October's Paper of the Month

Partly fossilized mycelium of fungal hyphae on a zeolite crystal from 740 m depth in fractured granite. Back-scattered Environmental Scanning Electron Microscopy image. Width of view 600 µm. Photo credit: Henrik Drake, Magnus Ivarsson.

Despite being considered vital for energy cycling of the earth; the deep biosphere is one of the least understood ecosystems. It is thought to have approximately 19% of the earth’s biomass yet samples are hard to come by, making their study difficult. Microorganisms from the deep biosphere that have been studied are generally prokaryotes, with microeukaryotes being largely ignored.

Recently samples were taken from a 740m deep drill core sample in Sweden after the site was investigated for its suitability for deep nuclear waste repositories. Findings have shown the presence of fossil and active fungi in these deep ecosystems, but little work has gone into understanding them.

Drake et al., studied the microorganisms in these deep crystalline fractured rock samples. Their aim was to gain a better understanding of the microbial processes in the continental crust. The knowledge of this vast realm is very scarce and tells us more about life forms and processes under extreme conditions which may also have important implications for nuclear waste storage. 

Their analyses found the microorganisms belonged to the Kingdom Fungi and were found to be anaerobic. The closest systems studied were that of anaerobic fungi in the rumina of ruminant animals. It was proposed that the fossilised fungi also shared a symbiotic relationship with bacteria in the deep biosphere. 

The group used a THMS600 to help indicate the approximate age of the fungi. Dr Drake said, “The THM600 was used to investigate fluid inclusions in calcite crystals that were spatially related to the fungi. The fluid inclusion signatures gave us information about past conditions (e.g. salinity) in the fracture void. Because no radiometric dating could be made of the fungi, the fluid inclusion signatures (when put in a paleohydrogeological context) serve as an important temporal indicator for when the fungi were active.” 

Their work highlighted an intimate relationship between the fungi and sulphate reducing bacteria, further drawing attention to the richness of the deep oligotrophic biosphere which is often neglected. These fungi were found to provide significant amounts of H2 to autotrophic microorganisms in the crystalline continental crust.

The group also looked at the biochemistry of these fungi and found they may pose a threat to repositories of toxic waste.  This is through either directly breaking down the barriers holding the waste, or by facilitating the bacterial community into doing so. 

Their work highlights the importance of studying these neglected geological microorganisms. With fossil fuels running out, nuclear energy may be the way forward. But to safely store away waste products, understanding their chemical and geological environment is of utmost importance as illustrated by Drake et al., As such it becomes vital to study ecosystems, such as the deep biosphere, in its entirety. 

By Tabassum Mujtaba

Drake et al., Anaerobic consortia of fungi and sulfate reducing bacteria in deep granite fractures. Nat. Comms 8, Article number: 55 doi:10.1038/s41467-017-00094-6 (2017)

September's Paper of the Month

Serpentinization is central to many theories of the origin of life. 

The hydrothermal alteration of mantle rocks, referred as serpentinization, occurs when the mantle is exposed to aqueous fluids circulating below 400°C, leading to the formation of serpentine, hydrogen and other minerals. It is a process heavily involved in mass exchange between the mantle and the surface and influences geochemical cycling and fluid-mobile elements. It occurs in various submarine environments including mid-ocean ridges and subduction zones and it affects the physical and chemical properties of the oceanic lithosphere.

 It is also pivotal to current theories on the origin of life. Serpentinization is likely to have provided the crucial chemical gradients required for life to being when the earth was simply rock, water and carbon dioxide. 

Despite being a process vital to our understanding of the origin of life and the Earth´s lithospheric mantle activity, the rates and the environmental factors affecting serpentinization are poorly understood. A collaborative effort from Virginia Tech, The Free University of Berlin, Woods Hole Oceanographic Institution and The University of Texas used synthetic fluid inclusions as micro-reactors in olivine crystals as a model to study the rate of serpentinization. This method allowed them to study mineral precipitation and water activity in real time and in situ.

When discussing their work, Dr. Lamadrid said “We trapped synthetic fluid inclusions (tiny droplets of fluid) with a seawater-like composition in gem quality olivine crystals and then we set the samples to serpentinization conditions (~280ºC). Within a few days, serpentine crystals begin to precipitate inside the synthetic fluid inclusions. Since the inclusions are isolated any changes inside the inclusion can be observed and we can model them as chemical micro-reactors. The serpentinization reaction consumes H2O, so the original salinity starts to increase as more H2O leaves the fluid to form new serpentine crystals. As such, we were able to monitor the amounts of H2O leaving the fluid by measuring changes of the salinity inside the inclusion. The salinity of the fluid inclusions were measured with high precision by measuring changes in the freezing point depression of the fluid inclusions with the Linkam THMSG600 stage.”

Their technique allowed them to study the mineralogy and chemistry of the reaction products. After carrying out experiments with different salinities and fluid compositions, they found the reaction to be highly sensitive to the salinity and chemistry of the fluid. This poses interesting concepts of where serpentinization may occur in the earth’s mantle as well on other planetary bodies. Their novel micro-reactor technique could also be applied to many other minerals, reaction products, and fluid compositions to study fluid-rock reactions in real time and in situ. 
 

By Tabassum Mujtaba

 Lamadrid, H. M. et al. Effect of water activity on rates of serpentinization of olivine. Nat. Commun. 8, 16107 doi: 10.1038/ncomms16107 (2017).

