R., Jørgensen, B.B.,
Witte, U., and Pfannkuche, O. (2000) A marine microbial consortium apparently mediating the anaerobic
oxidation of methane. Nature (London, U. K.), 407, 623–626.
Bohrmann, G., Linke, P., Suess, P., Pfannkuche, O. (2000) RV SONNE Cruise Report SO143: TECFLUX-I-1999.
GEOMAR Rep. 93.
Boone, D.R., Johnson, R.L., Liu,Y. (1989) Diffusion of the interspecies electron carriers H 2 and formate in
methanogenic ecosystems and its implications in the measurement of Km and H2 or formate uptake. Appl.
Environ. Microbiol. 55, 1735– 1741.
Coleman, D.F., Ballard, R.D. (2001). A highly concentrated region of cold hydrocarbon seeps in the southeastern
Mediterranean Sea. Geo-Marine Letters. 21: 162-167.
Hoehler, T.M., Alperin, M.J., Albert, D.B., Martens, C.S. (1994) Field and laboratory studies of methane oxidation
in an anoxic marine sediment: Evidence for a methanogen-sulfate reducer consortium. Global Biogeochemical
Cycles 8, 451-463.
Knittel, K., Losekann, T., Boetius, A., Kort, R., Amann, R. (2005). Diversity and Distribution of Methanotrophic
Archaea at Cold Seeps. Applied and Environmental Microbiology. 71 (1): 467-479.
Levin, L.A. (2005). Ecology of cold seep sediments: interactions of fauna with flow, chemistry and microbes.
Oceanography and Marine Biology: A Annual Review. 43 1-46.
Manz, W., Eisenbrecher, M., Neu, T.R., Szewzyk, U. (1998) Abundance and spatial organization of Gram-negative
sulfate-reducing bacteria in activated sludge investigated by in situ probing with specific 16S rRNA targeted
oligonucleotides. FEMS Microbiol. Ecol. 25, 43–61.
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Cold seeps - summary
Orphan, V.J., House, C.H., Hinrichs, K.-U., McKeegan, K.D., DeLong, E.F. (2002) Multiple archaeal groups
mediate methane oxidation in anoxic cold seep sediments. PNAS 99; 11, 7663-7668.
Orphan, V.J., House, C.H., Hinrichs, K.-U., McKeegan, K.D., DeLong, E.F. (2001) Methane-consuming archaea
revealed by direct coupled isotopic and phylogenetic analysis. Science 293, 484–487.
Sleigh, M.A. (ed.) (1987) Microbes in the sea. Ellis Horwood Limited, New York, p.84-86.
Sloan, E.D.D. (1990). Clathrate Hydrates of Natural Gases. Marcel Dekker, New York.
Sørensen K.B., Finster, K., Ramsing, N.B. (2001) Thermodynamic and kinetic requirements in anaerobic methane
oxidizing consortia exclude hydrogen, acetate and methanol as possible electron shuttles. Microb. Ecol. 42,110.
Teske, A., Hinrichs, K.-U., Edgcomb, V., Gomez, A. d. V., Kysela, D., Sylva, S.P., Sogin, M.L., Jannasch, H.W.
(2002) Microbial diversity of hydrothermal sediments in the Guaymas Basin: evidence for anaerobic
methanotrophic communities. Appl. Environ. Microbiol. 68, 1994–2007.
Thiel, V., Peckmann, J., Richnow, H.H., Luth, U., Reitner, J., Michaelis, W. (2001) Molecular signals for anaerobic
methane oxidation in Black Sea seep carbonates and a microbial mat. Marine Chemistry 73, 97-112.
Thomsen T.R., Finster, K., Ramsing, N.B. (2001) Biogeochemical and Molecular Signatures of Anaerobic Methane
Oxidation in a Marine Sediment. Appl Environ Microbiol. 67, 1646 -1656.
Tunnicliffe, V., Juniper, S.K., Sibuet, M. (2003). Reducing environments of the deep sea floor. In: TYLER, P.A.
Ecosystems of the Deep Oceans, Elsevier, Amsterdam. pp. 81-110.
Valentine, D.L., Reeburgh, W.S. (2000) New perspectives on anaerobic methane oxidation. Environmental
Microbiology 2, 477-484.
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Biogeochemical processes and global change coursework
Cold seeps - summary
COLD SEEPS IN THE OCEANS
By Romana Roje (37491), Shauna Narine (38546), Victoria Kessareva (36095) and Jeff Bogart
Abroguena (37489)
Cold seeps are deep-sea environments where methane gas or hydrogen sulfide is released from large storage of the seafloor
by slow diffusion. Fluid flow is driven by pressure gradients created through tectonic compaction, unsteady sedimentation
and diagenetic processes. Cold seeps are mainly located along subduction zones or continental margins and function as
habitat and energy source for chemosynthetic primary production, particularly for unique symbiotic marine communities
inhabiting depth about from15m to more than 7,500m. They are considered the most recent marine habitat first discovered
on the Florida Encampment, Gulf of Mexico in 1984. Brine pools or ‘seafloor lakes’ are hypersaline and methane-rich areas
in the deep sea environment and are linked to cold seep’s symbiotic communities of chemosynthetic microbes and
macrofauna inhabiting the pool edge. Brines evolve by fluid migration through faults which are established above salt
deposits. Mud volcanoes, also associated with seeps are active areas of fluid seepage, discovered in the 1990s. Chemoherms
are massive carbonate structures where discharged methane is converted to carbonate. Gas hydrates consist of water and
methane and are only stable under elevated pressure and low temperature, may evolve together with oil leakages from
hydrocarbon deposits and from decomposition of organic matter. More than 550 species have been identified in cold seeps
which are characterized by considerable variations in the concentrations of sulfide, methane and other chemical constituents
and mechanisms regulating fluid flow. Methane is formed in the marine environment by anaerobic decay of organic matter
in sediments and the water column, and in the form of gas hydrates and at cold water seeps in ocean sediments. Growth and
metabolism of the associated macrofauna are based on a chemoautotrophic endosymbiotic association with the bacteria
which has the ability to chemosynthetically derive energy from hydrogen sulfide when converting to sulphate. Dominant
seep macrofauna (usually also endemic) consists of bivalve families as Vesicomyidae (Calyptogena), Mytilidae,
Thyasiridae, Lucinidae and Solemyidae (Solemya and Acharax); agreggates of Vestimentiferan tube worms (siboglinid
polychaetes) including the most common genus Lamellibrachia; ice worms, pogonophora worms, and sponges as
Cladorhizidae and Hymedesmiidae. But there are also a lot of visiting scavenging and predatory fish (hakes, pancake bat
fish) and crustaceans, deposit-feeding gastropods and holothurians, suspension-feeding polychaetes and anemones.
