Genetic structure of three fosmid-fragments encoding 16S rRNA genes of the Miscellaneous Crenarchaeotic Group (MCG): implications for physiology and evolution of marine sedimentary archaea

Archaea of the Miscellaneous Crenarchaeotic Group (MCG) exist widely in soil, freshwater and marine sediments of both surface and subsurface. However, current knowledge about this group is limited to its phylogenetic diversity. An archaeal 16S library was constructed from a sediment sample from the South China Sea, which was dominated by MCG and Marine Group I (MG-I). A metagenomic library was constructed from the same sediment sample, and three MCG fosmids (E6-3G, E37-7F and E48-1C) containing 16S rRNA genes were screened. Annotation showed that the three genomic fragments encode a variety of open reading frames (ORFs) that are potentially homologous to important functional genes related to lipid biosynthesis, energy metabolism, and resistance to oxidants. No colinear regions were found between MCG fosmids and reported archaeal genomic fragments or genomes, suggesting that the MCG archaea are quite different from the sequenced archaea in gene arrangement. Analyses of both the phylogenies of 16S rRNA genes and several informational processing genes and nucleotide frequencies showed that MCG archaea are distinct from MG-I plus relatives. In addition, tetranucleotide frequency analysis in combination with phylogenetic analysis suggested that some fragments in the MCG fosmids are probably derived from non-MCG or non-archaeal genomes.     

Insights in the ecology and evolutionary history of the Miscellaneous Crenarchaeotic Group lineage

Members of the archaeal Miscellaneous Crenarchaeotic Group (MCG) are among the most successful microorganisms on the planet. During its evolutionary diversification, this very diverse group has managed to cross the saline–freshwater boundary, one of the most important evolutionary barriers structuring microbial communities. However, the current understanding on the ecological significance of MCG in freshwater habitats is scarce and the evolutionary relationships between freshwater and saline MCG remains poorly known. Here, we carried out molecular phylogenies using publicly available 16S rRNA gene sequences from various geographic locations to investigate the distribution of MCG in freshwater and saline sediments and to evaluate the implications of saline–freshwater transitions during the diversification events. Our approach provided a robust ecological framework in which MCG archaea appeared as a core generalist group in the sediment realm. However, the analysis of the complex intragroup phylogeny of the 21 subgroups currently forming the MCG lineage revealed that distinct evolutionary MCG subgroups have arisen in marine and freshwater sediments suggesting the occurrence of adaptive evolution specific to each habitat. The ancestral state reconstruction analysis indicated that this segregation was mainly due to the occurrence of a few saline–freshwater transition events during the MCG diversification. In addition, a network analysis showed that both saline and freshwater MCG recurrently co-occur with archaea of the class Thermoplasmata in sediment ecosystems, suggesting a potentially relevant trophic connection between the two clades.     

Archaea of the Miscellaneous Crenarchaeotal Group are abundant,diverse and widespread in marine sediments

Members of the highly diverse Miscellaneous Crenarchaeotal Group (MCG) are globally distributed in various marine and continental habitats. In this study, we applied a polyphasic approach (rRNA slot blot hybridization, quantitative PCR (qPCR) and catalyzed reporter deposition FISH) using newly developed probes and primers for the in situ detection and quantification of MCG crenarchaeota in diverse types of marine sediments and microbial mats. In general, abundance of MCG (cocci, 0.4 μm) relative to other archaea was highest (12–100%) in anoxic, low-energy environments characterized by deeper sulfate depletion and lower microbial respiration rates (P=0.06 for slot blot and P=0.05 for qPCR). When studied in high depth resolution in the White Oak River estuary and Hydrate Ridge methane seeps, changes in MCG abundance relative to total archaea and MCG phylogenetic composition did not correlate with changes in sulfate reduction or methane oxidation with depth. In addition, MCG abundance did not vary significantly (P>0.1) between seep sites (with high rates of methanotrophy) and non-seep sites (with low rates of methanotrophy). This suggests that MCG are likely not methanotrophs. MCG crenarchaeota are highly diverse and contain 17 subgroups, with a range of intragroup similarity of 82 to 94%. This high diversity and widespread distribution in subsurface sediments indicates that this group is globally important in sedimentary processes.     