August's Paper of the Month

Bacteria must be able to find food in order to survive. They have evolved various chemotactic strategies to efficiently locate and track nutrient gradients, several of which have been defined. The strategies usually consist of a series of run phases in which the bacteria swim in straight lines followed by phases of tumbles, arcs, stops and reversals. A tight control over these phases allows them to direct and adapt movements towards nutrient sources. 

Their intricate pathways of signalling proteins allow them to detect chemical changes in the environment which in turn will affect their run phase. Bacteria must maintain straight trajectories to pick up vital environmental cues and react appropriately. However due to their size and shape, the lengths of their movements are restricted by Brownian motion. 

The rotation friction (fr) co-efficient is the cell’s resistance to being rotated, which is dependent on both cell size and shape. Several models have been suggested for spherical and ellipsoidal cell types. However, despite theoretical modelling, there has been little empirical evidence. 

August’s Paper of the Month, from the Universities of York and Lincoln, focussed on validating the theoretical understanding of how cell size and shape affect bacteria run phases. 

To create bacteria with different aspect ratios they treated E.coli with cephalexin, which was found to elongate the cell. They compared this form to the normal wildtype E.coli. With increasing cell length, they found an increase in flagella along the cell body.
 

Flagella are primarily motile appendages, but also sensory, and are found commonly in the cell bodies of bacteria. 

Using phase contrast microscopy, they then recorded and tracked both the control and elongated group. Samples were imaged while placed on a Linkam PE-100 ZAL system heated to 33°C. 

Their results indicated the elongated cells had shorter runs but longer tumble phases. This finding agreed with the veto model which suggests an increase in flagella increases the average tumble time. 

Although mechanistically different, they also found elongated E.coli performed a run and reverse strategy. This pattern has been described within natural populations of marine and soil bacteria and has been found to be advantageous within these particular niches. 
When asked about the role of the stage, Dr Oscar Guadayol said, “For this kind of study, the ability to perfectly control the environment at the microscale is critical, and thus the PE100 has become an absolutely essential piece of equipment in our everyday exploration of the microbial behaviour.”

Their work experimentally demonstrated long-standing theoretical predictions about how cell elongation may affect the capability of bacteria to swim and to navigate their chemical landscape and how different morphologies can lead to vital changes in motility patterns. 

They are now taking their results one step further and using microfluidic devices with the PE100 to characterize bacterial chemotaxis.
 

A microfluidic chip placed on a Linkam PE100 ZAL system. 

By Tabassum Mujtaba

Guadayol et al., Cell morphology governs directional control in swimming bacteria. Sci Rep| 7: 2061 | DOI:10.1038/s41598-017-01565-y

July's Paper of the Month

A hexagonal ice crystal in the presence of birch pollen molecules. The shape is indicative of ice crystal growth inhibition.

Ice crystal growth through nucleation is an important natural process for atmospheric and cryobiological processes. For biological organisms, surviving sub-freezing temperatures requires tackling intracellular ice formation. Such organisms have evolved antifreeze proteins to inhibit ice crystal growth, thus preserving structural integrity. 

Ice crystals are formed in clouds triggered by ice nucleating particles. Originally it was believed these particles were forms of mineral dust but recent studies have found them to also include biological agents including pollen, bacteria, fungal spores, cellulose and microalgae. 

Active sites are regions on the ice nucleating particles where critical ice embryo formation occurs. These can be proteins or polysaccharides in the cell membrane although studies have found these are still active when separated from their original particles. 

Yet these biological molecules can act as both ice nucleators and ice inhibitors and consequently there has been much desire to further understand the manner in which these molecules interact with ice. The search for such answers may also help to further explain how biological organisms survive extreme climatic conditions.

July’s Paper of the Month comes from the Bielefeld University. They tested for the presence of antifreeze molecules in various types of known ice nucleating boreal pollen. The group conducted their temperature controlled experiment using the Linkam BCS196.

FTIR spectroscopy of the pollen highlighted two polysaccharides with similar chemical structures which differed in size. The larger (>100kD) of the two was responsible for the ice nucleating ability of the pollen while the smaller (<100kD) exhibited ice inhibiting abilities. 
Analysis of IR spectrum suggests the ice inhibiting molecules are either fragments of ice nucleating molecules, or ice nucleating molecules are clusters of smaller ice inhibiting molecules. The group’s results indicate both to have similar molecular moieties. Complementary findings in studies on boreal pollen suggest this may be a mechanism to protect pollen against springtime frosts. 

When asked about the role of the BCS196 stage, Professor Koop said: “For the ice growth inhibition experiments, we have developed an assay which makes use of the BCS196 stage while attached to a brightfield transmission optical microscope. The stage allows for a rapid cooling to about -50 °C in order to produce a film of polycrystalline ice and, subsequently, an accurate and constant hold temperature at -8 °C, during which we determine how the size of the ice crystals changes over several hours and how this is affected by the pollen molecules.”

Their valuable work better helps us to understand the way molecules may be interacting with ice in natural processes. 

By Tabassum Mujtaba

Dreischmeier, K. et al. Boreal pollen contain ice-nucleating as well as ice-binding ‘antifreeze’ polysaccharides. Sci. Rep. 7, 41890; doi: 10.1038/srep41890 (2017).