Microbial food web

The microbial food web refers to the combined trophic interactions among microbes in aquatic environments. These microbes include viruses, bacteria, algae, heterotrophic protists (such as ciliates and flagellates).

In aquatic environments, microbes constitute the base of the food web. Single celled photosynthetic organisms such as diatoms and cyanobacteria are generally the most important primary producers in the open ocean. Many of these cells, especially cyanobacteria, are too small to be captured and consumed by small crustaceans and planktonic larvae. Instead, these cells are consumed by phagotrophic protists which are readily consumed by larger organisms. Viruses can infect and break open bacterial cells and (to a lesser extent), planktonic algae (a.k.a. phytoplankton). Therefore, viruses in the microbial food web act to reduce the population of bacteria and, by lysing bacterial cells, release particulate and dissolved organic carbon (DOC). DOC may also be released into the environment by algal cells. One of the reasons phytoplankton release DOC termed "unbalanced growth" is when essential nutrients (e.g. nitrogen and phosphorus) are limiting. Therefore, carbon produced during photosynthesis is not used for the synthesis of proteins (and subsequent cell growth), but is limited due of a lack of the nutrients necessary for macromolecules. Excess photosynthate, or DOC is then released, or exuded.

The microbial loop describes a pathway in the microbial food web where DOC is returned to higher trophic levels via the incorporation into bacterial biomass.

See also

Aquatic ecosystem

An aquatic ecosystem is an ecosystem in a body of water. Communities of organisms that are dependent on each other and on their environment live in aquatic ecosystems. The two main types of aquatic ecosystems are marine ecosystems and freshwater ecosystems.


Benthos is the community of organisms that live on, in, or near the seabed, river, lake, or stream bottom, also known as the benthic zone. This community lives in or near marine or freshwater sedimentary environments, from tidal pools along the foreshore, out to the continental shelf, and then down to the abyssal depths.

Many organisms adapted to deep-water pressure cannot survive in the upperparts of the water column. The pressure difference can be very significant (approximately one atmosphere for each 10 metres of water depth).Because light is absorbed before it can reach deep ocean-water, the energy source for deep benthic ecosystems is often organic matter from higher up in the water column that drifts down to the depths. This dead and decaying matter sustains the benthic food chain; most organisms in the benthic zone are scavengers or detritivores.

The term benthos, coined by Haeckel in 1891, comes from the Greek noun βένθος "depth of the sea". Benthos is used in freshwater biology to refer to organisms at the bottom of freshwater bodies of water, such as lakes, rivers, and streams. There is also a redundant synonym, benthon.

Cascade effect (ecology)

An ecological cascade effect is a series of secondary extinctions that is triggered by the primary extinction of a key species in an ecosystem. Secondary extinctions are likely to occur when the threatened species are: dependent on a few specific food sources, mutualistic (dependent on the key species in some way), or forced to coexist with an invasive species that is introduced to the ecosystem. Species introductions to a foreign ecosystem can often devastate entire communities, and even entire ecosystems. These exotic species monopolize the ecosystem's resources, and since they have no natural predators to decrease their growth, they are able to increase indefinitely. Olsen et al. showed that exotic species have caused lake and estuary ecosystems to go through cascade effects due to loss of algae, crayfish, mollusks, fish, amphibians, and birds. However, the principal cause of cascade effects is the loss of top predators as the key species. As a result of this loss, a dramatic increase (ecological release) of prey species occurs. The prey is then able to overexploit its own food resources, until the population numbers decrease in abundance, which can lead to extinction. When the prey's food resources disappear, they starve and may go extinct as well. If the prey species is herbivorous, then their initial release and exploitation of the plants may result in a loss of plant biodiversity in the area. If other organisms in the ecosystem also depend upon these plants as food resources, then these species may go extinct as well. An example of the cascade effect caused by the loss of a top predator is apparent in tropical forests. When hunters cause local extinctions of top predators, the predators' prey's population numbers increase, causing an overexploitation of a food resource and a cascade effect of species loss. Recent studies have been performed on approaches to mitigate extinction cascades in food-web networks.

