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Elizabeth Saunders - One of the best experts on this subject based on the ideXlab platform.
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complete genome sequence of methanoculleus marisnigri romesser et al 1981 type strain jr1
Standards in Genomic Sciences, 2009Co-Authors: Iain Anderson, Eileen Dalin, Elizabeth Saunders, Kerrie Barry, Magdalena Sieprawskalupa, Alla Lapidus, Matt Nolan, Alex Copeland, Hope TiceAbstract:Methanoculleus marisnigri Romesser et al. 1981 is a methanogen belonging to the order Methanomicrobiales within the archaeal phylum Euryarchaeota. The type strain, JR1, was isolated from anoxic sediments of the Black Sea. M. marisnigri is of phylogenetic interest because at the time the sequencing project began only one genome had previously been sequenced from the order Methanomicrobiales. We report here the complete genome sequence of M. marisnigri type strain JR1 and its annotation. This is part of a Joint Genome Institute 2006 Community Sequencing Program to sequence genomes of diverse Archaea.
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complete genome sequence of methanoculleus marisnigri type strain jr1
Standards in Genomic Sciences, 2009Co-Authors: Iain Anderson, Eileen Dalin, Eugene Goltsman, Elizabeth Saunders, Kerrie Barry, Magdalena Sieprawskalupa, Alla Lapidus, Alex Copeland, Hope Tice, Thomas BrettinAbstract:Methanoculleus marisnigri Romesser et al. 1981 is a methanogen belonging to the order Methanomicrobiales within the archaeal phylum Euryarchaeota. The type strain, JR1, was isolated from anoxic sediments of the Black Sea. M. marisnigri is of phylogenetic interest because at the time the sequencing project began only one genome had previously been sequenced from the order Methanomicrobiales. We report here the complete genome sequence of M. marisnigri type strain JR1 and its annotation. This is part of a Joint Genome Institute 2006 Community Sequencing Program to sequence genomes of diverse Archaea.
Edward F Delong - One of the best experts on this subject based on the ideXlab platform.
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reply to schouten et al marine group ii planktonic Euryarchaeota are significant contributors to tetraether lipids in the ocean
Proceedings of the National Academy of Sciences of the United States of America, 2014Co-Authors: Sara A Lincoln, John M Eppley, Matthew J Church, Roger E Summons, Edward F DelongAbstract:Schouten et al. (1), referencing Lincoln et al. (2), question whether Marine Group II Euryarchaeota (MG-II) contribute significantly to glycerol dibiphytanyl glycerol tetraether (GDGT) lipids in the ocean. We respond below to what we believe are some mistaken claims and interpretations.
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planktonic Euryarchaeota are a significant source of archaeal tetraether lipids in the ocean
Proceedings of the National Academy of Sciences of the United States of America, 2014Co-Authors: Sara A Lincoln, John M Eppley, Matthew J Church, Roger E Summons, Edward F DelongAbstract:Archaea are ubiquitous in marine plankton, and fossil forms of archaeal tetraether membrane lipids in sedimentary rocks document their participation in marine biogeochemical cycles for >100 million years. Ribosomal RNA surveys have identified four major clades of planktonic archaea but, to date, tetraether lipids have been characterized in only one, the Marine Group I Thaumarchaeota. The membrane lipid composition of the other planktonic archaeal groups—all uncultured Euryarchaeota—is currently unknown. Using integrated nucleic acid and lipid analyses, we found that Marine Group II Euryarchaeota (MG-II) contributed significantly to the tetraether lipid pool in the North Pacific Subtropical Gyre at shallow to intermediate depths. Our data strongly suggested that MG-II also synthesize crenarchaeol, a tetraether lipid previously considered to be a unique biomarker for Thaumarchaeota. Metagenomic datasets spanning 5 y indicated that depth stratification of planktonic archaeal groups was a stable feature in the North Pacific Subtropical Gyre. The consistent prevalence of MG-II at depths where the bulk of exported organic matter originates, together with their ubiquitous distribution over diverse oceanic provinces, suggests that this clade is a significant source of tetraether lipids to marine sediments. Our results are relevant to archaeal lipid biomarker applications in the modern oceans and the interpretation of these compounds in the geologic record.
