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    Reserved for Pterophyta
    I'm in it for the tomatoes. I been growing tomatoes for a long long time. Sometimes I get to thinking I know everything about tomatoes.
    My tomatoes make me completely delusional.


      Also reserved for Pterophyta
      I'm in it for the tomatoes. I been growing tomatoes for a long long time. Sometimes I get to thinking I know everything about tomatoes.
      My tomatoes make me completely delusional.


        Reserved for Gymnosperms
        I'm in it for the tomatoes. I been growing tomatoes for a long long time. Sometimes I get to thinking I know everything about tomatoes.
        My tomatoes make me completely delusional.


          Also reserved for Gymnosperms
          I'm in it for the tomatoes. I been growing tomatoes for a long long time. Sometimes I get to thinking I know everything about tomatoes.
          My tomatoes make me completely delusional.


            Reserved for Angiosperms
            I'm in it for the tomatoes. I been growing tomatoes for a long long time. Sometimes I get to thinking I know everything about tomatoes.
            My tomatoes make me completely delusional.


              Also reserved for Angiosperms
              I'm in it for the tomatoes. I been growing tomatoes for a long long time. Sometimes I get to thinking I know everything about tomatoes.
              My tomatoes make me completely delusional.



                Thought I'd put some soil ecology in this thread for those who like a look at the bigger picture. Ecosystems can be very small, all ecosystems have inputs and outputs which we'll get into. A common misconception is that ecosystems are closed systems, not so.

                Great reading: Lavelle, Soil Ecology.

                Ecosystem Structure.

                An ecosystem is a bounded ecological system of all the organisms (biotic factors) in an area - and the physical environment (abiotic factors) with which they interact. Ecosystems can be defined over a large range of spatial scales from global to biomes to watersheds down to the biofilms on rocks. Also, a range of temporal scales exist e.g. instantaneous (light effects on photosynthesis), seasonal (production may exceed herbivory over season), plant succession, migration of species, and evolutionary and geologic history.

                The components of an ecosystem include: primary producers (plants); consumers (animals); decomposers (microbial species) and abiotic components water, atmosphere and soil minerals.

                The trophic structure of an ecosystems food web is characterized by trophic levels: from primary producers like plants to primary consumers (bugs) then secondary consumers (birds) and so on. A loss of energy occurs as it is passed through to the next trophic level leading to a point where no higher trophic level can be supported due to insufficient energy.

                The characteristics of an ecosystem include biomass – the mass of organisms per unit area (living things and dead bits stuck on them); dead organic matter; Gross primary productivity (total fixation of energy per unit area); Net primary productivity - the rate of production of new carbon based biomass available for consumers (live consumer system) and decomposers (bacteria and fungi).

                An ecosystem’s structure and function are determined by external and internal (interactive) factors. External factors are : time – disturbance regimes and plant succession; climate – important at large scales determining biomes; parent material – determining soil type and explaining much of regional variation; topography – influencing microclimate and local scale soil production; and potential biota – organisms in the region that could potentially occupy the site. Internal (interactive) factors are: Resource supply (consumables like light, water and nutrients); modulators (non consumables like temperature and pH); Disturbances (e.g tilling, fire, winds, flood); biotic community (e.g. special species present like the N fixer Myrica faya that invaded Hawaii) and human activities (having major impact on the structure and function of ecosystems).

                Ecosystems can be described as pools (quantities) and fluxes (flows). Ecosystem processes are the flow of energy and materials from one pool to the other.

                Natural ecosystems are complex networks of interacting feedbacks. Feedback regulates ecosystem dynamics. Negative feedback occurs when two components have the opposite effect on each other e.g. predator and prey. Positive feedback occurs when both organisms have a positive effect on each other eg mutualism or population growth. Negative feedbacks resist change in ecosystems and maintain them in the current state. Positive feedback includes low fertility soil producing slow growth producing plant defenses which makes for slow decomposition leading back to low soil fertility.

                Ecosystem goods and services encompass the idea that ecosystems provide goods and services to human populations. Alteration of an ecosystem changes provision of these goods and services. The valuation of ecosystem services can help decision making with economic and ecologic knowledge being integrated.

