Recent Submissions

  • Journal Article

    Identification of Candidate Signature Genes and Key Regulators Associated With Trypanotolerance in the Sheko Breed 

    Mekonnen, Yonatan Ayalew; Gültas, Mehmet; Effa, Kefena; Hanotte, Olivier; Schmitt, Armin O.
    Frontiers in Genetics 2019; 10: Art. 1095
    African animal trypanosomiasis (AAT) is caused by a protozoan parasite that affects the health of livestock. Livestock production in Ethiopia is severely hampered by AAT and various controlling measures were not successful to eradicate the disease. AAT affects the indigenous breeds in varying degrees. However, the Sheko breed shows better trypanotolerance than other breeds. The tolerance attributes of Sheko are believed to be associated with its taurine genetic background but the genetic controls of these tolerance attributes of Sheko are not well understood. In order to investigate the level of taurine background in the genome, we compare the genome of Sheko with that of 11 other African breeds. We find that Sheko has an admixed genome composed of taurine and indicine ancestries. We apply three methods: (i) The integrated haplotype score (iHS), (ii) the standardized log ratio of integrated site specific extended haplotype homozygosity between populations (Rsb), and (iii) the composite likelihood ratio (CLR) method to discover selective sweeps in the Sheko genome. We identify 99 genomic regions harboring 364 signature genes in Sheko. Out of the signature genes, 15 genes are selected based on their biological importance described in the literature. We also identify 13 overrepresented pathways and 10 master regulators in Sheko using the TRANSPATH database in the geneXplain platform. Most of the pathways are related with oxidative stress responses indicating a possible selection response against the induction of oxidative stress following trypanosomiasis infection in Sheko. Furthermore, we present for the first time the importance of master regulators involved in trypanotolerance not only for the Sheko breed but also in the context of cattle genomics. Our finding shows that the master regulator Caspase is a key protease which plays a major role for the emergence of adaptive immunity in harmony with the other master regulators. These results suggest that designing and implementing genetic intervention strategies is necessary to improve the performance of susceptible animals. Moreover, the master regulatory analysis suggests potential candidate therapeutic targets for the development of new drugs for trypanosomiasis treatment.
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  • Journal Article

    Mitigation efforts will not fully alleviate the increase in water scarcity occurrence probability in wheat-producing areas 

    Trnka, Miroslav; Feng, Song; Semenov, Mikhail A.; Olesen, Jørgen E.; Kersebaum, Kurt Christian; Rötter, Reimund P.; Semerádová, Daniela; Klem, Karel; Huang, Wei; Ruiz-Ramos, Margarita; et al.
    Hlavinka, PetrMeitner, JanBalek, JanHavlík, PetrBüntgen, Ulf
    Science Advances 2019; 5(9): Art. eaau2406
    Global warming is expected to increase the frequency and intensity of severe water scarcity (SWS) events, which negatively affect rain-fed crops such as wheat, a key source of calories and protein for humans. Here, we develop a method to simultaneously quantify SWS over the world’s entire wheat-growing area and calculate the probabilities of multiple/sequential SWS events for baseline and future climates. Our projections show that, without climate change mitigation (representative concentration pathway 8.5), up to 60% of the current wheat-growing area will face simultaneous SWS events by the end of this century, compared to 15% today. Climate change stabilization in line with the Paris Agreement would substantially reduce the negative effects, but they would still double between 2041 and 2070 compared to current conditions. Future assessments of production shocks in food security should explicitly include the risk of severe, prolonged, and near-simultaneous droughts across key world wheat-producing areas.
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  • Journal Article

    Classification of Pigs with Tail Lesions from Different Farrowing and Rearing Systems during Rearing and Fattening Period 

