Small Things Considered

The Art of Microbial Alchemy

by Gemma Reguera

“The Great Work of the Metal Lover” display, by Brown and Kashefi (Michigan State University) (top image). Included is the aesthetically-engaging, original glass chemostat used to grow the microbe, a metal manifold for gas distribution, and a heated glass copper column that removes any traces of oxygen from the gas supply. Cupriavidus biofilms and the gold grains they produce are visible at the bottom of the vessel (bottom image). Source.

In 2001, Kashefi and collaborators published an article in Applied and Environmental Microbiology reporting the surprising finding that several iron-reducing microbes can use gold as an electron acceptor for their respiration. These microbial alchemists included both mesophilic and thermophilic bacteria as well as hyperthermophilic archaea. The beauty of this process is that the oxidized form of gold provided to the microbes, Au(III), is soluble, whereas its reduced form, Au(0), is insoluble. Hence, the microbes respire soluble gold and precipitate it as gold nanoparticles on their outer surface plus, in the case of the Gram-negative bacteria, in the periplasmic space as well. These studies provided the first experimental evidence supporting the role of microbes in the formation of gold deposits in both hydrothermal and cooler environments, thus challenging the prevailing view that gold mineralization was an abiotic process.

Since then, the list of microbes with the ability to precipitate gold has grown. One of them, the Gram-negative bacterium Cupriavidus metallidurans, is an especially abundant component of the so-called gold nugget microbiota, i.e., the bacterial biofilms associated with gold grains. Elio covered this story previously in our blog. This bacterium grows at room temperature and its mechanism for gold biomineralization is one of the best characterized. For this reason, when artist Brown asked Kashefi, both at Michigan State University, to help him design an exhibit that allowed the audience to witness the process of microbial alchemy, Kashefi regarded Cupriavidus asthe microbe of choice.

A Day in the Life: Eavesdropping on Marine Picoplankton

by Heather Maughan

ESP being tested by divers at the Monterey Bay Aquarium Research Institute. Source.

Observing microbes in nature is a challenge. Compared to what goes on in the lab, there is not much one can do with them out there. So, instead of bringing the bacteria to the lab, why not bring the lab to the bacteria? Imagine being able to capture the expression of genes of a community of microbes in situ, and over multiple time points. This movement of the microbial stage to natural environments has been done for microbial niches that are easily accessible, such as agricultural soil, hot springs, or mine washes. But inhospitable sites far from a lab, sites such as hydrothermal vents and the open ocean, pose a bigger problem.

The solution? A steadfast robot designed and dispatched by researchers at MIT and the Monterey Bay Aquarium Research Institute. Known as the Environmental Sample Processor (ESP), this robot gathers samples of seawater and stores them temporarily so as to preserve the RNA transcripts for subsequent retrieval and analysis. ESP is also able to perform DNA and protein hybridization to identify and quantify specific molecules.

Bacterial Antidepressants: Avoiding Stationary Phase Stress

by S. Marvin Friedman

In bacterial quorum sensing, the absolute number of cells is irrelevant; only the number of bacteria in a given volume plays a role. (Credit: Copyright Wiley-VCH) Source.

High on the list of the exciting manners bacteria communicate with one another is quorum sensing (QS), a population-dependent gene regulation system that operates within a wide range of species. The general scheme of QS is as follows: at high population densities, signal molecules called autoinducers reach threshold levels, at which point they initiate a signal transduction pathway leading to transcription of specific genes. This altered gene expression allows the bacterial community to behave in a cooperative manner so as to achieve a common goal. In a sense, the bacterial population now functions like a multicellular organism. In many Proteobacteria, such as vibrios and pseudomonads, autoinducers are acyl-homoserine lactones (AHLs), compounds synthesized by the LuxI family of signal synthases and detected by the LuxR family of transcriptional regulators. Cellular activities regulated by AHLs include bioluminescence, biofilm formation, motility, and the making of virulence factors, among others. A large body of studies has illuminated the molecular mechanisms underlying QS, but identifying what’s in it for the species has not always been easy. In the paper to be discussed here, Goo and collaborators show how QS enables bacteria to avoid the perils of entry into stationary phase.

Death in the Stationary Phase

The researchers studied three closely-related species of the proteobacteria Burkholderia: the rice pathogen B. glumae, the opportunistic human pathogen B. pseudomallei, and the saprophyte, B. thailandensis. Each of these species has an N-octanoyl homoserine lactone (C8-HSL) signaling system. The basic experiment was to grow these three Burkholderia strains and their corresponding QS signal synthesis mutants in rich LB broth. (Elio pipes in: LB broth is actually a nutrient-scarce medium that supports exponential growth only at low bacterial density. Growth ceases soon, thus this medium may be an OK choice for studies of the stationary phase, all the more so because LB is scarcely buffered, which is relevant to this work. But for studies using growing cultures, LB is an abomination. For an erudite treatment of the limitations of LB medium, see here) The wild type strains survived long periods in stationary phase but the QS mutants died shortly after entering the stationary phase. These crashes were avoided by adding C8-HSL to the culture medium, indicating that QS was somehow involved in preventing death in the stationary phase.

