What can we learn with microbiology?
Microbiology
Microbiology (from Greek , "mīkros", "small"; , "bios", "life"; and , "-logia") is the study of microorganisms, those being unicellular (single cell), multicellular (cell colony), or acellular (lacking cells). Microbiology encompasses numerous sub-disciplines including virology, parasitology, mycology and bacteriology.
Pharmacomicrobiomics
Efforts to understand the interaction between specific xenobiotics and the microbiome have traditionally involved the use of "in vivo" as well as "in vitro" models. Recently, next generation sequencing of genomic DNA obtained from a community of microbes has been used to identify organisms within microbial communities, allowing for accurate profiles of the composition of microbes within an environment. Initiatives such as the Human Microbiome Project (HMP) have aimed to characterize the microbial composition of the oral, gut, vaginal, skin and nasal environments. This and other microbiome characterization projects have accelerated the study of pharmacomicrobiomics. An extensive understanding of the microbiome in the human body can lead to the development of novel therapeutics and personalized drug treatments that are not potentiated or activated by processes carried out by the microbiome.
Microorganism
The possible existence of unseen microbial life was suspected from ancient times, such as in Jain scriptures from 6th century BC India and the 1st century BC book "On Agriculture" by Marcus Terentius Varro. Microbiology, the scientific study of microorganisms, began with their observation under the microscope in the 1670s by Antonie van Leeuwenhoek. In the 1850s, Louis Pasteur found that microorganisms caused food spoilage, debunking the theory of spontaneous generation. In the 1880s, Robert Koch discovered that microorganisms caused the diseases tuberculosis, cholera and anthrax.
Microbial ecology
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, and these relationships affect the ecosystem in many ways.
Alison Murray (scientist)
Murray's research has provided critical insights into how microorganisms persist and function in extremely cold and harsh environments, including those that lack oxygen and biological sources of energy. Making use of molecular genomic tools to describe microbial life, her work has helped answer questions about how microbes function and survive in extremely cold environments and how environmental changes affect the functioning and diversity of these organisms, as well as potential feedbacks that might impact the sustainability of cold-environment ecosystems.
Environmental engineering science
This includes further education about microbial, molecular and cell biology. Classes can include cell biology, virology, microbial and plant biology
Viral shunt
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.
UCL Eastman Dental Institute
The Microbial Diseases Department examines the aetiology, pathogenesis and control of diseases caused by micro-organisms as well as the ecology of the indigenous microbiota and its contribution to health. The department also oversees the Swab and Send project and the Tn Registry, the latter designating Tn numbers to researchers publishing details of new transposable elements discovered in bacteria and archaea.
Transmission (medicine)
The mode of transmission is also an important aspect of the biology of beneficial microbial symbionts, such as coral-associated dinoflagellates or human microbiota. Organisms can form symbioses with microbes transmitted from their parents, from the environment or unrelated individuals, or both.
Microbiomes of the built environment
This field encompasses studies of any kind of microorganism (e.g. bacteria, archaea, viruses, various microbial eukaryotes including yeasts, and others sometimes generally referred to as protists) and studies of any kind of built environment such as buildings, vehicles, and water systems.
Microorganism
Microorganisms can form an endosymbiotic relationship with other, larger organisms. For example, microbial symbiosis plays a crucial role in the immune system. The microorganisms that make up the gut flora in the gastrointestinal tract contribute to gut immunity, synthesize vitamins such as folic acid and biotin, and ferment complex indigestible carbohydrates. Some microorganisms that are seen to be beneficial to health are termed probiotics and are available as dietary supplements, or food additives.
Biology
Ecology is the study of the distribution and abundance of living organisms, the interaction between them and their environment. An organism shares an environment that includes other organisms and biotic factors as well as local abiotic factors (non-living) such as climate and ecology. One reason that biological systems can be difficult to study is that so many different interactions with other organisms and the environment are possible, even on small scales. A microscopic bacterium responding to a local sugar gradient is responding to its environment as much as a lion searching for food in the African savanna. For any species, behaviors can be co-operative, competitive, parasitic, or symbiotic. Matters become more complex when two or more species interact in an ecosystem.
Microbial ecology
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 and coworkers calculated cells, eight orders of magnitude greater than the number of stars in the observable universe) microbes, by virtue of their biomass alone, constitute a significant 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.
Impedance microbiology
Impedance microbiology is a microbiological technique used to measure the microbial number density (mainly bacteria but also yeasts) of a sample by monitoring the electrical parameters of the growth medium. The ability of microbial metabolism to change the electrical conductivity of the growth medium was discovered by Stewart and further studied by other scientists such as Oker-Blom, Parson and Allison in the first half of 20th century. However, it was only in the late 1970s that, thanks to computer-controlled systems used to monitor impedance, the technique showed its full potential, as discussed in the works of Fistenberg-Eden & Eden, Ur & Brown and Cady.
List of Puerto Rican scientists and inventors
Microbiology is the study of "microorganisms", which are unicellular or cell-cluster microscopic organisms. This includes eukaryotes such as fungi and protists, and prokaryotes, which are bacteria and archaea. Viruses, though not strictly classed as living organisms, are also studied.
Conrad Weiser Area School District
The curriculum includes microbiology, environmental science, tissue culture, food science, animal science and entomology, with a focus on performance in the laboratory, independent reading and technical writing, professional communication, and self-directed study.
Biodiversity hypothesis of health
We are exposed to microbes via different ways from which the most important are respiratory tract, digestive system and skin contact. The habitat we live in and the food we eat influence greatly to our microbiota. Our own way of living and our choices — how we live, eat, move and what are our recreational activities — impacts on the amount of valuable microbe exposure. The amount as well as the microbial diversity of exposure are essential factors.
Microecology
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.
Microbiology
Eukaryotic microorganisms possess membrane-bound cell organelles and include fungi and protists, whereas prokaryotic organisms—all of which are microorganisms—are conventionally classified as lacking membrane-bound organelles and include Bacteria and Archaea. Microbiologists traditionally relied on culture, staining, and microscopy. However, less than 1% of the microorganisms present in common environments can be cultured in isolation using current means. Microbiologists often rely on molecular biology tools such as DNA sequence based identification, for example 16s rRNA gene sequence used for bacteria identification.
