bluuebunny/crossref_metadata_2025_split huggingface dataset:
Temporal change in culturable phenanthrene degraders in response to long‐term exposure to phenanthrene in a soil column system
Authors: Bodour Adria A. , Wang Jiann‐Ming , Brusseau Mark L. , Maier Raina M. 
Published: September 2003

SummaryWidespread environmental contamination by polycyclic aromatic hydrocarbons (PAH) has led to increased interest in the use of natural attenuation as a clean‐up strategy. However, few bioremediation studies have investigated the behaviour of the indigenous PAH‐degrading community after long‐term exposure to a PAH. In this study, a column packed with sandy loam soil was exposed to a solution saturated with phenanthrene (≈ 1.2 mg l−1) for a 6‐month period to examine the temporal response of the indigenous phenanthrene‐degrading community. Initial soil, effluent, and final soil samples were collected and analysed for phenanthrene concentration and culturable phenanthrene degraders. Phenanthrene‐degrading isolates were grouped by colony morphology. For each unique group, 16S rDNA polymerase chain reaction was performed, and then sequencing analysis was used to identify the isolate at the genus level. Twenty‐five phenanthrene‐degrading isolates, potentially representing 19 genera, were obtained from this analysis. Of these, eight genera have not been reported previously to degrade phenanthrene, including Afipia, Janthinobacterium, Leptothrix, Massilia, Methylobacterium, Rhizobium, Sinorhizobium and Thiobacillus. Results indicate that the dominant phenanthrene‐degrading population changed over the course of this 6‐month experiment. Specifically, the isolates obtained initially from the soil were not subsequently found in either effluent samples or the soil at the end of the experiment. Furthermore, several isolates that were found in the soil at the end of the experiment were not observed in the soil initially or in the effluent samples. This study confirms earlier findings indicating that a diverse community participates in phenanthrene degradation in the environment, and also suggests that the composition of this community is temporally variable.
New primers for the class Actinobacteria: application to marine and terrestrial environments
Authors: Stach James E. M. , Maldonado Luis A. , Ward Alan C. , Goodfellow Michael , Bull Alan T. 
Published: September 2003

SummaryIn this study, we redesigned and evaluated primers for the class Actinobacteria. In silico testing showed that the primers had a perfect match with 82% of genera in the class Actinobacteria, representing a 26–213% improvement over previously reported primers. Only 4% of genera that displayed mismatches did so in the terminal three bases of the 3′ end, which is most critical for polymerase chain reaction success. The primers, designated S‐C‐Act‐0235‐a‐S‐20 and S‐C‐Act‐0878‐a‐A‐19, amplified an ≈ 640 bp stretch of the 16S rRNA gene from all actinobacteria tested (except Rubrobacter radiotolerans) up to an annealing temperature of 72°C. An Actinobacteria Amplification Resource (http://microbe2.ncl.ac.uk/MMB/AAR.htm) was generated to provide a visual guide to aid the amplification of actinobacterial 16S rDNA. Application of the primers to DNA extracted from marine and terrestrial samples revealed the presence of actinobacteria that have not been described previously. The use of 16S rDNA similarity and DNA–DNA pairing correlations showed that almost every actinomycete clone represented either a new species or a novel genus. The results of this study reinforce the proposition that current culture‐based techniques drastically underestimate the diversity of Actinobacteria in the environment and highlight the need to evaluate taxon‐specific primers regularly in line with improvements in databases holding 16S rDNA sequences.
Comparative 16S rDNA and 16S rRNA sequence analysis indicates that Actinobacteria might be a dominant part of the metabolically active bacteria in heavy metal‐contaminated bulk and rhizosphere soil
Authors: Gremion Fabienne , Chatzinotas Antonis , Harms Hauke 
Published: September 2003

