Ecosystem Ecology

Now that we have studied the interaction between different species, populations, and communities, it is important to look at the larger scale and understand the functioning of an ecosystem. An ecosystem consists of all biotic and abiotic elements existing within a defined boundary. 

In this unit we will

1.       Understand the flow of energy beginning at the primary producer level of any (terrestrial, marine or freshwater) food chain and how it goes up the trophic levels passing through different functional groups.  An overview to complement your understanding of food chains and food webs can also be found in Chapter 46 of Biology 2e here. 

2.       Understand about the conversion, transfer and cycling of nutrients amongst the various constituents of an ecosystem and the influence of biotic and abiotic components on their cycling. Supplemental reading can be found in Chapter 46 of Biology 2e.

Ecosystem can be defined as a collection of all living and nonliving parts in a defined area, which interact with one another. It is an open system which means that there are constant inputs (solar radiation, carbon and nitrogen from the atmosphere, etc.) and there are outputs (nutrients that are lost and do not return to the soil). It involves the flow of energy and nutrients between different functional groups of organisms (A functional group consists of all organisms that acquire their energy in a similar way such as autotrophs).  

This transfer of energy follows the laws of thermodynamics.

A quick review of the laws of thermodynamics:

The 1st law of thermodynamics states that energy can neither be created nor destroyed. It can only be converted from one form to another.

The 2nd law states that during any energy transformations, a part of it will be lost as heat energy. In energy transfers happening in the food chain – only 10% energy is transferred to the next trophic level. 90% is lost as heat at each level. 

The transfer of energy is also accompanied by nutrients being transferred from one trophic level to the next. 

All energy on Earth is derived directly or indirectly from solar energy. Autotrophs (green plants in terrestrial and plankton in aquatic ecosystems) use this solar energy to convert carbon from the atmosphere (inorganic form) into organic molecules (sugars) that can be used by other living organisms. This is called photosynthesis. Some archaic bacteria use the energy from oxidation of chemical compounds for the synthesis of carbon containing organic molecules. This process is called chemosynthesis. Ultimately, the rate of conversion of inorganic carbon from the atmosphere, to organic carbon is termed primary productivity. This primary production is the source of energy for all living organisms, ranging from bacteria to humans. 

GPP (Gross Primary Productivity) describes the total amount of carbon assimilated by the autotrophs in an ecosystem.

NPP (Net Primary productivity) describes the amount of biomass gained by the autotrophs after assimilation of carbon and energy. This represents the energy that can be transferred on to herbivores and other trophic levels of the food chain.

NPP = GPP – Loss of C and energy through respiration

 This gross and net productivity of an ecosystem is heavily influenced by abiotic factors such as the temperature, precipitation, soil moisture, humidity, amount of available sunlight, etc. For example, the amount of water available in soil, affects the opening and closing of stomata in plants.  If enough moisture is available to the plant via its roots, stomata remain open, which allows the plant to also exchange gases with the atmosphere and perform photosynthesis. However, if soil moisture is low, stomata close to prevent water loss from the plant, preventing the uptake of CO2, which inhibits photosynthesis. 

Very high amount of precipitation could also create anoxic conditions (lack of oxygen) in soil, inhibiting root growth and preventing growth and assimilation of energy in autotrophs. 

Research shows that higher air temperatures also promote a faster rate of photosynthesis in plants and tend to extend the growing season for greater gain in biomass. Cooler air does not support high NPP irrespective of the amount of soil moisture available for plants. 

 Various other soil properties can also significantly impact the rate of photosynthesis, such as

1.       Higher amount of organic matter in soil will promote nutrient absorption by the roots, thereby promoting gain in biomass.

2.       A silty or loamy soil texture allows for more plant growth, as opposed to sandy soil which will not hold any moisture, or very clayey soil which will not allow for air or plant root penetration

3.       Presence of a good microbial diversity (consisting of bacteria, fungus and protozoa) in soil promotes faster breakdown of detritus, returning important nutrients to the soil for faster plant growth.

