Detecting macroecological patterns in bacterial communities across independent studies of global soils
Ramirez, Kelly S. ; Knight, Christopher G. ; Hollander, Mattias de; Brearley, Francis Q. ; Constantinides, Bede ; Cotton, Anne ; Creer, Si ; Crowther, Thomas W. ; Davison, John ; Delgado-Baquerizo, Manuel ; Dorrepaal, Ellen ; Elliott, David R. ; Fox, Graeme ; Griffiths, Robert I. ; Hale, Chris ; Hartman, Kyle ; Houlden, Ashley ; Jones, David L. ; Krab, Eveline J. ; Maestre, Fernando T. ; McGuire, Krista L. ; Monteux, Sylvain ; Orr, Caroline H. ; Putten, Wim H. van der; Roberts, Ian S. ; Robinson, David A. ; Rocca, Jennifer D. ; Rowntree, Jennifer ; Schlaeppi, Klaus ; Shepherd, Matthew ; Singh, Brajesh K. ; Straathof, Angela L. ; Bhatnagar, Jennifer M. ; Thion, Cécile ; Heijden, Marcel G.A. van der; Vries, Franciska T. de - \ 2018
Nature Microbiology 3 (2018). - ISSN 2058-5276 - p. 189 - 196.
The emergence of high-throughput DNA sequencing methods provides unprecedented opportunities to further unravel bacterial biodiversity and its worldwide role from human health to ecosystem functioning. However, despite the abundance of sequencing studies, combining data from multiple individual studies to address macroecological questions of bacterial diversity remains methodically challenging and plagued with biases. Here, using a machine-learning approach that accounts for differences among studies and complex interactions among taxa, we merge 30 independent bacterial data sets comprising 1,998 soil samples from 21 countries. Whereas previous meta-analysis efforts have focused on bacterial diversity measures or abundances of major taxa, we show that disparate amplicon sequence data can be combined at the taxonomy-based level to assess bacterial community structure. We find that rarer taxa are more important for structuring soil communities than abundant taxa, and that these rarer taxa are better predictors of community structure than environmental factors, which are often confounded across studies. We conclude that combining data from independent studies can be used to explore bacterial community dynamics, identify potential ‘indicator’ taxa with an important role in structuring communities, and propose hypotheses on the factors that shape bacterial biogeography that have been overlooked in the past.
Volatile-mediated suppression of plant pathogens is related to soil properties and microbial community composition
Agtmaal, Maaike van; Straathof, Angela L. ; Termorshuizen, Aad ; Lievens, Bart ; Hoffland, Ellis ; Boer, Wietse de - \ 2018
Soil Biology and Biochemistry 117 (2018). - ISSN 0038-0717 - p. 164 - 174.
Fusarium oxysporum - Phytopathology - Pythium intermedium - Rhizoctonia solani - Soil microbial ecology - Soil-borne plant pathogens - Volatile organic compounds
There is increasing evidence that the soil microbial community produces a suite of volatile organic compounds that suppress plant pathogens. However, it remains unknown which soil properties and management practices influence volatile-mediated pathogen suppression. The aim of this study was to relate soil properties to growth suppression of three plant pathogens by soil volatiles. We measured the effect of volatiles emitted from a broad range of agricultural soils on the in vitro growth of the plant pathogenic fungi Rhizoctonia solani and Fusarium oxysporum, and the oomycete Pythium intermedium. Growth suppression of pathogens by soil volatiles could be linked to various soil properties, and some aspects of microbial community composition and field history, using multiple linear regression. Volatile-mediated suppression of mycelial development occurred for each pathogen type, but the magnitude of inhibition differed among soils as well as pathogens. On average R. solani and P. ultimum appeared more sensitive to volatile suppression than F. oxysporum. Suppression of R. solani by volatiles was positively correlated with organic matter content, microbial biomass and proportion of litter saprotrophs in the microbial community, but negatively correlated with pH, microbial diversity (Shannon), and the proportion of Acidobacteria in the community. R. solani, F. oxysporum, and P. intermedium suppression by volatiles was affected by various management practices occurring in the soil's field history, such as reduced tillage, the presence of certain crops in the crop rotation, and the application of solid manure. P. intermedium suppression was also negatively correlated with soil sulphur content. This study identifies pathogen-specific drivers of growth-suppressive volatiles, a critical step in integrating soil volatiles into prediction and management of soil-borne plant diseases.
