A psychrophilic crenarchaeon inhabits a marine sponge: Cenarchaeum symbiosum gen. nov., sp. nov

Microbial community associated with the colonial ascidian Cystodytes dellechiajei

The ascidian Cystodytes dellechiajei (Della Valle, 1877) (phylum Chordata, class Ascidiacea, family Polycitoridae) is a colonial tunicate that inhabits benthic rock environments in the Atlantic, Pacific and Indian Oceans, as well as the Mediterranean Sea. Its life cycle has two phases, the adult sessile colony and the free-living larva. Both adult zooids and larvae are surrounded by a protective tunic that contains several eukaryotic cell lines, is composed mainly of acidic mucopolysacharides associated with collagen and elastin-like proteins, and is covered by a thin cuticle. The microbiota associated with the tunic tissues of adult colonies and larva of C. dellechiajei has been examined by optical, confocal and electron microscopy and by fluorescence in situ hybridization (FISH), denaturing gradient gel electrophoresis (DGGE), and 16S rRNA gene clone library analysis. Microscopy analyses indicated the presence inside the tunic, both for the adult and the larva, of a dense community of Bacteria while only the external surface of colony cuticle was colonized by diatoms, rodophyte algae and prokaryotic-like epiphytes. Transmission electron microscopy showed tunic eukaryotic cells that were engulfing and lysing bacteria. 16S rRNA gene analyses (DGGE and clone libraries) and FISH indicated that the community inside the tunic tissues of the adults and larvae was dominated by Alphaproteobacteria. Bacteria belonging to the phyla Gammaproteobacteria and Bacteroidetes were also detected in the adults. Many of the 16S rRNA gene sequences in the tunic tissues were related to known aerobic anoxygenic phototrophs (AAP), like Roseobacter sp. and Erythrobacter sp. In order to check whether the gene pufM, coding for the M subunit of the reaction centre complex of aerobic anoxygenic photosynthesis, was being expressed inside the ascidian tissues, two libraries, one for an adult colony and one for larva, of cDNA from the expressed pufM gene were also constructed. The sequences most frequently (64% for colony and 67% for larva) retrieved from these libraries presented > 90% aa identity with the pufM gene product of the Roseobacter-like group, a cluster of AAP widely detected in marine planktonic environments.

The bacterial species definition in the genomic era

The bacterial species definition, despite its eminent practical significance for identification, diagnosis, quarantine and diversity surveys, remains a very difficult issue to advance. Genomics now offers novel insights into intra-species diversity and the potential for emergence of a more soundly based system. Although we share the excitement, we argue that it is premature for a universal change to the definition because current knowledge is based on too few phylogenetic groups and too few samples of natural populations. Our analysis of five important bacterial groups suggests, however, that more stringent standards for species may be justifiable when a solid understanding of gene content and ecological distinctiveness becomes available. Our analysis also reveals what is actually encompassed in a species according to the current standards, in terms of whole-genome sequence and gene-content diversity, and shows that this does not correspond to coherent clusters for the environmental Burkholderia and Shewanella genera examined. In contrast, the obligatory pathogens, which have a very restricted ecological niche, do exhibit clusters. Therefore, the idea of biologically meaningful clusters of diversity that applies to most eukaryotes may not be universally applicable in the microbial world, or if such clusters exist, they may be found at different levels of distinction.

Biochemical characterisation of LigN, an NAD+-dependent DNA ligase from the halophilic euryarchaeon Haloferax volcanii that displays maximal in vitro activity at high salt concentrations

Background

DNA ligases are required for DNA strand joining in all forms of cellular life. NAD⁺-dependent DNA ligases are found primarily in eubacteria but also in some eukaryotic viruses, bacteriophage and archaea. Among the archaeal NAD⁺-dependent DNA ligases is the LigN enzyme of the halophilic euryarchaeon Haloferax volcanii, the gene for which was apparently acquired by Hfx.volcanii through lateral gene transfer (LGT) from a halophilic eubacterium. Genetic studies show that the LGT-acquired LigN enzyme shares an essential function with the native Hfx.volcanii ATP-dependent DNA ligase protein LigA.

Results

To characterise the enzymatic properties of the LigN protein, wild-type and three mutant forms of the LigN protein were separately expressed in recombinant form in E.coli and purified to apparent homogeneity by immobilised metal ion affinity chromatography (IMAC). Non-isotopic DNA ligase activity assays using λ DNA restriction fragments with 12 bp cos cohesive ends were used to show that LigN activity was dependent on addition of divalent cations and salt. No activity was detected in the absence of KCl, whereas maximum activity could be detected at 3.2 M KCl, close to the intracellular KCl concentration of Hfx.volcanii cells.

Conclusion

LigN is unique amongst characterised DNA ligase enzymes in displaying maximal DNA strand joining activity at high (> 3 M) salt levels. As such the LigN enzyme has potential both as a novel tool for biotechnology and as a model enzyme for studying the adaptation of proteins to high intracellular salt levels.

Vertical transmission of diverse microbes in the tropical sponge Corticium sp

Sponges are host to extremely diverse bacterial communities, some of which appear to be spatiotemporally stable, though how these consistent associations are assembled and maintained from one sponge generation to the next is not well understood. Here we report that a diverse group of microbes, including both bacteria and archaea, is consistently present in aggregates within embryos of the tropical sponge Corticium sp. The major taxonomic groups represented in bacterial 16S rRNA sequences amplified from the embryos are similar to those previously described in a variety of marine sponges. Three selected bacterial taxa, representing proteobacteria, actinobacteria, and a clade including recently described sponge-associated bacteria, were tested and found to be present in all adult samples tested over a 3-year period and in the embryos throughout development. Specific probes were used in fluorescence in situ hybridization to localize cells of the three types in the embryos and mesohyl. This study confirms the vertical transmission of multiple, phylogenetically diverse microorganisms in a marine sponge, and our findings lay the foundation for future work on exploring vertical transmission of specific, yet diverse, microbial assemblages in marine sponges.

Genomic analysis of the uncultivated marine crenarchaeote Cenarchaeum symbiosum

Crenarchaeota are ubiquitous and abundant microbial constituents of soils, sediments, lakes, and ocean waters. To further describe the cosmopolitan nonthermophilic Crenarchaeota, we analyzed the genome sequence of one representative, the uncultivated sponge symbiont Cenarchaeum symbiosum. C. symbiosum genotypes coinhabiting the same host partitioned into two dominant populations, corresponding to previously described a- and b-type ribosomal RNA variants. Although they were syntenic, overlapping a- and b-type ribotype genomes harbored significant variability. A single tiling path comprising the dominant a-type genotype was assembled and used to explore the genomic properties of C. symbiosum and its planktonic relatives. Of 2,066 ORFs, 55.6% matched genes with predicted function from previously sequenced genomes. The remaining genes partitioned between functional RNAs (2.4%) and hypotheticals (42%) with limited homology to known functional genes. The latter category included some genes likely involved in the archaeal-sponge symbiotic association. Conversely, 525 C. symbiosum ORFs were most highly similar to sequences from marine environmental genomic surveys, and they apparently represent orthologous genes from free-living planktonic Crenarchaeota. In total, the C. symbiosum genome was remarkably distinct from those of other known Archaea and shared many core metabolic features in common with its free-living planktonic relatives.

