The Experts below are selected from a list of 5118 Experts worldwide ranked by ideXlab platform
Jaap Sinninghe S Damste - One of the best experts on this subject based on the ideXlab platform.
-
intact membrane lipids of candidatus nitrosopumilus maritimus a cultivated representative of the cosmopolitan mesophilic group i Crenarchaeota
Applied and Environmental Microbiology, 2008Co-Authors: Stefan Schouten, Martin Könneke, Ellen C Hopmans, David A Stahl, Marianne Baas, Henry A. Boumann, Sonja Standfest, Jaap Sinninghe S DamsteAbstract:In this study we analyzed the membrane lipid composition of “Candidatus Nitrosopumilus maritimus,” the only cultivated representative of the cosmopolitan group I Crenarchaeota and the only mesophilic isolate of the phylum Crenarchaeota. The core lipids of “Ca. Nitrosopumilus maritimus” consisted of glycerol dialkyl glycerol tetraethers (GDGTs) with zero to four cyclopentyl moieties. Crenarchaeol, a unique GDGT containing a cyclohexyl moiety in addition to four cyclopentyl moieties, was the most abundant GDGT. This confirms unambiguously that crenarchaeol is synthesized by species belonging to the group I.1a Crenarchaeota. Intact polar lipid analysis revealed that the GDGTs have hexose, dihexose, and/or phosphohexose head groups. Similar polar lipids were previously found in deeply buried sediments from the Peru margin, suggesting that they were in part synthesized by group I Crenarchaeota.
-
Intact Membrane Lipids of “Candidatus Nitrosopumilus maritimus,” a Cultivated Representative of the Cosmopolitan Mesophilic Group I Crenarchaeota
Applied and environmental microbiology, 2008Co-Authors: Stefan Schouten, Martin Könneke, Ellen C Hopmans, David A Stahl, Marianne Baas, Henry A. Boumann, Sonja Standfest, Jaap Sinninghe S DamsteAbstract:In this study we analyzed the membrane lipid composition of "Candidatus Nitrosopumilus maritimus," the only cultivated representative of the cosmopolitan group I Crenarchaeota and the only mesophilic isolate of the phylum Crenarchaeota. The core lipids of "Ca. Nitrosopumilus maritimus" consisted of glycerol dialkyl glycerol tetraethers (GDGTs) with zero to four cyclopentyl moieties. Crenarchaeol, a unique GDGT containing a cyclohexyl moiety in addition to four cyclopentyl moieties, was the most abundant GDGT. This confirms unambiguously that crenarchaeol is synthesized by species belonging to the group I.1a Crenarchaeota. Intact polar lipid analysis revealed that the GDGTs have hexose, dihexose, and/or phosphohexose head groups. Similar polar lipids were previously found in deeply buried sediments from the Peru margin, suggesting that they were in part synthesized by group I Crenarchaeota.
-
archaeal tetraether membrane lipid fluxes in the northeastern pacific and the arabian sea implications for tex86 paleothermometry
Paleoceanography, 2006Co-Authors: Cornelia Wuchter, Stuart G Wakeham, Stefan Schouten, Jaap Sinninghe S DamsteAbstract:The newly introduced temperature proxy, the tetraether index of archaeal lipids with 86 carbon atoms (TEX86), is based on the number of cyclopentane moieties in the glycerol dialkyl glycerol tetraether (GDGT) lipids of marine Crenarchaeota. The composition of sedimentary GDGTs used for TEX86 paleothermometry is thought to reflect sea surface temperature (SST). However, marine Crenarchaeota occur ubiquitously in the world oceans over the entire depth range and not just in surface waters. We analyzed the GDGT distribution in settling particulate organic matter collected in sediment traps from the northeastern Pacific Ocean and the Arabian Sea to investigate the seasonal and spatial distribution of the fluxes of Crenarchaeotal GDGTs and the origin of the TEX86 signal transported to the sediment. In both settings the TEX86 measured at all trap deployment depths reflects SST. In the Arabian Sea, analysis of an annual time series showed that the SST estimate based on TEX86 in the shallowest trap at 500 m followed the in situ SST with a 1 to 3 week time delay, likely caused by the relatively low settling speed of sinking particles. This revealed that the GDGT signal that reaches deeper water is derived from the upper water column rather than in situ production of GDGTs. The GDGT temperature signal in deeper traps at 1500 m and 3000 m did not show a seasonal cyclicity observed in the 500 m trap but rather reflected the annual mean SST. This is probably due to a homogenization of the TEX86 SST signal carried by particles as they ultimately reach the interior of the ocean. Our data confirm the use of TEX86 as a temperature proxy of surface ocean waters.