Chuanlun Zhang - One of the best experts on this subject based on the ideXlab platform.
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evaluating production of cyclopentyl tetraethers by marine group ii Euryarchaeota in the pearl river estuary and coastal south china sea potential impact on the tex86 paleothermometer
Frontiers in Microbiology, 2017Co-Authors: Jinxiang Wang, Yi Ge Zhang, Travis B Meador, Chuanlun ZhangAbstract:TEX86 is built upon an empirically observed correlation between ring distribution of glycerol dialkyl glycerol tetraethers (GDGTs) and sea surface temperature. According to cultural and environmental studies, Marine Group I (MG-I) Thaumarchaeota are hypothesized to constitute the dominant source of TEX86-related GDGTs in the ocean. Recently, Marine Group II (MG-II) Euryarchaeota are suggested to contribute significantly to the GDGT pool in the ocean. However, due to the absence of MG-II cultures, little is known regarding the potential impact of MG-II Euryarchaeota-derived GDGTs on TEX86 in the water column and ultimately its export to the sediment. In this study, we assessed the relationship between distributions of intact polar lipids (IPLs) and core GDGTs and MG-II Euryarchaeota and evaluated its potential effect on the TEX86 proxy. Lipid and DNA analyses were performed on suspended particulate matter and surface sediments collected along a salinity gradient from the lower Pearl River (river water) and its estuary (mixing water) to the coastal South China Sea (SCS, seawater). TEX86-derived temperatures for both IPL- and core-GDGTs from the water column and surface sediments were significantly correlated and both were lower than satellite-based temperatures. The ring index (RI) values in these environments were higher than predicted from the calculated TEX86-RI correlation, indicating that the GDGT pool in the water column of the PR estuary and coastal SCS comprises relatively more cyclopentane rings, which thereby altered TEX86 values. Furthermore, the 16S rRNA gene abundance of MG-II Euryarchaeota in the mixing water was two to three orders of magnitude higher than those observed in the river or seawater. Significant linear correlations were observed between the gene abundance ratio of MG-II Euryarchaeota to total archaea and the fractional abundance of phosphatidic IPL-GDGTs with cyclopentane rings. Collectively, these results corroborate previous studies that have shown that MG-II Euryarchaeota likely produce GDGTs with 1–4 cyclopentane moieties, which may bias TEX86 values in the water column and sediments. As such, valid interpretation of TEX86 values in the sediment record, particularly in coastal oceans, should consider the contribution from MG-II Euryarchaeota.
Emilio O. Casamayor - One of the best experts on this subject based on the ideXlab platform.
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High occurrence of Pacearchaeota and Woesearchaeota (Archaea superphylum DPANN) in the surface waters of oligotrophic high-altitude lakes
Environmental Microbiology Reports, 2016Co-Authors: Rüdiger Ortiz-Álvarez, Emilio O. CasamayorAbstract:Summary We carried out a regional survey on the archaea composition from surface waters of > 300 high-altitude Pyrenean lakes (average altitude 2300 m, pH range 4.4–10.1) by 16S rRNA gene tag sequencing. Relative Archaea abundances ranged between 0% and 6.3% of total prokaryotes amplicons in the polymerase chain reaction (PCR) mixture, and we detected 769 operational taxonomic units (OTUs; grouped at 97% identity) that split into 13 different lineages, with altitude and pH having a significant effect on the community composition. Woesearchaeota and Pacearchaeota (formerly Euryarchaeota DHVEG-6 cluster) dominated the data set (83% of total OTUS), showed a high occurrence (presence in c. 75% of the lakes) and had relative abundances significantly and positively correlated with the phylogenetic diversity of bacterial communities. Micrarchaeota–Diapherotrites (formerly Euryarchaeota MEG cluster), Methanomicrobia, Thermoplasmata and ammonia-oxidizing thaumarchaeota (AOA) showed relative abundances between 1% and 3% and occurrences between 14% and 26%. Minor lineages were SM1K20, Aenigmarchaeota (formerly Euryarchaeota DSEG cluster), Methanobacteria, Bathyarchaeota and SCG. Environmental preferences substantially differed among lineages, with Aenigmarchaeota and Methanomicrobia having the largest habitat breadth, and Thermoplasmata, AOA and Micrarchaeota having the smallest. Pacearchaeota and Woesearchaeota had been mostly reported from saline habitats and sediments, but surface waters of oligotrophic alpine lakes are suitable environments for such ecologically spread and genetically diverse archaeal lineages.
