Archaeal Sequences Research Articles

The newly proposed TACK and DPANN archaea detected in the production waters from a high-temperature petroleum reservoir

Revealing the diversity and distribution of archaea is basically crucial to understanding their ecological functions in subsurface petroleum reservoir ecosystems. However, the knowledge about the abundance and distribution of newly proposed archaea (e.g. TACK and DPANN superphyla) in such environments is still limited. In the present work, archaeal communities from five production wells of a high-temperature petroleum reservoir were characterized by high-throughput sequencing. The outcome showed that in the five samples over 98% of archaeal sequences were affiliated to Euryarchaeota, and the rest belonged to newly proposed archaeal phyla (Thaumarchaeota, Verstraetearchaeota, Bathyarchaeota, Aigarchaeota and Woesearchaeota). Based on the defined criteria of rare taxa (<0.1%), OTUs affiliated within Bathyarchaeota, Thaumarchaeota and Woesearchaeota were mostly present as the rare biosphere in the samples. The archaeal communities were significantly shaped by different geochemical parameters of the production waters from the petroleum reservoir. The co-occurrence network analysis revealed the potential syntrophic interactions among the archaea themselves in the subterrestrial environments. Our results indicate that the newly proposed archaea are ubiquitous, also present in the petroleum reservoirs, where they contribute to the ecosystem diversity and play potential roles in the biogeochemical cycle of carbon. This work also provides an overall understanding of the identity, ecology, and functional diversity of newly proposed archaea in petroleum reservoirs.

A glimpse of the prokaryotic diversity of the Large Aral Sea reveals novel extremophilic bacterial and archaeal groups.

During the last five decades, the Aral Sea has gradually changed from a saline water body to a hypersaline lake. Microbial community inhabiting the Aral Sea has been through a succession and continuous adaptation during the last 50 years of increasing salinization, but so far, the microbial diversity has not been explored. Prokaryotic diversity of the Large Aral Sea using cultivation‐independent methods based on determination of environmental 16S rRNA gene sequences revealed a microbial community related to typical marine or (hyper) saline‐adapted Bacteria and Archaea. The archaeal sequences were phylogenetically affiliated with the order Halobacteriales, with a large number of operational taxonomic units constituting a novel cluster in the Haloferacaceae family. Bacterial community analysis indicated a higher diversity with representatives belonging to Proteobacteria, Actinobacteria and Bacteroidetes. Many members of Alphaproteobacteria and Gammaproteobacteria were affiliated with genera like Roseovarius, Idiomarina and Spiribacter which have previously been found in marine or hypersaline waters. The majority of the phylotypes was most closely related to uncultivated organisms and shared less than 97% identity with their closest match in GenBank, indicating a unique community structure in the Large Aral Sea with mostly novel species or genera.

Fluid inclusions from the deep Dead Sea sediment provide new insights on Holocene extreme microbial life

The Dead Sea Deep Drilling Project allowed us to retrieve a continuous sedimentary record spanning the two last glacial cycles. This unique archive, in such an extreme environment, has permitted the development of new proxies and the refinement of already available paleoenvironmental studies. Although life is pushed to its extremes in the Dead Sea environment, several studies have highlighted the impact of microbial activity on this harsh milieu. The identity and means of adaptation of these organisms are however partly ignored. We also know relatively little on the way this extreme ecosystem has evolved with time, and how it will react to growing pressure. In this study, we have used the fluid inclusions trapped in halite, the main evaporitic phase during arid periods in the Dead Sea, to investigate the way the Dead Sea ecosystem has evolved. By extracting ancient DNA from Holocene halite fluid inclusions, we have obtained fossil bacterial and archaeal 16S rRNA gene sequences that suggest that the main microbial actors of the present Dead Sea have been present in the lake for a relatively long period, emphasizing the stability of this extreme environment. This is the case of extreme halophilic archaea of the Salinarchaeum genera. Additionally, we show that current phylotypes of the deep biosphere, such as Acetothermia bacteria are present within the obtained fluid inclusions sequences, which would support seeding of the deep biosphere from the water column. Finally, through the retrieval of sequences assigned to Halodesulfurarchaeum and Desulfovermiculus genera, we shed light on putative new actors of the sulfur cycle involving respectively archaea and bacteria, which could play an unexpected role in the reduction of sulfur species. Together, these data provide new research avenues for both geologists and biologists working in this extreme environment, and help to increase understanding of the evolution of the Dead Sea ecosystem with time.