-
occurrence and distribution of tetraether membrane lipids in soils implications for the use of the tex86 proxy and the bit index
Organic Geochemistry, 2006Co-Authors: Johan W H Weijers, O.c. Spaargaren, Stefan Schouten, Jaap Sinninghe S DamsteAbstract:A diverse collection of globally distributed soil samples was analyzed for its glycerol dialkyl glycerol tetraether (GDGT) membrane lipid content. Branched GDGTs, derived from anaerobic soil bacteria, were the most dominant and were found in all soils. Isoprenoid GDGTs, membrane lipids of Archaea, were also present, although in considerably lower concentration. Crenarchaeol, a specific isoprenoid membrane lipid of the non-thermophilic Crenarchaeota, was also regularly detected and its abundance might be related to soil pH. The detection of crenarchaeol in nearly all of the samples is the first report of this type of GDGT membrane lipid in soils and is in agreement with molecular ecological studies, confirming the widespread occurrence of non-thermophilic Crenarchaeota in the terrestrial realm. The fluvial transport of crenarchaeol and other isoprenoid GDGTs to marine and lacustrine environments could possibly bias the BIT index, a ratio between branched GDGTs and crenarchaeol used to determine relative terrestrial organic matter (TOM) input. However, as crenarchaeol in soils is only present in low concentration compared to branched GDGTs, no large effect is expected for the BIT index. The fluvial input of terrestrially derived isoprenoid GDGTs could also bias the TEX86, a proxy used to determine palaeo surface temperatures in marine and lacustrine settings and based on the ratio of cyclopentane-containing isoprenoid GDGTs in marine and lacustrine Crenarchaeota. Indeed, it is shown that a substantial bias in TEX86-reconstructed sea and lake surface temperatures can occur if TOM input is high, e.g. near large river outflows.
-
membrane tetraether lipids of planktonic Crenarchaeota in pliocene sapropels of the eastern mediterranean sea
Palaeogeography Palaeoclimatology Palaeoecology, 2006Co-Authors: Diana Menzel, Ellen C Hopmans, Stefan Schouten, Jaap Sinninghe S DamsteAbstract:Abstract The distribution of glycerol dibiphytanyl glycerol tetraethers (GDGTs), predominantly derived from planktonic Crenarchaeota, were studied in three age-equivalent Pliocene sapropels as well as in the homogeneous intervals, below and above the sapropel. In both the homogeneous intervals and sapropels the dominance of GDGT-0 and crenarchaeol among the GDGTs indicated their origin from planktonic Crenarchaeota as it was found in many other marine sediments. In the homogeneous intervals highest GDGT abundances (normalized to TOC) were measured at the easternmost study Site 967 of the eastern Mediterranean Sea and decreased at the central and western Sites 969 and 964. Within the three studied sapropels large variations in GDGT abundance were observed. The newly established sea surface temperature (SST) proxy, the TEX 86 index, derived from GDGTs of planktonic Crenarchaeota was used to estimate past SST. Comparison with previous obtained SST data using the alkenones from haptophyte algae revealed substantial differences. Whereas the U 37 K′ -based SSTs were almost constant at ca. 25 °C in both the homogeneous intervals and the sapropels, the TEX 86 -based SSTs were 26–29 °C in the homogeneous intervals and decreased to 15–17 °C in the sapropels. The TEX 86 -based SST values outside the sapropel probably reflect summer SST based on a comparison with the present-day Mediterranean Sea. The surprisingly low TEX 86 -based SST estimates for the sapropels showed similarities with those obtained for the contemporary euxinic Black Sea. The distribution of marine Crenarchaeota in the modern Black Sea, i.e. thriving at the deeper and colder chemocline, suggests that this leads to a reduction in TEX 86 , resulting in artificially low SST estimates. A similar situation is inferred for the Pliocene eastern Mediterranean during sapropel deposition since the SST anomaly co-occurs with the build-up of a shallow chemocline.
Stefan Schouten - One of the best experts on this subject based on the ideXlab platform.
-
Diversity of Archaea and detection of Crenarchaeotal amoA genes in the rivers Rhine and Têt
Aquatic Microbial Ecology, 2009Co-Authors: Lydie Herfort, Ben Abbas, Marco J L Coolen, Stefan Schouten, Gerhard J HerndlAbstract:Pelagic archaeal phylogenetic diversity and the potential for Crenarchaeotal nitrification of Group 1.1a were determined in the rivers Rhine and Tet by 16S rRNA sequencing, catalyzed reported deposition-fluorescence in situ hybridization (CARD–FISH) and quantification of 16S rRNA and functional genes. Euryarchaeota were, for the first time, detected in temperate river water even though a net predominance of Crenarchaeotal phylotypes was found. Differences in phylogenic distribution were observed between rivers and seasons. Our data suggest that a few archaeal phylotypes (Euryarchaeota Groups RC-V and LDS, Crenarchaeota Group 1.1a) are widely distributed in pelagic riverine environments whilst others (Euryarchaeota Cluster Sagma-1) may only occur seasonally in river water. Crenarchaeota Group 1.1a has recently been identified as a major nitrifier in the marine environment and phylotypes of this group were also present in both rivers, where they represented 0.3% of the total pelagic microbial community. Interestingly, a generally higher abundance of Crenarchaeota Group 1.1a was found in the Rhine than in the Tet, and Crenarchaeotal ammonia monooxygenase gene (amoA) was also detected in the Rhine, with higher amoA copy numbers measured in February than in September. This suggests that some of the Crenarchaeota present in river waters have the ability to oxidize ammonia and that riverine Crenarchaeotal nitrification of Group 1.1a may vary seasonally.
