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Chromosomal integration of Golden Gate compatible plasmids in non-symbiotic Bradyrhizobium [Student report]
Nijhuis, P. \ 2018

Bradyrhizobium spp. are well known for their capacity to initiate a beneficial relationship with a large variety of legume species and the non-legume Parasponia. Through initiation of nodulogenesis in plants, Bradyrhizobium spp. are able to utilize organic molecules derived from photosynthesis in exchange for fixed nitrogen. The genes essential for the nitrogen-fixation and nodulation trait are clustered chromosomally on so called symbiotic islands, which are wildly accepted to be of foreign origin. However, previously published Bradyrhizobium ecotypes have been shown to be non-symbiotic. These non-symbionts were found to be highly abundant in soils lacking legumes and do not harbour the nitrogen fixation and nodulation gene clusters. Recently, a study showed that a multitude of Bradyrhizobium strains are highly abundant in the root endophytic compartment of eight different plant species originating from the same ecological test field. From a single Arabidopsis thaliana (Arabidopsis) root, four genetically and functionally highly diverse Bradyrhizobium strains were isolated. These isolates, designated Bradyrhizobium sp. MOS001 to MOS004, were shown to be nonsymbiotic. However, the nature of the interaction between these non-symbiotic Bradyrhizobium isolates and the root endophytic compartment remained elusive. In this study, we show the first step to identify the nature of this host-microbe interaction through localization of these non-symbionts on roots of model species Arabidopsis. Moreover, we show the construction of strain specific plasmids which become stably integrated at a uniform locus in the chromosome of MOS001, MOS004 and type strain Bradyrhizobium diazoefficiens USDA110 (USDA110). These constructs enable expression of a single copy gene for a Bradyrhizobium optimized green fluorescent protein. Here, we reportsuccessful construction of green fluorescent protein-expressing USDA110, MOS001 and MOS004 strains. In our experimental setup, we were unable to detect these labelled strains in the root endophytic compartment of Arabidopsis.

Emissies naar lucht uit de landbouw in 2016 : berekeningen met het model NEMA [Monograph]
Bruggen, C. van \ Bannink, A \ Groenestein, C.M. \ Huijsmans, J.F.M. \ Luesink, H.H. \ Sluis, S.M. van der \ Velthof, G.L. \ Vonk, J. \ 2018

Agricultural activities are in the Netherlands a major source of ammonia (NH3), nitrogen oxide (NO), nitrous oxide (N2O), methane (CH4) and particulate matter (PM10 and PM2.5). The emissions in 2016 were calculated using the National Emission Model for Agriculture (NEMA). Some figures in the time series 1990-2015 were revised. The method calculates the NH3 emission from livestock manure based on the total ammonia nitrogen (TAN) content in manure. In 2016 NH3 emissions from livestock manure, fertilizer and other sources in agriculture, from hobby farms, private parties and manure disposal in nature areas amounted to 116.8 million kg NH3, 1.3 million kg more than in 2015. Nitrogen excretion increased due to expansion of the dairy herd, but because of a larger share of low emission housing and more manure exports outside agriculture, the increase in NH3 emission remained limited. N2O emissions in 2016 were 21.1 million kg at virtually the same level as in 2015 (21.2). NO emissions in 2016 totaled 22.8 million kg compared to 22.6 million kg in 2015. CH4 emissions increased from 496 to 512 million kg due to the expansion of the dairy herd. Emissions of particulate matter PM10 and PM2.5, 6.5 and 0.6 million kg respectively, did not change compared to 2015. NH3 emissions from livestock manure in the Netherlands dropped by almost two thirds since 1990, mainly as a result of lower nitrogen excretion rates by livestock and lowemission manure application. Emissions of N2O and NO also decreased over the same period, but less strongly(38% and 31% respectively), due to higher emissions from manure injection into the soil and the shift from poultry housing systems with liquid manure towards solid manure systems. CH4 emissions reduced by 13% between 1990 and 2016 caused by a decreasein livestock numbers and increased feed efficiency of dairy cattle.