Phylogenetic characterization of eukaryotic and prokaryotic gut flora of Nile tilapia, Oreochromis niloticus, along niches of Lake Nasser, Egypt, based on rRNA gene high-throughput sequences

Abstract Studies of phylogenetic diversity of fish gut flora often focus on bacteria, leaving a gap in characterization of flora from other domains. This study focused on first exploring of phylogenetic composition of the gut flora, belonging to all domains, eukaryotes, bacteria and archaea, of the tilapia fish, Oreochromis niloticus, inhabiting Lake Nasser, Egypt, based on rRNA gene high-throughput sequencing. Specimens were collected from four distant lake natural fish feeding niches, Khor Kalabsha, Khor Wadi Abyad, Khor Korosko and Khor Toshka. Metagenomic DNA was extracted from fish gut contents, followed by PCR and next generation sequencing of both of eukaryotic 18S- and prokaryotic 16S rRNA genes. A total of 2491, 19005 and 9032 rRNA gene OTUs, were recorded, for eukaryotes, bacteria and archaea, respectively, in the guts from the four niches. Fish guts from Khor Toshka, harbored the highest diversity of bacterial and archaeal 16S rRNA gene sequences. Some 18S rRNA gene OTUs, belonging to members of class Ostracoda, molluscs, and phylum Bacillariophyta, diatoms, beside of 16S rRNA gene OTUs assigned to genus Synechococcus, phylum Cyanobacteria, were recorded in guts from all studied niches, suggesting favorite foods for the fish throughout the lake. Other rRNA gene OTUs, affiliated with the diatom genus Fragilaria, cyanobacterial family Pseudanabaenaceae and genus Oscillatoria, characterized guts from Khor Toshka and Khor Kalabsha, respectively. OTUs, belonging to genus Cetobacterium, phylum Fusobacteria; genera, Methanobacterium and Methanosaeta, phylum Euryarchaeota, constituted the core gut microbiome. Neoechinorhynchus-like OTUs were recorded in guts from all niches, implicating common tilapia gut parasites at Lake Nasser. Guts from all niches harbored several unique archaeal 16S rRNA gene OTUs, but did not match known archaeal phyla. Hence, a large number of phylogenetic shared taxa persist across guts from distant niches, with respect to some OTUs, characterizing gut contents of specific niches.

Evolutionary design principles in metabolism.

Microorganisms are ubiquitous and adapt to various dynamic environments to sustain growth. These adaptations accumulate, generating new traits forming the basis of evolution. Organisms adapt at various levels, such as gene regulation, signalling, protein-protein interactions and metabolism. Of these, metabolism forms the integral core of an organism for maintaining the growth and function of a cell. Therefore, studying adaptations in metabolic networks is crucial to understand the emergence of novel metabolic capabilities. Metabolic networks, composed of enzyme-catalysed reactions, exhibit certain repeating paradigms or design principles that arise out of different selection pressures. In this review, we discuss the design principles that are known to exist in metabolic networks, such as functional redundancy, modularity, flux coupling and exaptations. We elaborate on the studies that have helped gain insights highlighting the interplay of these design principles and adaptation. Further, we discuss how evolution plays a role in exploiting such paradigms to enhance the robustness of organisms. Looking forward, we predict that with the availability of ever-increasing numbers of bacterial, archaeal and eukaryotic genomic sequences, novel design principles will be identified, expanding our understanding of these paradigms shaped by varied evolutionary processes.