Other factors like – plant tissue chemistry, presence of natural or anthropogenic disturbances in the environment, presence of pests and pathogens, irreplaceable loss of nutrients from the ecosystem; all have an impact on the NPP pf the ecosystem. 

 On land, areas with highest NPP are generally tropical rain forests, due to their high temperature, high moisture and greater number of daylight hours. Near the coast, greater NPP can be observed in swamps, marshes and wetlands. This is because water entering these areas brings a lot of silt and nutrients along with it which promote plant growth. A greater amount of rainfall and higher temperatures also promote greater primary productivity near the coastlines. 

Plankton are the autotrophs of the marine ecosystems. Condition promoting the growth of plankton – such as addition of nutrients like N and P, greater light penetration in shallower depths, also results in very high NPP closer to the coastline in estuaries and coral reefs. 

 NPP also shows seasonal variation since the amount of light and nutrient available also varies with the different seasons. During summers, light penetration in water could be the limiting condition; whereas, during Fall and Spring, the availability of nutrients could be a limiting factor in NPP.

 The width of a stream could determine if the addition of organic carbon in a stream is a result of Autochotonous or Allochotonous process. 

Autochonous represents production of organic carbon within the stream itself. This is a feature of wider rivers, which are not under tree canopy and receive enough sunlight to promote growth of plankton, algae and underwater weeds. The carbon and energy fixed through photosynthesis can be used for NPP and passed on in the food chain. 

 Allochotonous represents the addition of organic carbon to a stream from external sources instead of internal production. This is more characteristic of a narrower stream, which is mostly under shade from trees growing on the river bank. This prevents light penetration and growth of underwater autotrophs in the system. Addition of carbon in water comes from dead organic material and particulate matter such as silt and sediments brought into the water from the river banks. 

 NPP is also be impacted by the age of a community. Plant communities that are still early in succession consist primarily of short lived, smaller sized, plant species such as grasses, weeds and herbs. These do not increase their biomass and spend more resources and energy in reproduction, dispersal and colonization. Plant communities that arrive during mid succession such as woody trees have greater NPP and tend to accumulate a greater amount of biomass. This can be used for transfer of energy to other trophic levels. As succession proceeds, resources get depleted and soil nutrients may become the limiting factors for NPP in the later years. Trees in this stage of succession spend most of the resources and energy acquired on their maintenance and very little is used in growth. 

Secondary production is the use of organic material by herbivores and other consumers to increase their biomass. This may be greatly limited by the amount of energy available from the autotrophs – exerting a bottom up control on the ecosystem. The total energy consumed by a heterotroph may be used in one of the following ways: for maintenance and repair of the body, it may be lost as heat, lost with secretion of waste material or through respiration, or be used for growth and reproduction. 

Secondary production (including the population size and reproduction in heterotrophs) depends on primary production by the autotrophs in an ecosystem.

The efficiency of the conversion of energy in heterotrophs and its use for secondary production, is defined as the production efficiency of a heterotroph. It is represented as P/A or the ratio of production to assimilation. It is seen to vary with different species such as ectotherms and endotherms. 

Ectotherms are organisms that depend on solar heat and energy to maintain their body temperatures. They cannot generate any heat on their own and hence, are generally limited in their body size. Endotherms, on the other hand, can generate their own heat within the body through mechanisms like shivering and are able to achieve a larger body size. 

The assimilation efficiency (A/I) of an endotherm is greater than that of an ectotherm. This means that out of all the food ingested, endotherms are able to assimilate it or extract energy from the food with a greater efficiency than ectotherms. They are able to use this energy to maintain homeostasis with respect to temperature. Similarly carnivores assimilate energy with a greater efficiency than herbivores from their food.  However, using this assimilated energy for growth and production of offspring is much better in ectotherms than endotherms; since they are not wasting a part of this energy to generate heat and maintain body temperature. 

