Archaea In Sediments Research Articles

Different Responses of Bacterial and Archaeal Communities in River Sediments to Water Diversion and Seasonal Changes.

In recent years, different responses of archaea and bacteria to environmental changes have attracted increasing scientific interest. In the mid-latitude region, Fen River receives water transferred from the Yellow River, electrical conductivity (EC), concentrations of Cl− and Na+ in water, total phosphorus (TP), and Olsen phosphorus (OP) in sediments were significantly affected by water transfer. Meanwhile, temperature and oxidation-reduction potential (ORP) of water showed significant seasonal variations. Based on 16S rRNA high-throughput sequencing technology, the composition of bacteria and archaea in sediments was determined in winter and summer, respectively. Results showed that the dominance of bacterial core flora decreased and that of archaeal core flora increased after water diversion. The abundance and diversity of bacterial communities in river sediments were more sensitive to anthropogenic and naturally induced environmental changes than that of archaeal communities. Bacterial communities showed greater resistance than archaeal communities under long-term external disturbances, such as seasonal changes, because of rich species composition and complex community structure. Archaea were more stable than bacteria, especially under short-term drastic environmental disturbances, such as water transfer, due to their insensitivity to environmental changes. These results have important implications for understanding the responses of bacterial and archaeal communities to environmental changes in river ecosystems affected by water diversion.

Impact of Terrestrial Input on Deep-Sea Benthic Archaeal Community Structure in South China Sea Sediments.

Archaea are widespread in marine sediments and play important roles in the cycling of sedimentary organic carbon. However, factors controlling the distribution of archaea in marine sediments are not well understood. Here we investigated benthic archaeal communities over glacial-interglacial cycles in the northern South China Sea and evaluated their responses to sediment organic matter sources and inter-species interactions. Archaea in sediments deposited during the interglacial period Marine Isotope Stage (MIS) 1 (Holocene) were significantly different from those in sediments deposited in MIS 2 and MIS 3 of the Last Glacial Period when terrestrial input to the South China Sea was enhanced based on analysis of the long-chain n-alkane C31. The absolute archaeal 16S rRNA gene abundance in subsurface sediments was highest in MIS 2, coincident with high sedimentation rates and high concentrations of total organic carbon. Soil Crenarchaeotic Group (SCG; Nitrososphaerales) species, the most abundant ammonia-oxidizing archaea in soils, increased dramatically during MIS 2, likely reflecting transport of terrestrial archaea during glacial periods with high sedimentation rates. Co-occurrence network analyses indicated significant association of SCG archaea with benthic deep-sea microbes such as Bathyarchaeota and Thermoprofundales in MIS 2 and MIS 3, suggesting potential interactions among these archaeal groups. Meanwhile, Thermoprofundales abundance was positively correlated with total organic carbon (TOC), along with n-alkane C31 and sedimentation rate, indicating that Thermoprofundales may be particularly important in processing of organic carbon in deep-sea sediments. Collectively, these results demonstrate that the composition of heterotrophic benthic archaea in the South China Sea may be influenced by terrestrial organic input in tune with glacial-interglacial cycles, suggesting a plausible link between global climate change and microbial population dynamics in deep-sea marine sediments.

Diversity of NC10 Bacteria and ANME-2d Archaea in Sediments of Fault Zones at Lake Baikal

Anaerobic oxidation of methane (AOM) reduces methane emissions from marine ecosystems, but we know little about AOM in freshwater reservoirs. Lake Baikal is the world’s only freshwater reservoir where gas hydrates (GH) are found. Despite that AOM has been demonstrated in deep sediments of Lake Baikal did not reveal methane-oxidizing archaea ANME1, 2, or 3, which are responsible for AOM in marine sediments. A search for representatives Candidatus Methylomirabilis oxyfera (M. oxyfera)-like bacteria (NC10) and Candidatus Methanoperedens nitroreducens (M. nitroreducens)-like archaea (ANME-2d) has been carried out in the different types of Lake Baikal methane enriched sediments. We used different molecular biology methods including high-throughput sequencing and PCR analysis, using 16S rRNA genes as well as different functional genes of AOM (mcrA and pmoA). We found diverse M. oxyfera-like bacteria and M. nitroreducens-like archaea in various geological structures in Lake Baikal (methane seep and mud volcano), which were different from the composition of the discharged fluid. We also considered possible electron acceptors for this process in the sediments of Lake Baikal.