Effects of Group Size on Approach to Novel Objects in Ravens (Corvus corax)

Neophobia may constrain explorative behaviour, learning and innovation, while social context may facilitate approach to novel objects and acceptance of novel food. We examined the effects of neophobia on the exploration of novel objects in relation to social context in ravens (Corvus corax). Ravens are suitable subjects for studying effects of social context, as they are highly neophobic scavengers that recruit conspecifics to food. We tested two groups of six and 11 hand‐raised birds in three conditions: single‐bird, in dyadic combinations and sibling sub‐groups of three to six birds. Contrary to expectation, individuals of both groups were quicker to approach novel objects when tested alone than when tested with conspecifics. However, they spent more time close to and manipulating the novel objects in the social conditions (dyadic and group) than when being alone. We discuss the possibility that the higher latencies of dyads and groups to approach novel objects may reflect a ‘negotiation’ process in a ‘war of attrition’ between the individuals over risk‐taking.     

Genome Sequence of Candidatus Nitrososphaera evergladensis from Group I.1b Enriched from Everglades Soil Reveals Novel Genomic Features of the Ammonia-Oxidizing Archaea

The activity of ammonia-oxidizing archaea (AOA) leads to the loss of nitrogen from soil, pollution of water sources and elevated emissions of greenhouse gas. To date, eight AOA genomes are available in the public databases, seven are from the group I.1a of the Thaumarchaeota and only one is from the group I.1b, isolated from hot springs. Many soils are dominated by AOA from the group I.1b, but the genomes of soil representatives of this group have not been sequenced and functionally characterized. The lack of knowledge of metabolic pathways of soil AOA presents a critical gap in understanding their role in biogeochemical cycles. Here, we describe the first complete genome of soil archaeon Candidatus Nitrososphaera evergladensis, which has been reconstructed from metagenomic sequencing of a highly enriched culture obtained from an agricultural soil. The AOA enrichment was sequenced with the high throughput next generation sequencing platforms from Pacific Biosciences and Ion Torrent. The de novo assembly of sequences resulted in one 2.95 Mb contig. Annotation of the reconstructed genome revealed many similarities of the basic metabolism with the rest of sequenced AOA. Ca. N. evergladensis belongs to the group I.1b and shares only 40% of whole-genome homology with the closest sequenced relative Ca. N. gargensis. Detailed analysis of the genome revealed coding sequences that were completely absent from the group I.1a. These unique sequences code for proteins involved in control of DNA integrity, transporters, two-component systems and versatile CRISPR defense system. Notably, genomes from the group I.1b have more gene duplications compared to the genomes from the group I.1a. We suggest that the presence of these unique genes and gene duplications may be associated with the environmental versatility of this group.     

Influence of Land Use Intensity on the Diversity of Ammonia Oxidizing Bacteria and Archaea in Soils from Grassland Ecosystems

In the present study, the influence of the land use intensity on the diversity of ammonia oxidizing bacteria (AOB) and archaea (AOA) in soils from different grassland ecosystems has been investigated in spring and summer of the season (April and July). Diversity of AOA and AOB was studied by TRFLP fingerprinting of amoA amplicons. The diversity from AOB was low and dominated by a peak that could be assigned to Nitrosospira. The obtained profiles for AOB were very stable and neither influenced by the land use intensity nor by the time point of sampling. In contrast, the obtained patterns for AOA were more complex although one peak that could be assigned to Nitrosopumilus was dominating all profiles independent from the land use intensity and the sampling time point. Overall, the AOA profiles were much more dynamic than those of AOB and responded clearly to the land use intensity. An influence of the sampling time point was again not visible. Whereas AOB profiles were clearly linked to potential nitrification rates in soil, major TRFs from AOA were negatively correlated to DOC and ammonium availability and not related to potential nitrification rates.     

