Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Exploring the usefulness of scenario archetypes in science-policy processes: Experience across IPBES assessments
Sitas, Nadia ; Harmáčková, Zuzana V. ; Anticamara, Jonathan A. ; Arneth, Almut ; Badola, Ruchi ; Biggs, Reinette ; Blanchard, Ryan ; Brotons, Lluis ; Cantele, Matthew ; Coetzer, Kaera ; Dasgupta, Rajarshi ; Belder, Eefje Den; Ghosh, Sonali ; Guisan, Antoine ; Gundimeda, Haripriya ; Hamann, Maike ; Harrison, Paula A. ; Hashimoto, Shizuka ; Hauck, Jennifer ; Klatt, Brian J. ; Kok, Kasper ; Krug, Rainer M. ; Niamir, Aidin ; O'farrell, Patrick J. ; Okayasu, Sana ; Palomo, Ignacio ; Pereira, Laura M. ; Riordan, Philip ; Santos-Martín, Fernando ; Selomane, Odirilwe ; Shin, Yunne Jai ; Valle, Mireia - \ 2019
Ecology and Society 24 (2019)3. - ISSN 1708-3087
Assessment - Biodiversity - Decision making - Ecosystem services - Futures - Nature - Regional - Scenarios

Scenario analyses have been used in multiple science-policy assessments to better understand complex plausible futures. Scenario archetype approaches are based on the fact that many future scenarios have similar underlying storylines, assumptions, and trends in drivers of change, which allows for grouping of scenarios into typologies, or archetypes, facilitating comparisons between a large range of studies. The use of scenario archetypes in environmental assessments foregrounds important policy questions and can be used to codesign interventions tackling future sustainability issues. Recently, scenario archetypes were used in four regional assessments and one ongoing global assessment within the Intergovernmental Science-Policy Platform for Biodiversity and Ecosystem Services (IPBES). The aim of these assessments was to provide decision makers with policy-relevant knowledge about the state of biodiversity, ecosystems, and the contributions they provide to people. This paper reflects on the usefulness of the scenario archetype approach within science-policy processes, drawing on the experience from the IPBES assessments. Using a thematic analysis of (a) survey data collected from experts involved in the archetype analyses across IPBES assessments, (b) notes from IPBES workshops, and (c) regional assessment chapter texts, we synthesize the benefits, challenges, and frontiers of applying the scenario archetype approach in a science-policy process. Scenario archetypes were perceived to allow syntheses of large amounts of information for scientific, practice-, and policy-related purposes, streamline key messages from multiple scenario studies, and facilitate communication of them to end users. In terms of challenges, they were perceived as subjective in their interpretation, oversimplifying information, having a limited applicability across scales, and concealing contextual information and novel narratives. Finally, our results highlight what methodologies, applications, and frontiers in archetype-based research should be explored in the future. These advances can assist the design of future large-scale sustainability-related assessment processes, aiming to better support decisions and interventions for equitable and sustainable futures.

Elucidating syntrophic butyrate-degrading populations in anaerobic digesters using stable-isotope-informed genome-resolved metagenomics
Ziels, Ryan M. ; Nobu, Masaru K. ; Sousa, Diana Z. - \ 2019
mSystems 4 (2019)4. - ISSN 2379-5077
Anaerobic catabolic pathways - Anaerobic digestion - Metagenomics - Methanogenesis - Stable-isotope probing - Syntrophy