Archaeal communities in sponge, sediment and water from marine lakes and open water habitats

ABSTRACTMarine lakes are characterized by higher temperatures and lower pH and salinity values compared to open-water environments. Microbial communities in these habitats are, thus, subjected to distinct environmental conditions. Understanding how these conditions influence marine lake microbial composition and function can be illuminating since global phenomena such as ocean acidification are predicted to profoundly affect the marine environment. Here we investigated the archaeal community composition and putative function in three biotopes (water, sediment, the sponge Biemna fortis) in three distinct habitats (Kakaban and Haji Buang Lakes and the surrounding open-water habitat of Berau, Indonesia). Both biotope and habitat were shown to be important predictors of variation in archaeal composition and higher taxon abundance, but habitat only proved to be a significant factor for water and sediment. The compositional differences among habitats were mainly driven by differences in sediment archaea. These differences were not only prevalent at a higher taxonomic level, but also at the level of OTU identity, suggesting a degree of environmental specialization of distinct Cenarchaeum symbiosum phylotypes. There were also differences in the abundance of predicted relative gene counts among biotopes and habitats with functions that favour the adaptation to stressful environmental conditions enriched in samples from marine lakes.

Vertical stratification of bacteria and archaea in sediments of a small boreal humic lake.

ABSTRACTAlthough sediments of small boreal humic lakes are important carbon stores and greenhouse gas sources, the composition and structuring mechanisms of their microbial communities have remained understudied. We analyzed the vertical profiles of microbial biomass indicators (PLFAs, DNA and RNA) and the bacterial and archaeal community composition (sequencing of 16S rRNA gene amplicons and qPCR of mcrA) in sediment cores collected from a typical small boreal lake. While microbial biomass decreased with sediment depth, viable microbes (RNA and PLFA) were present all through the profiles. The vertical stratification patterns of the bacterial and archaeal communities resembled those in marine sediments with well-characterized groups (e.g. Methanomicrobia, Proteobacteria, Cyanobacteria, Bacteroidetes) dominating in the surface sediment and being replaced by poorly-known groups (e.g. Bathyarchaeota, Aminicenantes and Caldiserica) in the deeper layers. The results also suggested that, similar to marine systems, the deep bacterial and archaeal communities were predominantly assembled by selective survival of taxa able to persist in the low energy conditions. Methanotrophs were rare, further corroborating the role of these methanogen-rich sediments as important methane emitters. Based on their taxonomy, the deep-dwelling groups were putatively organo-heterotrophic, organo-autotrophic and/or acetogenic and thus may contribute to changes in the lake sediment carbon storage.

Prevalence of ammonia-oxidizing bacteria over ammonia-oxidizing archaea in sediments as related to nutrient loading in Chinese aquaculture ponds

Nitrogen (N) application in excess of assimilatory capacity for aquaculture ponds can lead to water-quality deterioration through ammonia accumulation with toxicity to fish. Ammonia-oxidizing archaea (AOA) and bacteria (AOB) potentially process extra ammonium, so their abundance and diversity are of great ecological significance. This study aimed to reveal variations in communities of AOA and AOB as affected by aquaculture activities. From June to September 2012, water and sediments were sampled monthly in three ponds feeding Mandarin fish in a suburb of Wuhan City, China. Molecular methods based on ammonia monooxygenase (amoA) gene were used to determine abundance and diversity of AOA and AOB in the sediments. The pond with the highest fish stock had the highest nutrient loadings in terms of different forms of N and carbon (C) in both sediment and water. The abundance and diversity of AOB were significantly higher than those of AOA in the sediment. The AOB abundance showed a significantly positive relationship to concentration of soluble reactive phosphorus (SRP) in interstitial water, and both abundance and diversity of AOA were significantly negative to concentration of ammonium in interstitial water. Furthermore, AOA species affiliated to Nitrososphaera-like and Nitrosophaera Cluster was distinguishable from those observed in other aquaculture environments. Nutrients in sediment were enriched by intensive aquaculture activity, among which organic N and C, together with ammonium and SRP, shaped the communities of ammonia oxidizers, with AOB dominating over AOA in terms of abundance and diversity.

Differences in the Composition of Archaeal Communities in Sediments from Contrasting Zones of Lake Taihu.