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environmental distribution of two widespread uncultured freshwater Euryarchaeota clades unveiled by specific primers and quantitative pcr
Environmental Microbiology Reports, 2013Co-Authors: Claudia X Restrepoortiz, Emilio O. CasamayorAbstract:Abstract Quantitative environmental distribution of two widely distributed uncultured freshwater Euryarchaeota with unknown functional role was explored by newly designed quantitative PCR primers targeting the 16S rRNA gene of clades Miscellaneous Euryarchaeota Group (MEG, containing the groups pMC2A384 and VALII/Eury4) and Deep-Sea Euryarchaeotal Groups (DSEG, targeting the cluster named VALIII containing the DHVE-3/DSEG, BC07-2A-27/DSEG-3 and DSEG-2 groups), respectively. The summer surface plankton of 28 lakes was analysed, and one additional dimictic deep alpine lake, Lake Redon, was temporally and vertically surveyed covering seasonal limnological variability. A trophic range between 0.2 and 5.2 μg l(-1) Chl a, and pH span from 3.8 to 9.5 was explored at altitudes between 632 and 2590 m above sea level. The primers showed to be highly selective with c. 85% coverage and 100% specificity. Only pH significantly explained the changes observed in gene abundances and environment. In Lake Redon, DSEG bloomed in deep stratified waters both in summer and early spring, and MEG at intermediate depths during the ice-cover period. Overall, MEG and DSEG showed a differential ecological distribution although correlational analyses indicated lack of coupling of both Euryarchaeota with phytoplankton (chlorophyll a). However, an intriguing positive and significant relationship was found between DSEG and putative ammonia oxidizing thaumarchaeota.
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phylogenetic ecology of widespread uncultured clades of the kingdom Euryarchaeota
Molecular Ecology, 2011Co-Authors: Albert Barberan, Pierre E Galand, Jean-christophe Auguet, Antoni Fernandezguerra, Emilio O. CasamayorAbstract:Despite its widespread distribution and high levels of phylogenetic diversity, microbes are poorly understood creatures. We applied a phylogenetic ecology approach in the Kingdom Euryarchaeota (Archaea) to gain insight into the environmental distribution and evolutionary history of one of the most ubiquitous and largely unknown microbial groups. We compiled 16S rRNA gene sequences from our own sequence libraries and public genetic databases for two of the most widespread mesophilic Euryarchaeota clades, Lake Dagow Sediment (LDS) and Rice Cluster-V (RC-V). The inferred population history indicated that both groups have undergone specific nonrandom evolution within environments, with several noteworthy habitat transition events. Remarkably, the LDS and RC-V groups had enormous levels of genetic diversity when compared with other microbial groups, and proliferation of sequences within each single clade was accompanied by significant ecological differentiation. Additionally, the freshwater Euryarchaeota counterparts unexpectedly showed high phylogenetic diversity, possibly promoted by their environmental adaptability and the heterogeneous nature of freshwater ecosystems. The temporal phylogenetic diversification pattern of these freshwater Euryarchaeota was concentrated both in early times and recently, similarly to other much less diverse but deeply sampled archaeal groups, further stressing that their genetic diversity is a function of environment plasticity. For the vast majority of living beings on Earth (i.e. the uncultured microorganisms), how they differ in the genetic or physiological traits used to exploit the environmental resources is largely unknown. Inferring population history from 16S rRNA gene-based molecular phylogenies under an ecological perspective may shed light on the intriguing relationships between lineage, environment, evolution and diversity in the microbial world.
