1-20 von 480 Publikationen

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      Rural food security, subsistence agriculture, and seasonality. 

      Sibhatu, Kibrom T.; Qaim, Matin
      PloS one 2017; 12(10): Art. e0186406
      Many of the world's food-insecure and undernourished people are smallholder farmers in developing countries. This is especially true in Africa. There is an urgent need to make smallholder agriculture and food systems more nutrition-sensitive. African farm households are known to consume a sizeable part of what they produce at home. Less is known about how much subsistence agriculture actually contributes to household diets, and how this contribution changes seasonally. We use representative data from rural Ethiopia covering every month of one full year to address this knowledge gap. On average, subsistence production accounts for 58% of rural households' calorie consumption, that is, 42% of the calories consumed are from purchased foods. Some seasonal variation occurs. During the lean season, purchased foods account for more than half of all calories consumed. But even during the main harvest and post-harvest season, purchased foods contribute more than one-third to total calorie consumption. Markets are even more important for dietary quality. During all seasons, purchased foods play a much larger role for dietary diversity than subsistence production. These findings suggest that strengthening rural markets needs to be a key element in strategies to improve food security and dietary quality in the African small-farm sector.
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      Supermarket purchase contributes to nutrition-related non-communicable diseases in urban Kenya. 

      Demmler, Kathrin M.; Klasen, Stephan; Nzuma, Jonathan M.; Qaim, Matin
      PloS one 2017; 12(9): Art. e0185148
      BACKGROUND: While undernutrition and related infectious diseases are still pervasive in many developing countries, the prevalence of non-communicable diseases (NCD), typically associated with high body mass index (BMI), is rapidly rising. The fast spread of supermarkets and related shifts in diets were identified as possible factors contributing to overweight and obesity in developing countries. Potential effects of supermarkets on people's health have not been analyzed up till now. OBJECTIVE: This study investigates the effects of purchasing food in supermarkets on people's BMI, as well as on health indicators such as fasting blood glucose (FBG), blood pressure (BP), and the metabolic syndrome. DESIGN: This study uses cross-section observational data from urban Kenya. Demographic, anthropometric, and bio-medical data were collected from 550 randomly selected adults. Purchasing food in supermarkets is defined as a binary variable that takes a value of one if any food was purchased in supermarkets during the last 30 days. In a robustness check, the share of food purchased in supermarkets is defined as a continuous variable. Instrumental variable regressions are applied to control for confounding factors and establish causality. RESULTS: Purchasing food in supermarkets contributes to higher BMI (+ 1.8 kg/m2) (P<0.01) and an increased probability (+ 20 percentage points) of being overweight or obese (P<0.01). Purchasing food in supermarkets also contributes to higher levels of FBG (+ 0.3 mmol/L) (P<0.01) and a higher likelihood (+ 16 percentage points) of suffering from pre-diabetes (P<0.01) and the metabolic syndrome (+ 7 percentage points) (P<0.01). Effects on BP could not be observed. CONCLUSIONS: Supermarkets and their food sales strategies seem to have direct effects on people's health. In addition to increasing overweight and obesity, supermarkets contribute to nutrition-related NCDs. Effects of supermarkets on nutrition and health can mainly be ascribed to changes in the composition of people's food choices.
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      Gut microbiomes of mobile predators vary with landscape context and species identity. 

      Tiede, Julia; Scherber, Christoph; Mutschler, James; McMahon, Katherine D.; Gratton, Claudio
      Ecology and evolution 2017-10; 7(20) p.8545-8557
      Landscape context affects predator-prey interactions and predator diet composition, yet little is known about landscape effects on insect gut microbiomes, a determinant of physiology and condition. Here, we combine laboratory and field experiments to examine the effects of landscape context on the gut bacterial community and body condition of predatory insects. Under laboratory conditions, we found that prey diversity increased bacterial richness in insect guts. In the field, we studied the performance and gut microbiota of six predatory insect species along a landscape complexity gradient in two local habitat types (soybean fields vs. prairie). Insects from soy fields had richer gut bacteria and lower fat content than those from prairies, suggesting better feeding conditions in prairies. Species origin mediated landscape context effects, suggesting differences in foraging of exotic and native predators on a landscape scale. Overall, our study highlights complex interactions among gut microbiota, predator identity, and landscape context.
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      Performances of Different Fragment Sizes for Reduced Representation Bisulfite Sequencing in Pigs 

