Soil , also commonly referred to as earth , is a mixture of organic matter , minerals , gases , liquids , and organisms that together support the life of plants and soil organisms . Some scientific definitions distinguish dirt from soil by restricting the former term specifically to displaced soil.
120-748: Soil consists of a solid phase of minerals and organic matter (the soil matrix), as well as a porous phase that holds gases (the soil atmosphere) and water (the soil solution). Accordingly, soil is a three- state system of solids, liquids, and gases. Soil is a product of several factors: the influence of climate , relief (elevation, orientation, and slope of terrain), organisms, and the soil's parent materials (original minerals) interacting over time. It continually undergoes development by way of numerous physical, chemical and biological processes, which include weathering with associated erosion . Given its complexity and strong internal connectedness , soil ecologists regard soil as an ecosystem . Most soils have
240-409: A haploid chromosomal composition that is partially replicated, a condition known as merodiploidy . Prokaryotes lack mitochondria and chloroplasts . Instead, processes such as oxidative phosphorylation and photosynthesis take place across the prokaryotic cell membrane . However, prokaryotes do possess some internal structures, such as prokaryotic cytoskeletons . It has been suggested that
360-693: A paraphyletic group, just like dinosaurs without birds. Unlike the above assumption of a fundamental split between prokaryotes and eukaryotes, the most important difference between biota may be the division between Bacteria and the rest (Archaea and Eukaryota). For instance, DNA replication differs fundamentally between the Bacteria and Archaea (including that in eukaryotic nuclei), and it may not be homologous between these two groups. Moreover, ATP synthase , though common (homologous) in all organisms, differs greatly between bacteria (including eukaryotic organelles such as mitochondria and chloroplasts ) and
480-1088: A prokaryotic cytoskeleton that is more primitive than that of the eukaryotes. Besides homologues of actin and tubulin ( MreB and FtsZ ), the helically arranged building-block of the flagellum , flagellin , is one of the most significant cytoskeletal proteins of bacteria, as it provides structural backgrounds of chemotaxis , the basic cell physiological response of bacteria. At least some prokaryotes also contain intracellular structures that can be seen as primitive organelles. Membranous organelles (or intracellular membranes) are known in some groups of prokaryotes, such as vacuoles or membrane systems devoted to special metabolic properties, such as photosynthesis or chemolithotrophy . In addition, some species also contain carbohydrate-enclosed microcompartments, which have distinct physiological roles (e.g. carboxysomes or gas vacuoles). Most prokaryotes are between 1 μm and 10 μm, but they can vary in size from 0.2 μm ( Mycoplasma genitalium ) to 750 μm ( Thiomargarita namibiensis ). Prokaryotic cells have various shapes;
600-401: A taxon to be found nearby the then-unknown Asgard group). For example, histones which usually package DNA in eukaryotic nuclei, have also been found in several archaean groups, giving evidence for homology . This idea might clarify the mysterious predecessor of eukaryotic cells ( eucytes ) which engulfed an alphaproteobacterium forming the first eucyte ( LECA , l ast e ukaryotic c ommon
720-1203: A bacterium to bind, take up and recombine donor DNA into its own chromosome, it must first enter a special physiological state called competence . About 40 genes are required in Bacillus subtilis for the development of competence. The length of DNA transferred during B. subtilis transformation can be as much as a third to the whole chromosome. Transformation is a common mode of DNA transfer, and 67 prokaryotic species are thus far known to be naturally competent for transformation. Among archaea, Halobacterium volcanii forms cytoplasmic bridges between cells that appear to be used for transfer of DNA from one cell to another. Another archaeon, Sulfolobus solfataricus , transfers DNA between cells by direct contact. Frols et al. (2008) found that exposure of S. solfataricus to DNA damaging agents induces cellular aggregation, and suggested that cellular aggregation may enhance DNA transfer among cells to provide increased repair of damaged DNA via homologous recombination. While prokaryotes are considered strictly unicellular, most can form stable aggregate communities. When such communities are encased in
840-399: A better estimation can be obtained by examining the lithology of the particles. Porosity can be proportional to hydraulic conductivity ; for two similar sandy aquifers , the one with a higher porosity will typically have a higher hydraulic conductivity (more open area for the flow of water), but there are many complications to this relationship. The principal complication is that there
960-638: A dry bulk density (density of soil taking into account voids when dry) between 1.1 and 1.6 g/cm, though the soil particle density is much higher, in the range of 2.6 to 2.7 g/cm. Little of the soil of planet Earth is older than the Pleistocene and none is older than the Cenozoic , although fossilized soils are preserved from as far back as the Archean . Collectively the Earth's body of soil
1080-399: A higher metabolic rate , a higher growth rate, and as a consequence, a shorter generation time than eukaryotes. There is increasing evidence that the roots of the eukaryotes are to be found in (or at least next to) the archaean Asgard group, perhaps Heimdallarchaeota (an idea which is a modern version of the 1984 eocyte hypothesis , eocytes being an old synonym for Thermoproteota ,
1200-446: A medium for plant growth , making it a critically important provider of ecosystem services . Since soil has a tremendous range of available niches and habitats , it contains a prominent part of the Earth's genetic diversity . A gram of soil can contain billions of organisms, belonging to thousands of species, mostly microbial and largely still unexplored. Soil has a mean prokaryotic density of roughly 10 organisms per gram, whereas
1320-527: A ncestor) according to endosymbiotic theory . There might have been some additional support by viruses, called viral eukaryogenesis . The non-bacterial group comprising archaea and eukaryota was called Neomura by Thomas Cavalier-Smith in 2002. However, in a cladistic view, Eukaryota are Archaea in the same sense as birds are dinosaurs because they evolved from the Maniraptora dinosaur group. In contrast, archaea without eukaryota appear to be
SECTION 10
#17327724456821440-416: A net absorption of oxygen and methane and undergo a net release of carbon dioxide and nitrous oxide . Soils offer plants physical support, air, water, temperature moderation, nutrients, and protection from toxins. Soils provide readily available nutrients to plants and animals by converting dead organic matter into various nutrient forms. Components of a silt loam soil by percent volume A typical soil