-
intact membrane lipids of candidatus nitrosopumilus maritimus a cultivated representative of the cosmopolitan mesophilic group i Crenarchaeota
Applied and Environmental Microbiology, 2008Co-Authors: Stefan Schouten, Martin Könneke, Ellen C Hopmans, David A Stahl, Marianne Baas, Henry A. Boumann, Sonja Standfest, Jaap Sinninghe S DamsteAbstract:In this study we analyzed the membrane lipid composition of “Candidatus Nitrosopumilus maritimus,” the only cultivated representative of the cosmopolitan group I Crenarchaeota and the only mesophilic isolate of the phylum Crenarchaeota. The core lipids of “Ca. Nitrosopumilus maritimus” consisted of glycerol dialkyl glycerol tetraethers (GDGTs) with zero to four cyclopentyl moieties. Crenarchaeol, a unique GDGT containing a cyclohexyl moiety in addition to four cyclopentyl moieties, was the most abundant GDGT. This confirms unambiguously that crenarchaeol is synthesized by species belonging to the group I.1a Crenarchaeota. Intact polar lipid analysis revealed that the GDGTs have hexose, dihexose, and/or phosphohexose head groups. Similar polar lipids were previously found in deeply buried sediments from the Peru margin, suggesting that they were in part synthesized by group I Crenarchaeota.
-
Intact Membrane Lipids of “Candidatus Nitrosopumilus maritimus,” a Cultivated Representative of the Cosmopolitan Mesophilic Group I Crenarchaeota
Applied and environmental microbiology, 2008Co-Authors: Stefan Schouten, Martin Könneke, Ellen C Hopmans, David A Stahl, Marianne Baas, Henry A. Boumann, Sonja Standfest, Jaap Sinninghe S DamsteAbstract:In this study we analyzed the membrane lipid composition of "Candidatus Nitrosopumilus maritimus," the only cultivated representative of the cosmopolitan group I Crenarchaeota and the only mesophilic isolate of the phylum Crenarchaeota. The core lipids of "Ca. Nitrosopumilus maritimus" consisted of glycerol dialkyl glycerol tetraethers (GDGTs) with zero to four cyclopentyl moieties. Crenarchaeol, a unique GDGT containing a cyclohexyl moiety in addition to four cyclopentyl moieties, was the most abundant GDGT. This confirms unambiguously that crenarchaeol is synthesized by species belonging to the group I.1a Crenarchaeota. Intact polar lipid analysis revealed that the GDGTs have hexose, dihexose, and/or phosphohexose head groups. Similar polar lipids were previously found in deeply buried sediments from the Peru margin, suggesting that they were in part synthesized by group I Crenarchaeota.
-
Variations in spatial and temporal distribution of Archaea in the North Sea in relation to environmental variables
FEMS Microbiology Ecology, 2007Co-Authors: Lydie Herfort, Ben Abbas, Cornelia Wuchter, Jan P. Boon, Marcel J W Veldhuis, Marco J L Coolen, Stefan Schouten, Gerhard J HerndlAbstract:The spatial and temporal distribution of pelagic Archaea was studied in the southern North Sea by rRNA hybridization, sequencing and quantification of 16S rRNA gene and membrane lipid analyses and related to physical, chemical and biological parameters to determine the factors influencing archaeal biogeography. A clear temporal variability was observed, with marine Crenarchaeota (Group I.1a) being relatively more abundant in winter and Euryarchaeota dominating the archaeal assemblage in spring and summer. Spatial differences in the lateral distribution of Crenarchaeota were also evident. In fact, their abundance was positively correlated with the copy number of the gene encoding the α subunit of Crenarchaeotal ammonia monooxygenase (amoA) and with concentrations of ammonia, nitrate, nitrite and phosphorus. This suggests that most Crenarchaeota in the North Sea are nitrifiers and that their distribution is determined by nutrient concentrations. However, Crenarchaeota were not abundant when larger phytoplankton (>3 μm) dominated the algal population. It is hypothesized that together with nutrient concentration, phytoplankton biomass and community structure can predict Crenarchaeotal abundance in the southern North Sea. Euryarchaeotal abundance was positively correlated with chlorophyll a concentrations, but not with phytoplankton community structure. Whether this is related to the potential of Euryarchaeota to perform aerobic anoxygenic phototrophy remains to be shown, but the conspicuous seasonal distribution pattern of Crenarchaeota and Euryarchaeota suggests that they occupy a different ecological niche.
