Rice Cluster Research Articles

難培養性メタン生成古細菌Rice Cluster Iの分離と特性(生物多様性の中の機能ネットワークを探る,シンポジウム)

難培養性メタン生成古細菌Rice Cluster Iの分離と特性(生物多様性の中の機能ネットワークを探る,シンポジウム)

Methanogenic Community Was Stable in Two Contrasting Freshwater Marshes Exposed to Elevated Atmospheric CO2.

The effects of elevated atmospheric CO2 concentration on soil microbial communities have been previously recorded. However, limited information is available regarding the response of methanogenic communities to elevated CO2 in freshwater marshes. Using high-throughput sequencing and real-time quantitative PCR, we compared the abundance and community structure of methanogens in different compartments (bulk soil, rhizosphere soil, and roots) of Calamagrostis angustifolia and Carex lasiocarpa growing marshes under ambient (380 ppm) and elevated CO2 (700 ppm) atmospheres. C. lasiocarpa rhizosphere was a hotspot for potential methane production, based on the 10-fold higher abundance of the mcrA genes per dry weight. The two marshes and their compartments were occupied by different methanogenic communities. In the C. lasiocarpa marsh, archaeal family Methanobacteriaceae, Rice Cluster II, and Methanosaetaceae co-dominated in the bulk soil, while Methanobacteriaceae was the exclusively dominant methanogen in the rhizosphere soil and roots. Families Methanosarcinaceae and Methanocellaceae dominated in the bulk soil of C. angustifolia marsh. Conversely, Methanosarcinaceae and Methanocellaceae together with Methanobacteriaceae dominated in the rhizosphere soil and roots, respectively, in the C. angustifolia marsh. Elevated atmospheric CO2 increased plant photosynthesis and belowground biomass of C. lasiocarpa and C. angustifolia marshes. However, it did not significantly change the abundance (based on mcrA qPCR), diversity, or community structure (based on high-throughput sequencing) of methanogens in any of the compartments, irrespective of plant type. Our findings suggest that the population and species of the dominant methanogens had weak responses to elevated atmospheric CO2. However, minor changes in specific methanogenic taxa occurred under elevated atmospheric CO2. Despite minor changes, methanogenic communities in different compartments of two contrasting freshwater marshes were rather stable under elevated atmospheric CO2.

Localised learning in the Malaysian rice cluster: proximity, social capital and institutional dynamics

This paper takes a clustering approach as it attempts to investigate localised learning within a rice cluster in Malaysia and to examine the role of institutions, social capital and geographical proximity in helping promote localised learning. The paper argues that the development of social capital within a cluster needs to take place in its institutional context, and that development policies must address the ‘soft’ elements of the cluster in fostering cooperative relationships and ‘social contracts’ among the cluster actors. Evidence shows that learning processes and gains from learning in a cluster occur mainly in the form of informal learning – in which the effects of social cohesiveness, trust and connectedness are particularly important. Geographic proximity also plays an important role when it comes to the regional embedding of knowledge and learning processes. This paper shows supporting evidence that social proximity is the main dimension that should be embedded within the geographical and instit...

Perilaku Petani Pada Program Pengembangan Klaster Padi Binaan Bank Indonesia (Kasus Subak Pulagan, Desa Tampaksiring, Kecamatan Tampaksiring, Kabupaten Gianyar)

The Behavior of Farmers on Rice Cluster Development Program AssistedInonesian Bank (Case of Subak Pulagan, Tampaksiring Village, TampaksiringDistrict, Gianyar Regency)Bank Indonesia has been mentoring and coaching in the pass program developmentreal sector and UMKM. The purpose of this study to knowledge, attitudes, and skillof farmers on rice cluster development program assisted Indonesian Bank. This study took place in Subak Pulagan with the number of respondents 48 people. Methods ofdata collection by interview and analyzed by qualitative descriptive analysis. The results showed the behavior of farmers on rice cluster development program is inexcellent condition with a score of 85,1%. It can be seen from the three indicators. Excellent knowledge indicators category with a score of 84,4%, a very good attitudeindicator categories premises a score of 84,7%, and very good indicator oh the skillcategory with a score of 86,2%.Advice which may be recommended that the diversification of products is not good,it can be suggested that extension is to provide an understanding of the impotance ofdiversification benefits of products to enhance the competitiveness and obtaineconomic value higher.