中越茜草科栀子族植物拾零

报道了中国茜草科Rubiaceae栀子族tribe Gardcnieae一新记录属和二新记录种：越南茜属Rubovietnamia Tirveng．、长管越南茜R．aristata Tirveng．和中越大果茜Fosbergia pettelotii Merr．ex Tirveng．＆Sastre;以及越南茜草科栀子族的一新记录种,即大围山紫冠茜Rothmannia daweishanensis Y.M．Shui＆WH．Chen。     

Novel thermoactive glucoamylases from the thermoacidophilic Archaea Thermoplasma acidophilum,Picrophilus torridus and Picrophilus oshimae

The thermoacidophilic Archaea Thermoplasma acidophilum (optimal growth at 60 °C and pH 1–2), Picrophilus torridus and Picrophilus oshimae (optimal growth at 60 °C and pH 0.7) were able to utilize starch as sole carbon source. During growth these microorganisms secreted heat and acid-stable glucoamylases into the culture fluid. Applying SDS gel electrophoresis activity bands were detected with appearent molecular mass (Mw) of 141.0, 95.0 kDa for T. acidophilum, 133.0, 90.0 kDa for P. torridus and 140.0, 85.0 kDa for P. oshimae. The purified enzymes were incubated with various polymeric substrates such as starch, pullulan, panose and isomaltose. The product pattern, analyzed by HPLC, showed that in all cases glucose was formed as the sole product of hydrolysis. The purified glucoamylases were optimally active at pH 2.0 and 90 °C and have an isoelectric points (pI) between 4.5 and 4.8. Enzymatic activity was detected even at pH 1.0 and 100 °C. The glucoamylases were thermostable at elevated temperature with a half-life of 24 h at 90 °C for both P. torridus and T. acidophilum, and 20 h at 90 °C for P. oshimae. The enzyme system of T. acidophilum has a lower K _m value for soluble starch (1.06 mg/ml) than the enzymes from P. oshimae and P. torridus (4.35 mg/ml and 2.5 mg/ml), respectively. Enzyme activity was not affected by Na⁺, Mg⁺⁺, Ca⁺⁺, Ni⁺⁺, Zn⁺⁺, Fe⁺⁺, EDTA and DTT. This revised version was published online in August 2006 with corrections to the Cover Date.     

Archaebacteria (Archaea) and the origin of the eukaryotic nucleus

The eukaryotic nucleus is a unique structure. Because it lacks an obvious homologue or precursor among prokaryotes, ideas about its evolutionary origin are diverse. Current attempts to derive the nuclear membrane focus on invaginations of the plasma membrane in a prokaryote, endosymbiosis of an archaebacterium within a eubacterial host, or the origin of a genuinely new membrane system following the origin of mitochondria in an archaebacterial host. Recent reports point to ways in which different ideas regarding the origin of the nucleus might someday be discriminated.     

A Novel and Enantioselective Approach to the Synthesis of Cyclohexane Carbocyclic Nucleosides Starting from (-)-Carvone

Abstract

3,5-dihydroxy-4-(hydroxymethyl)-1-cyclohexanyl adenine has been synthesized starting from (-)-carvone. The adenine base was introduced via Mitsunobu reaction. Conformational analysis showed that the base still adopts the equatorial position at the expence of three axial substituents.     

Miscellaneous taxonomic notes on Elatostema (Urticaceae) from China and its adjacent area

Based on examination of specimens and field observations of Elatostema J. R. Forster & G. Forster (Urticaceae) from China and its adjacent area, one new species, E. vietnamense Q. Lin & L. D. Duan from Bach Ma Natl. Park, Thua Thien‐Hue Province, Vietnam, is described and illustrated. Pellionia ambigua Wedd. from Khasi Hills, Churra, Assam (=Meghalaya), India and P. rhizomatosa Gagnep. from Annam, Vietnam are transferred as Elatostema ambiguum (Wedd.) Q. Lin and E. rhizomatosum (Gagnep.) Q. Lin, respectively. Elatostema glochidioides W. T. Wang from Guangxi and Guizhou and Provinces, China is regarded as a new synonym of E. ramosissimum Rein.     

