Microbial ecology

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 (calculated as 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]

Great-plate-count-anomaly
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]

History

While microbes have been studied since the seventeenth-century, this research was from a primarily physiological perspective rather than an ecological one.[10] For instance, Louis Pasteur and his disciples were interested in the problem of microbial distribution both on land and in the ocean.[11] 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.[12] 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.[13]: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]

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.[14] 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,[15] microbial ecology is also of importance to studies of evolution.[16]

Symbiosis

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.[17][18] The types of symbiotic relationship that microbes participate in include mutualism, commensalism, parasitism,[19] and amensalism,[20] and these relationships affect the ecosystem in many ways.

Mutualism

Mutualism in microbial ecology is a relationship between microbial species and between microbial species and humans that allow for both sides to benefit.[21] One such example would be syntrophy, also known as cross-feeding,[20] which is clearly shown in Methanobacterium omelianskii. Although initially thought of as one microbial species, this system is actually two species - an S organism and Methabacterium bryantii. The S organism provides the bacterium with the H2, which the bacterium needs in order to grow and produce methane.[17][22] The reaction used by the S organism for the production of H2 is endergonic (and so thermodynamically unfavored) however, when coupled to the reaction used by Methabacterium bryantii in its production of methane, the overall reaction becomes exergonic.[17]  Thus the two organisms are in a mutualistic relationship which allows them to grow and thrive in an environment, deadly for either species alone. Lichen is an example of a symbiotic organism.[22]

Amensalism

Amensalism (also commonly known as antagonism) is a type of symbiotic relationship where one species/organism is harmed while the other remains unaffected.[21] One example of such a relationship that takes place in microbial ecology is between the microbial species Lactobacillus casei and Pseudomonas taetrolens.[23] 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.[24] However, Lactobacillus casei shows no difference in its behaviour, and such this relationship can be defined as amensalism.

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.[25] 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.[26]

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.[27]

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.[28]

The lifespan of microbes in the home varies similarly. Generally bacteria and viruses require a wet environment with a humidity of over 10 percent.[29] E. coli can survive for a few hours to a day.[29] Bacteria which form spores can survive longer, with Staphylococcus aureus surviving potentially for weeks or, in the case of Bacillus anthracis, years.[29]

In the home, pets can be carriers of bacteria; for example, reptiles are commonly carriers of salmonella.[30]

S. aureus is particularly common, and asymptomatically colonizes about 30% of the human population;[31] attempts to decolonize carriers have met with limited success[32] and generally involve mupirocin nasally and chlorhexidine washing, potentially along with vancomycin and cotrimoxazole to address intestinal and urinary tract infections.[33]

Antimicrobials

Some metals, particularly copper and silver, 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.[34] Silver nanoparticles have also begun to be incorporated into building surfaces and fabrics, although concerns have been raised about the potential side-effects of the tiny particles on human health.[35]

See also

References

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Applied and Environmental Microbiology

Applied and Environmental Microbiology is a biweekly peer-reviewed scientific journal published by the American Society for Microbiology. It was established in 1953 as Applied Microbiology and obtained its current name in 1975. Articles older than six months are available free of cost from the website, however, the newly published articles within six months are available to subscribers only. According to the Journal Citation Reports, the journal has a 2017 impact factor of 3.633. The journal has been ranked as one of the top 100 journals over the past 100 years in the fields of biology and medicine. The current editor-in-chief is Harold L. Drake (University of Bayreuth).

The journal's scope includes "(a) applied microbiology, including biotechnology, protein engineering, bioremediation, and food microbiology, (b) microbial ecology, including environmental, organismic, and genomic microbiology, and (c) interdisciplinary microbiology, including invertebrate microbiology, plant microbiology, aquatic microbiology, and geomicrobiology".

Aquatic Microbial Ecology

Aquatic Microbial Ecology is a monthly peer-reviewed scientific journal covering all aspects of aquatic microbial dynamics, in particular viruses, prokaryotes, and eukaryotes in marine, limnetic, and brackish habitats. The journal was originally established as Marine Microbial Food Webs by P. Bougis and F. Rassoulzadegan in 1985, and acquired its current name in 1995. The journal is currently published by Inter Research.

Bland Finlay

Bland J. Finlay FRS is a British biologist, and Professor of Microbial Ecology, Queen Mary, University of London.

Bruce Rittmann

Bruce E. Rittmann is Regents' Professor of Environmental Engineering and Director of the Swette Center for Environmental Biotechnology at the Biodesign Institute of Arizona State University, and a member of both the Civil Engineering and the Chemical Engineering Sections of the National Academy of Engineering. He was elected to the Academy in 2004.

Community Cyberinfrastructure for Advanced Microbial Ecology Research and Analysis

CAMERA, or the Community Cyberinfrastructure for Advanced Microbial Ecology Research and Analysis, is an online cloud computing service that provides hosted software tools and a high-performance computing infrastructure for the analysis of metagenomic data. The project was announced in January 2006, becoming Calit2's flagship project.

FEMS Microbiology Ecology

FEMS Microbiology Ecology is one of the five FEMS, free to publish, print and online peer-reviewed scientific journals, which covers all aspects of microbial ecology.