1560-659: A nucleus. Both eukaryotes and prokaryotes contain large RNA / protein structures called ribosomes , which produce protein , but the ribosomes of prokaryotes are smaller than those of eukaryotes. Mitochondria and chloroplasts , two organelles found in many eukaryotic cells, contain ribosomes similar in size and makeup to those found in prokaryotes. This is one of many pieces of evidence that mitochondria and chloroplasts are descended from free-living bacteria. The endosymbiotic theory holds that early eukaryotic cells took in primitive prokaryotic cells by phagocytosis and adapted themselves to incorporate their structures, leading to
1680-545: A pH of 9, plant growth is reduced. High pH results in low micro-nutrient mobility, but water-soluble chelates of those nutrients can correct the deficit. Sodium can be reduced by the addition of gypsum (calcium sulphate) as calcium adheres to clay more tightly than does sodium causing sodium to be pushed into the soil water solution where it can be washed out by an abundance of water. There are acid-forming cations (e.g. hydronium, aluminium, iron) and there are base-forming cations (e.g. calcium, magnesium, sodium). The fraction of
1800-726: A result of a trade-off between toxicity and requirement most nutrients are better available to plants at moderate pH, although most minerals are more soluble in acid soils. Soil organisms are hindered by high acidity, and most agricultural crops do best with mineral soils of pH 6.5 and organic soils of pH 5.5. Given that at low pH toxic metals (e.g. cadmium, zinc, lead) are positively charged as cations and organic pollutants are in non-ionic form, thus both made more available to organisms, it has been suggested that plants, animals and microbes commonly living in acid soils are pre-adapted to every kind of pollution, whether of natural or human origin. In high rainfall areas, soils tend to acidify as
1920-399: A result, layers (horizons) form in the soil profile. The alteration and movement of materials within a soil causes the formation of distinctive soil horizons . However, more recent definitions of soil embrace soils without any organic matter, such as those regoliths that formed on Mars and analogous conditions in planet Earth deserts. An example of the development of a soil would begin with
2040-690: A similar group of selfish individuals (see inclusive fitness and Hamilton's rule ). Should these instances of prokaryotic sociality prove to be the rule rather than the exception, it would have serious implications for the way we view prokaryotes in general, and the way we deal with them in medicine. Bacterial biofilms may be 100 times more resistant to antibiotics than free-living unicells and may be nearly impossible to remove from surfaces once they have colonized them. Other aspects of bacterial cooperation—such as bacterial conjugation and quorum-sensing-mediated pathogenicity , present additional challenges to researchers and medical professionals seeking to treat
2160-473: A single founder (in the way that animals and plants are founded by single cells), which presents a number of theoretical issues. Most explanations of co-operation and the evolution of multicellularity have focused on high relatedness between members of a group (or colony, or whole organism). If a copy of a gene is present in all members of a group, behaviors that promote cooperation between members may permit those members to have (on average) greater fitness than
2280-505: A small, insoluble particle ranging in size from 1 nanometer to 1 micrometer , thus small enough to remain suspended by Brownian motion in a fluid medium without settling. Most soils contain organic colloidal particles called humus as well as the inorganic colloidal particles of clays . The very high specific surface area of colloids and their net electrical charges give soil its ability to hold and release ions . Negatively charged sites on colloids attract and release cations in what
2400-411: A soil can be said to be developed, and can be described further in terms of color, porosity, consistency, reaction ( acidity ), etc. Water is a critical agent in soil development due to its involvement in the dissolution, precipitation, erosion, transport, and deposition of the materials of which a soil is composed. The mixture of water and dissolved or suspended materials that occupy the soil pore space
2520-401: A soil determines its ability to supply available plant nutrients and affects its physical properties and the health of its living population. In addition, a soil's chemistry also determines its corrosivity , stability, and ability to absorb pollutants and to filter water. It is the surface chemistry of mineral and organic colloids that determines soil's chemical properties. A colloid is
SECTION 20
#17327724456822640-679: A stabilizing polymer matrix ("slime"), they may be called " biofilms ". Cells in biofilms often show distinct patterns of gene expression (phenotypic differentiation) in time and space. Also, as with multicellular eukaryotes, these changes in expression often appear to result from cell-to-cell signaling , a phenomenon known as quorum sensing . Biofilms may be highly heterogeneous and structurally complex and may attach to solid surfaces, or exist at liquid-air interfaces, or potentially even liquid-liquid interfaces. Bacterial biofilms are often made up of microcolonies (approximately dome-shaped masses of bacteria and matrix) separated by "voids" through which
2760-435: A third domain: Eukaryota . Prokaryotes evolved before eukaryotes, and lack nuclei, mitochondria , and most of the other distinct organelles that characterize the eukaryotic cell. It was once thought that prokaryotic cellular components were unenclosed within the cytoplasm except for an outer cell membrane , but bacterial microcompartments , which are thought to be quasi-organelles enclosed in protein shells (such as
2880-471: A valence of two, converts to (40 ÷ 2) × 1 milliequivalent = 20 milliequivalents of hydrogen ion per 100 grams of dry soil or 20 meq/100 g. The modern measure of CEC is expressed as centimoles of positive charge per kilogram (cmol/kg) of oven-dry soil. Most of the soil's CEC occurs on clay and humus colloids, and the lack of those in hot, humid, wet climates (such as tropical rainforests ), due to leaching and decomposition, respectively, explains
3000-404: Is evidence on Mars of fossil or living prokaryotes. However, this possibility remains the subject of considerable debate and skepticism. The division between prokaryotes and eukaryotes is usually considered the most important distinction or difference among organisms. The distinction is that eukaryotic cells have a "true" nucleus containing their DNA , whereas prokaryotic cells do not have
3120-549: Is 0.04%, but in the soil pore space it may range from 10 to 100 times that level, thus potentially contributing to the inhibition of root respiration. Calcareous soils regulate CO 2 concentration by carbonate buffering , contrary to acid soils in which all CO 2 respired accumulates in the soil pore system. At extreme levels, CO 2 is toxic. This suggests a possible negative feedback control of soil CO 2 concentration through its inhibitory effects on root and microbial respiration (also called soil respiration ). In addition,