                Goods include: Food, construction materials, medicine, genetic pool, tourism and recreation. Ecosystem services include hydrological cycles, regulating climate, cleaning water and air, maintaining gaseous atmosphere, pollination, soil generation and maintenance, nutrient cycling and storage, detoxification of pollutants, and aesthetic beauty, inspiration and recreation. Water for New York from Catskills Mountains would cost $6 - $8 Billion to supply via a filtration plant with $300m annual operating costs. Restoration in Catskills cost $1B. They purchased critical lands in water catchment and subsidized improvements in sewage systems.
                I'm in it for the tomatoes. I been growing tomatoes for a long long time. Sometimes I get to thinking I know everything about tomatoes.
                My tomatoes make me completely delusional.


                  Primary Production and Energy Flow.

                  Light energy enters an ecosystem through solar radiation. Most of this is lost as heat, reflection or powering evapotranspiration. Plants absorb about 2.2% of the available light, and 1.2% is used in respiration. GPP (2.2%) – respiration (1.2%) = NPP (1%).

                  Gross Primary Production (GPP) is the sum of all leaves photosynthesis in an ecosystem. NPP = GPP – respiration. The amount of GPP is determined by photosynthetic rates of individual leaves, amount of leaf area, photosynthetic capacity, LAI (leaf area index) and the length of the growing season.

                  Net Primary Production (NPP) is the net carbon gain including new biomass (leaves stems roots and shoots), root exudations including mycorrhizal transfers, losses to herbivores mortality and fire, and volatile emissions.

                  Carbon and energy enter an ecosystem via photosynthesis. At leaf scale photosynthesis is controlled by available light, water and CO2, the air temperature (warmer speeds reaction rates) and leaf nitrogen content (for enzymes e.g. Betula pendula 5x photosynthetic rate with N increase). At ecosystem scale photosynthesis is controlled by available leaf area (dependant on water and nutes) and length of growing season (active photosynthesis duration).

                  Plants lose water (which must be replaced by absorption) from leaves during uptake of CO2 (for photosynthesis) and so limited water will reduce photosynthetic capacity. Plants change the size of their stomata openings to regulate CO2 uptake (and H2O losses).

                  Gradients from low to high NPP and evapotranspiration below:

                  Desert -> Grassland -> Tundra -> Dune -> Subalpine forest -> Grass prairie -> Temperate -> Tropical.

                  This is the traditional view but see below for recent research suggesting temperate zones have higher NPP. This relates to decomposition rates being slower, and so recycling is slower, and so... soil is built.

                  As precipitation increases, NPP increases (to a point ~2m rain). NPP increases exponentially with temperature. High variance in NPP due to soil variation etc.

                  Leaf longevity (from low nute environs or plants that take up little) results in increased exposure to seasonal variation and herbivory. To counteract this plants with long lived leaves have other compounds to protect from herbivory and dessication within their leaves. This leaves less room for photosynthetic activity.

                  NPP was traditionally though to be the highest in the tropical rainforests. In marine ecosystems the opposite occurs with the highest productivity near the poles. Huston & Wolverton (2009) conclude ecologically relevant terrestrial productivity is highest between the latitudes of 30 – 50 degrees.
                  I'm in it for the tomatoes. I been growing tomatoes for a long long time. Sometimes I get to thinking I know everything about tomatoes.
                  My tomatoes make me completely delusional.


                    Nutrients in Ecosystems.

                    Nutrients flow through ecosystems with inputs and outputs.

                    The majorities of nutrients stay within an ecosystem and are recycled, or transferred between plants and soil. Internal cycling of nutrients includes switching of organic and inorganic forms, changes in ionic forms, biological uptake, and interactions with mineral surfaces.

                    Inputs come from weathering, deposition, biological fixation and fertilization.

                    Losses are incurred via leaching, trace gas emissions, wind and water erosion, fire and harvest.

                    Nutrient supply is a critical controller of net primary production in ecosystems.

                    The primary method of P entering ecosystems is through the chemical weathering of rocks (Apatite mineral and carbonic acid form mono hydrogen phosphate which is biologically available). Highest during early primary succession parent materials are exposed to water and acidity releasing elements in biologically available forms. Primary P from parent materials will over time be transformed into other forms - organic P, stable organic P, labile and occluded P. Some farmers practice putting rocks in their fields to increase fertility. Rock phosphate is a mined (and ground) substance used by many farmers. Phosphate availability is influenced by soil pH.

                    Some elements arrive in ecosystems through deposition in rain, dust and gases, and through lightning which forms nitrogenous species adding to N deposition. N deposition is small in unpolluted ecosystems but can be substantial in N hemisphere due to human activity. The ocean also contributes some N in “background” levels.

