Effects of Abiotic Factors on the Phylogenetic Diversity of Bacterial Communities in Acidic Thermal Springs

Acidic thermal springs offer ideal environments for studying processes underlying extremophile microbial diversity. We used a carefully designed comparative analysis of acidic thermal springs in Yellowstone National Park to determine how abiotic factors (chemistry and temperature) shape acidophile microbial communities. Small-subunit rRNA gene sequences were PCR amplified, cloned, and sequenced, by using evolutionarily conserved bacterium-specific primers, directly from environmental DNA extracted from Amphitheater Springs and Roaring Mountain sediment samples. Energy-dispersive X-ray spectroscopy, X-ray diffraction, and colorimetric assays were used to analyze sediment chemistry, while an optical emission spectrometer was used to evaluate water chemistry and electronic probes were used to measure the pH, temperature, and E_h of the spring waters. Phylogenetic-statistical analyses found exceptionally strong correlations between bacterial community composition and sediment mineral chemistry, followed by weaker but significant correlations with temperature gradients. For example, sulfur-rich sediment samples contained a high diversity of uncultured organisms related to Hydrogenobaculum spp., while iron-rich sediments were dominated by uncultured organisms related to a diverse array of gram-positive iron oxidizers. A detailed analysis of redox chemistry indicated that the available energy sources and electron acceptors were sufficient to support the metabolic potential of Hydrogenobaculum spp. and iron oxidizers, respectively. Principal-component analysis found that two factors explained 95% of the genetic diversity, with most of the variance attributable to mineral chemistry and a smaller fraction attributable to temperature.     

Characterization of a sulfide-oxidizing biofilm developed in a packed-column reactor.

The potential of microbial mats to develop sulfide-oxidizing biofims was explored. A bioreactor specially designed for the treatment of sulfide-containing effluents was inoculated with a microbial-mat sample, and a complex microbial biofilm with sulfide-oxidation activity developed. The microbial composition of the biofilm was studied by pigment, microscopy, and 16S rRNA gene analyses. Purple sulfur bacteria and diatoms were observed by microscopy, chlorophyll a and bacteriochlorophyll a were detected in the pigment analysis, and high genetic diversity was found in the 16S rRNA gene library. Specialized anaerobic sulfur oxidizers (i.e., phototrophic purple and green sulfur bacteria) dominated the library. Aerobic phototrophs (diatoms) also developed and the oxygen produced allowed the growth of aerobic sulfide oxidizers, such as Thiomicrospira-like spp. Cyanobacteria, which are significant organisms in natural microbial mats, did not develop in the reactor but unexpected uncultured members from the Epsilonproteobacteria developed profusely. Moreover, a variety of more minor organisms, such as members of the Cytophaga-Flavobacterium-Bacteroides (CFB) and purple non-sulfur bacteria (Roseospirillum sp.), were also present. The results showed that a complex community with high genetic and metabolic diversity, including many uncultured organisms, can develop in a laboratory-scale reactor.     

Assessment of Microbial Diversity in Saudi Springs by Culture-Dependent and Culture-Independent Methods

Culture-dependent and culture-independent methods were used to evaluate the microbial diversity in two hot springs of the Aljouf region in Saudi Arabia, including Qasr Kaff and Ain Hawas. Physicochemical characteristics of the springs were examined to establish their effect on the biodiversity of thermophilic bacteria and fungi. We employed culture-dependent techniques to study microbial diversity using four different complex media for bacteria and fungi. In addition, the direct count for algal populations from two springs was investigated. We surveyed the microbial diversity in water and sediment samples from both springs by denaturing gradient gel electrophoresis (DGGE) and clone library construction. Bacillariophycaea (18 species) was the most diverse group, followed by Cyanophyceaea. Bacterial isolates closer to the genera Bacillus spp., Geobacillus, Thermoactinomyces, and unidentified actinobacteria were recovered. Fungal isolates were related to Aspergillus, Pezizaceae, Penicillium, Acremonium, Fusarium, Chrysosporium, and Stachybotrys. Using molecular-based techniques, the results were slightly different from those obtained by culture-dependent methods, and more genera were obtained. However, most genera were uncultured microbes, particularly from bacterial communities.     

