Great Boiling Spring is a large, circumneutral, geothermal spring in the US Great Basin. Twelve samples were collected from water and four different sediment sites on four different dates. Microbial community composition and diversity were assessed by PCR amplification of a portion of the small subunit rRNA gene using a universal primer set followed by pyrosequencing of the V8 region. Analysis of 164 178 quality-filtered pyrotags clearly distinguished sediment and water microbial communities. Water communities were extremely uneven and dominated by the bacterium Thermocrinis. Sediment microbial communities grouped according to temperature and sampling location, with a strong, negative, linear relationship between temperature and richness at all taxonomic levels. Two sediment locations, Site A (87-80 1C) and Site B (79 1C), were predominantly composed of single phylotypes of the bacterial lineage GAL35 ( p ¼ 36.1%), Aeropyrum ( p ¼ 16.6%), the archaeal lineage pSL4 ( p ¼ 15.9%), the archaeal lineage NAG1 ( p ¼ 10.6%) and Thermocrinis ( p ¼ 7.6%). The ammonia-oxidizing archaeon 'Candidatus Nitrosocaldus' was relatively abundant in all sediment samples o82 1C ( p ¼ 9.51%), delineating the upper temperature limit for chemolithotrophic ammonia oxidation in this spring. This study underscores the distinctness of water and sediment communities in GBS and the importance of temperature in driving microbial diversity, composition and, ultimately, the functioning of biogeochemical cycles.

Biological soil crusts (BSCs) are bio-sedimentary complexes that play critical ecological roles in arid landscapes; however, the interactions between component biota and sediments are poorly understood. A detailed micromorphological investigation of BSC development and crust microstructure in the Muddy Mountains Wilderness Area, Nevada, examined features in thin section using pétrographie microscopy, light microscopy, scanning electron microscopy, and energy dispersive x-ray spectroscopy. The >1800 microscopic observations were linked to crust macroscale features and soil geomorphology. Complex bio-sedimentary structures of BSCs reflect a dynamic genetic history and diverse formative processes, including: (i) stabilization and authigenic mineral precipitation; (ii) wetting-drying and expansion-contraction; (iii) dust capture; (iv) microscale mass wasting; and (v) vesicular (Av) horizon formation. A new conceptual model for hot deserts illustrates how these processes co-develop with BSC succession, during countless wet-dry cycles, to huild up pinnacle microtopography while simultaneously forming Av horizons in the bio-rich and hio-poor zones. Complex surficial and internal hio-sedimentary structures, which vary as a function of crust morphology, trap surface water for uptake hy crust organisms, while dust influx provides a source of nutrients. These phenomena influence landscape-scale water dynamics and biogeochemical cycling, increasing the availability of soil resources during times of biotic stress. Biological soil crusts uniquely facilitate the accumulation, morphology, and ecosystem function of dust and should, therefore, be considered critical agents in arid pedogenesis and landscape development.Abbreviations: BSC, biological soil crust; EPS, extracellular polymeric secretions; XPL, cross-polarized light.

The Rehai Geothermal Field, located in Tengchong County, in central-western Yunnan Province, is the largest and most intensively studied geothermal field in China. A wide physicochemical diversity of springs (ambient to w97 C; pH from 1.8 to !9.3) provides a multitude of niches for extremophilic microorganisms. A variety of studies have focused on the cultivation, identification, basic physiology, taxonomy, and biotechnological potential of thermophilic microorganisms from Rehai. Thermophilic bacteria isolated from Rehai belong to the phyla Firmicutes and Deinococcus-Thermus. Firmicutes include neutrophilic or alkaliphilic Anoxybacillus, Bacillus, Caldalkalibacillus, Caldanaerobacter, Laceyella, and Geobacillus, as well as thermoacidophilic Alicyclobacillus and Sulfobacillus. Isolates from the Deinococcus-Thermus phylum include several Meiothermus and Thermus species. Many of these bacteria synthesize thermostable polymer-degrading enzymes that may be useful for biotechnology. The thermoacidophilic archaea Acidianus, Metallosphaera, and Sulfolobus have also been isolated and studied. A few studies have reported the isolation of thermophilic viruses belonging to Siphoviridae (TTSP4 and TTSP10) and Fuselloviridae (STSV1) infecting Thermus spp. and Sulfolobus

BACKGROUND The characterization of differentially expressed genes between cancerous and normal tissues is an important step in the understanding of tumorigenesis. Global gene expression profiling with microarrays has now offered a powerful tool to measure the changes of thousands of genes in any carcinoma tissues in an effort to identify these key disease‐related genes. To compare the gene expression of a primary liver carcinoma, metastatic carcinoma to the liver, and normal liver, the authors analyzed tissue from six primary hepatocellular carcinomas (HCCs), five colorectal adenocarcinoma metastases to the liver, and eight normal livers. METHODS Samples were processed from total RNA to fragmented cRNA and hybridized onto Affymetrix GeneChip® expression arrays. Analyses were performed to determine the consensus pattern of gene expression for primary liver carcinoma, metastatic liver carcinoma, and normal liver tissue and their changes in expression level. RESULTS In hepatocellular carcinoma, 842 genes were overexpressed, and 393 genes were underexpressed in comparison with genes of normal liver tissue. Of note, 7 of the 20 most increased identified known genes previously have been associated with liver carcinoma or other types of cancers. The 13 additional identified genes until now have not previously shown strong association with cancers. Furthermore, the authors identified 42 genes and 24 expressed sequence tags that are expressed at a significant level in both HCC and metastastic tumors, presenting a list of marker genes indicative of cancerous liver tissue. CONCLUSIONS In this study, genes that can be involved in the production of and maintenance of hepatic carcinomas were identified. These data offer new insight into genes that are potentially important in the pathogenesis of liver carcinoma, as well as additional targets for new strategies for cancer therapy and treatment. Cancer 2001;92:395–405. © 2001 American Cancer Society.