In shallow lakes, different primary producers might impact the physiochemical characteristics of the sediment and the associated microbial communities. Until now, little was known about the features of sediment Archaea and their variation across different primary producer-dominated ecosystems. Lake Taihu provides a suitable study area with cyanobacteria- and macrophyte-dominated zones co-occurring in one ecosystem. The composition of the sediment archaeal community was assessed using 16S rRNA gene amplicon sequencing technology, based on which the potential variation with respect to the physiochemical characteristics of the sediment was analyzed. Euryarchaeota (30.19% of total archaeal sequences) and Bathyarchaeota (28.00%) were the two most abundant phyla, followed by Crenarchaeota (11.37%), Aigarchaeota (10.24%) and Thaumarchaeota (5.98%). The differences found in the composition of the archaeal communities between the two zones was significant (p = 0.005). Sediment from macrophyte-dominated zones had high TOC and TN content and an abundance of archaeal lineages potentially involved in the degradation of complex organic compounds, such as the order Thermoplasmatales. In the area dominated by Cyanobacteria, archaeal lineages related to sulfur metabolism, for example, Sulfolobales and Desulfurococcales, were significantly enriched. Among Bathyarchaeota, subgroups MCG-6 and MCG-15 were significantly accumulated in the sediment of areas dominated by macrophytes whereas MCG-4 was consistently dominant in both type of sediments. The present study contributes to the knowledge of sediment archaeal communities with different primary producers and their possible biogeochemical functions in sediment habitats.

The Distribution Pattern of Sediment Archaea Community of the Poyang Lake, the Largest Freshwater Lake in China.

Archaea plays an important role in the global geobiochemical circulation of various environments. However, much less is known about the ecological role of archaea in freshwater lake sediments. Thus, investigating the structure and diversity of archaea community is vital to understand the metabolic processes in freshwater lake ecosystems. In this study, sediment physicochemical properties were combined with the results from 16S rRNA clone library-sequencing to examine the sediment archaea diversity and the environmental factors driving the sediment archaea community structures. Seven sites were chosen from Poyang Lake, including two sites from the main lake body and five sites from the inflow river estuaries. Our results revealed high diverse archaea community in the sediment of Poyang Lake, including Bathyarchaeota (45.5%), Euryarchaeota (43.1%), Woesearchaeota (3.6%), Pacearchaeota (1.7%), Thaumarchaeota (1.4%), suspended Lokiarchaeota (0.7%), Aigarchaeota (0.2%), and Unclassified Archaea (3.8%). The archaea community compositions differed among sites, and sediment property had considerable influence on archaea community structures and distribution, especially total organic carbon (TOC) and metal lead (Pb) (p < 0.05). This study provides primary profile of sediment archaea distribution in freshwater lakes and helps to deepen our understanding of lake sediment microbes.

Habitat and water quality variables as predictors of community composition in an Indonesian coral reef: a multi-taxon study in the Spermonde Archipelago

Assemblages of corals, sponges, foraminifera, sediment bacteria and sediment archaea were assessed at two depths in the Spermonde Archipelago. Our goal was to assess to what extent variation in composition could be explained by habitat and water quality variables. The habitat variables consisted of depth, substrate type and scleractinian coral cover while water quality variables were derived from ocean color satellite imagery, including the colored dissolved organic matter index (CDOM), chlorophyll-a (Chlor-a) and remote sensing reflectance at 645nm (Rrs_645). Together, habitat and water quality variables explained from 31% (sediment bacteria) to 80% (forams) of the variation in composition. The variation in composition of corals, sponges, forams and sediment archaea was primarily related to habitat variables, while the variation in composition of sediment bacteria was primarily related to water quality variables. Habitat and water quality variables explained similar amounts of variation in the composition of corals and sediment bacteria. CDOM (sponges, sediment bacteria and sediment archaea), Chlor-a (corals and forams) and Rrs_645 (sponges and forams) proved significant predictors of variation in composition for the studied taxa. In addition to water quality variables, all taxa responded to a range of habitat variables including depth and the percentage cover of various benthic life forms including coral cover variables, rubble and sand. Sand cover was the most important habitat variable for corals, sponges, sediment bacteria and sediment archaea. Coral life forms including the cover of branching and tabular corals were important habitat variables for sponges and forams. These results show marked differences in how various taxa respond to variation in habitat and water quality in the Spermonde Archipelago. Moreover, our results indicate that variables estimated from ocean color satellite imagery proved to be better predictors of variation in marine community composition than commonly-used proxies such as the distance offshore or distance to the nearest river.

Archaeal community diversity and abundance changes along a natural salinity gradient in estuarine sediments.