Exploring the reservoir of potential fungal plant pathogens in agricultural soil
Agtmaal, M. van; Straathof, Angela ; Termorshuizen, Aad ; Teurlincx, Sven ; Hundscheid, Maria ; Ruyters, Stefan ; Busschaert, Pieter ; Lievens, Bart ; Boer, Wietse de - \ 2017
Applied Soil Ecology 121 (2017). - ISSN 0929-1393 - p. 152 - 160.
Community dynamics - Fungi - Oomycetes - Soil-borne plant pathogens - Surviving propagules
Soil-borne pathogens cause great crop losses in agriculture. Because of their resilience in the soil, these pathogens persist in a population reservoir, causing future outbreaks of crop diseases. Management focus is usually on the most common pathogens occurring, but it is likely that a mixed population of pathogens together affect crops. Next generation sequencing of DNA from environmental samples can provide information on the presence of potential pathogens. The aim of this study was to obtain insight into the factors that drive the composition of potential plant pathogen populations in agricultural soils. To this end, the alpha and beta diversity of fungal OTUs that were assigned as potential plant pathogens for 42 agricultural soils were assessed. The presented study is the first inventory of the pool of pathogens and its correlating factors. The results of this inventory indicate that the composition of pathogens in soil is driven by pH, soil type, crop history, litter saprotrophic fungi and spatial patterns. The major driving factors differed between potential root- and shoot-infecting fungi, suggesting interactions among environmental factors and pathogen traits like reproduction, survival and dispersal. This information is important to understand risks for disease outbreaks and to recommend management strategies to prevent such outbreaks.
Recovery and esterification of aqueous carboxylates by using CO2-expanded alcohols with anion exchange
Cabrera-Rodríguez, Carlos I. ; Paltrinieri, Laura ; Smet, Louis C.P.M. De; Wielen, Luuk A.M. Van Der; Straathof, Adrie J.J. - \ 2017
Green Chemistry 19 (2017)3. - ISSN 1463-9262 - p. 729 - 738.
The recovery of carboxylic acids from fermentation broth is one of the main bottlenecks for the industrial production of bio-based esters. This paper proposes an alternative for the recovery of carboxylates produced by fermentations at pH values above the pKa of the carboxylic acid. In this approach, the aqueous carboxylate anion is recovered using anion exchange, followed by desorption and esterification with CO2-expanded alcohols. Using CO2-expanded methanol, we achieved a high desorption yield at 10 bar of CO2 and 20 °C. An ester yield of 1.03 ± 0.07 mol methyl acetate/acetatein was obtained for the combined desorption-esterification at 5 bar of CO2 and 60 °C. The proposed process has low chemical consumption and low waste production. The proposed process works, with a lower yield, for other carboxylates (e.g. lactate and succinate) and alcohols (e.g. ethanol).
Changes in body weight in patients with colorectal cancer treated with surgery and adjuvant chemotherapy: An observational study
Winkels, Renate M. ; Snetselaar, Teunise ; Adriaans, Anika ; Warmerdam, Laurens J.C. van; Vreugdenhil, A. ; Slooter, G.D. ; Straathof, J.W. ; Kampman, Ellen ; Lieshout, Rianne van; Beijer, Sandra - \ 2016
Cancer Treatment and Research Communications 9 (2016). - ISSN 2468-2942 - p. 111 - 115.
