Bacteria in a wastewater treatment plant

Bacteria in activated sludge from a wastewater treatment plant

It is a remarkable fact that we fully depend on microbes to treat or sewage water. In every wastewater treatment plant, from the simplest to the most modern ones, the essential activity is biological and is mainly carried out by bacteria. In modern plants, sewage water is directed to large aerated tanks in which the pollution is consumed by a mixture of microbes and organic matter known as  activated sludge.

The video below shows how an aerated tank looks like. You don’t want to take a swim in there… 

For a microbiologist, a wastewater treatment plant is a delight: I’ve never seen another environment with as much diversity in the size and shapes of cells. It is a true microbial jungle containing countless bacteria and many protozoans that feed on them.

Should science be apolitical?

Read the other day in the magazine the Atlantic: “The danger of making science political”, by Puneet Opal, medical doctor and professor of neurology at the Northwestern University Feinberg School of Medicine. Opal reflects on the relation between science and politics; he observes that, in the US, science is associated with the Democrat party, and he asks the question: why is it so?

Opal’s article is echoing another piece published recently in Nature, “Science must be seen to bridge the political divide”, by Daniel Sarewitz, from the Consortium for Science, Policy and Outcomes at Arizona State University. Sarewitz complains about a very US-centered situation, that is, the fact that most American scientists seem to side with the Democrats against the Republicans. He takes as an example the letter written by many Nobel laureates in support of Obama’s reelection in 2012. This bias, Sarewitz claims, is a bad thing for science. He writes:

“To prevent science from continuing its worrying slide towards politicization, here’s a New Year’s resolution for scientists, especially in the United States: gain the confidence of people and politicians across the political spectrum by demonstrating that science is bipartisan.”

Plant pathogen focus: Pierce's disease and the vineyards of California

Grapevine dying of Pierce's disease. Photo courtesy of PD-GWSS/CDFA.

Xylella fastidiosa  is not your ordinary kind of bug. It made it to the list of the most wanted plant pathogenic bacteria in 2012! (Mansfield, 2012.)

This is well deserved: X. fastidiosa can infect over a hundred species (grapevine, oleander, citrus, almonds,…), and it causes severe symptoms that can kill the infected plant. The Xylella bacteria colonize the xylem vessels, and by doing so they block the transport of water in the plant. The water-deprived leaves dry and scorch, until finally they drop to the ground. 

In 1892, Newton Pierce, California’s first professional plant pathologist, described the disease that now bears his name, although he failed to identify the causative agent of the disease (X. fastidiosa). Around the end of the 19^th century, an epidemic of Pierce’s disease devastated thousands of hectares of vineyards in the Los Angeles Basin. Since then, southern California has considerably reduced its viticulture; this also explains why present-day Californian vineyards are mostly restricted to the north of the state. There is currently no other cure than getting rid of the infected plants!

The new biology of Carl Woese

Carl Woese. Photo courtesy of Don Hamerman.

Carl Woese, one of the giants of contemporary biology, passed away a day before New Year’s Eve (see the NY Times obituary). Woese, an American microbiologist from the University of Illinois, revolutionized our understanding of life with the discovery of a new domain of living organisms, the Archaea, and the creation of a universal tree of life made of three main branches (Bacteria, Archaea and Eukarya) (Woese, 1990). This discovery is already more than thirty years old, but is not very well known to the general public, to say the least… And now with Woese’s death the possibility of a Nobel nomination vanishes.

Everything we do nowadays in microbiology labs is to some extent influenced by the work done by Woese in the seventies and eighties. This is one reason why I entitled this post “The new biology of Carl Woese”. The other reason is a 2004 article by Woese, “A new biology for anew century”, which offers a great perspective on our job and which contains some juicy controversial elements. But let’s begin with the landmark contribution of Woese to the field of biology.

Before the sixties and the advent of molecular phylogeny, the classification of bacteria seemed an insoluble problem, since morphology and metabolism were not good enough to allow us to order the bacterial life forms. Woese, a physicist by training, decided in 1966 that he could give it a try using the powerful tools of molecular biology. At that time many researchers had turned towards proteins in order to build phylogenetic trees, following the pioneer work of Linus Pauling on hemoglobin. Woese didn’t follow the consensus and decided to use ribosomal RNA as source material. Thanks to a tedious technique called oligonucleotide cataloging, he was able to reconstruct the rRNA sequence and did that for about sixty bacteria. It took ten years.

Macroscopic fungi

In the lab I have only dealt with microscopic fungi, such as yeasts, but a couple of weeks ago I had the privilege to accompany a group of UC Davis students and staff on a mushroom hunting trip! This excursion was led by the very knowledgeable mycologist Dr. Mike Davis, author of the Field Guide to Mushrooms of Western North America, and Professor of Plant Pathology at UCD.

Fungi are curious organisms, neither animal nor plant, with unique chemical traits such as the presence of chitin in the wall of their cells. My beloved Brock Biology of Microorganims reminds me that there are three major groups of fungi: the molds (the type you don't want in your household); the yeasts, which we commonly use to ferment sugars; and finally the mushrooms, or macroscopic fungi.

Scientists keep an eye on a new SARS-like virus

Coronavirus. Electron microscope photo by Phil Murphy/CDC.

In 2003, a coronavirus named SARS (for Severe Acute Respiratory Syndrome) made nine hundreds victims, most of them in Asia. Usually coronaviruses are not dangerous - they cause a cold or stomach flu -, but this one killed one among ten infected human beings. Thanks to the prompt response of the sanitary authorities all over the world, SARS was relatively rapidly controlled.

This year, a SARS-like virus has appeared in Middle East, and scientists and health officers keep a very close eye on it, as Nature News reports. At present it remains unclear whether this new virus could become a real worldwide threat, but it killed five of the nine cases known so far. 
The first cases were reported this Summer in Saudi Arabia and in Qatar, but in November evidence showed that people had been infected by the new virus in Jordan already this Spring.

A Planet of Viruses by Carl Zimmer

Published by University of Chicago Press

This is popular science writing at its best: concise, edifying and not condescending. But I did not expect less from Carl Zimmer, a seasoned science writer and the author of many books (e.g. Microcosm, Soul Made Flesh, Evolution:Making Sense of Life), as well as a contributor to many high profiles newspapers and magazines (e. g. NYT, Time, Scientific American). On top of that he's a widely read blogger (The Loom).

You can tell that it is good when you would recommend the book to a non-scientist, and at the same time you find plenty in the book to enjoy for yourself.

A Planet of Viruses is a short book, so don’t expect an exhaustive treatise on viruses. But if the scope is narrow, it is due to clever choices that help keep the book focused.  For instance, Zimmer doesn’t discuss the molecular details so much. We won’t learn here about RNA vs. DNA viruses, single vs. double stranded, and so forth. Neither will we learn the elaborated tricks of viral replication or the taxonomy of viruses – but textbooks are just for that, aren’t they?