Linking the genomic content of uncultivated microbes to their metabolic functions remains a critical challenge in microbial ecology. Resolving this challenge has implications for improving our management of key microbial interactions in biotechnologies such as anaerobic digestion, which relies on slow-growing syntrophic and methanogenic communities to produce renewable methane from organic waste. In this study, we combined DNA stable-isotope probing (SIP) with genome-centric metagenomics to recover the genomes of populations enriched in 13C after growing on [13C]butyrate. Differential abundance analysis of recovered genomic bins across the SIP metagenomes identified two metagenome-assembled genomes (MAGs) that were significantly enriched in heavy [13C]DNA. Phylogenomic analysis assigned one MAG to the genus Syntrophomonas and the other MAG to the genus Methanothrix. Metabolic reconstruction of the annotated genomes showed that the Syntrophomonas genome encoded all the enzymes for beta-oxidizing butyrate, as well as several mechanisms for interspecies electron transfer via electron transfer flavoproteins, hydrogenases, and formate dehydrogenases. The Syntrophomonas genome shared low average nucleotide identity (<95%) with any cultured representative species, indicating that it is a novel species that plays a significant role in syntrophic butyrate degradation within anaerobic digesters. The Methanothrix genome contained the complete pathway for acetoclastic methanogenesis, indicating that it was enriched in 13C from syntrophic acetate transfer. This study demonstrates the potential of stable-isotope-informed genome-resolved metagenomics to identify in situ interspecies metabolic cooperation within syntrophic consortia important to anaerobic waste treatment as well as global carbon cycling. IMPORTANCE Predicting the metabolic potential and ecophysiology of mixed microbial communities remains a major challenge, especially for slow-growing anaerobes that are difficult to isolate. Unraveling the in situ metabolic activities of uncultured species may enable a more descriptive framework to model substrate transformations by microbiomes, which has broad implications for advancing the fields of biotechnology, global biogeochemistry, and human health. Here, we investigated the in situ function of mixed microbiomes by combining stable-isotope probing with metagenomics to identify the genomes of active syntrophic populations converting butyrate, a C4 fatty acid, into methane within anaerobic digesters. This approach thus moves beyond the mere presence of metabolic genes to resolve "who is doing what" by obtaining confirmatory assimilation of the labeled substrate into the DNA signature. Our findings provide a framework to further link the genomic identities of uncultured microbes with their ecological function within microbiomes driving many important biotechnological and global processes.

Meer overstromingen rivieren in Noordwest-Europa
Teuling, Ryan - \ 2019
Nú weten we hoe hittegolven ontstaan
Teuling, Ryan - \ 2019
European mega-heatwaves linked to drought
Vila-Guerau de Arellano, Jordi ; Heerwaarden, Chiel van; Teuling, Ryan - \ 2019

Heatwaves in Europe have become increasingly frequent and intense in recent years. This summer, Western Europe has already been hit by two severe heatwaves. Researchers from Ghent University and Wageningen University & Research have found a common ingredient of such European mega-heatwaves: drought conditions in the regions the wind blows from.

Nmr spectroscopy for metabolomics research
Emwas, Abdul Hamid ; Roy, Raja ; McKay, Ryan T. ; Tenori, Leonardo ; Saccenti, Edoardo ; Nagana Gowda, G.A. ; Raftery, Daniel ; Alahmari, Fatimah ; Jaremko, Lukasz ; Jaremko, Mariusz ; Wishart, David S. - \ 2019
Metabolites 9 (2019)7. - ISSN 2218-1989
Analytical platform - GC-MS - LC-MS - Metabolomics - MS - NMR - Resolution - Sensitivity

Over the past two decades, nuclear magnetic resonance (NMR) has emerged as one of the three principal analytical techniques used in metabolomics (the other two being gas chromatography coupled to mass spectrometry (GC-MS) and liquid chromatography coupled with single-stage mass spectrometry (LC-MS)). The relative ease of sample preparation, the ability to quantify metabolite levels, the high level of experimental reproducibility, and the inherently nondestructive nature of NMR spectroscopy have made it the preferred platform for long-term or large-scale clinical metabolomic studies. These advantages, however, are often outweighed by the fact that most other analytical techniques, including both LC-MS and GC-MS, are inherently more sensitive than NMR, with lower limits of detection typically being 10 to 100 times better. This review is intended to introduce readers to the field of NMR-based metabolomics and to highlight both the advantages and disadvantages of NMR spectroscopy for metabolomic studies. It will also explore some of the unique strengths of NMR-based metabolomics, particularly with regard to isotope selection/detection, mixture deconvolution via 2D spectroscopy, automation, and the ability to noninvasively analyze native tissue specimens. Finally, this review will highlight a number of emerging NMR techniques and technologies that are being used to strengthen its utility and overcome its inherent limitations in metabolomic applications.

