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Complete Dissertation VU Research Portal Stress-free springtails de Boer, T.E. 2010 document version Publisher's PDF, also known as Version of record Link to publication in VU Research Portal citation for published version (APA) de Boer, T. E. (2010). Stress-free springtails: Determining natural gene expression profiles in collembolans. Ipskamp Drukkers B.V. General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. • Users may download and print one copy of any publication from the public portal for the purpose of private study or research. • You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying the publication in the public portal ? Take down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. E-mail address: [email protected] Download date: 25. Sep. 2021 Stress-free springtails – Determining natural gene expression profiles in collembolans Cover design: Janine Mariën Lay-out: Désirée Hoonhout Printing: Ipskamp Drukkers B.V., Enschede VRIJE UNIVERSITEIT Stress-free springtails Determining natural gene expression profiles in collembolans ACADEMISCH PROEFSCHRIFT ter verkrijging van de graad Doctor aan de Vrije Universiteit Amsterdam, op gezag van de rector magnificus prof.dr. L.M. Bouter, in het openbaar te verdedigen ten overstaan van de promotiecommissie van de faculteit der Aard- en Levenswetenschappen op woensdag 1 december 2010 om 11.45 uur in de aula van de universiteit, De Boelelaan 1105 door Tjalf Elmer de Boer geboren te Alkmaar promotor: prof.dr. N.M. van Straalen copromotor: dr.ir. D. Roelofs Contents Page Chapter 1: Introduction 7 Chapter 2: Reference genes for QRT-PCR tested under various stress conditions 23 in Folsomia candida and Orchesella cincta (Insecta, Collembola) Chapter 3: The effect of soil pH and temperature on Folsomia candida 47 transcriptional regulation Chapter 4: Transcriptional plasticity of a soil arthropod across different 65 ecological conditions Chapter 5: The effects of aged copper pollution on Folsomia candida physiology 89 Chapter 6: Discussion 109 Summary 117 Samenvatting 121 Dankwoord 125 Curriculum Vitae 126 Publications 127 Chapter 1 General introduction All over the world, from mountains to deserts, soil fulfills many important functions for plants, animals and humans. Plants grow in it while extracting nutrients and water from the soil. Animals and humans are exposed to it directly by walking on it, or living in it, or indirectly by eating plants or other animals. There are theories that soil, in the form of clay particles, played a major role in the origins of life. This theory states that clay particles are able to catalyze the reactions needed for the formation of primitive life (Ponnamperuma et al., 1982). In 2003 Hanczyc et al (2003) reported that particles of a certain type of clay, called Montmorrilonite, is able to catalyze the formation of lipid bi-layers, simple forms of cell membranes, from single fatty acids. Because soil plays an important role in organismal functioning, soil pollution can have a major impact on plants and animals. Soil pollutants can be taken up by plants and animals where they can cause adverse effects on their development and ultimately threaten the survival of species (McGrath et al., 1995, Lande, 1998). Soil pollution can be formed by natural phenomena, such as volcanic eruptions, or caused by human society. The latter, also called anthropogenic pollution, is the result of an overburden of substances emitted into the environment faster than natural systems can eliminate them. Anthropogenic pollution can be historic; an example is heavy metal pollution. In the Bronze Age (3300 - 1200 BC) human civilization started working metals on a large scale. The production of these metals, first copper and tin but later also iron and zinc, requires mining and smelting of the various metal containing ores. During the smelting process other metals such as lead and cadmium were also emitted. This is why soils and litter in many historic smelting sites in Europe are heavily polluted with these heavy metals (Nriagu, 1996). To understand the effect of soil pollutants on soil flora and fauna, it is important to know the interaction between soil properties and pollutants. The origin of soil To understand the functional properties of soil we need to understand its composition and how it was formed. Soil is generally made up by minerals, metals, organic molecules, water 7 and air. The distribution of these elements in the earth crust was established during the formation of our solar system and the earth. The earth took shape approximately 4.5 billion years ago. After its formation the young planet heated up rapidly due to different processes, after which it entered a mostly liquid state. In that phase and as it still is today, 93% of the planet’s mass is made up of only four elements: iron (35%), oxygen (30%), silicon (15%) and magnesium (13%). However, due to its mass and under the influence of gravity, Iron started to fall down into the centre of the planet making up the core. This process is called chemical zonation (Rama Murthy and Hall, 1972) in which lighter elements aggregate in the crust of the planet while heavier elements fall in and concentrate in the centre. This is why the crust of the planet has a different relative abundance compared to the planet as a whole. 