Variations in microbial community composition through two soil depth profiles

Soil profiles are often many meters deep, but with the majority of studies in soil microbiology focusing exclusively on the soil surface, we know very little about the nature of the microbial communities inhabiting the deeper soil horizons. We used phospholipid fatty acid (PLFA) analysis to examine the vertical distribution of specific microbial groups and to identify the patterns of microbial abundance and community-level diversity within the soil profile. Samples were collected from the soil surface down to 2 m in depth from two unsaturated Mollisol profiles located near Santa Barbara, CA, USA. While the densities of microorganisms were generally one to two orders of magnitude lower in the deeper horizons of both profiles than at the soil surface, approximately 35% of the total quantity of microbial biomass found in the top 2 m of soil is found below a depth of 25 cm. Principal components analysis of the PLFA signatures indicates that the composition of the soil microbial communities changes significantly with soil depth. The differentiation of microbial communities within the two profiles coincides with an overall decline in microbial diversity. The number of individual PLFAs detected in soil samples decreased by about a third from the soil surface down to 2 m. The ratios of cyclopropyl/monoenoic precursors and total saturated/total monounsaturated fatty acids increased with soil depth, suggesting that the microbes inhabiting the deeper soil horizons are more carbon limited than surface-dwelling microbes. Using PLFAs as biomarkers, we show that Gram-positive bacteria and actinomycetes tended to increase in proportional abundance with increasing soil depth, while the abundances of Gram-negative bacteria, fungi, and protozoa were highest at the soil surface and substantially lower in the subsurface. The vertical distribution of these specific microbial groups can largely be attributed to the decline in carbon availability with soil depth.     

Genetic methods for the detection of microbial pathogens. Identification of enterotoxigenic Escherichia coli by DNA colony hybridization: collaborative study

Enteropathogenic Escherichia coli strains may produce a cholera-like, heat-labile enterotoxin (LT) as a virulence factor. The gene that codes for LT can be purified by recombinant DNA techniques and used as a genetic probe for DNA hybridization. These probes detect enterotoxigenic strains as well as strains that may not manifest toxin production but carry the genetic information to do so. In this study, 13 laboratories tested 3 known and 25 unknown (10 positive and 15 negative) cultures of E. coli for the presence of the LT gene. The isolates had been tested and classified by the mouse Y-1 adrenal cell test and an enzyme-linked immunosorbent assay. Cultures were spotted on nitrocellulose filters on MacConkey agar and incubated. Colonies were lysed in situ and their DNA was hybridized to 32P-labeled, purified LT gene DNA (provided to the collaborators). Positive colonies were identified by autoradiography. Of 325 samples, 315 (96.9%) were identified correctly and 10 were misclassified; there were 6 false negative and 4 false positive identifications. Chi-square values indicated that the method agreed with the previous classification and was equally efficient in distinguishing positive and negative samples (95.7 and 98.1%, respectively). The method has been adopted official first action.     

Detection of Rhodococcus equi by polymerase chain reaction using species-specific nonproprietary primers.

Species-specific primers for the polymerase chain reaction (PCR) for the detection of Rhodococcus equi were developed. These primers were based on unique DNA fragments produced from R. equi reference strains and field isolates. Following random amplification of polymorphic DNA from R. equi and R. rhodochrous with a set of 40 arbitrary 10-base pair (bp) primers, a pair of species-specific primers was designed to detect a unique 700-bp fragment of R. equi chromosomal DNA. This PCR product was limited to R. equi and was not detectable in other Rhodococcus species or in a panel of additional gram-positive and gram-negative bacteria.     

Disseminated Intravascular Coagulation Associated with Colic in 23 Horses (1984–1989)

Disseminated intravascular coagulation (DIC) secondary to colic was diagnosed in 23 horses. Each horse was categorized retrospectively as to the cause of the colic based on surgical and/or necropsy findings: group 1 consisted of 14 horses with compromised intestine that required resection and anastomosis; group 2 consisted of 3 horses with nonstrangulating intestinal displacement and/or impactions; and group 3 consisted of 6 horses with colic associated with enteritis and/or colitis. Horses were considered to be affected with DIC if at least three of five hemostatic parameters were significantly abnormal: decreased antithrombin III (AT III) values, increased level of fibrin degradation products (FDP), thrombocytopenia, prolonged activated partial thromboplastin time, and prolonged prothrombin time. The most consistent hemostatic abnormalities were decreased AT III activity, increased FDP titers, and thrombocytopenia. Clotting times were more variable and did not always correlate with the presence of excessive hemorrhage. Excessive hemorrhage was present during surgery in seven horses and occurred within 1 to 12 hours after surgery in nine other horses. In addition to treatment of the primary disease, 19 horses received treatment for DIC consisting of heparin and/or plasma or fresh whole blood transfusions. Heparin alone was used in 12 horses. Heparin, in addition to fresh whole blood transfusions or fresh plasma, was administered to four horses. Three horses were treated with plasma alone. Four other horses were not treated specifically for the DIC. Eight horses (34%) survived the acute coagulopathy. Although a greater proportion of the surviving horses received heparin therapy (87.5%; 7/8) than did those that died (60%; 9/15), the difference was not statistically significant (P = 0.345).(ABSTRACT TRUNCATED AT 250 WORDS)     