Transmission electron microscopy DNA sequencing
The microbiome refers the total collection of microbes present in a microenvironment and their respective genomes. For example, an estimated 100 trillion microbial cells colonize the human body at any given time. The human microbiome is of particular interest, as these commensal bacteria are important for human health and immunity. Most of the Earth's bacterial genomes have not yet been sequenced; undertaking a microbiome sequencing project would require extensive "de novo" genome assembly, a prospect which is daunting with short read DNA sequencing technologies. Longer reads would greatly facilitate the assembly of new microbial genomes.
Bibliography of biology
Biology is a natural science concerned with the study of life and living organisms, including their structure, function, growth, origin, evolution, distribution, and taxonomy. Biology is a vast subject containing many subdivisions, topics, and disciplines. Subdisciplines of biology are recognized on the basis of the scale at which organisms are studied and the methods used to study them.
Microbial genetics
Since the discovery of microorganisms by Robert Hooke and Antoni van Leeuwenhoek during the period 1665-1885 they have been used to study many processes and have had applications in various areas of study in genetics.
For example: Microorganisms' rapid growth rates and short generation times are used by scientists to study evolution. Robert Hooke and Antoni van Leeuwenhoek discoveries involved depictions, observations, and descriptions of microorganisms. Mucor is the microfungus that Hooke presented and gave a depiction of. His contribution being, Mucor as the first microorganism to be illustrated. Antoni van Leeuwenhoek’s contribution to the microscopic protozoa and microscopic bacteria yielded to scientific observations and descriptions. These contributions were accomplished by a simple microscope, which led to the understanding of microbes today and continues to progress scientists understanding.  
Microbial genetics also has applications in being able to study processes and pathways that are similar to those found in humans such as drug metabolism.
Microorganism
Antonie Van Leeuwenhoek is considered to be the father of microbiology. He was the first in 1673 to discover, observe, describe, study and conduct scientific experiments with microoorganisms, using simple single-lensed microscopes of his own design. Robert Hooke, a contemporary of Leeuwenhoek, also used microscopy to observe microbial life in the form of the fruiting bodies of moulds. In his 1665 book "Micrographia", he made drawings of studies, and he coined the term "cell".
Geobiology
Geomicrobiology traditionally studies the interactions between microbes and minerals. While it is generally reliant on the tools of microbiology, microbial geochemistry uses geological and chemical methods to approach the same topic from the perspective of the rocks. Geomicrobiology and microbial geochemistry (GMG) is a relatively new interdisciplinary field that more broadly takes on the relationship between microbes, Earth, and environmental systems. Billed as a subset of both geobiology and geochemistry, GMG seeks to understand elemental biogeochemical cycles and the evolution of life on Earth. Specifically, it asks questions about where microbes live, their local and global abundance, their structural and functional biochemistry, how they have evolved, biomineralization, and their preservation potential and presence in the rock record. In many ways, GMG appears to be equivalent to geobiology, but differs in scope: geobiology focuses on the role of all life, while GMG is strictly microbial. Regardless, it is these tiniest creatures that dominated to history of life integrated over time and seem to have had the most far-reaching effects.
Pharmaceutical microbiology
Pharmaceutical Microbiology is an applied branch of Microbiology. It involves the study of microorganisms associated with the manufacture of pharmaceuticals e.g. minimizing the number of microorganisms in a process environment, excluding microorganisms and microbial biproducts like exotoxin and endotoxin from water and other starting materials, and ensuring the finished pharmaceutical product is sterile. Other aspects of pharmaceutical microbiology include the research and development of anti-infective agents, the use of microorganisms to detect mutagenic and carcinogenic activity in prospective drugs, and the use of microorganisms in the manufacture of pharmaceutical products like insulin and human growth hormone.
Microbial genetics
Microbial genetics is a subject area within microbiology and genetic engineering. Microbial genetics studies microorganisms for different purposes. The microorganisms that are observed are bacteria, and archaea. Some fungi and protozoa are also subjects used to study in this field. The studies of microorganisms involve studies of genotype and expression system. Genotypes are the inherited compositions of an organism. (Austin, "Genotype," n.d.) Genetic Engineering is a field of work and study within microbial genetics. The usage of recombinant DNA technology is a process of this work. The process involves creating recombinant DNA molecules through manipulating a DNA sequence. That DNA created is then in contact with a host organism. Cloning is also an example of genetic engineering.
Ecological succession
Succession of micro-organisms including fungi and bacteria occurring within a microhabitat is known as microsuccession or serule. Like in plants, microbial succession can occur in newly available habitats (primary succession) such as surfaces of plant leaves, recently exposed rock surfaces (i.e., glacial till) or animal infant guts , and also on disturbed communities (secondary succession) like those growing in recently dead trees or animal droppings. Microbial communities may also change due to products secreted by the bacteria present. Changes of pH in a habitat could provide ideal conditions for a new species to inhabit the area. In some cases the new species may outcompete the present ones for nutrients leading to the primary species demise. Changes can also occur by microbial succession with variations in water availability and temperature. Theories of macroecology have only recently been applied to microbiology and so much remains to be understood about this growing field. A recent study of microbial succession evaluated the balances between stochastic and deterministic processes in the bacterial colonization of a salt marsh chronosequence. The results of this study show that, much like in macro succession, early colonization (primary succession) is mostly influenced by stochasticity while secondary succession of these bacterial communities was more strongly influenced by deterministic factors.
Bibliography of biology
This section contains a list of works in ecology, the scientific study of the relations that living organisms have with respect to each other and their natural environment.This section contains a list of works on evolution, the change across successive generations in the heritable characteristics of biological populations.This section contains a list of works on genetics, the science of genes, heredity, and variation in living organisms.This section contains a list of publications on microbiology. Microbiology is the study of "microorganisms", which are defined as any microscopic organism that comprises either a single cell (unicellular), cell clusters or no cell at all (acellular).
