What are algae and why study them?     "Algae" refers to a diverse group of protists (structurally simple eukaryotes = organisms whose cells contain a nucleus and other internal structures surrounded by membranes).  Most, but not all, are photosynthetic, producing their own organic material from sunlight, CO2 and mineral nutrients.  Algal species range from tiny single cells to the plant-like kelps, which may reach tens of meters in length.  Most algae that live in extreme environments are small, often single-celled species.  What are often erroneously called "blue-green algae" are actually cyanobacteria, a type of photosynthetic bacteria (see below).     Algae and cyanobacteria are important primary producers (base of the food chain) in freshwater and marine ecosystems.  They perform an ecological role similar to plants in terrestrial (land) ecosystems.  Without algae, there could be little animal life in aquatic habitats.  Sometimes algae also become a nuisance, as when your neighborhood pond turns green, or a red tide occurs in the coastal ocean.  In both cases the probable cause is eutrophication: excess nutrient (nitrogen and/or phosphorus) input, largely from human sources such as farm, lawn and golf course fertilizers, and human and livestock sewage.

What are Bacteria and why study them?     The domain Bacteria includes prokaryotes, whose cells lack a nucleus or other internal structures surrounded by membranes.  Cyanobacteria are a class of photosynthetic bacteria.  Although some bacteria cause disease in  humans, plants and animals, most species are probably free-living (not parasites), and thus harmless.  Bacteria are critical for the proper functioning of ecosystems because they decompose dead organisms and thereby recycle organic material back into mineral nutrients.

What are Archaea and why study them?      The domain Archaea, like Bacteria, includes prokaryotes.  Although they look superficially the same, Bacteria and Archaea differ in some major genetic and biochemical ways.  In fact, the genetic differences between these two domains is greater than between all organisms within the domain Eukarya (protists, fungi, plants, animals).  In other words, you may have more in common genetically with a mushroom than do bacteria and archaea!  Archaea were discovered and recognized as a distinct domain of life only within the last couple decades.  They tend to be extremophiles, but more are being discovered from all sorts of habitats in recent years.  They probably fill ecological roles similar to bacteria.

What are Bacteriophages and why study them?     Bacteriophages (or just phages) are viruses that survive by infecting bacteria.  Phages take over the bacterial host's enzymes and metabolism to make many copies of the virus.  In the process, the phages often pick up one or more bacterial genes which may be transferred to other bacteria, a genetic exchange mechanism called transduction.

What are extremophiles?      Extremophiles are organisms (life forms), often microbes (bacteria, archaea, algae) that live in habitats where one or more environmental conditions are far beyond the range tolerated by most organisms on Earth.  For example, this may include extreme heat (thermophiles), cold (psychrophiles), pH (acidophiles or alkaliphiles), ultraviolet radiation, dryness, salt (halophiles), or toxic chemicals.  It also may include wide fluctuations in one or more of these conditions, even if the average condition is not particularly extreme.  At the SPMO, we study primarily halophiles.

 

Why study extremophiles? It is useful to study extremophiles for several reasons: They help us to understand the process of evolution, that is, how organisms adapt to their environment and become reproductively/genetically isolated from similar organisms. They provide models for early life on Earth and how and where we might search for life on other planets. They often have unusual physiological and metabolic properties, such as enzymes that can be used in industrial processes under harsh physical or chemical conditions.

How and why do we isolate microbes? Although modern molecular biology techniques can give us a broad perspective on which types of microbes are present in a given sample, that information alone does not necessarily tell us much about the physiological properties of those organisms.  To obtain such information, microbes must be isolated in pure living cultures and then studied in laboratory experiments.  There are various methods used to isolate microbes, involving either liquid media (a water solution of various nutrients) or solid media (basically the same as liquid, but with agar added as an inert gelling agent).  Physical/chemical conditions (temperature, light, salt concentration, pH, etc.) and which nutrients to add, and in what concentrations, are critical to successful isolation.  Of course, different organisms prefer different physical/chemical conditions and types and amounts of nutrients, so it is best to try a wide variety of media and conditions.  In fact, current dogma is that most bacteria present in nature have never been successfully cultivated, perhaps because standard culture media and procedures are designed for biomedical study of human pathogens, but most bacteria don't live under those conditions.  Also, some bacteria from nature may have unknown chemical needs or limited tolerances.  For example they may prefer very low nutrient concentrations, whereas standard media recipes use extremely high concentrations.  As for techniques: To isolate Bacteria and Archaea, a sample of soil or water may be added to sterile liquid medium containing organic compounds (e.g. sugars) that many/most known microbes can live on as an energy source.  Once the bacteria reach a high enough density, a sample of this crude culture, which may contain numerous species, may be "streaked" (smeared) onto sterile agar plates, such that individual cells can grow separately into discrete "colonies".  By repeating this procedure several times, we can ultimately get a colony of a single species that can be studied separately from all others. The procedures for algae and cyanobacteria are much the same, except that these are photosynthetic organisms that require light rather than organic compounds as their energy source.  See photos on the "Activities" link at left.