Consistent bacterial community structure associated with the surface of the sponge Mycale adhaerens bowerbank

As a crucial step in the identification of possible association between bacteria and sponges, we investigated if a unique bacterial population community was consistently associated with the surface of the sponge Mycale adhaerens, irrespective of environmental conditions. The composition of bacterial communities associated with the surface of sponges at three geographically distinctive sites in Hong Kong waters over four seasons was examined by analyzing terminal restriction fragment length polymorphism of the bacterial 16S rRNA genes. Statistical analysis indicated that bacterial communities on inanimate reference surfaces (polystyrene dishes deployed in the close vicinity of the sponge colonies for 7 days) had a relatively high degree of both site and seasonal specificities (R statistics of pairwise comparisons approximately 1), which might be attributed to the differences in environmental conditions at different sites and seasons. On the contrary, the sponge-surface-associated bacterial communities from different sites and seasons were hardly distinguishable from each other (lowest R = -0.16) but were rather distinctive from the reference bacterial communities (R approximately 1), suggesting a highly stable and distinctive bacteria-sponge association irrespective of the environmental conditions. The occurrence of some unique bacterial types in the sponge-surface-associated communities over space and time suggests that the associations are consistent and specific.

Molecular analyses of microbial diversity associated with the Lonar soda lake in India: an impact crater in a basalt area

The prokaryotic diversity associated with an Indian soda lake (Lonar Crater Lake) located in a basaltic soil area was investigated using a culture-independent approach. Community DNA was extracted directly from four sediment samples obtained by coring to depths of 10-20 cm. Small subunit rRNA genes (16S rDNA) were amplified by PCR using primers specific to the domains Bacteria and Archaea. The PCR products were cloned and sequenced. For the bacterial rDNA clone library, 500 clones were randomly selected for further analysis. After restriction fragment length polymorphism (RFLP) analysis and subsequent sequencing, a total of 44 unique phylotypes were obtained. These phylotypes spanned a wide range within the domain Bacteria, occupying eight major lineages/phyla. 34% of the clones were classified as firmicutes. The other clones were grouped into proteobacteria (29.5%), actinobacteria (6.8%), deinococcus-thermus (4.5%), cytophages-flavobacterium-bacteroidetes (13.3%), planctomycetes (6.8%), cyanobacteria (4.5%) and spirochetes (2.27%). In the case of the archaeal 16S rDNA library, analysis of 250 randomly selected clones revealed the presence of 13 distinct phylotypes; 5 phylotypes were associated with Crenarchaeota and 8 with Euryarchaeota. Most of the euryarchaeota sequences were related to methanogens. Findings from this molecular study of a site investigated for the first time have revealed the presence of a highly diverse bacterial population and a comparatively less diverse archaeal population. The majority ( approximately 80%) of the cloned sequences show little affiliation with known taxa (<97% sequence similarity) and may represent novel taxa/sequences and organisms specifically adapted to this basaltic soda lake environment. Diversity analyses demonstrate greater diversity and evenness of bacterial species compared to a skewed representation of species for Archaea.

Stratified communities of active Archaea in deep marine subsurface sediments

Archaeal 16S rRNA was extracted from samples of deep marine subsurface sediments from Peru Margin site 1227, Ocean Drilling Program leg 201. The amounts of archaeal 16S rRNA in each extract were quantified by serial dilution and reverse transcription (RT)-PCR. The results indicated a 1,000-fold variation in rRNA content with depth in the sediment, with the highest concentrations found near the sediment surface and in the sulfate-methane transition zone (SMTZ). The phylogenetic composition of the active archaeal population revealed by cloning and sequencing of RT-PCR products changed with depth. Several phylotypes affiliated with marine benthic group B (MBGB) dominated clone libraries from the upper part of the SMTZ and were detected only in this layer. Members of the miscellaneous crenarchaeotal group (MCG) dominated clone libraries from the other layers. These results demonstrate that archaeal communities change in activity and community composition over short distances in geochemically distinct zones of deep subseafloor sediments and that these changes are traceable in the rRNA pool. It was shown for the first time that members of both the MCG and MBGB Archaea are more active in the SMTZ than in layers above and below. This indicates that they benefit either directly or indirectly from the anaerobic oxidation of methane. They also appear to be ecophysiologically flexible, as they have been retrieved from a wide range of marine sediments of various geochemical properties.

Thermophilic temperature optimum for crenarchaeol synthesis and its implication for archaeal evolution

The isoprenoid lipid crenarchaeol is widespread in hot springs of California and Nevada. Terrestrial and marine data together suggest a maximum relative abundance of crenarchaeol at approximately 40 degrees C. This warm temperature optimum may have facilitated colonization of the ocean by (hyper)thermophilic Archaea and the major marine radiation of Crenarchaeota.

Diversity of polyketide synthase genes from bacteria associated with the marine sponge Pseudoceratina clavata: culture-dependent and culture-independent approaches

Diverse ketosynthase (KS) genes were retrieved from the microbial community associated with the Great Barrier Reef sponge Pseudoceratina clavata. Bacterial isolation and metagenomic approaches were employed. Phylogenetic analysis of 16S rRNA of culturable sponge-associated bacterial communities comprised eight groups over four phyla. Ten KS domains were amplified from four genera of isolates and phylogenetics demonstrated that these KS domains were located in three clusters (actinobacterial, cyanobacterial and trans-AT type). Metagenomic DNA of the sponge microbial community was extracted to explore community KS genes by two approaches: direct amplification of KS domains and construction of fosmid libraries for KS domain screening. Five KS domains were retrieved from polymerase chain reaction (PCR) amplification using sponge metagenome DNA as template and five fosmid clones containing KS domains found using multiplex PCR screening. Analysis of selected polyketide synthase (PKS) from one fosmid showed that the PKS consists of two modules. Open reading frames located up- and downstream of the PKS displayed similarity with membrane synthesis-related proteins such as cardiolipin synthase. Metagenome approaches did not detect KS domains found in sponge isolates. All KS domains from both metagenome approaches formed a single cluster with KS domains originating from metagenomes derived from other sponge species from other geographical regions.