Research Needs for Understanding and Predicting the Behavior of Managed Ecosystems: Lessons from the Study of Agroecosystems

Managed ecosystems are complex, dynamic systems with spatially varying inputs and outputs that are the result of interrelated physical, biological, and human decision-making processes. To gain an adequate understanding of these systems and predict their behavior, we believe that it is necessary to move beyond stylized theoretical models and loosely coupled disciplinary simulation models to what we describe as “fully integrated models.” Herein we present a conceptual framework for a more integrated approach to the study of managed ecosystems using the example of agricultural ecosystems. We then propose the implementation of a research agenda that fosters coordinated disciplinary research aimed at a better understanding and quantification of linkages across disciplinary models. Key research issues include the effects of spatial scale, the assessment of uncertainty in coupled models, and methods for collecting and analyzing spatially referenced data. Received 6 October 2000; accepted 10 April 2001.     

Discontinuous Occurrence of the hsp70 (dnaK) Gene among Archaea and Sequence Features of HSP70 Suggest a Novel Outlook on Phylogenies Inferred from This Protein

Occurrence of the hsp70 (dnaK) gene was investigated in various members of the domain Archaea comprising both euryarchaeotes and crenarchaeotes and in the hyperthermophilic bacteria Aquifex pyrophilus and Thermotoga maritima representing the deepest offshoots in phylogenetic trees of bacterial 16S rRNA sequences. The gene was not detected in 8 of 10 archaea examined but was found in A. pyrophilus and T. maritima, from which it was cloned and sequenced. Comparative analyses of the HSP70 amino acid sequences encoded in these genes, and others in the databases, showed that (i) in accordance with the vicinities seen in rRNA-based trees, the proteins from A. pyrophilus and T. maritima form a thermophilic cluster with that from the green nonsulfur bacterium Thermomicrobium roseum and are unrelated to their counterparts from gram-positive bacteria, proteobacteria/mitochondria, chlamydiae/spirochetes, deinococci, and cyanobacteria/chloroplasts; (ii) the T. maritima HSP70 clusters with the homologues from the archaea Methanobacterium thermoautotrophicum and Thermoplasma acidophilum, in contrast to the postulated unique kinship between archaea and gram-positive bacteria; and (iii) there are exceptions to the reported association between an insert in HSP70 and gram negativity, or vice versa, absence of insert and gram positivity. Notably, the HSP70 from T. maritima lacks the insert, although T. maritima is phylogenetically unrelated to the gram-positive bacteria. These results, along with the absence of hsp70 (dnaK) in various archaea and its presence in others, suggest that (i) different taxa retained either one or the other of two hsp70 (dnaK) versions (with or without insert), regardless of phylogenetic position; and (ii) archaea are aboriginally devoid of hsp70 (dnaK), and those that have it must have received it from phylogenetically diverse bacteria via lateral gene transfer events that did not involve replacement of an endogenous hsp70 (dnaK) gene.     

Nitrous Oxide (N2O) Emissions from Subsurface Soils of Agricultural Ecosystems

Ecosystems - Nitrous oxide (N2O) is a major greenhouse gas and cultivated soils are the most important anthropogenic source. N2O production and consumption are known to occur at depths below the A...     