Living Wires of the Ocean Floor

by Gemma Reguera

In a recent post I shared with you how different microbes come together to breathe as one. In some cases, all it takes is the presence of conductive minerals such as magnetite to facilitate the exchange of metabolic electrons between two microbial partners. This allows the team to catalyze a redox reaction (for example, acetate oxidation coupled to nitrate reduction) that each organism could not have been able to achieve individually. The role of conductive minerals in such interspecies electron transfer is a good example of the diverse strategies that microorganisms have evolved to compete for the available electron acceptors, especially those with highest affinity for electrons (the most electropositive ones), as more energy is generated from the reactions.

The metabolic stratification of sediments reflects the reduction of the most energetic electron acceptor available for respiration: from oxygen reduction in the upper sediment region to sulfate (SO₄^2-) reduction and then methanogenesis in the deeper layers. Modified from source.

In marine sediments, for example, oxygen diffuses from the oxic waters into the underlying sediment and is rapidly consumed by microorganisms in the upper region. This limits its availability as a terminal electron acceptor in the deeper layers, which are largely anoxic. As a result, microbes in the anoxic zone rely on alternative electron acceptors, choosing the most electropositive first. This also stratifies the anoxic region of the sediment, with each layer reflecting, from top to bottom, the sequential reduction of nitrate (NO₃^-), manganese (Mn[IV]), iron (Fe[III], which is often present as insoluble iron oxide minerals) and sulfate (SO₄^-2). Methanogens, which use the most electronegative electron acceptor (CO₂), are usually active in the deepest stratum of the sediment. Interestingly, the reduction of sulfate generates hydrogen sulfide, a toxic gas with the chemical formula H₂S. Sulfide production can be high in marine sediments, leading to a characteristic foul smell similar to that of rotten eggs. Unless removed, sulfide can expand from its layer into the oxic layer and poison the respiratory enzymes of oxygen-respiring cells.

Some microbes have evolved mechanisms to detoxify sulfide and/or use it as a substrate for growth. Sulfide can, for example, be oxidized to sulfate or other sulfur compounds by some species even in the presence of oxygen. It can also serve as electron donor for photosynthetic purple and green sulfur bacteria or for nitrate reducers. In addition, sulfide can react strongly with iron and manganese oxides to form iron-sulfur and manganese-sulfur minerals, respectively, which can also be used as terminal electron acceptors. The integration of all these microbial activities in the sediments helps prevent the expansion of the sulfide layer and keep it at millimeter or even centimeters away from the oxic layer. It also creates a harmonic metabolic balance among all the microbes in the sediments, so although each carries out its own reaction they can respond and adapt to sediment disturbances as a whole, integrated system.

Love At First Zap

by Gemma Reguera

Source.

Although both cooperation and conflict are decisive forces in evolution, some of the most successful microbial strategies for survival have arisen from cooperation.  At times, two or more microorganisms can even come together to breathe as one. Breathing, or respiration, accomplishes a most challenging fête: the disposal of electrons generated in metabolic cellular reactions to gain energy for growth. The electron donors and acceptors that microorganisms can use for respiration can be aligned hierarchically on a tower based on their redox or reduction potential (to wit, their affinity for the electrons). The more positive the potential, the easiest it is for the molecule to capture the electrons (i. e., to be reduced) and the more energy that is gained from the reaction. The redox tower provides a visual reference of the energy that microorganisms may generate from the transfer of electrons to each chemical species. Oxygen, for example, has a higher redox potential (it is more electropositive) than nitrate [NO3-)] or iron ([Fe(III], often present in nature as hydrated iron oxide -FeOOH-). As a result, more energy is generated when oxygen is used as the terminal electron acceptor.

The Colors of the Microbial Rainbow

by Gemma Reguera

The only part of the electromagnetic spectrum that is visible to the human eye is in the narrow region between 390 and 750 nm, which contains all the colors of the rainbow and is referred to as the visible or vis light spectrum (vertical arrow at the bottom). Source.

Our appreciation of the colors of nature is limited by the narrow wavelengths of the electromagnetic spectrum that our eyes can detect. This portion of the electromagnetic spectrum between 390 and 750 nm is what we refer to as the visible (vis) light or, simply, light.  We cannot see below (ultraviolet light) or above (infrared light) these wavelengths. Yet this narrow margin of detection allows us to see all the colors of the rainbow, spreading across the visible spectrum from violet (shortest wavelength) to red (longest wavelength). You can see the color palette of visible light in the rainbow up in the sky on a rainy day, as light is dispersed by water droplets. You can also reveal the full color of the visible spectrum using a glass prism: the change of speed of the light as it crosses the glass medium changes the direction of the light waves and enables their dispersion.

Iridescence from soap bubbles (left), shells (middle) and the exoskeleton of a golden stag beetle (right). Source.

