MicrobiologyBytes

Four new fungi in the genus Ophiocordyceps have been identified. These fungi belong to a group of “zombifying” fungi that infect ants and then manipulate their behavior, eventually killing the ants after securing a prime location for spore dispersal.

Beyond this important milestone, the paper also draws attention to undiscovered, complex, biological interactions in threatened habitats. The four new species all come from the Atlantic Rainforest of Brazil which is the most heavily degraded biodiversity hotspot on the planet. Ninety-two percent of its original coverage is gone. The effect of biodiversity loss on community structure is well known. What researchers don’t know is how parasites, such as these zombie-inducing fungi, cope with fragmentation. The authors show that each of the four species is highly specialized on one ant species and has a suite of adaptations and spore types to ensure infection. The life-cycle of these fungi that infect, manipulate and kill ants before growing spore producing stalks from their heads is remarkably complicated. The present work establishes the identification tools to move forward and ask how forest fragmentation affects such disease dynamics.

Hidden Diversity Behind the Zombie-Ant Fungus Ophiocordyceps unilateralis: Four New Species Described from Carpenter Ants in Minas Gerais, Brazil. (2011) PLoS ONE 6(3): e17024. doi:10.1371/journal.pone.0017024
Background: Ophiocordyceps unilateralis (Clavicipitaceae: Hypocreales) is a fungal pathogen specific to ants of the tribe Camponotini (Formicinae: Formicidae) with a pantropical distribution. This so-called zombie or brain-manipulating fungus alters the behaviour of the ant host, causing it to die in an exposed position, typically clinging onto and biting into the adaxial surface of shrub leaves. We (HCE and DPH) are currently undertaking a worldwide survey to assess the taxonomy and ecology of this highly variable species.
Methods: We formally describe and name four new species belonging to the O. unilateralis species complex collected from remnant Atlantic rainforest in the south-eastern region (Zona da Mata) of the State of Minas Gerais, Brazil. Fully illustrated descriptions of both the asexual (anamorph) and sexual (teleomorph) stages are provided for each species. The new names are registered in Index Fungorum (registration.indexfungorum.org) and have received IF numbers. This paper is also a test case for the electronic publication of new names in mycology.
Conclusions: We are only just beginning to understand the taxonomy and ecology of the Ophiocordyceps unilateralis species complex associated with carpenter ants; macroscopically characterised by a single stalk arising from the dorsal neck region of the ant host on which the anamorph occupies the terminal region and the teleomorph occurs as lateral cushions or plates. Each of the four ant species collected – Camponotus rufipes, C. balzani, C. melanoticus and C. novogranadensis – is attacked by a distinct species of Ophiocordyceps readily separated using traditional micromorphology. The new taxa are named according to their ant host.

Chemists and engineers taught us how to wring fuels and chemicals out of rock – the word petroleum derives from Latin roots meaning “rock oil”. In the current world, amid concerns that our sources of petroleum are dwindling, we are turning over all stones for suitable alternatives to petroleum. We need to replace an essentially non-renewable resource, petroleum, with renewable fuels and thus make our future sustainable. The major renewable materials on Earth are derived from biological systems that reproduce and replenish themselves. So it is natural to turn to biological systems for producing renewable fuels. This short review focuses on recent advances in engineering organisms and processes to make renewable fuels.

Engineering microbes to produce biofuels. Curr Opin Biotechnol. Nov 9 2010
The current biofuels landscape is chaotic. It is controlled by the rules imposed by economic forces and driven by the necessity of finding new sources of energy, particularly motor fuels. The need is bringing forth great creativity in uncovering new candidate fuel molecules that can be made via metabolic engineering. These next generation fuels include long-chain alcohols, terpenoid hydrocarbons, and diesel-length alkanes. Renewable fuels contain carbon derived from carbon dioxide. The carbon dioxide is derived directly by a photosynthetic fuel-producing organism(s) or via intermediary biomass polymers that were previously derived from carbon dioxide. To use the latter economically, biomass depolymerization processes must improve and this is a very active area of research. There are competitive approaches with some groups using enzyme based methods and others using chemical catalysts. With the former, feedstock and end-product toxicity loom as major problems. Advances chiefly rest on the ability to manipulate biological systems. Computational and modular construction approaches are key. For example, novel metabolic networks have been constructed to make long-chain alcohols and hydrocarbons that have superior fuel properties over ethanol. A particularly exciting approach is to implement a direct utilization of solar energy to make a usable fuel. A number of approaches use the components of current biological systems, but re-engineer them for more direct, efficient production of fuels.