Adjuvant therapy - Colon and rectal cancer - Survivorship
Background and objectives Prevalence of overweight and obesity is high among colorectal cancer patients upon diagnosis. Body weight may change substantially during treatment for colorectal cancer. In this study, we describe changes in body weight in colorectal cancer patients during three periods: the period of surgery, during adjuvant chemotherapy and during oncological follow-up; in addition, we assess which clinical/personal factors were associated with weight change. Subject/Methods 485 stage II/III colorectal cancer patients diagnosed between 2007 and 2012 and treated with surgery and adjuvant chemotherapy in three hospitals in the Netherlands were identified through the Netherlands Cancer Registry. Data on changes in body weight were retrieved from medical records. Results Over the period of surgery, patients on average lost weight (mean −1.9 kg, SD 4.6 kg) (n=357). Weight increased during chemotherapy (2.9 kg, SD 5.8 kg) (n=291) and increased during oncological follow-up (2.2 kg, SD 6.6 kg) (n=242). Mean weight change over the total period was +2.0 kg (SD 6.8 kg) (n=283). Factors univariately associated with weight gain were normal BMI (vs a BMI of 25–30), open surgery (vs laparoscopic surgery) and Capecitabine monotherapy (vs Capecitabine plus Oxaliplatin). In a multivariate model, factors were no longer associated with weight gain. Conclusions Body weight generally decreased during surgery and increased during and after chemotherapy. During oncological follow-up, body weight generally was higher than upon diagnosis. Studies among other patient groups suggest that weight changes may primarily affect muscle mass, and may lead to e.g. sarcopenic obesity. Future prospective studies are needed to explore this in colorectal cancer patients.
Een indicator voor de bodemweerbaarheid
Os, G.J. van; Straathof, A.L. ; Bloem, J. ; Berg, W. van den; Hoffland, E. - \ 2016
Gewasbescherming 47 (2016)3. - ISSN 0166-6495 - p. 67 - 67.
|The IsoButanol Rotterdam Platform Project
Dijkstra, J.W.H. ; Straathof, A.J.J. ; Lopez Contreras, A.M. ; Zirkzee, H. ; Wermink, W. ; Ramirez-Ramirez, A. ; Hal, J.W. van - \ 2016
An indicator for disease suppresion: linking soil chemistry to microbiology using dissolved organic carbon fractionation
Os, G.J. van; Straathof, A.L. ; Bloem, J. ; Berg, W. van den; Hoffland, E. - \ 2015
- 1 p.
Soil organic matter (SOM) is a major component of soil quality, contributing to physical, chemical and biological properties of the soil. Incorporation of organic matter may stimulate the soil microflora, increase microbial activity and biodiversity and thus enhance suppression of soil borne pathogens by competition, predation and/or specific antagonism.
In a field experiment, a mixture of peat (95%) and manure (5%) was incorporated, creating three levels of SOM: 10, 20 and 30 g kg-1. Soil samples were analysed for a range of physical, chemical and biological soil parameters. Samples were also tested in bioassays for disease suppression against Pythium intermedium, Rhizoctonia solani and Melodogyne hapla using Hyacinth, Tulip and Lettuce respectively as test crops. SOM levels had no effect on sprout infection by Rhizoctonia. For both Pythium and Melodogyna, less disease symptoms were observed at higher SOM contents. It was concluded that higher SOM induced disease suppression against these two pathogens and that this suppression was mainly due to biological activity since in sterilized soil little or no suppression occurred. Multivariate analyses and multiple regressions obtained with model selection, showed positive correlation between disease suppression, SOM and hot water extractable carbon (HWC). Based on these results, SOM and soluble organic carbon have been proposed as indicators for disease suppression. Fractionation of soil dissolved organic carbon (DOC) may even give more detailed information on SOM quality as a substrate for the soil microflora and subsequent antagonistic activities. In another field trial, four different types of organic inputs were incorporated in the soil: compost, coconut fibre, cacao shells and biochar. The raw materials differed significantly in DOC concentrations, ranging from 4 mg kg-1 to more than 9000 mg kg-
1. DOC was further qualified by fractionation into pools of humic acids, fulvic acids, hydrophobic neutrals, and hydrophilic compounds. After amendment, soil physical, chemical and biological parameters were measured, including total DOC, DOC fractions and disease suppression. Statistical analyses showed that variation in disease suppression was best explained with models including total DOC, humic acids and fulvic acids, rather than SOM or HWC. Based on these results, qualification of DOC pools through fractionation may be an informative tool in predicting soil functional processes such as disease suppression.
