ESM 2022 poster: Patterns of bacterial-fungal co-occurrence in European beech (Fagus sylvatica L.) deadwood

For those that were not able to attend the Ecology of Soil Microorganisms 2022 conference (which ran from 19-23 July in Prague, Czech Republic) I got permission to upload the poster which I presented. Being a scientist can also mean doing a bit of public speaking and graphic design. Below, you will find the abstract and poster.

Patterns of bacterial-fungal co-occurrence in European beech (Fagus sylvatica L.) deadwood

Jason Bosch, Ema Némethová, Vojtěch Tláskal, Vendula Brabcová, Petr Baldrian

Deadwood represents an important nutrient source and microbial habitat in forest ecosystems. Its decomposition is one of the key processes of global carbon turnover considering that European natural forests can contain up to 1200 m3 of deadwood per hectare. This deadwood is primarily decomposed by saprotrophic fungi but bacteria also have a role to play, particularly in the provision of nitrogen. Previous work has shown that the first fungi to become established will physically prevent further colonisation by other fungi. As bacteria and fungi can interact in both synergistic and antagonistic ways, we expect that these fungal zones of control will also influence the bacterial community composition at local scales.

We investigated the patterns of microbial diversity and co-occurrence in 1 cm3 blocks of European beech (Fagus sylvatica L.) deadwood collected from the Žofínský prales National Nature Reserve in the Czech Republic, using 16S and ITS amplicon sequencing. Compared to previously-collected “whole log” communities, the small-scale communities showed less diversity both individually and in combination. By correlating fungal and bacterial species, we were able to expand on previous work which showed that fungi influence bacterial community composition. As small-scale microbial communities collected from the same log can differ dramatically from one another, we advise caution when interpreting “whole log” microbial community data as the results may not reflect the actual interactions which take place in the deadwood.

If you would like to cite the poster, you can use the abstract book citation:

Piché Choquette S., Slaninová Kyselková M., Pospíšek M., Baldrian P. (Eds.), 2022. Ecology of Soil Microorganisms – Book of Abstracts, Prague, June 19 – 23, 2022.

Photos from Prague

I’m ashamed at how little I have written this year, even though I have had several ideas for blog posts. To help assuage some of my guilt, I will share a few photographs I have taken.

I’m rather lucky to be living near the Krč forest where I can, regularly, go walking. At the beginning of the year it was still winter and most of the trees were bare.

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2022 Book List

We’re now in mid-March and I still haven’t written down my thoughts on the two books I read in January. A lot has been going on recently but, the longer I take to write these down, the worse my recollections become.

2021 Book List
2020 Book List
2019 Book List
2018 Book List
2017 Book List

The Philosopher and the Wolf (2008) by Mark Rowlands

In this book, Rowlands shares several of his experiences moving between countries and building a career in philosophy, all while raising a wolf. The anecdotes about Brenin, the wolf, invariably serve as the starting point for some sort of philosophical digression. While several of these digressions are indeed interesting, I was seldom convinced by his arguments (see my blog post on what makes a person evil for an example).

I would’ve preferred much more of a focus on the stories involving Brenin, but those that are there do provide some fascinating insights on animal behaviour and training. While not all of the methods will probably be approved of by everyone, Rowlands does make the point that wolves and dogs are quite different and, from the stories he gives, he managed to have a wolf which was much better behaved than many dogs. It’s also clear that he cared deeply for Brenin, and his other dogs, and, especially towards the end, many of the stories were quite emotional.

If you were planning to read The Philosopher and the Wolf to hear about what is like to have a wolf as a pet, you will probably be disappointed. I’d estimate that that about two thirds of the book are given over to his philosophical musings which, if nothing else, at least serve as food for thought. I can’t say that I agreed with most of them but I did still enjoy the book and think it is worth reading.

A Christmas Carol (1843) by Charles Dickens

There’s really little to say about this one. It’s an old story and, if you have any contact with Western culture, you have likely seen an adaption, homage or parody of this. I am, of course, familiar with the story but not the original work. In fact, I think this is my first time reading Dickens’ own words. I have no complaints but, given how well-known the story is, there were no real surprises.

What was special was that I was reading a copy which, I believe, had been my maternal grandmother’s. I can’t recall the exact printing date of the book but it was around 80-90 years old. While not as old as the story itself, it’s still quite a bit of history and all of the people who originally bought and read it are now dead. Yet the book is still there, can still be read and provides a tangible link to the past. Plus, a physical book has no battery issues or file type compatibility problems.

