Microbiology — Textbook Reader

Acquiring an antibiotic-resistant infection or “superbug” is one of medicine’s biggest nightmares. What can medical practitioners do to treat the patient? Besides drugs, viruses known as bacteriophages have been recruited to specifically target and kill bacteria.

Despite microbiologists’ tinkering with using bacteriophages as antimicrobials for decades, their actual application in medicine has been minimal. However, the emergence of antibiotic resistance has led to renewed focus on using these tiny microbes as therapeutic agents. The photo above shows Ella Balasa (right side of photo), a microbiologist who has cystic fibrosis. Cystic fibrosis is a genetic disease that results in a buildup of thick mucus in the lungs. This mucus allows bacteria to flourish in the lungs, which results in infections and subsequent lung damage that can be fatal. Ella had b…

Mammoth Hot Springs (MHS) in Yellowstone National Park (USA) displays many geochemical traits similar to those on Mars. Because of this, geomicrobiologists study these hot, oxygen-limited and sulfur-rich springs for microbial fossils whose fingerprints of life (biomarkers) could be used to detect life on other planets. The photo on the left shows filamentous microbial mats from MHS that resemble fettuccine pasta as a result of mineral encrustation. Tens of centimeters long, these streamers contain extremophilic microbes that entomb themselves in 5 millimeters of travertine (calcium carbonate) …

Using a combination of geochemical measurements, microscopy, and metagenomic, metatranscriptomic, and metaproteomic approaches, scientists have unraveled many of the mysteries surrounding the MHS streamers. These mats are dominated by the thermophilic, chemolithotrophic bacterium Sulfurihydrogenibium yellowstonense, which uses CO2 and reduced sulfur as carbon and energy sources, respectively. Multi-omic data sets indicate that these remarkable cells produce pili as well as extracellular polymeric substances to latch onto one another and form streamers in the fast-moving spring water. Once th…

A membrane-bound nucleus is a defining feature of eukaryotic cells that differentiates them from their prokaryotic counterparts. Remarkably, molecular biologists have discovered a group of large Pseudomonas bacteriophages whose genomes encode structures resembling the eukaryotic nucleus and mitotic spindle. The obvious question is why, and to understand these remarkable events, scientists needed to understand the roles of both eukaryotic-like structures.

Using fluorescent labeling and cryo-electron microscopy, it was determined that the phage-encoded nucleus contains enzymes specific for replicating and transcribing phage DNA. Once empty phage capsids are assembled at the host membrane, they move rapidly toward the phage nucleus to be filled with phage DNA. The top photo shows a cryo-tomogram slice of a Pseudomonas chlororaphis cell infected with the phage 201ϕ2-1 (phage virions are about 0.1 μm in diameter), and the bottom image highlights the following structures in color: nucleus-like structure (blue), capsids (light yellow), phage tails …

Antarctica is one of the harshest environments on Earth, experiencing extremely cold temperatures, high levels of ultraviolet radiation, and limited availability of carbon, nitrogen, and water. Even so, rocky desert Antarctic soils (photo) support microbial communities whose diversity rivals that of temperate soils. Cyanobacteria fix enough carbon dioxide (CO2) to support heterotrophic communities in many soils of Antarctica. However, the virtual absence of cyanobacteria in some other Antarctic soils raises the question of what energy source (other than light) sustains these microbial communit…

Researchers combined metagenomics with biochemical measurements to probe this mystery. The first hint was the discovery of Calvin cycle genes for CO2 fixation in Actinobacteria that composed about half of the total soil microbiota (the Calvin cycle is a major autotrophic pathway). Since these Actinobacteria are not phototrophic, CO2 fixation—which requires ATP—had to be supported by energy sources other than sunlight. The answer again emerged from metagenomics by identifying genes in the Actinobacteria encoding aerobic respiration of molecular hydrogen (H2) and carbon monoxide (CO) and t…

Carbon dioxide (CO2) released from the burning of fossil fuels is contributing to global warming and ocean acidification. Although all ecosystems will ultimately be impacted by this, coral reef ecosystems are particularly sensitive. About a quarter of the oceans’ coral reefs have already been lost to thermal stress and pollution, and ongoing acidification is impairing their formation of calcium carbonate skeletons. Although occupying less than 1% of the ocean floor, coral reefs support about one-quarter of all marine species that provide food for millions of people. Thus it is essential that w…

In an experimental study of adding CO2 to ocean waters bathing a natural coral reef ecosystem, it was clear that even a minor reduction in pH greatly reduces the rate of biogenic calcification. This study, performed at a section of the Great Barrier Reef (Australia), used tidal flow from an upper to a lower lagoon to adjust the pH of water bathing the lower section of reef. A 4000-gallon floating tank of seawater was first acidified by bubbling with CO2 and then pumped from the edge of the upper lagoon during tidal change, reducing the pH in the lower lagoon from ambient pH (8.13) to a treatme…