Small Things Considered

Talmudic Question #64

by Ramy Aziz

Are any human-associated biofilms "useful" or "beneficial" to human health?

A Giant Among Giants

A colorized SEM showing numerous particles
of the phycodnavirus PBCV-1 attached to a
chlorella NC64A host. Bar = 500 nm. Source.

by Merry

Without a doubt, Mimivirus is remarkable. For a virus, it is extraordinarily large and complex. But it is hardly one of a kind. The more that researchers look for large viruses, the more they find.

Although phages generally tend to have small genomes, some managing with but a handful of genes, a glance at the current NCBI list reveals that there are now eight with sequenced genomes that amount to more than 200 kb. A Pseudomonas phage tops the list with 317 kb, but the not-yet-sequenced genome of Bacteriophage G of Bacillus megaterium is reported to be ~670 kb.

EM of novel Bacillus thuringiensis phage from
soil—the first representative of a new group
of large myoviruses. Bar = 0.1 μm. Source.

Serwer and colleagues have pointed out that the procedures used to isolate phages are biased against the giants. Typical plaque assay protocols call for at least 0.3% agarose in the overlay. However large phages, such as Bacteriophage G, can't make plaques of significant size when the agarose concentration is 0.2% or higher. Using 0.15% agarose, these researchers isolated a novel Bacillus thuringiensis phage from soil—the first representative of a new group of large myoviruses. It too has a genome with more than 200 kb packaged inside a 95 nm capsid that sports a tail measuring half a micrometer!

Hello Again, Metabolism!

by Amy Cheng Vollmer

Source.

Years ago, pathways of intermediary metabolism made up a significant portion of biochemistry and microbiology courses. Therein, students learned about interconversions and connections between pathways, and they could follow the carbons as they moved from acetate into the cholesterol molecule and many others. But the advent of exciting new methodologies—structural biology, recombinant DNA, molecular genetics, immunochemistry, probes, blots, microarrays, metagenomics, and more—crowded much of metabolism right off the syllabus. Given that teaching pathways could be dry and boring, faculty often elected to substitute more trendy and exciting topics instead. To be sure, they thought metabolism was important, but assumed ‘someone else must be teaching it.’

Microbiology in the Andes: Ancient and Unexpected

by Elio

The Ancient Gate of the Universidad de San Gregorio
Magno.

Thanks to the investigations by the Ecuadorian physician and scientist, Dr. Byron Núñez Freile, I learned of a surprisingly high level of scientific development that took place long ago in a remote region of the world. Quito, the present-day capital of Ecuador, is nestled amidst the high Andes and was the northern capital of the Inca empire. It was conquered by the Spaniards in 1534. In this exceedingly distant land, Jesuits established a college within a year of their coming in the late 16th century. By 1622, they founded one of the oldest universities in the Americas, the Universidad de San Gregorio Magno. This was earlier than the founding of Harvard, which happened in 1642. With the passing years, the two universities may not have enjoyed a parallel development, but early on they were likely of comparable quality. Soon, San Gregorio became a major institution, with a most impressive library of 16,000 volumes, the largest in South America at the time. In its first thirty years of existence, the university granted 160 masters degrees and 120 doctorates, mostly in philosophy and theology. Nevertheless, the library holdings also included numerous scientific and medical treatises.

Power of Ten

Tenfold Power. A gorilla can lift 10 times its own
weight, it is said. It can also sit wherever it wants.
Source.

by Elio & Stanley

How often have you heard it said, or seen it stated in writing, that we carry ten times more microbial cells than cells of our own? We don't dispute this figure, at least not as a ballpark estimate. But we were curious to find out where it came from. The paper that seems to be quoted most often in this regard is Microbial Ecology of the Gastrointestinal Tract by Dwayne Savage in the Annual Review of Microbiology, 1977, 31:107-33. Savage was an eminent intestinal microbiologist and those of us who knew him believe that he was a stickler for details. So he should have known. He stated: The various body surfaces and the gastrointestinal canals of humans may be colonized by as many as 10¹⁴ indigenous prokaryotic and eukaryotic microbial cells (70).

So now let’s go to reference # 70. It is to a paper by T.D. Luckey in the American Journal of Clinical Nutrition. 1970, (11) 1430-1432. Now we’re getting somewhere. Luckey writes: Assume one viable microbial mutation each 10⁸ cells, a microbial count of 10¹¹/g intestinal contents and 10³ g intestinal contents, then at a given time each of us harbors about 1 million newly mutated microbes (10¹¹ x 10³/10⁸ = 10⁶).