      Yuan, Xiao-Long; Zhang, Zhe; Pan, Rong-Yang; Gao, Ning; Deng, Xi; Li, Bin; Zhang, Hao; Sangild, Per Torp; Li, Jia-Qi
      Biological Procedures Online 2017; 19(5)
      Reduced representation bisulfite sequencing (RRBS) has been widely used to profile genome-scale DNA methylation in mammalian genomes. However, the applications and technical performances of RRBS with different fragment sizes have not been systematically reported in pigs, which serve as one of the important biomedical models for humans. The aims of this study were to evaluate capacities of RRBS libraries with different fragment sizes to characterize the porcine genome. We found that the MspI-digested segments between 40 and 220 bp harbored a high distribution peak at 74 bp, which were highly overlapped with the repetitive elements and might reduce the unique mapping alignment. The RRBS library of 110–220 bp fragment size had the highest unique mapping alignment and the lowest multiple alignment. The cost-effectiveness of the 40–110 bp, 110–220 bp and 40–220 bp fragment sizes might decrease when the dataset size was more than 70, 50 and 110 million reads for these three fragment sizes, respectively. Given a 50-million dataset size, the average sequencing depth of the detected CpG sites in the 110–220 bp fragment size appeared to be deeper than in the 40–110 bp and 40–220 bp fragment sizes, and these detected CpG sties differently located in gene- and CpG island-related regions. In this study, our results demonstrated that selections of fragment sizes could affect the numbers and sequencing depth of detected CpG sites as well as the cost-efficiency. No single solution of RRBS is optimal in all circumstances for investigating genome-scale DNA methylation. This work provides the useful knowledge on designing and executing RRBS for investigating the genome-wide DNA methylation in tissues from pigs.
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      An effective molecular approach for assessing cereal aphid-parasitoid-endosymbiont networks 

      Ye, Zhengpei; Vollhardt, Ines M. G.; Girtler, Susanne; Wallinger, Corinna; Tomanovic, Zeljko; Traugott, Michael
      Scientific Reports 2017; 7(1): Art. 3138 (2017)
      Molecular approaches are increasingly being used to analyse host-parasitoid food webs as they overcome several hurdles inherent to conventional approaches. However, such studies have focused primarily on the detection and identification of aphids and their aphidiid primary parasitoids, largely ignoring primary parasitoid-hyperparasitoid interactions or limiting these to a few common species within a small geographical area. Furthermore, the detection of bacterial secondary endosymbionts has not been considered in such assays despite the fact that endosymbionts may alter aphid-parasitoid interactions, as they can confer protection against parasitoids. Here we present a novel two-step multiplex PCR (MP-PCR) protocol to assess cereal aphid-primary parasitoid-hyperparasitoid-endosymbiont interactions. The first step of the assay allows detection of parasitoid DNA at a general level (24 primary and 16 hyperparasitoid species) as well as the species-specific detection of endosymbionts (3 species) and cereal aphids (3 species). The second step of the MP-PCR assay targets seven primary and six hyperparasitoid species that commonly occur in Central Europe. Additional parasitoid species not covered by the second-step of the assay can be identified via sequencing 16S rRNA amplicons generated in the first step of the assay. The approach presented here provides an efficient, highly sensitive, and cost-effective (~consumable costs of 1.3 € per sample) tool for assessing cereal aphid-parasitoid-endosymbiont interactions.
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      Soil nitrogen transformation responses to seasonal precipitation changes are regulated by changes in functional microbial abundance in a subtropical forest 

