Microbial ecology

The great plate count anomaly. Counts of cells obtained via cultivation are orders of magnitude lower than those directly observed under the microscope. This is because microbiologists are able to cultivate only a minority of naturally occurring microbes using current laboratory techniques, depending on the environment.^[1]

Microbial ecology (or environmental microbiology) is the ecology of microorganisms: their relationship with one another and with their environment. It concerns the three major domains of life—Eukaryota, Archaea, and Bacteria—as well as viruses.^[2]

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.^[3][4] As a consequence of the quantitative magnitude of microbial life (Whitman and coworkers calculated 7030500000000000000♠5.0×10³⁰ cells, eight orders of magnitude greater than the number of stars in the observable universe^[5][6]) microbes, by virtue of their biomass alone, constitute a significant carbon sink.^[7] Aside from carbon fixation, microorganisms' key collective metabolic processes (including nitrogen fixation, methane metabolism, and sulfur metabolism) control global biogeochemical cycling.^[8] The immensity of microorganisms' production is such that, even in the total absence of eukaryotic life, these processes would likely continue unchanged.^[9]

History

While microbes have been studied since the seventeenth-century, this research was from a primarily physiological perspective rather than an ecological one.^[10] Martinus Beijerinck invented the enrichment culture, a fundamental method of studying microbes from the environment. He is often incorrectly credited with framing the microbial biogeographic idea that "everything is everywhere, but, the environment selects", which was stated by Lourens Baas Becking.^[11] Sergei Winogradsky was one of the first researchers to attempt to understand microorganisms outside of the medical context—making him among the first students of microbial ecology and environmental microbiology—discovering chemosynthesis, and developing the Winogradsky column in the process.^[12]:644

Beijerinck and Windogradsky, however, were focused on the physiology of microorganisms, not the microbial habitat or their ecological interactions.^[10] Modern microbial ecology was launched by Robert Hungate and coworkers, who investigated the rumen ecosystem. The study of the rumen required Hungate to develop techniques for culturing anaerobic microbes, and he also pioneered a quantitative approach to the study of microbes and their ecological activities that differentiated the relative contributions of species and catabolic pathways.^[10]

Symbiosis

Microbes, especially bacteria, often engage in symbiotic 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 gases might have triggered a global ice-age known as the Snowball Earth.

Roles

Microorganisms are the backbone of all ecosystems, but even more so in the zones where photosynthesis is unable to take place because of the absence of light. In such zones, chemosynthetic microbes provide energy and carbon to the other organisms.

Other microbes are decomposers, with the ability to recycle nutrients from other organisms' waste products. These microbes play a vital role in biogeochemical cycles.^[13] The nitrogen cycle, the phosphorus cycle, the sulphur cycle and the carbon cycle all depend on microorganisms in one way or another. For example, the nitrogen gas which makes up 78% of the earth's atmosphere is unavailable to most organisms, until it is converted to a biologically available form by the microbial process of nitrogen fixation.

Due to the high level of horizontal gene transfer among microbial communities,^[14] microbial ecology is also of importance to studies of evolution.^[15]

Microbial resource management

Biotechnology may be used alongside microbial ecology to address a number of environmental and economic challenges. For example, molecular techniques such as community fingerprinting can be used to track changes in microbial communities over time or assess their biodiversity. 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 cells. Microbial resource management advocates a more progressive attitude towards disease, whereby biological control agents are favoured over attempts at eradication. Fluxes in microbial communities has to be better characterized for this field's potential to be realised.^[16] 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.^[17]

In built environment and human interaction

Microbes exist in all areas, including homes, offices, commercial centers, and hospitals. In 2016, the journal Microbiome published a collection of various works studying the microbial ecology of the built environment.^[18]

A 2006 study of pathogenic bacteria in hospitals found that their ability to survive varied by the type, with some surviving for only a few days while others survived for months.^[19]

The lifespan of microbes in the home varies similarly. Generally bacteria and viruses require a wet environment with a humidity of over 10 percent.^[20] E. coli can survive for a few hours to a day.^[20] Bacteria which form spores can survive longer, with Staphylococcus aureus surviving potentially for weeks or, in the case of Bacillus anthracis, years.^[20]

In the home, pets can be carriers of bacteria; for example, reptiles in particular are commonly carriers of salmonella.^[21]

