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Intestinal colonization is influenced by the ability of the bacterium to inhabit a niche, which is based on the expression of colonization factors. Escherichia coli carries a broad range of virulence-associated genes (VAGs) which contribute to intestinal (inVAGs) and extraintestinal (exVAGs) infection. Moreover, initial evidence indicates that inVAGs and exVAGs support intestinal colonization. We developed new screening tools to genotypically and phenotypically characterize E. coli isolates originating in humans, domestic pigs, and 17 wild mammal and avian species. We analyzed 317 isolates for the occurrence of 44 VAGs using a novel multiplex PCR microbead assay (MPMA) and for adhesion to four epithelial cell lines using a new adhesion assay. We correlated data for the definition of new adhesion genes. inVAGs were identified only sporadically, particularly in roe deer (Capreolus capreolus) and the European hedgehog ( Erinaceus europaeus). The prevalence of exVAGs depended on isolation from a specific host. Human uropathogenic E. coli isolates carried exVAGs with the highest prevalence, followed by badger (Meles meles) and roe deer isolates. Adhesion was found to be very diverse. Adhesion was specific to cells, host, and tissue, though it was also unspecific. Occurrence of the following VAGs was associated with a higher rate of adhesion to one or more cell lines: afa-dra, daaD, tsh, vat, ibeA, fyuA, mat, sfa-foc, malX, pic, irp2, and papC. In summary, we established new screening methods which enabled us to characterize large numbers of E. coli isolates. We defined reservoirs for potential pathogenic E. coli. We also identified a very broad range of colonization strategies and defined potential new adhesion genes.
Abstract
BACKGROUND:
Different strategies of colonization or infection by E. coli result in formation of certain adhesion patterns which help also in classifying intestinal E. coli into pathotypes. Little is known about adhesion patterns and host- and tissue adaption of commensal E. coli and about E. coli originating in clinically healthy hosts carrying pathotype-specific virulence-associated genes.
FINDINGS:
Adhesion pattern of E. coli (n = 282) from humans and from 18 animal species were verified on intestinal human Caco-2 and porcine IPEC-J2 cells and, furthermore, for comparison on human urinary bladder 5637, porcine kidney PK-15 epithelial and HEp-2 cells. The analysis was carried out on 150,000 images of adhesion assays.Adhesion patterns were very diverse; 88 isolates were completely non-adherent, whereas 194 adhered to at least one cell line with the dominant adhesion patterns "diffusely distributed" and "microcolony formation". Adhesion patterns "chains" and "clumps" were also visible. Chain formation was mediated by the presence of epithelial cells. Clump formation was very specific on only the 5637 cell line. All enteropathogenic (eae+) E. coli (EPEC; n = 14) were able to form microcolonies which was cell line specific for each isolate. Most EPEC formed microcolonies on intestinal IPEC-J2 and Caco-2 but several also on urinary tract cells. Shigatoxin-producing (stx+) E. coli (n = 10) showed no specific adhesion patterns.
CONCLUSIONS:
E. coli isolates were highly diverse. Commensal and pathogenic isolates can adhere in various forms, including diffuse distribution, microcolonies, chains and clumps. Microcolony formation seems to be a global adhesion strategy also for commensal E. coli.
Short rotation coppice (SRC) is seen as a successful management system, which in addition to energy wood production may enhance soil carbon sequestration. The objective of this study was to investigate total, labile and stable soil carbon fractions at SRCs composed of poplar clones Max 1 (Populus nigra x P. maximowiczii), Muhle Larsen (Populus Trichocarpa), and black locust (Robinia pseudoacacia L.). Study was conducted at three SRC sites (Allendorf, Dornburg, and Forst) varying in age (1–4 years old), soil texture and climatic characteristics, in Germany. Composite soil samples collected at SRCs from 0 to 3; 0–10; 10–30; and 30–60 cm depth layers were compared with soils collected from adjacent crop strips. Samples were analysed for total organic carbon (TOC), hot-water extractable carbon (HWC), and organic carbon (OC) at 250–2,000; 53–250; and\53 lm soil-size aggregates. Total OC stocks in 0–60 cm soil layer were the highest at the site with the heaviest texture, Dornburg, followed by Forst and Allendorf, comprising 92–107; 59–74; and 53–64 Mg ha-1, respectively. Although no significant differences in the total OC stocks between SRCs and adjacent crops were found for the 0–60 cm layer, a significantly (p\0.05) higher TOC, HWC, OC at macroaggregates (250–2,000 lm), and the amount of macro-aggregates were found in the top 0–3 cm layer in all SRC sites (except the youngest poplar SRC in Forst) compared to adjacent crop strips. A greater macro-aggregate formation in SRCs related to the lower soil disturbance compared to the tilled crops, revealed a potential of SRC for C sequestration, as C occluded within soil aggregates has a slower decomposition rates and longer residence time.
Agroforestry is receiving increasing attention in Germany because of its capacity to address some of the negative consequences of intensive agriculture. However the actual uptake and maintenance of agroforestry by farmers remains low. The aim of this study was to identify the opportunities and obstacles to agroforestry in Germany and to identify potential measures which could address the obstacles and increase agroforestry adoption. Qualitative interviews with 32 farmers indicated that the legal framework and administrative burden associated with agroforestry in Germany was a major obstacle. The farmers recognised that agroforestry provided environmental benefits, but these do not always increase farm profitability. Agroforestry was identified as a viable alternative to conventional farming systems, especially in less productive areas, not profitable when managed in a conventional way. To enhance the implementation of agroforestry the simplification of the legal framework is crucial. Modern agroforestry should be better recognized by existing policy measures providing payments for environmentally friendly farming. Ultimately, an integrated approach for environmental benefits and production objectives is required, which is based on rewarding farmers for providing ecosystem services (ESs) and a stronger public involvement in sustainable land use practices. Rewarding farmers for ESs could increase the interest in agroforestry in highly productive areas, enhancing sustainable land use in the long term.
The aim of this study was to evaluate the potential of short rotation alley cropping systems (SRACS) to improve the soil fertility of marginal post-mining sites in Brandenburg, Germany. Therefore, we annually investigated the crop alleys (AC) and black locust hedgerows (ABL) of a SRACS field trail under initial soil conditions to identify the short-term effects of tree planting on the storage of soil organic carbon (SOC) and its degree of stabilization by density fractionation. We detected a significant increase in SOC and hot-water-extractable organic C (HWEOC) at ABL, which was mainly restricted to the uppermost soil layer (0–10 cm). After 6 years, the SOC and HWEOC accumulation rates at ABL were 0.6 Mg and 46 kg ha−1 year−1, which were higher than those in the AC. In addition, comparatively high stocks of approximately 4.6 Mg OC and 182 kg HWEOC ha−1 were stored in the ABL litter layer. Density fractionation of the 0–3 cm soil layer at ABL revealed that the majority of the total SOC (47%) was stored in the free particulate organic matter fraction, which was more than twice that of the AC. At the same time, a higher and steadily increasing amount of SOC was stored in the occluded particulate organic matter fraction at ABL, which indicated a high efficiency for SOC stabilization. Overall, our findings support the suitability of black locust trees for increasing the soil fertility of the reclaimed mining substrate and, consequently, the high potential for SRACS to serve as an effective recultivation measure at marginal sites.