Genomic reconstruction of multiple lineages of uncultured benthic archaea suggests distinct biogeochemical roles and ecological niches.

Genomic bins belonging to multiple archaeal lineages were recovered from distinct redox regimes in sediments of the White Oak River estuary. The reconstructed archaeal genomes were identified as belonging to the rice cluster subgroups III and V (RC-III, RC-V), the Marine Benthic Group D (MBG-D), and a newly described archaeal class, the Theionarchaea. The metabolic capabilities of these uncultured archaea were inferred and indicated a common capability for extracellular protein degradation, supplemented by other pathways. The multiple genomic bins within the MBG-D archaea shared a nearly complete reductive acetyl-CoA pathway suggesting acetogenic capabilities. In contrast, the RC-III metabolism appeared centered on the degradation of detrital proteins and production of H2, whereas the RC-V archaea lacked capabilities for protein degradation and uptake, and appeared to be specialized on carbohydrate fermentation. The Theionarchaea appeared as complex metabolic hybrids; encoding a complete tricarboxylic acid cycle permitting carbon (acetyl-CoA) oxidation, together with a complete reductive acetyl-CoA pathway and sulfur reduction by a sulfhydrogenase. The differentiated inferred capabilities of these uncultured archaeal lineages indicated lineage-specific linkages with the nitrogen, carbon and sulfur cycles. The predicted metabolisms of these archaea suggest preferences for distinct geochemical niches within the estuarine sedimentary environment.

Response of archaeal communities to water regimes under simulated warming and drought conditions in Tibetan Plateau wetlands

Understanding how archaeal communities are affected by water-table drawdown is essential for predicting soil functional responses to future climate change and the consequences of the responses on the soil carbon cycle. We investigated the effect of water-table drawdown, warming, drought, and combinations thereof on archaeal communities using terminal restriction fragment length polymorphism (T-RFLP) and quantitative PCR. Methanosarcinales, Methanosaeta, Methanomicrobiales, Methanobacteriales, uncultured Rice Cluster II (RC-II), and uncultured Crenarchaeota were detected. Water-table drawdown and drought exhibited significant effects on the archaeal communities. When the water table was at or above 10 cm, the archaeal abundance at 10 cm remained high (approximately 109 cells per gram dry soil), whereas the archaeal abundance at 10 cm was reduced to approximately 108 cells per gram dry soil where the water table was lowered to 20 cm or below. When the water table kept constant, warming caused a significant reduction in the archaeal abundance, whereas drought only caused a decrease in archaeal abundance when the water table was higher than −20 cm. Results suggest that changes in water table may directly impact archaeal community abundance and assemblage which can in turn influence methane emissions, potentially on a large scale. Our results also indicate that archaeal communities response to water-table drawdowns that are dependent on the initial ecohydrology.

Food Sufficiency in the Terraces: The Case of Globally-Important Agricultural Heritage Systems In Ifugao, Central Cordillera, Philippines

The rice terrace clusters in Nagacadan, Kiangan and those in Bocos, Banaue,Ifugao aside from recognized as UNESCO World Heritage Sites are nowregarded as relevant landscapes belonging to the so-called Globally-ImportantAgricultural Heritage Systems (GIAHS). These landscapes are characterizedby being sustainable showcase of one of humanity’s greatest human-natureinterrelationships, whose ecological flows have maintained these highlandagroecosystems for over two millennia and continuing to do so. Althoughdiffering in soil quality characteristics as a result of gradual introductions ofinorganic inputs into the production system, this rice terraced ecosystem remainspredominantly organic in terms of production. The focal dimension assessed in this paper is the food supply contributions of commonly cultivated native rice varieties to food sufficiency at the community level as well as the basic Ifugaohousehold level. These native rice varieties are, of course, raised in a primarilyorganic farming setting. It is revealed, however, that the average household inthese two study sites has their native rice supply lasting for about six months orless, both at 2001 and 2008 levels.Keywords: Ecology and environmental science, globally-important agricultural heritagesystems (GIAHS), food sufficiency, organic agriculture, descriptive survey,Philippines