Archaea are widespread in marine sediments, but their occurrence and relationship with natural salinity gradients in estuarine sediments is not well understood. This study investigated the abundance and diversity of Archaea in sediments at three sites [Brightlingsea (BR), Alresford (AR) and Hythe (HY)] along the Colne Estuary, using quantitative real-time PCR (qPCR) of 16S rRNA genes, DNA hybridization, Archaea 16S rRNA and mcrA gene phylogenetic analyses. Total archaeal 16S rRNA abundance in sediments were higher in the low-salinity brackish sediments from HY (2–8 × 107 16S rRNA gene copies cm−3) than the high-salinity marine sites from BR and AR (2 × 104–2 × 107 and 4 × 106–2 × 107 16S rRNA gene copies cm−3, respectively), although as a proportion of the total prokaryotes Archaea were higher at BR than at AR or HY. Phylogenetic analysis showed that members of the ‘Bathyarchaeota’ (MCG), Thaumarchaeota and methanogenic Euryarchaeota were the dominant groups of Archaea. The composition of Thaumarchaeota varied with salinity, as only ‘marine’ group I.1a was present in marine sediments (BR). Methanogen 16S rRNA genes from low-salinity sediments at HY were dominated by acetotrophic Methanosaeta and putatively hydrogentrophic Methanomicrobiales, whereas the marine site (BR) was dominated by mcrA genes belonging to methylotrophic Methanococcoides, versatile Methanosarcina and methanotrophic ANME-2a. Overall, the results indicate that salinity and associated factors play a role in controlling diversity and distribution of Archaea in estuarine sediments.

Community Composition and Abundance of Ammonia-Oxidizing Archaea in Sediments from the Changjiang Estuary and its Adjacent Area in the East China Sea

ABSTRACTCommunity composition and abundance of ammonia-oxidizing archaea (AOA) were investigated using ammonia monooxygenase α subunit (amoA) in sediments from the Changjiang estuary and its adjacent area in the East China Sea (ECS). Real-time quantitative polymerase chain reaction (qPCR), clone libraries and sequencing were performed to characterize the AOA community. Clone libraries analysis showed that the majority of amoA sequences fell within the Nitrosopumilus cluster. Correlation analysis showed that AOA diversity was closely related to the nitrite concentration, which was consistent with the canonical correspondence analysis (CCA) where a significant association between nitrite and AOA community composition was observed. The qPCR results were found to be significantly correlated with the environmental parameters. In the gravity cores, a significant positive correlation was found between ammonium concentrations and amoA gene copy numbers from different sediment depths at station S31. At station S33, however, ammonium concentration had a negative correlation and nitrite concentration had a positive correlation with amoA gene copy numbers. In the surface sediments, chlorophyll a concentration had a negative correlation and nitrate concentration had a positive correlation with amoA gene copy numbers. Compared amoA gene copy numbers from AOA with those from ammonia-oxidizing β-proteobacteria (β-AOB) in the same studied areas, the amoA gene copy ratio of β-AOB to AOA was negatively correlated with the phosphate concentration and dissolved oxygen concentration, but was not significantly correlated with either ammonium concentrations or salinity. Our data provided valuable information to achieve a better understanding of the potential role of ammonia oxidizers at the interface between terrestrial and marine environments.

Ammonia-oxidizing bacteria and archaea in sediments of the Gulf of Mexico

The diversity (richness and community composition) of ammonia-oxidizing archaea (AOA) and bacteria (AOB) within sediments of the Gulf of Mexico was examined. Using polymerase chain reaction primers designed to specifically target the archaeal ammonia monooxygenase-subunit (amoA) gene and bacterial amoA gene, we found AOA and AOB to be present in all three sampling sites. Archaeal amoA libraries were dominated by a few widely distributed Nitrosopumilus-like sequence types, whereas AOB diversity showed significant variation in both richness and community composition. Majority of the bacterial amoA sequences recovered belong to Betaproteobacteria and very few belong to Gammaproteobacteria. Results suggest that water depth and nutrient availability were identified as potential drivers that affected the selection of the AOA and AOB communities. Besides influencing the abundance of individual taxa, these environmental factors also had an impact on the overall richness of the overall AOA and AOB communities. The richness and diversity of AOA and AOB genes were higher at the shallowest sediments (100 m depth) and the deepest sediments (1300 m depth). The reduced diversity in the deepest sediments could be explained by much lower nutrient availability.