Bioinformatics Analysis of Metabolism Pathways of Archaeal Energy Reserves

Energy storage compounds play crucial roles in prokaryotic physiology. Five chemical compounds have been identified in prokaryotes as energy reserves: polyphosphate (polyP), polyhydroxyalkanoates (PHAs), glycogen, wax ester (WE) and triacylglycerol (TAG). Currently, no systematic study of archaeal energy storage metabolism exists. In this study, we collected 427 archaeal reference sequences from UniProt database. A thorough pathway screening of energy reserves led to an overview of distribution patterns of energy metabolism in archaea. We also explored how energy metabolism might have impact on archaeal extremophilic phenotypes. Based on the systematic analyses of archaeal proteomes, we confirmed that metabolism pathways of polyP, PHAs and glycogen are present in archaea, but TAG and WE are completely absent. It was also confirmed that PHAs are tightly related to halophilic archaea with larger proteome size and higher GC contents, while polyP is mainly present in methanogens. In sum, this study systematically investigates energy storage metabolism in archaea and provides a clear correlation between energy metabolism and the ability to survive in extreme environments. With more genomic editing tools developed for archaea and molecular mechanisms unravelled for energy storage metabolisms (ESMs), there will be a better understanding of the unique lifestyle of archaea in extreme environments.

Archaea dominate the microbial community in an ecosystem with low-to-moderate temperature and extreme acidity

BackgroundThe current view suggests that in low-temperature acidic environments, archaea are significantly less abundant than bacteria. Thus, this study of the microbiome of Parys Mountain (Anglesey, UK) sheds light on the generality of this current assumption. Parys Mountain is a historically important copper mine and its acid mine drainage (AMD) water streams are characterised by constant moderate temperatures (8–18 °C), extremely low pH (1.7) and high concentrations of soluble iron and other metal cations.ResultsMetagenomic and SSU rRNA amplicon sequencing of DNA from Parys Mountain revealed a significant proportion of archaea affiliated with Euryarchaeota, which accounted for ca. 67% of the community. Within this phylum, potentially new clades of Thermoplasmata were overrepresented (58%), with the most predominant group being “E-plasma”, alongside low-abundant Cuniculiplasmataceae, ‘Ca. Micrarchaeota’ and ‘Terrestrial Miscellaneous Euryarchaeal Group’ (TMEG) archaea, which were phylogenetically close to Methanomassilicoccales and clustered with counterparts from acidic/moderately acidic settings. In the sediment, archaea and Thermoplasmata contributed the highest numbers in V3-V4 amplicon reads, in contrast with the water body community, where Proteobacteria, Nitrospirae, Acidobacteria and Actinobacteria outnumbered archaea. Cultivation efforts revealed the abundance of archaeal sequences closely related to Cuniculiplasma divulgatum in an enrichment culture established from the filterable fraction of the water sample. Enrichment cultures with unfiltered samples showed the presence of Ferrimicrobium acidiphilum, C. divulgatum, ‘Ca. Mancarchaeum acidiphilum Mia14’, ‘Ca. Micrarchaeota’-related and diverse minor (< 2%) bacterial metagenomic reads.ConclusionContrary to expectation, our study showed a high abundance of archaea in this extremely acidic mine-impacted environment. Further, archaeal populations were dominated by one particular group, suggesting that they are functionally important. The prevalence of archaea over bacteria in these microbiomes and their spatial distribution patterns represents a novel and important advance in our understanding of acidophile ecology. We also demonstrated a procedure for the specific enrichment of cell wall-deficient members of the archaeal component of this community, although the large fraction of archaeal taxa remained unculturable. Lastly, we identified a separate clustering of globally occurring acidophilic members of TMEG that collectively belong to a distinct order within Thermoplasmata with yet unclear functional roles in the ecosystem.

Biogeographic Distribution Patterns of the Archaeal Communities Across the Black Soil Zone of Northeast China.