      Chen, Jie; Xiao, Guoliang; Kuzyakov, Yakov; Jenerette, G. Darrel; Ma, Ying; Liu, Wei; Wang, Zhengfeng; Shen, Weijun
      Biogeosciences 2017; 14(9) p.2513-2525
      The frequency of dry-season droughts and wet-season storms has been predicted to increase in subtropical areas in the coming decades. Since subtropical forest soils are significant sources of N2O and NO3−, it is important to understand the features and determinants of N transformation responses to the predicted precipitation changes. A precipitation manipulation field experiment was conducted in a subtropical forest to reduce dry-season precipitation and increase wet-season precipitation, with annual precipitation unchanged. Net N mineralization, net nitrification, N2O emission, nitrifying (bacterial and archaeal amoA) and denitrifying (nirK, nirS and nosZ) gene abundance, microbial biomass carbon (MBC), extractable organic carbon (EOC), NO3−, NH4+ and soil water content (SWC) were monitored to characterize and explain soil N transformation responses. Dry-season precipitation reduction decreased net nitrification and N mineralization rates by 13–20 %, while wet-season precipitation addition increased both rates by 50 %. More than 20 % of the total variation of net nitrification and N mineralization could be explained by microbial abundance and SWC. Notably, archaeal amoA abundance showed the strongest correlation with net N transformation rates (r  ≥  0.35), suggesting the critical role of archaeal amoA abundance in determining N transformations. Increased net nitrification in the wet season, together with large precipitation events, caused substantial NO3− losses via leaching. However, N2O emission decreased moderately in both dry and wet seasons due to changes in nosZ gene abundance, MBC, net nitrification and SWC (decreased by 10–21 %). We conclude that reducing dry-season precipitation and increasing wet-season precipitation affect soil N transformations through altering functional microbial abundance and MBC, which are further affected by changes in EOC and NH4+ availabilities.
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      What do consumers think about farm animal welfare in modern agriculture? Attitudes and shopping behaviour 

      Heise, Heinke; Theuvsen, Ludwig
      International Food and Agribusiness Management Review 2017; 20(3) p.379-399
      Several food crises damaged the image of the agricultural sector and consumers have lost trust, especially in animal production practices. Large parts of society believe that animal welfare standards in livestock production need to be improved. As a result, numerous animal welfare products have emerged on the market. This consumer paper identifies five clusters and, thus, strategic groups for the purchase of animal welfare products within the large group of consumers that differ significantly in their attitudes towards modern agriculture, their perception of animal welfare, their social acceptance of meat consumption and their shopping behaviour. Even personal differences are found between the clusters. Based on the results, we derived specific marketing implications for each cluster. These implications can help to develop a more differentiated market segment for animal welfare products in terms of animal welfare level and required price premium, enabling consumers to make product choices according to their preferences.
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      CSR activities in the German poultry sector: differencing preference groups 

      Luhmann, Henrike; Theuvsen, Ludwig
      International Food and Agribusiness Management Review 2017; 20(3) p.321-334
      Corporate Social Responsibility (CSR) has long been an issue worldwide, and more and more industries are taking note. One important example is the poultry industry in Germany, which has become a focal point of public debate. Increasingly, consumers are demanding that firms take responsibility for their corporate actions. The goals of this study were, first, to analyze consumers’ preferences for poultry firms’ CSR commitment with the help of an adaptive conjoint analysis. Second, a cluster analysis is set out to define consumer groups according to their preferences. With regard to CSR, consumers in this study were most concerned with product quality, animal welfare and employee issues. TV, newspaper and product packaging are their most preferred information sources. Three clusters were identified. Firms should focus more on communicating what their firm’s commitment comprises and should adapt their CSR activities and firm communication methods to the preferences of different target groups.
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      Conservation of Erwinia amylovora pathogenicity-relevant genes among Erwinia genomes 

      Borruso, Luigimaria; Salomone-Stagni, Marco; Polsinelli, Ivan; Schmitt, Armin Otto; Benini, Stefano
      Archives of Microbiology
      The Erwinia genus comprises species that are plant pathogens, non-pathogen, epiphytes, and opportunistic human pathogens. Within the genus, Erwinia amylovora ranks among the top 10 plant pathogenic bacteria. It causes the fire blight disease and is a global threat to commercial apple and pear production. We analyzed the presence/ absence of the E. amylovora genes reported to be important for pathogenicity towards Rosaceae within various Erwinia strains genomes. This simple bottom-up approach, allowed us to correlate the analyzed genes to pathogenicity, host specificity, and make useful considerations to drive targeted studies.
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      ddRADseq reveals determinants for temperature-dependent sex reversal in Nile tilapia on LG23 

      Wessels, Stephan; Krause, Ina; Floren, Claudia; Schütz, Ekkehard; Beck, Jule; Knorr, Christoph
      BMC Genomics 2017; 18(1)
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      Developing a 670k genotyping array to tag ~2M SNPs across 24 horse breeds 