3240-428: Is a fraction between 0 and 1, typically ranging from less than 0.005 for solid granite to more than 0.5 for peat and clay . The porosity of a rock, or sedimentary layer, is an important consideration when attempting to evaluate the potential volume of water or hydrocarbons it may contain. Sedimentary porosity is a complicated function of many factors, including but not limited to: rate of burial, depth of burial,
3360-595: Is a measure of the acidity or alkalinity of the soil. More precisely, it is a measure of hydronium concentration in an aqueous solution and ranges in values from 0 to 14 (acidic to basic) but practically speaking for soils, pH ranges from 3.5 to 9.5, as pH values beyond those extremes are toxic to life forms. At 25 °C an aqueous solution that has a pH of 3.5 has 10 moles H 3 O (hydronium ions) per litre of solution (and also 10 moles per litre OH). A pH of 7, defined as neutral, has 10 moles of hydronium ions per litre of solution and also 10 moles of OH per litre; since
3480-455: Is a measure of the void (i.e. "empty") spaces in a material , and is a fraction of the volume of voids over the total volume, between 0 and 1, or as a percentage between 0% and 100%. Strictly speaking, some tests measure the "accessible void", the total amount of void space accessible from the surface (cf. closed-cell foam ). There are many ways to test porosity in a substance or part, such as industrial CT scanning . The term porosity
3600-409: Is about 50% solids (45% mineral and 5% organic matter), and 50% voids (or pores) of which half is occupied by water and half by gas. The percent soil mineral and organic content can be treated as a constant (in the short term), while the percent soil water and gas content is considered highly variable whereby a rise in one is simultaneously balanced by a reduction in the other. The pore space allows for
3720-418: Is also a net sink of methane (CH 4 ) but a net producer of methane (a strong heat-absorbing greenhouse gas ) when soils are depleted of oxygen and subject to elevated temperatures. Soil atmosphere is also the seat of emissions of volatiles other than carbon and nitrogen oxides from various soil organisms, e.g. roots, bacteria, fungi, animals. These volatiles are used as chemical cues, making soil atmosphere
Soil - Misplaced Pages Continue
3840-453: Is an associated concept. The ratio of holes to solid that the wind "sees". Aerodynamic porosity is less than visual porosity, by an amount that depends on the constriction of holes. Casting porosity is a consequence of one or more of the following: gasification of contaminants at molten-metal temperatures; shrinkage that takes place as molten metal solidifies; and unexpected or uncontrolled changes in temperature or humidity. While porosity
3960-552: Is an important characteristic of soil. This ventilation can be accomplished via networks of interconnected soil pores , which also absorb and hold rainwater making it readily available for uptake by plants. Since plants require a nearly continuous supply of water, but most regions receive sporadic rainfall, the water-holding capacity of soils is vital for plant survival. Soils can effectively remove impurities, kill disease agents, and degrade contaminants , this latter property being called natural attenuation . Typically, soils maintain
4080-462: Is assumed acid-forming cations). Base saturation is almost in direct proportion to pH (it increases with increasing pH). It is of use in calculating the amount of lime needed to neutralise an acid soil (lime requirement). The amount of lime needed to neutralize a soil must take account of the amount of acid forming ions on the colloids (exchangeable acidity), not just those in the soil water solution (free acidity). The addition of enough lime to neutralize
4200-425: Is between 1.5 and 1.7 g/cm . This calculates to a porosity between 0.43 and 0.36. Typical bulk density of clay soil is between 1.1 and 1.3 g/cm . This calculates to a porosity between 0.58 and 0.51. This seems counterintuitive because clay soils are termed heavy , implying lower porosity. Heavy apparently refers to a gravitational moisture content effect in combination with terminology that harkens back to
4320-412: Is called the pedosphere . The pedosphere interfaces with the lithosphere , the hydrosphere , the atmosphere , and the biosphere . Soil has four important functions : All of these functions, in their turn, modify the soil and its properties. Soil science has two basic branches of study: edaphology and pedology . Edaphology studies the influence of soils on living things. Pedology focuses on
4440-401: Is called the soil solution. Since soil water is never pure water, but contains hundreds of dissolved organic and mineral substances, it may be more accurately called the soil solution. Water is central to the dissolution , precipitation and leaching of minerals from the soil profile . Finally, water affects the type of vegetation that grows in a soil, which in turn affects the development of
4560-469: Is complex. Traditional models regard porosity as continuous. This fails to account for anomalous features and produces only approximate results. Furthermore, it cannot help model the influence of environmental factors which affect pore geometry. A number of more complex models have been proposed, including fractals , bubble theory, cracking theory, Boolean grain process, packed sphere, and numerous other models. The characterisation of pore space in soil
4680-421: Is dependent on the type of parent material , the processes that modify those parent materials, and the soil-forming factors that influence those processes. The biological influences on soil properties are strongest near the surface, though the geochemical influences on soil properties increase with depth. Mature soil profiles typically include three basic master horizons: A, B, and C. The solum normally includes
4800-399: Is induced. Capillary action is responsible for moving groundwater from wet regions of the soil to dry areas. Subirrigation designs (e.g., wicking beds , sub-irrigated planters ) rely on capillarity to supply water to plant roots. Capillary action can result in an evaporative concentration of salts, causing land degradation through salination . Soil moisture measurement —measuring
4920-459: Is inherent in die casting manufacturing, its presence may lead to component failure where pressure integrity is a critical characteristic. Porosity may take on several forms from interconnected micro-porosity, folds, and inclusions to macro porosity visible on the part surface. The end result of porosity is the creation of a leak path through the walls of a casting that prevents the part from holding pressure. Porosity may also lead to out-gassing during
Soil - Misplaced Pages Continue
5040-530: Is likely home to 59 ± 15% of the species on Earth. Enchytraeidae (worms) have the greatest percentage of species in soil (98.6%), followed by fungi (90%), plants (85.5%), and termites ( Isoptera ) (84.2%). Many other groups of animals have substantial fractions of species living in soil, e.g. about 30% of insects , and close to 50% of arachnids . While most vertebrates live above ground (ignoring aquatic species), many species are fossorial , that is, they live in soil, such as most blind snakes . The chemistry of