SummaryBacterial diversity in 16S ribosomal DNA and reverse‐transcribed 16S rRNA clone libraries originating from the heavy metal‐contaminated rhizosphere of the metal‐hyperaccumulating plant Thlaspi caerulescens was analysed and compared with that of contaminated bulk soil. Partial sequence analysis of 282 clones revealed that most of the environmental sequences in both soils affiliated with five major phylogenetic groups, the Actinobacteria, α‐Proteobacteria, β‐Proteobacteria, Acidobacteria and the Planctomycetales. Only 14.7% of all phylotypes (sequences with similarities> 97%), but 45% of all clones, were common in the rhizosphere and the bulk soil clone libraries. The combined use of rDNA and rRNA libraries indicated which taxa might be metabolically active in this soil. All dominant taxa, with the exception of the Actinobacteria, were relatively less represented in the rRNA libraries compared with the rDNA libraries. Clones belonging to the Verrucomicrobiales, Firmicutes, Cytophaga–Flavobacterium–Bacteroides and OP10 were found only in rDNA clone libraries, indicating that they might not represent active constituents in our samples. The most remarkable result was that sequences belonging to the Actinobacteria dominated both bulk and rhizosphere soil libraries derived from rRNA (50% and 60% of all phylotypes respectively). Seventy per cent of these clone sequences were related to the Rubrobacteria subgroups 2 and 3, thus providing for the first time evidence that this group of bacteria is probably metabolically active in heavy metal‐contaminated soil.
Molecular investigation on strain genetic relatedness and population structure of Beauveria bassiana
Authors: Wang Chengshu , Shah Farooq A. , Patel Nita , Li Zengzhi , Butt Tariq M. 
Published: September 2003

SummaryTriplicate molecular methods, i.e. polymerase chain reaction‐restriction fragment length polymorphism of the pr1 gene, microsatellite markers and 28S rDNA haplotyping by detecting the presence or absence of group I introns, were used for population study of the entomopathogenic fungus, Beauveria bassiana. The findings showed that the average genetic diversity index of geographical populations was significantly smaller than that of populations derived from insect host orders, indicating that the genetic relatedness of B. bassiana strains was highly associated with geographical locality rather than insect host species. The reproductive style of all the B. bassiana populations was found to be non‐clonal. Population structure analysis revealed that the average divergent coefficient among populations of B. bassiana was far below 1 (0.1112), which indicated that there was no significant genetic differentiation between populations, and that the overall genetic diversity mainly resulted from the genetic variations within geographical populations. Statistically, genetic distances between populations were positively correlated with geographical distances, suggesting that geographical separation poses an obstacle to the possibility and frequency of genetic exchanges between populations. On the other hand, gene flow was indirectly established to occur between B. bassiana populations.
Effect of thorium on the growth and capsule morphology of Bradyrhizobium
Authors: Santamaría Mónica , Díaz‐Marrero Ana R. , Hernández Jairo , Gutiérrez‐Navarro Angel M. , Corzo Javier 
Published: September 2003

SummaryThe thorium effect on Bradyrhizobium growth was assayed in liquid media. Th4+ inhibited the growth of Bradyrhizobium (Chamaecytisus) BGA‐1, but this effect decreased in the presence of suspensions of live or dead bacterial cells. Th4+ induced the formation of a gel‐like precipitate when added to a dense suspension of B. (Chamaecytisus) BGA‐1 cells. Viable Bradyrhizobium cells remained in suspension after precipitate formation. Thorium was recovered in the precipitate, in which polysaccharide, lipopolysaccharide and proteins were also found. After Th4+ addition, the morphology of B. (Chamaecytisus) BGA‐1 or Bradyrhizobium japonicum USDA 110 sedimented cells studied by scanning electron microscopy changed from an entangled network of capsulated bacteria to uncapsulated individual cells and an amorphous precipitate. Energy‐dispersive X‐ray spectroscopy showed that thorium was mainly in the amorphous fraction. Precipitate was also formed between B. (Chamaecytisus) BGA‐1 and Al3+, which was also toxic to this bacterium. Precipitate induced by Th4+ or Al3+ was found in all Bradyrhizobium and Sinorhizobium strains tested, but not in Rhizobium, Salmonella typhimurium, Aerobacter aerogenes or Escherichia coli. These results suggest a specific defence mechanism based on metal precipitation by extracellular polymers.
Stationary phase mutagenesis: mechanisms that accelerate adaptation of microbial populations under environmental stress
Authors: Kivisaar Maia 
Published: September 2003