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• Microdiesel: microbiology can reduce your carbon footprint
• New Microbial Fuels

The availability of nitrogen (N) is one of the factors that controls the productivity of the oceans, and there has been great interest in determining the magnitudes and pathways of N inputs to the world’s oceans through biological N₂ fixation. Biological N₂ fixation is the reduction of N₂ gas to biologically available ammonium, and this is performed by a diverse but limited number of bacterial and archaeal genera. Cyanobacteria are generally assumed to be the major N₂-fixing microorganisms in the open ocean. Atmospheric N₂ is one of the important external sources of N to the surface waters of the oceans, and thus provides the stoichiometric nutrient flux to support the export of carbon to the deep ocean. This is of importance in ocean–atmosphere fluxes and feedbacks that help to constrain the atmospheric concentrations of the greenhouse gas CO₂. There continues to be controversy over whether the oceanic denitrification losses of N are balanced by N₂ fixation inputs. There are large uncertainties in the estimates of basin- and global-scale denitrification and N₂ fixation rates from biogeochemical calculations, perhaps due to the many assumptions required to scale these processes globally from either biogeochemical or biological data. Conversely, there is also a general lack of data on the distributions and activities of N₂-fixing microorganisms over the vast scales of the ocean. At the core of resolving these issues is the identification of the organisms involved and determining how they function, the factors that limit their growth, and their roles in food webs. The difficulties in determining the roles of open ocean microorganisms in N₂ fixation are the nature of N₂-fixing microorganisms themselves, the dilute nature of microbial populations in the oligotrophic ocean, and the general difficulty in cultivating microorganisms from the ocean. Despite these hurdles, over the past few years much has been learned about the microorganisms primarily responsible for N₂ fixation in the surface waters of the open ocean.

Nitrogen fixation by marine cyanobacteria. Trends Microbiol. Jan 10 2011
Discrepancies between estimates of oceanic N₂ fixation and nitrogen (N) losses through denitrification have focused research on identifying N₂-fixing cyanobacteria and quantifying cyanobacterial N₂ fixation. Previously unrecognized cultivated and uncultivated unicellular cyanobacteria have been discovered that are widely distributed, and some have very unusual properties. Uncultivated unicellular N₂-fixing cyanobacteria (UCYN-A) lack major metabolic pathways including the tricarboxylic acid cycle and oxygen-evolving photosystem II. Genomes of the oceanic N₂-fixing cyanobacteria are highly conserved at the DNA level, and genetic diversity is maintained by genome rearrangements. The major cyanobacterial groups have different physiological and ecological constraints that result in highly variable geographic distributions, with implications for the marine N-cycle budget.

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• Cyanobacteria
• Calcifying cyanobacteria and carbon capture
• A day in the life of a cyanobacterium

Emerging infectious diseases arise by a range of distinct phenomena, such as the resurgence or upsurge of pre-existing endemic infections, the arrival of exotic microorganisms and the appearance of genetically new microorganisms. The evolutionary emergence of new human pathogens is driven by changes in the biological barriers that determine host-pathogen interactions and therefore the transmission competence of any new partnership. True evolutionary emergence is rare. Among emerging infectious diseases other than infection by drug-resistant bacteria, there is a high percentage of zoonoses. This review focuses on infectious diseases that have emerged recently in new areas, where selection may favour microbial genetic novelties. Among these, vector-borne pathogens are particularly common.

The arrival, establishment and spread of exotic diseases: patterns and predictions. Nature Rev Microbiol. 2010 8(5): 361-371 doi: 10.1038/nrmicro2336
The impact of human activities on the principles and processes governing the arrival, establishment and spread of exotic pathogens is illustrated by vector-borne diseases such as malaria, dengue, chikungunya, West Nile, bluetongue and Crimean-Congo haemorrhagic fevers. Competent vectors, which are commonly already present in the areas, provide opportunities for infection by exotic pathogens that are introduced by travel and trade. At the same time, the correct combination of environmental conditions (both abiotic and biotic) makes many far-flung parts of the world latently and predictably, but differentially, permissive to persistent transmission cycles. Socioeconomic factors and nutritional status determine human exposure to disease and resistance to infection, respectively, so that disease incidence can vary independently of biological cycles.