      Schaefer, Robert J.; Schubert, Mikkel; Bailey, Ernest; Bannasch, Danika L.; Barrey, Eric; Bar-Gal, Gila Kahila; Brem, Gottfried; Brooks, Samantha A.; Distl, Ottmar; Fries, Ruedi; et al.
      Finno, Carrie J.Gerber, VinzenzHaase, BiancaJagannathan, VidhyaKalbfleisch, TedLeeb, TossoLindgren, GabriellaLopes, Maria SusanaMach, Núriada Câmara Machado, ArturMacLeod, James N.McCoy, AnnetteMetzger, JuliaPenedo, CeciliaPolani, SagiRieder, StefanTammen, ImkeTetens, JensThaller, GeorgVerini-Supplizi, AndreaWade, Claire M.Wallner, BarbaraOrlando, LudovicMickelson, James R.McCue, Molly E.
      BMC Genomics 2017; 18(1)
      BACKGROUND: To date, genome-scale analyses in the domestic horse have been limited by suboptimal single nucleotide polymorphism (SNP) density and uneven genomic coverage of the current SNP genotyping arrays. The recent availability of whole genome sequences has created the opportunity to develop a next generation, high-density equine SNP array. RESULTS: Using whole genome sequence from 153 individuals representing 24 distinct breeds collated by the equine genomics community, we cataloged over 23 million de novo discovered genetic variants. Leveraging genotype data from individuals with both whole genome sequence, and genotypes from lower-density, legacy SNP arrays, a subset of ~5 million high-quality, high-density array candidate SNPs were selected based on breed representation and uniform spacing across the genome. Considering probe design recommendations from a commercial vendor (Affymetrix, now Thermo Fisher Scientific) a set of ~2 million SNPs were selected for a next-generation high-density SNP chip (MNEc2M). Genotype data were generated using the MNEc2M array from a cohort of 332 horses from 20 breeds and a lower-density array, consisting of ~670 thousand SNPs (MNEc670k), was designed for genotype imputation. CONCLUSIONS: Here, we document the steps taken to design both the MNEc2M and MNEc670k arrays, report genomic and technical properties of these genotyping platforms, and demonstrate the imputation capabilities of these tools for the domestic horse.
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      The Value of Environmental and Health Claims on New Legume Products: A Non-Hypothetical Online Auction 

      Lemken, Dominic; Knigge, Mandy; Meyerding, Stephan; Spiller, Achim
      Sustainability 2017; 9(8): Art. 1340
      Legumes are valued in agricultural systems, as they can contribute to a more sustainable land use. However, their economic value is low. Despite health and environmental benefits, marketers struggle to communicate the worth of legumes to consumers. We evaluate the worth of health and, in particular, environmental claims that would spread consumers’ awareness of ecological advantages. Utilizing a large consumer sample, we execute binding online auctions. Comparing claim-treated and untreated subjects (between design), we model the price premium that potential customers are willing to pay (WTP) for having pasta in a legume instead of a wheat version. We find that claims may increase the WTP, however, a mix of environmental and health claims is superior to individual claims. Effect sizes suggest that the mix of claims increases the WTP by roughly 35% (20 cents). The link of WTP and food attitudes, such as concern for health in eating habits or social reservations towards legumes, varies depending on whether the green-pea or chickpea pasta was evaluated. A critical perception of legumes’ association with flatulence reduces the WTP. Developing the online auction may enable researchers to increase the external validity of consumer samples. We discuss implications for researchers and marketers.
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      A structural variant in the 5'-flanking region of the TWIST2 gene affects melanocyte development in belted cattle. 