SummaryMicroorganisms are exposed to constantly changing environmental conditions. In a growth‐restricting environment (e.g. during starvation), mutants arise that are able to take over the population by a process known as stationary phase mutation. Genetic adaptation of a microbial population under environmental stress involves mechanisms that lead to an elevated mutation rate. Under stressful conditions, DNA synthesis may become more erroneous because of the induction of error‐prone DNA polymerases, resulting in a situation in which DNA repair systems are unable to cope with increasing amounts of DNA lesions. Transposition may also increase genetic variation. One may ask whether the rate of mutation under stressful conditions is elevated as a result of malfunctioning of systems responsible for accuracy or are there specific mechanisms that regulate the rate of mutations under stress. Evidence for the presence of mutagenic pathways that have probably been evolved to control the mutation rate in a cell will be discussed.
Marine prosthecate bacteria involved in the ennoblement of stainless steel
Authors: Baker Paul W. , Ito Kimio , Watanabe Kazuya 
Published: September 2003

SummaryEnnoblement, a phenomenon in which open‐circuit potential is elevated to a noble value, triggers metal corrosion in the environment and is considered to be biologically catalysed. This study investigated the involvement of marine microorganisms in the ennoblement of stainless steel coupons in sea water pumped from Kamaishi Bay. Scanning electron microscopy (SEM) showed significant attachment of prosthecate bacteria on the surfaces of stainless steel coupons in the course of ennoblement. In denaturing gradient gel electrophoresis (DGGE) analyses of polymerase chain reaction‐amplified bacterial 16S rDNA fragments, several major bands were detected from the surface of the ennobled coupons, including those affiliated with the α and γ subclasses of the Proteobacteria. After these observations, bacterial strains were isolated from the surface of the ennobled coupon. The 16S rDNA analysis revealed that a bacterial isolate (designated PWB3) corresponded to a major DGGE band representing an α‐Proteobacterial population; a database analysis showed that its closest relative was Rhodobium spp., albeit with low homology (≈ 89%). SEM indicated that this bacterium was a prosthecate bacterium that was morphologically similar to those observed on the ennobled coupons. In pure culture of strain PWB3, stainless steel coupons were ennobled when the culture was supplemented with MnCl2. Manganese was recovered from the surface of the ennobled coupons after treatment with a reducing agent. These results suggest that the attachment of manganese‐oxidizing prosthecate bacteria triggered the ennoblement of stainless steel in Kamaishi Bay sea water.
Validation of a more sensitive method for using spotted oligonucleotide DNA microarrays for functional genomics studies on bacterial communities
Authors: Denef Vincent J. , Park Joonhong , Rodrigues Jorge L. M. , Tsoi Tamara V. , Hashsham Syed A. , Tiedje James M. 
Published: September 2003

SummarySpotted oligonucleotide microarrays potentially offer a wide scope of applications for microbial ecology, especially as they improve the flexibility of design and the specificity of detection compared to PCR product based microarrays. Sensitivity, however, was expected to be problematic, as studies with the more sensitive PCR‐based cDNA microarrays indicate that only genes from populations contributing to more than 5% of the community DNA can be detected. We evaluated several parameters to increase sensitivity and then tested applicability for bacterial functional genomics. The optimal parameters were the use of 5′‐C6‐amino‐modified 70‐mers printed on CMT‐GAPS II substrates at a 40 µM concentration combined with the use of Tyramide Signal Amplification labelling. This protocol allowed detection of single copy genes belonging to an organism contributing to 1% or more of the total community. To demonstrate its application, we detected the specific aromatic oxygenase genes in a soil community degrading polychlorinated biphenyls (PCBs). This increase in sensitivity is important if oligonucleotide microarrays are to be used for simultaneous monitoring of a range of functions performed by different microorganisms in the environment.
Effect of N‐fertilization, plant genotype and environmental conditions on nifH gene pools in roots of rice
Authors: Tan Zhiyuan , Hurek Thomas , Reinhold‐Hurek Barbara 
Published: September 2003