Mesopelagic zone
Very little is known about the microbial community of the mesopelagic zone because it is a difficult part of the ocean to study. Recent work using DNA from seawater samples emphasized the importance of viruses and microbes role in recycling organic matter from the surface ocean, known as the microbial loop. These many microbes can get their energy from different metabolic pathways. Some are autotrophs, heterotrophs, and a 2006 study even discovered chemoautotrophs. This chemoautotrophic Archaea crenarchaeon "Candidatus" can oxidize ammonium as their energy source without oxygen, which could significantly impact the nitrogen and carbon cycles. One study estimates these ammonium-oxidizing bacteria, which are only 5% of the microbial population, can annually capture 1.1 Gt of organic carbon.
History of molecular biology
The successes of molecular biology derived from the exploration of that unknown world by means of the new technologies developed by chemists and physicists: X-ray diffraction, electron microscopy, ultracentrifugization, and electrophoresis. These studies revealed the structure and function of the macromolecules.
Microorganism
Microbes are important in human culture and health in many ways, serving to ferment foods, treat sewage, produce fuel, enzymes and other bioactive compounds. They are essential tools in biology as model organisms and have been put to use in biological warfare and bioterrorism. They are a vital component of fertile soils. In the human body microorganisms make up the human microbiota including the essential gut flora. They are the pathogens responsible for many infectious diseases and as such are the target of hygiene measures.
American Microscopical Society
The current research goals of "Invertebrate Biology" describes its research goals as spanning the fields of "morphology and ultrastructure, genetics and phylogenetics, evolution, physiology and ecology, neurobiology, behavior and biomechanics, reproduction and development" and includes "cell and molecular biology related to all types of invertebrates: protozoan and metazoan, aquatic and terrestrial, free-living and symbiotic".
Geomicrobiology
A common field of study within geomicrobiology is origin of life on earth or other planets. Various rock-water interactions, such as serpentinization and water radiolysis, are possible sources of metabolic energy to support chemolithoautotrophic microbial communities on Early Earth and on other planetary bodies such as Mars, Europa and Enceladus.
Journal of Medical Microbiology
The Journal of Medical Microbiology is a peer-reviewed academic journal that covers microbiological research relevant to human and animal disease. Topics covered include pathogenicity, virulence, host response, epidemiology, microbial ecology, diagnostics, typing, models for infection and antimicrobial agents relating to viruses, bacteria, fungi and eukaryotic parasites. The journal is published monthly by the Microbiology Society, from Reading, UK.
Branches of science
Some branches of biology include: microbiology, anatomy, neurology and neuroscience, immunology, genetics, physiology, pathology, biophysics, biolinguistics, and ophthalmology.
List of life sciences
The life sciences or biological sciences comprise the branches of science that involve the scientific study of life and organisms – such as microorganisms, plants, and animals including human beings.
Biology
Molecular biology is the study of biology at the molecular level. This field overlaps with other areas of biology, particularly those of genetics and biochemistry. Molecular biology is a study of the interactions of the various systems within a cell, including the interrelationships of DNA, RNA, and protein synthesis and how those interactions are regulated.
Microbiologist
A microbiologist (from Greek ) is a scientist who studies microscopic life forms and processes. This includes study of the growth, interactions and characteristics of microscopic organisms such as bacteria, algae, fungi, and some types of parasites and their vectors. Most microbiologists work in offices and/or research facilities, both in private biotechnology companies as well as in academia. Most microbiologists specialize in a given topic within microbiology such as bacteriology, parasitology, virology, or immunology.
Human interactions with microbes
Microbes can form an endosymbiotic relationship with larger organisms. For example, the bacteria that live within the human digestive system contribute to human health through gut immunity, the synthesis of vitamins such as folic acid and biotin, and the fermentation of complex indigestible carbohydrates. Future drugs and food chemicals may need to be tested on the gut microbiota; it is already clear that probiotic supplements can promote health, and that gut microbes are affected by both diet and medicines.
Microbial biogeography
Microbial biogeographic patterns are often similar to those of macro-organisms. Microbes generally follow well-known patterns such as the distance decay relationship, the abundance-range relationship, and Rapoport's rule. This is surprising given the many disparities between microorganisms and macro-organisms, in particular their size (micrometers vs. meters), time between generations (minutes vs. years), and dispersibility (global vs. local). However, important differences between the biogeographical patterns of microorganism and macro-organism do exist, and likely result from differences in their underlying biogeographic processes (e.g., drift, dispersal, selection, and mutation). For example, dispersal is an important biogeographical process for both microbes and larger organisms, but small microbes can disperse across much greater ranges and at much greater speeds by traveling through the atmosphere (for larger animals dispersal is much more constrained due to their size). As a result, many microbial species can be found in both northern and southern hemispheres, while larger animals are typically found only at one pole rather than both.
ABI Solid Sequencing
The ability to learn more about methylation and TF binding sites on a genome wide scale is a valuable resource and could teach us much about disease and molecular biology in general.
Monserrate Román
In 1989, she applied and was hired as a microbiologist by NASA's Marshall Space Flight Center (MSFC) at Huntsville, Alabama. As a microbiologist, Román studies microbes, living organisms including viruses, bacteria, fungi and parasites, which are only visible under a microscope.
Microorganism
Microorganisms can be found almost anywhere on Earth. Bacteria and archaea are almost always microscopic, while a number of eukaryotes are also microscopic, including most protists, some fungi, as well as some micro-animals and plants. Viruses are generally regarded as not living and therefore not considered as microorganisms, although a subfield of microbiology is virology, the study of viruses.
Microbial population biology
Microbial population biology can (and often does) involve the testing of more-general ecological and evolutionary hypotheses. Again, it is important to retain some emphasis on the microbe since at some point this "question-driven" microbial population biology becomes instead population biology using microorganisms. Because the point of departure of these potentially disparate emphases can be somewhat arbitrary, there exist vague and not universally accepted delimits around what the discipline of microbial population biology does and does not constitute.
