Analysis of soil microbial communities based on amplicon sequencing of marker genes

The use of cultivation independent methods has revolutionized soil biology in the last decades. Most popular approaches are based on directly extracted DNA from soil and subsequent analysis of PCR-amplified marker genes by next-generation sequencing. While these high-throughput methods offer novel possibilities over cultivation-based approaches, several key points need to be considered to minimize potential biases during library preparation and downstream bioinformatic analysis. This opinion paper highlights crucial steps that should be considered for accurate analysis and data interpretation.     

Feasibility of Locating Leakages in Sewage Pressure Pipes Using the Distributed Temperature Sensing Technology

The cost effective maintenance of underwater pressure pipes for sewage disposal in Austria requires the detection and localization of leakages. Extrusion of wastewater in lakes can heavily influence the water and bathing quality of surrounding waters. The Distributed Temperature Sensing (DTS) technology is a widely used technique for oil and gas pipeline leakage detection. While in pipeline leakage detection, fiber optic cables are installed permanently at the outside or within the protective sheathing of the pipe; this paper aims at testing the feasibility of detecting leakages with temporary introduced fiber optic cable inside the pipe. The detection and localization were tested in a laboratory experiment. The intrusion of water from leakages into the pipe, producing a local temperature drop, served as indicator for leakages. Measurements were taken under varying measurement conditions, including the number of leakages as well as the positioning of the fiber optic cable. Experiments showed that leakages could be detected accurately with the proposed methodology, when measuring resolution, temperature gradient and measurement time were properly selected. Despite the successful application of DTS for leakage detection in this lab environment, challenges in real system applications may arise from temperature gradients within the pipe system over longer distances and the placement of the cable into the real pipe system.     

Population structure and genetic diversity in elite sugar beet germplasm investigated with SSR markers

The assessment of genetic diversity and structuration of germplasm is essential for the efficient organization of breeding material. The objectives of the study were to (i) examine the population structure of elite sugar beet germplasm, (ii) investigate genetic diversity within and among subgroups of elite sugar beet germplasm, and (iii) assess the extent of linkage disequilibrium (LD) within elite sugar beet germplasm. A total of 111 and 178 inbred lines from the seed and pollen parent (SP and PP) heterotic gene pools, respectively, which had been genotyped with 23 SSR markers, were used in this study. Two distinct subgroups were detected within the entire germplasm set by STRUCTURE and principal coordinate analysis (PCoA). This observation was not expected because the SP heterotic pool of sugar beet was developed out of the PP heterotic pool in the late 1970s. Our observation of high LD in elite sugar beet germplasm suggests that association mapping will be possible in the examined germplasm set using a relatively low numbers of markers. However, to reduce the problem of false-positive marker-phenotype association, it might be necessary to examine the subgroups separately or apply association mapping methods which take into account this structure.     

Factors affecting radial growth of the invasive <Emphasis Type="Italic">Prunus serotina</Emphasis> in pine plantations in Flanders

Prunus serotina is an invasive species that causes problems mainly in pine forests on sandy soils in Western Europe. Thus far, there have been almost no studies considering the diameter growth of P. serotina in its introduced range. We analysed the radial growth of P. serotina in seven Scots pine (Pinus sylvestris) plantations in Flanders (Belgium) using multiple linear regression and a potential × modifier approach. The radial growth of P. serotina in the understory of the studied pine plantations was reduced by up to 50% when compared to potential P. serotina growth in full light conditions. Size and site effects were strongly growth-reducing; crowding effects were important only for small individuals. The actual radial growth of P. serotina below pines was determined primarily by the diameter and age of the P. serotina tree and by competition with neighbouring trees.     

Measurement of digestibility in agastric fish based on stripping method – apparent nutrient,energy and amino acid digestibilities of common feed ingredients for carp diets (Cyprinus carpio)