SummaryTerminal restriction fragment length polymorphism (T‐RFLP) analysis of PCR‐amplified nitrogenase gene (nifH) fragments is a rapid technique for profiling of diazotrophic microbial communities without the necessity of cultures for study. Here, we examined the impact of N‐fertilization, plant genotype and environmental conditions on diazotrophic microbial populations in association with roots of rice (Oryza species) by T‐RFLP community profiling and found marked effects on the composition of the microbial community. We found a rapid change of the diazotrophic population structure within 15 days after application of nitrogen fertilizer and a strong effect of environmental conditions and plant genotype. Control experiments revealed that phylogenetically distantly related nifH genes were proportionately amplified, and that signal strength reflected the relative abundance of nifH genes in the sample within a 10‐fold range of template concentrations. These results clearly demonstrated that our T‐RFLP method was suitable to reflect compositional differences in the diazotrophic community in a semiquantitative manner and that the diazotrophic rhizosphere communities of rice are not static but presumably rather highly dynamic.
A novel pathway for mineralization of the thiocarbamate herbicide molinate by a defined bacterial mixed culture
Authors: Barreiros Luísa , Nogales Balbina , Manaia Célia M. , Ferreira António C. Silva , Pieper Dietmar H. , Reis Maria A. , Nunes Olga C. 
Published: September 2003

SummaryA bacterial mixed culture able to mineralize molinate was established, through enrichment, using mineral medium with molinate as the only carbon, nitrogen and energy source. The combination of five cultivable isolates, purified from the enrichment culture, permitted the reconstitution of a degrading consortium. Both enrichment and defined cultures were able to mineralize molinate without accumulation of degradation products by the end of the growth. Among the five isolates constituting the defined mixed culture, an actinomycete, strain ON4, was essential for biodegradation, being involved in the cleavage of the thioester bond of molinate, the initial step of the degradation pathway. Isolate ON4 was able to grow on molinate at concentrations below 2 mM, with the accumulation of ethanethiol and diethyl disulphide. These sulphur compounds were toxic to strain ON4 when accumulating at higher concentrations. However, this inhibitory effect was avoided by the presence of other members of the mixed culture, out of which isolates ON1 and ON2 were observed to consume ethanethiol and diethyl disulphide. In this way, interactions among defined mixed culture members involve metabolic and detoxifying association.
Novel Proteorhodopsin variants from the Mediterranean and Red Seas
Authors: Sabehi Gazalah , Massana Ramon , Bielawski Joseph P. , Rosenberg Mira , Delong Edward F. , Béjà Oded 
Published: September 2003

SummaryProteorhodopsins, ubiquitous retinylidene photoactive proton pumps, were recently found in the widespread uncultured SAR86 bacterial group in oceanic surface waters. To survey proteorhodopsin diversity, new degenerate sets of proteorhodopsin primers were designed based on a genomic proteorhodopsin gene sequence originating from an Antarctic fosmid library. New proteorhodopsin variants were identified in Red Sea samples that were most similar to the original green‐light absorbing proteorhodopsins found in Monterey Bay California. Unlike green‐absorbing proteorhodopsins however, these new variants contained a glutamine residue at position 105, the same site recently shown to control spectral tuning in naturally occurring proteorhodopsins. Different proteorhodopsin variants were also found in the Mediterranean Sea. These proteorhodopsins formed new and distinctive proteorhodopsin groups. Phylogenetic analyses show that some of the new variants were very different from previously characterized proteorhodopsins, and formed the deepest branching groups found so far among marine proteorhodopsins. The existence of these varied proteorhodopsin sequences suggests that this class of proteins has undergone substantial evolution. These variants could represent functionally divergent paralogous genes, derived from the same or similar species, or orthologous proteorhodopsins that are distributed amongst divergent planktonic microbial taxa.
Microbially mediated sulphide production in a thermal, acidic algal mat community in Yellowstone National Park
Authors: Ferris Michael J. , Magnuson Timothy S. , Fagg Jennifer A. , Thar Roland , Kühl Michael , Sheehan Kathy B. , Henson Joan M. 
Published: September 2003

