Small Things Considered

Fine Reading: The gut microbiota of insects – diversity in structure and function

by Elio

Now that the mammalian intestinal microbiome has been promoted to organ status, might not such stately respectability be granted to the gut microbiota of other metazoans? If looking for a worthy candidate for such recognition, one could not do better than to consider the varied communities dwelling in the guts of insects. A recent review by Engel and Moran points out that beneficial intestinal microbes here: upgrade nutrient-poor diets, aid digestion of recalcitrant food components, protect from predators, parasites and pathogens, contribute to inter- and intraspecific communication, affect efficiency as disease vectors, and govern mating and reproductive systems. Microbes, it is clear, have contributed mightily to insect success.

A. Generalized gut structure of insects. The foregut and hindgut are lined by a cuticle layer (black line), the midgut secretes a peritrophic matrix (dashed line). B-M: Gut structures of insects from different orders. If not specifically indicated, the gut of an adult insect is shown. Stipples depict the predominant localization of the gut bacteria. For plataspid stinkbug, the magnification shows bacteria localized in the midgut crypts. Source.

The microbial landscape of the insect gut microbiome is much different from that of mammals. The great diversity of insects is reflected in their digestive tracts that also differ greatly in anatomy and physiology, and thus accommodate microbiotas that vary in composition and number. The total number of bacteria present range from 10⁹ per honey bee, to 10⁵ in a fruit fly, to negligible numbers in the sap-feeders, the latter often carrying instead an abundance of bacterial endosymbionts. Pick any individual insect and likely it will have fewer species in its gut than you do, although there are exceptions. Perhaps the most diverse communities among the insects are those in the termites, which are teeming with bacteria and protists. The 19th century American paleontologist and biologist Joseph Leidy observed that when one ruptures the intestine of a termite, myriads of the living occupants escape, reminding one of the turning out of a multitude of persons from the door of a crowded meeting-house.

The authors of this review article serve as expert guides to the anatomic complexity of the insect digestive system—with it distinguishable fore-, mid-, and hindgut. Each molt brings marked changes that disrupt or discard the microbiota, thus calling for extensive re-seeding. The routes of acquisition of these varied partners are likewise diverse. Some insects tend their eggs, thus facilitating vertical transmission, while the social insects have opportunities for transmission within the group. Both of these routes favor the development of gut communities’ characteristic of that species. The interests of the Moran lab being centered on bacterial endosymbionts, those associated with the gut receive considerable attention and serve to contrast with the free-living members of the microbiome.

Bacteria arriving by any route encounter powerful host defensive mechanisms. These barriers vary among the different groups of insects, and so do the bacterial strategies for surmounting them. As expected, the mighty subject of insect innate immunity, which is so conducive to understanding its equivalent in mammals, is treated here in detail. So are nutritional symbioses, the role of the microbes in insect development and physiology, and, especially thought provoking, their participation in intraspecific and interspecific communication. But be prepared for a specialized language: you will encounter terms such as proctodeal trophallaxis (anus-to anus feeding), peritrophic matrix (a layer of chitin fibrils that protects the intestinal epithelium), paratransgenesis (the elimination of a pathogen via the introduction of a symbiont) and others that may prompt a Google search.

This review will acquaint you with what we currently know about the great variety of bacteria found in the guts of insects, and at the same time will convince you that much remains to be explored before we have the grand picture of the inner life in insects. This is to be expected, insects being the most varied and abundant animal clade of all.

Engel P, & Moran NA (2013). The gut microbiota of insects - diversity in structure and function. FEMS microbiology reviews PMID: 23692388

O'Hara AM, & Shanahan F (2006). The gut flora as a forgotten organ. EMBO reports, 7 (7), 688-93 PMID: 16819463

Terraforming Mars With Microbes

by Ben Auch

Using new advances in synthetic biology and our updated understanding of Martian geochemical conditions, we should be able to inoculate the planet Mars with specially designed extremophilic microbes in an attempt to start (or re-start) life on its surface. This could be the largest and most audacious scientific experiment ever undertaken, aimed at one of the greatest puzzles in biology: how does life evolve on a planet? In so doing, the microbial pioneers we launch could pave the way for future human colonization of Mars and beyond.

A Biosphere is Born

Fig. 1. Source: Jackson Moore.