Effects of global warming on marine mammals

The effect of global warming on marine mammals is a growing concern. Many of the effects of global warming are currently unknown due to unpredictability, but many are becoming increasingly evident today. Some effects are very direct such as loss of habitat, temperature stress, and exposure to severe weather. Other effects are more indirect, such as changes in host pathogen associations, changes in body condition because of predator–prey interaction, changed in exposure to toxins, and increased human interactions. Marine mammals that have been affected by climate change include walruses, seals, and polar bears.

Floodplain restoration

Floodplain restoration is the process of fully or partially restoring a river's floodplain to its original conditions before having been affected by the construction of levees (dikes) and the draining of wetlands and marshes.

The objectives of restoring floodplains include the reduction of the incidence of floods, the provision of habitats for aquatic species, the improvement of water quality and the increased recharge of groundwater.


Limnology ( lim-NOL-ə-jee; from Greek λίμνη, limne, "lake" and λόγος, logos, "knowledge"), is the study of inland aquatic ecosystems.

The study of limnology includes aspects of the biological, chemical, physical, and geological characteristics and functions of inland waters (running and standing waters, fresh and saline, natural or man-made). This includes the study of lakes, reservoirs, ponds, rivers, springs, streams, wetlands, and groundwater. A more recent sub-discipline of limnology, termed landscape limnology, studies, manages, and seeks to conserve these ecosystems using a landscape perspective, by explicitly examining connections between an aquatic ecosystem and its watershed. Recently, the need to understand global inland waters as part of the Earth System created a sub-discipline called global limnology. This approach considers processes in inland waters on a global scale, like the role of inland aquatic ecosystems in global biogeochemical cycles.Limnology is closely related to aquatic ecology and hydrobiology, which study aquatic organisms and their interactions with the abiotic (non-living) environment. While limnology has substantial overlap with freshwater-focused disciplines (e.g., freshwater biology), it also includes the study of inland salt lakes.

List of watershed topics

This list embraces topographical watersheds and drainage basins and other topics focused on them.

Mary Ann Moran

Mary Ann Moran is a distinguished research professor of marine sciences at the University of Georgia in Athens. She studies the role of bacteria in Earth's marine nutrient cycles, and is a leader in the fields of marine sciences and biogeochemistry. Her work is focused on how microbes interact with dissolved organic matter and the impact of microbial diversity on the global carbon and sulfur cycles. By defining the roles of diverse bacteria in the carbon and sulfur cycles, she connects the biogeochemical and organismal approaches in marine science.For her leadership and contributions to science, Moran is a recipient of many awards and honors including a Creative Research Medal from the University of Georgia and the White Research and Mentoring Award from the American Society for Microbiology. She is also a Fellow of the American Academy of Microbiology and the American Association for the Advancement of Science.

Mesopredator release hypothesis

The mesopredator release hypothesis is an ecological theory used to describe the interrelated population dynamics between apex predators and mesopredators within an ecosystem, such that a collapsing population of the former results in dramatically-increased populations of the latter. This hypothesis describes the phenomenon of trophic cascade in specific terrestrial communities.

A mesopredator is a medium-sized, middle trophic level predator, which both preys and is preyed upon. Examples are raccoons, skunks, snakes, cownose rays, and small sharks.