                    The biological fixation of atmospheric N2 to NH4+ is the main way by which N enters ecosystems. A process requiring abundant energy and P, N fixation is carried out by symbiotic bacteria in association with leguminous and other plant types, by heterotrophic N fixation in the rhizosphere and other carbon rich environments, and by phototrophic cyanobacteria (formerly bluegreen algae) either free living or associated with lichens, liverworts, mosses cycads and ferns. Nitrogen is the most abundant component of the atmosphere yet it is also the most frequent element to limit terrestrial NPP. N fixation is constrained by its high energy cost and so is restricted to high light environments. It can also be limited by other nutrients used in the process of fixation e.g. P, Mo, Fe, S. Grazing also slows N fixation as many N fixers are preferable foliage for animals. N limitation is maintained in many ecosystems due to these three factors (energy and nutrients required, and grazing).

                    Imported nutrients are only a small part of the total pool of nutrients in a terrestrial ecosystem. Nitrogen is 93% recycled, and only 7% deposited or fixed. P around 1% deposited or fixed, more than 10% input from weathering, and less than 90 percent recycled, etc. The mineral that is recycled the least is calcium’s 65%, with 31% from weathering and around 4% from deposition.

                    Nutrients get to roots via diffusion, mass flow, and root interception. Diffusion is the movement of ions along gradients of concentration. Diffusion is driven by nutrient uptake and mineralization. Mass flow can be important in some systems and is the movement of ions in flowing soil water. Root interception is as it suggests.

                    To increase nutrient uptake plants increase their root/shoot ratio by generating roots in the areas where it does the most good. Roots proliferate in nutrient hotspots. Longer root hairs result from reducing nitrate or phosphate.

                    Some plants can tap nutrients other plants can’t use e.g. high latitude plants absorb amino acids, prefer ammonium over nitrate but will take whatever they can get. Some plants access different pools of nutrients than others can: some roots can produce phosphatase enzymes and cleave P from stable organic matter. Others release siderophores (chelates) , and solubilize mineral P. The chelate-P complex diffuses to root.

                    The nutrient ratios vary little between plant species so the availability of growth limiting nutrients like N and P, or both, govern the uptake of all other nutrients. When nutrients are in short supply plants become more efficient in their use to produce biomass.

                    Mycorrhizae increase the soil volume used by plants. They trade carbs for nutrients and are most advantageous to plants for immobile nutrients like P. Ectomycorrhizae (e.g. Amanita muscaria) form sheaths around the root and are typically found on woody plant species like pines and oaks, endomycorrhizae (e.g. Glomus spp.) enter the root cells and form arbuscles, these are typically associated with grasses, herbs and trees. When looking for mycorrhizal infection on a plants root system look for swollen ‘Y’ tips on the roots and discoloration (compared to bare roots of same species) – e.g. y branching root tips, swollen more than normal, often bulbous ends to them with two tone colour scheme to root system (not just difference between new and old roots).

                    Plants lose nutrients via senescence and death, leaching of dissolved nutrients, consumption by herbivores, exudations into soils and disturbances.

                    Tissue senescence is the major means of nutrient loss from many plants.

                    All plant species, both evergreen and deciduous, lose similar amounts of their annual nutrients due to leaching. N and P around 15%, K around 60%, Ca and Mg around 30%.

                    Loss of nutrients from ecosystems involves microbial nitrification and denitrification, leaching, erosion, fire, harvest and animal movement.

                    Nitrification converts NH4+ to NO3- which is then taken up by plants. During the process NH3 NO and N2O are often lost. Denitrification involves converting nitrate to N2, with NO and N2O as side products in the process. The majority of N loss is N2. Dissolved Organic N is the dominant form of leaching loss in most undisturbed systems. NO3- is the major species lost in disturbed systems (e.g. tilled), in systems where N is in excess (over fertilization) and thawing permafrost.
                    I'm in it for the tomatoes. I been growing tomatoes for a long long time. Sometimes I get to thinking I know everything about tomatoes.
                    My tomatoes make me completely delusional.



                      Soils are the thin film over the Earth’s surfaces that intersect geological and biological processes. Soils are a multi-phasic system: consisting of solids (roughly 50%), liquids (15-35%) and gases (15-35%). Soil provides: water and nutrients for plants and microbes; anchorage and support for plants, and habitat for many animals and decomposer organisms. Soils influence all aspects of ecosystem functioning and their characteristics are influenced by the external (state) factors of the ecosystems they support: parent material; climate; topography, potential biota and time.