Patterns of nitrogen-fixing tree abundance in forests across Asia and America
Menge, Duncan N.L. ; Chisholm, Ryan A. ; Davies, Stuart J. ; Abu Salim, Kamariah ; Allen, David ; Alvarez, Mauricio ; Bourg, Norm ; Brockelman, Warren Y. ; Bunyavejchewin, Sarayudh ; Butt, Nathalie ; Cao, Min ; Chanthorn, Wirong ; Chao, Wei Chun ; Clay, Keith ; Condit, Richard ; Cordell, Susan ; Silva, João Batista da; Dattaraja, H.S. ; Andrade, Ana Cristina Segalin de; Oliveira, Alexandre A. de; Ouden, Jan den; Drescher, Michael ; Fletcher, Christine ; Giardina, Christian P. ; Savitri Gunatilleke, C.V. ; Gunatilleke, I.A.U.N. ; Hau, Billy C.H. ; He, Fangliang ; Howe, Robert ; Hsieh, Chang Fu ; Hubbell, Stephen P. ; Inman-Narahari, Faith M. ; Jansen, Patrick A. ; Johnson, Daniel J. ; Kong, Lee Sing ; Král, Kamil ; Ku, Chen Chia ; Lai, Jiangshan ; Larson, Andrew J. ; Li, Xiankun ; Li, Yide ; Lin, Luxiang ; Lin, Yi Ching ; Liu, Shirong ; Lum, Shawn K.Y. ; Lutz, James A. ; Ma, Keping ; Malhi, Yadvinder ; McMahon, Sean ; McShea, William ; Mi, Xiangcheng ; Morecroft, Michael ; Myers, Jonathan A. ; Nathalang, Anuttara ; Novotny, Vojtech ; Ong, Perry ; Orwig, David A. ; Ostertag, Rebecca ; Parker, Geoffrey ; Phillips, Richard P. ; Abd. Rahman, Kassim ; Sack, Lawren ; Sang, Weiguo ; Shen, Guochun ; Shringi, Ankur ; Shue, Jessica ; Su, Sheng Hsin ; Sukumar, Raman ; Fang Sun, I. ; Suresh, H.S. ; Tan, Sylvester ; Thomas, Sean C. ; Toko, Pagi S. ; Valencia, Renato ; Vallejo, Martha I. ; Vicentini, Alberto ; Vrška, Tomáš ; Wang, Bin ; Wang, Xihua ; Weiblen, George D. ; Wolf, Amy ; Xu, Han ; Yap, Sandra ; Zhu, Li ; Fung, Tak - \ 2019
Journal of Ecology 107 (2019)6. - ISSN 0022-0477 - p. 2598 - 2610.
forest - legume - nitrogen fixation - nutrient limitation - Smithsonian ForestGEO - symbiosis

Symbiotic nitrogen (N)-fixing trees can provide large quantities of new N to ecosystems, but only if they are sufficiently abundant. The overall abundance and latitudinal abundance distributions of N-fixing trees are well characterised in the Americas, but less well outside the Americas. Here, we characterised the abundance of N-fixing trees in a network of forest plots spanning five continents, ~5,000 tree species and ~4 million trees. The majority of the plots (86%) were in America or Asia. In addition, we examined whether the observed pattern of abundance of N-fixing trees was correlated with mean annual temperature and precipitation. Outside the tropics, N-fixing trees were consistently rare in the forest plots we examined. Within the tropics, N-fixing trees were abundant in American but not Asian forest plots (~7% versus ~1% of basal area and stems). This disparity was not explained by mean annual temperature or precipitation. Our finding of low N-fixing tree abundance in the Asian tropics casts some doubt on recent high estimates of N fixation rates in this region, which do not account for disparities in N-fixing tree abundance between the Asian and American tropics. Synthesis. Inputs of nitrogen to forests depend on symbiotic nitrogen fixation, which is constrained by the abundance of N-fixing trees. By analysing a large dataset of ~4 million trees, we found that N-fixing trees were consistently rare in the Asian tropics as well as across higher latitudes in Asia, America and Europe. The rarity of N-fixing trees in the Asian tropics compared with the American tropics might stem from lower intrinsic N limitation in Asian tropical forests, although direct support for any mechanism is lacking. The paucity of N-fixing trees throughout Asian forests suggests that N inputs to the Asian tropics might be lower than previously thought.