Although archaea are ubiquitous in various environments, the knowledge gaps still exist regarding the biogeographical distribution of archaeal communities at regional scales in agricultural soils compared with bacteria and fungi. To provide a broader biogeographical context of archaeal diversity, this study quantified the abundance and community composition of archaea across the black soil zone in northeast China using real-time PCR and high-throughput sequencing (HTS) methods. Archaeal abundances across all soil samples ranged from 4.04 × 107 to 26.18 × 107 16S rRNA gene copies per gram of dry soil. Several soil factors were positively correlated with the abundances including soil pH, concentrations of total C, N, and P, and available K in soil, and soil water content. Approximately 94.2, 5.7, and 0.3% of archaeal sequences, and 31, 151, and 3 OTUs aligned within the phyla Thaumarchaeota, Euryarchaeota, and Crenarchaeota, respectively. Within the phylum of Thaumarchaeota, group 1.1b was a dominating genus accounting for an average of 87% archaeal sequences and phylogenetically classified as Nitrososphaera, a genus of ammonia oxidizing archaea. The response of dominating OTUs to environmental factors differed greatly, suggesting the physiological characteristics of different archaeal members is diversified in the black soils. Although the number of OTUs was not related with any particular soil parameters, the number of OTUs within Thaumarchaeota and Euryarchaeota was marginally related with soil pH. Archaeal community compositions differed between samples, and a Canonical correspondence analysis (CCA) analysis indicated that soil pH and the latitude of sampling locations were two dominating factors in shifting community structures. A variance partitioning analysis (VPA) analysis showed that the selected soil parameters (32%) were the largest drivers of community variation, in particular soil pH (21%), followed by geographic distances (19%). These findings suggest that archaeal communities have distinct biogeographic distribution pattern in the black soil zone and soil pH was the key edaphic factor in structuring the community compositions.

Effects of pig slurry acidification on methane emissions during storage and subsequent biogas production

In addition to undesirable odorous gases, substantial amounts of greenhouse gases (GHG), particularly methane (CH4), are generated during the storage of livestock manure. To reduce the CH4 emissions, first, pig slurry (PS) was stored for 40 d at 30 °C after adjusting the pH at 5.0–7.0 using H2SO4 solution. In the control (non-acidified PS), 3.7 kg CO2 eq./ton PS of CH4 emissions was detected, which was reduced to 1.8, 0.9, 0.4, 0.2, and 0.1 kg CO2 eq./ton PS at pH 7.0, 6.5, 6.0, 5.5, and 5.0, respectively. Methanosarcina was found to be the dominant genus (67% of the total archaeal sequence) in the control, whose dominance was reduced as storage pH decreased. The results of ribonucleic acid analysis and specific methanogenic activity test further confirmed the inhibition of indigenous methanogens by acidification. Later, the biochemical CH4 potential of stored PS was tested. Compared to the control (10.6 L CH4/L PS), the acidified PS showed higher CH4 yields of 12.7–14.6 L CH4/L PS, presumably by keeping degradable organic matters in PS under acidic condition. Among different acidification pHs tested, the maximum amount of GHG reduction was achieved at pH 6.0 by reducing CH4 emission to +0.4 kg CO2 eq./ton PS during storage while increasing biogas production potential equivalent to 48.3 kWh/ton PS (−22.5 kg CO2 eq./ton PS), resulting in a further reduction of (−)9.6 kg CO2 eq./ton PS compared to the control.

Salino-alkaline lime of anthropogenic origin a reservoir of diverse microbial communities

This paper presents study on the microbiome of a unique extreme environment - saline and alkaline lime, a by-product of soda ash and table salt production in Janikowo, central Poland. High-throughput 16S rDNA amplicon sequencing was used to reveal the structure of bacterial and archaeal communities in the lime samples, taken from repository ponds differing in salinity (2.3–25.5% NaCl). Surprisingly abundant and diverse bacterial communities were discovered in this extreme environment. The most important geochemical drivers of the observed microbial diversity were salinity, calcium ions, nutrients, and water content. The bacterial and archaeal communities in saline, alkaline lime were similar to those found in natural haloalkaline environments. Although the archaeal contribution to the whole microbial community was lower than 4%, the four archaeal genera Natronomonas, Halorubrum, Halobellus, and Halapricum constituted the core microbiome of saline, alkaline lime - a set of OTUs (> 0.1% of total archaeal relative abundance) present in all samples under study. The high proportion of novel, unclassified archaeal and bacterial sequences (not identified at 97% similarity level) in the 16S rRNA gene libraries indicated that potentially new genera, especially within the class of Thermoplasmata inhabit this unique environment.

