The influence of soil properties on the structure of bacterial and fungal communities across land-use types

Land-use change can have significant impacts on soil conditions and microbial communities are likely to respond to these changes. However, such responses are poorly characterized as few studies have examined how specific changes in edaphic characteristics do, or do not, influence the composition of soil bacterial and fungal communities across land-use types. Soil samples were collected from four replicated (n = 3) land-use types (hardwood and pine forests, cultivated and livestock pasture lands) in the southeastern US to assess the effects of land-use change on microbial community structure and distribution. We used quantitative PCR to estimate bacterial–fungal ratios and clone libraries targeting small-subunit rRNA genes to independently characterize the bacterial and fungal communities. Although some soil properties (soil texture and nutrient status) did significantly differ across land-use types, other edaphic factors (e.g., pH) did not vary consistently with land-use. Bacterial–fungal ratios were not significantly different across the land-uses and distinct land-use types did not necessarily harbor distinct soil fungal or bacterial communities. Rather, the composition of bacterial and fungal communities was most strongly correlated with specific soil properties. Soil pH was the best predictor of bacterial community composition across this landscape while fungal community composition was most closely associated with changes in soil nutrient status. Together these results suggest that specific changes in edaphic properties, not necessarily land-use type itself, may best predict shifts in microbial community composition across a given landscape. In addition, our results demonstrate the utility of using sequence-based approaches to concurrently analyze bacterial and fungal communities as such analyses provide detailed phylogenetic information on individual communities and permit the robust assessment of the biogeographical patterns exhibited by soil microbial communities.     

Evaluation of equine breeding farm characteristics as risk factors for development of Rhodococcus equi pneumonia in foals

OBJECTIVE: To identify farm characteristics as risk factors for the development of Rhodococcus equi pneumonia in foals. DESIGN: Prospective matched case-control study. ANIMALS: 2,764 foals on 64 equine breeding farms with 9,991 horses. PROCEDURE: During 1997, participating veterinarians completed paired data collection forms, 1 for a farm with > or = 1 foal with R equi pneumonia and 1 for an unaffected control farm. Matched data were compared by use of conditional logistic regression analysis. RESULTS: Farm characteristics found in bivariate analyses to be associated with increased risk for pneumonia caused by R equi in foals included > 200 farm acres, > or = 60 acres used in the husbandry of horses, > 160 horses, > or = 10 mares housed permanently on the farm (resident mares), > 17 foals, > 0.25 foals/acre, and the presence of transient mares (mares brought temporarily to the farm for breeding or foaling) and their foals. Affected farms were significantly more likely to be > 200 acres in size and have > or = 10 resident dam-foal pairs, whereas control farms were significantly more likely to have > or = 75% of their dam-foal pairs housed permanently on the farm. CONCLUSIONS AND CLINICAL RELEVANCE: Breeding farms with large acreage, a large number of mares and foals, high foal density, and a population of transient mares and foals are at high risk for foals developing pneumonia caused by R equi.     

Association of racing performance with specific abnormal radiographic findings in Thoroughbred yearlings sold in Texas

The objective of this prospective study was to determine the association between presence of abnormal radiographic findings attributed to orthopedic disorders of development (ARF) with subsequent performance among yearlings in Texas. The study population was 348 yearlings offered for sale at the Texas Summer Yearling Sale during 2002 and 2003 for which presale radiographs of limbs were available for review. Radiographs of yearlings were reviewed and presence of ARF were recorded. Additionally, the following data were recorded for each horse: identifiers [name of dam, name of sire, hip number, and name (when available)], year of sale, state of birth, and sales price. Subsequent performance data were obtained for each horse at the conclusion of their 2^nd and 3^rd years of life. Results indicated that no ARF was significantly associated with performance outcomes. Lesions of the proximal dorsal aspect of the sagittal ridge of the 3^rd metacarpus/metatarsus resulted in significantly lower sales prices than either horses without this ARF or horses without any ARF. In conclusion, multiple radiographic abnormalities of Thoroughbred yearlings were not associated with reduced performance during the first 2 years of the racing careers of horses studied. Presence of some abnormalities, however, may be associated with reduced sales price.     