      Awasthi Mishra, Nivedita; Drögemüller, Cord; Jagannathan, Vidhya; Keller, Irene; Wüthrich, Daniel; Bruggmann, Rémy; Beck, Julia; Schütz, Ekkehard; Brenig, Bertram; Demmel, Steffi; et al.
      Moser, SimonSigner-Hasler, HeidiPieńkowska-Schelling, AldonaSchelling, ClaudeSande, MarcosRongen, RonaldRieder, StefanKelsh, Robert N.Mercader, NadiaLeeb, Tosso
      PloS one 2017; 12(6): Art. e0180170
      Belted cattle have a circular belt of unpigmented hair and skin around their midsection. The belt is inherited as a monogenic autosomal dominant trait. We mapped the causative variant to a 37 kb segment on bovine chromosome 3. Whole genome sequence data of 2 belted and 130 control cattle yielded only one private genetic variant in the critical interval in the two belted animals. The belt-associated variant was a copy number variant (CNV) involving the quadruplication of a 6 kb non-coding sequence located approximately 16 kb upstream of the TWIST2 gene. Increased copy numbers at this CNV were strongly associated with the belt phenotype in a cohort of 333 cases and 1322 controls. We hypothesized that the CNV causes aberrant expression of TWIST2 during neural crest development, which might negatively affect melanoblasts. Functional studies showed that ectopic expression of bovine TWIST2 in neural crest in transgenic zebrafish led to a decrease in melanocyte numbers. Our results thus implicate an unsuspected involvement of TWIST2 in regulating pigmentation and reveal a non-coding CNV underlying a captivating Mendelian character.
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      Morgagnian cataract resulting from a naturally occurring nonsense mutation elucidates a role of CPAMD8 in mammalian lens development. 

      Hollmann, Anne K.; Dammann, Insa; Wemheuer, Wiebke M.; Wemheuer, Wilhelm E.; Chilla, Almuth; Tipold, Andrea; Schulz-Schaeffer, Walter J.; Beck, Julia; Schütz, Ekkehard; Brenig, Bertram
      PloS one 2017; 12(7): Art. e0180665
      To investigate the genetic basis of hereditary lens opacities we analyzed 31 cases of bilateral congenital cataract in Red Holstein Friesian cattle. A genome-wide association study revealed a significant association on bovine chromosome 7 at positions 6,166,179 and 12,429,691. Whole genome re-sequencing of one case and four relatives showed a nonsense mutation (g.5995966C>T) in the PZP-like, alpha-2-macroglobulin domain containing 8 (CPAMD8) gene leading to a premature stop codon (CPAMD8 p.Gln74*) associated with cataract development in cattle. With immunohistochemistry we confirmed a physiological expression of CPAMD8 in the ciliary body epithelium of the eye in unaffected cattle, while the protein was not detectable in the ciliary body of cattle with cataracts. RNA expression of CPAMD8 was detected in healthy adult, fetal and cataractous lenses.
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      Evaluation of nine genotypes of oilseed rape (Brassica napus L.) for larval infestation and performance of rape stem weevil (Ceutorhynchus napi Gyll.). 

      Schaefer, Heike L; Brandes, Haiko; Ulber, Bernd; Becker, Heiko C; Vidal, Stefan
      PloS one 2017; 12(7): Art. e0180807
      The rape stem weevil, Ceutorhynchus napi Gyll., is a serious pest of winter oilseed rape (Brassica napus L.) crops in Europe causing severe yield loss. In currently used oilseed rape cultivars no resistance to C. napi has been identified. Resynthesized lines of B. napus have potential to broaden the genetic variability and may improve resistance to insect pests. In this study, the susceptibility to C. napi of three cultivars, one breeding line and five resynthesized lines of oilseed rape was compared in a semi-field plot experiment under multi-choice conditions. Plant acceptance for oviposition was estimated by counting the number of C. napi larvae in stems. The larval instar index and the dry body mass were assessed as indicators of larval performance. The extent of larval feeding within stems was determined by the stem injury coefficient. Morphological stem traits and stem contents of glucosinolates were assessed as potential mediators of resistance. The resynthesized line S30 had significantly fewer larvae than the cultivars Express617 and Visby and the resynthesized lines L122 and L16. The low level of larval infestation in S30 was associated with a low larval instar and stem injury index. Low numbers of larvae were not correlated with the length or diameter of stems, and the level of stem glucosinolates. As indicated by the low larval infestation and slow larval development the resistance of S30 to C. napi is based on both antixenotic and antibiotic properties of the genotypes. The resynthesized line S30 should therefore be introduced into B. napus breeding programs to enhance resistance against C. napi.
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      Rhizosphere hydrophobicity: A positive trait in the competition for water. 