According to the Journal Citation Reports, the journal has a 2017 impact factor of 3.495 and a five-year impact factor of 4.188, ranking it 42nd out of 126 journals in the category "Microbiology".The editor-in-chief is Max Häggblom.

Hybridization probe

In molecular biology, a hybridization probe is a fragment of DNA or RNA of variable length (usually 100–10000 bases long) which can be radioactively or fluorescently labeled. It can then be used in DNA or RNA samples to detect the presence of nucleotide substances (the RNA target) that are complementary to the sequence in the probe. The probe thereby hybridizes to single-stranded nucleic acid (DNA or RNA) whose base sequence allows probe–target base pairing due to complementarity between the probe and target. The labeled probe is first denatured (by heating or under alkaline conditions such as exposure to sodium hydroxide) into single stranded DNA (ssDNA) and then hybridized to the target ssDNA (Southern blotting) or RNA (northern blotting) immobilized on a membrane or in situ.

To detect hybridization of the probe to its target sequence, the probe is tagged (or "labeled") with a molecular marker of either radioactive or (more recently) fluorescent molecules; commonly used markers are 32P (a radioactive isotope of phosphorus incorporated into the phosphodiester bond in the probe DNA) or digoxigenin, which is a non-radioactive, antibody-based marker. DNA sequences or RNA transcripts that have moderate to high sequence similarity to the probe are then detected by visualizing the hybridized probe via autoradiography or other imaging techniques. Normally, either X-ray pictures are taken of the filter, or the filter is placed under UV light. Detection of sequences with moderate or high similarity depends on how stringent the hybridization conditions were applied—high stringency, such as high hybridization temperature and low salt in hybridization buffers, permits only hybridization between nucleic acid sequences that are highly similar, whereas low stringency, such as lower temperature and high salt, allows hybridization when the sequences are less similar. Hybridization probes used in DNA microarrays refer to DNA covalently attached to an inert surface, such as coated glass slides or gene chips, to which a mobile cDNA target is hybridized.

Depending on the method, the probe may be synthesized using the phosphoramidite method, or it can be generated and labeled by PCR amplification or cloning (both are older methods). In order to increase the in vivo stability of the probe RNA is not used, instead RNA analogues may be used, in particular morpholino- derivatives. Molecular DNA- or RNA-based probes are now routinely used in screening gene libraries, detecting nucleotide sequences with blotting methods, and in other gene technologies, such as nucleic acid and tissue microarrays.

International Society for Microbial Ecology

The International Society for Microbial Ecology (ISME) is the principal scientific society for the burgeoning field of microbial ecology and its related disciplines. ISME is a non-profit association and is owner of the International Symposia on Microbial Ecology and also owner of The ISME Journal which is published by Springer Nature (impact factor 2016 9.6 - Reuters Thomson). The ISME Office is based at the Netherlands Institute of Ecology (NIOO-KNAW) in Wageningen, The Netherlands.

James Tiedje

James Tiedje is University Distinguished Professor and the director of the NSF Center for Microbial Ecology (CME) at Michigan State University, as well as a Professor of Crop and Soil Sciences and Microbiology. He was elected to the National Academy of Sciences in 2003 and served as president of the American Society for Microbiology from 2004-2005. The Center he directed developed novel methods for microbial community analysis that have greatly expanded knowledge about complex microbial communities in soil, sediments, engineered systems, the oceans and within animals. He also created experiments to detect life on Mars that were carried aboard the Viking Mars landers.

He received a B.S. degree (1964) from Iowa State University and earned his M.S. (1966) and Ph.D. 1968 degrees from Cornell University.ASM Election

CME

Journal of Ecology

The Journal of Ecology is a bimonthly peer-reviewed scientific journal covering all aspects of the ecology of plants. It was established in 1913 and is published by Wiley-Blackwell on behalf of the British Ecological Society.

The journal publishes papers on plant ecology (including algae) in both terrestrial and aquatic ecosystems. In addition to population and community ecology, articles on biogeochemistry, ecosystems, microbial ecology, physiological plant ecology, climate change, molecular genetics, mycorrhizal ecology, and the interactions between plants and organisms such as animals or bacteria, are published regularly. Besides primary research articles, it publishes "Essay Reviews" and "Forum" articles. In 2008, the first papers in a new series called "Future Directions" were published. These short papers are intended to stimulate debate as to where a field within plant ecology is going, or needs to go.

In addition, the journal contains a long-running series on the "Biological Flora of the British Isles". Over 300 accounts (each of a different species) have been published so far, all of which, from 1998 onwards, can be accessed free of charge via the journal's website. The site also has a list of the species covered.In celebration of the journal’s 100th anniversary, a Centenary Symposium was held during the British Ecological Society’s Annual Meeting in Sheffield (United Kingdom) in September 2011. A group of researchers were invited to talk on topics in which the journal has published major contributions over the last century and in which significant progress is currently being made. The contributors to the Centenary Symposium produced written versions of their papers for publication in the journal's Centenary Special Issue.

According to the Journal Citation Reports, the journal has a 2017 impact factor of 5.172.

