BackgroundDespite the decades-long use of Bacillus atrophaeus var. globigii (BG) as a simulant for biological warfare (BW) agents, knowledge of its genome composition is limited. Furthermore, the ability to differentiate signatures of deliberate adaptation and selection from natural variation is lacking for most bacterial agents. We characterized a lineage of BGwith a long history of use as a simulant for BW operations, focusing on classical bacteriological markers, metabolic profiling and whole-genome shotgun sequencing (WGS).ResultsArchival strains and two “present day” type strains were compared to simulant strains on different laboratory media. Several of the samples produced multiple colony morphotypes that differed from that of an archival isolate. To trace the microevolutionary history of these isolates, we obtained WGS data for several archival and present-day strains and morphotypes. Bacillus-wide phylogenetic analysis identified B. subtilis as the nearest neighbor to B. atrophaeus. The genome of B. atrophaeus is, on average, 86% identical to B. subtilis on the nucleotide level. WGS of variants revealed that several strains were mixed but highly related populations and uncovered a progressive accumulation of mutations among the “military” isolates. Metabolic profiling and microscopic examination of bacterial cultures revealed enhanced growth of “military” isolates on lactate-containing media, and showed that the “military” strains exhibited a hypersporulating phenotype.ConclusionsOur analysis revealed the genomic and phenotypic signatures of strain adaptation and deliberate selection for traits that were desirable in a simulant organism. Together, these results demonstrate the power of whole-genome and modern systems-level approaches to characterize microbial lineages to develop and validate forensic markers for strain discrimination and reveal signatures of deliberate adaptation.

g Desulfosporosinus species are sulfate-reducing bacteria belonging to the Firmicutes. Their genomes will give insights into the genetic repertoire and evolution of sulfate reducers typically thriving in terrestrial environments and able to degrade toluene (Desulfosporosinus youngiae), to reduce Fe(III) (Desulfosporosinus meridiei, Desulfosporosinus orientis), and to grow under acidic conditions (Desulfosporosinus acidiphilus).T he sequenced Desulfosporosinus type strains (2,3,14,20) represent four out of eight described species belonging to the genus Desulfosporosinus and cover its phylogenetic and physiological breadth. Besides their ability to reduce sulfate for energy conservation, some Desulfosporosinus species can also grow by using nitrate, Fe(III), or As(V) as terminal electron acceptors or by fermentative processes. They can utilize a wide spectrum of energy sources, ranging from aromatic compounds to short-chained fatty acids. A characteristic feature of many Desulfosporosinus species, distinguishing them from their closest sulfate-reducing relatives of the genus Desulfotomaculum, is their ability to grow chemolithoautotrophically on hydrogen (3,14,15,19,(21)(22)(23). Members of the genus Desulfosporosinus are found in low-sulfate freshwater and soil environments but also in sulfate-rich heavymetal-contaminated environments, such as acid mine/rock drainage sites. In addition, Desulfosporosinus species are often observed in low-pH habitats (1, 3, 5-7, 12, 13, 17, 18), with the sequenced Desulfosporosinus acidiphilus strain being the first validly described sulfate-reducing acidophile (3).Genomic DNA was isolated using the Jetflex genomic DNA purification kit (GENOMED, Löhne, Germany) and subjected to sequencing using a combination of 454 Titanium (16) and Illumina (4) technologies. Sequences were assembled with Newbler (version 2.3-PreRelease-6/30/2009) and Velvet (version 1.0.13) (24) for 454 and Illumina data, respectively. Consensus sequences were obtained using computationally shredded Illumina and 454 reads together with 454 paired-end data using parallel Phrap (version SPS-4.24; High Performance Software, LLC). Identification of sequencing errors and improvement of consensus quality were done with Polisher (A. Lapidus, unpublished data) using Illumina data. GapResolution (C. Han, unpublished data), Dupfinisher (11), or sequencing cloned bridging PCR fragments with subcloning were used to correct misassemblies. Gaps between contigs were closed by editing in Consed (8-10), by PCR, and by Bubble PCR (J.-F. Cheng, unpublished data) primer walks. Automated genome annotation was performed at the Oak Ridge National Laboratory and is available at http://genome.ornl.gov/.The circular chromosomes of Desulfosporosinus orientis, Desulfosporosinus youngiae, Desulfosporosinus meridiei, and D. acidiphilus have sizes of 5,863,081 bp, 5,660,978 bp, 4,873,567 bp, and 4,926,837 bp, respectively. The genome of D. acidiphilus additionally harbors two plasmids of 60,447 bp and 3,897 bp. The genomes, in the order listed...

We present the complete genome assembly of Escherichia coli ATCC 25922 as submitted to NCBI under accession no. CP009072. This strain was originally isolated from a clinical sample in Seattle, Washington (1946), and is often used in quality control testing. The assembled genome is 5.20 Mb (50.4% G+C content) and includes two plasmids.

Among the bacteria, members of the order are considered quintessential degraders of complex polysaccharides in soils. However, studies examining complex polysaccharide degradation by (other than spp.) in soils are limited. Here, we examine the lignocellulolytic and chitinolytic potential of 112 strains, encompassing 13 families, isolated from a semiarid grassland of the Colorado Plateau in Utah. Members of the ,, , and families exhibited robust activity against carboxymethyl cellulose, xylan, chitin, and pectin substrates (except for low/no pectinase activity by the). When incubated in a hydrated mixture of blended and grass biomass over a 5-week period, and (a member of the ) isolates produced high levels of extracellular enzyme activity, such as endo- and exocellulase, glucosidase, endo- and exoxylosidase, and arabinofuranosidase. These characteristics make them well suited to degrade the cellulose and hemicellulose components of grass cell walls. On the basis of the polysaccharide degradation profiles of the isolates, relative abundance of sequences in 16S rRNA gene surveys of Colorado Plateau soils, and analysis of genes coding for polysaccharide-degrading enzymes among 237 genomes in the CAZy database and 5 genomes from our isolates, we posit that spp. and select members of the and likely play an important role in the degradation of hemicellulose, cellulose, and chitin substances in dryland soils. Shifts in the relative abundance of taxa have been observed in soil microbial community surveys during large, manipulated climate change field studies. However, our limited understanding of the ecophysiology of diverse taxa in soil systems undermines attempts to determine the underlying causes of the population shifts or their impact on carbon cycling in soil. This study combines a systematic analysis of the polysaccharide degradation potential of a diverse collection of isolates from surface soils of a semiarid grassland with analysis of genomes from five of these isolates and publicly available genomes for genes encoding polysaccharide-active enzymes. The results address an important gap in knowledge of ecophysiology-identification of key taxa capable of facilitating lignocellulose degradation in dryland soils. Information from this study will benefit future metagenomic studies related to carbon cycling in dryland soils by providing a baseline linkage of phylogeny with lignocellulolytic functional potential.