Monitoring microbial community composition by fluorescence in situ hybridization during cultivation of the marine cold-water sponge Geodia barretti

To determine the stability and specificity of microbes associated with the marine cold-water sponge Geodia barretti during cultivation, we compared the microbial community of freshly retrieved specimens to that of cultivated explants by fluorescence in situ hybridization (FISH). G. barretti hosts a specific homogeneous microbial community in its mesohyl, which is maintained during a cultivation period of 8 months. In 10-day-old explants, bright colonies of unusually large bacterial cells, located predominantly at canal walls, were observed in addition to the common bacteria. Bacteria of the aberrant type included both lineages present in whole sponges and foreign ones, notably numerous genera of sulfate-reducing bacteria. We assume that these represent infectious bacteria that eluded the innate immune system of the sponge. Explants that resist these microbial attacks during the critical phase of cultivation eliminate infectious bacteria. The intrinsic microbial community of G. barretti is not affected by these infections and remains persistent over a cultivation period of at least several months.

Archaeal pre-mRNA splicing: a connection to hetero-oligomeric splicing endonuclease

Eukaryotic Cbf5 is a protein subunit of the small nucleolar RNA-protein complex. Previously, we identified, in archaeal homologs of cbf5 of the crenarchaea, Aeropyrum pernix, Sulfolobus solfataricus, and Sulfolobus tokodaii, the first examples of introns of archaeal protein-coding genes. Here, we report the immunological detection of Cbf5 protein of S. tokodaii, the product of the spliced cbf5 mRNA. The hetero-oligomeric splicing endonuclease activity from recombinant S. tokodaii subunits cleaved at the exon-intron boundaries of cbf5 pre-mRNA fragments,suggesting that synthesis of full-length Cbf5 protein requires this activity. Database searches and PCR screens identified additional cbf5 introns in some, but not all sequenced crenarchaeal genomes. The predicted secondary structures of exon-intron boundaries of many of the newly identified intron-containing cbf5 pre-mRNAs contained relaxed forms of the bulge-helix-bulge motif similar to that of S. tokodaii. These observations are consistent with previous reports indicating that subunit composition of the splicing endonuclease contributes to substrate specificity.

Comparison of prokaryotic diversity at offshore oceanic locations reveals a different microbiota in the Mediterranean Sea

The bacterial and archaeal assemblages at two offshore sites located in polar (Greenland Sea; depth: 50 and 2000 m) and Mediterranean (Ionian Sea; depth 50 and 3000 m) waters were studied by PCR amplification and sequencing of the last 450-500 bp of the 16S rRNA gene. A total of 1621 sequences, together with alignable 16S rRNA gene fragments from the Sargasso Sea metagenome database, were analysed to ascertain variations associated with geographical location and depth. The Ionian 50 m sample appeared to be the most diverse and also had remarkable differences in terms of the prokaryotic groups retrieved; surprisingly, however, many similarities were found at the level of large-scale diversity between the Sargasso database fragments and the Greenland 50 m sample. Most sequences with more than 97% sequence similarity, a value often taken as indicative of species delimitation, were only found at a single location/depth; nevertheless, a few examples of cosmopolitan sequences were found in all samples. Depth was also an important factor and, although both deep-water samples had overall similarities, there were important differences that could be due to the warmer waters at depth of the Mediterranean Sea.

Ammonia-oxidising Crenarchaeota: important players in the nitrogen cycle?

Cultivation-independent molecular surveys show that members of the kingdom Crenarchaeota within the domain Archaea represent a substantial component of microbial communities in aquatic and terrestrial environments. Recently, metagenomic studies have revealed that such Crenarchaeota contain and express genes related to those of bacterial ammonia monooxygenases. Furthermore, a marine chemolithoautotrophic strain was isolated that uses ammonia as a sole energy source. Considering the ubiquity and abundance of Crenarchaeota, these findings considerably challenge the accepted view of the microbial communities involved in global nitrogen cycling. However, the quantitative contribution of Archaea to nitrification in marine and terrestrial environments still remains to be elucidated.

Diversity and biotechnological potential of the sponge-associated microbial consortia

Sponges are well known to harbor diverse microbes and represent a significant source of bioactive natural compounds derived from the marine environment. Recent studies of the microbial communities of marine sponges have uncovered previously undescribed species and an array of new chemical compounds. In contrast to natural compounds, studies on enzymes with biotechnological potential from microbes associated with sponges are rare although enzymes with novel activities that have potential medical and biotechnological applications have been identified from sponges and microbes associated with sponges. Both bacteria and fungi have been isolated from a wide range of marine sponge, but the diversity and symbiotic relationship of bacteria has been studied to a greater extent than that of fungi isolated from sponges. Molecular methods (e.g., rDNA, DGGE, and FISH) have revealed a great diversity of the unculturable bacteria and archaea. Metagenomic approaches have identified interesting metabolic pathways responsible for the production of natural compounds and may provide a new avenue to explore the microbial diversity and biotechnological potential of marine sponges. In addition, other eukaryotic organisms such as diatoms and unicellular algae from marine sponges are also being described using these molecular techniques. Many natural compounds derived from sponges are suspected to be of bacterial origin, but only a few studies have provided convincing evidence for symbiotic producers in sponges. Microbes in sponges exist in different associations with sponges including the true symbiosis. Fungi derived from marine sponges represent the single most prolific source of diverse bioactive marine fungal compounds found to date. There is a developing interest in determining the true diversity of fungi present in marine sponges and the nature of the association. Molecular methods will allow scientists to more accurately identify fungal species and determine actual diversity of sponge-associated fungi. This is especially important as greater cooperation between bacteriologists, mycologists, natural product chemists, and bioengineers is needed to provide a well-coordinated effort in studying the diversity, ecology, physiology, and association between bacteria, fungi, and other organisms present in marine sponges.

Cold-adapted archaea

Many archaea are extremophiles. They thrive at high temperatures, at high pressure and in concentrated acidic environments. Nevertheless, the largest proportion and greatest diversity of archaea exist in cold environments. Most of the Earth's biosphere is cold, and archaea represent a significant fraction of the biomass. Although psychrophilic archaea have long been the neglected majority, the study of these microorganisms is beginning to come of age. This review casts a spotlight on the ecology, adaptation biology and unique science that is being realized from studies on cold-adapted archaea.