                      Parent materials (rocks) go through a cycle: the rock cycle. Weathering and erosion of landscapes take sediments to the oceans where burial and lithification (change from loose sediments to rock) produce sedimentary rocks e.g. greywacke. Sedimentary rocks under heat and pressure make metamorphic rocks e.g. schist. Melting of metamorphic rocks produces magma which cools making igneous rocks e.g. granite. Igneous rocks can become metamorphic rocks under pressure and heat. Sedimentary, metamorphic and igneous rocks may all be subject to uplift through volcanic or tectonic activity exposing them to weathering and erosion where the rock cycle begins again. Products of parent materials include P, layered silicate clay minerals and hydrated silicates of Al, Fe, and Mg in crystalline structure.

                      Climate factors like temperature and precipitation influence a soil’s weathering rates, decomposition and nutrient cycling rates, and loss rates.

                      Topography influences microclimate differences through the effects of aspect and slope position. Erosion is more likely on the convex upper bounds of slopes with deposition likely further down where the slope is shallower and/or concave. Organic carbon moves down the slope over time depositing into and creating many richer valley soils. Physics determine that steeper slopes are more prone to slippage due to downslope force while shallow slopes have friction to assist in preventing slippage.

                      Potential biota is dependent on organic matter quantity and quality, and the types of disturbance effects that take place in the system e.g. cyclones, fires, floods. The latitude will also greatly influence the potential biota e.g. evergreens typically present in temperate, but not semi arid regions which have succulents bromeliads and other species not typically in temperate zones.

                      Time interacts with parent materials, climate, topography and potential biota.

                      Soil development involves the additions of organic matter and precipitation (including ions and solid particles), dust, and deposition to the parent material. Transformations turn organic matter to humus and primary minerals into hydrous oxides, clays, ions and silicic acid. Over time losses of ions and silicic acids occur. Litterfall and root turnover input nutrients from within the ecosystem.

                      Fertile soils are often rich in humus. Humus is a complex mixture of organic chemical compounds with highly irregular structure containing abundant aromatic rings. It colours brown soil to black. Humus is slow to decompose, and is a long term reservoir of soil C and N.

                      Soil transfers generate distinctive soil profiles – they layer the soil. Vertically from top to bottom soils typically include several of the following horizons: O – organic; A – mineral mixed with humus, dark coloured; E – Horizon of maximum leaching of silicate clays, Fe, Al oxides etc; B – Zone of Fe and Al accumulation; C - Zone of least weathering and accumulation, contains unweathered parent material; R – Bedrock.

                      Soil losses include anions like Cl- and NO3- which are easily leached from soil as are cations Na+, K+, and NH4+. Gaseous losses of nitrogenous species and methane are also common.

                      Downward leaching via precipitation to a certain depth and upward capillary rise (salinization) plus soil mixing by animals all contribute to soil transfers. Materials in soils undergo changes in physical or chemical states through dissolving, dehydrating or chemical change e’g. migration to new chemical environment with different redox or pH.

                      Some soil types are: Aridisol (desert), Mollisol (Grassland and deciduous forest), Spodisol (Acidic Conifer forests), Oxisol (Tropical wet forest), Gelisol (Tundra, Bog).

                      Soil properties include texture, bulk density,water holding capacity and soil chemical properties.

                      The texture of soil is the relative proportions of sand silt and clay. Texture is important as sand silt and clay’s particle sizes have different surface areas per unit of volume. Clay < 0.002mm, Silt 0.002 – 0.05mm and Sand 0.05-2mm. Aggregates of soil particles create cracks and channels for infiltration by water roots and soil invertebrates and microbes.

                      Bulk density is the mass of dry soil per unit volume e.g. kg/L. Bulk density influences nutrient and water characteristics of a site. Denser (compacted) soils can impede root growth, soil animals and gas and liquid infiltration.

                      Water holding capacity refers mainly to plant available water. When water is high (but not flooded) it is at field capacity - the quantity of water obtained by saturated soil after gravitational drainage – at this point there is plenty of plant available water. Permanent wilting point is where the soil has only unavailable water left. Across a gradient from sand to sandy loam to loam to silt loam to clay loam to clay soils more water is held at field capacity but the permanent wilting point is also higher with more unavailable water present in the finer compositional soils.