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vertical distribution of ammonia oxidizing crenarchaeota and methanogens in the epipelagic waters of lake kivu rwanda democratic republic of the congo
Applied and Environmental Microbiology, 2010Co-Authors: M Lliros, Emilio O. Casamayor, Jean-christophe Auguet, Frederic Gich, Anna Plasencia, Francois Darchambeau, Jeanpierre Descy, Carles M. BorregoAbstract:Four stratified basins in Lake Kivu (Rwanda-Democratic Republic of the Congo) were sampled in March 2007 to investigate the abundance, distribution, and potential biogeochemical role of planktonic archaea. We used fluorescence in situ hybridization with catalyzed-reported deposition microscopic counts (CARD-FISH), denaturing gradient gel electrophoresis (DGGE) fingerprinting, and quantitative PCR (qPCR) of signature genes for ammonia-oxidizing archaea (16S rRNA for marine Crenarchaeota group 1.1a [MCG1] and ammonia monooxygenase subunit A [amoA]). Abundance of archaea ranged from 1 to 4.5% of total DAPI (4′,6-diamidino-2-phenylindole) counts with maximal concentrations at the oxic-anoxic transition zone (∼50-m depth). Phylogenetic analysis of the archaeal planktonic community revealed a higher level of richness of crenarchaeal 16S rRNA gene sequences (21 of the 28 operational taxonomic units [OTUs] identified [75%]) over Euryarchaeotal ones (7 OTUs). Sequences affiliated with the kingdom Euryarchaeota were mainly recovered from the anoxic water compartment and mostly grouped into methanogenic lineages (Methanosarcinales and Methanocellales). In turn, crenarchaeal phylotypes were recovered throughout the sampled epipelagic waters (0- to 100-m depth), with clear phylogenetic segregation along the transition from oxic to anoxic water masses. Thus, whereas in the anoxic hypolimnion crenarchaeotal OTUs were mainly assigned to the miscellaneous crenarchaeotic group, the OTUs from the oxic-anoxic transition and above belonged to Crenarchaeota groups 1.1a and 1.1b, two lineages containing most of the ammonia-oxidizing representatives known so far. The concomitant vertical distribution of both nitrite and nitrate maxima and the copy numbers of both MCG1 16S rRNA and amoA genes suggest the potential implication of Crenarchaeota in nitrification processes occurring in the epilimnetic waters of the lake.
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High archaeal richness in the water column of a freshwater sulfurous karstic lake along an interannual study
FEMS Microbiology Ecology, 2008Co-Authors: M Lliros, Emilio O. Casamayor, Carles M. BorregoAbstract:We surveyed the archaeal assemblage in a stratified sulfurous lake (Lake Vilar, Banyoles, Spain) over 5 consecutive years to detect potential seasonal and interannual trends in the free-living planktonic Archaea composition. The combination of different primer pairs and nested PCR steps revealed an unexpectedly rich archaeal community. Overall, 140 samples were analyzed, yielding 169 different 16S rRNA gene sequences spread over 14 Crenarchaeota (109 sequences) and six Euryarchaeota phylogenetic clusters. Most of the Crenarchaeota (98% of the total crenarchaeotal sequences) affiliated within the Miscellaneous Crenarchaeota Group (MCG) and were related to both marine and freshwater phylotypes. Euryarchaeota mainly grouped within the Deep Hydrothermal Vent Euryarchaeota (DHVE) cluster (80% of the Euryarchaeotal sequences) and the remaining 20% distributed into three less abundant taxa, most of them composed of soil and sediment clones. The largest fraction of phylotypes from the two archaeal kingdoms (79% of the Crenarchaeota and 54% of the Euryarchaeota) was retrieved from the anoxic hypolimnion, indicating that these cold and sulfide-rich waters constitute an unexplored source of archaeal richness. The taxon rank-frequency distribution showed two abundant taxa (MCG and DHVE) that persisted in the water column through seasons, plus several rare ones that were only detected occasionally. Differences in richness distribution and seasonality were observed, but no clear correlations were obtained when multivariate statistical analyses were carried out.
Jinxiang Wang - One of the best experts on this subject based on the ideXlab platform.