Pathways of carbon assimilation and ammonia oxidation suggested by environmental genomic analyses of marine Crenarchaeota

Marine Crenarchaeota represent an abundant component of oceanic microbiota with potential to significantly influence biogeochemical cycling in marine ecosystems. Prior studies using specific archaeal lipid biomarkers and isotopic analyses indicated that planktonic Crenarchaeota have the capacity for autotrophic growth, and more recent cultivation studies support an ammonia-based chemolithoautotrophic energy metabolism. We report here analysis of fosmid sequences derived from the uncultivated marine crenarchaeote, Cenarchaeum symbiosum, focused on the reconstruction of carbon and energy metabolism. Genes predicted to encode multiple components of a modified 3-hydroxypropionate cycle of autotrophic carbon assimilation were identified, consistent with utilization of carbon dioxide as a carbon source. Additionally, genes predicted to encode a near complete oxidative tricarboxylic acid cycle were also identified, consistent with the consumption of organic carbon and in the production of intermediates for amino acid and cofactor biosynthesis. Therefore, C. symbiosum has the potential to function either as a strict autotroph, or as a mixotroph utilizing both carbon dioxide and organic material as carbon sources. From the standpoint of energy metabolism, genes predicted to encode ammonia monooxygenase subunits, ammonia permease, urease, and urea transporters were identified, consistent with the use of reduced nitrogen compounds as energy sources fueling autotrophic metabolism. Homologues of these genes, recovered from ocean waters worldwide, demonstrate the conservation and ubiquity of crenarchaeal pathways for carbon assimilation and ammonia oxidation. These findings further substantiate the likely global metabolic importance of Crenarchaeota with respect to key steps in the biogeochemical transformation of carbon and nitrogen in marine ecosystems.

Sequence data reveal the presence of key genes from pathways for carbon assimilation and ammonia oxidation in marine microbiota, supporting their importance in regulating the biogeochemistry of marine ecosystems.

Paths of lateral gene transfer of lysyl-aminoacyl-tRNA synthetases with a unique evolutionary transition stage of prokaryotes coding for class I and II varieties by the same organisms

Background

While the premise that lateral gene transfer (LGT) is a dominant evolutionary force is still in considerable dispute, the case for widespread LGT in the family of aminoacyl-tRNA synthetases (aaRS) is no longer contentious. aaRSs are ancient enzymes, guarding the fidelity of the genetic code. They are clustered in two structurally unrelated classes. Only lysine aminoacyl-tRNA synthetase (LysRS) is found both as a class 1 and a class 2 enzyme (LysRS1-2). Remarkably, in several extant prokaryotes both classes of the enzyme coexist, a unique phenomenon that has yet to receive its due attention.

Results

We applied a phylogenetic approach for determining the extent and origin of LGT in prokaryotic LysRS. Reconstructing species trees for Archaea and Bacteria, and inferring that their last common ancestors encoded LysRS1 and LysRS2, respectively, we studied the gains and losses of both classes. A complex pattern of LGT events emerged. In specific groups of organisms LysRS1 was replaced by LysRS2 (and vice versa). In one occasion, within the alpha proteobacteria, a LysRS2 to LysRS1 LGT was followed by reversal to LysRS2. After establishing the most likely LGT paths, we studied the possible origins of the laterally transferred genes. To this end, we reconstructed LysRS gene trees and evaluated the likely origins of the laterally transferred genes. While the sources of LysRS1 LGTs were readily identified, those for LysRS2 remain, for now, uncertain. The replacement of one LysRS by another apparently transits through a stage simultaneously coding for both synthetases, probably conferring a selective advantage to the affected organisms.

Conclusion

The family of LysRSs features complex LGT events. The currently available data were sufficient for identifying unambiguously the origins of LysRS1 but not of LysRS2 gene transfers. A selective advantage is suggested to organisms encoding simultaneously LysRS1-2.

Archaeal habitats — from the extreme to the ordinary

The domain Archaea represents a third line of evolutionary descent, separate from Bacteria and Eucarya. Initial studies seemed to limit archaea to various extreme environments. These included habitats at the extreme limits that allow life on earth, in terms of temperature, pH, salinity, and anaerobiosis, which were the homes to hyper thermo philes, extreme (thermo)acidophiles, extreme halophiles, and methanogens. Typical environments from which pure cultures of archaeal species have been isolated include hot springs, hydrothermal vents, solfataras, salt lakes, soda lakes, sewage digesters, and the rumen. Within the past two decades, the use of molecular techniques, including PCR-based amplification of 16S rRNA genes, has allowed a culture-independent assessment of microbial diversity. Remarkably, such techniques have indicated a wide distribution of mostly uncultured archaea in normal habitats, such as ocean waters, lake waters, and soil. This review discusses organisms from the domain Archaea in the context of the environments where they have been isolated or detected. For organizational purposes, the domain has been separated into the traditional groups of methanogens, extreme halophiles, thermoacidophiles, and hyperthermophiles, as well as the uncultured archaea detected by molecular means. Where possible, we have correlated known energy-yielding reactions and carbon sources of the archaeal types with available data on potential carbon sources and electron donors and acceptors present in the environments. From the broad distribution, metabolic diversity, and sheer numbers of archaea in environments from the extreme to the ordinary, the roles that the Archaea play in the ecosystems have been grossly underestimated and are worthy of much greater scrutiny.Key words: Archaea, methanogen, extreme halophile, hyperthermophile, thermoacidophile, uncultured archaea, habitats.

Archaeal chromatin proteins: different structures but common function?

Chromatin proteins promote chromosome flexibility in vivo, maintaining a compact yet decondensed template that permits polymerase accessibility. All Archaea have at least two types of chromatin proteins, and diversity in the chromatin protein population appears to prevent polymerization of a single type of protein. Of the numerous chromatin proteins that have been described in Archaea, only two--histones and Alba homologs--are present in all archaeal phyla. Although their structures and complexes with DNA have no similarities, their functions probably overlap as mutants that lack single chromatin proteins are viable.

Isolation of an autotrophic ammonia-oxidizing marine archaeon

For years, microbiologists characterized the Archaea as obligate extremophiles that thrive in environments too harsh for other organisms. The limited physiological diversity among cultivated Archaea suggested that these organisms were metabolically constrained to a few environmental niches. For instance, all Crenarchaeota that are currently cultivated are sulphur-metabolizing thermophiles. However, landmark studies using cultivation-independent methods uncovered vast numbers of Crenarchaeota in cold oxic ocean waters. Subsequent molecular surveys demonstrated the ubiquity of these low-temperature Crenarchaeota in aquatic and terrestrial environments. The numerical dominance of marine Crenarchaeota--estimated at 10(28) cells in the world's oceans--suggests that they have a major role in global biogeochemical cycles. Indeed, isotopic analyses of marine crenarchaeal lipids suggest that these planktonic Archaea fix inorganic carbon. Here we report the isolation of a marine crenarchaeote that grows chemolithoautotrophically by aerobically oxidizing ammonia to nitrite--the first observation of nitrification in the Archaea. The autotrophic metabolism of this isolate, and its close phylogenetic relationship to environmental marine crenarchaeal sequences, suggests that nitrifying marine Crenarchaeota may be important to global carbon and nitrogen cycles.