                      The redox (electrical) potential, pH, cation exchange capacity and organic content all make up soils chemical properties. Stable organic matter is a critical component of soils affecting weathering rates and soil development, water holding capacity, soil structure and nutrient retention. CEC is the capacity of the soil to hold exchangeable cations on negatively charged sites on the surfaces of soil minerals and organic matter.

                      The engineers of soils include (from small to big): Bacteria, fungi, nematodes, protists, rotifers, acari, collembola, protura, diptura, symphyta, enchytraeidae, chelonethi, isoptera, opiliones, isopoda, amphipoda, chilopoda, diplopoda, megadrili, coleopteran, araneida, mollusca.
                      I'm in it for the tomatoes. I been growing tomatoes for a long long time. Sometimes I get to thinking I know everything about tomatoes.
                      My tomatoes make me completely delusional.



                        Decomposition is the physical and chemical breakdown of dead organic matter (DOM). It provides energy for microbial growth, releases nutrients for plant uptake and releases carbon to the atmosphere. The balance between net primary production and decomposition influences ecosystem carbon storage and carbon cycling and therefore climate.

                        Decomposition consists of three phases:

                        1. Leaching by water transfers soluble materials to the soil matrix; also moving soluble compounds away from decomposing material. Leaching begins while leaves are still on the plant, it is most important in early decomposition. Fresh litter can lose 5% of its mass in a day.

                        2. Fragmentation is mainly carried out by soil animals. Fresh litter is protected from microbial attack with plant cuticles, bark etc. Soil animals pierce these barriers which increases the surface area for microbial attack. Litter particles become small enough that soil invertebrates can ingest them where enzymes in their guts digest the microbe layer that coats the surface of the litter particles.

                        3. Chemical alteration breaks down organic matter to CO2 and nutrients, forms complex recalcitrant compounds, and is carried out mostly by fungi and bacteria.

                        Solubles will generally be broken down first followed by cellulose and hemicelluloses (sugars) then microbial products and finally lignin. Decomposition rate is temperature dependant. It takes 100 years in the arctic to break DOM down to roughly the same extent as it takes 3 years to do in the tropics.

                        Decomposition is merely the result of decomposer organisms feeding activities and population dynamics. Decomposers are not performing a community service, they don’t care about their activities promoting nutrient cycling and ecosystem productivity, they’re just feeding and breeding and as plants and weather cycles remove their ‘wastes’ they have survived, and if litter continues to fall, they’ll continue to survive. Decomposer organisms are many (see previous post for list of soil engineers).

                        Fungi account for the majority of decomposition in aerobic environments. Fungi are absent from anaerobic environments. Fungi can be 60 – 90% of the microbial mass in forests and about half the microbial mass in grasslands. Fungi have broad enzymatic capability and digest cellulose, hemicelluloses and lignin of cell walls and proteins sugars and lipids from cell interiors. Fungi’s hyphae can transport metabolites through them so they can travel through nutrient poor terrain in search of substrate by importing nutrients to the growing tips from elsewhere - unlike bacteria, that depend on substrates moving to them. Surface litter fungi import nitrogen and wood degraders do the same. Mycorrhizae take carbohydrates from plants in exchange for nutrients.

                        Bacteria grow rapidly some with doubling times below 20 minutes, they specialize on easy to decompose (labile) substrates producing exoenzymes (enzymes they exude) to initiate breakdown of litter. Bacteria are dependent on the substrates that diffuse to them (unlike fungi). Bacteria are the specialists of small spaces – the rhizosphere, macropores, interior of aggregates and other species and as biofilms on particle surfaces. Bacteria are chemistry savvy. Different bacteria produce different enzymes and as a collective (consortia) they break down DOM and create many useful metabolic products for themselves and other biota. Bacteria become inactive when a substrate is exhausted. It’s estimated 50 – 80% of soil bacteria are inactive being activated only by the presence of substrate e.g. root grows past.

                        Microfauna <2mm includes the aquatic protozoans ciliates and amoebae. These bacterial predators are rhizosphere specialists that engulf their prey whole via phagocytosis. Nematodes have many trophic roles and are extremely abundant often eating as much as aboveground grazers. Mites of various roles are also typically abundant.

                        Mesofauna >2mm have the greatest effect on decomposition by fragmenting litter and ingesting particles of litter. Collembola are important species amongst the mesofauna.