Controlling Superstructure-Property Relationships via Critical Casimir Assembly of Quantum Dots
Marino, Emanuele ; Balazs, Daniel M. ; Crisp, Ryan W. ; Hermida-Merino, Daniel ; Loi, Maria A. ; Kodger, Thomas E. ; Schall, Peter - \ 2019
The Journal of Physical Chemistry Part C: Nanomaterials and Interfaces 123 (2019)22. - ISSN 1932-7447 - p. 13451 - 13457.

The assembly of colloidal quantum dots (QDs) into dense superstructures holds great promise for the development of novel optoelectronic devices. Several assembly techniques have been explored; however, achieving direct and precise control over the interparticle potential that controls the assembly has proven to be challenging. Here, we exploit the application of critical Casimir forces to drive the growth of QDs into superstructures. We show that the exquisite temperature-dependence of the critical Casimir potential offers new opportunities to control the assembly process and morphology of the resulting QD superstructures. The direct assembly control allows us to elucidate the relation between structural, optical, and conductive properties of the critical Casimir-grown QD superstructures. We find that the choice of the temperature setting the interparticle potential plays a central role in maximizing charge percolation across QD thin-films. These results open up new directions for controlling the assembly of nanostructures and their optoelectronic properties.

Enzyme promiscuity shapes adaptation to novel growth substrates
Guzmán, Gabriela I. ; Sandberg, Troy E. ; LaCroix, Ryan A. ; Nyerges, Ákos ; Papp, Henrietta ; Raad, Markus de; King, Zachary A. ; Hefner, Ying ; Northen, Trent R. ; Notebaart, Richard A. ; Pál, Csaba ; Palsson, Bernhard O. ; Papp, Balázs ; Feist, Adam M. - \ 2019
Molecular Systems Biology 15 (2019)4. - ISSN 1744-4292 - p. e8462 - e8462.
adaptive evolution - enzyme promiscuity - genome‐scale modeling - systems biology

Evidence suggests that novel enzyme functions evolved from low-level promiscuous activities in ancestral enzymes. Yet, the evolutionary dynamics and physiological mechanisms of how such side activities contribute to systems-level adaptations are not well characterized. Furthermore, it remains untested whether knowledge of an organism's promiscuous reaction set, or underground metabolism, can aid in forecasting the genetic basis of metabolic adaptations. Here, we employ a computational model of underground metabolism and laboratory evolution experiments to examine the role of enzyme promiscuity in the acquisition and optimization of growth on predicted non-native substrates in Escherichia coli K-12 MG1655. After as few as approximately 20 generations, evolved populations repeatedly acquired the capacity to grow on five predicted non-native substrates-D-lyxose, D-2-deoxyribose, D-arabinose, m-tartrate, and monomethyl succinate. Altered promiscuous activities were shown to be directly involved in establishing high-efficiency pathways. Structural mutations shifted enzyme substrate turnover rates toward the new substrate while retaining a preference for the primary substrate. Finally, genes underlying the phenotypic innovations were accurately predicted by genome-scale model simulations of metabolism with enzyme promiscuity.

‘Warm voorjaar riskant voor natuur’
Teuling, Ryan - \ 2019
Lactobacillus mucosae DPC 6426 as a bile-modifying and immunomodulatory microbe
Ryan, Paul M. ; Stolte, Ellen H. ; London, Lis E.E. ; Wells, Jerry M. ; Long, Sarah L. ; Joyce, Susan A. ; Gahan, Cormac G.M. ; Fitzgerald, Gerald F. ; Ross, R.P. ; Caplice, Noel M. ; Stanton, Catherine - \ 2019
BMC Microbiology 19 (2019)1. - ISSN 1471-2180
Bile acid - Bile salt hydrolase (BSH) - CVD - Exopolysaccharide - Hypercholesterolaemia