Lipid metabolism in Nannochloropsis gaditana during nitrogen starvation [PhD thesis]
Full text publicly available; under embargo until:2019-06-20
Janssen, Jorijn H. \ 2018
Disentangling microbial decomposition networks : linking detritus-based soil microbial food webs to ecosystem processes [PhD thesis]
Full text publicly available; under embargo until:2019-06-06
Heijboer, Amber \ 2018
Relating N2O emissions during biological nitrogen removal with operating conditions using multivariate statistical techniques \ Water research : the journal of the International Association on Water Quality [Article]
Vasilaki, V. \ Volcke, E.I.P. \ Nandi, A.K. \ Loosdrecht, M.C.M. van \ Katsou, E. \ 2018
water pollution - water quality - water supply - waste water treatment - government policy - environmental policy - environmental legislation - air pollution - soil pollution - aquatic environment

Multivariate statistical analysis was applied to investigate the dependencies and underlying patterns between N2O emissions and online operational variables (dissolved oxygen and nitrogen component concentrations, temperature and influent flow-rate) during biological nitrogen removal from wastewater. The system under study was a full-scale reactor, for which hourly sensor data were available. The 15-month long monitoring campaign was divided into 10 sub-periods based on the profile of N2O emissions, using Binary Segmentation.

Wettelijk instrumentarium voor landbouwmaatregelen om waterkwaliteit te verbeteren : realisatie van nutriëntendoelstellingen uit de Kaderrichtlijn Water [Monograph]
Velthof, G.L. \ Kistenkas, F.H. \ Groenendijk, P. \ Boekel, E.M.P.M. van \ Oenema, O. \ 2018

De doelstellingen voor stikstof- en fosforconcentraties in grond- en oppervlaktewater uit de Kaderrichtlijn Water en Nitraatrichtlijn worden in bepaalde regio’s in Nederland op dit moment nog niet gehaald. Op basis van afspraken in de Stuurgroep Water en in opdracht van het Bestuurlijk Overleg Delta-aanpak Waterkwaliteit en Zoetwater is onderzocht of er voldoende inzetbaar juridisch instrumentarium is en of er aanvullend instrumentarium nodig is om aanvullende maatregelen te nemen om de waterkwaliteit te verbeteren. De Commissie Deskundigen Meststoffenwet (CDM) heeft het project uitgevoerd, onder begeleiding van een ambtelijke projectgroep bestaande uit vertegenwoordigers van de Regionaal Bestuurlijke Overleggen (RBO-en), Interprovinciaal Overleg (IPO), Unie van Waterschappen (UvW) alsook de ministeries van Infrastructuur en Waterstaat (IenW) en Landbouw, Natuur en Voedsel-kwaliteit (LNV). Het generieke spoor om nutriëntenuitspoeling te reguleren loopt via gebruiksnormen en –voorschriften in de Meststoffenwet en het Besluit gebruik meststoffen (Wet bodembescherming). Mits deze wetgeving wordt aangepast, kan het Rijk alle in deze studie geïnventariseerde maatregelen regionaal inzetten. Het generieke spoor biedt zonder aanpassing geen delegatiemogelijkheid naar decentrale overheden. In het gebied-specifieke spoor heeft de provincie via de provinciale milieuverordening mogelijkheden tot het nemen van enkele maatregelen in grondwaterbeschermingsgebieden en kunnen waterschappen teeltvrije (mestvrije) zones langs waterlopen via maatwerkvoorschriften voorschrijven in specifieke gebieden. Deze mogelijkheden voor regionale overheden kunnen alleen in specifieke situaties worden gebruikt. Met de komst van het nieuwe stelsel van het omgevingsrecht (de Omgevingswet) zullen deze mogelijkheden worden verruimd. Nader jurisprudentie-onderzoek is nodig om de mogelijkheden na te gaan om nutriënten-uitspoeling te beperken via het ruimtelijke ordeningsspoor, het natuurbeschermingsrechtelijke spoor en het privaatrechtelijke spoor. Er zou nader onderzoek moeten worden uitgevoerd om te bepalen of het wenselijk is om de mogelijkheden voor provincies en/of waterschappen uit te breiden om gebiedsgericht aanvullende maatregelen te nemen---The targets for nitrogen and phosphorous concentrations in groundwater and surface water under the Water Framework Directive and the Nitrates Directive are currently not being met in certain regions of the Netherlands. The Scientific Committee on the Nutrient Management Policy (CDM) has studied the relevant legal instruments to determine whether or not these provide sufficient means to introduce the additional measures required to improve water quality. The generic approach to controlling nutrient leaching involves the application of use standards and conditions under the Act on Manures and Fertilisers and the Decree on Fertiliser Use (Soil Protection Act). If this legislation is amended, the national government will be able to deploy all the measures examined in this study on a regional scale. Without any legislative amendment, it will not be possible to delegate powers to subnational authorities for the application of generic measures. In the place-based approach the provincial authorities can deploy certain measures in groundwater protection areas via the provincial environmental regulation. Water authorities can issue individual regulations declaring crop-free zones (no fertiliser use) along watercourses in specified areas. These possibilities available to regional authorities can only be used in specific situations. When the Environment and Planning Act comes into force these powers will be expanded. Further research will be needed to determine whether or not it will be necessary to extend the powers available to provincial and/or water authorities to include the imposition of supplementary place-based measures

