Tag Archives: fungus

Cyborg soil?

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Edith Hammer, lecturer (Biology) at Lund University (Sweden) has written a July 22, 2021 essay for The Conversation (h/t July 23, 2021 news item on phys.org) that has everything.: mystery, cyborgs, unexpected denizens, and a phenomenon explored for the first time (Note: Links have been removed),

Dig a teaspoon into your nearest clump of soil, and what you’ll emerge with will contain more microorganisms than there are people on Earth. We know this from lab studies that analyse samples of earth scooped from the microbial wild to determine which forms of microscopic life exist in the world beneath our feet.

The problem is, such studies can’t actually tell us how this subterranean kingdom of fungi, flagellates and amoebae operates in the ground. Because they entail the removal of soil from its environment, these studies destroy the delicate structures of mud, water and air in which the soil microbes reside.

This prompted my lab to develop a way to spy on these underground workers, who are indispensable in their role as organic matter recycling agents, without disturbing their micro-habitats.

Our study revealed the dark, dank cities in which soil microbes reside [emphasis mine]. We found labyrinths of tiny highways, skyscrapers, bridges and rivers which are navigated by microorganisms to find food, or to avoid becoming someone’s next meal. This new window into what’s happening underground could help us better appreciate and preserve Earth’s increasingly damaged soils.

Here’s how the soil scientists probed the secrets buried in soil (Note: A link has been removed),

In our study, we developed a new kind of “cyborg soil”, which is half natural and half artificial. It consists of microengineered chips that we either buried in the wild, or surrounded with soil in the lab for enough time for the microbial cities to emerge within the mud.

The chips literally act like windows to the underground. A transparent patch in the otherwise opaque soil, the chip is cut to mimic the pore structures of actual soil, which are often strange and counter-intuitive at the scale that microbes experience them.

Different physical laws become dominant at the micro scale compared to what we’re acquainted to in our macro world. Water clings to surfaces, and resting bacteria get pushed around by the movement of water molecules. Air bubbles form insurmountable barriers for many microorganisms, due to the surface tension of the water around them.

Here’s some of the what they found,

When we excavated our first chips, we were met with the full variety of single-celled organisms, nematodes, tiny arthropods and species of bacteria that exist in our soils. Fungal hyphae, which burrow like plant roots underground, had quickly grown into the depths of our cyborg soil pores, creating a direct living connection between the real soil and our chips.

This meant we could study a phenomenon known only from lab studies: the “fungal highways” along which bacteria “hitchhike” to disperse through soil. Bacteria usually disperse through water, so by making some of our chips air-filled we could watch how bacteria smuggle themselves into new pores by following the groping arms of fungal hyphae.

Unexpectedly, we also found a high number of protists – enigmatic single-celled organisms which are neither animal, plant or fungus – in the spaces around hyphae. Clearly they too hitch a ride on the fungal highway – a so-far completely unexplored phenomenon.

…

The essay has a number of embedded videos and images illustrating a fascinating world in a ‘teaspoon of soil’.

Here’s a link to and a citation for the study by the researchers at Lund University,

Microfluidic chips provide visual access to in situ soil ecology by Paola Micaela Mafla-Endara, Carlos Arellano-Caicedo, Kristin Aleklett, Milda Pucetaite, Pelle Ohlsson & Edith C. Hammer. Communications Biology volume 4, Article number: 889 (2021) DOI: https://doi.org/10.1038/s42003-021-02379-5 Published: 20 July 2021

This paper is open access.

X-raying fungus on paper to conserve memory

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Civilization is based on memory. Our libraries and archives serve as memories of how things are made, why we use certain materials rather than others, how the human body is put together, what the weather patterns have been, etc. For centuries we have preserved our memories on paper. While this has many advantages, there are some drawbacks including fungus infestations.