Structure and specificity of novel aminopeptidase from marine sediment Archaea

The Earth's microbial diversity remained largely unexplored until recent developments in DNA sequencing. Novel methods enabled us to access genomic information of uncultured microbial organisms and create hypotheses about their metabolic capabilities. These predictions primarily rely on the sequence similarity between a novel protein and characterized proteins. Such an approach introduces a "culture" bias: the well-understood proteins come from a set of laboratory-grown bacteria, while novel microbial proteins are obtained from a variety of environments, including the most extreme. One such niche is ocean sediment – an unexplored ecosystem that plays important roles in geochemical cycles. Single-cell genomics targeting sedimentary populations identified four new archaeons encoding putative intra- and extra-cellular proteases [1]. This discovery suggests that heterotrophic marine Archaea evolved to degrade detrital proteins and might contribute to global carbon cycling. The novel proteases share some sequence similarity with well-known protein-degrading enzymes, but generally are distant homologs. Thus, functional screening is necessary to validate sequence-based predictions. One of the proteases shares sequence similarity with S15 peptidases, cocaine esterases and α-amino acid ester hydrolases (AEH). Phylogeny indicates that the gene is of bacterial origin. Enzymatic assays reveal α-aminopeptidase activity towards dipeptides with a preference for a small, L-configured hydrophobic residue at the N-terminus. The crystal structure shows a homotetrameric, self-compartmentalizing enzyme with four independent active sites localized inside the oligomeric assembly accessible from the internal channel. The active site contains a serine protease triad (Ser-His-Asp) and a cluster of negatively charged residues that bind the N-terminal NH3+ group of the substrate molecule. Therefore, the observed activity suggests that the enzyme (designated as AP TA1) may act on di- or tri-peptides produced during extracellular degradation and subsequently imported to the cell. As a close homolog of AEHs, it is also possible that AP TA1 might participate in the synthesis of yet-to-be-discovered secondary metabolites. Supported by NIH GM094585, DOE/BER DE-AC02-06CH11357 &amp; C-DEBI 36202823 &amp; 157595.

Archaeal Diversity and Spatial Distribution in the Surface Sediment of the South China Sea

Archaea represent a significant portion of biomass in the marine sediments and may play an important role in global carbon cycle. However, the identity and composition of deep sea sediment Archaea are unclear. Here, we used the archaeal 16S rRNA gene primers to determine the diversity and community structure of Archaea from shallow water (<100 m) and deep water (>1500 m) sediments in the South China Sea. Phylogenetically the archaeal community is separated between the shallow- and deep sea sediments, with the former being dominated by the Thaumarchaeota and the latter by the Marine Benthic Group B, E and the South African GoldMine Euryarchaeotal Group as well as Thaumarchaeota. Sand content showed significant correlation with Thaumarchaeota, suggesting that the porous media may create an oxic environment that allowed these aerobic organisms to thrive in the surface sediments. The carbon isotope composition of total organic carbon was significantly correlated to the distribution of archaeal groups, suggesting that Archaea overall may be constrained by the availability or sources of organic carbon in the sediments of the South China Sea.

Stratified Communities of Active Archaea in Shallow Sediments of the Pearl River Estuary, Southern China

Marine subsurface sediments represent a novel archaeal biosphere with unknown physiology. To get to know the composition and ecological roles of the archaeal communities within the sediments of the Pearl River Estuary, Southern China, the diversity and vertical distribution of active archaea in a sediment core were characterized by 16S rRNA phylogenetic analysis of clone libraries derived from RNA. In this study, the archaeal diversity above, within, and beneath the sulfate-methane transition zone (SMTZ) in the Pearl River Estuary sediment core was described. The majority of the clones obtained from the metabolically active fraction of the archaeal community were most closely related to miscellaneous crenarchaeotal group and terrestrial miscellaneous euryarchaeotal group. Notably, although the Pearl River Estuary sediment belong to high methane and high organic carbon environment, sequences affiliated with methanotrophic and methanogenic archaea were detected as minor group in 16S rRNA clone libraries. No obvious evidence suggested that these unknown archaeal phylotypes related directly to anaerobic oxidation of methane in SMTZ. This is the first phylogenetic analysis of the metabolically active fraction of the archaeal community in the coastal sediment environments.

Dynamics of the methanogenic archaea in tropical estuarine sediments.

Methanogenesis may represent a key process in the terminal phases of anaerobic organic matter mineralization in sediments of coastal lagoons. The aim of the present work was to study the temporal and spatial dynamics of methanogenic archaea in sediments of tropical coastal lagoons and their relationship with environmental changes in order to determine how these influence methanogenic community. Sediment samples were collected during the dry (February, May, and early June) and rainy seasons (July, October, and November). Microbiological analysis included the quantification of viable methanogenic archaea (MA) with three substrates and the evaluation of kinetic activity from acetate in the presence and absence of sulfate. The environmental variables assessed were temperature, pH, Eh, salinity, sulfate, solids content, organic carbon, and carbohydrates. MA abundance was significantly higher in the rainy season (106–107 cells/g) compared with the dry season (104–106 cells/g), with methanol as an important substrate. At spatial level, MA were detected in the two layers analyzed, and no important variations were observed either in MA abundance or activity. Salinity, sulfate, solids, organic carbon, and Eh were the environmental variables related to methanogenic community. A conceptual model is proposed to explain the dynamics of the MA.