Four billion years ago the Earth was entirely hostile to the life we find on it today. Our home-to-be was harsh and unrecognizable, with high volcanic activity, asteroid impacts, 1000-foot tides, and a toxic, anaerobic atmosphere. But then something amazing and maybe unique happened: through some mechanism life appeared. No, it did more than that: it exploded, and it changed the planet forever. How this happened is far from clear. The first microbes may well have been chemoautotrophs, using widely available sulfur and iron as a substrate for growth. These early anaerobes were largely supplanted by the photosynthetic cyanobacteria, which released large amounts of toxic oxygen into the atmosphere, killing their predecessors and causing Earth’s longest ice age. When the dust settled, a new Earth was born, rich in oxygen and a protective ozone layer, and eventually permissive to the aptly named Cambrian explosion, the root of most eukaryotic domain of life. Said another way, the initial genesis of life was the spark that unlocked a vast array of biochemical reactions on a global scale, creating an environment and atmosphere capable of supporting the vast diversity of life we see, study, and even represent today. This was the evolution of a biosphere.

A Whiff of Taxonomy – The Phylum Elusimicrobia

by Elio

If you happen to look, you’ll find that new bacterial phyla spring up with amazing frequency, and that taxonomic names and facts accumulate at a staggering rate. As a public service, we’ll try from time to time to nibble away at this huge salami, slicing off and serving up one unfamiliar phylum at a time. Today it’s the turn of the Elusimicrobia. I admit that I chose them on account of their name. What could be more enticing than an elusive living being? (BTW, the name is derived from the Latin elusus, escaped from capture.)

An unrooted maximum-likelihood tree of 280 bacterial genomes, including the two sequenced representatives of the phylum Elusimicrobia, representing the regions of the bacterial domain currently mapped by genome sequences. Source.

This phylum used to be referred to as Termite Group 1, a monophyletic group of bacteria found as endosymbionts of flagellates in the hindguts of termites and other insects. Actually, Elusimicrobia are far less constrained than that, inhabiting also the ocean, soils, and sewage sludge. Since they form a deep branch of the bacterial tree, they are thought of as being quite old. The first one to be cultivated was given the apt name Elusimicrobium minutum. It is minute, an “ultramicrobacterium” only 0.17- 0.3 μm wide and variable in length. For an organism that can be grown in the lab, its genome is a puny 1.64 Mbp. It is a strict anaerobe but can grow on a variety of organic substrates. No pili have been seen on its surface although it is equipped with many of the genes needed for constructing pili. It presents the typical Gram-negative two-membrane system at its surface, but, perhaps due to its extreme thinness, it displays an interesting partitioning of its nucleoid (see the electron micrograph).

Tit-for-Tat: A Bacterial Counterattack System

by Spencer Scott & John De Friel

Schematic diagram of a type VI secretion system by Y. M. Cully, C. Cambillau, and E. Cascales. The lower bilayer membrane is the attacker’s, the upper one the host’s. Notice the complex structure of the Type VI secretory apparatus. Source.

Microbial ecology may be a young field but it is well understood already that there is a broad spectrum of interactions between bacterial species, ranging from cooperative to competitive. In a recent paper researchers from John Mekalanos’ lab further characterized a recently discovered mechanism for inter-cell communication. This system, called the Type VI secretion system (T6SS), is a multi-protein complex native to many bacterial strains and structurally and functionally similar to a bacteriophage tail. The T6SS system is unique in that it is used as a weapon for injecting toxic proteins into the cytoplasm not only of animal host cells but also of neighboring bacterial cells by propelling its components through the neighbors’ membrane. The toxic effector proteins, Tse1 and Tse3, are peptidoglycan-degrading enzymes that can cause cell lysis in the absence of antitoxin proteins. For reviews, click here and here.

The Type VI Secretion System Differs in Two Species

To elucidate how and when a cell decides to inject a neighboring cell with its T6SS, these workers studied its behavior in Vibrio cholerae and Pseudomonas aeruginosa. In V. cholerae, the T6SS seems to shoot off at random, constantly showing up in different areas on the cell, which endows it with high pathogenicity and with the ability to kill off many other species of cells. In this light, V. cholerae can be seen as a sort of Yosemite Sam, a character renowned for his excessive and poorly aimed shooting. The analogy to this character and to Batman (see below) was thought up by Robert Cooper and appeared in his fine blog at Science 2.0.

Little Known Glomalin, a Key Protein in Soils

by Elio

A visible portion of the rhizosphere. Source.

If you had heard of glomalin, you are a better person than I am. Until a couple of months ago I wasn’t aware of its existence, which is close to sinful: it happens to be a very abundant protein in the soil rhizosphere, playing a key role in the soil’s mechanical properties and as repository of soil carbon. Glomalin is a glycoprotein (although the “glyco-“ may be overused here, as biochemical analyses suggest that it contains little in the way of sugars) that binds together silt, sand, or clay soil particles. By ‘supergluing’ the small, loose particles, this gooey protein makes larger granules or aggregates and protect the soils from the eroding forces of winds and water. So, where does glomalin come from? It is thought to be made by fungi, more specifically by members of the arbuscular mycorrhizal fungi, the Glomales (hence the name ‘glomalin’). The hyphae of these fungi synthesize glomalin as part of their stress response. They coat their outer surface with the protein to make a protective waxy coat that keeps the water and nutrients inside the cells. The glomalin coating also makes the fungal strings sticky so they bind soil particles, thus creating an protective ‘armor’ against environmental insults and microbial predators. Most importantly, the fungal “string bags” make soil aggregates. This improves water infiltration and retention in the soils and gas exchange, which makes them more fertile. For more information on glomalin click here.