Background: Lactobacillus mucosae DPC 6426 has previously demonstrated potentially cardio-protective properties, in the form of dyslipidaemia and hypercholesterolemia correction in an apolipoprotein-E deficient mouse model. This study aims to characterise the manner in which this microbe may modulate host bile pool composition and immune response, in the context of cardiovascular disease. Lactobacillus mucosae DPC 6426 was assessed for bile salt hydrolase activity and specificity. The microbe was compared against several other enteric strains of the same species, as well as a confirmed bile salt hydrolase-active strain, Lactobacillus reuteri APC 2587. Results: Quantitative bile salt hydrolase assays revealed that enzymatic extracts from Lactobacillus reuteri APC 2587 and Lactobacillus mucosae DPC 6426 demonstrate the greatest activity in vitro. Bile acid profiling of porcine and murine bile following incubation with Lactobacillus mucosae DPC 6426 confirmed a preference for hydrolysis of glyco-conjugated bile acids. In addition, the purified exopolysaccharide and secretome of Lactobacillus mucosae DPC 6426 were investigated for immunomodulatory capabilities using RAW264.7 macrophages. Gene expression data revealed that both fractions stimulated increases in interleukin-6 and interleukin-10 gene transcription in the murine macrophages, while the entire secretome was necessary to increase CD206 transcription. Moreover, the exopolysaccharide elicited a dose-dependent increase in nitric oxide and interleukin-10 production from RAW264.7 macrophages, concurrent with increased tumour necrosis factor-α secretion at all doses. Conclusions: This study indicates that Lactobacillus mucosae DPC 6426 modulates both bile pool composition and immune system tone in a manner which may contribute significantly to the previously identified cardio-protective phenotype.

Sneeuwpret wordt steeds zeldzamer
Teuling, Ryan - \ 2018
Call 2013: Roads and Wildlife : The Roads and Wildlife Manual
OBrien, Eugene ; Grift, E.A. van der; Elmeros, M. ; Wilson-Parr, Ryan ; Carey, Ciaràn - \ 2018
- 131 p.
Transnational Road Research Programme, Call 2013: Roads and Wildlife : Final Programme Report
Grift, E.A. van der; OBrien, Eugene ; Elmeros, M. ; Grift-Simeonova, V.S. van der; MacGearailt, Seamus ; Corrigan, Barry ; Wilson-Parr, Ryan ; Carey, Ciaràn - \ 2018
- 34 p.
The potential of unmanned aerial systems for sea turtle research and conservation : A review and future directions
Rees, Alan F. ; Avens, Larisa ; Ballorain, Katia ; Bevan, Elizabeth ; Broderick, Annette C. ; Carthy, Raymond R. ; Christianen, Marjolijn J.A. ; Duclos, Gwénaël ; Heithaus, Michael R. ; Johnston, David W. ; Mangel, Jeffrey C. ; Paladino, Frank ; Pendoley, Kellie ; Reina, Richard D. ; Robinson, Nathan J. ; Ryan, Robert ; Sykora-Bodie, Seth T. ; Tilley, Dominic ; Varela, Miguel R. ; Whitman, Elizabeth R. ; Whittock, Paul A. ; Wibbels, Thane ; Godley, Brendan J. - \ 2018
Endangered Species Research 35 (2018). - ISSN 1863-5407 - p. 81 - 100.
Aerial survey - Behaviour - Conservation - Drone - Ecology - Population biology - Sea turtle - UAV

The use of satellite systems and manned aircraft surveys for remote data collection has been shown to be transformative for sea turtle conservation and research by enabling the collection of data on turtles and their habitats over larger areas than can be achieved by surveys on foot or by boat. Unmanned aerial vehicles (UAVs) or drones are increasingly being adopted to gather data, at previously unprecedented spatial and temporal resolutions in diverse geographic locations. This easily accessible, low-cost tool is improving existing research methods and enabling novel approaches in marine turtle ecology and conservation. Here we review the diverse ways in which incorporating inexpensive UAVs may reduce costs and field time while improving safety and data quality and quantity over existing methods for studies on turtle nesting, at-sea distribution and behaviour surveys, as well as expanding into new avenues such as surveillance against illegal take. Furthermore, we highlight the impact that high-quality aerial imagery captured by UAVs can have for public outreach and engagement. This technology does not come without challenges. We discuss the potential constraints of these systems within the ethical and legal frameworks which researchers must operate and the difficulties that can result with regard to storage and analysis of large amounts of imagery. We then suggest areas where technological development could further expand the utility of UAVs as data-gathering tools; for example, functioning as downloading nodes for data collected by sensors placed on turtles. Development of methods for the use of UAVs in sea turtle research will serve as case studies for use with other marine and terrestrial taxa.