Therefore, although assimilation efficiency of endotherms is greater than that of ectotherms, the production efficiency of ectotherms is much higher than that of endotherms.

 Apart from the NPP, other factors could also affect secondary production, such as: amount of water, availability of appropriate habitat, intraspecific and interspecific competition for resources, predation and the loss of energy as it passes from one trophic level to the next. 

According to the second law of thermodynamics only 10% of energy from the previous level ends up being passed to the next trophic level and hence the secondary production in higher trophic levels is always less than the previous one. If one was to observe the biomass production in every level of a food chain, it would look like a pyramid with the top predator levels gaining the minimum amount of biomass. 

 A food chain represents the direction of flow of energy in an ecosystem. It represents the prey and predator relationship. It generally begins with the autotrophs (green plants and plankton) which are eaten by herbivores (the primary consumers), which are eaten by carnivores (the secondary consumers) which are then consumed by the top predators (the top level of the food chain). Any terrestrial or aquatic ecosystem generally has two major kinds of food chains. 

The first kind is the grazing food chain, where the first consumer or herbivores obtain their energy from living green plants or plankton. 

A second kind of food chain called the detrital food chain is one where the first consumer level obtain their energy from the dead decaying organic material. This food chain is made up of the decomposers and saprophytic organisms found at different trophic levels. The primary consumer level may consist of microscopic organisms like bacteria and fungus or soil dwelling macroscopic snail and millipedes. These may be eaten by soil dwelling decomposers at the secondary consumer level such as worms and nematodes. 

Decomposition is an important process at every level of the food chain, to break down the dead organic material and release those nutrients back into the soil or atmosphere. Decomposition breaks down the chemical bonds made through photosynthesis and converts organic material back to inorganic minerals and nutrients along with the release of energy. This recycling of nutrients plays a very important role in NPP and can sometimes also be the limiting factor in NPP especially in aquatic ecosystems where nutrient input from external sources may be low. 

A variety of decomposers from microscopic bacteria, fungus, nematodes and protists to macroscopic worms, millipedes, snails are important in the process. 

Decomposition is a complex process which involves 2 major steps – mineralization and immobilization.

Mineralization refers to the conversion of the organic form of nutrients back to their inorganic form and releasing them into the soil. 

Immobilization is the uptake of these released minerals by the decomposer and other autotrophs for their growth and reproduction. 

Decomposition can be studied with the help of fine mesh litter bags. A weighed amount of plant litter (dead leaves) is placed in a mesh bag, with holes big enough to allow small invertebrate decomposers to enter the bag. These bags may be buried in soil or placed on the surface and monitored periodically. A decrease in their weight over time indicates the degradation of organic matter and loss of C to the atmosphere. Nutrients from the organic matter undergo mineralization in to the soil and immobilization in the decomposers. This also results in the increase in biomass of decomposers like bacteria, fungus and worms. This is referred to as secondary biomass. This study can be performed in a variety of ecosystems.

Different types of plant materials decompose at different rates based on their carbon quality. Plant material with a higher content of simple sugars like glucose, undergo rapid decomposition since these molecules are easily broken down. They are the first molecules to be used in the assimilation process by decomposers. Complex sugars like chitin and lignin (long polysaccharide chains) are difficult to break down and tend to remain trapped in the plant material for a longer time. 

The physical environment also has a significant impact on the rate of decomposition. Warmer temperatures and higher moisture content in soil favor the growth of bacteria, fungus and smaller invertebrates, thereby, increasing the rate of decomposition. Cooler temperatures and dry condition do not promote decomposition. Microbial growth may also be inhibited in highly acidic soil, or in soil with high sand or clay content. Very sandy soils do not hold moisture and clayey soil do not have pore spaces to promote any invertebrate growth in it. 