      Zeppenfeld, Thorsten; Balkenhol, Niko; Kóvacs, Kristóf; Carminati, Andrea
      PloS one 2017; 12(7): Art. e0182188
      The ability to acquire water from the soil is a major driver in interspecific plant competition and it depends on several root functional traits. One of these traits is the excretion of gel-like compounds (mucilage) that modify physical soil properties. Mucilage secreted by roots becomes hydrophobic upon drying, impedes the rewetting of the soil close to the root, the so called rhizosphere, and reduces water availability to plants. The function of rhizosphere hydrophobicity is not easily understandable when looking at a single plant, but it may constitute a competitive advantage at the ecosystem level. We hypothesize that by making the top soil hydrophobic, deep-rooted plants avoid competititon with shallow-rooted plants. To test this hypothesis we used an individual-based model to simulate water uptake and growth of two virtual plant species, one deep-rooted plant capable of making the soil hydrophobic and a shallow-rooted plant. We ran scenarios with different precipitation regimes ranging from dry to wet (350, 700, and 1400 mm total annual precipitation) and from high to low precipitation frequencies (1, 7, and 14 days). Plant species abundance and biomass were chosen as indicators for competitiveness of plant species. At constant precipitation frequency mucilage hydrophobicity lead to a benefit in biomass and abundance of the tap-rooted population. Under wet conditions this effect diminished and tap-rooted plants were less productive. Without this trait both species coexisted. The effect of root exudation trait remained constant under different precipitation frequencies. This study shows that mucilage secretion is a competitive trait for the acquisition of water. This advantage is achieved by the modification of the soil hydraulic properties and specifically by inducing water repellency in soil regions which are shared with other species.
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      Rapid Prediction of Moisture Content in Intact Green Coffee Beans Using Near Infrared Spectroscopy 

      Adnan, Adnan; Hörsten, Dieter von; Pawelzik, Elke; Mörlein, Daniel
      Foods 2017; 6(6)
      Moisture content (MC) is one of the most important quality parameters of green coffee beans. Therefore, its fast and reliable measurement is necessary. This study evaluated the feasibility of near infrared (NIR) spectroscopy and chemometrics for rapid and non-destructive prediction of MC in intact green coffee beans of both Coffea arabica (Arabica) and Coffea canephora (Robusta) species. Diffuse reflectance (log 1/R) spectra of intact beans were acquired using a bench top Fourier transform NIR instrument. MC was determined gravimetrically according to The International Organization for Standardization (ISO) 6673. Samples were split into subsets for calibration (n = 64) and independent validation (n = 44). A three-component partial least squares regression (PLSR) model using raw NIR spectra yielded a root mean square error of prediction (RMSEP) of 0.80% MC; a four component PLSR model using scatter corrected spectra yielded a RMSEP of 0.57% MC. A simplified PLS model using seven selected wavelengths (1155, 1212, 1340, 1409, 1724, 1908, and 2249 nm) yielded a similar accuracy (RMSEP: 0.77% MC) which opens the possibility of creating cheaper NIR instruments. In conclusion, NIR diffuse reflectance spectroscopy appears to be suitable for rapid and reliable MC prediction in intact green coffee; no separate model for Arabica and Robusta species is needed.
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      The Effects of Cropping Regimes on Fungal and Bacterial Communities of Wheat and Faba Bean in a Greenhouse Pot Experiment Differ between Plant Species and Compartment 

      Granzow, Sandra; Kaiser, Kristin; Wemheuer, Bernd; Pfeiffer, Birgit; Daniel, Rolf; Vidal, Stefan; Wemheuer, Franziska
      Frontiers in Microbiology 2017; 8: Art. 902
      Many bacteria and fungi in the plant rhizosphere and endosphere are beneficial to plant nutrient acquisition, health, and growth. Although playing essential roles in ecosystem functioning, our knowledge about the effects of multiple cropping regimes on the plant microbiome and their interactions is still limited. Here, we designed a pot experiment simulating different cropping regimes. For this purpose, wheat and faba bean plants were grown under controlled greenhouse conditions in monocultures and in two intercropping regimes: row and mixed intercropping. Bacterial and fungal communities in bulk and rhizosphere soils as well as in the roots and aerial plant parts were analyzed using large-scale metabarcoding. We detected differences in microbial richness and diversity between the cropping regimes. Generally, observed effects were attributed to differences between mixed and row intercropping or mixed intercropping and monoculture. Bacterial and fungal diversity were significantly higher in bulk soil samples of wheat and faba bean grown in mixed compared to row intercropping. Moreover, microbial communities varied between crop species and plant compartments resulting in different responses of these communities toward cropping regimes. Leaf endophytes were not affected by cropping regime but bacterial and fungal community structures in bulk and rhizosphere soil as well as fungal community structures in roots. We further recorded highly complex changes in microbial interactions. The number of negative inter-domain correlations between fungi and bacteria decreased in bulk and rhizosphere soil in intercropping regimes compared to monocultures due to beneficial effects. In addition, we observed plant species-dependent differences indicating that intra- and interspecific competition between plants had different effects on the plant species and thus on their associated microbial communities. To our knowledge, this is the first study investigating microbial communities in different plant compartments with respect to multiple cropping regimes using large-scale metabarcoding. Although a simple design simulating different cropping regimes was used, obtained results contribute to the understanding how cropping regimes affect bacterial and fungal communities and their interactions in different plant compartments. Nonetheless, we need field experiments to properly quantify observed effects in natural ecosystems.
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      Microbial Metabolism in Soil at Subzero Temperatures: Adaptation Mechanisms Revealed by Position-Specific 13C Labeling 

