Rearrangement of bacterial community structure during peat diagenesis

The relationship between microbial diagenesis of Sphagnum peat (SP) and reed-sedge peat (RSP) and the spatial organization of peat bacterial communities was studied. Peats were aerobically incubated at 18-22 °C for 4 months. Changes in molecular composition of peat organic matter were monitored with solid-state ¹³C NMR, and the respective amount of functional groups was determined by integration of corresponding peaks. No abiotic peat transformation was detected. SP diagenesis caused about a 4% loss of parent materials with a similar yield of ketones, phenols, aromatic, and carbonyl compounds; whereas about 20% of RSP carbohydrates, along with ketones and methoxyl compounds were gradually transformed into carbonyl and aliphatic compounds. SP and RSP substantially varied in bacterial composition. To address spatial community structure, bacterial populations were dissected by a differential elution technique into three fractions based on the degree of their attachment to peat. Community composition was surveyed with T-RFLP (HhaI, MspI, and RsaI). The fragments were further attributed to freely-dispersed (FD), particle-associated (PA), or omnipresent (OMN) bacterial fractions. In both peats, bacterial communities have gradually shifted with the progress of diagenesis. In SP, numbers of exclusively FD or PA bacteria slightly decreased while in RSP their numbers more than doubled after 4-month incubation, and the number of OMN bacteria respectively decreased. The substantially greater changes in the spatial structure of RSP bacterial community compared to SP were consistent with the chemical transformations detected in these peats suggesting the diagenesis-driven divergence of RSP bacterial community into FD and PA sub-communities.     

Assessing the Potential of Rhizobacteria to Survive under Phenanthrene Pollution

Rhizobacteria possess a wide variety of qualities governing their pollutant-catabolic and rhizospheric competences. We investigated how the abilities to degrade phenanthrene and other polycyclic aromatic hydrocarbons (PAHs), to synthesize surfactants and the phytohormone indole-3-acetic acid (IAA), to be motile, and to perform chemotaxis toward phenanthrene and some potential root-exudate components were manifested in rhizobacteria isolated from oil-polluted sites. We observed that most of the examined rhizobacteria had the abilities under consideration and that in some strains, these were strongly affected by the bacterial environment. Only one strain—Sinorhizobium meliloti P221—exhibited increased PAH-degrading, surfactant-producing, and IAA-synthesizing activities, as well as distinct behavioral responses. We conclude that S. meliloti P221 can be used as a model to assess the contributions of all these activities to plant-inoculation-induced reduction in the soil PAH contents. This strain also may be useful for phytoremediation applications.     

Experimental oral transmission of chronic wasting disease to red deer (Cervus elaphus elaphus): Early detection and late stage distribution of protease-resistant prion protein

Chronic wasting disease (CWD), an important emerging prion disease of cervids, is readily transmitted by intracerebral or oral inoculation from deer-to-deer and elk-to-elk, suggesting the latter is a natural route of exposure. Studies of host range susceptibility to oral infection, particularly of those species found in habitats where CWD currently exists are imperative. This report describes the experimental transmission of CWD to red deer following oral inoculation with infectious CWD material of elk origin. At 18 to 20 months post-inoculation, mild to moderate neurological signs and weight loss were observed and animals were euthanized and tested using 3 conventional immunological assays. The data indicate that red deer are susceptible to oral challenge and that tissues currently used for CWD diagnosis show strong abnormal prion (PrP^CWD) accumulation. Widespread peripheral PrP^CWD deposition involves lymphoreticular tissues, endocrine tissues, and cardiac muscle and suggests a potential source of prion infectivity, a means of horizontal transmission and carrier state.     

Persistence and Profiles of Tetracycline Resistance Genes in Swine Farms and Impact of Operational Practices on Their Occurrence in Farms’ Vicinities

