Persistence of a biocontrol Pseudomonas inoculant as high populations of culturable and non-culturable cells in 200-cm-deep soil profiles

Little is known about the ecology of soil inoculants used for pathogen biocontrol, biofertilization and bioremediation under field conditions. We investigated the persistence and the physiological states of soil-inoculated Pseudomonas protegens (previously Pseudomonas fluorescens) CHA0 (10⁸ CFU g^?1 surface soil) in different soil microbial habitats in a planted ley (Medicago sativa L.) and an uncovered field plot. At 72 days, colony counts of the inoculant were low in surface soil (uncovered plot) and earthworm guts (ley plot), whereas soil above the plow pan (uncovered plot), and the rhizosphere and worm burrows present until 1.2 m depth (ley plot) were survival hot spots (10⁵–10⁶ CFU g^?1 soil). Interestingly, strain CHA0 was also detected in the subsoil of both plots, at 10²–10⁵ CFU g^?1 soil between 1.8 and 2 m depth. However, non-cultured CHA0 cells were also evidenced based on immunofluorescence microscopy. Kogure's direct viable counts of nutrient-responsive cells showed that many more CHA0 cells were in a viable but non-culturable (VBNC) or a non-responsive (dormant) state than in a culturable state, and the proportion of cells in those non-cultured states depended on soil microbial habitat. At the most, cells in a VBNC state amounted to 34% (above the plow pan) and those in a dormant state to 89% (in bulk soil between 0.6 and 2 m) of all CHA0 cells. The results indicate that field-released Pseudomonas inoculants may persist at high cell numbers, even in deeper soil layers, and display a combination of different physiological states whose prevalence fluctuates according to soil microbial habitats.     

Impact of ecologically different earthworm species on soil water characteristics

A laboratory experiment was performed to assess the impact of ecologically different earthworm species on soil water characteristics, such as soil tension, water content, and water infiltration rate. Three earthworm species (Lumbricus rubellus, Aporrectodea caliginosa, Lumbricus terrestris) were exposed in soil columns (diameter 30 cm, height 50 cm) for 100 days with a total fresh earthworm biomass of 22.7 ± 0.4 g per column, each in duplicate. Each column was equipped with tensiometers at 10 and 40 cm and FD-probes at 10 cm depth, to continuously measure the temporal development of soil tension and soil moisture. Additionally, 30 g of sieved and rewetted horse manure was placed on the soil surface as a food source. Precipitation events (10 mm) were simulated at day 28 and day 64. At the end of the experiment the water infiltration rate and the runoff at 55 cm depth were determined.The results showed considerable evidence, that ecologically different earthworms modify soil water characteristics in different ways. The anecic L. terrestris and the endogeic A. caliginosa showed the tendency to enhance the drying of the topsoil and subsoil. Their intensive and deep burrowing activity might enhance the exchange of water vapor due to a better aeration in soil. In contrast, the epigeic L. rubellus tended to enhance the storage of soil moisture in the topsoil, which might be linked to lower rates of litter loss from soil surface and thus a thicker litter layer remaining. A. caliginosa led to considerable higher water infiltration rates and faster water discharges in the subsoil, relative to the other species, probably due to a high soil dwelling activity.     

Analysis of Flavan-3-ols and procyanidins in food samples by reversed phase high-performance liquid chromatography coupled to electrospray ionization tandem mass spectrometry (RP-HPLC-ESI-MS/MS)

Concentrations of the main dimeric and trimeric procyanidins (PC) and their monomeric constitutive units catechin (CT) and epicatechin (EC) were determined in food samples by using reversed phase high-performance liquid chromatography coupled to electrospray ionization tandem mass spectrometry (RP-HPLC-ESI-MS/MS). In a first step, 12 PCs (PC B1, B2, B3, B4, B5, B6, B7, B8, C1, C2, and A2 and cinnamtannin B1), of which most are not commercially available, were isolated from plant materials or synthesized and purified by a combination of column chromatographic separation techniques with different stationary phases. These PCs in combination with CT and EC were used as standard substances for identification and quantification during the following screening of food samples by RP-HPLC-ESI-MS/MS analysis. The main focus of the newly developed RP-HPLC-ESI-MS/MS method is the compensation of matrix effects by using the echo-peak technique simulating internal standard injection. The suitability of this new method was demonstrated by the determination of recovery rates being 90% or higher. Use of this method allowed the determination of patterns and concentrations of PCs in 55 food samples.     

Detection of ruminant meat and bone meals in animal feed by real-time polymerase chain reaction: result of an interlaboratory study

The commercialization of animal feeds infected by prions proved to be the main cause of transmission of bovine spongiform encephalopathy (BSE). Therefore, feed bans were enforced, initially for ruminant feeds, and later for all feeds for farmed animals. The development and validation of analytical methods for the species-specific detection of animal proteins in animal feed has been indicated in the TSE (Transmissible Spongiform Encephalopathies) Roadmap (European Commission. The TSE (Transmissible Spongiform Encephalopathy) roadmap. URL: http://europa.eu.int/comm/food/food/biosafety/bse/roadmap_en.pdf, 2005) as the main condition for lifting the extended feed ban. Methods based on polymerase chain reaction (PCR) seem to be a promising solution for this aim. The main objective of this study was to determine the applicability of four different real-time PCR methods, developed by three National expert laboratories from the European Union (EU), for the detection and identification of cattle or ruminant species in typical compound feeds, fortified with meat and bone meals (MBM) from different animal species at different concentration levels. The MBM samples utilized in this study have been treated using the sterilization condition mandatory within the European Union (steam pressure sterilization at 133 degrees C, 3 bar, and 20 min), which is an additional challenge to the PCR methods evaluated in this study. The results indicate that the three labs applying their PCR methods were able to detect 0.1% of cattle MBM, either alone or in mixtures with different materials such as fishmeal, which demonstrates the improvement made by this technique, especially when compared with results from former interlaboratory studies.     