-
occurrence and distribution of tetraether membrane lipids in soils implications for the use of the tex86 proxy and the bit index
Organic Geochemistry, 2006Co-Authors: Johan W H Weijers, O.c. Spaargaren, Stefan Schouten, Jaap Sinninghe S DamsteAbstract:A diverse collection of globally distributed soil samples was analyzed for its glycerol dialkyl glycerol tetraether (GDGT) membrane lipid content. Branched GDGTs, derived from anaerobic soil bacteria, were the most dominant and were found in all soils. Isoprenoid GDGTs, membrane lipids of Archaea, were also present, although in considerably lower concentration. Crenarchaeol, a specific isoprenoid membrane lipid of the non-thermophilic Crenarchaeota, was also regularly detected and its abundance might be related to soil pH. The detection of crenarchaeol in nearly all of the samples is the first report of this type of GDGT membrane lipid in soils and is in agreement with molecular ecological studies, confirming the widespread occurrence of non-thermophilic Crenarchaeota in the terrestrial realm. The fluvial transport of crenarchaeol and other isoprenoid GDGTs to marine and lacustrine environments could possibly bias the BIT index, a ratio between branched GDGTs and crenarchaeol used to determine relative terrestrial organic matter (TOM) input. However, as crenarchaeol in soils is only present in low concentration compared to branched GDGTs, no large effect is expected for the BIT index. The fluvial input of terrestrially derived isoprenoid GDGTs could also bias the TEX86, a proxy used to determine palaeo surface temperatures in marine and lacustrine settings and based on the ratio of cyclopentane-containing isoprenoid GDGTs in marine and lacustrine Crenarchaeota. Indeed, it is shown that a substantial bias in TEX86-reconstructed sea and lake surface temperatures can occur if TOM input is high, e.g. near large river outflows.
Christa Schleper - One of the best experts on this subject based on the ideXlab platform.
-
Distribution of Crenarchaeota representatives in terrestrial hot springs of Russia and Iceland.
Applied and environmental microbiology, 2008Co-Authors: Anna A Perevalova, Christa Schleper, T V Kolganova, Elizaveta Bonch-osmolovskaya, Nils-kåre Birkeland, Aleksander V LebedinskyAbstract:Culture-independent (PCR with Crenarchaeota-specific primers and subsequent denaturing gradient gel electrophoresis) and culture-dependent approaches were used to study the diversity of Crenarchaeota in terrestrial hot springs of the Kamchatka Peninsula and the Lake Baikal region (Russia) and of Iceland. Among the phylotypes detected there were relatives of both cultured (mainly hyperthermophilic) and uncultured Crenarchaeota. It was found that there is a large and diverse group of uncultured Crenarchaeota that inhabit terrestrial hot springs with moderate temperatures (55 to 70°C). Two of the lineages of this group were given phenotypic characterization, one as a result of cultivation in an enrichment culture and another one after isolation of a pure culture, “Fervidococcus fontis,” which proved to be a moderately thermophilic, neutrophilic (optimum pH of 6.0 to 7.5), anaerobic organotroph.
-
Genomic analysis of the uncultivated marine crenarchaeote Cenarchaeum symbiosum.
Proceedings of the National Academy of Sciences of the United States of America, 2006Co-Authors: Steven J. Hallam, Christa Schleper, Christina M. Preston, Paul G. Richardson, Konstantinos T. Konstantinidis, Nik Putnam, Yoh-ichi Watanabe, Junichi Sugahara, Jose De La Torre, Edward F. DelongAbstract:Crenarchaeota are ubiquitous and abundant microbial constituents of soils, sediments, lakes, and ocean waters. To further describe the cosmopolitan nonthermophilic Crenarchaeota, we analyzed the genome sequence of one representative, the uncultivated sponge symbiont Cenarchaeum symbiosum. C. symbiosum genotypes coinhabiting the same host partitioned into two dominant populations, corresponding to previously described a- and b-type ribosomal RNA variants. Although they were syntenic, overlapping a- and b-type ribotype genomes harbored significant variability. A single tiling path comprising the dominant a-type genotype was assembled and used to explore the genomic properties of C. symbiosum and its planktonic relatives. Of 2,066 ORFs, 55.6% matched genes with predicted function from previously sequenced genomes. The remaining genes partitioned between functional RNAs (2.4%) and hypotheticals (42%) with limited homology to known functional genes. The latter category included some genes likely involved in the archaeal-sponge symbiotic association. Conversely, 525 C. symbiosum ORFs were most highly similar to sequences from marine environmental genomic surveys, and they apparently represent orthologous genes from free-living planktonic Crenarchaeota. In total, the C. symbiosum genome was remarkably distinct from those of other known Archaea and shared many core metabolic features in common with its free-living planktonic relatives.