5160-475: Is more advanced. Most plant nutrients, with the exception of nitrogen , originate from the minerals that make up the soil parent material. Some nitrogen originates from rain as dilute nitric acid and ammonia , but most of the nitrogen is available in soils as a result of nitrogen fixation by bacteria . Once in the soil-plant system, most nutrients are recycled through living organisms, plant and microbial residues (soil organic matter), mineral-bound forms, and
5280-402: Is more easily measured through the volume of gas or liquid that can flow into the rock, whereas fluids cannot access unconnected pores. Porosity is the ratio of pore volume to its total volume. Porosity is controlled by: rock type, pore distribution, cementation, diagenetic history and composition. Porosity is not controlled by grain size, as the volume of between-grain space is related only to
5400-478: Is not a direct proportionality between porosity and hydraulic conductivity but rather an inferred proportionality. There is a clear proportionality between pore throat radii and hydraulic conductivity. Also, there tends to be a proportionality between pore throat radii and pore volume. If the proportionality between pore throat radii and porosity exists then a proportionality between porosity and hydraulic conductivity may exist. However, as grain size or sorting decreases
5520-409: Is referred to as cation exchange . Cation-exchange capacity is the amount of exchangeable cations per unit weight of dry soil and is expressed in terms of milliequivalents of positively charged ions per 100 grams of soil (or centimoles of positive charge per kilogram of soil; cmol c /kg ). Similarly, positively charged sites on colloids can attract and release anions in the soil, giving
5640-455: Is the initial porosity of the sediment at the surface of soil (before its burial), and k {\displaystyle k} is the compaction coefficient (m ). The letter e {\displaystyle e} with a negative exponent denotes the decreasing exponential function. The porosity of the sediment exponentially decreases with depth, as a function of its compaction. A value for porosity can alternatively be calculated from
5760-418: Is used in multiple fields including pharmaceutics , ceramics , metallurgy , materials , manufacturing , petrophysics , hydrology , earth sciences , soil mechanics , rock mechanics , and engineering . In gas-liquid two-phase flow , the void fraction is defined as the fraction of the flow-channel volume that is occupied by the gas phase or, alternatively, as the fraction of the cross-sectional area of
5880-542: Is very little organic material. Basaltic minerals commonly weather relatively quickly, according to the Goldich dissolution series . The plants are supported by the porous rock as it is filled with nutrient-bearing water that carries minerals dissolved from the rocks. Crevasses and pockets, local topography of the rocks, would hold fine materials and harbour plant roots. The developing plant roots are associated with mineral-weathering mycorrhizal fungi that assist in breaking up
6000-537: The Ancient Greek πρό ( pró ), meaning 'before', and κάρυον ( káruon ), meaning 'nut' or 'kernel'. In the two-empire system arising from the work of Édouard Chatton , prokaryotes were classified within the empire Prokaryota . However in the three-domain system , based upon molecular analysis , prokaryotes are divided into two domains : Bacteria (formerly Eubacteria) and Archaea (formerly Archaebacteria). Organisms with nuclei are placed in
6120-489: The aeration of the soil and the ability of water to infiltrate and to be held within the soil. Soil water content can be measured as volume or weight . Soil moisture levels, in order of decreasing water content, are saturation, field capacity , wilting point , air dry, and oven dry. Field capacity describes a drained wet soil at the point water content reaches equilibrium with gravity. Irrigating soil above field capacity risks percolation losses. Wilting point describes
SECTION 50
#17327724456826240-626: The bulk density ρ bulk {\displaystyle \rho _{\text{bulk}}} , saturating fluid density ρ fluid {\displaystyle \rho _{\text{fluid}}} and particle density ρ particle {\displaystyle \rho _{\text{particle}}} : If the void space is filled with air, the following simpler form may be used: A mean normal particle density can be taken as approximately 2.65 g/cm ( silica , siliceous sediments or aggregates), or 2.70 g/cm ( calcite , carbonate sediments or aggregates), although
6360-555: The encapsulin protein cages ), have been discovered, along with other prokaryotic organelles . While being unicellular, some prokaryotes, such as cyanobacteria , may form colonies held together by biofilms , and large colonies can create multilayered microbial mats . Others, such as myxobacteria , have multicellular stages in their life cycles . Prokaryotes are asexual , reproducing via binary fission without any fusion of gametes , although horizontal gene transfer may take place. Molecular studies have provided insight into
6480-559: The humus form ), the copedon (in intermediary position, where most weathering of minerals takes place) and the lithopedon (in contact with the subsoil). The soil texture is determined by the relative proportions of the individual particles of sand , silt , and clay that make up the soil. The interaction of the individual mineral particles with organic matter, water, gases via biotic and abiotic processes causes those particles to flocculate (stick together) to form aggregates or peds . Where these aggregates can be identified,
6600-424: The mineralogy of those particles can strongly modify those properties. The mineralogy of the finest soil particles, clay, is especially important. Large numbers of microbes , animals , plants and fungi are living in soil. However, biodiversity in soil is much harder to study as most of this life is invisible, hence estimates about soil biodiversity have been unsatisfactory. A recent study suggested that soil
6720-447: The A and B horizons. The living component of the soil is largely confined to the solum, and is generally more prominent in the A horizon. It has been suggested that the pedon , a column of soil extending vertically from the surface to the underlying parent material and large enough to show the characteristics of all its horizons, could be subdivided in the humipedon (the living part, where most soil organisms are dwelling, corresponding to
6840-584: The CEC increases. Hence, pure sand has almost no buffering ability, though soils high in colloids (whether mineral or organic) have high buffering capacity . Buffering occurs by cation exchange and neutralisation . However, colloids are not the only regulators of soil pH. The role of carbonates should be underlined, too. More generally, according to pH levels, several buffer systems take precedence over each other, from calcium carbonate buffer range to iron buffer range. Porosity Porosity or void fraction
6960-404: The acronym CROPT. The physical properties of soils, in order of decreasing importance for ecosystem services such as crop production , are texture , structure , bulk density , porosity , consistency, temperature , colour and resistivity . Soil texture is determined by the relative proportion of the three kinds of soil mineral particles, called soil separates: sand , silt , and clay . At