Microalgae or microphytes are microscopic algae, typically found in freshwater and marine systems, living in both the water column and sediment. They are unicellular species which exist individually, or in chains or groups. Depending on the species, their sizes can range from a few micrometers (µm) to a few hundred micrometers. Unlike higher plants, microalgae do not have roots, stems, or leaves. They are specially adapted to an environment dominated by viscous forces. Microalgae, capable of performing photosynthesis, are important for life on earth; they produce approximately half of the atmospheric oxygen and use simultaneously the greenhouse gas carbon dioxide to grow photoautotrophically. Microalgae, together with bacteria, form the base of the food web and provide energy for all the trophic levels above them. Microalgae biomass is often measured with chlorophyll a concentrations and can provide a useful index of potential production. The standing stock of microphytes is closely related to that of its predators. Without grazing pressures the standing stock of microphytes dramatically decreases.The biodiversity of microalgae is enormous and they represent an almost untapped resource. It has been estimated that about 200,000-800,000 species in many different genera exist of which about 50,000 species are described. Over 15,000 novel compounds originating from algal biomass have been chemically determined. Most of these microalgae species produce unique products like carotenoids, antioxidants, fatty acids, enzymes, polymers, peptides, toxins and sterols.

Microbial loop

The microbial loop describes a trophic pathway in the marine microbial food web where dissolved organic carbon (DOC) is returned to higher trophic levels via its incorporation into bacterial biomass, and then coupled with the classic food chain formed by phytoplankton-zooplankton-nekton. The term microbial loop was coined by Farooq Azam and Tom Fenchel et al. to include the role played by bacteria in the carbon and nutrient cycles of the marine environment.

In general, dissolved organic carbon (DOC) is introduced into the ocean environment from bacterial lysis, the leakage or exudation of fixed carbon from phytoplankton (e.g., mucilaginous exopolymer from diatoms), sudden cell senescence, sloppy feeding by zooplankton, the excretion of waste products by aquatic animals, or the breakdown or dissolution of organic particles from terrestrial plants and soils (Van den Meersche et al. 2004). Bacteria in the microbial loop decompose this particulate detritus to utilize this energy-rich matter for growth. Since more than 95% of organic matter in marine ecosystems consists of polymeric, high molecular weight (HMW) compounds (e.g., protein, polysaccharides, lipids), only a small portion of total dissolved organic matter (DOM) is readily utilizable to most marine organisms at higher trophic levels. This means that dissolved organic carbon is not available directly to most marine organisms; marine bacteria introduce this organic carbon into the food web, resulting in additional energy becoming available to higher trophic levels. Recently the term "microbial food web" has been substituted for the term "microbial loop".

Microbial population biology

Microbial population biology is the application of the principles of population biology to microorganisms.

Particle (ecology)

In marine and freshwater ecology, a particle is a small object. Particles can remain in suspension in the ocean or freshwater. However, they eventually settle (rate determined by Stokes' law) and accumulate as sediment. Some can enter the atmosphere through wave action where they can act as cloud condensation nuclei (CCN). Many organisms filter particles out of the water with unique filtration mechanisms (filter feeders). Particles are often associated with high loads of toxins which attach to the surface. As these toxins are passed up the food chain they accumulate in fatty tissue and become increasingly concentrated in predators (see bioaccumulation). Very little is known about the dynamics of particles, especially when they are re-suspended by dredging. They can remain floating in the water and drift over long distances. The decomposition of some particles by bacteria consumes a lot of oxygen and can cause the water to become hypoxic.

Photic zone

The photic zone, euphotic zone (Greek for "well lit": εὖ "well" + φῶς "light"), or sunlight (or sunlit) zone is the uppermost layer of water in a lake or ocean that is exposed to intense sunlight. It corresponds roughly to the layer above the compensation point, i.e. depth where the rate of carbon dioxide uptake, or equivalently, the rate of photosynthetic oxygen production, is equal to the rate of carbon dioxide production, equivalent to the rate of respiratory oxygen consumption, i.e. the depth where net carbon dioxide assimilation is zero.

It extends from the surface down to a depth where light intensity falls to one percent of that at the surface, called the euphotic depth. Accordingly, its thickness depends on the extent of light attenuation in the water column. Typical euphotic depths vary from only a few centimetres in highly turbid eutrophic lakes, to around 200 meters in the open ocean. It also varies with seasonal changes in turbidity.

Since the photic zone is where almost all of the photosynthesis occurs, the depth of the photic zone is generally proportional to the level of primary production that occurs in that area of the ocean. About 90% of all marine life lives in the photic zone. A small amount of primary production is generated deep in the abyssal zone around the hydrothermal vents which exist along some mid-oceanic ridges.