-
Ammonia-oxidising Crenarchaeota: important players in the nitrogen cycle?
Trends in microbiology, 2006Co-Authors: Graeme W Nicol, Christa SchleperAbstract:Cultivation-independent molecular surveys show that members of the kingdom Crenarchaeota within the domain Archaea represent a substantial component of microbial communities in aquatic and terrestrial environments. Recently, metagenomic studies have revealed that such Crenarchaeota contain and express genes related to those of bacterial ammonia monooxygenases. Furthermore, a marine chemolithoautotrophic strain was isolated that uses ammonia as a sole energy source. Considering the ubiquity and abundance of Crenarchaeota, these findings considerably challenge the accepted view of the microbial communities involved in global nitrogen cycling. However, the quantitative contribution of Archaea to nitrification in marine and terrestrial environments still remains to be elucidated.
-
Pathways of carbon assimilation and ammonia oxidation suggested by environmental genomic analyses of marine Crenarchaeota.
PLoS biology, 2006Co-Authors: Steven J. Hallam, Christa Schleper, Tracy J. Mincer, Christina M. Preston, Katie Roberts, Paul G. Richardson, Edward F. DelongAbstract:Marine Crenarchaeota represent an abundant component of oceanic microbiota with potential to significantly influence biogeochemical cycling in marine ecosystems. Prior studies using specific archaeal lipid biomarkers and isotopic analyses indicated that planktonic Crenarchaeota have the capacity for autotrophic growth, and more recent cultivation studies support an ammonia-based chemolithoautotrophic energy metabolism. We report here analysis of fosmid sequences derived from the uncultivated marine crenarchaeote, Cenarchaeum symbiosum, focused on the reconstruction of carbon and energy metabolism. Genes predicted to encode multiple components of a modified 3-hydroxypropionate cycle of autotrophic carbon assimilation were identified, consistent with utilization of carbon dioxide as a carbon source. Additionally, genes predicted to encode a near complete oxidative tricarboxylic acid cycle were also identified, consistent with the consumption of organic carbon and in the production of intermediates for amino acid and cofactor biosynthesis. Therefore, C. symbiosum has the potential to function either as a strict autotroph, or as a mixotroph utilizing both carbon dioxide and organic material as carbon sources. From the standpoint of energy metabolism, genes predicted to encode ammonia monooxygenase subunits, ammonia permease, urease, and urea transporters were identified, consistent with the use of reduced nitrogen compounds as energy sources fueling autotrophic metabolism. Homologues of these genes, recovered from ocean waters worldwide, demonstrate the conservation and ubiquity of crenarchaeal pathways for carbon assimilation and ammonia oxidation. These findings further substantiate the likely global metabolic importance of Crenarchaeota with respect to key steps in the biogeochemical transformation of carbon and nitrogen in marine ecosystems.
-
Archaea predominate among ammonia-oxidizing prokaryotes in soils
Nature, 2006Co-Authors: S. Leininger, S. C. Schuster, James Ivor Prosser, J Qi, Tim Urich, Lorenz Schwark, Michael Schloter, Graeme W Nicol, Christa SchleperAbstract:Ammonia oxidation is the first step in nitrification, a key process in the global nitrogen cycle that results in the formation of nitrate through microbial activity. The increase in nitrate availability in soils is important for plant nutrition, but it also has considerable impact on groundwater pollution owing to leaching. Here we show that archaeal ammonia oxidizers are more abundant in soils than their well-known bacterial counterparts. We investigated the abundance of the gene encoding a subunit of the key enzyme ammonia monooxygenase (amoA) in 12 pristine and agricultural soils of three climatic zones. amoA gene copies of Crenarchaeota (Archaea) were up to 3,000-fold more abundant than bacterial amoA genes. High amounts of Crenarchaeota-specific lipids, including crenarchaeol, correlated with the abundance of archaeal amoA gene copies. Furthermore, reverse transcription quantitative PCR studies and complementary DNA analysis using novel cloning-independent pyrosequencing technology demonstrated the activity of the archaea in situ and supported the numerical dominance of archaeal over bacterial ammonia oxidizers. Our results indicate that Crenarchaeota may be the most abundant ammonia-oxidizing organisms in soil ecosystems on Earth.
Elizaveta Bonch-osmolovskaya - One of the best experts on this subject based on the ideXlab platform.