7080-443: The addition of any more hydronium ions or aluminum hydroxyl cations drives the pH even lower (more acidic) as the soil has been left with no buffering capacity. In areas of extreme rainfall and high temperatures, the clay and humus may be washed out, further reducing the buffering capacity of the soil. In low rainfall areas, unleached calcium pushes pH to 8.5 and with the addition of exchangeable sodium, soils may reach pH 10. Beyond
7200-449: The apparent sterility of tropical soils. Live plant roots also have some CEC, linked to their specific surface area. Anion exchange capacity is the soil's ability to remove anions (such as nitrate , phosphate ) from the soil water solution and sequester those for later exchange as the plant roots release carbonate anions to the soil water solution. Those colloids which have low CEC tend to have some AEC. Amorphous and sesquioxide clays have
7320-608: The archaea/eukaryote nucleus group. The last common antecessor of all life (called LUCA , l ast u niversal c ommon a ncestor) should have possessed an early version of this protein complex. As ATP synthase is obligate membrane bound, this supports the assumption that LUCA was a cellular organism. The RNA world hypothesis might clarify this scenario, as LUCA might have been a ribocyte (also called ribocell) lacking DNA, but with an RNA genome built by ribosomes as primordial self-replicating entities . A Peptide-RNA world (also called RNP world) hypothesis has been proposed based on
SECTION 60
#17327724456827440-478: The associated diseases. Prokaryotes have diversified greatly throughout their long existence. The metabolism of prokaryotes is far more varied than that of eukaryotes, leading to many highly distinct prokaryotic types. For example, in addition to using photosynthesis or organic compounds for energy, as eukaryotes do, prokaryotes may obtain energy from inorganic compounds such as hydrogen sulfide . This enables prokaryotes to thrive in harsh environments as cold as
7560-435: The atmosphere due to increased biological activity at higher temperatures, a positive feedback (amplification). This prediction has, however, been questioned on consideration of more recent knowledge on soil carbon turnover. Soil acts as an engineering medium, a habitat for soil organisms , a recycling system for nutrients and organic wastes , a regulator of water quality , a modifier of atmospheric composition , and
7680-450: The bacterial phylum Planctomycetota has a membrane around the nucleoid and contains other membrane-bound cellular structures. However, further investigation revealed that Planctomycetota cells are not compartmentalized or nucleated and, like other bacterial membrane systems, are interconnected. Prokaryotic cells are usually much smaller than eukaryotic cells. Therefore, prokaryotes have a larger surface-area-to-volume ratio , giving them
7800-424: The basic cations are forced off the soil colloids by the mass action of hydronium ions from usual or unusual rain acidity against those attached to the colloids. High rainfall rates can then wash the nutrients out, leaving the soil inhabited only by those organisms which are particularly efficient to uptake nutrients in very acid conditions, like in tropical rainforests . Once the colloids are saturated with H 3 O,
7920-421: The biofilm—has led some to speculate that this may constitute a circulatory system and many researchers have started calling prokaryotic communities multicellular (for example ). Differential cell expression, collective behavior, signaling, programmed cell death , and (in some cases) discrete biological dispersal events all seem to point in this direction. However, these colonies are seldom if ever founded by
8040-495: The bodies of other organisms, including humans. Prokaryotes have high populations in the soil - including the rhizosphere and rhizosheath . Soil prokaryotes are still heavily undercharacterized despite their easy proximity to humans and their tremendous economic importance to agriculture . In 1977, Carl Woese proposed dividing prokaryotes into the Bacteria and Archaea (originally Eubacteria and Archaebacteria) because of
8160-503: The channel that is occupied by the gas phase. Void fraction usually varies from location to location in the flow channel (depending on the two-phase flow pattern). It fluctuates with time and its value is usually time averaged. In separated (i.e., non- homogeneous ) flow, it is related to volumetric flow rates of the gas and the liquid phase, and to the ratio of the velocity of the two phases (called slip ratio ). Used in geology , hydrogeology , soil science , and building science ,
8280-454: The current set of prokaryotic species may have evolved from more complex eukaryotic ancestors through a process of simplification. Others have argued that the three domains of life arose simultaneously, from a set of varied cells that formed a single gene pool. This controversy was summarized in 2005: There is no consensus among biologists concerning the position of the eukaryotes in the overall scheme of cell evolution. Current opinions on
8400-435: The dry limit for growing plants. During growing season, soil moisture is unaffected by functional groups or specie richness. Available water capacity is the amount of water held in a soil profile available to plants. As water content drops, plants have to work against increasing forces of adhesion and sorptivity to withdraw water. Irrigation scheduling avoids moisture stress by replenishing depleted water before stress
8520-530: The evolution and interrelationships of the three domains of life. The division between prokaryotes and eukaryotes reflects the existence of two very different levels of cellular organization; only eukaryotic cells have an enveloped nucleus that contains its chromosomal DNA , and other characteristic membrane-bound organelles including mitochondria. Distinctive types of prokaryotes include extremophiles and methanogens ; these are common in some extreme environments. The distinction between prokaryotes and eukaryotes
8640-432: The formation of the Earth's crust. Eukaryotes only appear in the fossil record later, and may have formed from endosymbiosis of multiple prokaryote ancestors. The oldest known fossil eukaryotes are about 1.7 billion years old. However, some genetic evidence suggests eukaryotes appeared as early as 3 billion years ago. While Earth is the only place in the universe where life is known to exist, some have suggested that there
8760-525: The formation, description (morphology), and classification of soils in their natural environment. In engineering terms, soil is included in the broader concept of regolith , which also includes other loose material that lies above the bedrock, as can be found on the Moon and other celestial objects . Soil is a major component of the Earth 's ecosystem . The world's ecosystems are impacted in far-reaching ways by
8880-909: The four basic shapes of bacteria are: The archaeon Haloquadratum has flat square-shaped cells. Bacteria and archaea reproduce through asexual reproduction, usually by binary fission . Genetic exchange and recombination still occur, but this is a form of horizontal gene transfer and is not a replicative process, simply involving the transference of DNA between two cells, as in bacterial conjugation . DNA transfer between prokaryotic cells occurs in bacteria and archaea, although it has been mainly studied in bacteria. In bacteria, gene transfer occurs by three processes. These are (1) bacterial virus ( bacteriophage )-mediated transduction , (2) plasmid -mediated conjugation , and (3) natural transformation . Transduction of bacterial genes by bacteriophage appears to reflect an occasional error during intracellular assembly of virus particles, rather than an adaptation of
