Editors in Conversation

Host: Jeff Fox with special guest, Jon Telling.

Jon Telling of Bristol University in Bristol, United Kingdom talks with Jeff Fox about his findings suggesting that the grinding of glaciers over rocks can liberate hydrogen, which, in turn, drives the growth of methanogens within microbial ecosystems.

Telling and his collaborators provide evidence that the grinding of rocks beneath glaciers can free hydrogen gas from minerals in those rocks. In turn, that hydrogen provides energy to furnish the metabolic needs of particular microorganisms, called methanogens, that produce methane and other organic molecules from carbon dioxide through a non-photosynthetic process.

“This is an important new mechanism for hydrogen production,” says Christopher McKay, senior planetary scientist at the NASA Ames Research Center at Moffett Field, Calif., who was not involved in conducting this research. “Water-water reactions producing hydrogen are usually associated with high temperature systems, and it has been thought that they could not operate at low temperatures. This shows how hydrogen can be produced in an ice-covered system and has huge implications for ice-sealed Antarctic ecosystems such as Lake Vida and for the ice-covered ocean moons of the outer Solar System, Europa and Enceladus.” The research also has important implications for subglacial environments that acted as refuges during the early history of our planet, enabling microorganisms to survive during the Neoproterozoic glaciations, also called Snowball Earth.

This story was featured in the April 2016 issue of Microbe Magazine.

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Host: Jeff Fox with special guests, Øjvind Moestrup, Peter Ulvskov, and Jesper Harholt.

Øjvind Moestrup and Peter Ulvskov, both at the University of Copenhagen and Jesper Harholt at Carlsberg Laboratory, also in Copenhagen, Denmark, talk with Jeff Fox about their hypothesis about terrestrial plants, based on analyses of the cell walls of charophycean green algae.

Moestrup, Peter Ulvskov, and Jesper Harholt thought that something was amiss with our current understanding of the evolutionary development of terrestrial plants after they carefully examined features of the cell walls of charophycean green algae. “Our hypothesis is simple,” they note. “Charophycean green algae ancestors were already living on land and had been doing so for some time before the emergence of land plants.” This new hypothesis takes issue with the widely accepted view that land plants originated from a charophycean green alga. "You have to be patient and sometimes pursue your crazy ideas, even when they differ from the dogmatic thinking in the field," Harholt says. "If you pile up enough evidence, at some point you may realize that you might be correct."

This story was featured in the March 2016 issue of Microbe Magazine.

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Host: Jeff Fox with special guests, Cecil M. Lewis, Jr. and Krithivasan Sankaranarayanan.

Lewis and Krithivasan Sankaranarayanan—“Krithi”-- both from the University of Oklahoma in Norman talk with Jeff Fox about their analyses of the gut microbiomes of American Indians of Cheyenne and Arapaho ancestry.

Lewis, Krithi, and their collaborators learned that the gut microbial taxonomic profiles of these Native Americans are characterized by a reduced abundance of anti-inflammatory bacteria and also that their fecal metabolite profiles are similar to those found in individuals with metabolic disorders. Although this was a random sampling from a generally healthy group of individuals, their gut microbiota suggests that some of them might have health problems brewing below the surface—not a surprise among a population prone to metabolic disorders such as obesity and type 2 diabetes. “For three years, we collaborated with the Cheyenne and Arapaho to discuss these topics and identify common ground for the research process, including our microbiome data," Lewis says. I don't believe the microbiome pattern resulted from the genetics of the American Indian. It is likely related to the socioeconomic challenges and resource availability in rural areas of Oklahoma."

This story was featured in the February 2016 issue of Microbe Magazine.

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Host: Jeff Fox with special guest, Timothy Lu.

Lu, an Associate Professor of Biological Engineering and Electrical Engineering and Computer Science at Massachusetts Institute of Technology in Cambridge, Massachusetts, talks with Jeff Fox about efforts to develop new phage varieties, swapping in phage tail genes that enable them to target specific bacterial pathogens, including those carrying virulence or antibiotic resistance factors.

Lu and other members of the MIT team worked with T7 phages that ordinarily act only against Escherichia coli. However, by substituting genes from other phages for the T7 gp17 gene, engineering them to target other bacteria, including pathogens such as Yersinia and Klebsiella. “We used this technology to redirect E. coli phage scaffolds to target pathogenic Yersinia and Klebsiella bacteria, and conversely, Klebsiella phage scaffolds to target E. coli by modular swapping of phage tail components,” Lu says. Phages also can be used to speed diagnostic testing of clinical as well as environmental and food pathogens, and such diagnostic tools might be needed to optimize the use of narrow-range antimicrobial products that target very specific bacterial pathogens , he points out.

This story was featured in the January 2016 issue of Microbe Magazine.

Subscribe to MMP (free) on iTunes, Stitcher, Android, RSS, or by email. You can also listen on your mobile device with the Microbeworld app.

Send your microbiology questions and comments (email or audio file) to [email protected].