A July 21, 2015 news item on ScienceDaily describes how a technique used to x-ray rocks has provided insights into paper and its fungal infestations,

Believe it or not: X-ray works a lot better on rocks than on paper. This has been a problem for conservators trying to save historical books and letters from the ravages of time and fungi. They frankly did not know what they were up against once the telltale signs of vandals such as Dothidales or Pleosporales started to spot the surface of their priceless documents

Now Diwaker Jha, an imaging specialist from Department of Chemistry, University of Copenhagen, has managed to adapt methods developed to investigate interiors of rocks to work on paper too, thus getting a first look at how fungus goes about infesting paper. …

A July 21, 2015 University of Copenhagen press release (also on EurekAlert), which originated the news item, expands on the theme,

This is good news for paper conservators and others who wish to study soft materials with X-ray tomography. “Rocks are easy because they are hard. The X-ray images show a very good contrast between the solid and the pores or channels, which are filled with low density materials such as air or fluids. In this case, however, paper and fungi, both are soft and carbon based, which makes them difficult to distinguish,” says Diwaker.

Diwaker Jha is a PhD student in the NanoGeoScience group, which is a part of the Nano-Science Center at Department of Chemistry. He investigates methods to improve imaging techniques used by chemists and physicists to investigate how fluids move in natural porous materials. At a recent conference, he was presenting an analysis method he developed for X-ray tomography data, for which he was awarded the Presidential Scholar Award by the Microscopy Society of America. And this sparked interest with a conservator in the audience.

Hanna Szczepanowska works as a research conservator with the Smithsonian Institution in the USA. She had been wondering how fungi interact with the paper. Does it sit on the surface, or does it burrow deeper? If they are surface dwellers, it should be easy to just brush them off, but no such luck, says Jha.

“As it turns out, microscopic fungi that infest paper grow very much the same way as mushrooms on a forest floor. However, unlike mushrooms, where the fruiting body emerges out of the soil to the surface, here the fruiting bodies can be embedded within the paper fibres, making it difficult to isolate them. This is not great news for conservators because the prevalent surface cleaning approaches are not adequate,” explains Diwaker Jha.

In working out a way to see into the paper, Jha investigated a 17th century letter on a handmade sheet and a 1920 engraving on machine-made paper. Compared with mushrooms, these fungi are thousands of times smaller, which required an advanced X-ray imaging technique available at the European Synchrotron Radiation Facility (ESRF), Grenoble, France. The technique is very similar to medical tomography (CT scanning) done at hospitals but in Grenoble the X-ray is produced by electrons accelerated to about the speed of light in an 844 meter long circular tube. A handy comparison: “If I were to use medical X-ray tomography to look at an Olympic village, I would be able to make out only the stadium. With the synchrotron based X-ray tomography, I would be able to distinguish individual blades of grass on the field..”

Diwaker hopes that conservators will be able to use the new insight to develop conservation strategies not just for paper artefacts but for combating biodegradation on a host of other types of cultural heritage materials. And that the developed methods can be extended to other studies related to soft matter.

Here’s a citation and a link for the paper,

Morphology and characterization of Dematiaceous fungi on a cellulose paper substrate using synchrotron X-ray microtomography, scanning electron microscopy and confocal laser scanning microscopy in the context of cultural heritage by H. M. Szczepanowska, D. Jha, and Th. G. Mathia. Anal. At. Spectrom. (Journal of Analystical Atomic Spetrometry), 2015,30, 651-657 DOI: 10.1039/C4JA00337C First published online 27 Nov 2014

This paper is behind a paywall. By the way, it is part of something the journal calls a themed collection:  Synchrotron radiation and neutrons in art and archaeology. Clicking on the ‘themed collection’ link will give you a view of the collection, i.e., titles, authors and brief abstracts.

Dyeing textiles naturally when enabled by nanotechnology

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The May 15, 2012 news item on Nanowerk is intriguing,

Nanoparticles from a fungus could lead to new eco friendly dyes claim scientists from the Catholic University of Louvain.