9000-705: The gaps between larger particles). The graphic illustrates how some smaller grains can effectively fill the pores (where all water flow takes place), drastically reducing porosity and hydraulic conductivity, while only being a small fraction of the total volume of the material. For tables of common porosity values for earth materials , see the "further reading" section in the Hydrogeology article. Consolidated rocks (e.g., sandstone , shale , granite or limestone ) potentially have more complex "dual" porosities, as compared with alluvial sediment . This can be split into connected and unconnected porosity. Connected porosity
9120-413: The highest AEC, followed by the iron oxides. Levels of AEC are much lower than for CEC, because of the generally higher rate of positively (versus negatively) charged surfaces on soil colloids, to the exception of variable-charge soils. Phosphates tend to be held at anion exchange sites. Iron and aluminum hydroxide clays are able to exchange their hydroxide anions (OH) for other anions. The order reflecting
9240-432: The host bacteria. The transfer of bacterial DNA is under the control of the bacteriophage's genes rather than bacterial genes. Conjugation in the well-studied E. coli system is controlled by plasmid genes, and is an adaptation for distributing copies of a plasmid from one bacterial host to another. Infrequently during this process, a plasmid may integrate into the host bacterial chromosome, and subsequently transfer part of
9360-537: The host bacterial DNA to another bacterium. Plasmid mediated transfer of host bacterial DNA (conjugation) also appears to be an accidental process rather than a bacterial adaptation. Natural bacterial transformation involves the transfer of DNA from one bacterium to another through the intervening medium. Unlike transduction and conjugation, transformation is clearly a bacterial adaptation for DNA transfer, because it depends on numerous bacterial gene products that specifically interact to perform this complex process. For
9480-426: The idea that oligopeptides may have been built together with primordial nucleic acids at the same time, which also supports the concept of a ribocyte as LUCA. The feature of DNA as the material base of the genome might have then been adopted separately in bacteria and in archaea (and later eukaryote nuclei), presumably by help of some viruses (possibly retroviruses as they could reverse transcribe RNA to DNA). As
9600-629: The infiltration and movement of air and water, both of which are critical for life existing in soil. Compaction , a common problem with soils, reduces this space, preventing air and water from reaching plant roots and soil organisms. Given sufficient time, an undifferentiated soil will evolve a soil profile that consists of two or more layers, referred to as soil horizons. These differ in one or more properties such as in their texture , structure , density , porosity, consistency, temperature, color, and reactivity . The horizons differ greatly in thickness and generally lack sharp boundaries; their development
9720-424: The major differences in the structure and genetics between the two groups of organisms. Archaea were originally thought to be extremophiles, living only in inhospitable conditions such as extremes of temperature , pH , and radiation but have since been found in all types of habitats . The resulting arrangement of Eukaryota (also called "Eucarya"), Bacteria, and Archaea is called the three-domain system , replacing
9840-406: The medium (e.g., water) may flow easily. The microcolonies may join together above the substratum to form a continuous layer, closing the network of channels separating microcolonies. This structural complexity—combined with observations that oxygen limitation (a ubiquitous challenge for anything growing in size beyond the scale of diffusion) is at least partially eased by movement of medium throughout
9960-597: The method of grain packing. Rocks normally decrease in porosity with age and depth of burial. Tertiary age Gulf Coast sandstones are in general more porous than Cambrian age sandstones. There are exceptions to this rule, usually because of the depth of burial and thermal history. Porosity of surface soil typically decreases as particle size increases. This is due to soil aggregate formation in finer textured surface soils when subject to soil biological processes. Aggregation involves particulate adhesion and higher resistance to compaction. Typical bulk density of sandy soil
10080-571: The mitochondria and chloroplasts. The genome in a prokaryote is held within a DNA/protein complex in the cytosol called the nucleoid , which lacks a nuclear envelope . The complex contains a single, cyclic, double-stranded molecule of stable chromosomal DNA, in contrast to the multiple linear, compact, highly organized chromosomes found in eukaryotic cells. In addition, many important genes of prokaryotes are stored in separate circular DNA structures called plasmids . Like eukaryotes, prokaryotes may partially duplicate genetic material, and can have
10200-545: The nature of the connate fluids , the nature of overlying sediments (which may impede fluid expulsion). One commonly used relationship between porosity and depth is the decreasing exponential function given by the Athy (1930) equation: where, ϕ ( z ) {\displaystyle \phi (z)} is the porosity of the sediment at a given depth ( z {\displaystyle z} ) (m), ϕ 0 {\displaystyle \phi _{0}}
10320-427: The negatively charged colloids resist being washed downward by water and are out of reach of plant roots, thereby preserving the soil fertility in areas of moderate rainfall and low temperatures. There is a hierarchy in the process of cation exchange on colloids, as cations differ in the strength of adsorption by the colloid and hence their ability to replace one another ( ion exchange ). If present in equal amounts in
10440-412: The negatively-charged soil colloid exchange sites (CEC) that are occupied by base-forming cations is called base saturation . If a soil has a CEC of 20 meq and 5 meq are aluminium and hydronium cations (acid-forming), the remainder of positions on the colloids ( 20 − 5 = 15 meq ) are assumed occupied by base-forming cations, so that the base saturation is 15 ÷ 20 × 100% = 75% (the compliment 25%
10560-417: The next larger scale, soil structures called peds or more commonly soil aggregates are created from the soil separates when iron oxides , carbonates , clay, silica and humus , coat particles and cause them to adhere into larger, relatively stable secondary structures. Soil bulk density , when determined at standardized moisture conditions, is an estimate of soil compaction . Soil porosity consists of
10680-403: The nucleus, that eukaryotes arose without endosymbiosis, and that eukaryotes arose through a symbiotic event entailing a simultaneous endosymbiotic origin of the flagellum and the nucleus, in addition to many other models, which have been reviewed and summarized elsewhere. The oldest known fossilized prokaryotes were laid down approximately 3.5 billion years ago, only about 1 billion years after