Changes in microbial communities and associated water and gas geochemistry across a sulfate gradient in coal beds: Powder River Basin, USA

Competition between microbial sulfate reduction and methanogenesis drives cycling of fossil carbon and generation of CH4 in sedimentary basins. However, little is understood about the fundamental relationship between subsurface aqueous geochemistry and microbiology that drives these processes. Here we relate elemental and isotopic geochemistry of coal-associated water and gas to the microbial community composition from wells in two different coal beds across CH4 and SO42− gradients (Powder River Basin, Montana, USA). Areas with high CH4 concentrations generally have higher alkalinity and δ13C-DIC values, little to no SO42−, and greater conversion of coal-biodegradable organics to CH4 (based on δ13C-CH4 and δ13C-CO2 values). Wells with SO42− concentrations from 2 to 10 mM had bacterial populations dominated by several different sulfate-reducing bacteria and archaea that were mostly novel and unclassified. In contrast, in wells with SO42− concentrations <1 mM, the sequences were dominated by presumptive syntrophic bacteria as well as archaeal Methanosarcinales and Methanomicrobiales. The presence of sequences indicative of these bacteria in low SO42− methanogenic wells may suggest a syntrophic role in coal biodegradation and/or the generation of methanogenic substrates from intermediate organic compounds. Archaeal sequences were observed in all sampled zones, with an enrichment of sequences indicative of methanogens in low SO42− zones and unclassified sequences in high SO42− zones. However, sequences indicative of Methanomassiliicoccales were enriched in intermediate SO42− zones and suggest tolerance to SO42− and/or alternative metabolisms in the presence of SO42−. Moreover, sequences indicative of methylotrophic methanogens were more prevalent in an intermediate SO42− and CH4 well and results suggest an important role for methylotrophic methanogens in critical zone transitions. The presented results demonstrate in situ changes in bacterial and archaeal population distributions along a SO42− gradient associated with recalcitrant, organic carbon that is biodegraded and converted to CO2 and/or CH4.

Petroleum hydrocarbon rich oil refinery sludge of North-East India harbours anaerobic, fermentative, sulfate-reducing, syntrophic and methanogenic microbial populations

BackgroundSustainable management of voluminous and hazardous oily sludge produced by petroleum refineries remains a challenging problem worldwide. Characterization of microbial communities of petroleum contaminated sites has been considered as the essential prerequisite for implementation of suitable bioremediation strategies. Three petroleum refinery sludge samples from North Eastern India were analyzed using next-generation sequencing technology to explore the diversity and functional potential of inhabitant microorganisms and scope for their on-site bioremediation.ResultsAll sludge samples were hydrocarbon rich, anaerobic and reduced with sulfate as major anion and several heavy metals. High throughput sequencing of V3-16S rRNA genes from sludge metagenomes revealed dominance of strictly anaerobic, fermentative, thermophilic, sulfate-reducing bacteria affiliated to Coprothermobacter, Fervidobacterium, Treponema, Syntrophus, Thermodesulfovibrio, Anaerolinea, Syntrophobacter, Anaerostipes, Anaerobaculum, etc., which have been well known for hydrocarbon degradation. Relatively higher proportions of archaea were detected by qPCR. Archaeal 16S rRNA gene sequences showed presence of methanogenic Methanobacterium, Methanosaeta, Thermoplasmatales, etc. Detection of known hydrocarbon utilizing aerobic/facultative anaerobic (Mycobacterium, Pseudomonas, Longilinea, Geobacter, etc.), nitrate reducing (Gordonia, Novosphigobium, etc.) and nitrogen fixing (Azovibrio, Rhodobacter, etc.) bacteria suggested niche specific guilds with aerobic, facultative anaerobic and strict anaerobic populations. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) predicted putative genetic repertoire of sludge microbiomes and their potential for hydrocarbon degradation; lipid-, nitrogen-, sulfur- and methane- metabolism. Methyl coenzyme M reductase A (mcrA) and dissimilatory sulfite reductase beta-subunit (dsrB) genes phylogeny confirmed methanogenic and sulfate-reducing activities within sludge environment endowed by hydrogenotrophic methanogens and sulfate-reducing Deltaproteobacteria and Firmicutes members.ConclusionRefinery sludge microbiomes were comprised of hydrocarbon degrading, fermentative, sulfate-reducing, syntrophic, nitrogen fixing and methanogenic microorganisms, which were in accordance with the prevailing physicochemical nature of the samples. Analysis of functional biomarker genes ascertained the activities of methanogenic and sulfate-reducing organisms within sludge environment. Overall data provided better insights on microbial diversity and activity in oil contaminated environment, which could be exploited suitably for in situ bioremediation of refinery sludge.