Reproductive patterns of species occurring at vents and seeps are similar to those of species from the same phyla found in
non-chemosynthetic environments. The most common species, Lamellibrachia sp., grows very slowly (averaging 0.77
cm/year) and commonly reaches lengths over 2 m. It was calculated that individuals in mature aggregations are a minimum
of 100 years old. Three types of bacteria are found ii cold seeps aerobic symbiotic (in gill of clam) or free living on the
surface of sediment (depend on H2S) that make mats, or anaerobic bacteria in the sediment that produce methane and
sulfide. Several archaeal assemblages (dependant on specific environmental conditions) are involved in the anaerobic
consumption of methane. Microbial mediated anaerobic oxidation of methane (AOM) includes methane oxidation with
sulfate and yielding equimolar amounts of carbonate and sulfide. AOM can be mediated by structured consortia consisting
of methanotrophic archaea (ANME group 2) belonging to the order Methanosarcinales (or a second archaeal group
(ANME-1) distantly related to the Methanosarcinales and Methanomicrobiales) and sulfate-reducing bacteria (SRB)
belonging to the Desulfosarcina-Desulfococcus branch (DSS) of the Deltaproteobacteria, as syntrophic partners. Anaerobic
2-
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methane oxidation is coupled to sulfate reduction:
CH4 + SO4 → HCO3 + HS + H2O. At methane seeps authigenic
carbonates may be generated from the biogeochemical turnover yielding hydrogen sulfide and bicarbonate ions which
subsequently react with ions derived from pore waters and the water column to form sulfidic and carbonaceous minerals,
accompanied by an increase in pore water alkalinity, performed by various archaeal assemblages working in syntrophic cooperation with sulfate-reducing bacteria. AOM processes are important for transferring hydrocarbon-derived energy and
carbon to higher trophic levels via grazing or symbiotic interactions, and reducing the accumulation of toxic petroleum
hydrocarbon compounds. And AOM is the major biological sink of the greenhouse gas methane in marine sediments,
consuming up to 90 % of the methane produced there.
MAIN REFERENCES:
Cordes, E. E., Bergquist, D. C., Fisher, C. R., 2009. Macro-Ecology of Gulf of Mexico Cold Seeps. Ann. Rev. of Mar. Sci.,
1: 143-168.
Elvert, M., Suess, E., Greinert, J., Whiticar, M.J.,2000. Archaea mediating anaerobic methane oxidation in deep-sea
sediments at cold seeps of the eastern Aleutian subduction zone. Organ. Geochem. 31:1175-1187.
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Biogeochemical processes and global change coursework
Cold seeps - summary
Juniper, S.K., Sibuet, M., 1987. Cold seep benthic communities in Japan subduction zones. Spatial organization, trophic
strategies and evidence for temporal evolution. Mar.Ecology.Prog. Ser. 40:115-126.
Knittel, K., Losekann, T., Boetius, A., Kort, R., Amann, R., 2005. Diversity and distribution of methanotrophic archaea at
cold seeps. Appl. Environ. Microb. 71: 467–479.
Levin, L., 2005. Ecology of cold seep sediments: interactions of fauna with flow, chemistry and microbes. Oceanogr. and
Mar. Biol. 43: 1-46.
Macdonald, I.R., Reilly, J.F., Guinasso, N.L., Brooks, J.M., Carney, R.S., Bryant, W.A., Bright. T.J., 1990. Chemosynthetic
Mussels at a Brine-Filled Pockmark in the Northern Gulf of Mexico. Sci. 248: 1096-1099.
Orphan, V. J., House, C. H., Hinrichs, K.-U., McKeegan, K. D. & DeLong, E. F., 2001. Multiple archaeal groups mediate
methane oxidation in anoxic cold seep sediments. Sci. 293: 484–487.
Pape, T., Blumenberg, M., Seifert, R., Bohrmann, G., Michaelis, W., 2008. Marine methane biogeochemistry of the Black
Sea: A review. Spring. Sci. & Business Media B.V. 281-311.
Redmond, M., 2002. Indicators of microbial activity in the formation of cold seep carbonates in the Mendocino fracture
zone. MBARI.
Wasmund, K., Kurtböke, D. I., Burns, K. A., Bourne, D. G., 2009. Microbial diversity in sediments associatedwith a
shallowmethane seep in the tropical Timor Sea ofAustralia reveals a novel aerobic methanotroph diversity. FEMS
Microbiology Ecology, 68: 142 – 15.
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