Dominated Clone Libraries Research Articles

Hydrocarbon-degrading bacteria in deep-water subarctic sediments (Faroe-Shetland Channel).

AimsThe aim of this study was the baseline description of oil‐degrading sediment bacteria along a depth transect in the Faroe‐Shetland Channel (FSC) and the identification of biomarker taxa for the detection of oil contamination in FSC sediments.Methods and ResultsOil‐degrading sediment bacteria from 135, 500 and 1000 m were enriched in cultures with crude oil as the sole carbon source (at 12, 5 and 0°C respectively). The enriched communities were studied using culture‐dependent and culture‐independent (clone libraries) techniques. Isolated bacterial strains were tested for hydrocarbon degradation capability. Bacterial isolates included well‐known oil‐degrading taxa and several that are reported in that capacity for the first time (Sulfitobacter, Ahrensia, Belliella, Chryseobacterium). The orders Oceanospirillales and Alteromonadales dominated clone libraries in all stations but significant differences occurred at genus level particularly between the shallow and the deep, cold‐water stations. Alcanivorax constituted 64% of clones at FSC135 but was absent at deeper stations. Pseudoalteromonas and Oleispira dominated the bacterial community at 500 and 1000 m.ConclusionsThe genus Oleispira emerged as a major player in the early stages of crude oil degradation in deep‐sea sediments of the FSC particularly at subzero temperatures. This finding is offering a direction for future research into biomonitoring tools for the detection of low levels of crude oil contamination in the deep FSC, and possibly high latitude cold waters in general.Significance and Impact of the StudyOil and gas exploration in the FSC occurs at depths >1000 m but baseline environmental data necessary for the assessment of ecosystem recovery to prespill conditions in the event of an oil spill are lacking. This study will contribute to our ability to assess the impact of oil release in the FSC and guide the direction of bioremediation strategies tailored to the area.

Increased Variability of Microbial Communities in Restored Salt Marshes nearly 30 Years After Tidal Flow Restoration

We analyzed microbial diversity and community composition from four salt marsh sites that were impounded for 40–50 years and subsequently restored and four unimpounded sites in southeastern Connecticut over one growing season. Community composition and diversity were assessed by terminal restriction fragment length polymorphism (TRFLP) and sequence analysis of 16S ribosomal RNA (rRNA) genes. Our results indicated diverse communities, with sequences representing 14 different bacterial divisions. Proteobacteria, Bacteroidetes, and Planctomycetes dominated clone libraries from both restored and unimpounded sites. Multivariate analysis of the TRFLP data suggest significant site, sample date, and restoration status effects, but the exact causes of these effects are not clear. Composition of clone libraries and abundance of bacterial 16S rRNA genes were not significantly different between restored sites and unimpounded sites, but restored sites showed greater temporal and spatial variability of bacterial communities based on TRFLP profiles compared with unimpounded sites, and variability was greatest at sites more recently restored. In summary, our study suggests there may be long-lasting effects on stability of bacterial communities in restored salt marshes and raises questions about the resilience and ultimate recovery of the communities after chronic disturbance.

Lipid biomarker and phylogenetic analyses to reveal archaeal biodiversity and distribution in hypersaline microbial mat and underlying sediment

This study has utilized the tools of lipid biomarker chemistry and molecular phylogenetic analyses to assess the archaeal contribution to diversity and abundance within a microbial mat and underlying sediment from a hypersaline lagoon in Baja California. Based on abundance of ether-linked isoprenoids, archaea made up from 1 to 4% of the cell numbers throughout the upper 100 mm of mat and sediment core. Below this depth archaeal lipid was two times more abundant than bacterial. Archaeol was the primary archaeal lipid in all layers. Relatively small amounts of caldarchaeol (dibiphytanyl glyceroltetraether) were present at most depths with phytanyl to biphytanyl molar ratios lowest (approximately 10 : 1) in the 4-17 mm and 100-130 mm horizons, and highest (132 : 1) in the surface 0-2 mm. Lipids with cyclic biphytanyl cores were only detected below 100 mm. A novel polar lipid containing a C(30) isoprenoid (squalane) moiety was isolated from the upper anoxic portion of the core and partially characterized. Hydrocarbon biomarker lipids included pentamethylicosane (2-10 mm) and crocetane (primarily below 10 mm). Archaeal molecular diversity varied somewhat with depth. With the exception of samples at 0-2 mm and 35-65 mm, Thermoplasmatales of marine benthic group D dominated clone libraries. A significant number of phylotypes representing the Crenarchaeota from marine benthic group B were generally present below 17 mm and dominated the 35-65 mm sample. Halobacteriaceae family made up 80% of the clone library of the surface 2 mm, and consisted primarily of sequences affiliated with the haloalkaliphilic Natronomonas pharaonis.

Molecular identification of bacteria in bronchoalveolar lavage fluid from children with cystic fibrosis

Culture of bronchoalveolar lavage fluid (BALF) is the gold standard for detection of pathogens in the lower airways in cystic fibrosis (CF). However, current culture results do not explain all clinical observations in CF, including negative culture results during pulmonary exacerbation and inflammation in the absence of pathogens. We hypothesize that organisms not routinely identified by culture occur in the CF airway and may contribute to disease. To test this hypothesis we used a culture-independent molecular approach, based on use of rRNA sequence analysis, to assess the bacterial composition of BALF from children with CF and disease controls (DC). Specimens from 42 subjects (28 CF) were examined, and approximately 6,600 total clones were screened to identify 121 species of bacteria. In general, a single rRNA type dominated clone libraries from CF specimens, but not DC. Thirteen CF subjects contained bacteria that are not routinely assessed by culture. In four CF subjects, candidate pathogens were identified and include the anaerobe Prevotella denticola, a Lysobacter sp., and members of the Rickettsiales. The presumptive pathogens Tropheryma whipplei and Granulicatella elegans were identified in cases from the DC group. The presence of unexpected bacteria in CF may explain inflammation without documented pathogens and consequent failure to respond to standard treatment. These results show that molecular techniques provide a broader perspective on airway bacteria than do routine clinical cultures and thus can identify targets for further clinical evaluation.