Some natural surfaces can produce even more complex optical effects than rain droplets or a glass prism by selectively reflecting light of specific wavelengths and, therefore, specific colors. One optical effect, in particular, the one called iridescence, produces some of the most intense colorations in nature such as the rainbow-like coloration of soap bubbles, the inside of some shells, and the bright colors of the exoskeleton of some insects. The word iridescence originates from the Greek iris, which means ‘rainbow’, and refers to the optical property of some surfaces to change color and its intensity with the illumination or the viewing angle. Iridescent surfaces are uniquely structured in a way that causes the reflected light waves to interact physically with each other. The crests and troughs of the reflected light waves sometimes align (they are ‘in phase’) and reinforce each other, thus increasing the intensity of the reflected color. By contrast, if the reflected light waves are out of phase, they can cancel each other out and those particular colors never manifest. The final effect of this optical interference is the production of one or more predominant colors, the type and intensity changing with the angle of illumination and/or observation. Thus, iridescent colors are ‘structural’: they do not result from pigmentation but from physical interactions between light and surfaces.

Begetting the Eukarya: An Unexpected Light

by Franklin M. Harold

Peach Tree in Bloom by Vincent Van Gogh. Source.

Concerning the origin of eukaryotic cells, much has been written but almost everything remains to be settled. No one disputes that mitochondria derive from free-living bacteria that established an intimate symbiotic relationship with a host of some kind and progressively turned into organelles, workhorses of metabolism, and a hallmark of eukaryotic organization. But consensus ends here; the nature of that host, the timing and circumstances of the partnership, and its role in generating the conspicuous complexity of eukaryotic cells all remain elusive and entangled in controversy. In a comprehensive review of the subject published in 2006, Martin Embley and William Martin (6) concluded bleakly that the evolutionary gap between prokaryotes and eukaryotes is now deeper, and the nature of the host that acquired the mitochondrion more obscure, than ever before. No one will claim that the darkness has been lifted, but just in the past few years this intractable subject has begun to appear in a fresh light.

Life On the Edge: What Happens When Phosphorus Is Limiting?

by Howard Goldfine

Schematic drawing of a lipid bilayer. Source.

For many bacteria, scarcity of phosphorus—serious though it may sound—is not insurmountable. True, phosphorus is needed for nucleic acids and phospholipids, but many prokaryotes have found a way to reduce their need of this element for phospholipid synthesis. But first, why are there phospholipids in the first place? In these compounds the phosphate links the glycerol lipid backbone to a polar “head group” that possesses a free hydroxyl group. In bacteria, the most common head groups contain ethanolamine, glycerol, or, less frequently, serine or choline (Fig. 1). These polar ends can interact with water or with each other, while the hydrocarbon tails interact with each other to form the lipid bilayer. Provided with such amphipathic constituents, a cell can surround the rest of the cell machinery with a semipermeable membrane containing proteins embedded for various functions.

But what happens when phosphorus is in short supply, as it is in the oceans and some inland environments? The cells still need lipids with polar head groups. Bacteria have evolved a number of clever (some may say fiendishly clever) ways to nevertheless make membranes without phosphorus. Let me divide these strategies into two groups, those that use sugars and those that use an amino acid or parts thereof.

Where Mathematicians & Biologists Meet

by Joe Mahaffy

Source.

Mathematics and Biology have a long history together. It goes back to early studies on epidemiology (such as John Snow‘s on cholera and the Broad Street pump), and includes Ross’s quantitative studies that show how malaria can be controlled by careful analysis of data. And, of course, there are many others. In the early 20^th century, population models with differential equations were developed to describe the dynamics of populations, such as the studies of Alfred Lotka, who felt that natural selection could be quantified by physical laws, and Vito Volterra, who created a model to explain the predator-prey ratios in the Italian fish markets. These early models provide excellent tools because in their simplicity they show biologists how mathematics can help explain noteworthy biological phenomena. Mathematicians enjoy such models because the examples themselves make it easier to explain what the equations are describing.

The Bacterial Resistome is Both Ancient and Surprising

by S. Marvin Friedman

The Soda Straw Room in the Lechuguilla Cave. These pencil-thin
stalactites are called soda straws from their size and the fact
they have a central canal through which mineral-laden water flows.
Although it is not uncommon for soda straws to grow three to five
feet long, the ones in this room are as long as 15 feet. Credit: Norm
Thompson. Source.

One of the many interesting controversies that microbiologists can ponder today is whether the alarming proliferation of antibiotic-resistant strains is primarily a consequence of the widespread use of antibiotics in humans and in animal husbandry. An examination of bacteria isolated from terrestrial animals in the Galapagos, a remote location with limited exposure to humans, revealed  an absence of antibiotic resistance genes. Likewise, plasmids from bacterial collections that predate the antibiotic era were mostly devoid of resistance elements. Furthermore, a study of Dutch soil samples showed an increase in antibiotic resistance genes in contemporary samplings as compared to those from the pre-antibiotic era. On the other hand, antibiotic resistance genes were both abundant and diverse in ancient DNA recovered from Pleistocene deposits (30,000 years ago). Likewise, a survey of present-day actinomycetes revealed that multidrug resistance was prevalent even though human sources of antibiotics were presumed absent in this environment. It should be noted, however, that the actinomycetes are prolific antibiotic producers and thus it is not surprising to find resistance elements enriched in this group.