Factors Associated with Survival in Septicemic Foals: 65 Cases (1988–1995)

In order to identify variables obtained at admission that could be used to predict survival in septicemic foals, medical records of 65 foals diagnosed with septicemia were reviewed. Initially, variables were analyzed independently (univariate analysis) for association with survival. Of the physical examination and historical data examined using univariate analysis, the ability to stand at admission, respiratory rate ≥ 60 breaths per minute (bpm), and normal-appearing mucous membranes were significantly associated with survival. Foals with history of induced parturition were significantly less likely to survive. The following hematologic and serum biochemical variables determined at admission were significantly associated with survival: white blood cell count a 6,000 cells/μL, neutrophil count <4,000 cells/μL, serum albumin concentration <2.2 g/dL, serum glucose concentration <120 mg/ dL, blood pH ≥ 7.35, and positive base excess. The administration of plasma at admission was significantly associated with survival. Stepwise multiple logistic regression analysis was performed to evaluate the association between survival and variables identified as significantly associated with survival in bivariate analysis. The final multivariate model selected included the variables standing, duration of clinical signs (24-hour intervals) prior to admission, respiratory rate a 60 bpm, neutropenia (> 4,000 cells/μL), and neonatal age category. The probability of survival was significantly increased for foals that were standing, had a respiratory rate a 60 bpm, and that had a neutrophil count <4,000 cells/μL at admission. Probability of survival was significantly decreased for foals that had a longer duration of clinical signs prior to admission. For each 24 hours of duration, the estimated risk of death was increased by 5.8-fold.     

Seasonal Variations in Vertical Redox Stratification and Potential Influence on Trace Metal Speciation in Minerotrophic Peat Sediments

Seasonal variations in pore water and solid phase geochemistry were investigated in urbanized minerotrophic peat sediments located in southwestern Michigan, USA. Sediment pore waters were collected anaerobically, using pore water equilibrators with dialysis membranes (“peepers”) and analyzed for pH, alkalinity, dissolved ΣPO₄ ^?3, ΣNH₄ ⁺, ΣS^?2, SO₄ ^?2, Fe⁺³, Fe⁺², and Mn⁺² at 1-2 cm intervals to a depth of 50 cm. Cores collected adjacent to the peepers during all four seasons were analyzed for reactive solid phase Fe according to extraction methods proposed by Kostka and Luther (1994). The association of Fe and trace metals (Mn, Pb, Zn, Cu, Cr, Co, Cd, U) with operationally defined solid phase fractions (carbonates, iron and manganese oxides, sulfides/organics and residual) was assessed for cores extracted during winter and spring using extraction methods proposed by Tessier et al. (1979, 1982). Pore water Fe and S data demonstrate a clear seasonal variation in redox stratification of these sediments. The redox stratification becomes more compressed in spring and summer, with relatively more reducing conditions closer to the sediment water interface (SWI), and less reducing conditions near the SWI in fall and winter. In the upper 10–15 cm of sediment, the pool of ascorbate extractable Fe, thought to be indicative of reactive Fe(III) oxides, diminishes during spring and summer, in agreement with seasonal changes in redox stratification indicated by the pore water data. Tessier extractions indicate that the total extractable quantity of all metals analyzed in this study decrease with depth, and that the majority of the non-residual Fe, Pb, Zn, Cu, Cr, Co, Cd, and U is typically associated with the sulfide/organic fraction of the sediments at all depths. Non-residual Mn, in contrast, is significantly associated with carbonates in the upper 15–25 cm of the sediment, and predominantly associated with the sulfide/organic fraction only in deeper sediments.     

Genetic structure of human populations

We studied human population structure using genotypes at 377 autosomal microsatellite loci in 1056 individuals from 52 populations. Within-population differences among individuals account for 93 to 95% of genetic variation; differences among major groups constitute only 3 to 5%. Nevertheless, without using prior information about the origins of individuals, we identified six main genetic clusters, five of which correspond to major geographic regions, and subclusters that often correspond to individual populations. General agreement of genetic and predefined populations suggests that self-reported ancestry can facilitate assessments of epidemiological risks but does not obviate the need to use genetic information in genetic association studies.     