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.

A Passing Thought

by Elio

Sections of Rockyard Chalcedony (var. Agate) from Burns, OR. Except for the colors, might a section through feces look like this? Source.

In the celebrated novel The Rebel Angels, the famed Canadian author Robertson Davies mentions Ozias Froats, a fictional professor potentially on his way to a Nobel Prize for discovering that everyone’s feces reflect the maker’s personality. He did not have today’s ready recourse to metagenomics (that being still in the future), so he looked at "extremely thin slices of faeces, cut transversely, and examined microscopically and under special light.” He found that each person’s specimen reveals differences in individual temperament. It occurred to me that using this same approach could add another dimension to fecal metagenomics by determining the intra-turd location of individual species. This could readily be visualized using specific fluorescent-labeled antibodies on thin sections—merely a technical elaboration on Froats’ methods.

I know little about how feces are made (“turdopoiesis”) except that it involves dehydration of the colonic contents. In the process, some bacteria are surely displaced mechanically but others perhaps turn on their motility apparatus early in the process to travel to a preferred site, be it the edge or the interior of the creation. Do those species that cling to the mucosal surface or inhabit the mucus also get carried along? Or are they found mainly on the surface of the bolus? And what about prophages, which may well come to life as the result of bacterial stress? Sampling for metagenomics is easier to do with feces than with the insides of the gut, but at present we know little about the geometry of microbe-rich environments and their dynamics.

Froats saw much beauty in his work. He described what he saw in the sections as "splendid cuttings of moss-agate, brecciated agate, an extraordinary beauty reminiscent of ‘that chalcedony which John's Revelation tells us is part of the foundations of the Holy City’." Who knew? Anyhow, with individualized medicine upon us, perhaps standard laboratory tests in the future may include cutting sections of fecal samples for microscopic evaluation. Besides, this may give the person doing the examining unexpected visual pleasures.

Bdellovibrio’s Appetite for Metabolites

by Henry N. Williams

The Poly-hydroxyalkanoate repeating unit of PHA. (no source)

Not long ago, Elio said in this blog that predation, a major force in evolution, is somewhat neglected in microbiological circles. The full implications of predation are just beginning to be uncovered as more becomes known about the ecology, physiology, and genomics of predators against microbes and their interactions with their prey. The collective knowledge of how they influence each other will naturally feed curiosity of scientists regarding how some cellular characteristics evolved. Here, I address a new metabolic feature of a predatory bacterium that will certainly lend itself to evolutionary considerations.

Wolbachia Make Fruit Flies Lay More Eggs to Make More Wolbachia

by S. Marvin Friedman

S. Burt Wolbach (1880-1954), professor at Harvard Medical School. Source.

If you would like to have a particularly striking organism named after you, choose your collaborator well. The Harvard rickettsiologist S. Burt Wolbach was lucky to have such a colleague—the entomologist Marshall Hertig. In 1936, Hertig gave the name Wolbachia to the endosymbionts of mosquitoes they had jointly discovered in 1924. As is now widely known, Wolbachia are among the most common host-associated bacteria, infecting perhaps 70% of all insects, many spiders, and some worms to boot. And what they do for their hosts is mighty interesting. As an aside, it’s worth mentioning that the two discoverers were on the mark in deciding that the organism belongs to the Rickettsiales (Alphaproteobacteria). True enough, the genome sequence confirms that.

Wolbachia endosymbionts are transmitted maternally, hitching a ride on the zygote’s mitotic spindle. Among their most intriguing activities is their manipulation of the reproductive capabilities of their hosts. In females, they reside primarily in the ovaries, provoking a variety of reproductive consequences (some of which were described in earlier posts here and here). For instance, they skew the sex ratio in the population by killing male flies and enabling females to reproduce by parthenogenesis. They also reduce the number of uninfected flies in the population using a competitive strategy known as cytoplasmic incompatibility. Only uninfected females produce Wolbachia-free zygotes, but Wolbachia sees to it that infected males cannot mate productively with uninfected females. On the other hand, some species of flies cannot reproduce without their endosymbionts. In addition, some Wolbachia protect their host against infection by certain fungi and RNA viruses, including the agent of dengue fever.