Pharmacokinetics of gallium maltolate after intragastric administration in neonatal foals

OBJECTIVE: To determine the pharmacokinetics of gallium maltolate (GaM) after intragastric administration in healthy foals. ANIMALS: 6 healthy neonatal foals. PROCEDURES: Each foal received GaM (20 mg/kg) by intragastric administration. Blood samples were obtained before (time 0) and at 0.25, 0.5, 1, 2, 4, 8, 12, 24, 36, and 48 hours after GaM administration for determination of serum gallium concentrations by use of inductively coupled plasma mass spectroscopy. RESULTS: Mean +/- SD pharmacokinetic variables were as follows: peak serum gallium concentration, 1,079 +/- 311 ng/mL; time to peak serum concentration, 4.3 +/- 2.0 hours; area under the serum concentration versus time curve, 40,215 +/- 8,420 ng/mL/h; mean residence time, 39.5 +/- 17.2 hours; area under the moment curve, 1,636,554 +/- 931,458 ng([h](2)/mL); and terminal half-life, 26.6 +/- 11.6 hours. The mean serum concentration of gallium at 12 hours was 756 +/- 195 ng/mL. CONCLUSIONS AND CLINICAL RELEVANCE: Gallium maltolate administered via nasogastric tube at a dose of 20 mg/kg to neonatal foals resulted in gallium serum concentrations considered sufficient to suppress growth or kill Rhodococcus equi in macrophages and other infected tissues.     

Rhodococcus equi foal pneumonia: Update on epidemiology,immunity, treatment and prevention

Pneumonia in foals caused by the bacterium Rhodococcus equi has a worldwide distribution and is a common cause of disease and death for foals. The purpose of this narrative review was to summarise recent developments pertaining to the epidemiology, immune responses, treatment, and prevention of rhodococcal pneumonia of foals. Screening tests have been used to implement earlier detection and treatment of foals with presumed subclinical R. equi pneumonia to reduce mortality and severity of disease. Unfortunately, this practice has been linked to the emergence of antimicrobial-resistant R. equi in North America. Correlates of protective immunity for R. equi infections of foals remain elusive, but recent evidence indicates that innate immune responses are important both for mediating killing and orchestrating adaptive immune responses. A macrolide antimicrobial in combination with rifampin remains the recommended treatment for foals with R. equi pneumonia. Great need exists to identify which antimicrobial combination is most effective for treating foals with R. equi pneumonia and to limit emergence of antimicrobial-resistant strains. In the absence of an effective vaccine against R. equi, passive immunisation remains the only commercially available method for effectively reducing the incidence of R. equi pneumonia. Because passive immunisation is expensive, labour-intensive and carries risks for foals, great need exists to develop alternative approaches for passive and active immunisation.     

Epigenetic Regulation of Gene Expression: Emerging Applications for Horses

Epigenetic modifications play a central role in the cellular and developmental programming of gene expression, serving as a molecular code for regulating the spatial and temporal patterns of gene expression. Epigenetic modifications are unique as they are cell-specific, heritable, and dynamic. They provide a framework for regulating gene expression, a map of functional noncoding elements in the genome, a biological sensor of environmental conditions, and a window of opportunity for the potential development of therapeutic strategies. Here we provide a brief overview of our current understanding of the epigenetic mechanisms regulating gene expression, focusing on DNA methylation and posttranslational modifications of histone proteins. Furthermore, we explore the emerging field of epigenetics in the horse, including the identification of functional elements in the horse genome and the potential development of epigenetic therapies in horses.     

Searching for unifying principles in soil ecology

The field of soil ecology has relatively few fundamental unifying principles that can be used to explain and predict patterns and processes in belowground ecosystems. Here we propose that a first step towards developing a more comprehensive set of unifying principles in soil ecology is to identify and understand the characteristics shared by a wide range of soils, the common mechanisms driving soil biogeochemical processes, and the biogeochemical constraints imposed on soil biota regardless of soil type. Very often, soil ecologists focus on the differences between soils when, in fact, many soils share a common set of ecological mechanisms that govern biogeochemical processes. Here we explore evidence for the existence of unifying principles in soil ecology, highlighting some of the similarities in carbon dynamics and soil communities across widely different soil types and examining the various mechanisms that may drive these similarities. Given that soils are extremely complex environments that exhibit substantial spatial and temporal heterogeneity, defining overarching principles is, arguably, more challenging in soil ecology than in other disciplines. However, recent methodological advances hold great promise for testing and formulating unifying principles, particularly when such methods are used consistently, in concert with other interdisciplinary approaches, and across a range of sites. Soils are not identical, but they do exhibit consistent patterns and processes that, if explored more intensively, will affirm the existence of unifying principles in soil ecology.