Symbioses. Microbiota.
Last revised: Monday, April 14, 2003
Reading: Ch. 25 & 26 in text

Types of Symbiosis

• Symbiosis = "intimate living together" between different species
• Several possible types, ranging from harm to mutual benefit.
• Not clearly separated in nature; relationship may change from beneficial to harmful as environment changes.
  1. Commensalism
     One benefits, one (host) is not obviously affected either positively or negatively
  2. Mutualism
     Both benefit from the association
  3. Parasitism
     One benefits, the other (host) is (potentially) harmed

Some Examples of Microbial Symbioses

• Chlorochromatium aggregatum
• Remarkable symbiosis between two bacteria, so intimate that the two organisms were thought to be 1 species until recently.
• Name comes from aggregates often seen in aquatic communities.
• An example of "Phototrophic Consortia": associations of green sulfur bacteria that surround a central chemotrophic bacterium. Recent evidence suggests that such consortia may be the most common form of green sulfur bacteria in some aquatic systems.
• How does this symbiosis work? One bacterium is found at the center of the consortium, probably a chemotroph that is carrying out anaerobic respiration, using SO₄⁼ as an electron acceptor and producing H₂S as a waste product. This bacterium is surrounded bya cluster of anoxygenic green sulfur phototrophs, that use light as their energy source and H₂S as their reducing source to make NADPH.
• View phase micrograph of a bacterial consortium. A. is a phase contrast photomicrograph of P. roseum, the dominant bacterial community from a German lake. B: Fluorescent in situ hybridization of P. roseum with oligonucleotide GSB-532 [58] which is speci¢c for green sulfur bacteria. C: Transmission electron micrograph of P. roseum demonstrating the regular spatial arrangement of surrounding phototrophs. From "Microbial interactions involving sulfur bacteria: implications for the ecology and evolution of bacterial communities", Overmann and van Gemerden. FEMS Microbiology Reviews 24 (2000) 591-599
• Syntrophy between Bacteria and Archaea
• Syntrophy = metabolic relationship in which two (or more) species living together can utilize a substrate that neither could use by itself.
• Example: Bacterium Syntrophus aciditrophicus grows only on crotonate in pure culture. Archeaon Methanospirillum hungatei needs hydrogen-formate in pure culture. When both organisms are present, a variety of molecules can function as sole substrate, including benzoate, butyrate, etc. Syntrophus produces H₂ which in turn feeds Methanospirillum.
• View micrograph of a bacterial-archaeal consortium. In situ identification of archaea/SRB aggregates with fluorescently labelled rRNA-targeted oligonucleotide probes. The archaea are shown in red, and the SRB in green. From "A marine microbial consortium apparently mediating anaerobic oxidation of methane", 05 October 2000 Nature 407, 623 - 626 (2000).
• Plant-Microbe symbioses
• Many microbes (bacteria, fungi) have important symbioses with plants
• Rhizosphere = thin layer of soil immediately attached to root hairs of plants. Typically contains 10⁹ microbes/g of soil.
• Many rhizosphere organisms are ectosymbionts, living outside the roots. Others are endosymbionts, living inside or penetrating into plant roots.
• Many of these bacteria contribute Nitrogen fixation, obtain plant nutrients in return (see below for Rhizobium symbiosis).
• Rhizobium-Legume symbioses
• Plants of the legume family (soybeans, clover, alfalfa, beans, peas) can grow in soils lacking nitrogen compounds required by other plants. How?
• These plants contain endosymbiotic Rhizobium bacteria that grow in root nodules. Rhizobia can fix atmospheric Nitrogen gas (N₂)
  N₂ + 6[H] 2 NH₃
  