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• Emerging and re-emerging infectious diseases
• Hantaviruses as Emerging Pathogens
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Enteric bacteria such as Escherichia coli swim by rotating a set of flagella that forms a bundle when the flagellar motors turn in the counterclockwise (CCW) direction The bundle falls apart when one or more motors turns in the clockwise (CW) direction, and the bacterium tumbles. A new swimming direction is selected upon resuming the CCW rotation of the flagellar motors. By modulating the CCW and CW intervals according to external chemical cues, the cells are able to migrate toward attractants or away from repellents.

This paper report observations of motility patterns of marine bacterium Vibrio alginolyticus. The authors fround found that the bacteria employ a unique cyclic three-step (forward–reverse–flick) swimming pattern for chemotaxis; they regulate both forward and backward swimming times according to a given chemical profile. By employing the three-step chemotactic strategy, cells of V. alginolyticus are able to focus on a point source of attractant rapidly and form a compact swarm around it. This is apparently a significant niche for V. alginolyticus, which live in ocean where nutrients are scarce and rapidly dispersed by currents.

Bacterial flagellum as a propeller and as a rudder for efficient chemotaxis. PNAS USA 4th January 4 2011 doi: 10.1073/pnas.1011953108
We investigate swimming and chemotactic behaviors of the polarly flagellated marine bacteria Vibrio alginolyticus in an aqueous medium. Our observations show that V. alginolyticus execute a cyclic, three-step (forward, reverse, and flick) swimming pattern that is distinctively different from the run–tumble pattern adopted by Escherichia coli. Specifically, the bacterium backtracks its forward swimming path when the motor reverses. However, upon resuming forward swimming, the flagellum flicks and a new swimming direction is selected at random. In a chemically homogeneous medium (no attractant or repellent), the consecutive forward tf and backward tb swimming times are uncorrelated. Interestingly, although tf and tb are not distributed in a Poissonian fashion, their difference Δt = |tf – tb| is. Near a point source of attractant, on the other hand, tf and tb are found to be strongly correlated, and Δt obeys a bimodal distribution. These observations indicate that V. alginolyticus exploit the time-reversal symmetry of forward and backward swimming by using the time difference to regulate their chemotactic behavior. By adopting the three-step cycle, cells of V. alginolyticus are able to quickly respond to a chemical gradient as well as to localize near a point source of attractant.

Related:

• Bacterial Motility

Recent events have highlighted the damage our dependence on oil can wreak on the natural world. However, as Lena Ciric discusses in this article in Microbiology Today, communities of bacteria have evolved over billions of years to be rather better than we are at breaking down the complex hydrocarbons that are found in oil. How we can exploit this ability to improve our future clean-up strategies?

On 20th April 2010 a massive explosion rang out in the Gulf of Mexico. The source of the incident was the Deepwater Horizon drilling rig, situated about 84 km from the Louisiana coast, which had been drilling for oil at a depth of over 1,500 m. The explosion killed 11 people at the time and was the cause of what is now referred to as the worst environmental disaster in US history. It is difficult to state the exact volume of oil which has spilled into the Gulf of Mexico, the best estimate being put forward by the US government as 4.9 million barrels. That’s over 770 million litres, or over 300 full Olympic-size swimming pools. The well which was the source of the oil spill has since been plugged successfully and a US government report has stated that three-quarters of the spilled oil as now been ‘dealt with’. A considerable proportion of the removal of the spill is attributed to bacterial biodegradation of the hydrocarbons that constitute the crude oil. The huge oil spill in the Gulf of Mexico is only one of a huge number of oil spills that have taken place over the course of Earth’s history. For billions of years, our microbial neighbours have been evolving to utilize the molecules that constitute oil – and it turns out that they have now become quite
good at it.

Read more

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• Molecular approaches to bioremediation

Since the beginning of mankind, human beings have strived to pass on their thoughts and knowledge to other people and to future generations. In this respect, the cultural role played by paper has been immense: paper is used for drawings, books, archival documents, photographs, prints, and so forth. Paper was first made in China around 105 AD, and its history can be roughly divided into two major periods: before the 19th century, when paper was made by hand, cellulose from linen and cotton rags was used as the raw material; from the 19th century onwards, when paper was machine-made from wood pulp, paper has contained several other components in addition to cellulose; these include lignin, hemicellulose and pectin. Furthermore, paper is often coated with sizes (the sizing of paper is a process that renders the sheets impervious to ink) such as gelatine, or with minerals, pigments and other substances to impart desirable properties. Libraries, archives and museums preserve paper material, and such material is at risk of deterioration and needs to be protected from physicochemical and biological agents. In many cases, microbial processes have been implicated in paper deterioration.