Role of nucleotide identity in effective CRISPR target escape mutations
Künne, Tim ; Zhu, Yifan ; Silva, Fausia da; Konstantinides, Nico ; McKenzie, Rebecca E. ; Jackson, Ryan N. ; Brouns, Stan J.J. - \ 2018
Nucleic acids research 46 (2018)19. - ISSN 0305-1048 - p. 10395 - 10404.

Prokaryotes use primed CRISPR adaptation to update their memory bank of spacers against invading genetic elements that have escaped CRISPR interference through mutations in their protospacer target site. We previously observed a trend that nucleotide-dependent mismatches between crRNA and the protospacer strongly influence the efficiency of primed CRISPR adaptation. Here we show that guanine-substitutions in the target strand of the protospacer are highly detrimental to CRISPR interference and interference-dependent priming, while cytosine-substitutions are more readily tolerated. Furthermore, we show that this effect is based on strongly decreased binding affinity of the effector complex Cascade for guanine-mismatched targets, while cytosine-mismatched targets only minimally affect target DNA binding. Structural modeling of Cascade-bound targets with mismatches shows that steric clashes of mismatched guanines lead to unfavorable conformations of the RNA-DNA duplex. This effect has strong implications for the natural selection of target site mutations that lead to effective escape from type I CRISPR-Cas systems.

Kinetic analysis of the influenza A virus HA/NA balance reveals contribution of NA to virus-receptor binding and NA-dependent rolling on receptor-containing surfaces
Guo, Hongbo ; Rabouw, Huib ; Slomp, Anne ; Dai, Meiling ; Vegt, Floor van der; Lent, Jan W.M. van; McBride, Ryan ; Paulson, James C. ; Groot, Raoul J. de; Kuppeveld, Frank J.M. van; Vries, Erik de; Haan, Cornelis A.M. de - \ 2018
PLoS Pathogens 14 (2018)8. - ISSN 1553-7366

Interactions of influenza A virus (IAV) with sialic acid (SIA) receptors determine viral fitness and host tropism. Binding to mucus decoy receptors and receptors on epithelial host cells is determined by a receptor-binding hemagglutinin (HA), a receptor-destroying neuraminidase (NA) and a complex in vivo receptor-repertoire. The crucial but poorly understood dynamics of these multivalent virus-receptor interactions cannot be properly analyzed using equilibrium binding models and endpoint binding assays. In this study, the use of biolayer interferometric analysis revealed the virtually irreversible nature of IAV binding to surfaces coated with synthetic sialosides or engineered sialoglycoproteins in the absence of NA activity. In addition to HA, NA was shown to be able to contribute to the initial binding rate while catalytically active. Virus-receptor binding in turn contributed to receptor cleavage by NA. Multiple low-affinity HA-SIA interactions resulted in overall extremely high avidity but also permitted a dynamic binding mode, in which NA activity was driving rolling of virus particles over the receptor-surface. Virus dissociation only took place after receptor density of the complete receptor-surface was sufficiently decreased due to NA activity of rolling IAV particles. The results indicate that in vivo IAV particles, after landing on the mucus layer, reside continuously in a receptor-bound state while rolling through the mucus layer and over epithelial cell surfaces driven by the HA-NA-receptor balance. Quantitative BLI analysis enabled functional examination of this balance which governs this dynamic and motile interaction that is expected to be crucial for penetration of the mucus layer and subsequent infection of cells by IAV but likely also by other enveloped viruses carrying a receptor-destroying enzyme in addition to a receptor-binding protein.