INTRACELLULAR COMPARTMENTATION IN PLANCTOMYCETES

The phylum Planctomycetes of the domain Bacteria consists of budding, peptidoglycan-less organisms important for understanding the origins of complex cell organization. Their significance for cell biology lies in their possession of intracellular membrane compartmentation. All planctomycetes share a unique cell plan, in which the cell cytoplasm is divided into compartments by one or more membranes, including a major cell compartment containing the nucleoid. Of special significance is Gemmata obscuriglobus, in which the nucleoid is enveloped in two membranes to form a nuclear body that is analogous to the structure of a eukaryotic nucleus. Planctomycete compartmentation may have functional physiological roles, as in the case of anaerobic ammonium-oxidizing anammox planctomycetes, in which the anammoxosome harbors specialized enzymes and is wrapped in an envelope possessing unique ladderane lipids. Organisms in phyla other than the phylum Planctomycetes may possess compartmentation similar to that of some planctomycetes, as in the case of members of the phylum Poribacteria from marine sponges.

Incidence of novel and potentially archaeal nitrogenase genes in the deep Northeast Pacific Ocean

Archaea have been detected throughout the oceanic water column and are quantitatively important members of picoplankton in the deep ocean. Two common groups, group I Crenarchaeota and group II Euryarchaeota, are consistently detected in warm hydrothermal fluid and are assumed to have been drawn into the subseafloor, mixed with hydrothermal fluid and then expelled. However, because they remain resistant to cultivation, very little is known about their physiology. Here we show that cold deep-seawater from the axial valley of Endeavour Segment on the Juan de Fuca Ridge contains not only groups I and II archaea as expected, but also unique potentially archaeal nitrogenase (nifH) genes, which are required for nitrogen fixation. These nifH genes are phylogenetically distinct and have dissimilar G+C content compared with those of hydrothermal vent archaea, suggesting that they belong to non-thermophilic deep-sea archaea. Furthermore, this sample did not contain mcrA genes, which are present in methanogens, the only known archaeal nitrogen fixers. These nifH genes were not detected in upper water column samples, or in a deep-seawater sample 100 km away from the spreading axis of the Juan de Fuca Ridge. We propose that these unique nifH genes may be localized to archaea that circulate through the nitrogen-poor subseafloor at the mid-ocean ridge as part of their life cycle.

Recovery of partial 16S rDNA sequences suggests the presence of Crenarchaeota in the human digestive ecosystem

Human feces collected from 10 healthy teenagers was analyzed for the presence of Crenarchaeota. After a first polymerase chain reaction (PCR) with Archaea-specific primers, a nested real-time PCR was performed using Crenarchaeota-specific primers. Real-time Crenarchaeotal PCR products detected from four subjects were cloned and the sequencing revealed that most of the partial 16S rRNA gene sequences were highly similar (> or = 97% homology) to sequences affiliated to the Sulfolobus group of the Crenarchaeota phylum. Our findings suggest for the first time that Crenarchaeota might be present in the microbiota of the human digestive ecosystem in which this phylum has never been found yet.

Histones in crenarchaea

Archaeal histone-encoding genes have been identified in marine Crenarchaea. The protein encoded by a representative of these genes, synthesized in vitro and expressed in Escherichia coli, binds DNA and forms complexes with properties typical of an archaeal histone. The discovery of histones in Crenarchaea supports the argument that histones evolved before the divergence of Archaea and Eukarya.

Culturable bacterial symbionts isolated from two distinct sponge species (Pseudoceratina clavata and Rhabdastrella globostellata) from the Great Barrier Reef display similar phylogenetic diversity

The diversity of the culturable microbial communities was examined in two sponge species-Pseudoceratina clavata and Rhabdastrella globostellata. Isolates were characterized by 16S rRNA gene sequencing and phylogenetic analysis. The bacterial community structures represented in both sponges were found to be similar at the phylum level by the same four phyla in this study and also at a finer scale at the species level in both Firmicutes and Alphaproteobacteria. The majority of the Alphaproteobacteria isolates were most closely related to isolates from other sponge species including alpha proteobacterium NW001 sp. and alpha proteobacterium MBIC3368. Members of the low %G + C gram-positive (phylum Firmicutes), high %G + C gram-positive (phylum Actinobacteria), and Cytophaga-Flavobacterium-Bacteroides (phylum Bacteroidetes) phyla of domain Bacteria were also represented in both sponges. In terms of culturable organisms, taxonomic diversity of the microbial community in the two sponge species displays similar structure at phylum level. Within phyla, isolates often belonged to the same genus-level monophyletic group. Community structure and taxonomic composition in the two sponge species P. clavata and Rha. globostellata share significant features with those of other sponge species including those from widely separated geographical and climatic regions of the sea.

Cultivation of mesophilic soil crenarchaeotes in enrichment cultures from plant roots

Because archaea are generally associated with extreme environments, detection of nonthermophilic members belonging to the archaeal division Crenarchaeota over the last decade was unexpected; they are surprisingly ubiquitous and abundant in nonextreme marine and terrestrial habitats. Metabolic characterization of these nonthermophilic crenarchaeotes has been impeded by their intractability toward isolation and growth in culture. From studies employing a combination of cultivation and molecular phylogenetic techniques (PCR-single-strand conformation polymorphism, sequence analysis of 16S rRNA genes, fluorescence in situ hybridization, and real-time PCR), we present evidence here that one of the two dominant phylotypes of Crenarchaeota that colonizes the roots of tomato plants grown in soil from a Wisconsin field is selectively enriched in mixed cultures amended with root extract. Clones recovered from enrichment cultures were found to group phylogenetically with sequences from clade C1b.A1. This work corroborates and extends our recent findings, indicating that the diversity of the crenarchaeal soil assemblage is influenced by the rhizosphere and that mesophilic soil crenarchaeotes are found associated with plant roots, and provides the first evidence for growth of nonthermophilic crenarchaeotes in culture.

Microbial diversity of the freshwater sponge Spongilla lacustris

To provide insight into the phylogenetic bacterial diversity of the freshwater sponge Spongilla lacustris, a 16S rRNA gene libraries were constructed from sponge tissues and from lake water. Restriction fragment length polymorphism (RFLP) analysis of >190 freshwater sponge-derived clones resulted in six major restriction patterns, from which 45 clones were chosen for sequencing. The resulting sequences were affiliated with the Alpha proteobacteria (n=19), the Actinobacteria (n=15), the Beta proteobacteria (n=2), and the Chloroflexi (n=2) lineages. About half of the sequences belonged to previously described actinobacterial (hgc-I) and beta proteobacterial (beta-II) sequence clusters of freshwater bacteria that were also present in the lake water 16S rRNA gene library. At least two novel, deeply rooting alpha proteobacterial lineages were recovered from S. lacustris that showed <89% sequence similarity to known phylogenetic groups. Electron microscopical observations revealed that digested bacterial remnants were contained within food vacuoles of sponge archaeocytes, whereas the extracellular matrix was virtually free of bacteria. This study is the first molecular diversity study of a freshwater sponge and adds to a growing database on the diversity and community composition of sponge-associated microbial consortia.