SummaryOur objective in this study was to characterize prokaryotic sulphide production within the oxygenic, predominantly eukaryotic algal mat in an acidic stream, Nymph Creek, in Yellowstone National Park (YNP). We used microsensors to examine fluctuations in H2S and O2 concentrations over time through the vertical aspect of the ∼3 mm mat in a 46–48°C region of the creek. We also used analyses of PCR‐amplified 16S rRNA gene sequences obtained from denaturing gradient gels, and PCR‐amplified sequences of a functional gene associated with microbial sulphate respiration (dsrA) to characterize the bacterial community in the same region of the mat. During midday, photosynthesis rates were high within the first 500 µm interval of the mat and high oxygen concentrations (600% air saturation) penetrated deeply (>1800 µm) into the mat. During early evening and night, oxygen concentrations within the first 1100 µm of the mat decreased over time from 60% air saturation (a.s) to 12% a.s. A precipitous decline in oxygen concentration occurred at a depth of 1100 µm in all night measurements and anoxic conditions were present below 1200 µm. Within this anoxic region, sulphide concentrations increased from nearly 0 µM at 1200 µm depth to 100 µM at 2400 µm depth. Enrichment cultures inoculated with Nymph Creek mat organisms also produced H2S. Sequence analyses of 16S rRNA and dsrA genes indicated the presence of at least five bacterial genera including species involved in dissimilative sulphate or sulphur reduction.
Bacterial diversity in hydrothermal sediment and epsilonproteobacterial dominance in experimental microcolonizers at the Mid‐Atlantic Ridge
Authors: López‐García Purificación , Duperron Sébastien , Philippot Pascal , Foriel Julien , Susini Jean , Moreira David 
Published: September 2003

SummaryWe report here a molecular survey based on 16S rRNA genes of the bacterial diversity found in two deep‐sea vent niches at the Mid‐Atlantic Ridge: hydrothermal sediment (Rainbow site), and microcolonizers made of three different substrates (organic‐rich, iron‐rich and pumice) that were exposed for 15 days to a vent emission. Bacterial diversity in sediment samples was scattered through many bacterial divisions. The most abundant and diverse environmental sequences (phylotypes) in our libraries corresponded to the Gammaproteobacteria, followed by the Acidobacteria. We detected members of all the subdivisions within the Proteobacteria. Myxobacterial lineages were the most represented within the delta subdivision. Phylotypes ascribing to the Cytophaga‐Flavobacterium‐Bacteroides, Planctomycetales, high and low G + C Gram‐positives, Nitrospirae, and the candidate division TM7 were also identified. Compared to this broad taxonomic coverage, microcolonizers were almost exclusively colonized by epsilonproteobacteria, although these exhibited considerable morphological and phylogenetic in‐group diversity. No specificity for any of the substrates tested was seen. This observation further supports the idea of the ecological dominance of epsilonproteobacteria in the fluid–seawater interface environment. Because oxidation of reduced S species and/or sulphur‐reduction is thought to be essential for their energetic metabolism in these areas, we mapped different oxidation states of S in individual bacterial filaments from the iron‐rich microcolonizer. For this, we used high‐resolution, non‐destructive synchrotron micro‐X‐ray Absorption Near‐Edge Spectroscopy (micro‐XANES), which revealed the co‐existence of different S oxidation states, from sulphide to sulphate, at the level of individual cells. This suggests that these cells were metabolizing sulphur in situ.
Microbial characterization of the Mars Odyssey spacecraft and its encapsulation facility
Authors: La Duc Myron T. , Nicholson Wayne , Kern Roger , Venkateswaran Kasthuri 
Published: September 2003

SummaryMicrobial characterization of the Mars Odyssey spacecraft and the Kennedy Space Center Spacecraft Assembly and Encapsulation Facility II (SAEF‐II) was carried out by both culture‐based and molecular methods. The most dominant cultivable microbes were species of Bacillus, with comamonads, microbacteria and actinomycetales also represented. Several spore‐forming isolates were resistant to γ‐radiation, UV, H2O2 and desiccation, and one Acinetobacter radioresistens isolate and several Aureobasidium, isolated directly from the spacecraft, survived various conditions. Sequences arising in clone libraries were fairly consistent between the spacecraft and facility; predominant genera included Variovorax, Ralstonia and Aquaspirillum. This study improves our understanding of the microbial community structure, diversity and survival capabilities of microbes in an encapsulation facility and physically associated with colocated spacecraft.