-
Biodiversity of Thermophilic Prokaryotes with Hydrolytic Activities in Hot Springs of Uzon Caldera, Kamchatka (Russia)
Applied and Environmental Microbiology, 2009Co-Authors: Ilya V Kublanov, Anna A Perevalova, G B Slobodkina, Aleksander V Lebedinsky, Salima Kh Bidzhieva, T V Kolganova, E N Kaliberda, L D Rumsh, Thomas Haertle, Elizaveta Bonch-osmolovskayaAbstract:Samples of water from the hot springs of Uzon Caldera with temperatures from 68 to 87 C and pHs of 4.1 to 7.0, supplemented with proteinaceous (albumin, casein, or alpha- or beta-keratin) or carbohydrate (cellulose, carboxymethyl cellulose, chitin, or agarose) biological polymers, were filled with thermal water and incubated at the same sites, with the contents of the tubes freely accessible to the hydrothermal fluid. As a result, several enrichment cultures growing in situ on different polymeric substrates were obtained. Denaturing gradient gel electrophoresis (DGGE) analysis of 16S rRNA gene fragments obtained after PCR with Bacteria-specific primers showed that the bacterial communities developing on carbohydrates included the genera Caldicellulosiruptor and Dictyoglomus and that those developing on proteins contained members of the Thermotogales order. DGGE analysis performed after PCR with Archaea- and Crenarchaeota-specific primers showed that archaea related to uncultured environmental clones, particularly those of the Crenarchaeota phylum, were present in both carbohydrate- and protein-degrading communities. Five isolates obtained from in situ enrichments or corresponding natural samples of water and sediments represented the bacterial genera Dictyoglomus and Caldanaerobacter as well as new archaea of the Crenarchaeota phylum. Thus, in situ enrichment and consequent isolation showed the diversity of thermophilic prokaryotes competing for biopolymers in microbial communities of terrestrial hot springs.
-
Biodiversity of thermophilic prokaryotes with hydrolytic activities in hot springs of Uzon Caldera, Kamchatka (Russia).
Applied and environmental microbiology, 2008Co-Authors: Ilya V Kublanov, Anna A Perevalova, G B Slobodkina, Aleksander V Lebedinsky, Salima Kh Bidzhieva, T V Kolganova, E N Kaliberda, L D Rumsh, Thomas Haertle, Elizaveta Bonch-osmolovskayaAbstract:Samples of water from the hot springs of Uzon Caldera with temperatures from 68 to 87 degrees C and pHs of 4.1 to 7.0, supplemented with proteinaceous (albumin, casein, or alpha- or beta-keratin) or carbohydrate (cellulose, carboxymethyl cellulose, chitin, or agarose) biological polymers, were filled with thermal water and incubated at the same sites, with the contents of the tubes freely accessible to the hydrothermal fluid. As a result, several enrichment cultures growing in situ on different polymeric substrates were obtained. Denaturing gradient gel electrophoresis (DGGE) analysis of 16S rRNA gene fragments obtained after PCR with Bacteria-specific primers showed that the bacterial communities developing on carbohydrates included the genera Caldicellulosiruptor and Dictyoglomus and that those developing on proteins contained members of the Thermotogales order. DGGE analysis performed after PCR with Archaea- and Crenarchaeota-specific primers showed that archaea related to uncultured environmental clones, particularly those of the Crenarchaeota phylum, were present in both carbohydrate- and protein-degrading communities. Five isolates obtained from in situ enrichments or corresponding natural samples of water and sediments represented the bacterial genera Dictyoglomus and Caldanaerobacter as well as new archaea of the Crenarchaeota phylum. Thus, in situ enrichment and consequent isolation showed the diversity of thermophilic prokaryotes competing for biopolymers in microbial communities of terrestrial hot springs.
-
Distribution of Crenarchaeota representatives in terrestrial hot springs of Russia and Iceland.
Applied and environmental microbiology, 2008Co-Authors: Anna A Perevalova, Christa Schleper, T V Kolganova, Elizaveta Bonch-osmolovskaya, Nils-kåre Birkeland, Aleksander V LebedinskyAbstract:Culture-independent (PCR with Crenarchaeota-specific primers and subsequent denaturing gradient gel electrophoresis) and culture-dependent approaches were used to study the diversity of Crenarchaeota in terrestrial hot springs of the Kamchatka Peninsula and the Lake Baikal region (Russia) and of Iceland. Among the phylotypes detected there were relatives of both cultured (mainly hyperthermophilic) and uncultured Crenarchaeota. It was found that there is a large and diverse group of uncultured Crenarchaeota that inhabit terrestrial hot springs with moderate temperatures (55 to 70°C). Two of the lineages of this group were given phenotypic characterization, one as a result of cultivation in an enrichment culture and another one after isolation of a pure culture, “Fervidococcus fontis,” which proved to be a moderately thermophilic, neutrophilic (optimum pH of 6.0 to 7.5), anaerobic organotroph.
Cornelia Wuchter - One of the best experts on this subject based on the ideXlab platform.