Potential of insect proteins for food and feed : effect of endogenous enzymes and iron-phenolic complexation [PhD thesis]
Janssen, Renske H. \ 2018
Sodium and protein nutrition of lactating cows under tropical conditions [PhD thesis]
Thiangtum, Wandee \ 2018
Planty Organic 5 year: evaluation of soil fertility, nitrogen dynamics and production [Monograph]
Burgt, Geert-Jan van der \ Rietema, Carina \ Bus, Michiel \ 2018

In the Planty Organic experimental field, located at the SPNA location ‘Kollumerwaard’, an organic arable farming system is developed based on three principles: 1) Nitrogen input fully based on leguminous crops. 2) Use of farm-produced cut-and-carry fertilizers. 3) Reduced tillage; no ploughing. The results of this research will be available for improvements in both organic and conventional arable farming.

Scientific analysis of the status of designated Natura 2000 areas and the protection of nitrogen-sensitive species and habitats : Dutch contribution [Monograph]
Schmidt, A.M. \ Smidt, R.A. \ 2018
Effect of fire occurrence and frequency on topsoil properties and soil (fertility) losses by runoff [PhD thesis]
Hosseini, Mohammadreza \ 2018
Methodology for estimating emissions from agriculture in the Netherlands – update 2018 : calculations of CH4, NH3, N2O, NOx, PM10, PM2.5 and CO2 with the National Emission Model for Agriculture (NEMA) [Monograph]
Vonk, J. \ Sluis, S.M. van der \ Bannink, A. \ Bruggen, C. van \ Groenestein, C.M. \ Huijsmans, J.F.M. \ Kolk, J.W.H. van der \ Lagerwerf, L.A. \ Luesink, H.H. \ Oude Voshaar, S.V. \ Velthof, G.L. \ 2018

The National Emission Model for Agriculture (NEMA) is used to calculate emissions to air from agricultural activities in the Netherlands on a national scale. Emissions of ammonia (NH3) and other N-compounds (NOx and N2O) are calculated from animal housing, manure storage, manure application and grazing using a Total Ammoniacal Nitrogen (TAN) flow model. Furthermore, emissions from application of inorganic N fertilizer, compost and sewage sludge, cultivation of organic soils, crop residues, and ripening of crops are calculated. NEMA is also used to estimate emissions of methane (CH4) from enteric fermentation and manure management, particulate matter (PM) from manure management and agricultural soils and carbon dioxide (CO2) from liming. Emissions are calculated in accordance with international guidance criteria and reported in an annual Informative Inventory Report (IIR; for air pollutants) and National Inventory Report (NIR; for greenhouse gases). This methodology report describes the outline and backgrounds of the emission calculations with NEMA