Microbial community genomics in the ocean

Marine microbial communities were among the first microbial communities to be studied using cultivation-independent genomic approaches. Ocean-going genomic studies are now providing a more comprehensive description of the organisms and processes that shape microbial community structure, function and dynamics in the sea. Through the lens of microbial community genomics, a more comprehensive view of uncultivated microbial species, gene and biochemical pathway distributions, and naturally occurring genomic variability is being brought into sharper focus. Besides providing new perspectives on oceanic microbial communities, these new studies are now poised to reveal the fundamental principles that drive microbial ecological and evolutionary processes.

Genomic studies of uncultivated archaea

Archaea represent a considerable fraction of the prokaryotic world in marine and terrestrial ecosystems, indicating that organisms from this domain might have a large impact on global energy cycles. However, many novel archaeal lineages that have been detected by molecular phylogenetic approaches have remained elusive because no laboratory-cultivated strains are available. Environmental genomic analyses have recently provided clues about the potential metabolic strategies of several of the uncultivated and abundant archaeal species, including non-thermophilic terrestrial and marine crenarchaeota and methanotrophic euryarchaeota. These initial studies of natural archaeal populations also revealed an unexpected degree of genomic variation that indicates considerable heterogeneity among archaeal strains. Here, we review genomic studies of uncultivated archaea within a framework of the phylogenetic diversity and ecological distribution of this domain.

Metagenomics: genomic analysis of microbial communities

Uncultured microorganisms comprise the majority of the planet's biological diversity. Microorganisms represent two of the three domains of life and contain vast diversity that is the product of an estimated 3.8 billion years of evolution. In many environments, as many as 99% of the microorganisms cannot be cultured by standard techniques, and the uncultured fraction includes diverse organisms that are only distantly related to the cultured ones. Therefore, culture-independent methods are essential to understand the genetic diversity, population structure, and ecological roles of the majority of microorganisms. Metagenomics, or the culture-independent genomic analysis of an assemblage of microorganisms, has potential to answer fundamental questions in microbial ecology. This review describes progress toward understanding the biology of uncultured Bacteria, Archaea, and viruses through metagenomic analyses.

Diversity of thermophilic and non-thermophilic crenarchaeota at 80 °C

A hot spring in the solfataric field of Pisciarelli (Naples-Italy) was analysed for Archaeal diversity. Total DNA was extracted from the environment, archaeal 16S rRNA genes were amplified with Archaea specific primers, and a clone library consisting of 201 clones was established. The clones were grouped in 10 different groups each representing a specific band pattern using restriction fragment length polymorphism (RFLP). Members of all 10 groups were sequenced and phylogenetically analyzed. Surprisingly, a high abundance of clones belonging to non-thermophilic Crenarchaeal clusters were detected together with the thermophilic archaeon Acidianus infernus in this thermophilic environment. Neither Sulfolobus species nor other hyperthermophilic Crenarchaeota were detected in the clone library. The relative abundance of the sequenced clones was confirmed by terminal restriction fragment analyses. Amplification of 16S rRNA genes from Archaea transferred from the surrounding environment was considered negligible because DNA from non-thermophilic Crenarchaeota incubated under conditions similar to the solfatara could not be PCR amplified after 5 min.

Metagenomics: application of genomics to uncultured microorganisms

Metagenomics (also referred to as environmental and community genomics) is the genomic analysis of microorganisms by direct extraction and cloning of DNA from an assemblage of microorganisms. The development of metagenomics stemmed from the ineluctable evidence that as-yet-uncultured microorganisms represent the vast majority of organisms in most environments on earth. This evidence was derived from analyses of 16S rRNA gene sequences amplified directly from the environment, an approach that avoided the bias imposed by culturing and led to the discovery of vast new lineages of microbial life. Although the portrait of the microbial world was revolutionized by analysis of 16S rRNA genes, such studies yielded only a phylogenetic description of community membership, providing little insight into the genetics, physiology, and biochemistry of the members. Metagenomics provides a second tier of technical innovation that facilitates study of the physiology and ecology of environmental microorganisms. Novel genes and gene products discovered through metagenomics include the first bacteriorhodopsin of bacterial origin; novel small molecules with antimicrobial activity; and new members of families of known proteins, such as an Na(+)(Li(+))/H(+) antiporter, RecA, DNA polymerase, and antibiotic resistance determinants. Reassembly of multiple genomes has provided insight into energy and nutrient cycling within the community, genome structure, gene function, population genetics and microheterogeneity, and lateral gene transfer among members of an uncultured community. The application of metagenomic sequence information will facilitate the design of better culturing strategies to link genomic analysis with pure culture studies.

Rapid screening and dereplication of bacterial isolates from marine sponges of the sula ridge by intact-cell-MALDI-TOF mass spectrometry (ICM-MS)

Rapid grouping of bacterial isolates is critical in comprehensive microbial studies of environmental samples or screening programmes e.g. in unknown marine environments where large numbers of strains have to be isolated on different growth media. Sets of bacteria have been cultured from the marine sponges Isops phlegraei, Haliclona sp. 1, Phakellia ventilabrum and Plakortis sp. growing at a depth of about 300 m on the Sula Ridge close to the Norwegian coast. We employed Intact-Cell MALDI-TOF (ICM) mass spectrometry to achieve a rapid proteometric clustering of a subset of the strain collection including 456 isolates. Cluster analysis of mass spectra resolved the strains into 11 groups corresponding to species of Alteromonas (15), Bacillus (3), Colwellia (31), Erythrobacter (19), Marinobacter (14), Marinococcus (6), Pseudoalteromonas (297), Pseudomonas (56), Roseobacter (3), Sphingomonas (2) and Vibrio (10) as verified by 16 S rDNA analysis. A further discrimination into subgroups was demonstrated for different isolates from the genus Pseudoalteromonas. The approach described here permits the rapid identification of isolates for dereplication, and the selection of strains representing rare species for subsequent characterization.

Water table related variations in the abundance of intact archaeal membrane lipids in a Swedish peat bog

The presence and distribution of isoprenoid glycerol dialkyl glycerol tetraethers (GDGTs), lipids that constitute the membranes of Archaea, have been investigated in a 50-cm long core from a Swedish peat bog. In the acrotelm, the periodically water saturated and thus oxic upper layer of the peat bog, only minor amounts of GDGTs were found. These amounts increase considerably in the catotelm, the continuously water saturated and consequently anoxic lower layer of the peat bog. Based on earlier analyses of GDGTs in different settings and on 16S rDNA results from literature, these lipids are likely derived from methanogenic Archaea. Crenarchaeol, previously only found in marine settings and in fresh water lakes, has also been found in this peat bog. Contrary to the other GDGTs, crenarchaeol concentrations remain relatively constant throughout the peat core, suggesting that they are produced by Crenarchaeota thriving in the oxic part of the peat bog and possibly also in the anoxic part.