-
Variations in spatial and temporal distribution of Archaea in the North Sea in relation to environmental variables
FEMS Microbiology Ecology, 2007Co-Authors: Lydie Herfort, Ben Abbas, Cornelia Wuchter, Jan P. Boon, Marcel J W Veldhuis, Marco J L Coolen, Stefan Schouten, Gerhard J HerndlAbstract:The spatial and temporal distribution of pelagic Archaea was studied in the southern North Sea by rRNA hybridization, sequencing and quantification of 16S rRNA gene and membrane lipid analyses and related to physical, chemical and biological parameters to determine the factors influencing archaeal biogeography. A clear temporal variability was observed, with marine Crenarchaeota (Group I.1a) being relatively more abundant in winter and Euryarchaeota dominating the archaeal assemblage in spring and summer. Spatial differences in the lateral distribution of Crenarchaeota were also evident. In fact, their abundance was positively correlated with the copy number of the gene encoding the α subunit of Crenarchaeotal ammonia monooxygenase (amoA) and with concentrations of ammonia, nitrate, nitrite and phosphorus. This suggests that most Crenarchaeota in the North Sea are nitrifiers and that their distribution is determined by nutrient concentrations. However, Crenarchaeota were not abundant when larger phytoplankton (>3 μm) dominated the algal population. It is hypothesized that together with nutrient concentration, phytoplankton biomass and community structure can predict Crenarchaeotal abundance in the southern North Sea. Euryarchaeotal abundance was positively correlated with chlorophyll a concentrations, but not with phytoplankton community structure. Whether this is related to the potential of Euryarchaeota to perform aerobic anoxygenic phototrophy remains to be shown, but the conspicuous seasonal distribution pattern of Crenarchaeota and Euryarchaeota suggests that they occupy a different ecological niche.
-
archaeal tetraether membrane lipid fluxes in the northeastern pacific and the arabian sea implications for tex86 paleothermometry
Paleoceanography, 2006Co-Authors: Cornelia Wuchter, Stuart G Wakeham, Stefan Schouten, Jaap Sinninghe S DamsteAbstract:The newly introduced temperature proxy, the tetraether index of archaeal lipids with 86 carbon atoms (TEX86), is based on the number of cyclopentane moieties in the glycerol dialkyl glycerol tetraether (GDGT) lipids of marine Crenarchaeota. The composition of sedimentary GDGTs used for TEX86 paleothermometry is thought to reflect sea surface temperature (SST). However, marine Crenarchaeota occur ubiquitously in the world oceans over the entire depth range and not just in surface waters. We analyzed the GDGT distribution in settling particulate organic matter collected in sediment traps from the northeastern Pacific Ocean and the Arabian Sea to investigate the seasonal and spatial distribution of the fluxes of Crenarchaeotal GDGTs and the origin of the TEX86 signal transported to the sediment. In both settings the TEX86 measured at all trap deployment depths reflects SST. In the Arabian Sea, analysis of an annual time series showed that the SST estimate based on TEX86 in the shallowest trap at 500 m followed the in situ SST with a 1 to 3 week time delay, likely caused by the relatively low settling speed of sinking particles. This revealed that the GDGT signal that reaches deeper water is derived from the upper water column rather than in situ production of GDGTs. The GDGT temperature signal in deeper traps at 1500 m and 3000 m did not show a seasonal cyclicity observed in the 500 m trap but rather reflected the annual mean SST. This is probably due to a homogenization of the TEX86 SST signal carried by particles as they ultimately reach the interior of the ocean. Our data confirm the use of TEX86 as a temperature proxy of surface ocean waters.
-
Archaeal nitrification in the ocean
Proceedings of the National Academy of Sciences of the United States of America, 2006Co-Authors: Cornelia Wuchter, Ben Abbas, Marco J L Coolen, Lydie Herfort, Gerhard J Herndl, Eva Teira, Judith Van Bleijswijk, Peer H. A. Timmers, Marc Strous, Jack J. MiddelburgAbstract:Marine Crenarchaeota are the most abundant single group of prokaryotes in the ocean, but their physiology and role in marine biogeochemical cycles are unknown. Recently, a member of this clade was isolated from a sea aquarium and shown to be capable of nitrification, tentatively suggesting that Crenarchaeota may play a role in the oceanic nitrogen cycle. We enriched a crenarchaeote from North Sea water and showed that its abundance, and not that of bacteria, correlates with ammonium oxidation to nitrite. A time series study in the North Sea revealed that the abundance of the gene encoding for the archaeal ammonia monooxygenase alfa subunit (amoA) is correlated with a decline in ammonium concentrations and with the abundance of Crenarchaeota. Remarkably, the archaeal amoA abundance was 1–2 orders of magnitude higher than those of bacterial nitrifiers, which are commonly thought to mediate the oxidation of ammonium to nitrite in marine environments. Analysis of Atlantic waters of the upper 1,000 m, where most of the ammonium regeneration and oxidation takes place, showed that Crenarchaeotal amoA copy numbers are also 1–3 orders of magnitude higher than those of bacterial amoA. Our data thus suggest a major role for Archaea in oceanic nitrification.