Kartik Chandran

Kartik Chandran is an American environmental engineer at Columbia University, where he is a Professor in the Department of Earth and Environmental Engineering. He primarily works on the interface between environmental molecular and microbiology, environmental biotechnology and environmental engineering. The focus of his research is on elucidating the molecular microbial ecology and metabolic pathways of the microbial nitrogen cycle. Applications of his work have ranged from energy and resource efficient treatment of nitrogen containing wastewater streams, development and implementation of sustainable approaches to sanitation to novel models for resource recovery. Under his stewardship, the directions of biological wastewater treatment and biological nutrient removal were established for the first ever time in the history of Columbia University.

In 2015, he received the MacArthur Fellowship for his innovative work on "integrating microbial ecology, molecular biology, and engineering to transform wastewater from a troublesome pollutant to a valuable resource".

Kate Scow

Kate M. Scow is an American Professor of soil science and microbial ecology at the University of California, Davis.

Marine Biological Laboratory

The Marine Biological Laboratory (MBL) is an international center for research and education in biological and environmental science. Founded in Woods Hole, Massachusetts in 1888, the MBL is a private, nonprofit institution affiliated with the University of Chicago. After being independent for most of its history, it became officially affiliated with the university on July 1, 2013. It also collaborates with numerous other institutions.

As of 2018, 58 Nobel Prize winners have been affiliated with MBL as students, faculty members or researchers. In addition, there are 280 members of the National Academy of Sciences and 236 Members of the American Academy of Arts and Sciences who have been affiliated with the lab.

Microecology

Microecology means microbial ecology or ecology of a microhabitat. Human gut microecology is the study of microbial ecology of the human gut.Microecology is a large field which includes many topics such as evolution, biodiversity, exobiology, ecology, bioremediation, recycling, and food microbiology. There are an estimated 1,000,000 different type of microbes that live on this planet of which fewer than 4,500 have been described according to the General Biodiversity Assessment.

Neocallimastix

Neocallimastix is a genus of obligately anaerobic rumen fungi in the family Neocallimastigaceae. A specialised group of chytrids grow in the rumen of herbivorous animals, where they degrade cellulose and thus play a primary role in the complex microbial ecology of the rumen.

Olav Vadstein

Olav Vadstein (born 14 February 1955) is a Norwegian professor of Microbial Ecology at the Norwegian University of Science and Technology.According to his web page, Vadstein is interested in aquatic ecosystems

"both natural and un-natural (human created). Besides basic aspects, I’m interested in applied microbial ecology, which can be placed under the heading Environmental Biotechnology."

His most highly cited papers are:

J. Skjermo, O. Vadstein, Techniques for microbial control in the intensive rearing of marine larvae in Aquaculture, 77, Issues 1–4, 1 July 1999, Pages 333-343- cited 378 times according to Google Scholar

Vadstein O. (2000) Heterotrophic, Planktonic Bacteria and Cycling of Phosphorus. In: Schink B. (eds) Advances in Microbial Ecology vol 16. Springer, Boston, MA- cited 184 times

Vadstein, O. The use of immunostimulation in marine larviculture: possibilities and challenges. Aquaculture Volume 155, Issues 1–4, 20 September 1997, Pages 401-417 Cited 179 times

Temperature gradient gel electrophoresis

Temperature gradient gel electrophoresis (TGGE) and denaturing gradient gel electrophoresis (DGGE) are forms of electrophoresis which use either a temperature or chemical gradient to denature the sample as it moves across an acrylamide gel. TGGE and DGGE can be applied to nucleic acids such as DNA and RNA, and (less commonly) proteins. TGGE relies on temperature dependent changes in structure to separate nucleic acids. DGGE separates genes of the same size based on their different denaturing ability which is determined by their base pair sequence. DGGE was the original technique, and TGGE a refinement of it.

The ISME Journal

The ISME Journal: Multidisciplinary Journal of Microbial Ecology is a peer-reviewed scientific journal covering all areas of microbial ecology spanning the breadth of microbial life, including bacteria, archaea, microbial eukaryotes, and viruses. It is an official publication of the International Society for Microbial Ecology (ISME) and publishes original research articles, reviews, and commentaries. The founding editors-in-chief are Mark Bailey and George Kowalchuk. The journal is published on behalf of ISME by the Nature Publishing Group. According to the Journal Citation Reports, the journal had a 2017 impact factor of 9.520, ranking it 3rd out of 160 journals in the category "Ecology". and 9th out of 126 in the category "Microbiology".

UniFrac

UniFrac is a distance metric used for comparing biological communities. It differs from dissimilarity measures such as Bray-Curtis dissimilarity in that it incorporates information on the relative relatedness of community members by incorporating phylogenetic distances between observed organisms in the computation.

Both weighted (quantitative) and unweighted (qualitative) variants of UniFrac are widely used in microbial ecology, where the former accounts for abundance of observed organisms, while the latter only considers their presence or absence. The method was devised by Catherine Lozupone, when she was working under Rob Knight of the University of Colorado at Boulder in 2005.

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Producers
Consumers
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Microorganisms
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Example webs
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Ecology: Modelling ecosystems: Other components
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networks
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