World Community Grid
Microbiome Immunity Project (launched August 2017) is a study of proteins in bacteria located in and on the human body; the human microbiome, which is made of around 3 million separate bacterial genes. By learning bacteria genes, their individual shapes can be known, and each physical shape determines the function of bacteria. Collaborative institutions includes the University of California San Diego, Broad Institute of MIT and Harvard, and the Simons Foundation's Flatiron Institute.
Microbiomes of the built environment
Microbiomes of the built environment is a field of inquiry focusing on the study of the communities of microorganisms found in human constructed environments (i.e., the built environment). It is also sometimes referred to as "microbiology of the built environment".
Acanthamoeba
Because "Acanthamoeba" does not differ greatly at the ultrastructural-level from a mammalian cell, it is an attractive model for cell biology studies; it is important in cellular microbiology, environmental biology, physiology, cellular interactions, molecular biology, biochemistry, and evolutionary studies, due to the organisms' versatile roles in the ecosystem and ability to capture prey by phagocytosis, act as vectors and reservoirs for microbial pathogens, and to produce serious human infections. In addition, "Acanthamoeba" has been used extensively to understand the molecular biology of cell motility and cancer cell dormancy by in-depth exploration of the process of encystation.
Veterinary physician
Some veterinary school uses the same biochemistry, histology, and microbiology books as human medicine students; however, the course content is greatly supplemented to include the varied animal diseases and species specific differences. Many veterinarians were trained in pharmacology using the same text books as human physicians. As the specialty of veterinary pharmacology develop, more schools are using pharmacology textbooks written specifically for veterinarians. Veterinary physiology, anatomy, and histology is complex, as physiology often varies among species. Microbiology and virology of animals share the same foundation as human microbiology, but with grossly different disease manifestation and presentations. Epidemiology is focused on herd health and prevention of herd borne diseases, and foreign animal diseases. Pathology, like microbiology and histology, is very diverse and encompasses many species and organ systems. Most veterinary school have courses in small animal and also large animal nutrition, often taken as electives in the clinical years or as part of the core curriculum in the first two years.
Cellular microbiology
Recently, the field of Cellular Microbiology has been expanded to incorporate investigation of the cell biology of microbes themselves. "The field of cellular microbiology is a coalescence of two fields: molecular microbiology and cell biology," said Professor Jacek Hawiger, Chair of Microbiology and Immunology at Vanderbilt University. Particularly in the case of bacterial cells, new technology is starting to be used to reveal a high level of organization within the bacterial cells themselves. For example, high-resolution fluorescence microscopy and atomic force microscopy are both being used to show just how sophisticated bacterial cells are.
Oral ecology
Oral ecology refers to the organisms that live in a mouth. Bacteria in biofilm were first detected under the microscopes of Antony van Leeuwenhoek in the 17th century. Various bacteria and saliva are two of the major components in oral microbiology, having the capability to be harmful, but also performing beneficial and necessary roles in the immune system. Proper oral hygiene aims to control the harmful effects and prevent disease transmission.
Cryobiology
Cryobiology is the branch of biology that studies the effects of low temperatures on living things within Earth's cryosphere or in science. The word cryobiology is derived from the Greek words κρῧος [kryos], "cold", βίος [bios], "life", and λόγος [logos], "word" (hence science). In practice, cryobiology is the study of biological material or systems at temperatures below normal. Materials or systems studied may include proteins, cells, tissues, organs, or whole organisms. Temperatures may range from moderately hypothermic conditions to cryogenic temperatures.
Geobiology
Astrobiology is an interdisciplinary field that uses a combination of geobiological and planetary science data to establish a context for the search for life on other planets. The origin of life from non-living chemistry and geology, or abiogenesis, is a major topic in astrobiology. Even though it is fundamentally an earth-bound concern, and therefore of great geobiological interest, getting at the origin of life necessitates considering what life requires, what, if anything, is special about Earth, what might have changed to allow life to blossom, what constitutes evidence for life, and even what constitutes life itself. These are the same questions that scientists might ask when searching for alien life. In addition, astrobiologists research the possibility of life based on other metabolisms and elements, the survivability of Earth’s organisms on other planets or spacecrafts, planetary and solar system evolution, and space geochemistry.
Human Microbiome Project
Despite the staggering number of microbes in and on the human body, little was known about their roles in human health and disease. Many of the organisms that make up the microbiome have not been successfully cultured, identified, or otherwise characterized. Organisms thought to be found in the human microbiome, however, may generally be categorized as bacteria, members of domain Archaea, yeasts, and single-celled eukaryotes as well as various helminth parasites and viruses, the latter including viruses that infect the cellular microbiome organisms (e.g., bacteriophages). The HMP set out to discover and characterize the human microbiome, emphasizing oral, skin, vaginal, gastrointestinal, and respiratory sites.
The HMP will address some of the most inspiring, vexing and fundamental scientific questions today. Importantly, it also has the potential to break down the artificial barriers between medical microbiology and environmental microbiology. It is hoped that the HMP will not only identify new ways to determine health and predisposition to diseases but also define the parameters needed to design, implement and monitor strategies for intentionally manipulating the human microbiota, to optimize its performance in the context of an individual's physiology.
The HMP has been described as "a logical conceptual and experimental extension of the Human Genome Project." In 2007 the HMP was listed on the NIH Roadmap for Medical Research as one of the "New Pathways to Discovery". Organized characterization of the human microbiome is also being done internationally under the auspices of the International Human Microbiome Consortium. The Canadian Institutes of Health Research, through the CIHR Institute of Infection and Immunity, is leading the Canadian Microbiome Initiative to develop a coordinated and focused research effort to analyze and characterize the microbes that colonize the human body and their potential alteration during chronic disease states.
Geobiology
Microbiology is a broad scientific discipline pertaining to the study of that life which is best viewed under a microscope. It encompasses several fields that are of direct relevance to geobiology, and the tools of microbiology all pertain to geobiology. Environmental microbiology is especially entangled in geobiology since it seeks an understanding of the actual organisms and processes that are relevant in nature, as opposed to the traditional lab-based approach to microbiology. Microbial ecology is similar, but tend to focus more on lab studies and the relationships between organisms within a community, as well as within the ecosystem of their chemical and geological physical environment. Both rely on techniques such as sample collection from diverse environments, metagenomics, DNA sequencing, and statistics.