Apparent nutrient, energy and amino acid (AA) digestibilities of wheat starch (WS), corn starch (CS), pea protein concentrate (PPC), soy protein concentrate (SPC), corn gluten meal (CGM) and soybean meal (SM) were assessed indirectly in common carp by applying the marker‐based indicator method. Each test diet consisted of 70% reference diet and 30% test ingredient. Stripping as faeces collection technique was applied to obtain faecal material two times a day for 9 weeks. Apparent digestibilities of ingredients (ADIs) for crude protein (CP) were higher in SM (79.5 ± 5.1%) and SPC (75.2 ± 4.8%) than in CGM (59.2 ± 6.6%). Regarding ADIs of individual AAs, SM and SPC always showed higher values than CGM and PPC. ADIs for crude carbohydrates in CS (90.4 ± 2.2%), WS (88.8 ± 2.0%) and CGM (82.3 ± 3.9%) exhibited higher amounts than in SM (26.3 ± 1.0%). Evaluated apparent digestibilities indicate that in particular SM and SPC are good protein and CGM, WS and CS are promising carbohydrate sources to be included in diets for common carp. A strong correlation between ADI_CP and ADI_AA was determined. Stripping used for digestibility measurement in carp was found to be a viable method as conventional passive faeces collecting techniques such as sedimentation or sieving.     

Use of specific peaks obtained by diffuse reflectance Fourier transform mid‐infrared spectroscopy to study the composition of organic matter in a Haplic Chernozem

This study assessed specific peaks obtained by diffuse reflectance Fourier transform mid‐infrared spectroscopy (DRIFTS) for characterizing the soil organic matter (SOM) composition of a Haplic Chernozem. Soils were collected from the Static Fertilization Experiment, Bad Lauchstädt, Germany, during 5 years from the farmyard manure (FYM), mineral fertilizer (NPK), combination (FYM + NPK) and no fertilizer (Control) treatments. Soils were extracted with hot water (HWE), and fractionated by size and density. Bulk soil and fractions were analysed by DRIFTS. Peak areas at 2930, 1620, 1530 and 1159 cm^?1 were selected as a range of organic functional groups (with limited mineral interference), integrated with a local baseline (corrected peak area) and each was divided by the summed area of the four peaks (relative peak area). Positive correlations between carbon (C) in fractions representing labile OM (<1.8 g cm^?3, 1.8–2.0 g cm^?3, C_HWE) and the corrected peak area at 2930 cm^?1 (3010–2800 cm^?1) in the bulk soil indicated that this aliphatic peak corresponded to the more labile C compounds. Negative correlations between the same fractions and the corrected area of the predominantly aromatic peak at 1620 cm^?1 (1660–1580 cm^?1) in the bulk soil suggested a relationship with more stable SOM compounds. All relative peak areas were significantly affected by fertilizer treatment, with an increasing relative peak area at 2930 cm^?1 in FYM compared with non‐FYM treatments. The ratio of the peaks at 1620 and 2930 cm^?1 was positively correlated with the ratio of stable C (sum of C in >1.8 g cm^?3 and clay fractions) to labile C (C content of <1.8 g cm^?3 fraction) and thus taken as an indicator of SOM stability. The DRIFTS peak area method reflected changes in SOM quality and composition under long‐term management as measured by size and density fractionation, indicating heterogeneous chemical composition of the latter. Further, the DRIFTS analysis of undiluted soil samples can be used to assess SOM composition in small sample sets if specular reflection and mineral interferences are considered.     

Development of soil organic matter stocks under different farm types and tillage systems in the Organic Arable Farming Experiment Gladbacherhof

In 1998, the Organic Arable Farming Experiment Gladbacherhof (OAFEG) was started in order to explore the impact of different organic arable production systems (mixed farming, stockless farming with rotational ley, stockless cash crop farming) and of different tillage intensities (conventional plough as a full inversion tillage, two-layer plough, inversion tillage at reduced depth, non-inversion tillage) on sustainability parameters. In this article, we present results on the development of soil organic matter (SOM) levels. Starting with organic mixed farming with approximately 0.7 livestock units (LU) per ha cattle before set-up of the experiment, only the mixed farming system in the experiment was able to maintain SOM levels. The stockless system with ley maintained soil organic carbon (SOC), but lost soil total nitrogen (STN), and the stockless cash crop system had a significant SOM loss in the magnitude of 7.7 t SOM ha^?1, or roughly 8.4% of the initial SOM mass. Reducing tillage intensity had no impact on SOM masses, but only on organic matter stratification in soils. We conclude that specialization of organic farms towards stockless arable crop production requires special attention on SOM reproduction to avoid detrimental effects. Further, reduced tillage intensity does not necessarily have a positive effect on SOM.     

Norchief,a new smooth type,high total solids,red-skinned potato variety

Norchief is a medium late maturing, red variety with high total solids. In yield, the new variety is quite comparable to Red Pontiac and La Rouge but higher than Norland. Norchief has shown a certain degree of field tolerance to potato flea beetle,Epitrix cucumeris.