Discovery of a novel methanogen prevalent in thawing permafrost

Thawing permafrost promotes microbial degradation of cryo-sequestered and new carbon leading to the biogenic production of methane, creating a positive feedback to climate change. Here we determine microbial community composition along a permafrost thaw gradient in northern Sweden. Partially thawed sites were frequently dominated by a single archaeal phylotype, Candidatus 'Methanoflorens stordalenmirensis' gen. nov. sp. nov., belonging to the uncultivated lineage 'Rice Cluster II' (Candidatus 'Methanoflorentaceae' fam. nov.). Metagenomic sequencing led to the recovery of its near-complete genome, revealing the genes necessary for hydrogenotrophic methanogenesis. These genes are highly expressed and methane carbon isotope data are consistent with hydrogenotrophic production of methane in the partially thawed site. In addition to permafrost wetlands, 'Methanoflorentaceae' are widespread in high methane-flux habitats suggesting that this lineage is both prevalent and a major contributor to global methane production. In thawing permafrost, Candidatus 'M. stordalenmirensis' appears to be a key mediator of methane-based positive feedback to climate warming.

Southern Appalachian Peatlands Support High Archaeal Diversity

Mid-latitude peatlands with a temperate climate are sparsely studied and as such represent a gap in the current knowledge base regarding archaeal populations present and their roles in these environments. Phylogenetic analysis of the archaeal populations among three peatlands in the Southern Appalachians reveal not only methanogenic species but also significant populations of thaumarchaeal and crenarchaeal-related organisms of the uncultured miscellaneous crenarchaeotal group (MCG) and the terrestrial group 1.1c, as well as deep-branching Euryarchaeota primarily within the Lake Dagow sediment and rice cluster V lineages. The Thaum/Crenarchaea and deep-branching Euryarchaea represented approximately 24-83% and 2-18%, respectively, of the total SSU rRNA clones retrieved in each library, and methanogens represented approximately 14-72% of the clones retrieved. Several taxa that are either rare or novel to acidic peatlands were detected including the euryarchaeal SM1K20 cluster and thaumarchaeal/crenarchaeal-related clusters 1.1a, C3, SAGMCG-1, pSL12, and AK59. All three major groups (methanogens, Thaumarchaea/Crenarchaea, and deep-branching Euryarchaea) were detected in the RNA library, suggesting at least a minimum level of maintenance activity. Compared to their northern counterparts, Southern Appalachian peatlands appear to harbor a relatively high diversity of Archaea and exhibit a high level of intra-site heterogeneity.

Methyl Coenzyme M Reductase A (mcrA) Gene-Based Investigation of Methanogens in the Mudflat Sediments of Yangtze River Estuary, China

Methanogen populations of an intertidal mudflat in the Yangtze River estuary of China were investigated based on the methyl coenzyme M reductase A (mcrA) gene using 454-pyrosequencing and quantitative real-time polymerase chain reaction (qPCR). Samples were collected at six depths from three locations. In the qPCR analyses, a mean depth-wise change of mcrA gene abundance was observed from (1.23 ± 0.13) × 10(7) to (1.16 ± 0.29) × 10(8) per g dried soil, which was inversely correlated with the depletion of sulfate (R(2) = 0.74; α = 0.05) and salinity (R (2) = 0.66; α = 0.05). The copy numbers of mcrA was at least 1 order of magnitude higher than dissimilatory sulfate reductase B (dsrB) genes, likely indicating the importance of methanogenesis at the mudflat. Sequences related to the orders Methanomicrobiales, Methanosarcinales, Methanobacteriales, Methanococcales and the uncultured methanogens; Rice Cluster I (RC-I), Zoige cluster I (ZC-I) and anaerobic methane oxidizing archaeal lineage-1 (ANME-1) were detected. Methanomicrobiales and Methanosarcinales dominated the entire sediment layers, but detectable changes of proportions were observed with depth. The hydrogenotrophic methanogens Methanomicrobiales slightly increased with depth while Methanosarcinales showed the reverse. Chao1 and ACE richness estimators revealed higher diversity of methanogens near the surface (0-10 cm) when compared with the bottom sediments. The near-surface sediments were mainly dominated by the family Methanosarcinaceae (45 %), which has members that can utilize substrates that cannot be used by sulfate-reducing bacteria. Overall, current data indicate that Methanosarcinales and Methanomicrobiales are the most dominant methanogens within the entire depth profile down to 100 cm, with higher abundance and diversity of methanogens in the deeper and upper sediment layers, respectively.