S. aureus is particularly common, and asymptomatically colonizes about 30% of the human population;^[22] attempts to decolonize carriers have met with limited success^[23] and generally involve mupirocin nasally and chlorhexidine washing, potentially along with vancomycin and cotrimoxazole to address intestinal and urinary tract infections.^[24]

Antimicrobials

Some metals, particularly copper and silver, are relatively microbial. Using antimicrobial copper-alloy touch surfaces is a technique which has began to be used in the 21st century to prevent transmission of bacteria.^[25] Silver, particularly in nanoparticle form, has also began to be incorporated into building surfaces and fabrics, although concerns have been raised about the potential unhealthy side-effects of the tiny particles on the body.^[26]

See also

• Microbial biogeography
• Microbial loop
• Outline of ecology
• International Society for Microbial Ecology
• The ISME Journal

References

Microorganisms
Microorganisms	Archaea Bacterium Cyanobacteria Fungi Nanobacterium Prokaryote Protist Protozoa Virus
Microbiology	Microbial biogeography Microbial genetics Microbial intelligence Microbial metabolism Microbial phylogenetics Microbial population biology Mycology Virology
Ecology	Microbial cooperation Microbial ecology Microbial food web Microbial loop Microbial synergy Host microbe interactions in Caenorhabditis elegans
Techniques	Dark field microscopy Impedance microbiology Microbial cytology Microbiological culture Staining
Marine	Marine microorganism Antarctic Marine microbial symbiosis International Census of Marine Microbes
Human related	Microbes in human culture Food microbiology Microbial oil Microbial symbiosis and immunity Nylon-eating Human microbiota asthma dysbiosis fecal Human Microbiome Project gut lung mouth skin vagina in pregnancy placenta uterus Protein production
Other	Lines on the Antiquity of Microbes Microbially induced sedimentary structure Microbial dark matter Physical factors affecting microbial life

Ecology: Modelling ecosystems: Trophic components
General	Abiotic component Abiotic stress Behaviour Biogeochemical cycle Biomass Biotic component Biotic stress Carrying capacity Competition Ecosystem Ecosystem ecology Ecosystem model Keystone species List of feeding behaviours Metabolic theory of ecology Productivity Resource
Producers	Autotrophs Chemosynthesis Chemotrophs Foundation species Mixotrophs Myco-heterotrophy Mycotroph Organotrophs Photoheterotrophs Photosynthesis Photosynthetic efficiency Phototrophs Primary nutritional groups Primary production
Consumers	Apex predator Bacterivore Carnivores Chemoorganotroph Foraging Generalist and specialist species Intraguild predation Herbivores Heterotroph Heterotrophic nutrition Insectivore Mesopredator release hypothesis Omnivores Optimal foraging theory Predation Prey switching
Decomposers	Chemoorganoheterotrophy Decomposition Detritivores Detritus
Microorganisms	Archaea Bacteriophage Environmental microbiology Lithoautotroph Lithotrophy Microbial cooperation Microbial ecology Microbial food web Microbial intelligence Microbial loop Microbial mat Microbial metabolism Phage ecology
Food webs	Biomagnification Ecological efficiency Ecological pyramid Energy flow Food chain Trophic level
Example webs	Cold seeps Hydrothermal vents Intertidal Kelp forests Lakes North Pacific Subtropical Gyre Rivers San Francisco Estuary Soil Tide pool
Processes	Ascendency Bioaccumulation Cascade effect Climax community Competitive exclusion principle Consumer-resource systems Copiotrophs Dominance Ecological network Ecological succession Energy quality Energy Systems Language f-ratio Feed conversion ratio Feeding frenzy Mesotrophic soil Nutrient cycle Oligotroph Paradox of the plankton Trophic cascade Trophic mutualism Trophic state index
Defense/counter	Animal coloration Antipredator adaptations Camouflage Deimatic behaviour Herbivore adaptations to plant defense Mimicry Plant defense against herbivory Predator avoidance in schooling fish