 The C:N ratio of plant material and decomposers also vary. Plants contain a greater amount of carbon as compared to decomposers. During the process of breakdown, decomposers assimilate their required carbon from the litter and mineralize the remaining nutrients into the soil. As decomposition continues, carbon is either lost to the atmosphere as CO2 by microbial respiration or assimilated as biomass by the decomposers, and the nitrogen content of the remaining litter goes on increasing. The material left behind is darker in color, and primarily composed of chitin and lignin which are more difficult to break down. This is called humus. 

 Decomposition involves the interaction of several different species and hence results in the formation of the soil microbial loop. 

The soil present around the roots of a plant is called the rhizosphere. It is a zone of high biological activity with a lot of bacterial, fungal and protozoan growth. Some plants secrete carbohydrate rich exudates from their roots to attract more fungus and bacteria. These bacteria carry out decomposition of organic matter in the rhizosphere, releasing nutrients in the soil, which the plant can absorb. They also assimilate carbon and nitrogen for their growth and reproduction. 

Attracted by the rich diversity of bacteria and fungus, their predators like nematodes and protozoans also aggregate in the rhizosphere.  Their presence is important to re-mobilize the nutrients assimilated by the decomposers. Due to a lower assimilation rate by the predators, they end up releasing the excess nitrogen back into the soil, in a more plant usable form like ammonia or nitrates and nitrites. This benefits the plants allowing them to grow with an increased supply of nutrients in the rhizosphere.

 Decomposition also takes place in the aquatic ecosystems, however the two processes of production and decomposition are vertically stratified. Production is limited to the top layers of a water body where light can penetrate and support photosynthesis – photic zone. When organic material dies, it settles down to the bottom of the water body – the aphotic zone, where decomposition proceeds. The nutrients released during decomposition can be brought up to the surface waters through tides, currents or other forms of water turbulence. 

Changes in seasons also causes upwelling of water, especially during the fall (called Fall turnover) when surface water starts to cool down and sink, displacing the lower nutrient rich water and pushing it to the surface. 

Decomposers present in a water body include microbial species such as bacteria and fungus, along with aquatic arthropods that perform a variety of functions such as shredding up the organic matter along with filtering, gathering, grazing and scrapping. All these breakdown the organic matter into finer dissolved and particulate organic matter which can undergo mineralization and immobilization.

 Now that we understand what decomposition is; and the fact that nutrients cycle between living organisms and the soil, let us look at the larger scale, which includes multiple ecosystems with all their biotic and abiotic components. This includes different nutrient reservoirs such as soil and rocks as well as the atmosphere. The cycling of nutrients through the terrestrial, aquatic and atmospheric components of various ecosystems is called biogeochemical cycles. 

Biogeochemical cycles may be gaseous or sedimentary. A gaseous biogeochemical has its primary nutrient source in the atmosphere. These includes cycling of nutrients such as nitrogen, oxygen and carbon. 

The main nutrient source for a sedimentary biogeochemical cycle would be soil, rocks and minerals. 

Nutrient deposition into these cycles can happen as wet fall or dry fall. 

Wet fall includes addition of nutrients into the soil along with any form of precipitation – rain or snow; whereas dry fall includes nutrient addition into the soil in the form of particulates from the oceans or as aerosols. 

Nutrient outputs describes the complete loss of nutrients from the cycle. For example, when harvesting a standing crop in agriculture, prevents the return of those nutrients assimilated by the crop, back to the soil upon decomposition. Due to this, farmers have to supplementing the soil with additional fertilizers to replenish its nutrient levels. 

 Let us begin with the Carbon cycle

The carbon cycle includes major steps such as photosynthesis, respiration, combustion and decomposition

The major pools of C include the 

1.       Atmosphere – almost 0.04% of air is made up of CO2

2.       Oceans

3.       Land surface - decomposition in soil and respiration from all animals releases CO2

4.       Sediments and rock – release C via weathering

99% of global C is trapped in sediments and rock; the most stable pool. It takes up and releases C on geological time scales. Soils contain twice as much C as plants.

