Microbial ecology
Encyclopedia
Microbial ecology is the ecology
of microorganism
s: their relationship with one another and with their environment. It concerns the three major domains
of life — Eukaryota
, Archaea
, and Bacteria
— as well as virus
es.
Microorganisms, by their omnipresence, impact the entire biosphere
. Microbial life plays a primary role in regulating biogeochemical
systems in virtually all of our planet's environments, including some of the most extreme, from frozen environments and acidic lakes, to hydrothermal vents at the bottom of deepest oceans, and some of the most familiar, such as the human small intestine
. As a consequence of the quantitative magnitude of microbial life (Whitman et al. (1998) calculated 5 × 10 30 cells, eight orders of magnitude greater than the number of stars in the observable universe
) microbes, by virtue of their biomass alone, constitute the single largest carbon sink. Aside from carbon fixation, microorganisms’ key collective metabolic processes (including nitrogen fixation
, methane metabolism
, and sulfur metabolism
) control global biogeochemical cycling. The immensity of microorganisms’ production is such that, even in the total absence of eukaryotic life these processes would likely continue unchanged.
relationships (either positive
or negative
) with other organisms, and these relationships affect the ecosystem. One example of these fundamental symbioses are chloroplasts, which allow eukaryotes to conduct photosynthesis
. Chloroplasts are considered to be endosymbiotic cyanobacteria, a group of bacteria
that are thought to be the origins of aerobic photosynthesis. Some theories state that this invention coincides with a major shift in the early earth's atmosphere, from a reducing atmosphere to an oxygen-rich atmosphere. Some theories go as far as saying that this shift in the balance of gasses might have triggered a global ice-age known as the Snowball Earth
.
s, but even more so in the zones where light cannot approach and thus photosynthesis cannot be the basic means to collect energy. In such zones, chemosynthetic microbes provide energy and carbon
to the other organism
s.
Other microbes are decomposer
s, with the ability to recycle nutrient
s from other organisms' waste poducts. These microbes play a vital role in biogeochemical cycles . The nitrogen cycle
, the phosphorus cycle
and the carbon cycle
all depend on microorganisms in one way or another. For example, nitrogen
which makes up 78% of the planet's atmosphere is "indigestible" for most organisms, and the flow of nitrogen into the biosphere depends on a microbial process called fixation.
Due to the high level of horizontal gene transfer
among microbial communities, microbial ecology is also of importance to studies of evolution
.
may be used alongside microbial ecology to address a number of environmental and economic challenges. Managing the carbon cycle to sequester carbon dioxide
and prevent excess methanogenesis
is important in mitigating global warming
, and the prospects of bioenergy
are being expanded by the development of microbial fuel cell
s. Microbial resource management advocates a more progressive attitude towards disease
, whereby biological control agents are favoured over attempts at eradicationJ. Fluxes in microbial communities has to be better characterized for this field's potential to be realised. In addition, there are also clinical implications, as marine microbial symbioses are a valuable source of existing and novel antimicrobial agents, and thus offer another line of inquiry in the evolutionary arms race of antibiotic resistance
, a pressing concern for researchers .
Ecology
Ecology is the scientific study of the relations that living organisms have with respect to each other and their natural environment. Variables of interest to ecologists include the composition, distribution, amount , number, and changing states of organisms within and among ecosystems...
of microorganism
Microorganism
A microorganism or microbe is a microscopic organism that comprises either a single cell , cell clusters, or no cell at all...
s: their relationship with one another and with their environment. It concerns the three major domains
Domain (biology)
In biological taxonomy, a domain is the highest taxonomic rank of organisms, higher than a kingdom. According to the three-domain system of Carl Woese, introduced in 1990, the Tree of Life consists of three domains: Archaea, Bacteria and Eukarya...
of life — Eukaryota
Eukaryote
A eukaryote is an organism whose cells contain complex structures enclosed within membranes. Eukaryotes may more formally be referred to as the taxon Eukarya or Eukaryota. The defining membrane-bound structure that sets eukaryotic cells apart from prokaryotic cells is the nucleus, or nuclear...
, Archaea
Archaea
The Archaea are a group of single-celled microorganisms. A single individual or species from this domain is called an archaeon...
, and Bacteria
Bacteria
Bacteria are a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals...
— as well as virus
Virus
A virus is a small infectious agent that can replicate only inside the living cells of organisms. Viruses infect all types of organisms, from animals and plants to bacteria and archaea...
es.
Microorganisms, by their omnipresence, impact the entire biosphere
Biosphere
The biosphere is the global sum of all ecosystems. It can also be called the zone of life on Earth, a closed and self-regulating system...
. Microbial life plays a primary role in regulating biogeochemical
Biogeochemistry
Biogeochemistry is the scientific discipline that involves the study of the chemical, physical, geological, and biological processes and reactions that govern the composition of the natural environment...
systems in virtually all of our planet's environments, including some of the most extreme, from frozen environments and acidic lakes, to hydrothermal vents at the bottom of deepest oceans, and some of the most familiar, such as the human small intestine
Small intestine
The small intestine is the part of the gastrointestinal tract following the stomach and followed by the large intestine, and is where much of the digestion and absorption of food takes place. In invertebrates such as worms, the terms "gastrointestinal tract" and "large intestine" are often used to...