Host: Jeff Fox with special guest, Stijn Mertens.

Mertens, a graduate student working with Kevin Verstrepen at the University of Leuven in Belgium, talks with Jeff Fox about their efforts to develop new yeast strains for making lager beers—imparting novel flavor and aroma notes without detracting from the freshness and drinkability of lagers.

Unlike other beers, lagers are brewed at low temperatures and with two special hybrid versions of yeast that date back about 600 years. Those hybrids aren’t so easy to produce, but Verstrepen and Mertens first made about 30 new varieties and, by now, about tenfold more, looking to find varieties that yield unusual flavors but still produce enough alcohol at cold temperatures to make lagers of acceptable uniformity and familiarity to brewers and to consumers. Underlying these practical challenges to make better beer are some important fundamental questions about what happens when two different species of yeast are forced to mate and produce stable hybrids. During that process, a good deal of genetic change takes place, but little is known about the details or what leads to genetic stability, according to Mertens. Part of his dissertation research entails investigating some of those processes at the molecular level.

This story was featured in the December 2015 issue of Microbe magazine

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Send your microbiology questions and comments (email or audio file) to [email protected].

Warren C. Ruder of Virginia Polytechnic Institute and State University (Virginia Tech) in Blacksburg, Virginia talks with Jeff Fox about efforts to develop an electronic model system that incorporates a robot for a host and two slightly different kinds of simulated bacteria for its microbiome.

The model carries an engineered bacterial population onboard to stand in for the microbiome, while the robot serves as a proxy for an animal host. When conditions are changed a bit, and the robot is made to send signals to its virtual microbiome, the robot’s behavior changes rather dramatically, making it look very much like the microbiome is pulling the robot’s “strings,” dictating to the host what to do next. This model system carries implications for fields ranging from synthetic biology and ecology to mobile robotics, according to Ruder and his collaborators. Details appeared in the July 2015 Scientific Reports (DOI: 10.1038/srep11988.)

This story was featured in the November 2015 issue of Microbe magazine.

Alexander Mankin –called Shura --of the University of Illinois, Chicago, and Michael Jewett at Northwestern University talk with Jeff Fox about their recent success in joining the 30S and 50S bacterial ribosomal subunits into a single, functioning entity and the implications of that work in terms of making specialized proteins and for studying antibiotics that target the ribosome.
 
This story was featured in the October 2015 issue of Microbe magazine.

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Jeremy Brownlie of Griffıth University in Brisbane, Australia, talks with Jeff Fox about how bacteria influence aggressive behavior in an animal. Fruit flies infected with the wMelPop strain of Wolbachia were less aggressive than their uninfected peers. The neurotransmitter octopamine regulates fruit fly aggression, and Brownlie and his collaborators found that the infected flies produce less of the compound than their uninfected peers, and expression of two genes that encode enzymes responsible for producing octopamine are present at lower levels in infected flies. “That suggested that Wolbachia directly affects fruit fly gene function,” he says.

This story was featured in the September 2015 issue of Microbe magazine. 

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Thijs Ettema of Uppsala University in Sweden talks with Jeff Fox about a deep-sea archaeon, named Lokiarchaeum for the underwater volcano between Greenland and Norway near where it was found, that might be related to the last common ancestor of eukaryotes.

“The shape-shifting deity ‘Loki’ is described as complex and confusing; thus, ‘Lokiarchaeum’ seems a very appropriate name for our typical prokaryote with a whole bunch of eukaryotic genes,” he says. “Importantly, the genes we found in Lokiarchaeum could have provided the archaeal ancestor of eukaryotes with a ‘starter kit’ for the cellular complexity typical in the eukaryotes we see today.” Genes usually associated with eukaryotes are found in Lokiarchaeota, including those enabling membrane remodeling and vesicular traffıcking, indicating that the onset of “cellular complexity was already underway before the acquisition of a mitochondrial endosymbiont.” The fındings favor a two-domain Tree of Life, in which eukaryotes are placed together with a diverse group of archaea known as the “TACK” superphylum because it includes Thaumarchaeota, Aigarchaeota, Crenarchaeota, and Korarchaeota, which share several signature proteins with eukaryotes.
This story was featured in the August 2015 issue of Microbe magazine.

Paul Kelton of the University of Kansas, Lawrence, talks with Jeff Fox about the introduction of infectious diseases among Native American populations.  Kelton’s book Cherokee Medicine, Colonial Germs: an Indigenous Nation’s Fight against Smallpox, 1518–1824, published in April 2015 by the University of Oklahoma Press, looks at how Native American communities responded to new diseases, including establishing quarantines, to protect themselves against smallpox and other diseases. He offers evidence that the high mortality rate ascribed to smallpox in native populations had as much to do with cultural factors and the ferment of trade and warfare during the colonial period, as to any lack of immunity to the new disease. Kelton also discusses the question of whether Europeans may have means to deliberately infect Native Americans.

This story was featured in the July 2015 issue of Microbe Magazine.