What makes a person evil?

The first book I’m reading this year is Mark Rowland‘s memoir, The Philosopher and the Wolf. For now, I will just say that it’s stories of having a wolf mixed with some philosophical musings. One of those musings concerned evil. He maintained that evil does exist, though not in a supernatural sense, and that it consists of “very bad things” and that people do those “very bad things” due to a failure on their part, both a failure of moral duty (to do the right thing) and epistemic duty (to properly subject one’s beliefs to scrutiny). He contrasted that with the modern view of evil which, he claimed, is seen as people doing “very bad things” because of an underlying medical or social issue. I think that both of those views are fundamentally flawed and want to describe a different way of viewing evil.

Let’s briefly consider the idea that evil actions are those actions which are very bad, i.e. at the extreme end of a scale of bad actions. Shoplifting a chocolate bar is bad but not very bad. It’s worse to steal a car but still not evil. Premeditated murder, especially if paired with some other crime, is now getting to the sort of thing we would nearly all agree is evil. But there’s a flaw; except for religious beliefs, there is no “objective” morality, so there is no objective and universal measurement which you can use to say something is bad. As there is insufficient evidence to support the claims of religion, we must discard it. We are left with secular morality.

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A literary return to the Namib Desert

I managed to finish off two more books for my 2021 Book List. It’s still fewer than I had hoped for this year but it’s better than nothing.

The Sheltering Desert (1956, translated 1957) by Henno Martin

This is a memoir which recounts the story of two German geologists stationed in South West Africa, now Namibia, which I bought during my trip to the Namib Desert. When WWII broke out, they wanted no part in it, nor did they wish to be interned by the police, so they resolved to hide out in the Namib Desert until it was all over. The pair of scientists and their dog travelled into the desert and remained there for two years until malnutrition forced them to abandon their plan.

Along with the descriptions of life in the desert are several philosophical musings on human society, evolution and the nature of man. A lot of it feels quite dated but I really enjoyed the discussions on the similarities and differences between humans and non-human animals. Even back then, many people living in cities and towns had little actual contact with wild, or even tame, animals; meaning no familiarity. Martin observed that, after time in the desert, with only the wild animals as their neighbours, they began to see the complexity in their behaviour and recognise the animals as being as unique as other people.

As the pair are scientists, the story is more than just a tale of survival. Scientific curiosity is evident in many observations and trips which include one to investigate why the rocks of a distant mountain were so white. If you’re at all interested in outdoor activities or the Namib, I think it will make for a great read.

Why Vegan? (2020) by Peter Singer

Why Vegan? is a collection of essays by the controversial, utilitarian philosopher Peter Singer. I had already read his classic book Animal Liberation but only after already becoming a vegetarian. These essays also revolve around the topic of animals and diet and span several decades, the earliest from 1973 and the most-recent from 2020. It’s a quick read, with some essays being incredibly short, but a very important topic.

Singer’s ethical approach is about avoiding causing unnecessary suffering, so several essays discuss cruelty in farming. In his introduction he does note that several practices documented in older works, such as Animal Liberation, have now been outlawed but not all problems have been fixed. In an essay from 2006 on chicken farming, he describes how many chickens are still kept in cramped conditions, standing in their own filth, where some starve to death and many others are boiled, alive and conscious, due to failures of the stunning system and manual oversight. These are things we ought to know if we are to be informed consumers.

If someone has never thought much about the practice of eating animals, because it is usually an unquestioned aspect of human society, then this collection will serve as a good introduction to the topic. This collection doesn’t go deep into details (I would recommend something like A Plea for the Animals to expand on the topic.) but it raises many of the questions and concerns which everyone should keep in mind. Regardless of the answers we eventually settle on, this is a pressing topic which we must think hard about and not allow the suffering of our fellow creatures to be hidden behind the veils of tradition and ignorance.

Updating my blogroll

The blogroll is on the main page of my blog and links to various other sites that I consider worth reading. The sites which were on there were from many years ago and included several which I no longer read. When I noticed that, I saw that it was time to update it. Here’s a new list of blogs which are worth reading. Go check them out.

Animal Emotions

Animal Emotions is written by Marc Bekoff, Professor Emeritus of Ecology and Evolutionary Biology at the University of Colorado, Boulder, United States and co-founder of the Jane Goodall Institute of Ethologists for the Ethical Treatment of Animals (ethology being the study of animal behaviour). The blog deals with various aspects of animal behaviour, welfare and ethics.