10800-469: The ocean has no more than 10 prokaryotic organisms per milliliter (gram) of seawater. Organic carbon held in soil is eventually returned to the atmosphere through the process of respiration carried out by heterotrophic organisms, but a substantial part is retained in the soil in the form of soil organic matter; tillage usually increases the rate of soil respiration , leading to the depletion of soil organic matter. Since plant roots need oxygen, aeration
10920-408: The origin and position of eukaryotes span a broad spectrum including the views that eukaryotes arose first in evolution and that prokaryotes descend from them, that eukaryotes arose contemporaneously with eubacteria and archaebacteria and hence represent a primary line of descent of equal age and rank as the prokaryotes, that eukaryotes arose through a symbiotic event entailing an endosymbiotic origin of
11040-633: The other cations more weakly bound to colloids are pushed into solution as hydrogen ions occupy exchange sites ( protonation ). A low pH may cause the hydrogen of hydroxyl groups to be pulled into solution, leaving charged sites on the colloid available to be occupied by other cations. This ionisation of hydroxy groups on the surface of soil colloids creates what is described as pH-dependent surface charges. Unlike permanent charges developed by isomorphous substitution , pH-dependent charges are variable and increase with increasing pH. Freed cations can be made available to plants but are also prone to be leached from
11160-426: The painting process, leaching of plating acids and tool chatter in machining pressed metal components. Several methods can be employed to measure porosity: where Prokaryote A prokaryote ( / p r oʊ ˈ k ær i oʊ t , - ə t / ; less commonly spelled procaryote ) is a single-cell organism whose cell lacks a nucleus and other membrane -bound organelles . The word prokaryote comes from
11280-490: The plant roots release hydrogen ions to the solution. CEC is the amount of exchangeable hydrogen cation (H) that will combine with 100 grams dry weight of soil and whose measure is one milliequivalents per 100 grams of soil (1 meq/100 g). Hydrogen ions have a single charge and one-thousandth of a gram of hydrogen ions per 100 grams dry soil gives a measure of one milliequivalent of hydrogen ion. Calcium, with an atomic weight 40 times that of hydrogen and with
11400-540: The porosity of a porous medium (such as rock or sediment ) describes the fraction of void space in the material, where the void may contain, for example, air or water. It is defined by the ratio : where V V is the volume of void-space (such as fluids) and V T is the total or bulk volume of material, including the solid and void components. Both the mathematical symbols ϕ {\displaystyle \phi } and n {\displaystyle n} are used to denote porosity. Porosity
11520-482: The porous lava, and by these means organic matter and a finer mineral soil accumulate with time. Such initial stages of soil development have been described on volcanoes, inselbergs, and glacial moraines. How soil formation proceeds is influenced by at least five classic factors that are intertwined in the evolution of a soil: parent material, climate, topography (relief), organisms, and time. When reordered to climate, relief, organisms, parent material, and time, they form
11640-411: The processes carried out in the soil, with effects ranging from ozone depletion and global warming to rainforest destruction and water pollution . With respect to Earth's carbon cycle , soil acts as an important carbon reservoir , and it is potentially one of the most reactive to human disturbance and climate change . As the planet warms, it has been predicted that soils will add carbon dioxide to
11760-677: The proportionality between pore throat radii and porosity begins to fail and therefore so does the proportionality between porosity and hydraulic conductivity. For example: clays typically have very low hydraulic conductivity (due to their small pore throat radii) but also have very high porosities (due to the structured nature of clay minerals ), which means clays can hold a large volume of water per volume of bulk material, but they do not release water rapidly and therefore have low hydraulic conductivity. Well sorted (grains of approximately all one size) materials have higher porosity than similarly sized poorly sorted materials (where smaller particles fill
11880-411: The rate of diffusion of gases into and out of soil. Platy soil structure and soil compaction (low porosity) impede gas flow, and a deficiency of oxygen may encourage anaerobic bacteria to reduce (strip oxygen) from nitrate NO 3 to the gases N 2 , N 2 O, and NO, which are then lost to the atmosphere, thereby depleting the soil of nitrogen, a detrimental process called denitrification . Aerated soil
12000-458: The relative force required to pull a tillage implement through the clayey soil at field moisture content as compared to sand. Porosity of subsurface soil is lower than in surface soil due to compaction by gravity. Porosity of 0.20 is considered normal for unsorted gravel size material at depths below the biomantle . Porosity in finer material below the aggregating influence of pedogenesis can be expected to approximate this value. Soil porosity
12120-438: The seat of interaction networks playing a decisive role in the stability, dynamics and evolution of soil ecosystems. Biogenic soil volatile organic compounds are exchanged with the aboveground atmosphere, in which they are just 1–2 orders of magnitude lower than those from aboveground vegetation. Humans can get some idea of the soil atmosphere through the well-known 'after-the-rain' scent, when infiltering rainwater flushes out
12240-427: The snow surface of Antarctica , studied in cryobiology , or as hot as undersea hydrothermal vents and land-based hot springs . Prokaryotes live in nearly all environments on Earth. Some archaea and bacteria are extremophiles , thriving in harsh conditions, such as high temperatures ( thermophiles ) or high salinity ( halophiles ). Many archaea grow as plankton in the oceans. Symbiotic prokaryotes live in or on
12360-440: The soil anion exchange capacity. The cation exchange, that takes place between colloids and soil water, buffers (moderates) soil pH, alters soil structure, and purifies percolating water by adsorbing cations of all types, both useful and harmful. The negative or positive charges on colloid particles make them able to hold cations or anions, respectively, to their surfaces. The charges result from four sources. Cations held to
12480-536: The soil by volatilisation (loss to the atmosphere as gases) or leaching. Soil is said to be formed when organic matter has accumulated and colloids are washed downward, leaving deposits of clay, humus , iron oxide , carbonate , and gypsum , producing a distinct layer called the B horizon. This is a somewhat arbitrary definition as mixtures of sand, silt, clay and humus will support biological and agricultural activity before that time. These constituents are moved from one level to another by water and animal activity. As
