Взаимодействие микроорганизмов с окружающей средой: современные методы изучения.

Study of the relationship of microorganisms with their environment

[[File:Great plate count anomaly. svg|thumb|upright=1.3|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. As a consequence of the quantitative magnitude of microbial life (calculated as 5.0 cells; eight orders of magnitude greater than the number of stars in the observable universe 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. These electrodes have a spatial resolution of 50–100 μm, and have allowed analysis of spatial and temporal biogeochemical dynamics in microbial mats and sediments. Although measuring biogeochemical process rates could analyse what processes were occurring, they were incomplete because they provided no information on which specific microbes were responsible. It was long known that 'classical' cultivation techniques recovered fewer than 1% of the microbes from a natural habitat. However, beginning in the 1990s, a set of cultivation independent techniques have evolved to determine the relative abundance of microbes in a habitat. Carl Woese first demonstrated that the sequence of the 16S ribosomal RNA molecule could be used to analyse phylogenetic relationships. Norm Pace took this seminal idea and applied it to analysfe 'who's there' in natural environments. The procedure involves (a) isolation of nucleic acids directly from a natural environment, (b) PCR amplification of small subunit rRNA gene sequences, (c) sequencing the amplicons, and (d) comparison of those sequences to a database of sequences from pure cultures and environmental DNA. This has provided tremendous insights into the diversity present within microbial habitats. However, it does not resolve how to link specific microbes to their biogeochemical role. Metagenomics, the sequencing of total DNA recovered from an environment, can provide insights into biogeochemical potential, whereas metatranscriptomics and metaproteomics can measure actual expression of genetic potential but remains more technically difficult.

Microbes, especially bacteria, often engage in symbiotic relationships (either positive or negative) with other microorganisms or larger organisms. Although physically small, symbiotic relationships amongst microbes are significant in eukaryotic processes and their evolution. The types of symbiotic relationship that microbes participate in include mutualism, commensalism, parasitism, and amensalism which affect the ecosystem in many ways.

Mutualism in microbial ecology is a relationship between microbial species and humans that allows for both sides to benefit. One such example would be syntrophy, also known as cross feeding, Syntrophy has been hypothesized to play a significant role in energy and nutrient limited environments, such as deep subsurface, where it can help the microbial community with diverse functional properties to survive, grow and produce maximum amount of energy. Anaerobic oxidation of methane (AOM) is carried out by mutualistic consortium of a sulfate reducing bacterium and an anaerobic methane oxidizing archaeon. The reaction used by the bacterial partner for the production of H2 is endergonic (and so thermodynamically unfavored) however, when coupled to the reaction used by archaeal partner, the overall reaction becomes exergonic. Metabolic products of one microbial population are used by another microbial population without either gain or harm for the first population. There are many "pairs "of microbial species that perform either oxidation or reduction reaction to the same chemical equation. For example, methanogens produce methane by reducing CO2 to CH4, while methanotrophs oxidise methane back to CO2.

Amensalism (also commonly known as antagonism) is a type of symbiotic relationship where one species/organism is harmed while the other remains unaffected. When co existing in an environment, Pseudomonas taetrolens shows inhibited growth and decreased production of lactobionic acid (its main product) most likely due to the byproducts created by Lactobacillus casei during its production of lactic acid. However, Lactobacillus casei shows no difference in its behaviour, and such this relationship can be defined as amensalism.

Biotechnology may be used alongside microbial ecology to address a number of environmental and economic challenges. For example, molecular techniques such as community fingerprinting or metagenomics 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. 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. The lifespan of microbes in the home varies similarly. Generally bacteria and viruses require a wet environment with a humidity of over 10 percent. E. coli can survive for a few hours to a day. S. aureus is particularly common, and asymptomatically colonizes about 30% of the human population; attempts to decolonize carriers have met with limited success and generally involve mupirocin nasally and chlorhexidine washing, potentially along with vancomycin and cotrimoxazole to address intestinal and urinary tract infections.

Some metals, particularly copper, silver, and gold have antimicrobial properties. Using antimicrobial copper alloy touch surfaces is a technique which has begun to be used in the 21st century to prevent transmission of bacteria. Due to the antimicrobial properties certain metals possess, products such as medical devices are made using those metals.