Microbial Activity of Soil Following Steam Treatment

The effect of steam treatment on subsurface aerobic and anaerobic microbial communities was investigated using multiple microbial assays. Soil samples were gathered and analyzed prior to, one month after, and eight months after a five-month field pilot test of steam injection and extraction. Aerobic soil samples were analyzed by respirometry, plate counts, and direct microscopic counts. Anaerobic microbial activity was examined by monitoring methane generation in anaerobic microcosms with gas chromatography. Respirometry showed pre-steam CO2 production was consistent with natural attenuation, post-steam (one month) CO2 production was below detection, and post-steam (eight months) CO2 production was about half of pre-steam. Post-steam (one and eight month) plate counts were one to four orders of magnitude lower than the pre-steam samples. Direct microscopic counts showed post-steam (one and eight month) cell numbers were higher than the pre-steam counts, but based on plate counts these cells were mostly non-viable. Significant amounts of methane and hydrogen were generated from pre-steam anaerobic microcosms, but post-steam microcosms had no detectable methane, and only trace amounts of hydrogen. Terminal restriction fragment (TRF) analysis was performed to determine the diversity of the microbial community before and after steam treatment. Pre-steam TRF analysis showed distinct differences in the microbial communities above and below the smear zone. Post-steam TRF analyses were not possible because insufficient DNA could be extracted from the soil

Complete Genomic Sequence of Bacteriophage B3, a Mu-Like Phage of \u3ci\u3ePseudomonas aeruginosa\u3c/i\u3e

Bacteriophage B3 is a transposable phage of Pseudomonas aeruginosa. In this report, we present the complete DNA sequence and annotation of the B3 genome. DNA sequence analysis revealed that the B3 genome is 38,439 bp long with a G+C content of 63.3%. The genome contains 59 proposed open reading frames (ORFs) organized into at least three operons. Of these ORFs, the predicted proteins from 41 ORFs (68%) display significant similarity to other phage or bacterial proteins. Many of the predicted B3 proteins are homologous to those encoded by the early genes and head genes of Mu and Mu-like prophages found in sequenced bacterial genomes. Only two of the predicted B3 tail proteins are homologous to other well-characterized phage tail proteins; however, several Mu-like prophages and transposable phage D3112 encode approximately 10 highly similar proteins in their predicted tail gene regions. Comparison of the B3 genomic organization with that of Mu revealed evidence of multiple genetic rearrangements, the most notable being the inversion of the proposed B3 immunity/early gene region, the loss of Mu-like tail genes, and an extreme leftward shift of the B3 DNA modification gene cluster. These differences illustrate and support the widely held view that tailed phages are genetic mosaics arising by the exchange of functional modules within a diverse genetic pool

Diversity of Microorganisms Isolated from Amber

Claims that organisms can be cultured from amber, if substantiated, would be significant contributions to our understanding of the evolution, tenacity, and potential spread of life. Three reports on the isolation of organisms from amber have been published. Cano and Borucki recently reported the isolation of Bacillus sphaericus and Lambert et al. have described a new species designated Staphylococcus succinus from 25–40 million year old Dominican amber. These characterized organisms were phylogenetically distant from extant relatives and the Staphylococcus sp. sufficiently far removed from other extant staphylococci to be considered a new species. Here we report the culture of bacteria from Dominican and previously untested 120 million year old Israeli (Lebanese lode) amber. Twenty-seven isolates from the amber matrix have been characterized by fatty-acid profiles (FAME) and/or 16S rRNA sequencing. We also performed a terminal restriction fragment pattern (TRF) analysis of the original amber before prolonged culture by consensus primer amplification of the 16S rRNA followed by restriction enzyme digestion of the amplicons. Sample TRFs were consistent with a sparse bacterial assemblage and included at least five of the isolated organisms. Finally, we microscopically mapped the internal topography of an amber slice

Nanosail-D: The Small Satellite That Could!

Three years from its initial design review, NanoSail-D successfully deployed its sail on January 20th, 2011. It became the first solar sail vehicle to orbit the earth and the second sail ever unfurled in space. The NanoSail-D mission had two main objectives: eject a nanosatellite from a microsatellite; deploy its sail from a highly compacted volume and low mass system to validate large structure deployment and potential de-orbit technologies. These objectives were successfully achieved and the de-orbit analysis is in process. This paper presents an overview of the NanoSail-D project and insights into how potential setbacks were overcome. Many lessons have been learned during these past three years and are discussed in light of the phenomenal success and interest that this small satellite has generated. NanoSail-D was jointly designed and built by NASA's Marshall Space Flight Center and NASA's Ames Research Center. ManTech/NeXolve Corporation also provided key sail design support. The NanoSail-D experiment is managed by Marshall and jointly sponsored by the Army Space and Missile Defense Command, the Von Braun Center for Science and Innovation and Dynetics Inc. Ground operations support was provided by Santa Clara University, with radio beacon packets received from amateur operators around the world