Interactions of Nitrifying Bacteria and Heterotrophs: Identification of a Micavibrio-Like Putative Predator of Nitrospira spp.

Chemolithoautotrophic nitrifying bacteria release soluble organic compounds, which can be substrates for heterotrophic microorganisms. The identities of these heterotrophs and the specificities of their interactions with nitrifiers are largely unknown. In this study, we incubated nitrifying activated sludge with ¹³C-labeled bicarbonate and used stable isotope probing of 16S rRNA to monitor the flow of carbon from uncultured nitrifiers to heterotrophs. To facilitate the identification of heterotrophs, the abundant 16S rRNA molecules from nitrifiers were depleted by catalytic oligonucleotides containing locked nucleic acids (LNAzymes), which specifically cut the 16S rRNA of defined target organisms. Among the ¹³C-labeled heterotrophs were organisms remotely related to Micavibrio, a microbial predator of Gram-negative bacteria. Fluorescence in situ hybridization revealed a close spatial association of these organisms with microcolonies of nitrite-oxidizing sublineage I Nitrospira in sludge flocs. The high specificity of this interaction was confirmed by confocal microscopy and a novel image analysis method to quantify the localization patterns of biofilm microorganisms in three-dimensional (3-D) space. Other isotope-labeled bacteria, which were affiliated with Thermomonas, colocalized less frequently with nitrifiers and thus were commensals or saprophytes rather than specific symbionts or predators. These results suggest that Nitrospira spp. are subject to bacterial predation, which may influence the abundance and diversity of these nitrite oxidizers and the stability of nitrification in engineered and natural ecosystems. In silico screening of published next-generation sequencing data sets revealed a broad environmental distribution of the uncultured Micavibrio-like lineage.     

高通量测序分析云南腾冲热海热泉微生物多样性

【背景】云南腾冲热海热泉中蕴含着丰富的极端微生物资源。【目的】揭示云南腾冲热海热泉中微生物物种多样性及群落结构差异,发掘酸性热泉中铁、硫氧化功能微生物。【方法】采用Illumina HiSeq高通量测序技术对3处热泉15个水体样品中微生物16SrRNA基因V4-V5区进行测序及生物信息学分析。【结果】3处热泉中共获得578061条有效序列,聚类为141个可操作分类单元(Operational taxonomic unit,OTU),包括19个门66个属。鼓鸣泉(GMQ)、蛤蟆嘴(HMZ)、黄瓜箐(HGQ)3处热泉均以泉古菌门(Crenarchaeota)和厚壁菌门(Firmicute)为主。从属水平分析,碱性热泉鼓鸣泉(GMQ)和中性热泉蛤蟆嘴(HMZ)分别注释到37、32个属,优势属均为芽孢杆菌属(Bacillus)和热棒菌属(Pyrobaculum)。酸性热泉黄瓜箐(HGQ)共注释到20个属,优势属为酸杆菌属(Acidibacillus)和酸硫杆状菌属(Acidithiobacillus),此外,具有铁、硫氧化潜力的菌属有喜酸菌属(Acidicaldus)、硫化芽孢杆菌属(Sulfobacillus)、硫化叶菌属(Sulfolobus)及生金球菌属(Metallosphaera)等,进一步通过硫氧化培养基分离获得了这些菌属中的纯菌株。【结论】云南腾冲热海热泉水体中蕴含丰富的微生物资源,热泉间微生物物种组成差异明显;酸性热泉中存在多种具有潜在铁、硫代谢功能的菌种;未分类类群、非培养类群丰度很高,尤其是蕴藏着可观的古菌资源。     