Stability of the 'L12 stalk' in ribosomes from mesophilic and (hyper)thermophilic Archaea and Bacteria

The ribosomal stalk complex, consisting of one molecule of L10 and four or six molecules of L12, is attached to 23S rRNA via protein L10. This complex forms the so-called ‘L12 stalk’ on the 50S ribosomal subunit. Ribosomal protein L11 binds to the same region of 23S rRNA and is located at the base of the ‘L12 stalk’. The ‘L12 stalk’ plays a key role in the interaction of the ribosome with translation factors. In this study stalk complexes from mesophilic and (hyper)thermophilic species of the archaeal genus Methanococcus and from the Archaeon Sulfolobus solfataricus, as well as from the Bacteria Escherichia coli, Geobacillus stearothermophilus and Thermus thermophilus, were overproduced in E.coli and purified under non-denaturing conditions. Using filter-binding assays the affinities of the archaeal and bacterial complexes to their specific 23S rRNA target site were analyzed at different pH, ionic strength and temperature. Affinities of both archaeal and bacterial complexes for 23S rRNA vary by more than two orders of magnitude, correlating very well with the growth temperatures of the organisms. A cooperative effect of binding to 23S rRNA of protein L11 and the L10/L12₄ complex from mesophilic and thermophilic Archaea was shown to be temperature-dependent.     

Novel dermaseptins from Phyllomedusa hypochondrialis (Amphibia)

Six new antimicrobial peptides structurally related to the dermaseptin family have been isolated from the skin secretion of the amphibian Phyllomedusa hypochondrialis. The primary structures of these molecules named as DShypo 01, 02, 03, 04, 06, and 07 were determined by de novo MS/MS experiments, Edman degradation, and cDNA sequencing. The fifth peptide was found to be precisely the same DS 01 from Phyllomedusa oreades previously described by our group. The majority of the peptides purified from the crude skin secretion could be directly localized and mapped onto a freshly dissected dorsal skin fragment using mass spectrometry-imaging techniques. Comparisons between peptides and commercial drugs on their antibacterial and anti-Leishmania amazonensis efficiencies, associated with peptide lytic effects on mammalian blood cells and surface plasmon resonance interaction studies on immobilized DMPC vesicles, were also performed.     

On the Classification of Ixeris Group (Compositae) from China

Ixeris Cass., strinctly speaking, is confined to plants which have achenes with sharply winged ribs. Ixeridium (A. Gray ) Tzvel. contains plants which have persistent radical leaves at anthesis and achenes with obtuse ribs and a fine rostrum at its apex. Paraixeris Nakai is restricted to plants which are of the same achenes as in the genus Ixeridium (A. Gray) Tzvel., but rostra of achenes are robust and radical leaves deciduous in flowering in the former. The Chorisis DC., a monotypic genus, is characterized by ternate palatisect leaves. In the light of the above mentioned understanding of these genera, the author thinks that the division of Chinese Ixeris group, a comparatively complex one, into four genera would be more reasonable than merging them into one genus, namely, Ixeris Cass. Based on the examination of specimens in the Herbarium of the Institute of Botany, Academia Sinica (PE), the author found that there are four species in the genus Ixeris Cass., including one new combination in China. They are I. polycephala Cass., I. dissecta (Makino) Shih, I. japonica (Burm. f. ) Nakai and I. stolonifera A. Gray. The genus Ixeridium (A. Gray ) Tzvel. has 13 species, including five new combinations and three new species in China, namely, I. sagittaroides (C. B. Clarke) Shih, I. gramineum (Ledb.) Tzvel., I. yunnarense Shih,I. graminifolium(Ledb.)Tzvel.,I, biparum Shih,I.aculeolatum Shih,I. chinense( Thunb. ) Tzvel., I. strigosum( Fisch. ) Tzvel., I. elegans( Franeh. ) Shih, I. sonchifolium (Maxim.)Shih,I. laevigatum (BI.)Shih,I. dentatum(Thunb. )Nakai and I. gracile(DC.)Shih, in China. There are six species in the genus Paraixeris Nakai, including One new combination, namely, P. denticulata(Houtt.) Nakai, P. humifusa(Dunn) Shih, P. cheldonifolia( Makino) Nakai, P. saxatilis( Baran. ) Tzvel., P.pinnatipartita (Makino)Tzvel. and P.serotina(Maxim.)Tzvel.in China.