An Initial Inventory of Bacteria Found within the Soils and Waters of Great Smoky Mountains National Park

Abstract Soils and waters were collected from Great Smoky Mountains National Park (GSMNP), and bacteria were cultured or DNA cloned from the samples. Oconaluftee Visitors Center and Kephart Prong Trail were sampled to examine distributions of heterotrophs inhabiting streams and riparian soil. Soil from All Taxa Biodiversity Inventory plots at Albright Grove, Cataloochee, and Purchase Knob were also sampled. A total of eleven phyla were detected, of which six were only found via culture-independent techniques. Overall, 69 genera were documented, with differences in their detection in soil and water and by methodology. Firmicutes dominated cultures from soil, while Acidobacteria dominated clone libraries; Bacteroidetes was the dominant phylum in water. Three classes of the phylum Proteobacteria were commonly seen as isolates or clones. Prokaryotic diversity is extraordinary; this is the first inventory examining non-photosynthetic bacteria inhabiting GSMNP and it lays the groundwork for investigations explo...

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.

Fatty Acid-Oxidizing Consortia along a Nutrient Gradient in the Florida Everglades

The Florida Everglades is one of the largest freshwater marshes in North America and has been subject to eutrophication for decades. A gradient in P concentrations extends for several kilometers into the interior of the northern regions of the marsh, and the structure and function of soil microbial communities vary along the gradient. In this study, stable isotope probing was employed to investigate the fate of carbon from the fermentation products propionate and butyrate in soils from three sites along the nutrient gradient. For propionate microcosms, 16S rRNA gene clone libraries from eutrophic and transition sites were dominated by sequences related to previously described propionate oxidizers, such as Pelotomaculum spp. and Syntrophobacter spp. Significant representation was also observed for sequences related to Smithella propionica, which dismutates propionate to butyrate. Sequences of dominant phylotypes from oligotrophic samples did not cluster with known syntrophs but with sulfate-reducing prokaryotes (SRP) and Pelobacter spp. In butyrate microcosms, sequences clustering with Syntrophospora spp. and Syntrophomonas spp. dominated eutrophic microcosms, and sequences related to Pelospora dominated the transition microcosm. Sequences related to Pelospora spp. and SRP dominated clone libraries from oligotrophic microcosms. Sequences from diverse bacterial phyla and primary fermenters were also present in most libraries. Archaeal sequences from eutrophic microcosms included sequences characteristic of Methanomicrobiaceae, Methanospirillaceae, and Methanosaetaceae. Oligotrophic microcosms were dominated by acetotrophs, including sequences related to Methanosarcina, suggesting accumulation of acetate.

ABUNDANCE OF A NOVEL DINOFLAGELLATE PHYLOTYPE IN THE ROSS SEA, ANTARCTICA1

The biodiversity of protistan assemblages present in microhabitats of the Ross Sea, Antarctica, was examined using molecular biological methods to obtain a greater understanding of the genetic diversity present. Sequencing of 18S clone libraries indicated genetically diverse collections of organisms in the water column, ice, and meltwater layer (slush), but a single small subunit ribosomal DNA (srDNA) sequence type dominated clone libraries (>30%) from seawater and slush samples taken within the ice pack of this ecosystem. The BLAST searches indicated that this dominant clone was derived from a dinoflagellate, and that it shared sequence similarity (97.6%–98.3%) with both Karenia and Karlodinium species. Phylogenetic analyses based on small subunit ribosomal gene sequences supported its placement as a sister group to these taxa, and suggested that it represented a novel genus. The dinoflagellate was successfully recovered in culture, and morphological analyses have shown that it contains chloroplasts, is gymnodinoid, appears not to have thecal plates, and has an apical groove and sulcal structure that confirm its placement as a relative of the Karenia/Karlodinium group. The abundance of this phylotype in natural samples was confirmed by quantitative PCR analyses of water and slush communities, and suggests that this dinoflagellate can be a major constituent of the protistan assemblages of some Antarctic microhabitats of the Ross Sea.

Uranium (VI) Reduction by Denitrifying Biomass

ABSTRACT Groundwater near the S3 ponds at the US Department of Energy's Y-12 site in Oak Ridge, Tennessee, is contaminated by high levels of nitrate (up to 160 mM) and U(VI) (∼0.3 mM). To minimize nitrate inhibition, the authors proposed extraction of contaminated groundwater, nitrate removal in a denitrifying fluidized bed bioreactor (FBR), and return of nitrate-free effluent to the aquifer to stimulate in situ microbial reduction of U(VI). In the presence of carbonate, U(VI) sorption to biomass was negligible, but in its absence, sorption was significant. Biomass reduced U(VI) to U(IV), exhibiting slow first-order removal with respect to U(VI). Addition of electron donor increased rates. Addition of an inhibitor of sulfate reduction (molybdate) slowed the rate and inhibited sulfate reduction. Denitrifying β-Proteobacteria dominated clone libraries of SSU rRNA and dsrA gene sequences. Approximately 10% were low-G+C microorganisms that had 90% to 92% sequence identity with Sporomusa, Acetonema, and Propionispora. The dsrA sequences were dominated by a single clone with ∼80% nucleotide identity to dsrA of Desulfovibrio vulgaris sub sp. oxamicus. The authors conclude that some members of this denitrifyng community reduce uranium, and that sulfate-reducing bacteria likely contribute to this capability.