12600-419: The soil solution composition (attenuate changes in the soil solution) as soils wet up or dry out, as plants take up nutrients, as salts are leached, or as acids or alkalis are added. Plant nutrient availability is affected by soil pH , which is a measure of the hydrogen ion activity in the soil solution. Soil pH is a function of many soil forming factors, and is generally lower (more acidic) where weathering
12720-401: The soil solution. Both living soil organisms (microbes, animals and plant roots) and soil organic matter are of critical importance to this recycling, and thereby to soil formation and soil fertility . Microbial soil enzymes may release nutrients from minerals or organic matter for use by plants and other microorganisms, sequester (incorporate) them into living cells, or cause their loss from
12840-471: The soil voids are saturated with water vapour, at least until the point of maximal hygroscopicity , beyond which a vapour-pressure deficit occurs in the soil pore space. Adequate porosity is necessary, not just to allow the penetration of water, but also to allow gases to diffuse in and out. Movement of gases is by diffusion from high concentrations to lower, the diffusion coefficient decreasing with soil compaction . Oxygen from above atmosphere diffuses in
12960-429: The soil water solution will be insufficient to change the pH, as the acid forming cations stored on the soil colloids will tend to restore the original pH condition as they are pushed off those colloids by the calcium of the added lime. The resistance of soil to change in pH, as a result of the addition of acid or basic material, is a measure of the buffering capacity of a soil and (for a particular soil type) increases as
13080-424: The soil water solution: Al replaces H replaces Ca replaces Mg replaces K same as NH 4 replaces Na If one cation is added in large amounts, it may replace the others by the sheer force of its numbers. This is called law of mass action . This is largely what occurs with the addition of cationic fertilisers ( potash , lime ). As the soil solution becomes more acidic (low pH , meaning an abundance of H),
13200-461: The soil where it is consumed and levels of carbon dioxide in excess of above atmosphere diffuse out with other gases (including greenhouse gases ) as well as water. Soil texture and structure strongly affect soil porosity and gas diffusion. It is the total pore space ( porosity ) of soil, not the pore size, and the degree of pore interconnection (or conversely pore sealing), together with water content, air turbulence and temperature, that determine
13320-500: The soil, a complex feedback which is exemplified in the dynamics of banded vegetation patterns in semi-arid regions. Soils supply plants with nutrients , most of which are held in place by particles of clay and organic matter ( colloids ) The nutrients may be adsorbed on clay mineral surfaces, bound within clay minerals ( absorbed ), or bound within organic compounds as part of the living organisms or dead soil organic matter. These bound nutrients interact with soil water to buffer
13440-411: The soil, possibly making the soil less fertile. Plants are able to excrete H into the soil through the synthesis of organic acids and by that means, change the pH of the soil near the root and push cations off the colloids, thus making those available to the plant. Cation exchange capacity is the soil's ability to remove cations from the soil water solution and sequester those to be exchanged later as
13560-407: The strength of anion adhesion is as follows: The amount of exchangeable anions is of a magnitude of tenths to a few milliequivalents per 100 g dry soil. As pH rises, there are relatively more hydroxyls, which will displace anions from the colloids and force them into solution and out of storage; hence AEC decreases with increasing pH (alkalinity). Soil reactivity is expressed in terms of pH and
13680-426: The traditional two-empire system . According to the phylogenetic analysis of Hug (2016), the relationships could be the following: A widespread current model of the evolution of the first living organisms is that these were some form of prokaryotes, which may have evolved out of protocells , while the eukaryotes evolved later in the history of life. Some authors have questioned this conclusion, arguing that
13800-485: The two concentrations are equal, they are said to neutralise each other. A pH of 9.5 has 10 moles hydronium ions per litre of solution (and also 10 moles per litre OH). A pH of 3.5 has one million times more hydronium ions per litre than a solution with pH of 9.5 ( 9.5 − 3.5 = 6 or 10) and is more acidic. The effect of pH on a soil is to remove from the soil or to make available certain ions. Soils with high acidity tend to have toxic amounts of aluminium and manganese . As
13920-472: The void part of the soil volume and is occupied by gases or water. Soil consistency is the ability of soil materials to stick together. Soil temperature and colour are self-defining. Resistivity refers to the resistance to conduction of electric currents and affects the rate of corrosion of metal and concrete structures which are buried in soil. These properties vary through the depth of a soil profile, i.e. through soil horizons . Most of these properties determine
14040-552: The water content of the soil, as can be expressed in terms of volume or weight—can be based on in situ probes (e.g., capacitance probes , neutron probes ), or remote sensing methods. Soil moisture measurement is an important factor in determining changes in soil activity. The atmosphere of soil, or soil gas , is very different from the atmosphere above. The consumption of oxygen by microbes and plant roots, and their release of carbon dioxide, decreases oxygen and increases carbon dioxide concentration. Atmospheric CO 2 concentration
14160-461: The weathering of lava flow bedrock, which would produce the purely mineral-based parent material from which the soil texture forms. Soil development would proceed most rapidly from bare rock of recent flows in a warm climate, under heavy and frequent rainfall. Under such conditions, plants (in a first stage nitrogen-fixing lichens and cyanobacteria then epilithic higher plants ) become established very quickly on basaltic lava, even though there
14280-474: The whole soil atmosphere after a drought period, or when soil is excavated, a bulk property attributed in a reductionist manner to particular biochemical compounds such as petrichor or geosmin . Soil particles can be classified by their chemical composition ( mineralogy ) as well as their size. The particle size distribution of a soil, its texture, determines many of the properties of that soil, in particular hydraulic conductivity and water potential , but
14400-520: Was firmly established by the microbiologists Roger Stanier and C. B. van Niel in their 1962 paper The concept of a bacterium (though spelled procaryote and eucaryote there). That paper cites Édouard Chatton 's 1937 book Titres et Travaux Scientifiques for using those terms and recognizing the distinction. One reason for this classification was so that what was then often called blue-green algae (now called cyanobacteria ) would not be classified as plants but grouped with bacteria. Prokaryotes have
#681318