an autodidact meets a dilettante…

‘Rise above yourself and grasp the world’ Archimedes – attribution

Useful stuff on extremophiles and their tricks

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A tardigrade or water bear, emblematic creature for extremophile-philes everywhere. Look em up, cause they’re not mentioned in this article

I’ll try to wean myself from the largely thankless task of writing about politics by picking a topic, almost at random, though one that I know will keep me engaged once I get started.

I was reading an article on the geology of the Earth’s crust and upper mantle (aka lithosphere) the other day, which mentioned the possibility of life in the mantle. Little is known for sure about the mantle’s composition and activity, because until recently drilling down to that level has been just a pipe dream, so to speak. The mantle’s distance from the earth’s surface varies considerably from region to region, but the average depth of the crust at its thinnest, ie under the ocean, is about 6 kilometres. In 2011, microscopic nematodes, or roundworms, were found some 4 kilometres below the surface in a gold mine in South Africa. Other single-celled micro-organisms were found in the region, at depths of 5 kms. Since we’ve rarely plumbed such depths, it’s not unreasonable to suppose that life down that far may be commonplace. We already know that life exists under the sea floor, at immense pressures. At the bottom of the Mariana Trench in the western Pacific, bacteria thrive 11 kilometres below sea level, and some bacteria have been tested in the lab as tolerating 1000 atmospheres of pressure.

Of course, the term extremophile, applied to such life forms, is typically anthropocentric, as they would presumably shuffle off their mortal coils tout de suite when subjected to our torturous environment. Then again…

Extremophiles are of course termed as such when found in conditions that are far from what we would term normal. Such conditions include extremely hot or cold environments, highly acidic or alkaline environments, anaerobic environments, and extreme pressure. They include archaea, the earliest living organisms we know of, some of which have been found to be halophilic (thriving in high salt conditions) or hyperthermophilic (lovers of temps around 80°C).

So how far down can these organisms go? What do they live on? What do they look like and how do they relate to other organisms on the bush of life?

This article from National Geographic online suggests the possibility of an ecosystem existing some eight or nine kilometres below the Mariana Trench. The trench is a subduction zone, a region known to provide pro-life environments of sorts. Analysing such regions requires geological as well as microbiological expertise. A geological process known as serpentinisation provides an ecosystem for methane-consuming microbes. Serpentine is a mineral formed deep in the lithosphere ‘when olivine in the upper mantle reacts with water pushed up from within the subduction zone’, according to the article. Hydrogen and methane are by-products of this reaction, and this serpentinisation process is already known to create microbial habitats at oceanic hydrothermal vents. Furthermore, in recent years, serpentinisation has been found ‘everywhere’, at subduction zones and within mountain ranges, suggesting that methane-supported life may be commonplace, and may even exist elsewhere in the solar system where there is tectonic activity, and an abundance of olivine.

Organisms living at great depths, under great pressure, are called piezophiles. So what is it that permits these bacteria, archaea and other unicellular organisms to thrive – or perhaps only just survive – in such conditions? There’s no one-size-fits-all answer, as some, such as xenophyophores, which are found at depth throughout the world’s oceans, are relatively complex creatures that appear to have adapted over time to increased pressure in order to benefit from benthic provender, while others like Halomonas salaria, a proteobacterium, are obligate piezophiles, unable to survive in under 1000 atmospheres. Unsurprisingly the outer membranes of these organisms are necessarily different in structure and composition from your common or garden microbes, but also unsurprisingly, it has proved difficult to analyse the structural features of piezophiles under lab conditions, though it’s clear that regulation of membrane phospholipids is key to maintaining a stable internal environment, which can not only withstand pressure, but also extremes of heat or cold or acidity. Proteins are also modified to maintain function. Although little is yet known about these organisms, the variety of their environments suggest a variety of adaptations independently arrived at. Most are autotrophs, or self-feeders, able to build organic compounds such as proteins through chemosynthesis in the absence of light. Many of them appear able to slow their metabolism and their reproduction rate by many factors.

Researchers are becoming increasingly interested in extremophiles in general, as they’ve widened the possibilities of life in environments hitherto dismissed as unviable – in boiling water or under mountains of ice for example – just as we’ve begun to discover or further explore other planets (and moons) within and beyond our solar system. The field of microbiology has also made great strides in recent decades. Don Cowan, a senior researcher at the University of Pretoria, describes the microbiological ‘revolution’ of the eighties:

In less than a decade, a combination of conceptual, scientific and technical developments all came together. These included the ability to purify total environmental DNA, the development of special marker sequences that can identify different microbial species, and the advent of very fast, very cheap DNA sequencing techniques.

Collectively known as metagenomics, these developments hugely stimulated the field of microbiology. They have done so across diverse areas of science, from biological methods for cleaning up environmental pollution and contamination, to human disease.

Researchers are applying these techniques to the examination and possible exploitation of extremophiles, for example to improve drought or temperature tolerance in plant species, for various pharmaceutical applications and possibly for the development of biofuels, as heat-tolerant enzymes enable plant tissues to be broken down more readily. The range of products and processes that can be improved by tapping into the enzyme production of various types of extremophiles is potentially vast, according to James Coker, a researcher at the University of Maryland’s Department of Biotechnology. In a 2016 paper, Coker admits that research in this field is new, but real progress has already been made:

Four success stories are the thermostable DNA polymerases used in the polymerase chain reaction (PCR) 17, various enzymes used in the process of making biofuels 18, organisms used in the mining process 19, and carotenoids used in the food and cosmetic industries 20. Other potential applications include making lactose-free milk 1; the production of antibiotics, anticancer, and antifungal drugs 6; and the production of electricity or, more accurately, the leaching of electrons to generate current that can be used or stored 21

That last-mentioned application is of particular interest (as are all the others), as clean electricity production and storage is a high priority issue for some. Extremophile microbial catalysts can be used to drive microbial electrochemical systems (MES), a new TLA which may or may not catch on. Related TLAs include the MFC (microbial fuel cell) and the MEC (microbial electrolysis cell). Without losing myself in too much detail here, the exploitation of these microbes to help drive reactions at the electrodes has a number of useful applications, such as the remediation of waste-water, desalination, biosensing and ‘generating electrical energy from marine sediment microbial fuel cells at low temperatures’ (Dopson et al, 2016). None of this is, as yet, set to revolutionise the clean energy industry, but these are just some of the largely unsung incremental developments that are, in fact, moving us towards more clever and efficient use of previously untapped renewable resources. I was about to use the metaphor ‘at the coalface’ – which would’ve been appropriately inappropriate.

It’s impossible for we dilettantes to keep up with all these discoveries and developments in a detailed way, but we can at least feel the excitement of work being done and advances being collaboratively made, as well as sensing the many obstacles and unforeseen complexities involved in transforming the viability of these amazing life-forms and their products into something viable and possibly life-transforming for the humans who have discovered them and unlocked their secrets. When politics and our inhumanity to others (human and non-human) lets us down, we can still marvel at our relentless drive and ingenuity.

 

Written by stewart henderson

July 14, 2018 at 8:50 am

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