Researchers working for the EU-funded research project SOPHIED have discovered that a fungus from the Solomon Islands produces special enzymes that act as nano-bio-catalysts.  These components help to trigger a chemical reaction between two different basic ingredients and turn it into a dye.

On digging into the matter a little further I found a Sept. 2, 2011 article by Elena Ledda for YOURIS; European Research Media Center about the reasons for the work and about the researcher who’s  focusing on the fungus, Estelle Enaud at Catholic University  of Louvain in Belgium,

The problems encountered by the traditional European colour industry go from lack of innovation and weak market competitiveness to toxicity, environmental hazards and health risks for those working in it. Dye-making industry is based on chemistry and processes designed more than a century ago, some of which are very energy consuming and potentially dangerous for the workers. In order to prevent explosive reactions when mixing the chemicals, the process has to be cooled down to ice cold temperatures, which consumes a lot of energy. Besides, some dyes can be toxic and there is a risk that they may pass the skin through perspiration. …

To overcome this bias scientists of the EU-funded research project SOPHIED led by the Catholic University of Louvain, in Belgium, have extracted special proteins, called enzymes, from fungi. …

“We already knew there is a whole spectrum of colours in the fungis and that the enzymes can form new color compounds during the bioremediation part, that is the process through which the metabolisms of microorganism removes pollutants. What we didn’t know was if it was possible to make textile dyes because these have special properties and chemical functions that you cannot find in nature”, says Estelle Enaud of the Earth and Life Institute – Applied Microbiology at the Université Catholique de Louvain. Enaud was a post-doc researcher in Sophie Vanhulle’s team. Sophie Vanhulle, the project co-ordinator, died two years ago. “The challenge was if it was possible to use the enzyme on a substance that is not natural, and it turned out it was!”

Here’s an interview with Enaud discussing her project (from the YOURIS website),

My curiosity still not satisfied, I researched SOPHIED to find out it is a European Union-funded project (Framework Project 6) with the tagline, novel sustainable bioprocess for European colour industries.  Here’s a 2008 interview with Magalie Foret, another researcher on the project discussing he SOPHIED project and her specialty wetlands engineering  (in French), from the SOPHIED website,

Getting back to Enaud and her latest work (from the Ledda article),

To extract the enzymes the fungi are put into a liquid that contains nutrients, which allows them to grow and release the desired proteins. After taking out the fungi, silica particles are added to the fluid. “The combination of enzymes and silica particles brings to a stabilization of the enzyme and eliminates proteins at the end in our dye product, since they might provoke allergies”, Estelle Enaud points out. “The particle we used the most had a mean size of 100 µm, much bigger than nano. The nano size and the nano part of the project concern the enzymes that are nanocatalysts and can also be called biological nano tools”, she explains. “I must admit I do not really like to use the word nano because although everything I work with as a biochemist is nano, biochemistry is not a new science area”.

The new colorants possess chemical features that allow them to adhere directly to the fibers of polyamide, wool or silk, making it unnecessary to add extra chemicals that can pollute water and provoke allergies. “Before putting this product on the market, it would be important to check its toxicity”, Victor Puntes, responsible of the ‘Inorganic nanoparticles group’ at the ICN (Institut Català de Nanotecnologia) points out. “In principle, large silica particles are more toxic than their nano counterpart: on the one hand, being larger they have a hard time to enter into the cell, on the other, once a few of them have entered, they can produce chronic inflammation that can result, maybe 20 years later, in some kind of cancer”, Puntes explains. Enaud ensures that the silica particles that they use are not toxic. She adds that the particles are customarily used in tooth paste, as ingredient in horticulture, and in concrete are not classified as dangerous substances.

Some interesting possibilities here assuming toxicity and scaling issues are dealt with. One final thought, I wonder if there might be some sort of ‘property’ issues. Given that the fungus under discussion comes from the Solomon Islands, it seems possible that indigenous peoples might feel proprietary, especially if they’ve been making using of it themselves thereby piquing the scientists’ interest in the first place.