The genome of deep-sea vent chemolithoautotroph Thiomicrospira crunogena XCL-2.

Presented here is the complete genome sequence of Thiomicrospira crunogena XCL-2, representative of ubiquitous chemolithoautotrophic sulfur-oxidizing bacteria isolated from deep-sea hydrothermal vents. This gammaproteobacterium has a single chromosome (2,427,734 base pairs), and its genome illustrates many of the adaptations that have enabled it to thrive at vents globally. It has 14 methyl-accepting chemotaxis protein genes, including four that may assist in positioning it in the redoxcline. A relative abundance of coding sequences (CDSs) encoding regulatory proteins likely control the expression of genes encoding carboxysomes, multiple dissolved inorganic nitrogen and phosphate transporters, as well as a phosphonate operon, which provide this species with a variety of options for acquiring these substrates from the environment. Thiom. crunogena XCL-2 is unusual among obligate sulfur-oxidizing bacteria in relying on the Sox system for the oxidation of reduced sulfur compounds. The genome has characteristics consistent with an obligately chemolithoautotrophic lifestyle, including few transporters predicted to have organic allocrits, and Calvin-Benson-Bassham cycle CDSs scattered throughout the genome.

The effectiveness of soil amendments, biochar and lime, in mitigating cadmium bioaccumulation in Theobroma cacao L.

Cocoa (Theobroma cacao L.) is an important neotropical tree crop grown for its seeds or beans used in global chocolate and confectionary industries. Following studies showing ill effects of long-term dietary exposure of cadmium (Cd) on human health, a number of countries including the European Union (EU) have developed stringent regulations to protect consumers from exposure to cadmium. Cocoa is capable of bioaccumulating Cd in the cocoa beans when grown in soils high in cadmium and hence livelihood of cocoa farmers can be at risk if methods to mitigate the bioaccumulation of Cd are not developed. In vitro, greenhouse and field experiments were established with four, three and three replications respectively to evaluate the effectiveness of soil amendments, biochar and lime, at various application rates (0, 0.5×, 1×, 1.5× and 2× of the recommended rate), on soil pH, Cd phytoavailability and Cd bioaccumulation in Theobroma cacao L. For the in vitro study, Cd-containing soil was amended with 5 levels of biochar and lime, while for the greenhouse and field study four application rates were tested. The study showed that while lower rates were effective under in vitro conditions as you progressed from in vitro to greenhouse to field conditions the application rates and application frequency had to be increased, as the effectiveness and longevity of the treatments were compromised by environmental factors. Our study implies that the two amendments were complementary in their action and can be used in the recommended rated to reduce Cd bioaccumulation. However further studies are required on the placement of amendments to improve their effectiveness and longevity particularly under field conditions.

Two-year study evaluating the potential loss of methicillin resistance in a methicillin-resistant Staphylococcus aureus culture collection.

A reported loss of mecA prompted us to monitor 360 cryostocked methicillin-resistant Staphylococcus aureus strains for stability. Concurrently, 14 well-characterized strains were stored in a Microbank preservation system and subjected to multiple freeze-thaw events. There were no significant declines in the methicillin-resistant populations with either method over a two-year period.

Molecular characterization of Vibrio parahaemolyticus strains associated with foodborne illness in Florida.

Vibrio parahaemolyticus is the leading cause of bacterial seafood-based illness in the United States. Real-time PCR, pandemic group-specific PCR, ribotyping, and multilocus sequence typing were used to characterize 30 strains of V. parahaemolyticus including 11 strains associated with foodborne outbreaks in Florida and 6 known pandemic strains. Thirteen strains were positive for four pandemic group-specific PCR markers, including 5 strains associated with outbreaks in Florida. Molecular typing methods were used to further define the pandemic status of these strains because the current PCR markers are not sufficient to identify pandemic isolates. Nine of the Florida strains clustered with a majority of the known pandemic strains, based on ribotyping patterns using PvuII, but no isolated pandemic branch was formed. Using multilocus sequence typing, it was determined that 14 strains possess a previously determined pandemic sequence type. This study identified 13 novel sequence types and seven to nine novel alleles for each locus. Furthermore, the results indicate that seven of the strains from recent foodborne outbreaks in Florida are pandemic strains, and that multilocus sequence typing was the most accurate molecular method to identify these strains.

Real-time PCR detection of the thermostable direct hemolysin and thermolabile hemolysin genes in a Vibrio parahaemolyticus cultured from mussels and mussel homogenate associated with a foodborne outbreak.

Molecular methods have become vital epidemiological tools in the detection and characterization of bacteria associated with a foodborne outbreak. We used both culture and real-time PCR to detect a Vibrio parahaemolyticus isolate associated with a foodborne outbreak. The outbreak occurred in July 2002 in Polk County, Florida, and originated at a Chinese buffet, with one person being hospitalized. The hospital isolated V. parahaemolyticus from the patient but destroyed the sample after diagnosis. From an onsite visit of the restaurant, food samples that possibly contributed to the outbreak were collected and sent to the Florida Department of Health, Tampa Branch Laboratory. Crab legs, crabsticks, and mussel samples were homogenized and incubated according to the Food and Drug Administration Bacteriological Analytical Manual culture protocol. Three sets of primers and a TaqMan probe were designed to target the tdh, trh, and tlh genes and used for real-time PCR. This study was successful in isolating V. parahaemolyticus from a mussel sample and detecting two of its genes (tdh and tlh) in food and pure culture by real-time PCR.

2,3,7,8-Tetrachlorodibenzo-p-dioxin: its effect on genes for mandible traits in mice.

2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) is a powerful toxicant that exerts its effects through the aryl hydrocarbon receptor (AHR) governed by the Ahr locus that in mice is located on chromosome 12. We used single marker analyses of the offspring of female mice treated/not treated with TCDD to search for a gene (quantitative trait locus or QTL) on chromosome 12 near the site of the Ahr locus to test whether this locus appeared to affect mandible size, shape, and/or asymmetry especially in the treated mice. These mice were sampled from the F(2) generation of an original intercross of two strains (C57BL/6J and AKR/J) known to be divergent in their response to TCDD. A QTL affecting mandible shape was found on chromosome 12, but its effect on mice in the treated and control groups did not differ and it was concluded that this QTL probably was not the Ahr locus itself. We also probed a second chromosome (11) and found a QTL whose effects on asymmetry of mandible shape differed in the two environments. These results suggested that the entire genome in these mice should be scanned to search for additional QTLs that might be affected by TCDD to learn more about the potential effects of this powerful toxicant on these genes.

Novel sample preparation method for safe and rapid detection of Bacillus anthracis spores in environmental powders and nasal swabs.

Bacillus anthracis spores have been used as a biological weapon in the United States. We wanted to develop a safe, rapid method of sample preparation that provided safe DNA for the detection of spores in environmental and clinical specimens. Our method reproducibly detects B. anthracis in samples containing <10 spores.

Comparison of methods for DNA isolation from food samples for detection of Shiga toxin-producing Escherichia coli by real-time PCR.

In this study, food samples were intentionally contaminated with Escherichia coli O157:H7, and then DNA was isolated by using four commercial kits. The isolated DNA samples were compared by using real-time PCR detection of the Shiga toxin genes. The four kits tested worked similarly.