Microbial cooperation
Although microbes are too small to see with the naked eye, they represent the overwhelming majority of biological diversity, and thus serve as an excellent system to study evolutionary questions. One such topic that scientists have examined in microbes is the evolution of social behaviors, including cooperation. A cooperative interaction benefits a recipient, and is selected for on that basis. In microbial systems, cells belonging to the same taxa have been documented partaking in cooperative interactions to perform a wide range of complex multicellular behaviors such as dispersal, foraging, construction of biofilms, reproduction, chemical warfare, and signaling. This article will outline the various forms of cooperative interactions seen in microbial systems, as well as the benefits that might have driven the evolution of these complex behaviors.
American Society for Microbiology
The American Society for Microbiology (ASM), originally the Society of American Bacteriologists, is a professional organization for scientists who study viruses, bacteria, fungi, algae, and protozoa as well as other aspects of microbiology. Founded in 1899, ASM has grown into the largest life science professional organization in the world. The Society publishes a variety of scientific journals, textbooks, and other educational materials related to microbiology and infectious diseases. Additionally, ASM organizes several large annual meetings, as well as workshops and professional development opportunities for its members.
Food microbiology
Food microbiology is the study of the microorganisms that inhibit, create, or contaminate food, including the study of microorganisms causing food spoilage, pathogens that may cause disease especially if food is improperly cooked or stored, those used to produce fermented foods such as cheese, yogurt, bread, beer, and wine, and those with other useful roles such as producing probiotics.
Natural science
Modern biology is divided into subdisciplines by the type of organism and by the scale being studied. Molecular biology is the study of the fundamental chemistry of life, while cellular biology is the examination of the cell; the basic building block of all life. At a higher level, anatomy and physiology look at the internal structures, and their functions, of an organism, while ecology looks at how various organisms interrelate.
Jacques Monod
In Monod's studies he discovered that the course work was decades behind the current biological science. He learned from other students a little older than himself, rather than from the faculty. "To George Teissier he owes a preference for quantitative descriptions; André Lwoff initiated him into the potentials of microbiology; to Boris Ephrussi he owes the discovery of physiological genetics, and to Louis Rapkine the concept that only chemical and molecular descriptions could provide a complete interpretation of the function of living organisms."
Metagenomics
The soils in which plants grow are inhabited by microbial communities, with one gram of soil containing around 10-10 microbial cells which comprise about one gigabase of sequence information. The microbial communities which inhabit soils are some of the most complex known to science, and remain poorly understood despite their economic importance. Microbial consortia perform a wide variety of ecosystem services necessary for plant growth, including fixing atmospheric nitrogen, nutrient cycling, disease suppression, and sequester iron and other metals. Functional metagenomics strategies are being used to explore the interactions between plants and microbes through cultivation-independent study of these microbial communities. By allowing insights into the role of previously uncultivated or rare community members in nutrient cycling and the promotion of plant growth, metagenomic approaches can contribute to improved disease detection in crops and livestock and the adaptation of enhanced farming practices which improve crop health by harnessing the relationship between microbes and plants.
Microbiomes of the built environment
Many methods are used to study microbes in built environment. A review of such methods are some of the challenges in using them was published by NIST. Hoisington et al. in 2015 reviewed methods that could be used by building professionals to study the microbiology of the built environment. Methods used in the study of microbes in the built environment include culturing (with subsequent studies of the cultured microbes), microscopy, air, water and surface sampling, chemical analyses, and culture independent DNA studies such as ribosomal RNA gene PCR and metagenomics.There are a growing number of research projects and groups focusing directly or indirectly on microbiomes of the built environment. Some of these are targeted towards specific environments (e.g., homes, hospitals, showerheads) and others are broader (e.g., BIMERC, the BioBE Center). More detail about some of these projects is below.
Petroleum microbiology
Petroleum microbiology is a branch of microbiology that deals with the study of microorganisms that can metabolize or alter crude or refined petroleum products. These microorganisms, also called hydrocarbonoclastic microorganisms, can degrade hydrocarbons and, include a wide distribution of bacteria, methanogenic archaea, and some fungi. Not all hydrocarbonoclasic microbes depend on hydrocarbons to survive, but instead may use petroleum products as alternative carbon and energy sources. Interest in this field is growing due to the increasing role of bioremediation in oil spill cleanup.
Geomicrobiology
Geomicrobiology is the scientific field at the intersection of geology and microbiology. It concerns the effect of microbes on geological and geochemical processes and vice versa. Such interactions occur in the geosphere (rocks, minerals, soils, and sediments), the atmosphere and the hydrosphere. Applications include aquifers and public drinking water supplies.
Geobiology
Geobiological research synthesizes the geologic record with modern biologic studies. It deals with process - how organisms affect the Earth and vice versa - as well as history - how the Earth and life have changed together. Much research is grounded in the search for fundamental understanding, but geobiology can also be applied, as in the case of microbes that clean up oil spills.
Bacteriology
Bacteriology is the branch and specialty of biology that studies the morphology, ecology, genetics and biochemistry of bacteria as well as many other aspects related to them. This subdivision of microbiology involves the identification, classification, and characterization of bacterial species. Because of the similarity of thinking and working with microorganisms other than bacteria, such as protozoa, fungi, and viruses, there has been a tendency for the field of bacteriology to extend as microbiology. The terms were formerly often used interchangeably. However, bacteriology can be classified as a distinct science.
Molecular virology
Molecular virology is the study of viruses on a molecular level. Viruses are submicroscopic parasites that replicate inside host cells. They are able to successfully infect and parasitize all kinds of life forms- from microorganisms to plants and animals- and as a result viruses have more biological diversity than the rest of the bacterial, plant, and animal kingdoms combined. Studying this diversity is the key to a better understanding of how viruses interact with their hosts, replicate inside them, and cause diseases.