82% of the earth’s crust is made up of oxygen (46%), silicon (28%) and aluminum (8%). iron, although the most abundant element in the whole planet, only accounts for only 6% of the mass in the crust (Press and Siever, 1986). As the planet cooled the first rock formations started to form the crust. The earth crust is mostly built up of minerals. Minerals are homogenous substances with a fixed composition and crystal structure. 98% of the minerals that make up the earth crust are composed out of different combinations of eight elements: (Si, O, Al, Fe, Ca, Na, K and Mg) (Yaroshevsky, 2006). Silicon and oxygen form the most common minerals in the form of silicon oxides. Silicon oxides form minerals in the ratio of one silicon atom and two oxygen atoms, the simplest being SiO2 also known as quartz (Lyon and Burns, 1963). In the crust, minerals form into larger aggregations called rock. Rock is formed out of one or multiple elements and sometimes out of organic substances. According to its origin rocks are classified generally into three classes; igneous rock, sedimentary rock and metamorphic rock. Igneous rock forms by cooling down and solidifying of volcanic magma (Le maitre, 2002). This can either be at the surface during a volcanic eruption or in between other rock layers when the pressure in the volcanic trench is not high enough to cause a surface eruption. Sedimentary rock is formed by the weathering down and erosion of other rock types, mainly igneous rock, into sediment which is deposited elsewhere after transportation by rivers, glaciers, wind and gravity. This sediment can, under the right conditions, lithify into rock. Sedimentary rock exists in many types and forms since there are many types of mineral or even organic sources of erosion (Einsele, 2000). Metamorphic rock is formed by the transformation of other rock, igneous, sedimentary or other metamorphic rock. This transformation is often caused by high pressure deep within the crust or by plate tectonics (Bucher and Frey, 2002). 8 The vertical soil profile Soil is formed by the deposition of sedimentary minerals eroded from rocks and from organic breakdown products of plants and animals. Soil specific structure is formed when both the mineral and the organic fraction of the soil are bound to each other. Sediment deposition is often a long-term process and can have multiple parent rock sources over time. This results in different layers, which can often be distinguished by eye from each other and are called soil horizons. There are many types of soil horizons but the most important ones are, from surface to deep soil, the O, A, B and C horizons (2000). The O (Organic) horizon is composed out of the litter layer on top of the soil. The A horizon is the surface soil in which most of the biological activity in the form of plant and animal life takes place. This part of the soil also contains most of the organic material. The B horizon, also referred to as the sub-soil, contains mineral layers which may contain different concentrations of clay. The C horizon is the parent rock on which the other horizons rest. There are different types of interaction possible between the soil horizons. Metal ions and clay particles, for example, are often transported by vertical water transport or chemical leaching, from the A to the B horizon where they accumulate, a process which is called illuvation (Lundström et al., 2000). In this thesis the top soil, or A horizon, is most important as this horizon has the greatest impact on plant and animal life. The soil samples used in Chapters 4 and 5 were taken from the top soil. The interaction between the two soil horizons however, cannot be neglected. In Chapter 5 for example an in situ spiked copper soil is investigated and the interaction between the A and B horizons has a major impact on copper behavior in the soil. Classification of soil texture according to particle size The soil type is often classified according to the size of the particles that make up the soil.
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