Effect of dissolved organic matter composition on metal speciation in soil solutions
Ren, Zong Ling ; Tella, Marie ; Bravin, M.N. ; Comans, R.N.J. ; Dai, Jun ; Garnier, Jean Marie ; Sivry, Yann ; Doelsch, Emmanuel ; Straathof, Angela ; Benedetti, M.F. - \ 2015
Chemical Geology 398 (2015). - ISSN 0009-2541 - p. 61 - 69.
Composition - Dissolved organic matter - Metal speciation - NICA-Donnan modeling - SC-DMT
Knowledge of the speciation of heavy metals and the role of dissolved organic matter (DOM) in soil solution is a key to understand metal mobility and ecotoxicity. In this study, soil column-Donnan membrane technique (SC-DMT) was used to measure metal speciation of Cd, Cu, Ni, Pb, and Zn in eighteen soil solutions, covering a wide range of metal sources and concentrations. DOM in these soil solutions was also fractionated into humic acid (HA), fulvic acid (FA), hydrophilic acid (Hy), and hydrophobic neutral organic matter (HON) by a rapid batch technique using DAX-8 resin. Our results show that in soil solution Pb and Cu are dominant in complex form, whereas Cd, Ni and Zn mainly exist as free ions; for the whole range of soil solutions, only 26.2% of DOM is humic substances and consists mainly of fulvic acid (FA). The metal speciation measured by SC-DMT was compared to the predicted ones obtained via the NICA-Donnan model using the measured FA concentrations. The free ion concentrations predicted by speciation modeling were in good agreement with the SC-DMT measurement. Moreover, we show that to make accurate modeling of metal speciation in soil solutions, the knowledge of DOM composition, especially FA fraction, is the crucial information, especially for Cu and Cd; like in previous studies the modeling of Pb speciation is not optimal and an update of Pb generic binding parameters is required to reduce model prediction uncertainties.
Explorations of soil microbial processes driven by dissolved organic carbon
Straathof, A.L. - \ 2015
Wageningen University. Promotor(en): Rob Comans; Ellis Hoffland. - Wageningen : Wageningen University - ISBN 9789462573277 - 146
organische koolstof - bodemmicrobiologie - bodem - microbiële ecologie - bodembiologie - bodemchemie - organic carbon - soil microbiology - soil - microbial ecology - soil biology - soil chemistry
Explorations of soil microbial processes driven by dissolved organic carbon
Angela L. Straathof
June 17, 2015, Wageningen UR
Dissolved organic carbon (DOC) is a complex, heterogeneous mixture of C compounds which, as a substrate, may influence various processes of the soil microbial community. Microbial respiration and volatile production are two such processes. These have both been linked to general disease suppression (GDS), a phenomenon in agricultural soils which inhibits pathogenic infestation in crops. The underlying hypothesis of this thesis is that the quality of DOC, via regulation of microbial processes, may be an important indicator of soil functions, including GDS. Properties of DOC quality include proportions of hydrophobic and hydrophilic fractions, and aromaticity. This thesis describes a high range in DOC fractions from various types of compost, which is often added to soil as an amendment to promote GDS. Differences in soil microbial respiration rates were attributed to differences in the composition of compost DOC added to soil in a laboratory incubation experiment. Compost DOC high in proportion of the hydrophilic (Hi) fraction promoted respiration rates. Depletion of the hydrophobic humic acid (HA) fraction was also observed. The relationship between DOC and microbial respiration was further explored in a survey of 50 arable soils. Both HA and Hi fractions of DOC that were found to be statistically, significantly related to respiration rates in these soils. Furthermore, in an assay measuring in vitro pathogen suppression by microbial volatile production, DOC concentration and microbial respiration were linked to growth suppression of Rhizoctonia solani, Fusarium oxysporum, and Pythium intermedium via multivariate regression modelling. This thesis provides evidence for the importance of DOC and DOC quality’s influence on microbial respiration and volatile production, thus supporting the hypothesis that DOC is a microbially-relevant soil chemical parameter, and potential indicator of general disease suppression in agricultural soils.