Archaea in protozoa and metazoa

The presence of Archaea is currently being explored in various environments, including extreme geographic positions and eukaryotic habitats. Methanogens are the dominating archaeal organisms found in most animals, from unicellular protozoa to humans. Many methanogens can contribute to the removal of hydrogen, thereby improving the efficiency of fermentation or the reductive capacity of energy-yielding reactions. They may also be involved in tissue damage in periodontal patients. Recent molecular studies demonstrated the presence of Archaea other than methanogens in some animals-but so far, not in humans. The roles of these microorganisms have not yet been established. In the present review, we present the state of the art regarding the archaeal microflora in animals.

Analysis of a genome fragment of a deep-sea uncultivated Group II euryarchaeote containing 16S rDNA, a spectinomycin-like operon and several energy metabolism genes

We have sequenced and analysed a 39.5 kbp genome fragment of a marine Group II euryarchaeote identified in a metagenomic library of 500 m deep plankton at the Antarctic Polar Front. The clone contains a 16S rRNA gene that is separated from the 23S rRNA gene in the genome. This appears to be a trait shared by Thermoplasmatales and Group II euryarchaeota. This genome fragment exhibits a compact organization, including a few overlapping genes in the canonical spectinomycin-like (spc) operon for ribosomal proteins that is immediately upstream the 16S rDNA. Most open reading frames (ORFs) encoded proteins involved in housekeeping processes and, as expected, exhibited a phylogenetic distribution congruent with that of the 16S rRNA. A considerable number of proteins with predicted transmembrane helices was identified. Among those, two proteins encoded by genes likely forming an operon appear to be part of a membrane terminal electron transport chain. One of these proteins has an unusual domain arrangement including ferredoxin, flavodoxin and one succinate dehydrogenase/fumarate reductase subunit. These proteins probably constitute a new succinate dehydrogenase-like oxidoreductase involved in what could be a novel pathway for energy metabolism in Group II euryarchaeota.

Spatial distribution of marine crenarchaeota group I in the vicinity of deep-sea hydrothermal systems

Distribution profiles of marine crenarchaeota group I in the vicinity of deep-sea hydrothermal systems were mapped with culture-independent molecular techniques. Planktonic samples were obtained from the waters surrounding two geographically and geologically distinct hydrothermal systems, and the abundance of marine crenarchaeota group I was examined by 16S ribosomal DNA clone analysis, quantitative PCR, and whole-cell fluorescence in situ hybridization. A much higher proportion of marine crenarchaeota group I within the microbial community was detected in deep-sea hydrothermal environments than in normal deep and surface seawaters. The highest proportion was always obtained from the ambient seawater adjacent to hydrothermal emissions and chimneys but not from the hydrothermal plumes. These profiles were markedly different from the profiles of epsilon-Proteobacteria, which are abundant in the low temperatures of deep-sea hydrothermal environments.

Prokaryote diversity and taxonomy: current status and future challenges

The prokaryotes are by far the most abundant organisms inhabiting planet Earth. They are also by far the most diverse, both metabolically and phylogenetically; they encompass the Bacteria and the Archaea, two out of the three major divisions of living organisms. The current prokaryote species classification is based on a combination of genomic and phenotypic properties. The recommended cut-off value of 70% DNA-DNA similarity to delineate species signifies an extremely broad species definition for the prokaryotes compared with the higher eukaryotes. The number of validly named species of prokaryotes is currently slightly more than 6200. However, on the basis of small-subunit rDNA characterization of whole communities and other approaches, the more exact number of species present can be inferred to be at least two orders of magnitude larger. Classic culturing methods based on colony formation on agar are generally unsatisfactory for the recovery of bacteria from the environment. Many of the most abundant prokaryotes in nature have not yet been brought into culture. Some of these may thrive by means of as yet unknown modes of energy generation. Several novel methods have recently enabled the isolation of some interesting organisms of environmental significance. A better coverage of the prokaryote diversity on Earth depends on such innovative approaches, combined with appropriate funding.

Discovery of the novel candidate phylum "Poribacteria" in marine sponges

Marine sponges (Porifera) harbor large amounts of commensal microbial communities within the sponge mesohyl. We employed 16S rRNA gene library construction using specific PCR primers to provide insights into the phylogenetic identity of an abundant sponge-associated bacterium that is morphologically characterized by the presence of a membrane-bound nucleoid. In this study, we report the presence of a previously unrecognized evolutionary lineage branching deeply in the domain Bacteria that is moderately related to the Planctomycetes, Verrucomicrobia, and Chlamydia lines of decent. Because members of this lineage showed <75% 16S rRNA gene sequence similarity to known bacterial phyla, we suggest the status of a new candidate phylum, named "Poribacteria", to acknowledge the affiliation of the new bacterium with sponges. The affiliation of the morphologically conspicuous sponge bacterium with the novel phylogenetic lineage was confirmed by fluorescence in situ hybridization with newly designed probes targeting different sites of the poribacterial 16S rRNA. Consistent with electron microscopic observations of cell compartmentalization, the fluorescence signals appeared in a ring-shaped manner. PCR screening with "Poribacteria"-specific primers gave positive results for several other sponge species, while samples taken from the environment (seawater, sediments, and a filter-feeding tunicate) were PCR negative. In addition to a report for Planctomycetes, this is the second report of cell compartmentalization, a feature that was considered exclusive to the eukaryotic domain, in prokaryotes.

Proteomic signatures: amino acid and oligopeptide compositions differentiate among phyla

Availability of complete genome sequences allows in-depth comparison of single-residue and oligopeptide compositions of the corresponding proteomes. We have used principal component analysis (PCA) to study the landscape of compositional motifs across more than 70 genera from all three superkingdoms. Unexpectedly, the first two principal components clearly differentiate archaea, eubacteria, and eukaryota from each other. In particular, we contrast compositional patterns typical of the three superkingdoms and characterize differences between species and phyla, as well as among patterns shared by all compositional proteomic signatures. These species-specific patterns may even extend to subsets of the entire proteome, such as proteins pertaining to individual yeast chromosomes. We identify factors that affect compositional signatures, such as living habitat, and detect strong eukaryotic preference for homopeptides and palindromic tripeptides. We further detect oligopeptides that are either universally over- or underabundant across the whole proteomic landscape, as well as oligopeptides whose over- or underabundance is phylum- or species-specific. Finally, we report that species composition signatures preserve evolutionary memory, providing a new method to compare phylogenetic relationships among species that avoids problems of sequence alignment and ortholog detection.