Ocean surface water takes up CO2 from the atmosphere by diffusion.

C is transferred to deeper water mostly as organic detritus (dead material) and carbonate shells.

Upwelling of water brings C-rich water to the surface, allowing it to be used by aquatic autotrophs and releasing CO2 to the atmosphere via diffusion and respiration. 

CO2 is exchanged with the atmosphere mostly by photosynthesis and respiration. Prior to the Industrial Revolution, these two fluxes were roughly equal, with no net change in atmospheric CO2.

The amount of C in the atmosphere varies daily and seasonally. Photosynthesis happing during the daytime can reduce C in air, while at night, lack of uptake of C by the plants increases its concentration in the air. Similarly, Spring and Summers see a much lower C concentration in air due to uptake by growing plants, whereas, fall and winter see a rise of C concentration in air due to lack of photosynthesis and higher amounts of decomposition.  

Green plants and oceans are the major sinks of C, absorbing large amounts from the atmosphere. Vegetation that was buried and converted to peat, coal, oil and gas was a big sink before industrial revolution, however, combustion of these fossil fuels is releasing large amounts of C in air, steadily increasing its concentration. 

 Nitrogen cycle

Nitrogen is required by all living organisms to form their DNA and proteins. It is present in the molecular N2 form in the atmosphere which cannot be used by living organisms. It has to be converted into NH4 and nitrites and nitrates to be taken up by green plants. This process is called nitrogen fixation and requires a high amount of energy input. 

Small amount of nitrogen fixation is carried out in the atmosphere by lightning. A majority of nitrogen fixation is done by free living and symbiotic soil bacteria such as Rhizobium. 

 The nitrogen cycle can be divided into 5 steps:

1.       Nitrogen fixation – converting N2 to NH3 – carried out by Rhizobium, Clostridium, Nosto bacteria species etc 

2.       Ammonification – NH3 à NH4+

performed in slightly acidic soil

3.       Nitrification -      NH4+ to NO2- by Nitrosomonas and 

NO2- to NO3- by Nitrobacter

4.       Assimilation - Plants are able to absorb these forms of nitrogen and often compete with other soil bacteria. Nitrogen passes through both the grazing and detritus food chains in this way

5.       Denitrification - NO3- to N2O and N2 by Pseudomonas bacteria. This is released to the atmosphere in the gaseous form. 

For all steps - bacterial activity is affected by temperature, moisture, and soil pH.

 Human have heavily altered this cycle through agriculture. Continuous monocrop systems deplete the soil of N which become a limiting factor in plant growth. This requires additional N addition in the form of fertilizers. When fertilizers are not mixed in the soil properly or are over applied – they get washed out/leach out of the soil and contaminate rivers, finally reaching the ocean. Here, they result in eutrophication – algal blooms that deplete the water of all its nutrients and oxygen, creating a dead zone beneath the algal surface, where no other aquatic organism grows. 

 Phosphorus cycle

P is unique in the fact that it only has sedimentary and aquatic components in its cycling. It does not exist in the atmosphere. 

Main pool of P – soil rocks and minerals. It is released via the processes of weathering and erosion, and is taken up by plants. It passes through both the grazing and the detrital food chains to be released back into the soil. 

P is also mined out of rocks to create fertilizers to supplement the loss in agriculture. It ends up in waters bodies due to over fertilization or improper mixing in soil. Along with N in water it contributes to Eutrophication. 

Waste from the poultry industry is another major P polluter in water. 

 It is important to understand that all biogeochemical cycles are connected to one another, and they impact one another. For example the amount of nitrogen available in soil (determined by nitrogen fixation and ammonification) will have an impact on plant growth and utilization of C – and hence the C cycle. This will impact the amount of oxygen released by the growing plants and hence will also affect the Oxygen cycle.