Seasonal Transition of Active Bacterial and Archaeal Communities in Relation to Water Management in Paddy Soils

Paddy soils have an environment in which waterlogging and drainage occur during the rice growing season. Fingerprinting analysis based on soil RNA indicated that active microbial populations changed in response to water management conditions, although the fundamental microbial community was stable as assessed by DNA-based fingerprinting analysis. Comparative clone library analysis based on bacterial and archaeal 16S rRNAs (5,277 and 5,436 clones, respectively) revealed stable and variable members under waterlogged or drained conditions. Clones related to the class Deltaproteobacteria and phylum Euryarchaeota were most frequently obtained from the samples collected under both waterlogged and drained conditions. Clones related to syntrophic hydrogen-producing bacteria, hydrogenotrophic methanogenic archaea, rice cluster III, V, and IV, and uncultured crenarchaeotal group 1.2 appeared in greater proportion in the samples collected under waterlogged conditions than in those collected under drained conditions, while clones belonging to rice cluster VI related to ammonia-oxidizing archaea (AOA) appeared at higher frequency in the samples collected under drained conditions than in those collected under waterlogged conditions. These results suggested that hydrogenotrophic methanogenesis may become active under waterlogged conditions, whereas ammonia oxidation may progress by rice cluster VI becoming active under drained conditions in the paddy field.

“Methanoplasmatales,” Thermoplasmatales-Related Archaea in Termite Guts and Other Environments, Are the Seventh Order of Methanogens

The Euryarchaeota comprise both methanogenic and nonmethanogenic orders and many lineages of uncultivated archaea with unknown properties. One of these deep-branching lineages, distantly related to the Thermoplasmatales, has been discovered in various environments, including marine habitats, soil, and also the intestinal tracts of termites and mammals. By comparative phylogenetic analysis, we connected this lineage of 16S rRNA genes to a large clade of unknown mcrA gene sequences, a functional marker for methanogenesis, obtained from the same habitats. The identical topologies of 16S rRNA and mcrA gene trees and the perfect congruence of all branches, including several novel groups that we obtained from the guts of termites and cockroaches, strongly suggested that they stem from the same microorganisms. This was further corroborated by two highly enriched cultures of closely related methanogens from the guts of a higher termite (Cubitermes ugandensis) and a millipede (Anadenobolus sp.), which represented one of the arthropod-specific clusters in the respective trees. Numerous other pairs of habitat-specific sequence clusters were obtained from the guts of other termites and cockroaches but were also found in previously published data sets from the intestinal tracts of mammals (e.g., rumen cluster C) and other environments. Together with the recently described Methanomassiliicoccus luminyensis isolated from human feces, which falls into rice cluster III, the results of our study strongly support the idea that the entire clade of "uncultured Thermoplasmatales" in fact represents the seventh order of methanogenic archaea, for which the provisional name "Methanoplasmatales" is proposed.