Biology
Biology began to quickly develop and grow with Anton van Leeuwenhoek's dramatic improvement of the microscope. It was then that scholars discovered spermatozoa, bacteria, infusoria and the diversity of microscopic life. Investigations by Jan Swammerdam led to new interest in entomology and helped to develop the basic techniques of microscopic dissection and staining.
Food science
Food microbiology is the study of the microorganisms that inhabit, create, or contaminate food, including the study of microorganisms causing food spoilage. "Good" bacteria, however, such as probiotics, are becoming increasingly important in food science. In addition, microorganisms are essential for the production of foods such as cheese, yogurt, bread, beer, wine and, other fermented foods.
Human microbiota
The problem of elucidating the human microbiome is essentially identifying the members of a microbial community which includes bacteria, eukaryotes, and viruses. This is done primarily using DNA-based studies, though RNA, protein and metabolite based studies are also performed. DNA-based microbiome studies typically can be categorized as either targeted amplicon studies or more recently shotgun metagenomic studies. The former focuses on specific known marker genes and is primarily informative taxonomically, while the latter is an entire metagenomic approach which can also be used to study the functional potential of the community. One of the challenges that is present in human microbiome studies, but not in other metagenomic studies is to avoid including the host DNA in the study.
Marine biology
The marine ecosystem is large, and thus there are many sub-fields of marine biology. Most involve studying specializations of particular animal groups, such as phycology, invertebrate zoology and ichthyology. Other subfields study the physical effects of continual immersion in sea water and the ocean in general, adaptation to a salty environment, and the effects of changing various oceanic properties on marine life. A subfield of marine biology studies the relationships between oceans and ocean life, and global warming and environmental issues (such as carbon dioxide displacement). Recent marine biotechnology has focused largely on marine biomolecules, especially proteins, that may have uses in medicine or engineering. Marine environments are the home to many exotic biological materials that may inspire biomimetic materials.
Isolation (microbiology)
In microbiology, the term isolation refers to the separation of a strain from a natural, mixed population of living microbes, as present in the environment, for example in water or soil flora, or from living beings with skin flora, oral flora or gut flora, in order to identify the microbe(s) of interest. Historically, the laboratory techniques of isolation first developed in the field of bacteriology and parasitology (during the 19th century), before those in virology during the 20th century. Methods of microbial isolation have drastically changed over the past 50 years, from a labor perspective with increasing mechanization, and in regard to the technology involved, and hence speed and accuracy.
Zoology
Cell biology studies the structural and physiological properties of cells, including their behavior, interactions, and environment. This is done on both the microscopic and molecular levels, for single-celled organisms such as bacteria as well as the specialized cells in multicellular organisms such as humans. Understanding the structure and function of cells is fundamental to all of the biological sciences. The similarities and differences between cell types are particularly relevant to molecular biology.
Minibeast
The study of minibeasts is common as part of the primary school curriculum. Studying minibeasts is a very effective way to observe many biological concepts first hand, which is not possible with many larger animals. Life cycles, food chains, and bodily structure and function are just some of the basic elements of biological science which can be easily explained using minibeasts. "Bugs Alive!" at Melbourne Museum features a huge number of live minibeasts with detailed information about them, while services such as "Minibeast Wildlife" and "Travelbugs" take live minibeast to school and provide educational resources.
State microbe
In April 2018, Dr Jeffrey Boyd spoke to students and teachers at the Bartle Elementary School in Highland Park, firing up their enthusiasm for microbial life in general and "S. griseus" in particular. The students were taught about microbiology, antibiotics, the interaction of science and public service, and how to contact their state legislators. In May, John Warhol introduced the topic of microbiology and the State Microbe to students at the Indian Hill School in Holmdel.
Biology
The next larger scale, cell biology, studies the structural and physiological properties of cells, including their internal behavior, interactions with other cells, and with their environment. This is done on both the microscopic and molecular levels, for unicellular organisms such as bacteria, as well as the specialized cells of multicellular organisms such as humans. Understanding the structure and function of cells is fundamental to all of the biological sciences. The similarities and differences between cell types are particularly relevant to molecular biology.
History of biology
Like biochemistry, the overlapping disciplines of bacteriology and virology (later combined as "microbiology"), situated between science and medicine, developed rapidly in the early 20th century. Félix d'Herelle's isolation of bacteriophage during World War I initiated a long line of research focused on phage viruses and the bacteria they infect.
Aerobiology
Aerobiology (from Greek ἀήρ, "aēr", "air"; βίος, "bios", "life"; and -λογία, "-logia") is a branch of biology that studies organic particles, such as bacteria, fungal spores, very small insects, pollen grains and viruses, which are passively transported by the air. Aerobiologists have traditionally been involved in the measurement and reporting of airborne pollen and fungal spores as a service to allergy sufferers.
Center for Microbial Oceanography: Research and Education
It has been said that more is known about the surface of the moon than about the Earth’s oceans. C-MORE was designed to explore the largely unknown world of microorganisms in the sea and to educate the public and other scientists about these organisms. The motto of the center is “From genomes to biomes” meaning that the researchers want to look at how the diversity of microbes in the ocean influences the structure and function of the world’s largest biome, the ocean.
Microbiota
A microbiota is an "ecological community of commensal, symbiotic and pathogenic microorganisms" found in and on all multicellular organisms studied to date from plants to animals. A microbiota includes bacteria, archaea, protists, fungi and viruses. Microbiota have been found to be crucial for immunologic, hormonal and metabolic homeostasis of their host.
The synonymous term microbiome describes either the collective genomes of the microorganisms that reside in an environmental niche or the microorganisms themselves.
International Society for Microbial Ecology
The new methods and techniques were proved to be successful for the analysis of microbial community in various fields, soil and water microbiology, food preservation and fermentation, and medical microbiology. The microbiologists working in different fields quickly became aware of the unified concept, microbial ecology. The work of T. Brock "Principles of Microbial Ecology" in 1964) gave a profound impact to the further development of microbial ecology in various countries.