    Gentz, Maria; Lange, Anita; Zeidler, Sebastian; Traulsen, Imke
    Animals 2019; 9(11): Art. 949
    The aim of the present study was to classify and characterise pigs with tail lesions using a combined parameter based on the frequency and duration of tail lesions and to find out whether biologically relevant groups could be separated by cluster analysis. Pigs (n = 677, 50% docked, 50% undocked) from three farrowing systems, as follows: (1) Conventional farrowing crate (FC), (2) free farrowing (FF), and (3) a group housing lactating sows (GH), were divided into two rearing systems as follows: (1) A conventional system (CONV) and (2) a wean-to-finish (W-F) system. Within 18 assessment weeks, starting after weaning, animal tail lesions were recorded individually. The animals were characterised into five lesion groups, as follows: (I) No lesions to (V) many long lasting lesions. The separability of the predefined lesion groups was checked by an animal individual lesion parameter. By using a k-means cluster analysis, it was shown that the docking status was the mainly affected parameter on the tail lesions. The separation of the groups only succeeded for the most distinct groups, I and V. The high impact of the docking status and the reduction of tail lesions by more space allowance was shown. More characterising information for the individual pigs would improve the separability of the lesion groups
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  • Journal Article

    Role of Salicylic Acid and Components of the Phenylpropanoid Pathway in Basal and Cultivar-Related Resistance of Oilseed Rape (Brassica napus) to Verticillium longisporum 

    Zheng, Xiaorong; Koopmann, Birger; von Tiedemann, Andreas
    Plants 2019; 8(11): Art. 491
    Enhanced resistance is a key strategy of controlling ‘Verticillium stem striping’ in Brassica napus caused by the soil-borne vascular pathogen Verticillium longisporum. The present study analyses the role of a broad range of components in the phenylpropanoid and salicylic acid (SA) pathways in basal and cultivar-related resistance of B. napus towards V. longisporum. A remarkable increase of susceptibility to V. longisporum in SA-deficient transgenic NahG plants indicated an essential role of SA in basal resistance of B. napus to V. longisporum. Accordingly, elevated SA levels were also found in a resistant and not in a susceptible cultivar during early asymptomatic stages of infection (7 dpi), which was associated with increased expression of PR1 and PR2. In later symptomatic stages (14 or 21 dpi), SA responses did not di er anymore between cultivars varying in resistance. In parallel, starting at 7 dpi, an overall increase in phenylpropanoid syntheses developed in the resistant cultivar, including the activity of some key enzymes, phenylalanine ammonium lyase (PAL), cinnamyl alcohol dehydrogenase (CAD) and peroxidase (POX) and the expression of key genes, PAL4, CCoAMT, CCR, POX. As a consequence, a remarkable increase in the levels of phenolic acids (t-cinnamic acid, p-coumaric acid, ca eic acid, ferulic acid, sinapic acid) occurred associated with cultivar resistance. A principal component analysis including all 27 traits studied indicated that component 1 related to SA synthesis (PR1, PR2, POX, level of free SA) and component 2 related to lignin synthesis (level of free ferulic acid, free p-coumaric acid, conjugated t-cinnamic acid) were the strongest factors to determine cultivar-related resistance. This study provides evidence that both SA and phenolic acid synthesis are important in cultivar-related resistance, however, with di erential roles during asymptomatic and symptomatic stages of infection.
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  • Journal Article

    Por que o Brasil precisa de suas Reservas Legais 

    Metzger, Jean Paul; Bustamante, Mercedes M.C.; Ferreira, Joice; Fernandes, Geraldo Wilson; Librán‐Embid, Felipe; Pillar, Valério D.; Prist, Paula R.; Rodrigues, Ricardo Ribeiro; Vieira, Ima Célia G.; Overbeck, Gerhard E.
    Perspectives in Ecology and Conservation 2019; 17(3) p.104-116
    A legislação ambiental brasileira requer que as propriedades privadas mantenham uma proporção de sua área coberta com vegetação nativa, as chamadas Reservas Legais. Essas áreas representam praticamente um terço da vegetação nativa do país e são reconhecidas pelo seu importante papel na proteção da biodiversidade e na provisão de uma vasta gama de serviços ecossistêmicos aos proprietários rurais e à sociedade. Apesar de sua relevância, o estabelecimento de Reservas Legais tem sido criticado por parte do agronegócio e seus representantes no Congresso Nacional. A exigência de Reservas Legais é considerada demasiadamente restritiva e impediria a plena expansão das atividades agrícolas e, por conseguinte, prejudicaria o desenvolvimento do país. Aqui, analisamos criticamente os argumentos de um projeto de lei recentemente proposto, que visa a extinguir completamente as Reservas Legais. Demonstramos que os argumentos usados não têm apoio em dados, evidências ou teorias, além de ser baseados em raciocínio ilógico. Além disso, sintetizamos os principais benefícios das Reservas Legais, inclusive benefícios econômicos e para a saúde humana, e enfatizamos a importância dessas reservas para as seguranças hídrica, energética, alimentar e climática, além de sua função primária de auxiliar na manutenção da biodiversidade em paisagens agrícolas. Destacamos também que as Reservas Legais são um componente‐chave para soluções baseadas na natureza, que são reconhecidamente mais eficazes e menos dispendiosas. Devem, assim, serum consideradas como ativos para o desenvolvimento do Brasil, e não como passivos. Baseados nas sólidas evidências científicas disponíveis e na concordância sobre a relevância das Reservas Legais, opomo‐nos veementemente a qualquer tentativa de extinguir ou enfraquecer a manutenção dessas áreas.
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  • Journal Article