Input materials and processing conditions control compost dissolved organic carbon quality
Straathof, A.L. ; Comans, R.N.J. - \ 2015
Bioresource Technology 179 (2015). - ISSN 0960-8524 - p. 619 - 623.
maturity - stability - parameters - fractions - matter - waste
Dissolved organic carbon (DOC) has been proposed as an indicator of compost maturity and stability. Further fractionation of compost DOC may be useful for determining how particular composting conditions will influence DOC quality. Eleven composts ranging in input materials and processing techniques were analyzed; concentrations of DOC ranged from 428 mg kg-1 to 7300 mg kg-1. Compost DOC was qualified by fractionation into pools of humic acids (HA), fulvic acids (FA), hydrophobic neutrals (HoN), and hydrophilic (Hi) compounds. The range in proportion of DOC pools was highly variable, even for composts with similar total DOC concentrations. Longer composting time and higher temperatures consistently corresponded with a depletion of hydrophilics, suggesting a preferential turnover of these compounds during the thermophilic composting phase. Qualification of DOC pools through fractionation may be an informative tool in predicting the effects of a processing technique on compost quality and, ultimately, soil functional processes.
A biorefinery in Rotterdam with isobutanol as platform molecule?
Posada Duque, J.A. ; Zirkzee, H. ; Hellemond, E.W. van; Lopez Contreras, A.M. ; Hal, J.W. van; Straathof, A.J.J. - \ 2014
ECN - 4 p.
The port area of Rotterdam with its concentration of chemical and petrochemical
industry is an important contributor to the emission of CO2 in this country. The
Rotterdam Climate Initiative (RCI) aims to reduce the CO2 emission in 2025 by 50%
compared to 1990 levels. The use of biomass as a raw material for the production
of bio-based chemicals to replace fossil-based chemicals is indispensable in
reaching this goal. This paper describes the assessment of the economic, technical
and ecological feasibility of an isobutanol based complex in the Rotterdam harbor
Bloembollen op pot
Kortstee, H.J.M. - \ 2014
bloembollen - verkoopbevordering - marketingtechnieken - agrarische handel - tuincentra - consumenten - potplanten - teleshopping - marketingkanalen - ondernemerschap - bedrijfseconomie - ornamental bulbs - sales promotion - marketing techniques - agricultural trade - garden centres - consumers - pot plants - marketing channels - entrepreneurship - business economics
Gebroeders Straathof over bloembollen op pot en hoe hij met behulp van een business model zich meer gaat inzetten op de verkoop van bloembollen in potten aan consumenten.
Dynamics of soil dissolved organic carbon pools reveal both hydrophobic and hydrophilic compounds sustain microbial respiration
Straathof, A.L. ; Chincarini, R. ; Comans, R.N.J. ; Hoffland, E. - \ 2014
Soil Biology and Biochemistry 79 (2014). - ISSN 0038-0717 - p. 109 - 116.
agricultural soils - humic substances - matter fractions - biodegradation - components - absorbency
The quality of dissolved organic carbon (DOC) released from soil organic amendments may influence soil microbial activity and the quality of the soil's DOC pools. Measurements of total DOC are often considered in relation to microbial activity levels but here we propose that quantification of DOC fractions is a more informative alternative. In a laboratory incubation, soil received DOC that was extracted from three organic matter sources: fresh compost, mature compost, and a mixture of the two. Soil microbial respiration (CO2 emission), and concentrations of hydrophobic (humic acids (HA), fulvic acids (FA) and neutrals (HoN)) and hydrophilic (Hi) DOC fractions were measured throughout the 35 d incubation. The A254 specific UV absorption of total and HA DOC were measured at the start and end of the incubation as an indicator of aromaticity. Microbial respiration rates were highest in soils amended with fresh compost DOC, which had a higher proportion of Hi compounds. Concentration of Hi was significantly and positively correlated with soil respiration, explaining 24% more variation than total DOC. Humic acid concentrations significantly decreased over 35 d, including a 33% reduction in HA from an unamended control soil. Compost treated soils' HA pools increased in aromaticity, suggesting preferential mineralization of the least aromatic HA molecules. A decrease in SUVA254 values in other HA pools may be the result of HA degradation in the absence of low-aromatic HA. Our observation of depletion of hydrophobic compounds from the HA fraction provides evidence that humic substances can be a relatively reactive pool, which can provide, together with hydrophilic compounds, a readily available C source to the microbial community.