Relevance of phenotypic information for the taxonomy of not-yet-cultured microorganisms

To date, far less than 1% of the estimated global species of Bacteria and Archaea have been described and their names validly published. Aside from these quantitative limitations, our understanding of phenotypic and functional diversity of prokaryotes is also highly biased as not a single species has been described for 85 of the 118 phyla that are currently recognized. Due to recent advances in sequencing technology and capacity, metagenomic datasets accumulate at an increasing speed and new bacterial and archaeal genome sequences become available at a faster rate than newly described species. The growing gap between the diversity of Bacteria and Archaea held in pure culture and that detected by molecular methods has led to the proposal to establish a formal nomenclature for not-yet-cultured taxa primarily based on sequence information. According to this proposal, the concept of Candidatus species would be extended to groups of closely related genome sequences and their names validly published following established rules of bacterial nomenclature. The corresponding sequences would be deposited in public databases as the type. The suggested alterations of the International Code of Nomenclature of Prokaryotes raise concerns regarding (1) the reliability and stability of nomenclature, (2) the technological and conceptual limitations as well as availability of reference genomes, (3) the information content of in silico functional predictions, and (4) the recognition of evolutionary units of microbial diversity. These challenges need to be overcome to arrive at a meaningful taxonomy of not-yet-cultured prokaryotes with so far poorly understood phenotypes.

Characteristics of archaea and bacteria in rice rhizosphere along a mercury gradient

Several strains of archaea have the ability to methylate or resist mercury (Hg), and the paddy field is regarded to be conducive to Hg methylation. However, our knowledge of Hg-methylating or Hg-resistant archaea in paddy soils is very limited so far. Therefore, the distribution of archaea and bacteria in the rhizosphere (RS) and bulk soil (BS) of the rice growing in Xiushan Hg-mining area of southwest China was investigated. Bacterial and archaeal 16S rRNA gene amplicon sequencing of the rice rhizosphere along the Hg gradient was conducted. THg concentrations in RS were significantly higher than that in BS at site S1 and S2, while MeHg concentrations in RS was always higher than that in BS, except S6. Bacterial species richness estimates were much higher than that in archaea. The bacterial α-diversity in high-Hg sites was significant higher than that in low-Hg sites based on ACE and Shannon indices. At the genus level, Thiobacillus, Xanthomonas, Defluviicoccus and Candidatus Nitrosoarchaeum were significantly more abundant in the rhizosphere of high-Hg sites, which meant that strains in these genera might play important roles in response to Hg stress. Hg-methylating archaea in the paddy field could potentially be affiliated to strains in Methanosarcina, but further evidence need to be found. The results provide reference to understand archaeal rhizosphere community along an Hg gradient paddy soils.

Stimulatory Effect of Magnetite Nanoparticles on a Highly Enriched Butyrate-Oxidizing Consortium.