    Why Brazil needs its Legal Reserves 

    Metzger, Jean Paul; Bustamante, Mercedes M.C.; Ferreira, Joice; Fernandes, Geraldo Wilson; Librán-Embid, Felipe; Pillar, Valério D.; Prist, Paula R.; Rodrigues, Ricardo Ribeiro; Vieira, Ima Célia G.; Overbeck, Gerhard E.
    Perspectives in Ecology and Conservation 2019; 17(3) p.91-103
    Brazil's environmental legislation obliges private properties to retain a fixed proportion of their total area with native vegetation, the so-called “Legal Reserves”. Those areas represent practically one third of the country's native vegetation and are well known for their role in biodiversity protection and in the provisioning of a wide range of ecosystem services for landowners and society. Despite their relevance, this instrument has been criticized by part of the agribusiness sector and its representatives in the Brazilian Congress. The Legal Reserve requirement is said to be too restrictive and to impede the full expansion of agricultural activities, and thus to be detrimental for the development of the country. Here, we critically analyze the arguments employed in the justification of a recently proposed bill that aims to completely extinguish Legal Reserves. We demonstrate that the arguments used are mostly unsupported by data, evidence or theory, besides being based on illogical reasoning. Further, we synthesize the principal benefits of Legal Reserves, including health and economic benefits, and emphasize the importance of these reserves for water, energy, food, and climate securities, in addition to their primary function of assisting in the maintenance of biodiversity in agricultural landscapes. We also highlight that Legal Reserves are a key-component for effective and less expensive nature-based solutions, and thus should be considered as assets for the development of Brazil rather than liabilities. Based on available sound scientific evidence and agreement on their relevance, we strongly oppose any attempt to extinguish or weaken the maintenance of Brazil's Legal Reserves.
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  • Journal Article

    Best Prediction of the Additive Genomic Variance in Random-Effects Models 

    Schreck, Nicholas; Piepho, Hans-Peter; Schlather, Martin
    Genetics 2019; 213(2) p.379-394
    The additive genomic variance in linear models with random marker effects can be defined as a random variable that is in accordance with classical quantitative genetics theory. Common approaches to estimate the genomic variance in random-effects linear models based on genomic marker data can be regarded as estimating the unconditional (or prior) expectation of this random additive genomic variance, and result in a negligence of the contribution of linkage disequilibrium (LD). We introduce a novel best prediction (BP) approach for the additive genomic variance in both the current and the base population in the framework of genomic prediction using the genomic best linear unbiased prediction (gBLUP) method. The resulting best predictor is the conditional (or posterior) expectation of the additive genomic variance when using the additional information given by the phenotypic data, and is structurally in accordance with the genomic equivalent of the classical additive genetic variance in random-effects models. In particular, the best predictor includes the contribution of (marker) LD to the additive genomic variance and possibly fully eliminates the missing contribution of LD that is caused by the assumptions of statistical frameworks such as the random-effects model. We derive an empirical best predictor (eBP) and compare its performance with common approaches to estimate the additive genomic variance in random-effects models on commonly used genomic datasets.
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  • Journal Article