西藏羊八井废弃热井沉积物中的真核微生物多样性

【目的】研究西藏羊八井废弃热井沉积物中的真核微生物多样性。【方法】采用ITS-rRNA基因分析法构建了沉积物中真核微生物的ITS-rRNA基因文库, 随机抽取文库中的克隆子进行扩增rDNA限制性酶切片段分析(ARDRA), 并对ITS-rRNA基因进行了系统发育分析。【结果】沉积物中主要的真核微生物有子囊菌、壶菌、担子菌、丝足虫、后生动物和非培养真菌。其中壶菌Chytridiales sp.、Physoderma maydis和Powellomyces sp., 子囊菌的假丝酵母(Candida parapsilosis)、鲁氏接合酵母(Zygosaccharomyces rouxii)和短梗霉(Aureobasidium pullulans)以及后生动物的轮虫(Lecane bulla)均未有报导存在于热泉或热井中。【结论】羊八井热井沉积物中具有丰富的真核微生物多样性。     

Characterization of Enrichment Cultures Involved in the Carbon,Sulfur and Iron Biogeochemical Cycles in French Guiana Mobile Muds

The fluidized sediment ecosystem off French Guiana is characterized by active physical reworking, diversity of electron acceptors and highly variable redox regime. It is well studied geochemically but little is known about specific microorganisms involved in its biogeochemistry. Based on the biogeochemical profiles and rate kinetics, several possible biotically mediated pathways of the carbon, sulfur and iron cycles were hypothesized. Enrichment studies were set up with a goal to culture microorganisms responsible for these pathways. Stable microbial consortia potentially capable of the following chemolithoautotrophic types were enriched from the environment and characterized: elemental sulfur/thiosulfate disproportionators, thiosulfate-oxidizing ferrihydrite and nitrate reducers, sulfide/ferrous sulfide oxidizers coupled with nitrate and microaerophilic iron oxidizers. Attempts to generate several enrichments (anoxic ammonia oxidation, and sulfide oxidizers with ferric iron or manganese oxide) were not successful. Heterotrophic sulfate and elemental sulfur reduction bacteria are prominent and dominate reductive sulfur transformations. We hypothesize that carbon dioxide fixation coupled with synthesis of organic matter happens mostly via sulfur disproportionation and sulfur species oxidation with iron oxidation playing a minor role.     

Neutrophilic lithotrophic iron-oxidizing prokaryotes and their role in the biogeochemical processes of the iron cycle

Biology of lithotrophic neutrophilic iron-oxidizing prokaryotes and their role in the processes of the biogeochemical cycle of iron are discussed. This group of microorganisms is phylogenetically, taxonomically, and physiologically heterogeneous, comprising three metabolically different groups: aerobes, nitratedependent anaerobes, and phototrophs; the latter two groups have been revealed relatively recently. Their taxonomy and metabolism are described. Materials on the structure and functioning of the electron transport chain in the course of Fe(II) oxidation by members of various physiological groups are discussed. Occurrence of iron oxidizers in freshwater and marine ecosystems, thermal springs, areas of hydrothermal activity, and underwater volcanic areas are considered. Molecular genetic techniques were used to determine the structure of iron-oxidizing microbial communities in various natural ecosystems. Analysis of stable isotope fractionation of ^56/54Fe in pure cultures and model experiments revealed a predominance of biological oxidation over abiotic ones in shallow aquatic habitats and mineral springs, which was especially pronounced under microaerobic conditions at the redox zone boundary. Discovery of anaerobic bacterial Fe(II) oxidation resulted in development of new hypotheses concerning the possible role of microorganisms and the mechanisms of formation of the major iron ore deposits during Precambrian era until the early Proterozoic epoch. Paleobiological data are presented on the microfossils and specific biomarkers retrieved from ancient ore samples and confirming involvement of anaerobic biogenic processes in their formation.     