Nitrogen retention and plant uptake on a highly weathered central Amazonian Ferralsol amended with compost and charcoal

Leaching losses of N are a major limitation of crop production on permeable soils and under heavy rainfalls as in the humid tropics. We established a field trial in the central Amazon (near Manaus, Brazil) in order to study the influence of charcoal and compost on the retention of N. Fifteen months after organic‐matter admixing (0–0.1 m soil depth), we added ¹⁵N‐labeled (NH₄)₂SO₄ (27.5 kg N ha^–1 at 10 atom% excess). The tracer was measured in top soil (0–0.1 m) and plant samples taken at two successive sorghum (Sorghum bicolor L. Moench) harvests. The N recovery in biomass was significantly higher when the soil contained compost (14.7% of applied N) in comparison to only mineral‐fertilized plots (5.7%) due to significantly higher crop production during the first growth period. After the second harvest, the retention in soil was significantly higher in the charcoal‐amended plots (15.6%) in comparison to only mineral‐fertilized plots (9.7%) due to higher retention in soil. The total N recovery in soil, crop residues, and grains was significantly (p < 0.05) higher on compost (16.5%), charcoal (18.1%), and charcoal‐plus‐compost treatments (17.4%) in comparison to only mineral‐fertilized plots (10.9%). Organic amendments increased the retention of applied fertilizer N. One process in this retention was found to be the recycling of N taken up by the crop. The relevance of immobilization, reduced N leaching, and gaseous losses as well as other potential processes for increasing N retention should be unraveled in future studies.     

Conversion of a tropical forest into agroforest alters the fine root-related carbon flux to the soil

Large areas of remaining tropical forests are affected by anthropogenic disturbances of various intensities. These disturbances alter the structure of the forest ecosystem and consequently its carbon budget. We analysed the role of fine root dynamics in the soil carbon budget of tropical moist forests in South-east Asia along a gradient of increasing disturbance intensity. Fine root production, fine root turnover, and the associated carbon fluxes from the fine root system to the soil were estimated with three different approaches in five stands ranging from an old growth forest with negligible anthropogenic disturbance to a cacao agroforestry system with planted shade trees. Annual fine root production and mortality in three natural forest sites with increasing canopy openness decreased continuously with increasing forest disturbance, with a reduction of more than 45% between the undisturbed forest and the forest with large timber extraction. Cacao agroforestry stands had higher fine root production and mortality rates than forest with large timber extraction but less than undisturbed forest. The amount of carbon annually transferred to the soil carbon pool through fine root mortality was highest in the undisturbed forest and generally decreased with increasing forest use intensity. However, root-related C flux was also relatively high in the plantation with planted shading trees. In contrast, the relative importance of C transfer from root death in the total above- and below-ground C input to the soil increased with increasing forest use intensity and was even similar to the C input via leaf litter fall in the more intensively managed agroforest. We conclude that moderate to heavy disturbance in South-east Asian tropical moist forests has a profound impact on fine root turnover and the related carbon transfer to the soil.     

Impact of nitrogen and phosphorus additions on soil gross nitrogen transformations in a temperate desert steppe

Nutrient addition has a significant impact on plant growth and nutrient cycling. Yet, the understanding of how the addition of nitrogen (N) or phosphorus (P) significantly affects soil gross N transformations and N availability in temperate desert steppes is still limited. Therefore, a ¹⁵N tracing experiment was conducted to study these processes and their underlying mechanism in a desert steppe soil that had been supplemented with N and P for 4 years in northwestern China. Soil N mineralization was increased significantly by P addition, and N and P additions significantly promoted soil autotrophic nitrification, rather than NH₄⁺-N immobilization. The addition of N promoted dissimilatory NO₃⁻ reduction to NH₄⁺, while that of P inhibited it. Soil NO₃⁻-N production was greatly increased by N added alone and by that of N and P combined, while net NH₄⁺-N production was decreased by these treatments. Soil N mineralization was primarily mediated by pH, P content or organic carbon, while soil NH₄⁺-N content regulated autotrophic nitrification mainly, and this process was mainly controlled by ammonia-oxidizing bacteria rather than archaea and comammox. NH₄⁺-N immobilization was mainly affected by functional microorganisms, the abundance of narG gene and comammox Ntsp-amoA. In conclusion, gross N transformations in the temperate desert steppe largely depended on soil inorganic N, P contents and related functional microorganisms. Soil acidification plays a more key role in N mineralization than other environmental factors or functional microorganisms.     

Oxidative degradation of lipids during mashing

Although hardly any polyunsaturated fatty acids (PUFAs) are present in the endproduct, the ingredients used for the production of beer contain a high concentration of PUFAs, such as linolic and linolenic acid. These compounds are readily oxidized, resulting in the formation of lipid-derived products that reduce the taste and quality of beer enormously. During mashing relatively high amounts of PUFAs are exposed to atmospheric oxygen at a relatively high temperature. This makes mashing a critical step in the brewing process with regard to the formation of lipid-derived off-taste products. F1 phytoprostane (PPF1) changes in antioxidant capacity and monohydroxy fatty acids (OH-FAs) were used as markers for the detection of oxidative damage to fatty acids during mashing. The pattern of OH-FA formation indicates that enzymatic oxidation of PUFAs is more important than nonenzymatic oxidation during the mashing process. Nevertheless, substantial nonenzymatic radical formation is evident from the increase of specific OH-FAs and PPF1s. It was found that a low oxygen tension reduces oxidative damage and gives a high antioxidant capacity of the mashing mixture. This indicates that mashing should be done under low oxygen pressure.