      Bore, Ezekiel K.; Apostel, Carolin; Halicki, Sara; Kuzyakov, Yakov; Dippold, Michaela A.
      Frontiers in Microbiology 2017; 8: Art. 946
      Although biogeochemical models designed to simulate carbon (C) and nitrogen (N) dynamics in high-latitude ecosystems incorporate extracellular parameters, molecular and biochemical adaptations of microorganisms to freezing remain unclear. This knowledge gap hampers estimations of the C balance and ecosystem feedback in high-latitude regions. To analyze microbial metabolism at subzero temperatures, soils were incubated with isotopomers of position-specifically 13C-labeled glucose at three temperatures: C5 (control), 􀀀5, and 􀀀20 C. 13C was quantified in CO2, bulk soil, microbial biomass, and dissolved organic carbon (DOC) after 1, 3, and 10 days and also after 30 days for samples at 􀀀20 C. Compared to C5 C, CO2 decreased 3- and 10-fold at 􀀀5 and 􀀀20 C, respectively. High 13C recovery in CO2 from the C-1 position indicates dominance of the pentose phosphate pathway at C5 C. In contrast, increased oxidation of the C-4 position at subzero temperatures implies a switch to glycolysis. A threefold higher 13C recovery in microbial biomass at 􀀀5 than C5 C points to synthesis of intracellular compounds such as glycerol and ethanol in response to freezing. Less than 0.4% of 13C was recovered in DOC after 1 day, demonstrating complete glucose uptake by microorganisms even at 􀀀20 C. Consequently, we attribute the fivefold higher extracellular 13C in soil than in microbial biomass to secreted antifreeze compounds. This suggests that with decreasing temperature, intracellular antifreeze protection is complemented by extracellular mechanisms to avoid cellular damage by crystallizing water. The knowledge of sustained metabolism at subzero temperatures will not only be useful for modeling global C dynamics in ecosystems with periodically or permanently frozen soils, but will also be important in understanding and controlling the adaptive mechanisms of food spoilage organisms.
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      The crystal structure of Erwinia amylovora AmyR, a member of the YbjN protein family, shows similarity to type III secretion chaperones but suggests different cellular functions 

      Bartho, Joseph D.; Bellini, Dom; Wuerges, Jochen; Demitri, Nicola; Toccafondi, Mirco; Schmitt, Armin O.; Zhao, Youfu; Walsh, Martin A.; Benini, Stefano
      PLOS ONE 2017; 12(4): Art. e0176049
      AmyR is a stress and virulence associated protein from the plant pathogenic Enterobacteriaceae species Erwinia amylovora, and is a functionally conserved ortholog of YbjN from Escherichia coli. The crystal structure of E. amylovora AmyR reveals a class I type III secretion chaperone-like fold, despite the lack of sequence similarity between these two classes of protein and lacking any evidence of a secretion-associated role. The results indicate that AmyR, and YbjN proteins in general, function through protein-protein interactions without any enzymatic action. The YbjN proteins of Enterobacteriaceae show remarkably low sequence similarity with other members of the YbjN protein family in Eubacteria, yet a high level of structural conservation is observed. Across the YbjN protein family sequence conservation is limited to residues stabilising the protein core and dimerization interface, while interacting regions are only conserved between closely related species. This study presents the first structure of a YbjN protein from Enterobacteriaceae, the most highly divergent and well-studied subgroup of YbjN proteins, and an in-depth sequence and structural analysis of this important but poorly understood protein family.
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