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evaluating production of cyclopentyl tetraethers by marine group ii Euryarchaeota in the pearl river estuary and coastal south china sea potential impact on the tex86 paleothermometer
Frontiers in Microbiology, 2017Co-Authors: Jinxiang Wang, Yi Ge Zhang, Travis B Meador, Chuanlun ZhangAbstract:TEX86 is built upon an empirically observed correlation between ring distribution of glycerol dialkyl glycerol tetraethers (GDGTs) and sea surface temperature. According to cultural and environmental studies, Marine Group I (MG-I) Thaumarchaeota are hypothesized to constitute the dominant source of TEX86-related GDGTs in the ocean. Recently, Marine Group II (MG-II) Euryarchaeota are suggested to contribute significantly to the GDGT pool in the ocean. However, due to the absence of MG-II cultures, little is known regarding the potential impact of MG-II Euryarchaeota-derived GDGTs on TEX86 in the water column and ultimately its export to the sediment. In this study, we assessed the relationship between distributions of intact polar lipids (IPLs) and core GDGTs and MG-II Euryarchaeota and evaluated its potential effect on the TEX86 proxy. Lipid and DNA analyses were performed on suspended particulate matter and surface sediments collected along a salinity gradient from the lower Pearl River (river water) and its estuary (mixing water) to the coastal South China Sea (SCS, seawater). TEX86-derived temperatures for both IPL- and core-GDGTs from the water column and surface sediments were significantly correlated and both were lower than satellite-based temperatures. The ring index (RI) values in these environments were higher than predicted from the calculated TEX86-RI correlation, indicating that the GDGT pool in the water column of the PR estuary and coastal SCS comprises relatively more cyclopentane rings, which thereby altered TEX86 values. Furthermore, the 16S rRNA gene abundance of MG-II Euryarchaeota in the mixing water was two to three orders of magnitude higher than those observed in the river or seawater. Significant linear correlations were observed between the gene abundance ratio of MG-II Euryarchaeota to total archaea and the fractional abundance of phosphatidic IPL-GDGTs with cyclopentane rings. Collectively, these results corroborate previous studies that have shown that MG-II Euryarchaeota likely produce GDGTs with 1–4 cyclopentane moieties, which may bias TEX86 values in the water column and sediments. As such, valid interpretation of TEX86 values in the sediment record, particularly in coastal oceans, should consider the contribution from MG-II Euryarchaeota.
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contribution of marine group ii Euryarchaeota to cyclopentyl tetraethers in the pearl river estuary and coastal south china sea impact on the tex 86 paleothermometer
Biogeosciences Discussions, 2015Co-Authors: Jinxiang Wang, Chen Zhang, Yue Zhang, Ping WangAbstract:TEX 86 (TetraEther indeX of glycerol dialkyl glycerol tetraethers (GDGTs) with 86 carbon atoms) has been widely applied to reconstruct (paleo-) sea surface temperature (SST). While Marine Group I (MG I) Thaumarchaeota have been commonly believed to be the source for GDGTs, Marine Group II (MG II Euryarchaeota ) have recently been suggested to contribute significantly to the GDGT pool in the ocean. However, little is known how the MG II Euryarchaeota -derived GDGTs may influence TEX 86 in marine sediment record. In this study, we characterize MG II Euryarchaeota -produced GDGTs and assess the likely effect of these tetraether lipids on TEX 86 . Analyses of core lipid (CL-) and intact polar lipid (IPL-) based GDGTs, 454 sequencing and quantitative polymerase chain reaction (qPCR) targeting MG II Euryarchaeota were performed on suspended particulate matter (SPM) and surface sediments collected along a salinity gradient from the lower Pearl River (river water) and its estuary (mixing water) to the coastal South China Sea (seawater). The results showed that the community composition varied along the salinity gradient with MG II Euryarchaeota as the second dominant group in the mixing water and seawater. qPCR data indicated that the abundance of MG II Euryarchaeota in the mixing water was three to four orders of magnitude higher than the river water and seawater. Significant linear correlations were observed between the gene abundance ratio of MG II Euryarchaeota vs. total archaea and the relative abundance of GDGTs-1, -2, -3, or -4 as well as the ring index based on these compounds, which collectively suggest that MG II Euryarchaeota may actively produce GDGTs in the water column. These results also show strong evidence that MG II Euryarchaeota synthesizing GDGTs with 1–4 cyclopentane moieties may bias TEX 86 in the water column and sediments. This study highlights that valid interpretation of TEX 86 in sediment record, particularly in coastal oceans, needs to consider the contribution from MG II Euryarchaeota .