Geobiology
Geobiology employs molecular biology, environmental microbiology, chemical analyses, and the geologic record to investigate the evolutionary interconnectedness of life and Earth. It attempts to understand how the Earth has changed since the origin of life and what it might have been like along the way. Some definitions of geobiology even push the boundaries of this time frame - to understanding the origin of life and to the role that man has played and will continue to play in shaping the Earth in the Anthropocene.
Flora (microbiology)
Bacterial flora is a community of bacteria that exists on or in the body, and possesses a unique ecological relationship with the host. Bacterial flora encompasses a wide variety microorganisms, and the interactions between microbes and host creates a mutualistic relationship that both entities benefit from. Humans, for example, provide a diversified ecosystem for a large variety of microbes. An average human adds 37 million bacteria to the air an hour in a given space. The mutualistic relationship has a significant impact on the host, and is thought to influence human traits such as obesity. In 2008, the National Institutes of Health started the Human Microbiome Project designed to help understand the health implications of human bacterial flora. Biologists believe that bacterial flora may play some role in disorders such as multiple sclerosis. Additionally, the study of flora can have industrial benefits such as dietary supplements like probiotics. The living microorganisms in probiotics are believed to have positive effects on health, and have been utilized in studies regarding gastrointestinal diseases and allergies.
Chemical ecology
Plants interact also with micro-organisms. For this to become possible the microbes have to establish an interface between them and the plant, by growing into the plant through its surface. To do so, the microbes need to break the protective hydrophobic waxy layer on the plant’s surface. To do this, the micro-organisms secrete special fluids which break down the fats from the cuticle.
Macrobiology
Macrobiology is the branch of biology that studies large living organisms (termed Macro organisms) that can be seen by the naked eye. Macrobiology is the opposite of Microbiology.
Soil microbiology
Soil microbiology is the study of microorganisms in soil, their functions, and how they affect soil properties. It is believed that between two and four billion years ago, the first ancient bacteria and microorganisms came about on Earth's oceans. These bacteria could fix nitrogen, in time multiplied, and as a result released oxygen into the atmosphere. This led to more advanced microorganisms, which are important because they affect soil structure and fertility. Soil microorganisms can be classified as bacteria, actinomycetes, fungi, algae and protozoa. Each of these groups has characteristics that define them and their functions in soil.
Marine life
In contemporary times, marine life is a field of study both in marine biology and in biological oceanography. In biology many phyla, families and genera have some species that live in the sea and others that live on land. Marine biology classifies species based on the environment rather than on taxonomy. For this reason marine biology encompasses not only organisms that live only in a marine environment, but also other organisms whose lives revolve around the sea. Biological oceanography is the study of how organisms affect and are affected by the physics, chemistry, and geology of the oceanographic system. Biological oceanography mostly focuses on the microorganisms within the ocean; looking at how they are affected by their environment and how that affects larger marine creatures and their ecosystem. Biological oceanography is similar to marine biology, but is different because of the perspective used to study the ocean. Biological oceanography takes a bottom up approach (in terms of the food web), while marine biology studies the ocean from a top down perspective. Biological oceanography mainly focuses on the ecosystem of the ocean with an emphasis on plankton: their diversity (morphology, nutritional sources, motility, and metabolism); their productivity and how that plays a role in the global carbon cycle; and their distribution (predation and life cycle). Biological oceanography also investigates the role of microbes in food webs, and how humans impact the ecosystems in the oceans.
Agricultural microbiology
Agricultural microbiology is a branch of microbiology dealing with plant-associated microbes and plant and animal diseases. It also deals with the microbiology of soil fertility, such as microbial degradation of organic matter and soil nutrient transformations.
Done by Alpha B S Conteh of Njala University.
Medical microbiology
Medical microbiology is not only about diagnosing and treating disease, it also involves the study of beneficial microbes. Microbes have been shown to be helpful in combating infectious disease and promoting health. Treatments can be developed from microbes, as demonstrated by Alexander Fleming's discovery of penicillin as well as the development of new antibiotics from the bacterial genus Streptomyces among many others. Not only are microorganisms a source of antibiotics but some may also act as probiotics to provide health benefits to the host, such as providing better gastrointestinal health or inhibiting pathogens.
Microbiologist
Entry-level microbiology jobs generally require at least a bachelor's degree in microbiology or a related field. These degree programs frequently include courses in chemistry, physics, statistics, biochemistry, and genetics, followed by more specialized courses in sub-fields of interest. Many of these courses have laboratory components to teach trainees basic and specialized laboratory skills.
Bruce Rittmann
Originally working in cooperation with Dr. David Stahl, Rittmann introduced the powerful tools of molecular biology to environmental engineering, helping create the exciting field known today as Environmental Biotechnology, in which the goal is to manage microbial communities so that they provide services to society. The tools of molecular microbial ecology directly interrogate the genetic information in microorganisms. They make it possible to determine what types of microorganisms are present in the complex communities of environmental biotechnologies, what reactions those microorganisms can carry out, what reactions they are carrying out, and how they interact with each other and their environment. Now working hand-in-glove with Center colleague Dr. Rosa Krajmalnik-Brown, Rittmann is using molecular microbial ecology to understand and manage microbial communities in a wide range of microbiological processes used for removing pollution from water, generating renewable resources, and improving human health.
Microbial ecology
While microbes have been studied since the seventeenth-century, this research was from a primarily physiological perspective rather than an ecological one. For instance, Louis Pasteur and his disciples were interested in the problem of microbial distribution both on land and in the ocean. 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. 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.
Biology
Biology is the natural science that studies life and living organisms, including their physical structure, chemical processes, molecular interactions, physiological mechanisms, development and evolution. Despite the complexity of the science, there are certain unifying concepts that consolidate it into a single, coherent field. Biology recognizes the cell as the basic unit of life, genes as the basic unit of heredity, and evolution as the engine that propels the creation and extinction of species. Living organisms are open systems that survive by transforming energy and decreasing their local entropy to maintain a stable and vital condition defined as homeostasis.