Syntrophic oxidation of butyrate is catabolized by a few bacteria specialists in the presence of methanogens. In the present study, a highly enriched butyrate-oxidizing consortium was obtained from a wetland sediment in Tibetan Plateau. During continuous transfers of the enrichment, the addition of magnetite nanoparticles (nanoFe3O4) consistently enhanced butyrate oxidation and CH4 production. Molecular analysis revealed that all bacterial sequences from the consortium belonged to Syntrophomonas with the closest relative of Syntrophomonas wolfei and 96% of the archaeal sequences were related to Methanobacteria with the remaining sequences to Methanocella. Addition of graphite and carbon nanotubes for a replacement of nanoFe3O4 caused the similar stimulatory effect. Silica coating of nanoFe3O4 surface, however, completely eliminated the stimulatory effect. The control experiment with axenic cultivation of a Syntrophomonas strain and two methanogen strains showed no effect by nanoFe3O4. Together, the results in the present study support that syntrophic oxidation of butyrate is likely facilitated by direct interspecies electron transfer in the presence of conductive nanomaterials.

Benthic archaea as potential sources of tetraether membrane lipids in sediments across an oxygen minimum zone

Abstract. Benthic archaea comprise a significant part of the total prokaryotic biomass in marine sediments. Recent genomic surveys suggest they are largely involved in anaerobic processing of organic matter, but the distribution and abundance of these archaeal groups are still largely unknown. Archaeal membrane lipids composed of isoprenoid diethers or tetraethers (glycerol dibiphytanyl glycerol tetraether, GDGT) are often used as archaeal biomarkers. Here, we compare the archaeal diversity and intact polar lipid (IPL) composition in both surface (0–0.5 cm) and subsurface (10–12 cm) sediments recovered within, just below, and well below the oxygen minimum zone (OMZ) of the Arabian Sea. Archaeal 16S rRNA gene amplicon sequencing revealed a predominance of Thaumarchaeota (Marine Group I, MG-I) in oxygenated sediments. Quantification of archaeal 16S rRNA and ammonia monoxygenase (amoA) of Thaumarchaeota genes and their transcripts indicated the presence of an active in situ benthic population, which coincided with a high relative abundance of hexose phosphohexose crenarchaeol, a specific biomarker for living Thaumarchaeota. On the other hand, anoxic surface sediments within the OMZ and all subsurface sediments were dominated by archaea belonging to the Miscellaneous Crenarchaeota Group (MCG), the Thermoplasmatales and archaea of the DPANN (superphylum grouping Micrarchaeota, Diapherotrites, Aenigmarchaeota, Nanohaloarchaeota, Parvarchaeota, Nanoarchaeota, Pacearchaeota and Woesearchaeota). Members of the MCG were diverse, with a dominance of subgroup MCG-12 in anoxic surface sediments. This coincided with a high relative abundance of IPL GDGT-0 with an unknown polar head group. Subsurface anoxic sediments were characterized by higher relative abundance of GDGT-0, -2 and -3 with dihexose IPL types, GDGT-0 with a cyclopentanetetraol molecule and hexose, as well as the presence of specific MCG subgroups, suggesting that these groups could be the biological sources of these archaeal lipids.

Compositional analysis of archaeal communities in high and low microbial abundance sponges in the Misool coral reef system, Indonesia

ABSTRACTThe high/low microbial abundance (HMA/LMA) dichotomy in sponges has been the subject of several studies over recent years, but few studies have analysed this dichotomy in terms of the sponge archaeal community and function. Using a 16S rRNA gene barcoded pyrosequencing approach and predictive functional analysis (PICRUSt) we compared the archaeal composition, richness and predicted function of one HMA sponge (Xestospongia testudinaria), one LMA sponge (Stylissa carteri) and one sponge species of unknown microbial abundance (Aaptos lobata). Although most of the archaeal sequences were assigned to the Crenarchaeota phylum, S. carteri had the highest percentage of sequences assigned to the Euryarchaeota phylum. Variation among sponge species explained >85% of the variation in archaeal operational taxonomic unit (OTU) composition with each sponge species forming a distinct cluster. There were significant differences in predicted PICRUSt profiles among sponge species, suggesting that archaeal communities present in the studied sponge species may perform different functions. X. testudinaria and A. lobata were similar both in terms of OTU and KEGG orthologues composition, which may indicate that A. lobata is a HMA sponge. Additionally, some of the most enriched functions seem to be related to traits associated with high and low microbial abundance sponges.