Scripta manent? Assessing microbial risk to paper heritage. Trends in Microbiol. Oct 22 2010
Paper, like all other cultural heritage materials, degrades over time, but conservation slows down the rate of its deterioration. There is a long history of cooperation between microbiologists and conservators of libraries and archival materials, but current approaches addressing paper deterioration need urgent reassessment to take full advantage of modern microbiological methodologies. This article discusses what we believe are the current priority research areas in assessing microbial risk to paper heritage, and reports studies on a 13th century Italian manuscript and on Leonardo da Vinci’s Atlantic Codex which illustrate the problems and challenges encountered when dealing with microbial investigations of paper artworks. The potential of using a more advanced microbiological approach is highlighted.

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• The Tomb of the Shroud
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• What have the Romans ever done for us?

I’ve written quite a lot on MicrobiologyBytes about the growing threat from Bluetongue virus. New figures from the European Commission now show that BTV 8, the epidemic strain of the virus, has been virtually eradicated from mainland Europe after an extensive vaccine campaign.

Tens of thousands of cases of bluetongue, predominantly the BTV8 strain, were identified across Europe in 2007 and 2008. The numbers dropped significantly in 2009 and are on course for a further significant decline this year.

The latest figures from the European Commission show incidence of BTV 8 has declined to just two recorded cases, while rare European cases of other strains are also on the way down.

Bluetongue virtually eradicated in Europe. Farmer’s Guardian, 2 November 2010

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• Bluetongue virus
• Midges and the emergence of bluetongue virus in northern Europe
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Marine natural products are a continued focus for drug discovery and have provided many important therapeutic agents. Lead compounds with biomedical potential have been isolated from marine invertebrates, bacteria, and fungi. Each year numerous compounds with an array of biological activities are reported, but to-date only 13 molecules have entered into the clinical pipeline. Four molecules have been approved for clinical use, one of which is approved only in the EU. The approved molecules include two nucleosides based on sponge-derived nucleosides, a cone snail peptide, and a metabolite isolated from a tunicate. Marine microbes have received growing attention as the sources for bioactive metabolites and have great potential to increase the number of marine natural products in clinical trials. The sustainable and economic supply of the active pharmaceutical ingredient is often easier to achieve for compounds produced through microbial fermentation approaches versus the cultivation of slower growing macroorganisms.

Marine natural products provide an excellent opportunity to study diverse and unique compounds not readily accessible from any other source leading to expansion of the pharmaceutical pipeline. Marine microbes can produce unique compounds covering new chemical space, and the utility of marine natural products is expanding beyond its original role in identification of new prototype drug leads into fields of study involving sustainable supplies of unique molecules using biosynthesis in conjunction with synthesis. Perhaps the greatest impact marine natural products has played is in revealing that unexplored and previously inaccessible chemical space can contribute to growth in the pharmaceutical pipeline. Improved methodologies in fermentation technologies, biosynthesis, and synthesis provide opportunities to both create and supply drug leads that would not be available by any single method independently. As a result pharmaceutical biotechnology in the future is certain to provide increasingly sophisticated molecular architecture assembled using biosynthesis and synthesis in concert.

The expanding role of marine microbes in pharmaceutical development. Curr Opin Biotechnol. Oct 16 2010
Marine microbes have received growing attention as sources of bioactive metabolites and offer a unique opportunity to both increase the number of marine natural products in clinical trials as well as expedite their development. This review focuses specifically on those molecules currently in the clinical pipeline that are established or highly likely to be produced by bacteria based on expanding circumstantial evidence. We also include an example of how compounds from harmful algal blooms may yield both tools for measuring environmental change as well as leads for pharmaceutical development. An example of the karlotoxin class of compounds isolated from the dinoflagellate Karlodinium veneficum reveals a significant environmental impact in the form of massive fish kills, but also provides opportunities to construct new molecules for the control of cancer and serum cholesterol assisted by tools associated with rational drug design.

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• Biofilms Use Chemical Weapons
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