Remote beneficials in soil; potential role of bacterial volatiles in suppression of soil-borne fungal pathogens
Agtmaal, M. van; Hundscheid, M.P.J. ; Straathof, A.L. ; Boer, W. de - \ 2013
Gewasbescherming 44 (2013)5. - ISSN 0166-6495 - p. 136 - 136.
Effect van grondstoffensamenstelling en aminozuurgehalte op technische resultaten van beren, borgen en zeugjes = Influence of diet composition and level of amino acids on performance of boars, barrows and gilts
Peet-Schwering, C.M.C. van der; Straathof, S.B. ; Binnendijk, G.P. ; Diepen, J.T.M. van - \ 2012
Lelystad : Wageningen UR Livestock Research (Rapport / Wageningen UR Livestock Research 563) - 56
varkenshouderij - vleesproductie - varkensvoeding - voersamenstelling - ruwe grondstoffen - effecten - pig farming - meat production - pig feeding - feed formulation - raw materials - effects
At Pig Innovation Centre Sterksel two experiments were done to find out what the effects are on the performance of boars, barrows and gilts of: 1) fine-tuning the composition of raw materials in starter, grower, and finisher diets; 2) fine-tuning the composition of raw materials plus extra amino acids in the diet; 3) alternating the composition of raw materials each week. The results are described in this report.
Effect van oplegbeleid, voersysteem en voersamenstelling op gedrag van beren en berengeur = Effect of mixing strategy, feeding system and feed composition on behaviour of boars and boar taint
Peet-Schwering, C.M.C. van der; Straathof, S.B. ; Dirx-Kuijken, N.C.P.M.M. ; Binnendijk, G.P. ; Vermeer, H.M. - \ 2012
Lelystad : Wageningen UR Livestock Research (Rapport / Wageningen UR Livestock Research 562) - 37
beren (varkens) - diergedrag - berengeur - voedersystemen - worpen - dierenwelzijn - varkenshouderij - varkensvoeding - varkens - dierlijke productie - boars - animal behaviour - boar taint - feeding systems - litters - animal welfare - pig farming - pig feeding - pigs - animal production
At Swine Innovation Centre Sterksel the effects of litters versus single sex groups, simultaneous feeding versus sequential feeding, and feeding a boar taint reducing diet versus a conventional diet on behaviour of boars, performance and boar taint were studied. The results are described in this report.
Houden van beren vak apart
Peet-Schwering, C.M.C. van der; Vermeer, H.M. ; Kluivers-Poodt, M. ; Straathof, B. ; Smolders, M.M.A.H.H. ; Bikker, A.M. - \ 2011
Lelystad : Wageningen UR Livestock Research
varkenshouderij - beren (varkens) - agrarische bedrijfsvoering - dierenwelzijn - diergedrag - varkens - dierlijke productie - huisvesting, dieren - pig farming - boars - farm management - animal welfare - animal behaviour - pigs - animal production - animal housing
De ervaringen met het houden van beren zijn wisselend. Tips van varkenshouders voor varkenshouders.
Optimalisatie van vraagarticulatie en kennisuitwisseling over de effecten van inundatie en waterberging (P2052) : eindrapport voor consortiumpartijen
Smit, A. ; Keijzer, T. ; Veld, M. ter; Straathof, J. ; Jaspers, A.M.J. ; Heuvelman, H. ; Koning, I.M. - \ 2010
Wageningen [etc.] : Alterra [etc.] - 42
wateropslag - inundatie - bodemwater - stroomgebieden - hydrologie - informatieverspreiding - water storage - flooding - soil water - watersheds - hydrology - diffusion of information
Doel van dit project was om via een participatief proces de relevante kennisvragen te identificeren die in de praktijk spelen bij waterberging en deze te confronteren met specialistische kennis en met de praktijkervaring over bodem en water. Het proces werd uitgevoerd met partijen in een of meerdere stroomgebieden (Hoog-Nederland en Laag-Nederland) met alle betrokken partijen die met kennisvragen zitten t.a.v. inundatie-effecten
Van Beemster wordt iedereen blij
Floris, J. ; Straathof, M. - \ 2008
Food Magazine 64 (2008). - ISSN 1383-4169