                        Macrofauna includes earthworms and termites. They fragment litter and ingest soil mixing it and carrying organic matter to depth, they reduce compaction and create channels for water and roots.
                        Litter mass declines almost exponentially with time. Temperature dependant for all substrate types, decomposition rates differs by litterfall type being faster for broadleaf then coniferous leaf litter then wood.

                        Decomposition is controlled by the physical environment: temperature – faster when hotter; moisture – bacteria function at lower water availability than plant roots and decomposition is sensitive to flooding SOM accumulates in waterlogged soils, leaching from higher precipitation will also speed up decomposition; pH – decomposition more rapid in neutral than acidic soils. Bacteria predominate at high pH, fungi at low pH; Soil texture – clays reduce SOM decomposition rate by protecting it and increase water holding capacity; soil disturbance – increases decomposition by promoting aeration and exposing new surfaces to microbial attack, reduces SOM protected by clays, breaks up soil aggregates.

                        The substrate quality is possibly the dominant control over decomposition. Substrate quality concerns the susceptibility to decomposition of carbon in a substrate. There is a 5-10 fold variation in decomposition rates of litter due to differences in substrate quality. Higher nitrogen containing leaves lose more mass quickly, higher lignin content mass is lost more slowly. N assists in the breaking down of carbon, and carbon assists in attracting N-fixing microbes.
                        I'm in it for the tomatoes. I been growing tomatoes for a long long time. Sometimes I get to thinking I know everything about tomatoes.
                        My tomatoes make me completely delusional.


                          Ecological Stability and Disturbance.

                          Ecological stability is the absence of change of an ecosystem in the face of a disturbance. Two types of stability occur: Resilience is the rate at which an ecosystem can return to its reference (original) state after a disturbance. Resistance is the tendency of an ecosystem to remain similar to its reference state when faced with disturbance. Resilience and resistance are measured in two ways: Response is the direction and magnitude of change after a disturbance. Recovery is the extent to which an ecosystem returns to its reference state.

                          Ecosystems experience many fluctuations. Daily changes in conditions; cyclic weather events e.g. el nino, glacial cycles; internal dynamics e.g. litterfall, seasonal plants; legacies are the persistent effects of past events e.g. stonewalls in regenerating farmland, and disturbance. Plants and their grazing animals also fluctuate in relative abundance to each other over time. More plants can support more grazers but then the plants decline,so the grazers decline, then the plants fare better, and repeat… The same thing may be applied to pathogens and hosts, pest insects and predators, etc.

                          Manmade disturbance to most ecosystems results from land use change e.g. clearing a wetland for farming or habitation, a forest for building etc. Land use changes favour generalist organisms, and lead to loss of diversity with many species adapted to an ecosystems reference state failing to survive. Many of our ecosystems types are depleted due to land use changes and the services the ecosystems provide are endangered. But change is not all bad for ecosystems; in fact, it is a part of life.

                          Ecosystems plant communities change over time. Specific species are adapted to primary succession (basically, no organic material available – rock - After a glacier, volcanic event, severe flood, or mining and war), to secondary succession (after an event removes initial vegetation e.g. flooding, fire, agricultural clearing) and to steady state (where relative stability is observed, herbivory/harvest may be occurring).

                          It was thought old ecosystems with established plant communities were in a state of equilibrium, with maximum number of species present due to long periods of undisturbed time to establish, but this is not the case. The current view is that ecosystems are always recovering from past changes, and are rarely if ever in equilibrium with the current environment. In fact, a decline in speciation can occur in ecosystems that undergo no disturbance events.

                          At a large scale a factor that keeps maximum species diversity in ecosystems is disturbance. No disturbance leads to a loss of diversity as the species best adapted to the conditions begin to dominate the landscape. Catastrophic events (high disturbance) may lead to a loss of diversity as much of life is simply wiped out, but small to medium amounts of disturbance (fire, wind, seasonal floods, senescence and windfalls etc) encourage maximum diversity.

                          Small disturbances have short periods of return to their original state (e.g. approx 200-250 yrs in temperate forests), large disturbances take longer. Tree fall creates microhabitats in the forest: mounds, pits and sites of varying levels of light exposure (and subsequent varying desiccation rates). Tree fall gaps can be from 10 – 1000m2. These gaps in old growth forest occur regularly and can be a significant portion of the forests total area e.g. 5 – 15% in temperate broadleaf-conifer forest. Recruitment of new plants (and possibly their microbial, insect and animal counterparts) is made possible in the gaps created by disturbances. Early succession plants arrive first, and then other plants shelter beneath the early plants, thus early, medium and late succession plants are all present in the wider ecosystem undergoing small disturbances.