Clinical handbook of air pollution-related diseases [Monograph]
Capello, Fabio \ Gaddi, Antonio Vittorino \ 2018
Environmentally induced diseases - Air Pollution - Environmentally induced diseases

This book examines in detail the clinical implications of those diseases that either are primarily triggered by air pollution or represent direct consequences of air pollutants. The aim is to provide medical practitioners with practical solutions to issues in diagnosis and treatment while simultaneously furnishing other interested parties with crucial information on the field. The book introduces the concept that air pollution-related diseases constitute a new class of pathologies. A wide range of conditions mainly attributable to air pollution are discussed, covering different body systems and pollution impacts in subsets of the population. In addition to presenting state of the art overviews of clinical aspects, the book carefully examines the implications of current knowledge for social and public health strategies aimed at disease prevention and prophylaxis. The Clinical Handbook of Air Pollution-Related Diseases will greatly assist doctors and healthcare workers when dealing with the consequences of air pollution in their everyday practice and will provide researchers, industry, and policymakers with valuable facts and insights.

Spatial patterns and mechanisms for terrestrial ecosystem carbon fluxes in the Northern Hemisphere [Monograph]
Chen, Zhi \ 2018
Carbon cycle (Biogeochemistry)

This book systematically illustrates the underlying mechanisms of spatial variation in ecosystem carbon fluxes. It presents the regulation of climate pattern, together with its impacts on ecosystem traits, which yields new insights into the terrestrial carbon cycle and offers a theoretic basis for large-scale carbon pattern assessment. By means of integrated analysis, the clear spatial pattern of carbon fluxes (including gross primary production, ecosystem respiration and net ecosystem production) along latitudes is clarified, from regions to the entire Northern Hemisphere. Temperature and precipitation patterns play a vital role in carbon spatial pattern formation, which strongly supports the application of the climate-driven theory to the Northern Hemisphere. With regard to the spatial pattern, the book demonstrates the covariation between production and respiration, offering new information to promote current respiration model development. Moreover, it reveals the high carbon uptake of subtropical forests across the East Asian monsoon region, which challenges the view that only mid- to high-latitude terrestrial ecosystems are principal carbon sink regions, and improves our understanding of carbon budgets and distribution. .

Termites and sustainable management. Volume 1, Biology, social behaviour and economic importance / [Monograph]
Khan, Md. Aslam \ Ahmad, Wasim \ 2018

This Volume comprises 12 chapters in an attempt to bring available information on biology, social behavour and economic importance of termites. Chapters in this book dealing with termites identification provide a review on most updated information of their systematics. Ecologically, termites interact with living and non-living surroundings and deliver a wide range of behaviors. In a separate chapter termites ecology is examined and explored. Termites depend on their gut microbes for digestion of complex polysaccharides of wood into simpler molecules. Information provided on termite gut microbiome and lignocellulose degradation constitutes an important contribution. Termite biology and social behaviour have been addressed comprehensively. Trail pheromones are responsible for the orientation and recruitment of nestmates to the food sources. Once arriving at a potential food source, termites assess its quality using a different set of cues. A separate chapter on trail pheromones, cues used during foraging and food assessment, with preferences for foraging sites, contributes a wealth of information. Emphasis has been given on reviewing ecological benefits of termites in other chapters. The information with respect to termite species as an edible insect and the overall role it plays in food and nutrition security in Africa is quite informative. A separate chapter dealing with importance of termites and termitaria in mineral exploration constitutes a significant step in addressing the economic importance of this insect group.