Recommended strategies for spectral processing and post-processing of 1D 1H-NMR data of biofluids with a particular focus on urine
Emwas, Abdul Hamid ; Saccenti, Edoardo ; Gao, Xin ; McKay, Ryan T. ; Martins dos Santos, Vitor A.P. ; Roy, Raja ; Wishart, David S. - \ 2018
Metabolomics 14 (2018)3. - ISSN 1573-3882
Baseline correction - Data post-processing - Metabolomics - NMR spectroscopy - Normalization - Scaling - Spectral alignment - Spectral binning - Spectral processing - Urine
1H NMR spectra from urine can yield information-rich data sets that offer important insights into many biological and biochemical phenomena. However, the quality and utility of these insights can be profoundly affected by how the NMR spectra are processed and interpreted. For instance, if the NMR spectra are incorrectly referenced or inconsistently aligned, the identification of many compounds will be incorrect. If the NMR spectra are mis-phased or if the baseline correction is flawed, the estimated concentrations of many compounds will be systematically biased. Furthermore, because NMR permits the measurement of concentrations spanning up to five orders of magnitude, several problems can arise with data analysis. For instance, signals originating from the most abundant metabolites may prove to be the least biologically relevant while signals arising from the least abundant metabolites may prove to be the most important but hardest to accurately and precisely measure. As a result, a number of data processing techniques such as scaling, transformation and normalization are often required to address these issues. Therefore, proper processing of NMR data is a critical step to correctly extract useful information in any NMR-based metabolomic study. In this review we highlight the significance, advantages and disadvantages of different NMR spectral processing steps that are common to most NMR-based metabolomic studies of urine. These include: chemical shift referencing, phase and baseline correction, spectral alignment, spectral binning, scaling and normalization. We also provide a set of recommendations for best practices regarding spectral and data processing for NMR-based metabolomic studies of biofluids, with a particular focus on urine.
Stripping away the soil : Plant growth promoting microbiology opportunities in aquaponics
Bartelme, Ryan P. ; Oyserman, Ben O. ; Blom, Jesse E. ; Sepulveda-Villet, Osvaldo J. ; Newton, Ryan J. - \ 2018
Frontiers in Microbiology 9 (2018)JAN. - ISSN 1664-302X
Aquaponics - Chlorosis - Microbiome - Plant growth promoting microorganisms - Recirculating aquaculture - Rhizosphere
As the processes facilitated by plant growth promoting microorganisms (PGPMs) become better characterized, it is evident that PGPMs may be critical for successful sustainable agricultural practices. Microbes enrich plant growth through various mechanisms, such as enhancing resistance to disease and drought, producing beneficial molecules, and supplying nutrients and trace metals to the plant rhizosphere. Previous studies of PGPMs have focused primarily on soil-based crops. In contrast, aquaponics is a water-based agricultural system, in which production relies upon internal nutrient recycling to co-cultivate plants with fish. This arrangement has management benefits compared to soil-based agriculture, as system components may be designed to directly harness microbial processes that make nutrients bioavailable to plants in downstream components. However, aquaponic systems also present unique management challenges. Microbes may compete with plants for certain micronutrients, such as iron, which makes exogenous supplementation necessary, adding production cost and process complexity, and limiting profitability and system sustainability. Research on PGPMs in aquaponic systems currently lags behind traditional agricultural systems, however, it is clear that certain parallels in nutrient use and plant-microbe interactions are retained from soil-based agricultural systems.
DNA-SIP based genome-centric metagenomics identifies key long-chain fatty acid-degrading populations in anaerobic digesters with different feeding frequencies
Ziels, Ryan M. ; Sousa, Diana Z. ; Stensel, H.D. ; Beck, David A.C. - \ 2018
ISME Journal 12 (2018)1. - ISSN 1751-7362 - p. 112 - 123.
Fats, oils and greases (FOG) are energy-dense wastes that can be added to anaerobic digesters to substantially increase biomethane recovery via their conversion through long-chain fatty acids (LCFAs). However, a better understanding of the ecophysiology of syntrophic LCFA-degrading microbial communities in anaerobic digesters is needed to develop operating strategies that mitigate inhibitory LCFA accumulation from FOG. In this research, DNA stable isotope probing (SIP) was coupled with metagenomic sequencing for a genome-centric comparison of oleate (C 18:1)-degrading populations in two anaerobic codigesters operated with either a pulse feeding or continuous-feeding strategy. The pulse-fed codigester microcosms converted oleate into methane at over 20% higher rates than the continuous-fed codigester microcosms. Differential coverage binning was demonstrated for the first time to recover population genome bins (GBs) from DNA-SIP metagenomes. About 70% of the 13 C-enriched GBs were taxonomically assigned to the Syntrophomonas genus, thus substantiating the importance of Syntrophomonas species to LCFA degradation in anaerobic digesters. Phylogenetic comparisons of 13 C-enriched GBs showed that phylogenetically distinct Syntrophomonas GBs were unique to each codigester. Overall, these results suggest that syntrophic populations in anaerobic digesters can have different adaptive capacities, and that selection for divergent populations may be achieved by adjusting reactor operating conditions to maximize biomethane recovery.
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