Removing contaminants from databases of draft genomes.

Metagenomic sequencing of patient samples is a very promising method for the diagnosis of human infections. Sequencing has the ability to capture all the DNA or RNA from pathogenic organisms in a human sample. However, complete and accurate characterization of the sequence, including identification of any pathogens, depends on the availability and quality of genomes for comparison. Thousands of genomes are now available, and as these numbers grow, the power of metagenomic sequencing for diagnosis should increase. However, recent studies have exposed the presence of contamination in published genomes, which when used for diagnosis increases the risk of falsely identifying the wrong pathogen. To address this problem, we have developed a bioinformatics system for eliminating contamination as well as low-complexity genomic sequences in the draft genomes of eukaryotic pathogens. We applied this software to identify and remove human, bacterial, archaeal, and viral sequences present in a comprehensive database of all sequenced eukaryotic pathogen genomes. We also removed low-complexity genomic sequences, another source of false positives. Using this pipeline, we have produced a database of “clean” eukaryotic pathogen genomes for use with bioinformatics classification and analysis tools. We demonstrate that when attempting to find eukaryotic pathogens in metagenomic samples, the new database provides better sensitivity than one using the original genomes while offering a dramatic reduction in false positives.

Operon-mapper: a web server for precise operon identification in bacterial and archaeal genomes.

SummaryOperon-mapper is a web server that accurately, easily and directly predicts the operons of any bacterial or archaeal genome sequence. The operon predictions are based on the intergenic distance of neighboring genes as well as the functional relationships of their protein-coding products. To this end, Operon-mapper finds all the ORFs within a given nucleotide sequence, along with their genomic coordinates, orthology groups and functional relationships. We believe that Operon-mapper, due to its accuracy, simplicity and speed, as well as the relevant information that it generates, will be a useful tool for annotating and characterizing genomic sequences.Availability and implementation http://biocomputo.ibt.unam.mx/operon_mapper/

Diversity and distribution of Archaea in global estuarine ecosystems

Estuarine ecosystem is a unique geographical transitional zone between freshwater and seawater, harboring a wide range of microbial communities including Archaea. Although a large number of Archaea have been detected in such ecosystem, the global patterns in archaeal diversity and distribution are extremely scarce. To bridge this gap, we carried out a comprehensive survey of archaeal communities using ca. 4000 publicly available archaeal 16S rRNA gene sequences (>300 bp) collected from 24 estuaries in different latitude regions. These sequences were divided into 1450 operational taxonomic units (OTUs) at 97% identity, suggesting a high biodiversity that increased gradually from the high- to low-latitude estuaries. Phylogenetic analysis showed that estuarine ecosystem was a large biodiversity pool of Archaea that was mainly composed of 12 phyla. Among them, the predominant groups were Bathyarchaeota, Euryarchaeota and Thaumarchaeota. Interestingly, archaeal distribution demonstrated a geographical differentiation in that Thaumarchaeota was dominated in the low-latitude estuaries, Bathyarchaeota in the mid-latitude estuaries, and Euryarchaeota in the high-latitude estuaries, respectively. Furthermore, the majority of the most abundant 20 OTUs demonstrated an overrepresented or underrepresented distribution pattern in some specific estuaries or latitude regions while a few were evenly distributed throughout the estuaries. This pattern indicates a potential selectivity of geographical distribution. In addition, the analysis of environmental parameters suggested that latitude would be one of the major factors driving the distribution of archaeal communities in estuarine ecosystem. This study profiles a clear framework on the diversity and distribution of Archaea in the global estuarine ecosystem and explores the general environmental factors that influence these patterns. Our findings constitute an important part of the exploration of the global ecology of Archaea.