    Transgenic cotton and farmers’ health in Pakistan 

    Kouser, Shahzad; Spielman, David J.; Qaim, Matin
    PLOS ONE 2019; 14(10): Art. e0222617
    Despite substantial research on the economic effects of transgenic insect-resistant Bacillus thuringiensis (Bt) cotton, there is still limited work on this technology's impacts on human health. Due to the inbuilt insect resistance, Bt cotton requires fewer pesticide sprays than conventional cotton, which is not only advantageous from economic and environmental perspectives, but may also result in health benefits for farmers. Using socioeconomic and biophysical data from Pakistan, we provide the first evidence of a direct association between Bt gene expression in the plant and health benefits. A key feature of this study is that Bt cotton cultivation in Pakistan occurs in a poorly regulated market: farmers are often mistaken in their beliefs about whether they have planted Bt cotton or conventional cotton, which may affect their pesticide-use strategies and thus their pesticide exposure. We employ a cost-of-illness approach and variations in the measurement of Bt adoption to estimate the relationship between Bt cotton and farmers' health. Bt adoption based on farmers' beliefs does not reduce the pesticide-induced cost of illness. However, adoption based on measuring Bt gene expression is associated with significant health cost savings. Extrapolating the estimates for true Bt seeds to Pakistan's entire Bt cotton area results in annual health cost savings of around US$ 7 million. These findings have important implications for the regulation of seed markets in Pakistan and beyond: improved regulations that ensure claimed crop traits are really expressed can increase the benefits for farmers and society at large.
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  • Journal Article

    Eliminating vicine and convicine, the main anti-nutritional factors restricting faba bean usage 

    Khazaei, Hamid; Purves, Randy W.; Hughes, Jessa; Link, Wolfgang; O'Sullivan, Donal M.; Schulman, Alan H.; Björnsdotter, Emilie; Geu-Flores, Fernando; Nadzieja, Marcin; Andersen, Stig U.; et al.
    Stougaard, JensVandenberg, AlbertStoddard, Frederick L.
    Trends in Food Science & Technology 2019; 91 p.549-556
    Background Faba bean (Vicia faba L.) seeds are an excellent source of plant-based protein. In spite of the vast nutritional and environmental benefits provided by faba bean cultivation, its use as a food crop has been restricted, primarily due to the presence of the pyrimidine glycosides vicine and convicine (v-c). Ingestion of v-c can cause favism in individuals with a genetically inherited deficiency in glucose-6-phosphate dehydrogenase (G6PD). In monogastric animals, v-c can cause decreased feeding efficiency. The elimination of these glucosides is a goal of most faba bean breeding programs worldwide. Scope and approach Our review focuses on the current genetic, molecular and biochemical knowledge surrounding the accumulation of v-c in faba beans. The gap between the current knowledge and what remains unknown is discussed. This review also explores historical and obscure information on v-c in faba bean. Key findings and conclusions A low-v-c faba bean line was identified in the 1980s and this trait has been introduced into several modern cultivars. It has been shown that low-v-c faba beans are safe for G6PD-deficient individuals. A robust molecular marker is now available for marker-assisted breeding to reduce levels of v-c. The biosynthetic pathway of v-c is not yet understood and is currently under investigation. An international coordinated effort, led by the authors of this paper, is making progress towards full elucidation of the pathway. Further efforts in this direction could lead to lower levels of these compounds than the current low v-c genotypes offer, perhaps even complete elimination.
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  • Journal Article

    Assessment of Fusarium Infection and Mycotoxin Contamination of Wheat Kernels and Flour Using Hyperspectral Imaging 

    Alisaac, Elias; Behmann, Jan; Rathgeb, Anna; Karlovsky, Petr; Dehne, Heinz-Wilhelm; Mahlein, Anne-Katrin
    Toxins 2019; 11(10): Art. 556
    Fusarium head blight (FHB) epidemics in wheat and contamination with Fusarium mycotoxins has become an increasing problem over the last decades. This prompted the need for non-invasive and non-destructive techniques to screen cereal grains for Fusarium infection, which is usually accompanied by mycotoxin contamination. This study tested the potential of hyperspectral imaging to monitor the infection of wheat kernels and flour with three Fusarium species. Kernels of two wheat varieties inoculated at anthesis with F. graminearum, F. culmorum, and F. poae were investigated. Hyperspectral images of kernels and flour were taken in the visible-near infrared (VIS-NIR) (400-1000 nm) and short-wave infrared (SWIR) (1000-2500 nm) ranges. The fungal DNA and mycotoxin contents were quantified. Spectral reflectance of Fusarium-damaged kernels (FDK) was significantly higher than non-inoculated ones. In contrast, spectral reflectance of flour from non-inoculated kernels was higher than that of FDK in the VIS and lower in the NIR and SWIR ranges. Spectral reflectance of kernels was positively correlated with fungal DNA and deoxynivalenol (DON) contents. In the case of the flour, this correlation exceeded r = -0.80 in the VIS range. Remarkable peaks of correlation appeared at 1193, 1231, 1446 to 1465, and 1742 to 2500 nm in the SWIR range.
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  • Journal Article