. As a consequence of the quantitative magnitude of microbial life (Whitman et al. (1998) calculated 5 × 10 30 cells, eight orders of magnitude greater than the number of stars in the observable universe
) microbes, by virtue of their biomass alone, constitute the single largest carbon sink. Aside from carbon fixation, microorganisms’ key collective metabolic processes (including nitrogen fixation
Nitrogen fixation
Nitrogen fixation is the natural process, either biological or abiotic, by which nitrogen in the atmosphere is converted into ammonia . This process is essential for life because fixed nitrogen is required to biosynthesize the basic building blocks of life, e.g., nucleotides for DNA and RNA and...
, methane metabolism
Methanogenesis
Methanogenesis or biomethanation is the formation of methane by microbes known as methanogens. Organisms capable of producing methane have been identified only from the domain Archaea, a group phylogenetically distinct from both eukaryotes and bacteria, although many live in close association with...
, and sulfur metabolism
Sulfur metabolism
Sulfur metabolism is vital for all living organisms as it is a constituent of a number of essential organic molecules like cysteine, methionine, coenzyme A, and iron-sulfur clusters. These compounds are involved in a number of essential cellular processes such as protein biosynthesis or the...
) control global biogeochemical cycling. The immensity of microorganisms’ production is such that, even in the total absence of eukaryotic life these processes would likely continue unchanged.
Symbiosis
Microbes, especially bacteria, often engage in symbioticSymbiosis
Symbiosis is close and often long-term interaction between different biological species. In 1877 Bennett used the word symbiosis to describe the mutualistic relationship in lichens...
relationships (either positive
Mutualism
Mutualism is the way two organisms of different species biologically interact in a relationship in which each individual derives a fitness benefit . Similar interactions within a species are known as co-operation...
or negative
Parasitism
Parasitism is a type of symbiotic relationship between organisms of different species where one organism, the parasite, benefits at the expense of the other, the host. Traditionally parasite referred to organisms with lifestages that needed more than one host . These are now called macroparasites...
) with other organisms, and these relationships affect the ecosystem. One example of these fundamental symbioses are chloroplasts, which allow eukaryotes to conduct photosynthesis
Photosynthesis
Photosynthesis is a chemical process that converts carbon dioxide into organic compounds, especially sugars, using the energy from sunlight. Photosynthesis occurs in plants, algae, and many species of bacteria, but not in archaea. Photosynthetic organisms are called photoautotrophs, since they can...
. Chloroplasts are considered to be endosymbiotic cyanobacteria, a group of bacteria
Bacteria
Bacteria are a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals...
that are thought to be the origins of aerobic photosynthesis. Some theories state that this invention coincides with a major shift in the early earth's atmosphere, from a reducing atmosphere to an oxygen-rich atmosphere. Some theories go as far as saying that this shift in the balance of gasses might have triggered a global ice-age known as the Snowball Earth
Snowball Earth
The Snowball Earth hypothesis posits that the Earth's surface became entirely or nearly entirely frozen at least once, some time earlier than 650 Ma . Proponents of the hypothesis argue that it best explains sedimentary deposits generally regarded as of glacial origin at tropical...
.
Roles
They are the backbone of all ecosystemEcosystem
An ecosystem is a biological environment consisting of all the organisms living in a particular area, as well as all the nonliving , physical components of the environment with which the organisms interact, such as air, soil, water and sunlight....
s, but even more so in the zones where light cannot approach and thus photosynthesis cannot be the basic means to collect energy. In such zones, chemosynthetic microbes provide energy and carbon
Carbon
Carbon is the chemical element with symbol C and atomic number 6. As a member of group 14 on the periodic table, it is nonmetallic and tetravalent—making four electrons available to form covalent chemical bonds...
to the other organism
Organism
In biology, an organism is any contiguous living system . In at least some form, all organisms are capable of response to stimuli, reproduction, growth and development, and maintenance of homoeostasis as a stable whole.An organism may either be unicellular or, as in the case of humans, comprise...
s.
Other microbes are decomposer
Decomposer
Decomposers are organisms that break down dead or decaying organisms, and in doing so carry out the natural process of decomposition. Like herbivores and predators, decomposers are heterotrophic, meaning that they use organic substrates to get their energy, carbon and nutrients for growth and...
s, with the ability to recycle nutrient
Nutrient
A nutrient is a chemical that an organism needs to live and grow or a substance used in an organism's metabolism which must be taken in from its environment. They are used to build and repair tissues, regulate body processes and are converted to and used as energy...
s from other organisms' waste poducts. These microbes play a vital role in biogeochemical cycles . The nitrogen cycle
Nitrogen cycle
The nitrogen cycle is the process by which nitrogen is converted between its various chemical forms. This transformation can be carried out by both biological and non-biological processes. Important processes in the nitrogen cycle include fixation, mineralization, nitrification, and denitrification...