Microbial and chemical characterization of underwater fresh water springs in the Dead Sea

Due to its extreme salinity and high Mg concentration the Dead Sea is characterized by a very low density of cells most of which are Archaea. We discovered several underwater fresh to brackish water springs in the Dead Sea harboring dense microbial communities. We provide the first characterization of these communities, discuss their possible origin, hydrochemical environment, energetic resources and the putative biogeochemical pathways they are mediating. Pyrosequencing of the 16S rRNA gene and community fingerprinting methods showed that the spring community originates from the Dead Sea sediments and not from the aquifer. Furthermore, it suggested that there is a dense Archaeal community in the shoreline pore water of the lake. Sequences of bacterial sulfate reducers, nitrifiers iron oxidizers and iron reducers were identified as well. Analysis of white and green biofilms suggested that sulfide oxidation through chemolitotrophy and phototrophy is highly significant. Hyperspectral analysis showed a tight association between abundant green sulfur bacteria and cyanobacteria in the green biofilms. Together, our findings show that the Dead Sea floor harbors diverse microbial communities, part of which is not known from other hypersaline environments. Analysis of the water's chemistry shows evidence of microbial activity along the path and suggests that the springs supply nitrogen, phosphorus and organic matter to the microbial communities in the Dead Sea. The underwater springs are a newly recognized water source for the Dead Sea. Their input of microorganisms and nutrients needs to be considered in the assessment of possible impact of dilution events of the lake surface waters, such as those that will occur in the future due to the intended establishment of the Red Sea-Dead Sea water conduit.     

Influence of Seasonal and Geochemical Changes on the Geomicrobiology of an Iron Carbonate Mineral Water Spring

Fuschna Spring in the Swiss Alps (Engadin region) is a bicarbonate iron(II)-rich, pH-neutral mineral water spring that is dominated visually by dark green microbial mats at the side of the flow channel and orange iron(III) (oxyhydr)oxides in the flow channel. Gradients of O₂, dissolved iron(II), and bicarbonate establish in the water. Our goals were to identify the dominating biogeochemical processes and to determine to which extent changing geochemical conditions along the flow path and seasonal changes influence mineral identity, crystallinity, and microbial diversity. Geochemical analysis showed microoxic water at the spring outlet which became fully oxygenated within 2.3 m downstream. X-ray diffraction and Mössbauer spectroscopy revealed calcite (CaCO₃) and ferrihydrite [Fe(OH)₃] to be the dominant minerals which increased in crystallinity with increasing distance from the spring outlet. Denaturing gradient gel electrophoresis banding pattern cluster analysis revealed that the microbial community composition shifted mainly with seasons and to a lesser extent along the flow path. 16S rRNA gene sequence analysis showed that microbial communities differ between the flow channel and the flanking microbial mat. Microbial community analysis in combination with most-probable-number analyses and quantitative PCR (qPCR) showed that the mat was dominated by cyanobacteria and the channel was dominated by microaerophilic Fe(II) oxidizers (1.97 × 10⁷ ± 4.36 × 10⁶ 16S rRNA gene copies g⁻¹ using Gallionella-specific qPCR primers), while high numbers of Fe(III) reducers (10⁹ cells/g) were identified in both the mat and the flow channel. Phototrophic and nitrate-reducing Fe(II) oxidizers were present as well, although in lower numbers (10³ to 10⁴ cells/g). In summary, our data suggest that mainly seasonal changes caused microbial community shifts, while geochemical gradients along the flow path influenced mineral crystallinity.     

Microbial communities of the discharge zone of oil- and gas-bearing fluids in low-mineral Lake Baikal

At the site of natural ingress of oil, microbial diversity in the Central Baikal bottom sediments differing in the chemical composition of pore waters was studied by molecular biological techniques. The sediments saturated with oil and methane were found to contain members of 10 bacterial and 2 archaeal phyla. The oxidized sediment layer contained methanotrophic bacteria belonging to the Alphaproteobacteria, which had a specific structure of the pmoA gene and clustered together with uncultured methanotrophs from cold ecosystems. The upper sediment layer also contained oil-oxidizing bacteria and the alkB genes most closely related to those of Rhodococcus. The microbial community of reduced sediments exhibited lower diversity and was represented mostly by the organisms involved in hydrocarbon biodegradation.     