    Food Security and Dietary Quality in African Slums 

    Wanyama, Rosina; Gödecke, Theda; Qaim, Matin
    Sustainability 2019; 11(21): Art. 5999
    More than half of Africa’s urban population lives in slums. Little is known about their nutritional situation, as slums are often underrepresented in standard surveys. This study analyzes issues of food security and dietary quality in East African slums using household-level and individual-level data collected in Nairobi and Kampala. The household food insecurity access scale (HFIAS) is used as a subjective measure of food security. Moreover, calorie availability and different dietary diversity scores are calculated based on 7-day food consumption recalls at the household level and 24-hour dietary recalls at the individual level. The large majority of the slum households are food insecure and suffer from low dietary quality. Rates of undernourishment are considerably higher than what country-level statistics report, suggesting that slum dwellers deserve more explicit attention in initiatives to improve nutrition. Household-level indicators are significantly correlated with individual-level indicators for women and children. This means that household-level data, which are easier to collect, can proxy for individual nutrition up to a certain extent when individual-level data are unavailable. Regression models show that household income is one of the main factors explaining dietary patterns. Hence, facilitating access to lucrative employment is an important entry point for improving nutrition in slums.
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  • Journal Article

    Different Components of the RNA Interference Machinery Are Required for Conidiation, Ascosporogenesis, Virulence, Deoxynivalenol Production, and Fungal Inhibition by Exogenous Double-Stranded RNA in the Head Blight Pathogen Fusarium graminearum 

    Gaffar, Fatima Yousif; Imani, Jafargholi; Karlovsky, Petr; Koch, Aline; Kogel, Karl-Heinz
    Frontiers in Microbiology 2019; 10: Art. 1662
    In filamentous fungi, gene silencing through RNA interference (RNAi) shapes many biological processes, including pathogenicity. We explored the requirement of key components of fungal RNAi machineries, including DICER-like 1 and 2 (FgDCL1, FgDCL2), ARGONAUTE 1 and 2 (FgAGO1, FgAGO2), AGO-interacting protein FgQIP (QDE2-interacting protein), RecQ helicase (FgQDE3), and four RNA-dependent RNA polymerases (FgRdRP1, FgRdRP2, FgRdRP3, FgRdRP4), in the ascomycete mycotoxin-producing fungal pathogen Fusarium graminearum (Fg) for sexual and asexual multiplication, pathogenicity, and its sensitivity to double-stranded (ds)RNA. We corroborate and extend earlier findings that conidiation, ascosporogenesis, and Fusarium head blight (FHB) symptom development require an operable RNAi machinery. The involvement of RNAi in conidiation is dependent on environmental conditions as it is detectable only under low light (<2 μmol m-2 s-1). Although both DCLs and AGOs partially share their functions, the sexual ascosporogenesis is mediated primarily by FgDCL1 and FgAGO2, while FgDCL2 and FgAGO1 contribute to asexual conidia formation and germination. FgDCL1 and FgAGO2 also account for pathogenesis as their knockout (KO) results in reduced FHB development. Apart from KO mutants Δdcl2 and Δago1, mutants Δrdrp2, Δrdrp3, Δrdrp4, Δqde3, and Δqip are strongly compromised for conidiation, while KO mutations in all RdPRs, QDE3, and QIP strongly affect ascosporogenesis. Analysis of trichothecenes mycotoxins in wheat kernels showed that the relative amount of deoxynivalenol (DON), calculated as [DON] per amount of fungal genomic DNA was reduced in all spikes infected with RNAi mutants, suggesting the possibility that the fungal RNAi pathways affect Fg's DON production. Moreover, silencing of fungal genes by exogenous target gene-specific double-stranded RNA (dsRNA) (spray-induced gene silencing, SIGS) is dependent on DCLs, AGOs, and QIP, but not on QDE3. Together these data show that in F. graminearum, different key components of the RNAi machinery are crucial in different steps of fungal development and pathogenicity.
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  • Journal Article