-
ecology and membrane lipid distribution of marine Crenarchaeota implications for tex86 paleothermometry
Geologica Ultraiectina, 2006Co-Authors: Cornelia WuchterAbstract:Archaea form one of the three domains of life on Earth and together with the bacteria form the prokaryotes. In the marine environment planktonic Archaea consist of two major groups, the Crenarchaeota and the Euryarchaeota of which the former appears to be the most abundant and may account for ca. 20% of all prokaryotic cells in the global ocean. Despite the fact that marine Crenarchaeota constitute a substantial fraction of the picoplankton in the world oceans, little is known about their basic metabolic requirements. Marine Crenarchaeota inherit unique tetraether membrane lipids and recent studies done on core top sediments showed that the distribution of sedimentary tetraether lipids from different geographic locations varies with sea surface temperature (SST). The change of the tetraether lipid distribution was expressed in an index of the lipid isomers, which was named the Tetraether Index of lipids with 86 carbon atoms, the TEX86. This index was considered as a new temperature proxy for reconstruction of SST in paleoenvironments. During my thesis, I focused on two major objectives. First, to shed more light on the physiology of marine Crenarchaeota and second, to validate the newly introduced temperature proxy TEX86. In order to study the carbon acquisition mechanism of marine Crenarchaeota, seawater-filled mesocosm tank were incubated with 13C bicarbonate and the results showed that the 13C was mainly incorporated in the Crenarchaeotal membrane lipids. This 13C tracer experiments demonstrated that at least some marine Crenarchaeota actively utilize bicarbonate and appear to be autotrophs. Field studies, applying functional gene analyses and quantitative PCR, revealed that marine Crenarchaeota occur highly seasonal in surface waters during the winter and were actively involved in the marine nitrogen cycle as nitrifiers. In the laboratory temperature experiments were performed on a Crenarchaeotal enrichment culture in order to validate the newly introduced temperature proxy TEX86. The results of this experiments showed that the membrane lipid distribution of the enriched marine Crenarchaeotal species is mainly determined by incubation temperature, thus, the TEX86 reflect mainly temperature. Marine Crenarchaeota occur throughout the water column so it was essential to study the origin of the tetraether lipids which reaches the sediment. Tetraether lipid studies done on suspended particulate organic matter (POM) samples and sediment trap material from different oceanic regimes showed that the TEX86 correlates best with SST in different depth of the water column. The archaeal lipid signal which reaches the sediment is mainly derived from the upper 100m of the water column probably due to more effective grazing and repackaging processes. In summary, the experimental work and field studies described in the first part revealed that at least some marine Crenarchaeota are chemolithoautotrophic organisms and thus, they may play an important but as yet not recognized part in the marine carbon and nitrogen cycle. The experimental work and field studies described in the second part validates the newly introduced temperature proxy TEX86. Therefore it should be possible to use the TEX86 for reconstruction of the upper water column temperatures in ancient environments.
-
temperature dependent variation in the distribution of tetraether membrane lipids of marine Crenarchaeota implications for tex86 paleothermometry
Paleoceanography, 2004Co-Authors: Cornelia Wuchter, Marco J L Coolen, Stefan Schouten, Jaap Sinninghe S DamsteAbstract:[1] Recently, a new geochemical temperature proxy, the TEX86, was introduced. This proxy is based on the number of cyclopentane moieties in the glycerol dialkyl glycerol tetraethers (GDGTs) of the membrane lipids of marine Crenarchaeota, which changes as a response to temperature. However, until now, only sediment data have been used to establish this proxy, and experimental work is missing. We performed mesocosm studies with marine Crenarchaeota incubated at temperatures ranging from 5 to 35°C and salinities of 27 and 35‰ to test the validity of the TEX86 proxy. Growth of marine Crenarchaeota in these mesocosms was evident from the substantial increase in the concentration of marine Crenarchaeotal membrane lipids with amounts up to 3400 ng/L. With increasing temperature, an increase in the number of cyclopentane moieties in the Crenarchaeotal membrane lipids was observed. Different salinities did not show any effect on the GDGT distribution. The TEX86 showed a significant linear correlation to incubation temperature: TEX86 = 0.015 × T + 0.10 (r2 = 0.79). This equation has a similar slope to the correlation obtained from core tops but differs in the intersection (TEX86 = 0.015 × T + 0.28, r2 = 0.92). This difference is mainly determined by the smaller amount of the regioisomer of crenarchaeol in the incubation series compared to core top samples. These incubation experiments indicates that water temperature is indeed the major controlling factor for the membrane distribution of marine Crenarchaeota and confirms that the TEX86 proxy depends on a physiological response to regulate membrane fluidity.