The Bowman Lab

This is the blog for the laboratory of Jeff Bowman from the Scripps Institution of Oceanography in the US. This is a blog that I started following more recently to get a wider view of microbial ecology. The Bowman lab works on different aspects of microbial ecology with many posts focussing on analytical tools as well as marine and polar microbial ecology.

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Rocks, (metaphorical) souls and His Dark Materials

Additions to my 2021 Book List.

Life at Rock Surfaces (2021) edited by Burkhard Büdel and Thomas Friedl

This is quite different to the other books I’ve been reading, both because it’s aimed at academics and because it’s not mine. I was lent a copy of the book by Pedro, my friend and colleague, who was an author of one of the chapters. Each chapter focusses on a different aspect of life, mostly microbial, at rock surfaces. Some of the chapters make for interesting reading on organisms living in quite an extreme habitat and some, like a taxonomy guide, are not chapters that lend themselves to normal reading.

As it’s aimed at an academic audience, it’s not really accessible unless you have a fair bit of familiarity with the field. Each chapter is written by a different set of authors and so the quality and style of writing varies wildly from chapter-to-chapter. The best chapters are fairly easy to read and follow but others are a slog. Part of this is due to the content of the chapters but, often, it is poor academic writing that is opaque or unnecessarily stilted. For example, there was one chapter written by a single author that repeatedly used phrases such as “The author hypothesises …” instead of “I think …” The former isn’t a more scientific way of writing; it’s stilted, it’s awkward and is the sort of thing that leads to multiple articles about why scientific writing needs to change.

Science in the Soul (2017) by Richard Dawkins

This is a collection of Dawkin’s essays and speeches from across the years. There is a lot of good content with a wide range of subjects, including science, religion, politics, humour and even a few eulogies. I had read probably about four of them before but that didn’t matter because it was still worthwhile reading them again. Out of the whole collection, there only a handful which I did not enjoy, which is a pleasant return to normality after Outgrowing God.

Despite the breadth of topics, there is an impressive depth of insight which one only gets from spending decades immersed in science. Dawkins’ clarity when writing and the knowledge beneath his writing is a welcome change from so much of the shallow and misguided thinking which is commonly seen today. Indeed, several chapters touch on issues which are still debated, even though they probably should’ve been settled many years ago. Dawkins is probably the best modern science writer and I can highly recommend this book.

His Dark Materials: The Amber Spyglass (2000) by Philip Pullman

The Amber Spyglass is the final book of the His Dark Materials trilogy and it is a great conclusion. I won’t say I am entirely happy with the way that everything ended, but I can see why it ended that way. I won’t say much of what happens to avoid spoilers, but I will say that it is a brilliant story, set in vivid worlds and overflowing with imagination.

I really enjoyed seeing some scientific musings in this book. During the story, the characters travel between different worlds and, in one of them, evolution followed a very different path. It’s not in any way a scientific book but it did a really cool job of pondering a different path of evolution and showing the interplay between different organisms as well as their environment. That was really cool.

The entire trilogy was well-written but I have to be clear how addictive and easy-to-read it is. There are good books that I’ve enjoyed reading but, when I finished a chapter, I was ready to stop. All of the His Dark Materials books are those wonderful sort where, after I finished a chapter, I just wanted to keep going. I thoroughly enjoyed it, highly recommend it and think I might need to look into the BBC series to see how it compares.

Science is universal

I’ve seen some rather disturbing reports recently that New Zealand is aiming to insert indigenous Mātauranga Māori beliefs into science classes. While there are, no doubt, many important bits of knowledge, there are also many superstitions such as the belief that “Rain happens when the goddess Papatuanuku sheds tears.” This is hardly the first time that unscientific, indigenous knowledge has been pushed in this way nor the first time that science has been, incorrectly, criticised as Western, white or European. In 2016, an infamous video did the rounds, showing a “ScienceMustFall” student at the University of Cape Town claiming that some people could use witchcraft to strike others with lightning. Mythical origin stories which claim that certain groups have always caused problems for those studying human migration in both North America and Australia. Many of these criticisms appear to be rooted in the negative way these communities have historically been treated. What becomes frustrating is that there are many legitimate concerns in those criticisms but the push-back becomes an over-correction which now demands an equal place for unscientific mythology which does not belong in a science classroom.

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