Summary Glycerol dialkyl glycerol tetraether (GDGT) membrane lipids of Archaea respond to gradients in temperature and pH; however, it is unclear how these lipids respond to gradients of other environmental variables. Here, we analysed water chemistry, archaeal lipids and amoA‐ and nirS genes from 37 Tibetan hot springs. Strong correlations between intact polar lipids and their degradation product core lipids indicate that these two pools of lipids are closely related and may be formed in situ in the hot springs. Cluster analysis resulted in three major groups, within each of which the individual samples showed better correlations between ring index or TEX86 (TetraEther Index of tetraethers with 86 carbons) and temperature, pH or geochemical variables (e.g. nitrite, phosphate) in the polar fraction than in the corresponding core fraction. Most of these relationships did not exist when all of the samples were considered as a whole. Abundances of amoA‐ and nirS genes were strongly correlated with some of the intact polar‐ or core lipids. Our results suggest link between specific microbial functions (e.g. ammonia oxidation or nitrite reduction) and the production of individual GDGT lipids and highlights the potential utility of GDGT lipids as proxies for biogeochemical processes.

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Branched glycerol dialkyl glycerol tetraethers (bGDGTs) are predominantly found in soils and peat bogs. In this study, we analyzed core (C)-bGDGTs after hydrolysis of polar fractions using liquid chromatography-atmospheric pressure chemical ionization-mass spectrometry and analyzed intact P-bGDGTs using total lipid extract (TLE) without hydrolysis by liquid chromatography-electrospray ionization-multiple stage mass spectrometry. Our results show multiple lines of evidence for the production of bGDGTs in sediments and cellulolytic enrichments in a hot spring (62–86°C) in the Great Basin (USA). First, in situ cellulolytic enrichment led to an increase in the relative abundance of hydrolysis-derived P-bGDGTs over their C-bGDGT counterparts. Second, the hydrolysis-derived P- and C-bGDGT profiles in the hot spring were different from those of the surrounding soil samples; in particular, a monoglycosidic bGDGT Ib containing 13,16-dimethyloctacosane and one cyclopentane moiety was detected in the TLE but it was undetectable in surrounding soil samples even after sample enrichments. Third, previously published 16S rRNA gene pyrotag analysis from the same lignocellulose samples demonstrated the enrichment of thermophiles, rather than mesophiles, and total bGDGT abundance in cellulolytic enrichments correlated with the relative abundance of 16S rRNA gene pyrotags from thermophilic bacteria in the phyla Bacteroidetes, Dictyoglomi, EM3, and OP9 (“Atribacteria”). These observations conclusively demonstrate the production of bGDGTs in this hot spring; however, the identity of organisms that produce bGDGTs in the geothermal environment remains unclear.

Over 100 hot spring sediment samples were collected from 28 sites in 12 areas/regions, while recording as many coincident geochemical properties as feasible (>60 analytes). PCR was used to screen samples for Korarchaeota 16S rRNA genes. Over 500 Korarchaeota 16S rRNA genes were screened by RFLP analysis and 90 were sequenced, resulting in identification of novel Korarchaeota phylotypes and exclusive geographical variants. Korarchaeota diversity was low, as in other terrestrial geothermal systems, suggesting a marine origin for Korarchaeota with subsequent niche-invasion into terrestrial systems. Korarchaeota endemism is consistent with endemism of other terrestrial thermophiles and supports the existence of dispersal barriers. Korarchaeota were found predominantly in >55°C springs at pH 4.7–8.5 at concentrations up to 6.6×106 16S rRNA gene copies g−1 wet sediment. In Yellowstone National Park (YNP), Korarchaeota were most abundant in springs with a pH range of 5.7 to 7.0. High sulfate concentrations suggest these fluids are influenced by contributions from hydrothermal vapors that may be neutralized to some extent by mixing with water from deep geothermal sources or meteoric water. In the Great Basin (GB), Korarchaeota were most abundant at spring sources of pH<7.2 with high particulate C content and high alkalinity, which are likely to be buffered by the carbonic acid system. It is therefore likely that at least two different geological mechanisms in YNP and GB springs create the neutral to mildly acidic pH that is optimal for Korarchaeota. A classification support vector machine (C-SVM) trained on single analytes, two analyte combinations, or vectors from non-metric multidimensional scaling models was able to predict springs as Korarchaeota-optimal or sub-optimal habitats with accuracies up to 95%. To our knowledge, this is the most extensive analysis of the geochemical habitat of any high-level microbial taxon and the first application of a C-SVM to microbial ecology.