• The reaction requires total lack of oxygen and lots of energy as ATP. To bind oxygen and get rid of it, bacteria use protein called leghemoglobin, somewhat similar to animal hemoglobin. Globin part is encoded in plant genome, heme group is encoded in bacterial genome. Neither partner can fix nitrogen alone, only in symbiosis.
• Hydrothermal vent Communities
• Occurs only near thermal springs on ocean floor, 2 miles or more below surface. Totally black, no sunlight penetrates below 600 feet.
• Associated with spreading centers of tectonic plates where hot magma close to surface causes area of floor to slowly drift apart.
• View diagram of sea floor at spreading junction.
• Seawater seeps down, mixes w/ minerals at high temperature comes back to ocean water in plumes at 270-380 deg. C. These are sometimes called black smokers since minerals precipitate as black cloud when in contact with cold sea water .
• View black smoker.
• See quicktime movie of hydrothermal vent (2 Meg)
• Contains high levels of inorganics: Mn²⁺, H₂, usually H₂S; very low in organic matter
• Astonishing discovery: such regions are densely populated by a community of unusual animals: 2 m long tube worms, giant clams, mussels, white shrimp.
• View image of sea floor in vent community. Notice tube worms.
• View image of tube worm community. Notice tube worms.
• View closeup of tube worms.
• What do they eat? Unlike earth's surface, there is no source of light to stimulate phototrophs.
• Answer: they "eat" chemolithotrophic bacteria!
• Example: Inside the tube worms live huge colonies of bacterial endosymbionts. These are autotrophic chemolithotrophs, oxidizing sulfide to sulfate as their energy source. As bacteria grow, they provide carbon and nitrogen compounds for worms to feed on. Have not been cultivated outside of host, so little is known about details of the bacterium.
• See "The Nemo Explorer for interactive exploration. Also explore Ocean Adventures.
• Ruminant Symbiosis
• Ruminants are the herbivorous mammals whose digestive tract contains four chambers. First chamber (largest) is the rumen, provides a place for bacteria to break down the fiber in the plants so the cow can use it for energy.Ý
• View diagram of rumen
• Includes cows, sheep, giraffes, buffalo, and elk.
• Ruminants eat grasses and other plant materials, but do not produce enzymes to digest cellulose, the primary plant metabolite.
• Instead, ruminants rely on huge microbial community in rumen to digest plant materials. Microbial densities can reach as high as 10¹² microorganisms/ml, the highest density found anywhere in nature.
• Ruminants feed off fermentation waste products of microorganisms; mainly acetic acid, propionic acid, and butyric acid.

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Normal Microbiota of Humans

• Internal body organs (heart, kidney, brain, blood) are usually free of microbes. But surface tissues have extensive populations of microbes, called the microbiota, also known as "normal flora" (term that implies some connection with plants, as contrasted with "normal fauna").
• Microbiota are specialists, able to colonize and survive on human tissue. Each body region has characteristic flora; e.g. many streptocococci inhabit nasopharyngeal cavity, while many enteric bacteria inhabit intestinal tract.
• Optional: For further information: Bacteriology 330 Lecture Topics: Normal Flora, from U. of Wisconsin.

Skin
• Not a great habitat; dries out, constantly being shed, secretions include fatty acids (lower pH to 4-6) and salt.
• Some skin regions better habitats than others: scalp, ears, underarms, anal region are all especially good habitats.
• Bacteria that can grow on skin must be able to survive these conditions.
• Typical bacteria: Propionobacterium acnes. Bacteria can live in sweat glands, hair follicles, so cannot be eliminated by washing skin. P. acnes grows esp. well in skin glands, causes acne when hormone activity in teen years causes overproduction of sebum (fluid secretion).
• Staphylococcus epidermidis, Staph aureus, are found on skin, thrive in nasal region esp. S. aureus is an opportunistic pathogen; rarely causes disease in healthy hosts, but can produce serious infections when skin lesions, burns, or general decrease in resistance occurs. S. aureus also has potent enterotoxin; if bacteria aget into food and grow in substantial numbers, can produce serious food poisoning. S. epidermidis not normally considered a pathogen: however, hospitalized patients may get infection in surgical implants and catheters; the bacteria produce a biofilm that

Mouth
• Saliva contains lysozyme, other enzymes that kill bacteria. Streptococci and Lactobacilli (gram-positive) are comon inhabitants.
• But bacteria thrive attached to teeth, esp in gum margins.
• Strep mutans, other streps secrete gooey polysaccharide ( plaque) that adheres to teeth, provides microhabitat for other bacteria to colonize.
• As food particles accumulate, bacterial growth anaerobic conditions fermentation production of acid wastes tooth decay, a.k.a gingivitis, periodontal disease.

Bacterial Disease Case Study: Dental caries and Streptococcus mutans

Teeth in skulls from Europeans prior to the 1500's showed remarkably well-preserved teeth. Once sucrose, a dissacharide from cane sugar, was introduced into the European diet, teeth deteriorated quickly and tooth decay became a widespread disease. The bacterium Streptococcus mutans (along with S. sobrinus) play an important role. In the process of breaking sucrose down into its component sugars, glucose and fructose, S. mutans polymerizes all the glucose units into a dextran polysaccharide, using the enzyme dextransucrase. Light micrograph of Strep. mutans. From Dr. Timothy Paustian, University of Wisconsin-Madison Since S. mutans uses lactic acid fermentation exclusively as its catabolic pathway, enormous quantities of dextran are produced when sucrose is present. This accumulates as a gooey polysaccharide matrix which initiates the formation of dental plaque. As plaque forms, other bacteria colonize and small food particles are trapped. Rapid bacterial metabolism causes anaerobic environments; lactic and other acids are produced, attacking tooth enamel and causing tooth decay (dental caries). Acids also attack surrounding tissues, producing gingivitis (periodontal disease).