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Terminal Restriction Fragment Patterns: A Tool for Comparing Microbial Communities and Assessing Community Dynamics

Terminal Restriction Fragment (TRF) patterns, also known as Terminal Restriction Fragment Length Polymorphisms (T-RFLP), are a recently introduced PCR-based tool for studying microbial community structure and dynamics. Since the first review of TRF methodology (Marsh, 1999. Curr. Op. Microbiol. 2: 323-7), at least 35 new research articles were published that include this powerful tool in some part of their reports. This review covers some of the applications that TRF patterns were used for and provides a discussion of how to create and analyze TRF pattern data. This data has the advantage of being simply and rapidly produced using standard DNA sequencing equipment. The raw data are automatically converted to a digitized form that can be easily analyzed with a variety of multivariate statistical techniques. The identification of specific elements in a TRF pattern is possible by comparison to entries in a good sequence database or by comparison to a clone library. As an added advantage when investigating complex microbial communities such as those in soils and intestines, TRF patterns are recognized as having better resolution than other DNA-based methods for evaluating community structure

Variation Between Observed and True Terminal Restriction Fragment Length is Dependent on True TRF Length and Purine Content

Terminal Restriction Fragment (TRF) pattern analysis has become a widely used and informative tool for studying microbial communities. Variation between sequence-determined or true TRF length and observed TRF length (TRF drift) has been previously reported and can significantly affect identification of bacterial species using TRF lengths predicted from sequence databases. In this study TRF drift was determined for 21 bacterial species using an ABI 310 Genetic Analyzer. TRF drift was positively correlated with true TRF length and negatively correlated with TRF purine content. This implies that subtle differences in molecular weight, whether from purine content or dye label, can significantly affect the observed TRF length

Bacterial Succession in a Petroleum Land Treatment Unit

Bacterial community dynamics were investigated in a land treatment unit (LTU) established at a site contaminated with highly weathered petroleum hydrocarbons in the C(10) to C(32) range. The treatment plot, 3,000 cubic yards of soil, was supplemented with nutrients and monitored weekly for total petroleum hydrocarbons (TPH), soil water content, nutrient levels, and aerobic heterotrophic bacterial counts. Weekly soil samples were analyzed with 16S rRNA gene terminal restriction fragment (TRF) analysis to monitor bacterial community structure and dynamics during bioremediation. TPH degradation was rapid during the first 3 weeks and slowed for the remainder of the 24-week project. A sharp increase in plate counts was reported during the first 3 weeks, indicating an increase in biomass associated with petroleum degradation. Principal components analysis of TRF patterns revealed a series of sample clusters describing bacterial succession during the study. The largest shifts in bacterial community structure began as the TPH degradation rate slowed and the bacterial cell counts decreased. For the purpose of analyzing bacterial dynamics, phylotypes were generated by associating TRFs from three enzyme digests with 16S rRNA gene clones. Two phylotypes associated with Flavobacterium and Pseudomonas were dominant in TRF patterns from samples during rapid TPH degradation. After the TPH degradation rate slowed, four other phylotypes gained dominance in the community while Flavobacterium and Pseudomonas phylotypes decreased in abundance. These data suggest that specific phylotypes of bacteria were associated with the different phases of petroleum degradation in the LTU

Weathering Effects on Biodegradation and Toxicity of Hydrocarbons in Groundwater

This study examined the effect of weathering on hydrocarbon biodegradation and toxicity at a former oil field near Guadalupe, California. Soil and groundwater at this site contains residual diesel-range hydrocarbons formerly used to dilute the viscous crude oil to facilitate pumping (Lundegard and Garcia, 2001). Natural attenuation is being considered at this site as a means of remediating residual hydrocarbons in soil and groundwater. To provide the lines of evidence required for use of natural attenuation at this site, this research was undertaken to determine if the hydrocarbons continue to be biodegradable after extensive weathering in the field. Observed hydrocarbon biodegradation rates were directly proportional to initial total petroleum hydrocarbon (TPH) con-centration, suggesting first-order kinetics. Highly weathered hydrocarbons most distant downgradient from the source zones exhibited slightly lower biodegradation rate con-stants. Microtox® toxicity decreased rapidly during 20 days of biodegradation in laboratory microcosms