Methane and Nitrous Oxide Productions and Community Structure of Methanogenic Archaea in Paddy Soil of South Sulawesi, Indonesia

The potential of methane and nitrous oxide productions and community structure of methanogenic archaeahas been characterized by incubation studies and PCR-DGGE approaches, respectively. The results showed thataddition of straw into the soil was the most important factor that influenced CH 4 production in this incubation 4 experiment, while N 2 O production was observed higher in soil without straw amendment under saturated 2 condition. Most of the clone sequences revealed from DGGE band was associated with a archaea lineage, Methanocellales ord. nov (Rice Cluster I). Other sequences belong to Methanomicrobiales , Methanosaetales and Rice Cluster 2 (RC-2). The study also showed that the hydrogenotrophic methanogens were the dominant members in methanogenic archaea community obtained from tropical paddy field soil, while acetoclastic methanogens present in relatively minor quantity in the soil.

Prokaryotic ultramicroforms in a Sphagnum peat bog of upper Volga catchment

The waters of small lakes located in swampy catchment areas of upper Volga contain considerable amounts of ultrasmall microbial cells that pass through 0.22-μm-pore-size filters. As shown in our previous study [1], most of these cells represent the bacterial genera Herbaspirillum, Herminiimonas, Curvibacter, and Burkholderia of the class Betaproteobacteria, as well as euryarchaea of the uncharacterized clade LDS. The aim of the present study was to investigate the possible effect of the waters draining swampy areas on the composition of the filterable microbial fraction in lakes fed by swampy catchments. To address this question molecular identification was performed of prokaryotic ultramicroforms in the peat of the ombrotrophic Sphagnum bog Obukhovskoe, located, like the lakes studied previously [1], in the Mologa-Sheksna catchment area. The number of filterable microorganisms in 1 g wet peat was 3.8 × 106 cells, or 0.5% of total microbial cell number in the peat. From the DNA of the filterable cell fraction, 100 clones of bacterial and 77 clones of archaeal 16S rRNA genes were obtained. The bacterial clone library contained 16S rRNA gene sequences representing the classes Beta- and Gammaproteobacteria (the genera Janthinobacterium and Pseudomonas, respectively) and the phylum Bacteroidetes (the genera Chryseobacterium and Epilithonimonas) and differed significantly from the clone library of bacterial ultramicroforms of lake water. By contrast, the pools of filterable archaea in bogs and lakes were essentially similar. They were represented by the euryarchaeal clade LDS and methanogens of the orders Methanobacteriales and Methanosarcinales. Additionally, the pool of filterable archaea of the bog included methanogens of the order Methanomicrobiales and representatives of the uncharacterized euryarchaeal clade RC-V (Rice Cluster V) and of the phylum Thaumarchaeota.

Local Conditions Structure Unique Archaeal Communities in the Anoxic Sediments of Meromictic Lake Kivu

Meromictic Lake Kivu is renowned for its enormous quantity of methane dissolved in the hypolimnion. The methane is primarily of biological origin, and its concentration has been increasing in the past half-century. Insight into the origin of methane production in Lake Kivu has become relevant with the recent commercial extraction of methane from the hypolimnion. This study provides the first culture-independent approach to identifying the archaeal communities present in Lake Kivu sediments at the sediment-water interface. Terminal restriction fragment length polymorphism analysis suggests considerable heterogeneity in the archaeal community composition at varying sample locations. This diversity reflects changes in the geochemical conditions in the sediment and the overlying water, which are an effect of local groundwater inflows. A more in-depth look at the archaeal community composition by clone library analysis revealed diverse phylogenies of Euryarchaeota and Crenarachaeota. Many of the sequences in the clone libraries belonged to globally distributed archaeal clades such as the rice cluster V and Lake Dagow sediment environmental clusters. Several of the determined clades were previously thought to be rare among freshwater sediment Archaea (e.g., sequences related to the SAGMEG-1 clade). Surprisingly, there was no observed relation of clones to known hydrogentrophic methanogens and less than 2 % of clones were related to acetoclastic methanogens. The local variability, diversity, and novelty of the archaeal community structure in Lake Kivu should be considered when making assumptions on the biogeochemical functioning of its sediments.