Analysis of the diversity of aerobic,thermophilic endospore-forming bacteria in two Algerian hot springs using cultural and non-cultural methods

Terrestrial hot environments are important resources for isolation of thermophilic microorganisms. Few studies have been made on microbial diversity of Algerian geothermal sites. This paper reports the diversity of thermophilic, aerobic endospore-forming bacteria from water and sediment samples taken from Hammam Ouled Ali and Hammam Debagh, two hot springs with a wide range of temperatures and a very rich mineral composition, located in the region of Guelma, north-east of Algeria using culture-dependent and culture-independent approaches Sequences of the V4 region of the 16S rRNA gene from environmental DNA extracted from sediment samples were analyzed and a set of isolates from water and sediment have been characterized by phenotypic and molecular methods. Phylogenetic surveys using environmental DNA sequences indicated that three families dominated the two hot springs: Planococcaceae, Bacillaceae, and Paenibacillaceae. Phenotypic characterization revealed the morphological, biochemical, and physiological properties of these microorganisms, all of which exhibited a range of common extracellular enzymatic activities. Amplified ribosomal DNA restriction analysis (ARDRA) was used to cluster isolates into different phylotypic groups and phylogenetic analysis of 16S rRNA gene sequences of selected isolates showed that all were closely related to four genera of thermophilic Bacilli: Bacillus, Anoxybacillus, Geobacillus, and Brevibacillus. Our results provide important insights into the microbial ecology of Guelma hot springs. They showed that the phylogenetic diversity of bacterial communities within the two studied hot springs was mostly aerobic, with the presence of taxonomic groups of great biotechnological interest. Bioprospection of thermozymes and other biomolecules within these communities will probably provide a data basis for their industrial exploitation.     

Microbial populations stimulated for hexavalent uranium reduction in uranium mine sediment

Uranium-contaminated sediment and water collected from an inactive uranium mine were incubated anaerobically with organic substrates. Stimulated microbial populations removed U almost entirely from solution within 1 month. X-ray absorption near-edge structure analysis showed that U(VI) was reduced to U(IV) during the incubation. Observations by transmission electron microscopy, selected area diffraction pattern analysis, and energy-dispersive X-ray spectroscopic analysis showed two distinct types of prokaryotic cells that precipitated only a U(IV) mineral uraninite (UO(2)) or both uraninite and metal sulfides. Prokaryotic cells associated with uraninite and metal sulfides were inferred to be sulfate-reducing bacteria. Phylogenetic analysis of 16S ribosomal DNA obtained from the original and incubated sediments revealed that microbial populations were changed from microaerophilic Proteobacteria to anaerobic low-G+C gram-positive sporeforming bacteria by the incubation. Forty-two out of 94 clones from the incubated sediment were related to sulfate-reducing Desulfosporosinus spp., and 23 were related to fermentative Clostridium spp. The results suggest that, if in situ bioremediation were attempted in the uranium mine ponds, Desulfosporosinus spp. would be a major contributor to U(VI) and sulfate reduction and Clostridium spp. to U(VI) reduction.     

Leaching of silica and uranium and other quantitative aspects of the lithobiontic colonization in a radioactive thermal spring

The formation of microbial mats by thermophilic organisms on submerged rocks in radioactive thermal springs was followed quantitatively in situ as well as under experimental conditions, by determining the change in dry weight and organic matter as a function of time. Furthermore, the decay of the rock occurring in the springs could be shown to be directly related to the microbial colonization. Early in that process the formation of silicious gels, facilitating the settling of the organisms, could be observed. Simultaneously, this was accompanied by the leaching of silica from the underlying rock. This resulted in the destruction of the rock, which had been altered to a fine-grained dust underneath the colonizing mats; the microorganisms were found to move further downward within this layer. From the heavy metals present in the rock—iron (Fe), copper (Cu), manganese (Mn), uranium (U)— the leaching of uranium could be demonstrated, leading to the acquisition of this metal in the microbial mats in concentrations up to 15.34g/mg dry weight. Direct evidence for the leaching of Si (silicon) and U could be obtained by measurement of these elements after their release from ground rock chips in cultures with microorganisms from the hot springs at 50°C. X-ray analysis of the biomats strongly suggested that Cu, Mn, and Fe are also accumulated.     

Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communities

The assessment of microbial diversity and distribution is a major concern in environmental microbiology. There are two general approaches for measuring community diversity: quantitative measures, which use the abundance of each taxon, and qualitative measures, which use only the presence/absence of data. Quantitative measures are ideally suited to revealing community differences that are due to changes in relative taxon abundance (e.g., when a particular set of taxa flourish because a limiting nutrient source becomes abundant). Qualitative measures are most informative when communities differ primarily by what can live in them (e.g., at high temperatures), in part because abundance information can obscure significant patterns of variation in which taxa are present. We illustrate these principles using two 16S rRNA-based surveys of microbial populations and two phylogenetic measures of community beta diversity: unweighted UniFrac, a qualitative measure, and weighted UniFrac, a new quantitative measure, which we have added to the UniFrac website (http://bmf.colorado.edu/unifrac). These studies considered the relative influences of mineral chemistry, temperature, and geography on microbial community composition in acidic thermal springs in Yellowstone National Park and the influences of obesity and kinship on microbial community composition in the mouse gut. We show that applying qualitative and quantitative measures to the same data set can lead to dramatically different conclusions about the main factors that structure microbial diversity and can provide insight into the nature of community differences. We also demonstrate that both weighted and unweighted UniFrac measurements are robust to the methods used to build the underlying phylogeny.     

Comparison of acid mine drainage microbial communities in physically and geochemically distinct ecosystems

This study presents population analyses of microbial communities inhabiting a site of extreme acid mine drainage (AMD) production. The site is the inactive underground Richmond mine at Iron Mountain, Calif., where the weathering of a massive sulfide ore body (mostly pyrite) produces solutions with pHs of approximately 0.5 to approximately 1.0. Here we used a suite of oligonucleotide probes, designed from molecular data recently acquired from the site, to analyze a number of microbial environments by fluorescent in situ hybridization. Microbial-community analyses were correlated with geochemical and mineralogical data from those environments. The environments investigated were within the ore body and thus at the site of pyrite dissolution, as opposed to environments that occur downstream of the dissolution. Few organism types, as defined by the specificities of the oligonucleotide probes, dominated the microbial communities. The majority of the dominant organisms detected were newly discovered or organisms only recently associated with acid-leaching environments. "Ferroplasma" spp. were detected in many of the communities and were particularly dominant in environments of lowest pH and highest ionic strength. Leptospirillum spp. were also detected in many slime and pyrite-dominated environments. In samples of an unusual subaerial slime, a new uncultured Leptospirillum sp. dominated. Sulfobacillus spp. were detected as a prominent inhabitant in warmer ( approximately 43 degrees C) environments. The information gathered here is critical for determining organisms important to AMD production at Iron Mountain and for directing future studies of this process. The findings presented here also have relevance to the microbiology of industrial bioleaching and to the understanding of geochemical iron and sulfur cycles.     

Electricity generation by microorganisms in the sediment-water interface of an extreme acidic microcosm

The attachment of microorganisms to electrodes is of great interest for electricity generation in microbial fuel cells (MFC) or other applications in bioelectrochemical systems (BES). In this work, a microcosm of the acidic ecosystem of Río Tinto was built and graphite electrodes were introduced at different points. This allowed the study of electricity generation in the sediment/water interface and the involvement of acidophilic microorganisms as biocatalysts of the anodic and cathodic reactions in a fuel-cell configuration. Current densities and power outputs of up to 3.5 A/m2 and 0.3 W/m2, respectively, were measured at pH 3. Microbial analyses of the electrode surfaces showed that Acidiphilium spp., which uses organic compounds as electron donors, were the predominant biocatalysts of the anodic reactions, whereas the aerobic iron oxidizers Acidithiobacillus ferrooxidans and Leptospirillum spp. were detected mainly on the cathode surface.     