GI tract
• Stomach is highly acidic (pH 2-3), kills most microbes.
• Some bacteria and yeasts can tolerate passage through stomach; few live in stomach.
• Ulcers, long thought to be a "stress disesase", recently shown to be infectious disease, due to Helicobacter pylori. Still not widely known or accepted by medical community.

  Bacterial Disease Case Study: Ulcers & Helicobacter pylori

  For centuries ulcers, a disease in which stomach acids attack the lining of the stomach, were thought to be caused by stress and diet. People afflicted with ulcers were taught to change their diet and reduce stress; in extreme cases surgical removal of the stomach was called for. About 4 million Americans have ulcers in any given year. See the NIH report on ulcers. In the early 1980's, Drs. Barry Marshall and Robin Warren in Australia identified a bacterium Helicobacter pylori in patients with ulcers. The bacterium survives inside the mucus lining of the stomach by neutralizing stomach acids around itself. Marshall and Warren found that antibiotics could be successfully used to treat ulcers. H. pylori is found in almost 1/2 of the human population; even though most don't have ulcers, all have some inflammation of the stomach lining (gastritis). Read more about the discovery of H. pylori in Jack Brown's "Bugs in the News"

• Small intestine has some bacteria, but digestive enzymes kill. As approach colon, find more and more bacteria, esp. Gram-negative Enterobacteria (e.g. E. coli).
• Colon has enormous bacterial population (1/3 of feces is bacteria). Up to 10¹² organisms/gram. Over 300 diff. bacterial species; majority are obligate anaerobes (300x more than facultative anaerobes). E. coli is only 0.1% of total population! Most abundant genus is anaerobic Bacteroides (~ 25% of microbiota)
• Bacteria in colon divide every 12-24 hours on average, much slower than laboratory batch culture rates.
• Major source of food = polysaccharides (least digestible part of human food); cellulose, pectin, lignin, xylan, collectively called "fiber"
• Colon microbes carry out colonic fermentation, produce wastes such as acetate, butyrate, propionate.
• Anaerobic colon pathogens are rare. Clostridium botulinum, cause of botulism, normally does not compete well, even though its endospores can survive passage through stomach. But in infant gut, far fewer microbes present. Infants are most at risk from honey, high level of C. botulinum endospores. Can produce infant botulism, fatal disease in which botulin toxin leads to paralysis.

Genitourinary tract
• Upper tract (kidney, bladder) usually sterile.
• Lower part of urethra gets some bacteria, but frequently "washed out" by urinary flow.
• When washout is reduced, more chances of urinary tract infections. More common in women because urethra is shorter.
• Vagina has complex microbiota. After women start periods, glycogen is secreted, and lactic acid bacteria produce lactic acid, maintain pH ~ 4.5. Most abundant bacteria are Lactobacilli.
• When this is disrupted (e.g. during antibiotic treatment, or if frequent intercourse leaves lots of semen which raise pH), can allow yeasts to grow = "honeymooner's disease".
• Pelvic Inflammatory Disease (PID): normally bacteria are not found in uterus or oviducts, but can pass through cervix (mouth of uterus) on occasion. Microbes normally found in vagina may infect upper female reproductive tract (PID), but uncertain whether microbiota cause the disease or colonize after damage caused by sexually-transmitted pathogens.

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Gnotobiotic Animals

• Gnotobiotic = "known microbiota"; animal host is either entirely free of microbes (aka "germfree", "axenic") or has a microbiota whose identity is completely known.
• Animals in utero are germfree, but acquire resident bacteria within hours of birth.
• Relatively easy to produce germfree animals for birds. Sterilize shell, use sterile incubator, keep animals in an environment where all air, food, water is sterilized before entry.
• More difficult to establish germfree animals other than birds. Need cesarean section of pgrenant females, germfree isolation chambers where all air, food, water is sterilized before entry.
• Germfree animals generally are less healthy than animals with normal microbiota. Defects include:
  1. Greater vitamin requirements for K and B complex
  2. lower cardiac output
  3. much more susceptible to pathogens -- normal microbiota colonize access sites, often compete successfully to prevent pathogens from binding to host tissues.
  4. much smaller infectious dose required to initiate an infection

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