Ecology: Modelling ecosystems: Other components
Population ecology	Abundance Allee effect Depensation Ecological yield Effective population size Intraspecific competition Logistic function Malthusian growth model Maximum sustainable yield Overpopulation in wild animals Overexploitation Population cycle Population dynamics Population modeling Population size Predator–prey (Lotka–Volterra) equations Recruitment Resilience Small population size Stability
Species	Biodiversity Density-dependent inhibition Ecological effects of biodiversity Ecological extinction Endemic species Flagship species Gradient analysis Indicator species Introduced species Invasive species Latitudinal gradients in species diversity Minimum viable population Neutral theory Occupancy–abundance relationship Population viability analysis Priority effect Rapoport's rule Relative abundance distribution Relative species abundance Species diversity Species homogeneity Species richness Species distribution Species-area curve Umbrella species
Species interaction	Antibiosis Biological interaction Commensalism Community ecology Ecological facilitation Interspecific competition Mutualism Storage effect
Spatial ecology	Biogeography Cross-boundary subsidy Ecocline Ecotone Ecotype Disturbance Edge effects Foster's rule Habitat fragmentation Ideal free distribution Intermediate Disturbance Hypothesis Island biogeography Landscape ecology Landscape epidemiology Landscape limnology Metapopulation Patch dynamics r/K selection theory Source–sink dynamics
Niche	Ecological niche Ecological trap Ecosystem engineer Environmental niche modelling Guild Habitat Marine habitats Limiting similarity Niche apportionment models Niche construction Niche differentiation
Other networks	Assembly rules Bateman's principle Bioluminescence Ecological collapse Ecological debt Ecological deficit Ecological energetics Ecological indicator Ecological threshold Ecosystem diversity Emergence Extinction debt Kleiber's law Liebig's law of the minimum Marginal value theorem Thorson's rule Xerosere
Other	Allometry Alternative stable state Balance of nature Biological data visualization Constructal theory Ecocline Ecological economics Ecological footprint Ecological forecasting Ecological humanities Ecological stoichiometry Ecopath Ecosystem based fisheries Endolith Evolutionary ecology Functional ecology Industrial ecology Macroecology Microecosystem Natural environment Regime shift Systems ecology Urban ecology Theoretical ecology
List of ecology topics

Aquatic ecosystem topics
Aquatic ecosystems – general and freshwater components General Acoustic ecology Adaptation Agent-based models Algal bloom Anoxic waters Aquatic animals (Insects Mammals) Aquatic plants Aquatic science Benthos Biodiversity research Bioluminescence Biomass Biomonitoring Cascade effect Colored dissolved organic matter Camouflage and mimicry Dead zone Ecohydrology Ecosystems Eutrophication Fisheries science Food chain Food web GIS and aquatic science Hydrobiology Hypoxia Isotope analysis Microbial ecology Microbial food web Microbial loop Nekton Neuston Particle Pelagic zone Photic zone Phytoplankton Plankton Pleuston Predation Productivity Ramsar Convention Respiration Schooling Sediment trap Siltation Spawning Substrate Thermal pollution Toxicology Trophic level Water column Zooplankton More... Freshwater Biology Biomes Ecosystems freshwater lake river Fish Hyporheic zone Limnology Lake stratification Macrophyte Pond Fish pond Rheotaxis Stream bed Stream pool Trophic state index Upland and lowland Water garden Wetland brackish marsh freshwater marsh swamp bog fen Environmental quality More... Ecoregions Freshwater (List) Marine (List) The Everglades Maharashtra The North Pacific Subtropical Gyre The San Francisco Estuary
Aquatic ecosystems – marine components Marine Marine biology Marine chemistry Deep scattering layer Diel vertical migration Ecosystems large marine marine) f-ratio Iron fertilization Marine snow Ocean nourishment Oceanic physical-biological process Ocean turbidity Photophore Thorson's rule Upwelling Whale fall More... Marine life Bacteriophages Census Fish coastal coral reef deep sea demersal pelagic Deep sea communities Deep sea creature Deep-water coral Invertebrates Larvae Mammals Marine life Microorganisms Paradox of the plankton Reptiles Seabirds Seashore wildlife Vertebrates Wild fisheries Marine habitats Bay mud Black smokers Coastal biogeomorphology Cold seeps Coral reefs Davidson Seamount Estuaries Intertidal ecology Intertidal wetlands Kelp forests Hydrothermal vents Lagoons Mangroves Marine biomes Marine habitats Mudflats Rocky shores Salt marshes Salt pannes and pools Seagrass meadows Sponge reefs Tide pools Issues Ecological values of mangroves Fisheries and climate change HERMIONE Marine conservation Marine conservation activism Marine pollution Marine Protected Area