Animal farms are recognized as a major contributor to environmental pollution with antibiotic resistance genes, the persistence at the source and the discharge routes to the environment of which need better understanding. The presence of 16 tetracycline resistance genes (TRG) was assessed in feed, feces, manure lagoons, and the vicinities of three Georgia swine farms varied on antibiotic usage and other operational characteristics. In these farms, TRG profiles of feces and lagoons were composed of the same “persistent” and “transient” genes, with the former consistently observed in farms’ proximities and the latter quickly attenuated in the lagoons. Fourteen TRG incidents, 13 of which occurred in gullies, ponds, and creeks, were detected around farms. Their frequency correlated to the cumulative antibiotic usage (R ² = 0.99), number of lagoons (R ² = 0.73), and precipitation (R ² = 0.83), but not to the size of herd or the amount of manure used for fertilization. Gene-specific amplicons of TRG from the farms’ proximities were similar to those of “persistent” TRG from corresponding farms. Our data suggested the independency of TRG profiles of antibiotic usage, variability in TRG persistence in manure lagoons, correlations between operational practices and TRG incidence in farms’ vicinities, and spills and seepage from lagoons as TRG environmental routes.     

Investigation of the effects of experimental autolysis on the detection of abnormal prion protein in lymphoid and central nervous system tissues from elk and sheep using the Western blotting method

Tissues unsuitable for standard immunohistochemical and histopathological examinations for chronic wasting disease (CWD) in cervids and for scrapie in sheep are frequently submitted for testing. This study investigated the effects of experimental autolysis on the detection of abnormal prion protein (PrPsc) in lymphoid and central nervous system (CNS) tissues from elk and sheep. The PrPsc was detected using a Western blotting (WB) test following PrPsc enrichment using sodium phosphotungstic acid (PTA) precipitation (PTA-WB). A commercial enzyme-linked immunosorbent assay (ELISA) was used as a reference test for quantitative measurement. This study showed that the amount of PrPsc in lymphoid and CNS tssues from elk and sheep decreased gradually as a result of autolysis, but PrPsc was still detectable after 5 and 15 d incubation at 37°C by PTA-WB for all lymphoid and CNS samples. The results of the ELISA supported those of PTA-WB, particularly for CNS tissues. In conclusion, autolysis at 37°C for 15 d would not significantly affect the detection of PrPsc in lymphoid and CNS tissues by WB and ELISA and, particularly, PTA-WB is a valuable and alternative confirmatory test to detect PrPsc in autolyzed lymphoid and CNS samples.     

Do carbon farming practices build bioavailable nitrogen pools?

Agricultural soils contain large amounts of nitrogen (N), but only a small fraction is readily available to plants. Despite several methods developed to estimate the bioavailability of N, there is no consensus on which extraction methods to use, and which N pools are critically important. In this study, we measured six soil N pools from 20 farms, which were part of a multi-year soil carbon sequestration on-farm experiment (Carbon action, 2019–2023). The aim was to quantify the N pools and to evaluate if farming practices that aim to build soil carbon pools, also build bioavailable N pools. We also aimed to test if the smaller and rapidly changing N pools could serve as an indicator for the slower change in soil organic matter. The measured N pools decreased in size, when moving from total N (7700 ± 1500 kg/ha) to slowly cycling (Illinois Soil Nitrogen Test ISNT-N: 1063 ± 220 kg/ha, autoclave citrate-extracted ACE protein N: 633 ± 440 kg/ha), water-soluble organic N (50 ± 17 kg/ha), potentially mineralizable N (33 ± 13 kg/ha) and finally readily plant available inorganic pools (nitrate and ammonium, total: 14 ± 8 kg/ha). In total, the measured pools covered only 18%–44% of total N, indicating a large unidentified N pool, which is either tightly bound to soil mineral fraction and not easily extractable or is bound to undecomposed plant residues and not hydrolysed by the methods. Of the large N pools (ISNT-N, ACE protein and unidentified residual N), clay, carbon (C) and C:Clay ratios explained most of the variability (R² = .90–.93), leaving a minor part of the variation to the management effect. A pairwise comparison of carbon farming and control plots concluded that farming practices had a small (3%–5%) but statistically significant (p < .05) effect on soil total N and ISNT-N pools, and a moderate and significant effect (18%, p < .01) on potentially mineralizable N. The large variation in protein N, water-soluble organic N and inorganic N reduced statistical significance, although individual C sequestration practices had large effects (−30% to +50%). In conclusion, carbon sequestration practices can build both slowly cycling N pools (ISNT) and increase the mineralisation rate of these pools to release plant available forms, resulting in an additional benefit to agriculture through reduced fertilizer application needs.     