, the phosphorus cycle
Phosphorus cycle
The phosphorus cycle is the biogeochemical cycle that describes the movement of phosphorus through the lithosphere, hydrosphere, and biosphere. Unlike many other biogeochemical cycles, the atmosphere does not play a significant role in the movement of phosphorus, because phosphorus and...
and the carbon cycle
Carbon cycle
The carbon cycle is the biogeochemical cycle by which carbon is exchanged among the biosphere, pedosphere, geosphere, hydrosphere, and atmosphere of the Earth...
all depend on microorganisms in one way or another. For example, nitrogen
Nitrogen
Nitrogen is a chemical element that has the symbol N, atomic number of 7 and atomic mass 14.00674 u. Elemental nitrogen is a colorless, odorless, tasteless, and mostly inert diatomic gas at standard conditions, constituting 78.08% by volume of Earth's atmosphere...
which makes up 78% of the planet's atmosphere is "indigestible" for most organisms, and the flow of nitrogen into the biosphere depends on a microbial process called fixation.
Due to the high level of horizontal gene transfer
Horizontal gene transfer
Horizontal gene transfer , also lateral gene transfer , is any process in which an organism incorporates genetic material from another organism without being the offspring of that organism...
among microbial communities, microbial ecology is also of importance to studies of evolution
Evolution
Evolution is any change across successive generations in the heritable characteristics of biological populations. Evolutionary processes give rise to diversity at every level of biological organisation, including species, individual organisms and molecules such as DNA and proteins.Life on Earth...
.
Microbial resource management
BiotechnologyBiotechnology
Biotechnology is a field of applied biology that involves the use of living organisms and bioprocesses in engineering, technology, medicine and other fields requiring bioproducts. Biotechnology also utilizes these products for manufacturing purpose...
may be used alongside microbial ecology to address a number of environmental and economic challenges. Managing the carbon cycle to sequester carbon dioxide
Carbon dioxide
Carbon dioxide is a naturally occurring chemical compound composed of two oxygen atoms covalently bonded to a single carbon atom...
and prevent excess methanogenesis
Methanogenesis
Methanogenesis or biomethanation is the formation of methane by microbes known as methanogens. Organisms capable of producing methane have been identified only from the domain Archaea, a group phylogenetically distinct from both eukaryotes and bacteria, although many live in close association with...
is important in mitigating global warming
Global warming
Global warming refers to the rising average temperature of Earth's atmosphere and oceans and its projected continuation. In the last 100 years, Earth's average surface temperature increased by about with about two thirds of the increase occurring over just the last three decades...
, and the prospects of bioenergy
Bioenergy
Bioenergy is renewable energy made available from materials derived from biological sources. Biomass is any organic material which has stored sunlight in the form of chemical energy. As a fuel it may include wood, wood waste, straw, manure, sugarcane, and many other byproducts from a variety of...
are being expanded by the development of microbial fuel cell
Microbial fuel cell
A microbial fuel cell or biological fuel cell is a bio-electrochemical system that drives a current by mimicking bacterial interactions found in nature....
s. Microbial resource management advocates a more progressive attitude towards disease
Disease
A disease is an abnormal condition affecting the body of an organism. It is often construed to be a medical condition associated with specific symptoms and signs. It may be caused by external factors, such as infectious disease, or it may be caused by internal dysfunctions, such as autoimmune...
, whereby biological control agents are favoured over attempts at eradicationJ. Fluxes in microbial communities has to be better characterized for this field's potential to be realised. In addition, there are also clinical implications, as marine microbial symbioses are a valuable source of existing and novel antimicrobial agents, and thus offer another line of inquiry in the evolutionary arms race of antibiotic resistance
Antibiotic resistance
Antibiotic resistance is a type of drug resistance where a microorganism is able to survive exposure to an antibiotic. While a spontaneous or induced genetic mutation in bacteria may confer resistance to antimicrobial drugs, genes that confer resistance can be transferred between bacteria in a...
, a pressing concern for researchers .
See also
- Environmental microbiologyEnvironmental microbiologyEnvironmental microbiology is the study of the composition and physiology of microbial communities in the environment. The environment in this case means the soil, water, air and sediments covering the planet and can also include the animals and plants that inhabit these areas...
- International Society for Microbial EcologyInternational Society for Microbial EcologyThe International Society for Microbial Ecology is the principle scientific society for the burgeoning field of Microbial Ecology and its related disciplines. ISME fosters the exchange of scientific information by organizing international symposia as well as specific workshops, sponsoring...
- The ISME JournalThe ISME JournalThe ISME Journal: Multidisciplinary Journal of Microbial Ecology is the official publication of the International Society for Microbial Ecology . The journal covers all areas of microbial ecology spanning the breadth of microbial life, including bacteria, archaea, microbial eukaryotes, and viruses...