    Mucilage Facilitates Nutrient Diffusion in the Drying Rhizosphere 

    Zarebanadkouki, Mohsen; Fink, Theresa; Benard, Pascal; Banfield, Callum C.
    Vadose Zone Journal 2019; 18(1)
    Despite detailed investigations of its distinct biochemical properties and their effects on the availability of nutrients for plants, the biophysical aspects of the rhizosphere, particularly the effect of mucilage on the transport of water and nutrients, are poorly understood. The aim of this study was to investigate the effect of mucilage on the diffusion of nutrients and consequently their transport through the rhizosphere into the plant roots. Phosphor imaging technique determined the temporospatial distribution of 137Cs in a model rhizosphere (a sandy soil mixed with chia seed (Salvia hispanica L) mucilage. The observed profiles of activities were used to estimate the diffusion coefficient of K in soils. A diffusion–convection equation was numerically solved to predict the transport of K and its uptake by a single plant root in drying soil. The results suggest that mucilage (i) keeps the rhizosphere wet and (ii) maintains the connectivity of the liquid phase in drying soil. In these ways, mucilage moderates the drop in diffusive transport. The modeling results showed that the presence of mucilage in the rhizosphere (i) prevents depletion of nutrients in soils with a low nutrient concentration in the soil solution and (ii) delays the risk of nutrient and/or salt accumulation in the vicinity of the root in soils with a high concentration nutrient and/or salt the soil solution. In conclusion, mucilage appears to mitigate the risk of nutrient deficiency and salinity stress as it enhances the diffusive transport in drying soil. In this way, mucilage may favor the transport of nutrients within the rhizosphere and their uptake by plant roots in drying soil.
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  • Journal Article

    Meta‐analysis of the role of entomopathogenic and unspecialized fungal endophytes as plant bodyguards 

    Gange, Alan C.; Koricheva, Julia; Currie, Amanda F.; Jaber, Lara R.; Vidal, Stefan
    New Phytologist 2019; 223(4) p.2002-2010
    Herbaceous plants harbour species-rich communities of asymptomatic endophytic fungi. Although some of these endophytes are entomopathogenic, many are not, and remarkably little is known about how the presence of these fungi in plant tissues affects phytophagous insects. Here we show through a meta-analysis that both entomopathogenic and nonentomopathogenic endophytes have a negative effect on insect herbivores. Growth and performance of polyphagous and sucking insects are reduced by nonentomopathogenic endophytes, but monophages are unaffected, likely because the latter are better adapted to secondary metabolites produced or induced by the fungi. Furthermore, studies using excised leaves report weaker effects than those with intact plants, likely caused by chemical changes being masked by leaf excision. Most surprisingly, endophyte infection of seeds produces the greatest effect on insect herbivores in subsequent mature plants, even though the usual mode of fungal transmission is infection of leaves by airborne spores. We conclude that these ubiquitous hidden fungi may be important bodyguards of plants. However, in order to fully understand their roles in plant protection, we must be aware that minor differences in experimental design can lead to contradictory results.
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  • Journal Article

    Feed Intake of Small Ruminants on Spring and Summer Pastures in the Mongolian Altai Mountains 

    Tsevegemed, Munkhnasan; Norovsambuu, Togtokhbayar; Jordan, Greta; Schlecht, Eva
    Sustainability 2019; 11(20): Art. 5759
    Climate variability, rising livestock numbers, decreasing herd mobility, and clustered grazing patterns have incited concern about the sustainable use of Mongolia’s natural pastures as the nutritional backbone of the country’s livestock sector. In 2013 and 2014 we studied daily itineraries, grazing behaviour, and feed and nutrient intake of small ruminants on spring and summer pastures in the southern Mongolian Altai, a remote livestock-dependent region. O er of herbage dry matter (DM, kg ha􀀀1) along the daily itinerary was higher in 2014 than in 2013 (837 versus 711; p > 0.05) but was comparable to previously reported values. Concentration of cell wall constituents in herbage increased from June to August in both years, whereas crude protein and phosphorus concentrations declined (p < 0.05). Animals grazed most actively at noon and in the afternoon; their daily DM intake amounted to 1151 300.8 g per head, with 60–72% of the ingested feed being digested. Feed intake enabled the animals to cover their nutritional requirements for maintenance, locomotion, and sizeable growth, rebutting the notion of unsustainable use of the regional spring and summer pastures. However, crude protein and phosphorus intake were deficient, pointing to a decline in vegetation quality that has to be counteracted with appropriate herd and pasture management strategies.
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  • Journal Article