Ionizing radiation effects on soil biota: Application of lessons learned from Chernobyl accident for radioecological monitoring

Russia, Ukraine, Belarus, Kazakhstan and some other neighboring countries bear the heritage of several Soviet era nuclear disasters and the resulting severe radioactive pollution of vast territories. The most famous of them is the Chernobyl catastrophe on April 26, 1986 which resulted in a massive radioisotope fallout (0.185 MBq m⁻² or higher) over about 25,000 km² of the territory of the former USSR alone. Extensive radioecological research around Chernobyl demonstrated that despite high resistance of most of soil-dwelling organisms to ionizing radiation, some soil animals were very vulnerable to radioactive pollution due to low motility, direct contact with hot particles and radioisotope accumulation in soil. These are the reasons that soil organisms are very important organisms for long-term radioecological observations. In this review, we analyze published data on the response of different soil taxa to radioisotope contamination of soil near Chernobyl and other nuclear accident locations. Field results are compared with the available experimental data. Earthworms, millipedes, collembolans and oribatid mites were recognized as the most appropriate biomonitors of different radioactivity levels and types of radioactive pollution. Synthesis of this knowledge allowed us to propose a multilevel system of soil radioecological monitoring, which may be useful for studying the short- and long-term environmental consequences of the recent catastrophe at Fukushima-1 nuclear power plant in Japan, as well as other locations vulnerable to radioactive pollution.     

Metabolic signature of spent culture media shows lipid metabolism as a determinant of pregnancy outcomes

In the present study, we investigated the spent culture media of in vitro produced (IVP) bovine embryos which did (group Pregnant) or did not (group Non-pregnant) establish pregnancy after transfer. For that purpose, IVP embryos on D5 were transferred to individual droplets for the last 48 h of culture. Embryos at the blastocyst stage were then transferred to synchronized recipients, while respective culture media drops were collected and evaluated individually. The list of metabolites present in spent culture media was obtained by electrospray ionization mass spectrometry (ESI-MS) and analysed with Metaboanalyst® to characterize the metabolic profile of each group. The spectrometric analysis showed that pathways related to lipid metabolism, particularly fatty acids degradation via beta-oxidation, were more present in the Pregnant group whereas no significant pathway was identified in the group Non-pregnant. By using this method, we were able to identify a metabolic signature in culture media that allows for a better comprehension of preferential metabolic routes taken by the most viable embryos. These findings offer great insights into the biochemistry of embryo development and reveal a potential target for the development of better-quality IVP systems, as well as tools to identify bovine embryos with greater chances to establish and maintain pregnancy.     

Copromicroscopic and molecular assays for the detection of cancer-causing parasitic nematode Spirocerca lupi

Spirocerca lupi (Nematoda, Spirurida) is a life-threatening parasitic nematode of dogs that is presently emerging in several countries. Nonetheless, canine spirocercosis is neglected and underestimated, mainly due to diagnostic limitations inherent to clinico-pathologic, diagnostic imaging and laboratory methodologies. Given the significant benefit of improved diagnosis, the present work evaluated the reliability of a recently described copromicroscopic approach, the FLOTAC technique, as well as a PCR-based assay with that of traditional coproscopic techniques to diagnose S. lupi infection. Ninety-four faecal field samples were collected from two endemic areas (i.e. 29 and 65 from Kenya and Israel, respectively) and processed using different coproscopic examination techniques. In particular, set I (Kenyan samples) comprised the modified flotation with Sheather's sugar solution and merthiolate-iodine-formalin technique, while set II (Israeli samples) comprised a flotation technique with zinc sulphate solution, a modified sugar flotation procedure and the FLOTAC method. All samples were also subjected to a semi-nested PCR protocol specific for a region internal to the mitochondrial cytochrome c oxidase subunit 1 gene of S. lupi. The coproscopic examinations showed low sensitivity and high variability, demonstrating the unreliability of the conventional methods for detecting S. lupi eggs. Nonetheless, the FLOTAC technique scored the highest number of positives and significantly higher number of S. lupi eggs per microscopic field compared to the other coproscopic methods. Additionally, of the coproscopically negative samples, 9 (45%) Kenyan and 21 (38.2%) Israeli samples scored molecularly positive using the PCR-based approach. The potential implications and perspectives for canine spirocercosis of these coproscopic and molecular diagnostic methodologies evaluated herein are discussed.