                          Disturbance is a common and major cause of long term fluctuations in the structure and functioning of ecosystems. Disturbances can disrupt ecosystem processes, communities, resources, substrates and the physical environment. The displacement or removal of individuals directly or indirectly creates opportunity for new individuals to establish. Disturbances give rise to adaptations over evolutionary time as adaptations to disturbance aid survival e.g. seeds that germinate better in the presence of terpenoids from smoke, seeds that need freezing, or fire.

                          The severity, frequency, size, type and timing of all disturbances are described as an ecosystems disturbance regime. Severity measures the physical changes, intensity the energy released in an area over a given time. Ecosystems adapt to their disturbance regimes e.g. fire frequency is correlated to the rate at which an ecosystem can reestablish biomass. Ecosystems with frequent fires support fire adapted species that recover quickly.

                          Larger disturbance events occur frequently enough (1-5 centuries at my house) that it is likely most large trees will experience at least one significant disturbance (earthquake, fire, volcanic ash shower, etc) in their lives. In fact disturbance is so frequent it is a major selective force on the life histories of organisms and a major factor in landscape development.
                          I'm in it for the tomatoes. I been growing tomatoes for a long long time. Sometimes I get to thinking I know everything about tomatoes.
                          My tomatoes make me completely delusional.



                            Succession is the predictable and orderly change in the composition or structure of an ecological community over time after a disturbance. Succession can be primary (no soil) or secondary (soil present).

                            Classical theory (Clements 1916) is that initial colonists change site conditions for other species. Ecological stability was thought to have a stable end stage called the climax, shaped primarily by local climate. Now it is thought that succession is more probabilistic than this model suggests, and that disturbance is experienced too frequently for climax communities to be the norm.

                            Species replace each other through differential access to a new site (deep or shallow rooters, temporal niches etc), differential life history traits and species interactions, and modification of the site over time.

                            Life history attributes change through succession. Pioneer plants have small seeds that disperse over long distances. They have rapid growth rates, short lives, small stature and are tolerant of environmental extremes. Later successional plants have larger seeds, slower growth rates, longer lives larger stature and are intolerant of environmental extremes. Succession involves a change from a colonization governed community to one governed by competition for resources. One can almost predict the stage of succession a plant is involved in by its seed mass.

                            Photosynthetic rates also differ according to successional role of plants. Roughly, annuals and herbaceous perennials have higher photosynthetic rates than early succession trees followed by late succession trees. Some successions are driven by original floristic composition. Dependant on the seed pool, all trees colonize in early succession and changes are reflective of dominance of sizes and growth rates.

                            Herbivory may promote or retard succession depending on its impact on early vs late species (based on palatability). Herbivory may enhance dispersal of early successional species and this can in turn enhance succession in forests. Herbivores can retard succession in grasslands and savannahs ecosystems by grazing tree seedlings, or speed succession up by eating grass and reducing tree seedling competition.

                            Many early succession plants are nitrogen fixers. 75% of primary successions studied have a vascular N fixing plant. Generally promote the establishment and growth of later succession species. The environmental change though succession involves this accumulation of N, an increase in soil organic matter, moisture holding capacity and CEC in primary succession. Often accompanied by a decrease in P, bulk density and pH.

                            The types of plants that first establish set much of the scene for succession. Some e.g. pines make the environment less suitable for establishment by other species and the climax community persists as these species until disturbed. Some early plants facilitate environmental changes for other species to establish. These often die out as late successional species arrive. Late succession species are ones that do not change environment to suit other species. Some species change the environment so it is less suitable for early species but give no advantage to later species. Eventually plants are there than can tolerate early species environmental changes and others can’t grow in the conditions. Disturbance destroys all climax stages.

                            Bracken inhibits many species via a dense litter layer, allelopathic chemicals which make it inedible and hard to decay, and possibly prevent ingress of other species. Bracken has a large rhizome system and high productivity.

                            Gorse facilitates establishment for other plants via N fixation.