Adsorption of cadmium to kaolinite in the presence of organic material

Kaolinite was equilibrated with Cd and with varying amounts of the individual compounds: EDTA, NTA, alginic acid, and humic acid. In experiments in which the Cd and kaolinite concentrations were held constant, and the ligand concentration allowed to vary, conditions under which ligand enhanced and inhibited Cd association with the solid phase were noted. Further experiments at constant Cd: ligand confirmed that, for alginic acid and humic acid, enhancement of uptake occurred, while EDTA diminished uptake. These results were compared with the adsorption of ligand by clay in the absence of organic, and it is suggested that the enhancement of uptake is due to the formation of an adsorbed organic layer on the clay serving as a solid phase ligand.     

Evaluation of a multiplex polymerase chain reaction assay for simultaneous detection of Rhodococcus equi and the vapA gene

OBJECTIVE: To evaluate sensitivity and specificity of a multiplex polymerase chain reaction (PCR) assay for simultaneous detection of Rhodococcus equi and differentiation of strains that contain the virulence-associated gene (vapA) from strains that do not. SAMPLE POPULATION: 187 isolates of R equi from equine and nonequine tissue and environmental specimens and 27 isolates of bacterial species genetically or morphologically similar to R equi. PROCEDURE: The multiplex PCR assay included 3 gene targets: a universal 311-bp bacterial 16S ribosomal RNA amplicon (positive internal control), a 959-bp R equi-specific target in the cholesterol oxidase gene (choE), and a 564-bp amplicon of the vapA gene. Duplicate multiplex PCR assays for these targets and confirmatory singleplex PCR assays for vapA and choE were performed for each R equi isolate. An additional PCR assay was used to examine isolates for the vapB gene. RESULTS: Results of duplicate multiplex and singleplex PCR assays were correlated in all instances, revealing high specificity and reliability (reproducibility) of the vapA multiplex assay. Of the pulmonary isolates from horses with suspected R equi pneumonia, 97.4% (76/78) yielded positive results for vapA. Seven of 50 (14%) human isolates of R equi yielded positive results for vapA. Six human R equi isolates and 1 porcine isolate yielded positive results for vapB. No isolates with vapA and vapB genes were detected. CONCLUSIONS AND CLINICAL RELEVANCE: The multiplex PCR assay is a sensitive and specific method for simultaneous confirmation of species identity and detection of the vapA gene. The assay appeared to be a useful tool for microbiologic and epidemiologic diagnosis and research.     

Concentrations of serum amyloid A and lipopolysaccharide-binding protein in horses with colic

OBJECTIVE: To determine concentrations of 2 acute-phase proteins (serum amyloid A [SAA] and lipopolysaccharide-binding protein [LBP]) in serum samples obtained from horses with colic and identify relationships among these acute-phase proteins and clinical data. ANIMALS: 765 horses with naturally developing gastrointestinal tract diseases characterized by colic (ie, clinical signs indicative of abdominal pain) and 79 healthy control horses; all horses were examined at 2 university teaching hospitals. PROCEDURE: Serum concentrations of SAA and LBP were determined by immunoturbidometric and dot-blot assays, respectively. RESULTS: SAA and LBP concentrations were determined for 718 and 765 horses with colic, respectively. Concentrations of SAA were significantly higher in nonsurvivors than in survivors, and horses with enteritis or colitis and conditions characterized by chronic inflammation (eg, abdominal abscesses, peritonitis, or rectal tears) had SAA concentrations significantly greater than those for horses with other conditions. Serum concentrations of LBP did not correlate with outcome, disease process, or portion of the gastrointestinal tract affected. CONCLUSIONS AND CLINICAL RELEVANCE: Circulating concentrations of SAA were significantly higher at admission in horses with colic attributable to conditions having a primary inflammatory cause (eg, enteritis, colitis, peritonitis, or abdominal abscesses) and were higher in horses that failed to survive the episode of colic, compared with concentrations in horses that survived. Serum concentrations of LBP did not correlate with survival. Analysis of these findings suggests that evaluation of SAA concentrations may be of use in identifying horses with colic attributable to diseases that have inflammation as a primary component of pathogenesis.