Just how authoritative is that? References to experimental work? None are given. Surely, the number of bacteria in feces must have been determined countless times through the years. A search of older literature is called for (but who’s got the time!). Moreover, is the number of human cells based on more solid ground? We have no idea.

Nowadays, a quantitative PCR using universal bacterial primers should give a reasonable estimate of the total intestinal bacterial DNA, a figure that can be converted with some assurance to the number of bacteria present. For good measure, add a few percent to account for eukaryotic microbes. Note, however, that we take leave from a good portion of our intestinal microbiome every day, the lucky among us with satisfying regularity. So, the ratio fluctuates daily. No big deal, but let’s qualify the ten-to-one mantra by saying “estimated.” To say the least.

Stanley Maloy is Dean of Sciences and Associate Director of the Center for Microbial Sciences at San Diego State University.

The Uncultured Bacteria

by Kim Lewis

Fig. 1. "The Great Plate Count Anomaly."

The majority of bacteria will not grow on nutrient medium in the lab. The basic experiment is simple: take a sample from the environment, such as marine sediment or soil, mix with water, vortex, allow it to settle, dilute supernatant and take two droplets. Plate one on a Petri dish with LB medium, and place the other on a microscope slide (adding a dye such as DAPI helps). Count the number of cells under the microscope and the number of colonies on the Petri dish – the result will be “The Great Plate Count Anomaly.” About 100 times more cells will be observed microscopically than colonies counted on the Petri dish (Fig. 1). This simple result is one of the most profound puzzles in microbiology, and one of the most significant unsolved questions in biology. Indeed, microorganisms probably make up the bulk of the total biodiversity of species on the planet, but we do not have access to the vast majority of them. Importantly, most Divisions—the largest taxonomic units—do not have a single cultivable representative, and we know of their existence only from 16S rDNA isolated directly from the environment.

There are two basic approaches to solving a problem, and one of them is to decide that it does not exist. It has been suggested on the pages of Nature and Microbe that the anomaly only exists in our minds and results from the insufficient number of microbiologists with a “green thumb” willing to tinker with growth conditions. However, the anomaly has existed for over 100 years, and tinkering by generations of scientists produced only minor improvements. A serious effort was mounted by several groups to culture representatives from the ubiquitous TM7 division, for example, but produced no results.

Comments on the “Synthetic Cell”

Creation of Light, by Gustave Doré (1832-1883).
Source.

by Elio & Merry

The now famous announcement by the Venter group is based on their paper in Science entitled Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome. We applaud this work for its impressive technical achievement and we acknowledge its future potential. However, we find the term “creation” to be misleading because the "new" cell was assembled using mainly preexisting constituents. We also find the term worrisome because, somewhat perversely, it may bring up creationism. We reprint a comment submitted by Bernie Strauss in response to the timely article published in Nature: Life After the Synthetic Cell. His words accurately express our sentiments.

Bernard S. Strauss wrote:

The first time I recall reading that biochemists had succeeded in synthesizing life was in 1967 when Arthur Kornberg and his colleagues succeeded in replicating a øX174 DNA template with E. coli polymerase I and ligase. According to the National Library of Medicine, U.S. President Lyndon Johnson looked at the Stanford press release and to Kornberg's dismay announced: "Some geniuses at Stanford University have created life in the test tube!" There was much discussion at the time including arguments similar to those published in the May 27th issue of Nature. The accomplishments are reasonably similar making allowance for the increase in technology over the past 40 years. A sequence of DNA has been replicated and then introduced into a cell where it takes over the functional apparatus to produce materials specified by the introduced DNA. This is certainly an important technical achievement and one with potential practical application. Does it tell us much about the origin or nature of life?

I would argue that the result is of little theoretical importance. The critical part of Kornberg's work 40 years ago (and one which he acknowledged) and of Venter's work this year is the necessity of a preformed cell. It is only this preformed cell that can convert the coded information in the DNA into functional products. In addition, that cell is not only a passive translator of genetic information but seems to include inherited information of its own, apart from the nucleic acid. As an example, membrane structures require preexisting structures as a template. It may be that at some date it will be possible to mix component membrane parts to form a structure into which all of the other cytoplasmic components can be added along with a synthetic DNA. So far however, all that has been done is to insert programming instructions into a completed machine. The basic unit of biology, and of life, remains the cell. Recent work emphasizes just how malleable the cell is but still requires the preexistence of this elementary life unit.