Calculation of total free energy yield as an alternative approach for predicting the importance of potential chemolithotrophic reactions in geothermal springs

To inform hypotheses regarding the relative importance of chemolithotrophic metabolisms in geothermal environments, we calculated free energy yields of 26 chemical reactions potentially supporting chemolithotrophy in two US Great Basin hot springs, taking into account the effects of changing reactant and product activities on the Gibbs free energy as each reaction progressed. Results ranged from 1.2 × 10(-5) to 3.6 J kg(-1) spring water, or 3.7 × 10(-5) to 11.5 J s(-1) based on measured flow rates, with aerobic oxidation of CH(4) or NH4 + giving the highest average yields. Energy yields calculated without constraining pH were similar to those at constant pH except for reactions where H(+) was consumed, which often had significantly lower yields when pH was unconstrained. In contrast to the commonly used normalization of reaction chemical affinities per mole of electrons transferred, reaction energy yields for a given oxidant varied by several orders of magnitude and were more sensitive to differences in the activities of products and reactants. The high energy yield of aerobic ammonia oxidation is consistent with previous observations of significant ammonia oxidation rates and abundant ammonia-oxidizing archaea in sediments of these springs. This approach offers an additional lens through which to view the thermodynamic landscape of geothermal springs.

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.

Temporal evolution of methane cycling and phylogenetic diversity of archaea in sediments from a deep-sea whale-fall in Monterey Canyon, California

Whale-falls represent localized areas of extreme organic enrichment in an otherwise oligotrophic deep-sea environment. Anaerobic remineralization within these habitats is typically portrayed as sulfidogenic; however, we demonstrate that these systems are also favorable for diverse methane-producing archaeal assemblages, representing up to 40% of total cell counts. Chemical analyses revealed elevated methane and depleted sulfate concentrations in sediments under the whale-fall, as compared to surrounding sediments. Carbon was enriched (up to 3.5%) in whale-fall sediments, as well as the surrounding sea floor to at least 10 m, forming a 'bulls eye' of elevated carbon. The diversity of sedimentary archaea associated with the 2893 m whale-fall in Monterey Canyon (California) varied both spatially and temporally. 16S rRNA diversity, determined by both sequencing and terminal restriction fragment length polymorphism analysis, as well as quantitative PCR of the methyl-coenzyme M reductase gene, revealed that methanogens, including members of the Methanomicrobiales and Methanosarcinales, were the dominant archaea (up to 98%) in sediments immediately beneath the whale-fall. Temporal changes in this archaeal community included the early establishment of methylotrophic methanogens followed by development of methanogens thought to be hydrogenotrophic, as well as members related to the newly described methanotrophic lineage, ANME-3. In comparison, archaeal assemblages in 'reference' sediments collected 10 m from the whale-fall primarily consisted of Crenarchaeota affiliated with marine group I and marine benthic group B. Overall, these results indicate that whale-falls can favor the establishment of metabolically and phylogenetically diverse methanogen assemblages, resulting in an active near-seafloor methane cycle in the deep sea.

Carbon isotope effects associated with aceticlastic methanogenesis.

The carbon isotope effects associated with synthesis of methane from acetate have been determined for Methanosarcina barkeri 227 and for methanogenic archaea in sediments of Wintergreen Lake, Michigan. At 37 degrees C, the 13C isotope effect for the reaction acetate (methyl carbon) --> methane, as measured in replicate experiments with M. barkeri, was - 21.3% +/- 0.3%. The isotope effect at the carboxyl portion of acetate was essentially equal, indicating participation of both positions in the rate-determining step, as expected for reactions catalyzed by carbon monoxide dehydrogenase. A similar isotope effect, - 19.2% +/- 0.3% was found for this reaction in the natural community (temperature = 20 degrees C). Given these observations, it has been possible to model the flow of carbon to methane within lake sediment communities and to account for carbon isotope compositions of evolving methane. Extension of the model allows interpretation of seasonal fluctuations in 13C contents of methane in other systems.