Chemolithotrophic acetogenic H2/CO2 utilization in Italian rice field soil

Acetate oxidation in Italian rice field at 50 °C is achieved by uncultured syntrophic acetate oxidizers. As these bacteria are closely related to acetogens, they may potentially also be able to synthesize acetate chemolithoautotrophically. Labeling studies using exogenous H(2) (80%) and (13)CO(2) (20%), indeed demonstrated production of acetate as almost exclusive primary product not only at 50 °C but also at 15 °C. Small amounts of formate, propionate and butyrate were also produced from (13)CO(2). At 50 °C, acetate was first produced but later on consumed with formation of CH(4). Acetate was also produced in the absence of exogenous H(2) albeit to lower concentrations. The acetogenic bacteria and methanogenic archaea were targeted by stable isotope probing of ribosomal RNA (rRNA). Using quantitative PCR, (13)C-labeled bacterial rRNA was detected after 20 days of incubation with (13)CO(2). In the heavy fractions at 15 °C, terminal restriction fragment length polymorphism, cloning and sequencing of 16S rRNA showed that Clostridium cluster I and uncultured Peptococcaceae assimilated (13)CO(2) in the presence and absence of exogenous H(2), respectively. A similar experiment showed that Thermoanaerobacteriaceae and Acidobacteriaceae were dominant in the (13)C treatment at 50 °C. Assimilation of (13)CO(2) into archaeal rRNA was detected at 15 °C and 50 °C, mostly into Methanocellales, Methanobacteriales and rice cluster III. Acetoclastic methanogenic archaea were not detected. The above results showed the potential for acetogenesis in the presence and absence of exogenous H(2) at both 15 °C and 50 °C. However, syntrophic acetate oxidizers seemed to be only active at 50 °C, while other bacterial groups were active at 15 °C.

Archaeal Populations in Hypersaline Sediments Underlying Orange Microbial Mats in the Napoli Mud Volcano

Microbial mats in marine cold seeps are known to be associated with ascending sulfide- and methane-rich fluids. Hence, they could be visible indicators of anaerobic oxidation of methane (AOM) and methane cycling processes in underlying sediments. The Napoli mud volcano is situated in the Olimpi Area that lies on saline deposits; from there, brine fluids migrate upward to the seafloor. Sediments associated with a brine pool and microbial orange mats of the Napoli mud volcano were recovered during the Medeco cruise. Based on analysis of RNA-derived sequences, the "active" archaeal community was composed of many uncultured lineages, such as rice cluster V or marine benthic group D. Function methyl coenzyme M reductase (mcrA) genes were affiliated with the anaerobic methanotrophic Archaea (ANME) of the ANME-1, ANME-2a, and ANME-2c groups, suggesting that AOM occurred in these sediment layers. Enrichment cultures showed the presence of viable marine methylotrophic Methanococcoides in shallow sediment layers. Thus, the archaeal community diversity seems to show that active methane cycling took place in the hypersaline microbial mat-associated sediments of the Napoli mud volcano.

Characterization of Archaeal Community in Contaminated and Uncontaminated Surface Stream Sediments

Archaeal communities from mercury and uranium-contaminated freshwater stream sediments were characterized and compared to archaeal communities present in an uncontaminated stream located in the vicinity of Oak Ridge, TN, USA. The distribution of the Archaea was determined by pyrosequencing analysis of the V4 region of 16S rRNA amplified from 12 streambed surface sediments. Crenarchaeota comprised 76% of the 1,670 archaeal sequences and the remaining 24% were from Euryarchaeota. Phylogenetic analysis further classified the Crenarchaeota as a Freshwater Group, Miscellaneous Crenarchaeota group, Group I3, Rice Cluster VI and IV, Marine Group I and Marine Benthic Group B; and the Euryarchaeota into Methanomicrobiales, Methanosarcinales, Methanobacteriales, Rice Cluster III, Marine Benthic Group D, Deep Sea Hydrothermal Vent Euryarchaeota 1 and Eury 5. All groups were previously described. Both hydrogen- and acetate-dependent methanogens were found in all samples. Most of the groups (with 60% of the sequences) described in this study were not similar to any cultivated isolates, making it difficult to discern their function in the freshwater microbial community. A significant decrease in the number of sequences, as well as in the diversity of archaeal communities was found in the contaminated sites. The Marine Group I, including the ammonia oxidizer Nitrosopumilus maritimus, was the dominant group in both mercury and uranium/nitrate-contaminated sites. The uranium-contaminated site also contained a high concentration of nitrate, thus Marine Group I may play a role in nitrogen cycle.Electronic supplementary materialThe online version of this article (doi:10.1007/s00248-010-9734-2) contains supplementary material, which is available to authorized users.