Seasonal and spatial diversity of microbial communities in marine sediments of the South China Sea

This study was conducted to characterize the diversity of microbial communities in marine sediments of the South China Sea by means of 16S rRNA gene clone libraries. The results revealed that the sediment samples collected in summer harboured a more diverse microbial community than that collected in winter, Deltaproteobacteria dominated 16S rRNA gene clone libraries from both seasons, followed by Gammaproteobacteria, Acidobacteria, Nitrospirae, Planctomycetes, Firmicutes. Archaea phylotypes were also found. The majority of clone sequences shared greatest similarity to uncultured organisms, mainly from hydrothermal sediments and cold seep sediments. In addition, the sedimentary microbial communities in the coastal sea appears to be much more diverse than that of the open sea. A spatial pattern in the sediment samples was observed that the sediment samples collected from the coastal sea and the open sea clustered separately, a novel microbial community dominated the open sea. The data indicate that changes in environmental conditions are accompanied by significant variations in diversity of microbial communities at the South China Sea.     

Comparison of PCR primer-based strategies for characterization of ammonia oxidizer communities in environmental samples

PCR-based techniques are commonly used to characterize microbial communities, but are subject to bias that is difficult to assess. This study aimed to evaluate bias of several PCR primer-based strategies used to study diversity of autotrophic ammonia oxidizers. 16S rRNA genes from soil- or sediment-DNA were amplified using primers considered either selective or specific for betaproteobacterial ammonia oxidizers. Five approaches were assessed: (a) amplification with primers betaAMO143f-betaAMO1315r; (b) amplification with primers CTO189f-CTO654r; (c) nested amplification with betaAMO143f-betaAMO1315r followed by CTO189f-CTO654r primers; (d) nested amplification with betaAMO143f-betaAMO1315r and CTO189f-Pf1053r primers; (e) nested amplification with 27f-1492r and CTO189f-CTO654r primers. Amplification products were characterized by denaturing gradient gel electrophoresis (DGGE) analysis after further amplification with 357f-GC-518r primers. DGGE profiles of soil communities were heterogeneous and depended on the approach followed. Ammonia oxidizer diversity was higher using approaches (b), (c) and (e) than using (a) and (d), where sequences of the most prominent bands showed similarities to nonammonia oxidizers. Profiles from marine sediments were more consistent, regardless of the approach adopted, and sequence analysis of excised bands indicated that these consisted of ammonia oxidizers only. The study demonstrates the importance of choice of primer, of screening for sequences of nontarget organisms and use of several approaches when characterizing microbial communities in natural environments.     

Microbiology and geochemistry of great boiling and mud hot springs in the United States Great Basin

A coordinated study of water chemistry, sediment mineralogy, and sediment microbial community was conducted on four >73°C springs in the northwestern Great Basin. Despite generally similar chemistry and mineralogy, springs with short residence time (~5–20 min) were rich in reduced chemistry, whereas springs with long residence time (>1 day) accumulated oxygen and oxidized nitrogen species. The presence of oxygen suggested that aerobic metabolisms prevail in the water and surface sediment. However, Gibbs free energy calculations using empirical chemistry data suggested that several inorganic electron donors were similarly favorable. Analysis of 298 bacterial 16S rDNAs identified 36 species-level phylotypes, 14 of which failed to affiliate with cultivated phyla. Highly represented phylotypes included Thermus, Thermotoga, a member of candidate phylum OP1, and two deeply branching Chloroflexi. The 276 archaeal 16S rDNAs represented 28 phylotypes, most of which were Crenarchaeota unrelated to the Thermoprotei. The most abundant archaeal phylotype was closely related to “Candidatus Nitrosocaldus yellowstonii”, suggesting a role for ammonia oxidation in primary production; however, few other phylotypes could be linked with energy calculations because phylotypes were either related to chemoorganotrophs or were unrelated to known organisms. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.