 

How do we know what organisms we have isolated? Once microbes are isolated, there are various ways to identify them and to determine if they are "new" to science or essentially the same as previously known species.  The methods depend on which group of microbes one is working with.  Bacteria and Archaea are tiny, so all one can tell in a light microscope is their shape (rods, spheres) and if they are motile (can move) with flagella.  Bacteria also can be stained to determine if they fall into one of two major groups based on cell wall chemistry: Gram positive (absorbs stain) or Gram negative (doesn't absorb stain).  Even without a microscope, they can be characterized by the shape and color of colonies they form on agar plates.  Further traditional methods for classifying Bacteria/Archaea involve a series of biochemical tests to determine what specific chemicals they can use for "food" (sugars, amino acids, etc.) and to which antibiotics they are sensitive/resistant.  Cyanobacteria and algae are larger than Bacteria/Archaea, so they often can be identified to genus (and sometimes to species, depending on the expertise of the individual) by their shape, size and cell appearance using a light microscope at magnifications of 100 to 1000X.  Various identification keys are available for this purpose.  Some key visible characteristics include whether cells are solitary, colonial or filamentous; absence/presence/number of flagella; color; number of chloroplasts (subcellular structures containing the green pigment chlorophyll and responsible for photosynthesis) present per cell; presence/absence of starch grains and/or pyrenoids (protein structures possibly related to photosynthesis) inside chloroplasts; how cells divide and reproduce sexually; etc.  One can also do various tests to determine which photosynthetic pigments (light-absorbing colored compounds), cell wall chemicals, and carbohydrate storage compounds they possess, all of which are evolutionarily conservative (present in virtually all members of a given class of algae).  The modern way to quickly classify microbes of all types is to extract and "digest" (with enzymes) their DNA (genetic material), then "amplify" it - make millions of copies of a selected gene (functional unit of genetic information) by a process called PCR (polymerase chain reaction).  (This is the same procedure crime labs use to identify human DNA.)  The gene is then "sequenced" by an automated machine, that is, the order of its individual nucleotides (the four basic structural units of DNA abbreviated as A, T, C and G);  usually the gene will have >1000 nucleotides, so there is a good chance of detecting at least one difference between closely related organisms.  So, for example, the corresponding sections of two related species might be ...AACTGCCCG... vs. ...AACTGCGCG...  The specific gene(s) used for this purpose is arbitrary and sometimes disputed among specialists, but to make it useful there are standard genes that most scientists use for this purpose.  The goal is to use gene(s) that are sufficiently variable (due to natural genetic mutations that accumulate over evolutionary time) to be able to distinguish closely related organisms (say species within a genus), but not so variable that the sequences show little similarity even between close relatives.  Think of it like doing "compare documents" in a word processing program to check for small differences in spelling or sentence organization.  Most commonly, we use the "16S rRNA" gene for prokaryotes and the "18S rRNA" gene for eukaryotes, and there are thousands of such sequences available on the internet through GenBank.  So, by "blasting" (searching) through all of the sequences of a particular gene in GenBank, one can look for exact or close matches to a known organism.  One can also use statistical programs to create a "phylogenetic tree" showing the similarity among a group of organisms, interpreted as indicating evolutionary relatedness.  Organisms in the same "clade" (branch of the phylogenetic tree) are more closely related to each other than to organisms in other clades.

 

How do we know whether the organisms we have isolated are representative of those present in nature? Microbes isolated in culture from soil or water samples in principle could be contaminants from the laboratory, although the great care taken in the isolation process makes this a relatively infrequent problem.  If one isolates a bacterium whose properties and sequence indicates that it is a common occupant of human skin, it is probably safe to assume that it is a contaminant.  Of greater scientific concern is whether the microbes isolated are really an accurate representation of the types of microbes present in the native environment.  In many cases this is NOT the case, because we can only employ a limited number of culture media and conditions, which are certainly not equally favorable for all microbes.  This biases the isolates toward microbes that grow quickly under laboratory conditions.  To determine just how biased the isolates may be, one can use various types of culture-independent molecular methods to probe for the presence of uncultured organisms directly in field samples.  One such method is to construct a "clone library", i.e. a collection of (supposedly) all the types of a particular marker gene (e.g. 16/18S rRNA gene) present in the sample(s).  These gene sequences can be used to construct a phylogenetic tree, just as we do with the genes of culture isolates.  If the sequences match (or are very closely related to) those of culture isolates, we're doing pretty well.  When many "library" sequences don't have close matches in the culture isolates, we're obviously not doing a thorough job of isolating all the microbes present.  One can then try to devise procedures to isolate those types of microbes previously missed.  Clone libraries also sometimes reveal "deeply branching" sequences, that is, microbes that have no known close relative.  These are especially exciting as they may represent microbes that are entirely new to science and may have interesting or useful properties, or may fill a previously unknown ecological role.  However, even such molecular probing may be somewhat biased, because not all microbes' DNA is equally extracted and amplified.