Advances in soil microbiology : recent trends and future prospects. Volume 1, Soil-microbe interaction / [Monograph]
Adhya, Tapan Kumar \ Lal, Banwari \ Mohapatra, Balaram \ Paul, Dhiraj \ Das, Subhasis \ 2018
Soil microbiology

This book presents a comprehensive collection of articles illustrating the importance of microbial community structure and function for ecosystem sustainability and environmental reclamation. It addresses a diverse range of topics, including microbial diversity, physiology, genomics, ecosystem function, interaction, metabolism, and the fruitful use of microbial communities for crop productivity and environmental remediation. In addition, the book explores issues ranging from general concepts on the diversity of microorganisms in soil, and ecosystem function to the evolution and taxonomy of soil microbiota, with future prospects. It covers cutting-edge methods in soil microbial ecological studies, rhizosphere microflora, the role of organic matter in plant productivity, biological nitrogen fixation and its genetics, microbial transformation of plant nutrients in soil, plant-growth-promoting rhizobacteria, and organic matter transformation. The book also discusses the application of microbes in biodegradation of xenobiotic contaminants. It covers bio-fertilizers and their role in sustainable agriculture and soil health, biological control of insect pests and plant pathogens, and the latest tools of omics in soil microbiology, i.e. genomics, proteomics, transcriptomics and metabolomics, which offer pioneering approaches to the exploration of microbial structure and function.

Alternative fuels for compression ignition engines [Monograph]
Abdul Karim, Zainal Ambri \ Sulaiman, Shaharin Anwar Bin \ 2018
Fuel switching - Synthetic fuels

This book examines the development and utilization of alternative fuels in order to reduce or control the environmental impact of internal combustion engine exhaust gases. Discussing alternative fuels such as dual fuel techniques, rubber seed/palm oil biodiesel, syngas dual-fuelling, water-in-diesel emulsions and gasification of date palm seeds, it is a valuable resource for researchers in the field of engine development and on alternative fuels.

Wastewater Management Through Aquaculture [Monograph]
Jana, B. B. \ Mandal, R. N. \ Jayasankar, P. \ 2018
Environment - Aquatic ecology - Environmental law - Environmental policy - Environmental management - Sustainable development - Water Pollution - Aquaculture Environmental aspects - Sewage disposal - Water conservation - Water quality management

This volume provides state-of-the-art information on soil-water interactions in wastewater systems, characterization of wastewater, modes of treatment, safety of wastewater use, water conservation technologies involved in recycling of sewage in fish culture, biogeochemical cycling bacteria and nutrient dynamics, ecosystem resilient driven wastewater reclamation, bioremediation, aquaponics, ecological integrity, culture practices of fish farming, microbial food web phenomena, fish diseases, environmental economics of wastewater, environmental risk assessment, environmental law and regulations. Given its breadth of coverage, the book will be useful to researchers, teachers, students, administrators, planners, farmers and entrepreneurs interested in the profitable use of wastewater in the wastes-into-wealth framework of for the benefit of humanity, and in achieving the targets for sanitation and safe wastewater reuse by 2030, specified in the United Nations’ Sustainable Development Goals. Concerns are growing about the quality and quantity of fresh water, as severe crises are expected in the near future. Climate change has further worsened the strain on inland water resources, with its major impacts on ecosystems and human life. It is most urgent to protect and conserve inland water resources to maintain vital ecosystem functions. Despite the immense nutrient potentials of wastewater in terms of phosphorus, nitrogen and potassium and increasingly high rates of urbanization-based wastewater generation, wastewater has traditionally been overlooked as a resource. This produces a threefold loss – environmental degradation, monetary losses from fertilizers, and water. As a result, municipal wastewater offers a win-win strategy for water conservation and environmental protection, while also turning waste into wealth in the form of fish biomass and allied cash crops. Wastewater-fed aquaculture refers to a unique, integrated biosystem in which the wastes generated by the first system are used by the next subsystem. In wastewater-fed aquaculture biosystems, the organic wastes are recycled into fish biomass mediated through a complex microbial/autotrophic/heterotrophic food web mechanism. .

Agronomy and photosynthesis physiology of hemp (Cannabis sativa L.) [PhD thesis]
Full text publicly available; under embargo until:2019-03-23
Tang, Kailei \ 2018
Identification and functional analyses of genes regulating seed dormancy, longevity and germination [PhD thesis]
Full text publicly available; under embargo until:2019-03-20
Yazdanpanah, Farzaneh \ 2018
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