The zone which extends from the base of the euphotic zone to about 200 metres is sometimes called the disphotic zone. While there is some light, it is insufficient for photosynthesis, or at least insufficient for photosynthesis at a rate greater than respiration. The euphotic zone together with the disphotic zone coincides with the epipelagic zone. The bottommost zone, below the euphotic zone, is called the aphotic zone. Most deep ocean waters belong to this zone.

The transparency of the water, which determines the depth of the photic zone, is measured simply with a Secchi disk. It may also be measured with a photometer lowered into the water.


Plankton are the diverse collection of organisms that live in large bodies of water and are unable to swim against a current. The individual organisms constituting plankton are called plankters. They provide a crucial source of food to many large aquatic organisms, such as fish and whales.

These organisms include bacteria, archaea, algae, protozoa and drifting or floating animals that inhabit—for example—the pelagic zone of oceans, seas, or bodies of fresh water. Essentially, plankton are defined by their ecological niche rather than any phylogenetic or taxonomic classification.

Though many planktonic species are microscopic in size, plankton includes organisms over a wide range of sizes, including large organisms such as jellyfish.

Technically the term does not include organisms on the surface of the water, which are called pleuston—or those that swim actively in the water, which are called nekton.

Productivity (ecology)

In ecology, productivity refers to the rate of generation of biomass in an ecosystem. It is usually expressed in units of mass per unit surface (or volume) per unit time, for instance grams per square metre per day (g m−2 d−1). The mass unit may relate to dry matter or to the mass of carbon generated. Productivity of autotrophs such as plants is called primary productivity, while that of heterotrophs such as animals is called secondary productivity.

Ramsar site

A Ramsar site is a wetland site designated to be of international importance under the Ramsar Convention.The Convention on Wetlands, known as the Ramsar Convention, is an intergovernmental environmental treaty established in 1971 by UNESCO, which came into force in 1975. It provides for national action and international cooperation regarding the conservation of wetlands, and wise sustainable use of their resources.Ramsar identifies wetlands of international importance, especially those providing waterfowl habitat.

As of 2016, there were 2,231 Ramsar sites, protecting 214,936,005 hectares (531,118,440 acres), and 169 national governments are currently participating.

Sustainable gardening

Sustainable gardening includes the more specific sustainable landscapes, sustainable landscape design, sustainable landscaping, sustainable landscape architecture, resulting in sustainable sites. It comprises a disparate group of horticultural interests that can share the aims and objectives associated with the international post-1980s sustainable development and sustainability programs developed to address the fact that humans are now using natural biophysical resources faster than they can be replenished by nature.Included within this compass are those home gardeners, and members of the landscape and nursery industries, and municipal authorities, that integrate environmental, social, and economic factors to create a more sustainable future.

Organic gardening and the use of native plants are integral to sustainable gardening.

Viral shunt

The viral shunt pathway is a mechanism that prevents (prokaryotic and eukaryotic) marine microbial particulate organic matter (POM) from migrating up trophic levels by recycling them into dissolved organic matter (DOM), which can be readily taken up by microorganisms. Viral shunting helps maintain diversity within the microbial ecosystem by preventing a single species of marine microbe from dominating the micro-environment. The DOM recycled by the viral shunt pathway is comparable to the amount generated by the other main sources of marine DOM.Viruses can easily infect microorganisms in the microbial loop due to their relative abundance compared to microbes. Prokaryotic and eukaryotic mortality contribute to carbon nutrient recycling through cell lysis. There is evidence as well of nitrogen (specifically ammonium) regeneration. This nutrient recycling helps stimulates microbial growth. As much as 25% of the primary production from phytoplankton in the global oceans may be recycled within the microbial loop through viral shunting.

Aquatic ecosystems
Food webs
Example webs
Ecology: Modelling ecosystems: Other components

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