                            Both competitive inhibition and positive facilitation act together during succession and the balance of the two determine vegetations composition. (Chapin et al 1994) shows factors determining succession are the life history traits (dispersal, growth rate, life expectancy), facilitation (shade or shelter, nutrient provision), inhibition, selective herbivory and modification of the environment from internal activity.
                            I'm in it for the tomatoes. I been growing tomatoes for a long long time. Sometimes I get to thinking I know everything about tomatoes.
                            My tomatoes make me completely delusional.


                              sweet i love this, thanks a lot.


                                Forest Dynamics & Regeneration.

                                What determines the changes in composition and structure of forests over time?

                                Forest structure can be represented as a mosaic of patches each representing either patchiness in physical environment (mountain, plain, wetland) or vegetation recovery after disturbance. The scale of observation is important as a canopy may be changing within tree gaps but over the entire area relative species abundance is maintained.

                                The mosaic of patches can be categorized into 4 (Oliver 1981) basic stages of forest development: Stand initiation where open space is filled by plants via seed, sprouting or advance regeneration; Stem exclusion or thinning is where crown enclosure occurs and competition becomes intense, self thinning occurs, sparse on ground level; understory reinitiation, overstory becomes less dense allowing redevelopment underneath and new seedling cohorts (sometimes different species); and old growth where a mixed age mixed species forest has developed.

                                Plants regeneration strategies are partitioned somewhat with differences in shade tolerance, ability to exploit gaps, requirements for seedling establishment, and parts of the gap environment (aspect, slope etc).

                                Shade tolerance is a major factor in determining where and when different species will regenerate. Plants need special adaptations to tolerate full sun conditions. They have to conserve water and protect themselves from UV rays, the tradeoff is abundant energy to grow fast. In the shade the need for water conservation and UV protection is lessened.

                                The regeneration mode is a species regeneration behavior in relation to disturbance. Catastrophic mode – light tolerant seedling species that establish massively as even aged cohort. Don’t tend to generate under their own canopy. Gap-phase mode – intermediate shade tolerance, exposure intolerant seedlings that occupy single to several tree fall gaps with a few individuals. Continuous mode (rare) – shade tolerant seedlings that grow through to maturity in canopy, incl root epiphytes (plants that grow from a root system over the top of other plants).

                                Gap and gap phase: Around 5-10% of a forested area is in fallen tree gaps at any given time. There is a short period of time for new individuals to compete for canopy dominance. The palm Astrocaryum mexicanum forms a kink when knocked over by a tree and continues to grow. In a five hectare plot, 52% of the palms were bent.

                                Seeds are dispersed via wind water and fauna; and are in banks (built up in soil). Treefalls often trigger germination in response to higher soil temps and light levels and quality. Advance generation is species developing suppressed seedlings that hang on for decades waiting for a light gap. They get a head start in the gap if they get light. Resprouting can outcompete seedlings coming from existing trees on the edge of gaps. Generally angiosperms are better at this than conifers. Serotiny is the condition where seeds are maintained in cones or capsules and require high heat for release. Some species respond to smoke: an Australian woodland soil germinated 56 species in response to treatment with smoke and 33 species without.

                                Establishment of seedlings is determined largely by substrate. Some seedlings survive better on logs (nurse log syndrome). Logs occur in gaps and raise the seedlings above the understory and out of the litter. In the pacific northwest hemlock recruited 98% of juveniles on decaying douglas fir logs even though the fir logs only occupied 6% of the area. Tree ferns are a dominant site for regeneration of some trees. Griselina littoralis and weinmannia racemosa establish on both logs and tree ferns. Red beech survivorship on logs was 41% on logs compared to 14% in bare areas and 0% in fern.

                                Compositional equilibrium is where stands of species persist for a generation in relatively constant proportions. Species distribution on a map shows species positioned where they achieve maximum abundance then tapering away from this central region. Ranges in temperature, precipitation levels etc results in ranges of plants. The history of past disturbances reflect opportunities for regeneration or succession affecting age structure of species in forests.

                                Conifers live longer than angiosperms but grow slower. Slow growth is helpful in obtaining old age.

                                The mean canopy residence time (MCRT) refers to average age of a tree before it falls, in NZ it is 80 yrs. Some North American forests have MCRTs of 150-200 yrs. Climax forests mortality rates roughly equal their recruitment rates.
                                I'm in it for the tomatoes. I been growing tomatoes for a long long time. Sometimes I get to thinking I know everything about tomatoes.
                                My tomatoes make me completely delusional.