Anyone who has done science knows just how much work it takes to make any new finding. It is perhaps inevitable that having done all that work, one wants to make the most of it.

This brings to mind two earlier contributions to this blog by Franklin Harold (click here and here) where he discusses the essentialness of pre-existing membranes. It also prompts us to muse that every virus does something similar, with less expense and fanfare.

As always, we welcome your comments.

Bernard Strauss is Professor Emeritus, Department of Molecular Genetics and Cell Biology, The University of Chicago.

It's a Book!

by Merry

Well over two years ago, through this blog I had the opportunity to edit a research paper for Forest Rohwer. One thing led to another, and we then spent the better part of two years writing a book together—the first book for either of us. Coral Reefs in the Microbial Seas is now published! It is a relatively small book written for a broad audience. Minimal science background is required, even though we weave together concepts from many scientific disciplines as we discuss how coral reefs work and what might be ailing them today. And, of course, the microbes are front and center. There is a bit of metagenomics, some epidemiology, an ode to the microbial members of the coral holobiont, the effects of rising atmospheric CO₂ on the oceans, fish farming in the Gulf of Aqaba, and on and on, all spiced with playful stories from Forest's research expeditions and illustrations by Derek Vosten, sculptor and tattoo artist. Forest has been studying coral reefs for nearly a decade, and has ~25 coral-related research papers and book chapters to his credit.

To sample the book, visit our book page at Amazon and use "look inside this book." Or click here to download a book excerpt (1.5 Megs) that includes the Table of Contents, Preface, Introduction, two of the anecdotal stories, and more. You are welcome to distribute the excerpt to others, make it available on your blog, etc. And then please do let me know what you think.

The Sea Slug's Guide to Plastid Adoption

by Merry

A handsome E. chlorotica. Its rich green
pigmentation is courtesy of plastids captured
from its food source, the siphonaceous marine
alga Vaucheria litorea (seen in the background).
Source.

Having an intimate relationship with photosynthetic microbes is a widespread strategy adopted by numerous unicellular and multicellular organisms. Some eschew a committed relationship, and simply nab the plastids, sequestering them inside vacuoles where they continue to photosynthesize for a while. Previously we reported on a ciliate that captures the algal nuclei, as well, to support the plastids, and a flagellate that seems to in the process of converting their plastid into a well-mannered organelle. What about us metazoans? So far there is only one group known to practice this kleptoplasty—the sap-sucking sacoglossan sea slugs—and, so far, only one genus among them is known to have made this a long-term relationship.

The best-studied species here is Elysia chlorotica. These naked molluscs pass their quiet lives in salt marshes from Chesapeake Bay to Nova Scotia. Eggs laid each spring hatch into planktonic veliger larvae that home-in on the one particular species of algae that they use for food, Vaucheria litorea. The larvae attach to the algae where, within 24 hours, they metamorphose into hungry juvenile slugs that begin feeding. During winter months the slugs are inactive; with the arrival of spring and warmer water, the hermaphroditic adults lay their eggs and die soon thereafter.

Of Ancient Curses, Microbes, and the ASM

It is our pleasure to begin an annual tradition of hosting a few reflections from the incoming president of the ASM.

by Bonnie L. Bassler

On July 1, as I start my term as ASM President, I am reminded of three ominous curses of dubious ancient origin:

1. May you live in interesting times.
2. May you come to the attention of those in authority.
3. May you find what you are seeking.

May you live in interesting times: Clearly, these times qualify. Microbes will be at the heart of solutions to our most pressing problems: the environment, food, energy, and health. The BP oil spill began on day -79 of my term. Microbes are coming to the rescue and ASM expertise is on the scene (see the earlier post in this blog). Let us hope that lessons have been learned. In his inauguration address, President Obama promised to “restore science to its rightful place.” It may be happening. The National Academy of Science’s Board on Life Sciences recently released their report: A New Biology for the Twenty First Century. The US Cabinet Secretaries of Energy and Agriculture requested a series of workshops to discuss how to implement the new biology. A first workshop, focused on food and fuel, was held in DC last month and I was invited to participate (day -27 of my term). Workshop members were asked to develop scientific challenges for the decade to be proposed to Congress for funding. Together with several other ASM members in attendance, I strongly advocated the understanding and appropriate use of microbes to synthesize new fuels, clean up the environment, optimize crop production, etc. Our rallying sound bite: Microbes: the world’s only unlimited renewable resource!