    Microbial spatial footprint as a driver of soil carbon stabilization 

    Kravchenko, A. N.; Guber, A. K.; Razavi, B. S.; Koestel, J.; Quigley, M. Y.; Robertson, G. P.; Kuzyakov, Y.
    Nature Communications 2019; 10(1): Art. 3121
    Increasing the potential of soil to store carbon (C) is an acknowledged and emphasized strategy for capturing atmospheric CO2. Well-recognized approaches for soil C accretion include reducing soil disturbance, increasing plant biomass inputs, and enhancing plant diversity. Yet experimental evidence often fails to support anticipated C gains, suggesting that our integrated understanding of soil C accretion remains insufficient. Here we use a unique combination of X-ray micro-tomography and micro-scale enzyme mapping to demonstrate for the first time that plant-stimulated soil pore formation appears to be a major, hitherto unrecognized, determinant of whether new C inputs are stored or lost to the atmosphere. Unlike monocultures, diverse plant communities favor the development of 30-150 µm pores. Such pores are the micro-environments associated with higher enzyme activities, and greater abundance of such pores translates into a greater spatial footprint that microorganisms make on the soil and consequently soil C storage capacity.
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  • Journal Article

    Regulation of Symbiotic Nitrogen Fixation in Legume Root Nodules 

    Schwember, Andrés R.; Schulze, Joachim; del Pozo, Alejandro; Cabeza, Ricardo A.
    Plants 2019; 8(9): Art. 333
    In most legume nodules, the di-nitrogen (N2)-fixing rhizobia are present as organelle-like structures inside their root host cells. Many processes operate and interact within the symbiotic relationship between plants and nodules, including nitrogen (N)/carbon (C) metabolisms, oxygen flow through nodules, oxidative stress, and phosphorous (P) levels. These processes, which influence the regulation of N2 fixation and are finely tuned on a whole-plant basis, are extensively reviewed in this paper. The carbonic anhydrase (CA)-phosphoenolpyruvate carboxylase (PEPC)-malate dehydrogenase (MDH) is a key pathway inside nodules involved in this regulation, and malate seems to play a crucial role in many aspects of symbiotic N2 fixation control. How legumes specifically sense N-status and how this stimulates all of the regulatory factors are key issues for understanding N2 fixation regulation on a whole-plant basis. This must be thoroughly studied in the future since there is no unifying theory that explains all of the aspects involved in regulating N2 fixation rates to date. Finally, high-throughput functional genomics and molecular tools (i.e., miRNAs) are currently very valuable for the identification of many regulatory elements that are good candidates for accurately dissecting the particular N2 fixation control mechanisms associated with physiological responses to abiotic stresses. In combination with existing information, utilizing these abundant genetic molecular tools will enable us to identify the specific mechanisms underlying the regulation of N2 fixation.
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  • Journal Article

    Genetic diversity of common guava in Kenya: an underutilized naturalized fruit species 

    Chiveu, J.C.; Mueller, M.; Krutovsky, K.V.; Kehlenbeck, K.; Pawelzik, E.; Naumann, M.
    Fruits 2019; 74(5) p.236-248
    Introduction – Common guava (Psidium guajava L.) fruit has a significant nutritional and medicinal potential besides its economic importance. Currently, the world guava fruit production is based only on a few cultivars. It is not clear when guava was introduced in Kenya, but the species is currently naturalized. There is no detailed study on guava diversity in Kenya to enable a comparison with other guava-producing countries for purposes of characterization and improvement. Objectives – The main objective of the study was to analyse the genetic diversity and differentiation of guava accessions from four geographically diverse regions of Kenya. Materials and methods – The genetic diversity of 177 guava accessions collected from four regions of Kenya (Coast, Eastern, Rift Valley, and Western) was assessed using 13 simple sequence repeat (SSR) markers. Results and discussion – The neighbour-joining (NJ) phylogenetic tree revealed most accessions generally clustering into multiple weakly supported groups. Only 46 out of 177 accessions were supported by bootstrap values above 50% and clustered in twenty-two groups, each comprising two or three individual accessions only. The principle coordinates analysis (PCoA) did not reveal clear-cut clusters along geographic origins or fruit flesh colour of the samples. The fixation index (FIS) was very high (FIS=0.511), which could be due to a high level of either inbreeding and/or differentiation. The white-fleshed accessions were clustered together with the red-fleshed types, indicative of some degree of genetic similarity, but also pointing to a possibility of shared ancestry between them. Conclusion – For guava conservation and selection for breeding and utilization purposes in Kenya, sampling of many individual accessions covering the geographical range of the species is recommended.
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  • Journal Article