Food and biological process engineering
Creating, processing, and storing food to support the world's population requires extensive interdisciplinary knowledge. Notably, there are many biological engineering processes within food engineering to manipulate the multitude of organisms involved in our complex food chain. Food safety in particular requires biological study to understand the microorganisms involved and how they affect humans. However, other aspects of food engineering, such as food storage and processing, also require extensive biological knowledge of both the food and the microorganisms that inhabit it. This food microbiology and biology knowledge becomes biological engineering when systems and processes are created to maintain desirable food properties and microorganisms while providing mechanisms for eliminating the unfavorable or dangerous ones.
Aerobiological engineering
Since healthcare facilities can house a number of different types of patients who potentially have weakened immune systems, aerobiological engineering is of significant importance to engineers of hospitals. The aerobiology that concerns designers of hospitals includes viruses, bacteria, fungi, and other microbiological products such as endotoxins, mycotoxins, and microbial volatile organic compounds (MVOC's). Bacteria and viruses, because of their small size, readily become airborne as bacterial aerosols and can remain suspended in the air for hours. Because of this, adequate precautions and mitigation techniques need to be taken with indoor air quality in hospitals dealing with infectious diseases.
Center for Microbial Oceanography: Research and Education
C-MORE scientists want to understand biological processes that begin at microscopic scales and are expressed in vitally significant issues such as climate change. Areas of research range from genomic surveys, to studies of the genetic basis of marine microbial biogeochemistry to building ecosystem models. One of the strengths of the Center is its seagoing capability, as well as the long term studies that have been conducted by the Hawaii Ocean Time-series (HOT) Program in the North Pacific Subtropical Gyre. In addition to extensive laboratory experimentation, C-MORE also stages cruises to examine marine microbes in their environment. One example was the SUPER HI-CAT cruise, which was the first effort to study the microbiology associated with the plastic particles in the Great Pacific Garbage Patch.
Medical microbiology
Epidemiology, the study of the patterns, causes, and effects of health and disease conditions in populations, is an important part of medical microbiology, although the clinical aspect of the field primarily focuses on the presence and growth of microbial infections in individuals, their effects on the human body, and the methods of treating those infections. In this respect the entire field, as an applied science, can be conceptually subdivided into academic and clinical subspecialties, although in reality there is a fluid continuum between public health microbiology and clinical microbiology, just as the state of the art in clinical laboratories depends on continual improvements in academic medicine and research laboratories.
Cryobiology
At least six major areas of cryobiology can be identified: 1) study of cold-adaptation of microorganisms, plants (cold hardiness), and animals, both invertebrates and vertebrates (including hibernation), 2) cryopreservation of cells, tissues, gametes, and embryos of animal and human origin for (medical) purposes of long-term storage by cooling to temperatures below the freezing point of water. This usually requires the addition of substances which protect the cells during freezing and thawing (cryoprotectants), 3) preservation of organs under hypothermic conditions for transplantation, 4) lyophilization (freeze-drying) of pharmaceuticals, 5) cryosurgery, a (minimally) invasive approach for the destruction of unhealthy tissue using cryogenic gases/fluids, and 6) physics of supercooling, ice nucleation/growth and mechanical engineering aspects of heat transfer during cooling and warming, as applied to biological systems. Cryobiology would include cryonics, the low temperature preservation of humans and mammals with the intention of future revival, although this is not part of mainstream cryobiology, depending heavily on speculative technology yet to be invented. Several of these areas of study rely on cryogenics, the branch of physics and engineering that studies the production and use of very low temperatures
Arnold Demain
The work done under Demain's direction in Rahway has been described in "Microbiology Australia" as “remarkable” in its “level of innovation,” in that it identified “novel biochemical pathways” that improved “natural levels of production” several thousandfold. Demain himself has said that thanks to Merck, “I learned early in my career that there was a lot more to applied microbiology than pickles and sauerkraut, and that microbes could be used to make antibiotics, produce commercial enzymes, convert steroids to be used for arthritis and rheumatism, make amino acids and vitamins for human and animal nutrition, and make many medicinals for human and animal health.”
Astro microbiology
Modern technology has already allowed us to use microbes to assist us in extracting materials on Earth, including over 25% of the our current copper supply. Similarly, microbes could help serve a similar purpose on other planets to mine resources, extract useful materials, or create self-sustaining reactors. The most promising of these candidates known to date is cyanobacteria. Billions of years ago, cyanobacteria originally helped us create a habitable Earth by pumping oxygen into the atmosphere, and manage to exist in the darkest corners of the Earth. Cyanobacteria, along with some other rock-eating microbes, seem to be able to withstand the harsh conditions of the vacuum of space without much effort. On Mars, however, cyanobacteria will not even have to endure such harsh conditions.
Forensic biology
“Post-mortem microbiology (PMM) aims to detect unexpected infections causing sudden deaths; confirm clinically suspected but unproven infection; evaluate the efficacy of antimicrobial therapy; identify emergent pathogens; and recognize medical errors. Additionally, the analysis of the thanatomicrobiome may help to estimate the post-mortem interval.”. There is currently an extensive amount of research being performed, most notably using the famous “body farms” throughout the United States, to determine if there is a consistent microbial decomposition “clock” that could be used by itself, or in conjunction with other techniques (such as forensic entomology) to help estimate postmortem intervals. One such group has made extensive headway into describing such a microbial clock, and “believes she’s within two to five years of testing her clock in a real crime scene scenario”. However, if a reliable and consistent microbial clock is determined to exist, “it’s too soon to know whether the microbial clock will pass scientific and legal muster,” (Beans) and “a judge would also have to determine that the microbial clock meets the standard for admission of expert testimony”.
Microbial population biology
Microbial population biology can include aspects of molecular evolution or phylogenetics. Strictly, however, these emphases should be employed toward understanding issues of microbial evolution and ecology rather than as a means of understanding more universal truths applicable to both microscopic and macroscopic organisms. The microorganisms in such endeavors consequently should be recognized as organisms rather than simply as molecular or evolutionary reductionist model systems. Thus, the study of RNA "in vitro" evolution is not microbial population biology and nor is the "in silico" generation of phylogenies of otherwise non-microbial sequences, even if aspects of either may in some (especially unintentional) manner be analogous to evolution in actual microbial populations.