Diverse microbial communities inhabit Antarctic sponges

Genetic techniques were employed to investigate the archaeal, bacterial and eukaryotic communities associated with the Antarctic sponges Kirkpatrickia varialosa, Latrunculia apicalis, Homaxinella balfourensis, Mycale acerata and Sphaerotylus antarcticus. The phylogenetic affiliation of sponge-derived bacteria was assessed by 16S rRNA sequencing of cloned DNA fragments. Denaturing gradient gel electrophoresis (DGGE) was used to determine the stability of bacterial associations within each sponge species and across spatial scales. Of the 150 archaeal clones from L. apicalis, K. varialosa and M. acerata screened by restriction fragment length polymorphism (RFLP) analysis, four unique operational taxonomic units (OTUs) were observed and all clustered closely together within the Crenarchaeota. Of the 250 sponge-derived bacterial clones screened by RFLP analysis, 61 were unique OTUs that were not detected during examination of 160 seawater-derived clones. Rarefaction analysis indicated that the clone libraries represented between 44 and 83% of the total estimated diversity. Phylogenetic analysis of sequence data revealed that the bacterial communities present in Antarctic sponges primarily clustered within the Gamma and Alpha proteobacteria and the Cytophaga/Flavobacterium of Bacteroidetes group. Bacterial DGGE analysis for replicate sponge and seawater samples at each Antarctic site revealed that bacterial communities were consistently detected within a particular species regardless of the collection site, with six bacterial bands exclusively associated with a single sponge species. Phylogenetic analysis of sequence data from eukaryotic DGGE analysis revealed that the communities present in Antarctic sponges fell into diatom and dinoflagellate clusters with many sequences having no known close relatives. In addition, seven eukaryotic sequences that were not detected in seawater samples or other sponge species were observed in K. varialosa.

Translocation of proteins across archaeal cytoplasmic membranes

All cells need to transport proteins across hydrophobic membranes. Several mechanisms have evolved to facilitate this transport, including: (i) the universally-conserved Sec system, which transports proteins in an unfolded conformation and is thought to be the major translocation pathway in most organisms and (ii) the Tat system, which transports proteins that have already obtained some degree of tertiary structure. Here, we present the current understanding of these processes in the domain Archaea, and how they compare to the corresponding pathways in bacteria and eukaryotes.

Scaling up: the next challenge in environmental microbiology

Great strides have recently been made in identifying and characterizing the staggering diversity of microorganisms conducting primary and secondary production, nutrient transformation and mineralization processes that underlie ecosystem and regional biogeochemical, trophodynamic and ecological change. We are now faced with the challenge of assigning and coupling function to structure in highly complex and interactive microbial communities mediating such change. Previous and ongoing ecophysiological work has shown that microbial processes controlled by environmental variables and limiting resources are highly specific in terms of what, when, where and why they are active, not to mention how they impact ecosystem dynamics. As such, it is imperative that we assess the activities and roles of key microbial 'players' along the appropriate environmental scales and gradients catalysing ecological change. Here, we discuss conceptual and technical challenges for some key microbially mediated environmental processes, problems and extremes that require synthesizing our growing knowledge of microbial community structure with emerging knowledge of function in aquatic ecosystems. We emphasize the importance of assessing ecological change over a range of relevant time scales that vary from minutes to millennia and spatial scales that range from microscale aggregates to ocean basins.

Biotechnological uses of archaeal extremozymes

Archaea have developed a variety of molecular strategies to survive the often harsh environments in which they exist. Although the rules that allow archaeal enzymes to fulfill their catalytic functions under extremes of salinity, temperature or pressure are not completely understood, the stability of these extremophilic enzymes, or extremozymes, in the face of adverse conditions has led to their use in a variety of biotechnological applications in which such tolerances are advantageous. In the following, examples of commercially important archaeal extremozymes are presented, potentially useful archaeal extremozyme sources are identified and solutions to obstacles currently hindering wider use of archaeal extremozymes are discussed.

Exocellular cyclic dipeptides from a Ruegeria strain associated with cell cultures of Suberites domuncula

From cell cultures of Suberites domuncula was isolated a bacterial strain, SDC-1, which was identified by 16S ribosomal RNA sequence analysis as an alpha-Proteobacterium of the genus Ruegeria. The occurrence of the strain in sponge cell culture could be explained by its resistance to the antibiotics used in the isolation of sponge cell cultures or by the preservation of SDC-1 by host sponge cells. The fatty acid composition of SDC-1 is characterized by branched C-12 methyl fatty acids. Two new and 8 known cyclic dipeptides were isolated and characterized from the fermentation broth of SDC-1. Cyclodipeptides are one of the families of cell-cell signaling compounds and may have some role to play in sponge-bacteria interactions.

Comparative analysis of a genome fragment of an uncultivated mesopelagic crenarchaeote reveals multiple horizontal gene transfers

Marine planktonic crenarchaeota have escaped all cultivation attempts to date, all crenarchaeota growing in pure culture so far being hyperthermophiles. Here, we present a comparative genomic analysis of a 16S- plus 23S-rDNA-containing fragment of a crenarchaeote retrieved from an environmental genomic library constructed from picoplankton collected at 500 m depth in the Antarctic Polar Front. The clone DeepAnt-EC39 contained an insert of 33.3 kbp, which was completely sequenced. DeepAnt-EC39 appears to represent a lineage specific to deep-sea waters but widespread geographically, as revealed by the analysis of the 16S-23S-rDNA intergenic spacer region. A comparison with previously sequenced marine crenarchaeotal genomic clones also containing an rrn operon (74A4, 4B7 and Cenarchaeum symbiosum strains A and B) revealed a highly variable structure involving gene rearrangements and insertions/deletions. The surroundings of the rrn operon and the contiguous glutamate-1-semialdehyde aminotransferase gene appear hot spots for recombination. Phylogenetic analyses of all individual predicted proteins revealed the existence of several likely cases of horizontal gene transfer both, between the two archaeal kingdoms and between the two prokaryotic domains. The most frequent horizontal transfers appear to involve genes from mesophilic methanogenic euryarchaeota related to Methanosarcinales. We hypothesise that the acquisition of genes from mesophilic bacteria and euryarchaeota has played a major role in the adaptation of Group I crenarchaeota to life at lower temperatures.

Pathogenic archaea: do they exist?

Archaea are microorganisms that are distinct from bacteria and eukaryotes. They are prevalent in extreme environments, and yet found in most ecosystems. They are a natural component of the microbiota of most, if not all, humans and other animals. Despite their ubiquity and close association with humans, animals and plants, no pathogenic archaea have been identified. Because no archaeal pathogens have yet been identified, there is a general assumption that archaeal pathogens do not exist. This review examines whether this is a good assumption by investigating the potential for archaea to be or become pathogens. This is achieved by addressing: the diversity of archaea versus known pathogens, opportunities for archaea to demonstrate pathogenicity and be detected as pathogens, reports linking archaea with disease, and immune responses to archaea. In addition, molecular and genomic data are examined for the presence of systems utilised in pathogenesis. The view of this report is that, although archaea can presently be described as non-pathogenic, they have the potential to be (discovered as) pathogens. The present optimistic view that there are no archaeal pathogens is tainted by a severe lack of relevant knowledge, which may have important consequences in the future.