    The NLRX R package: A next‐generation framework for reproducible NetLogo model analyses 

    Salecker, Jan; Sciaini, Marco; Meyer, Katrin M.; Wiegand, Kerstin
    Methods in Ecology and Evolution
    1. Agent‐based models find wide application in all fields of science where large‐scale patterns emerge from properties of individuals. Due to increasing capacities of computing resources it was possible to improve the level of detail and structural realism of nextgeneration models in recent years. However, this is at the expense of increased model complexity, which requires more efficient tools for model exploration, analysis and documentation that enable reproducibility, repeatability and parallelization. NetLogo is a widely used environment for agent‐based model development, but it does not provide sufficient built‐in tools for extensive model exploration, such as sensitivity analyses. One tool for controlling NetLogo externally is the r‐package RNetLogo. However, this package is not suited for efficient, reproducible research as it has stability and resource allocation issues, is not straightforward to be setup and used on high performance computing clusters and does not provide utilities, such as storing and exchanging metadata, in an easy way. 2. We present the r‐package nlrx, which overcomes stability and resource allocation issues by running NetLogo simulations via dynamically created XML experiment files. Class objects make setting up experiments more convenient and helper functions provide many parameter exploration approaches, such as Latin Hypercube designs, Sobol sensitivity analyses or optimization approaches. Output is automatically collected in user‐friendly formats and can be post‐processed with provided utility functions. nlrx enables reproducibility by storing all relevant information and simulation output of experiments in one r object which can conveniently be archived and shared. 3. We provide a detailed description of the nlrx package functions and the overall workflow. We also present a use case scenario using a NetLogo model, for which we performed a sensitivity analysis and a genetic algorithm optimization. 4. The nlrx package is the first framework for documentation and application of reproducible NetLogo simulation model analysis.
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  • Journal Article

    CO2 conversion to methane and biomass in obligate methylotrophic methanogens in marine sediments 

    Yin, Xiuran; Wu, Weichao; Maeke, Mara; Richter-Heitmann, Tim; Kulkarni, Ajinkya C.; Oni, Oluwatobi E.; Wendt, Jenny; Elvert, Marcus; Friedrich, Michael W.
    The ISME Journal 2019; 13(8) p.2107-2119
    Methyl substrates are important compounds for methanogenesis in marine sediments but diversity and carbon utilization by methylotrophic methanogenic archaea have not been clarified. Here, we demonstrate that RNA-stable isotope probing (SIP) requires 13C-labeled bicarbonate as co-substrate for identification of methylotrophic methanogens in sediment samples of the Helgoland mud area, North Sea. Using lipid-SIP, we found that methylotrophic methanogens incorporate 60-86% of dissolved inorganic carbon (DIC) into lipids, and thus considerably more than what can be predicted from known metabolic pathways (~40% contribution). In slurry experiments amended with the marine methylotroph Methanococcoides methylutens, up to 12% of methane was produced from CO2, indicating that CO2-dependent methanogenesis is an alternative methanogenic pathway and suggesting that obligate methylotrophic methanogens grow in fact mixotrophically on methyl compounds and DIC. Although methane formation from methanol is the primary pathway of methanogenesis, the observed high DIC incorporation into lipids is likely linked to CO2-dependent methanogenesis, which was triggered when methane production rates were low. Since methylotrophic methanogenesis rates are much lower in marine sediments than under optimal conditions in pure culture, CO2 conversion to methane is an important but previously overlooked methanogenic process in sediments for methylotrophic methanogens.
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