Active Archaeal Communities at Cold Seep Sediments Populated by Siboglinidae Tubeworms from the Storegga Slide

Siboglinid tubeworms in cold seep sediments can locally modify the geochemical gradients of electron acceptors and donors, hence creating potential microhabitats for prokaryotic populations. The archaeal communities associated with sediments populated by Oligobrachia haakonmosbiensis and Sclerolinum contortum Siboglinid tubeworms in the Storegga Slide were examined in this study. Vertical distribution of archaeal communities was investigated using denaturing gradient gel electrophoresis based on 16S rRNA genes. The active fraction of the archaeal community was assessed by using reverse-transcribed rRNA. Archaeal communities associated with sediments colonized by tubeworms were affiliated with uncultivated archaeal lineages of the Crenarchaeota and Euryarchaeota. The composition of the active archaeal populations changed with depth indicating a reorganization of microbial communities. 16S rRNA gene libraries were dominated by sequences affiliated to the Rice Cluster V which are unusual in marine sediment samples. Moreover, this study provides the first evidence of living Crenarchaeota of the Rice Cluster V in cold seep sediments. Furthermore, the Storegga Slide sediments harbored a high diversity of other minor groups of uncultivated lineages including Terrestrial Miscellaneous Euryarchaeotal Group, Marine Benthic Group (MBG)-D, MBG-E, Deep-Sea Hydrothermal Vent Euryarchaeotal Group, Lake Dagow Sediment, Val Kotinen Lake clade III, and Sippenauer Moor 1. Thus, we hypothesize that the vertical geochemical imprint created by the tubeworms could support broad active archaeal populations in the Siboglinidae-populated Storegga Slide sediments.

Methanocella arvoryzae sp. nov., a hydrogenotrophic methanogen isolated from rice field soil

A novel hydrogenotrophic methanogen, designated strain MRE50(T), was isolated from a methanogenic consortium, which was originally established from an Italian rice field soil. Cells were non-motile rods, 1.3-2.8 μm long and 0.4-0.7 μm wide. Coccoid cells were also observed in cultures at the late-exponential phase of growth. Strain MRE50(T) grew at 37-55 °C (optimally at 45 °C), at pH 6-7.8 (optimally at pH 7.0) and in the presence of 0-20 g NaCl l(-1). The isolate utilized H(2)/CO(2) and formate for growth and methane production. Phylogenetic analyses of the 16S rRNA gene and the methanogen-specific marker gene mcrA showed that strain MRE50(T) is affiliated with the order Methanocellales, previously known as uncultured archaeal group Rice Cluster I. Based on both 16S rRNA gene and mcrA gene sequences, strain MRE50(T) was related most closely to Methanocella paludicola SANAE(T). Levels of sequence similarity were 92.5 and 86.1 %, respectively, indicating that strains MRE50(T) and Methanocella paludicola SANAE(T) represent different species within the genus Methanocella. In addition, although these strains shared phenotypic properties including cell morphology and substrate utilization, they differed with respect to susceptibility to antibiotics, and temperature and NaCl ranges for growth. Given the phenotypic differences and the distinct phylogenetic placement of the new isolate relative to the type species of the genus Methanocella, strain MRE50(T) is considered to represent a novel species of the genus Methanocella, for which the name Methanocella arvoryzae sp. nov. is proposed. The type strain is MRE50(T) (=NBRC 105507(T) =DSM 22066(T)).