Small Things Considered

A blog for sharing appreciation of the width and depth of microbes and microbial activities on this planet.

Small Things Considered
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Welcome to Small Things Considered (STC)! In this blog we share our excitement about unexpected and unusual stories of the microbial world. The "About" page describes who we are. But we do not just publish our own writing. We very much enjoy posting contributions from students, postdocs, and others. Don't think that we do this to avoid work, we spend a lot of time editing the material we receive. Do send us your comments, criticisms, submissions, ideas, or whatever else comes to you mind; we are very eager to hear from you. See the "Contact" for directions on how to reach us. Thank you for visiting and, before you go, consider taking a moment to "Subscribe."
  • Safeguarding Beetle Development
  • Molecular Fossils of Microbial Interactions
  • A New Look and Other Changes
  • Christopher T. Walsh (1944–2023)
  • The Who-Ate-Whom of Terms in Biology: Virovory
  • Winter Vacation
  • Retrospective, July to December 2022
  • Luciferin in Scintillons at Sea
  • Applied Molecular Microbiology at Dubrovnik

First the Fire, Then the Fungus

by Roberto
 

FigureFigure 1. View from space of the wildfires raging in the Western United States, July 2021. Source

Fire is a fundamental eco­lo­gi­cal pro­cess. Through­out the his­tor­y of life on Earth, fire has been a re­gu­latory force that great­ly in­flu­en­ces eco­sys­tem func­tion and evo­lu­tion. Its ef­fects are not felt gra­du­al­ly but rather through pe­ri­od­ic, sud­den, and ca­tas­troph­ic ef­fects on po­pu­la­tion siz­es, com­mu­ni­ty com­po­si­tion, and nu­trient cyc­ling (par­ti­cu­lar­ly car­bon.) Fire's be­ne­fi­cial ef­fects in in­vi­go­rat­ing eco­sys­tems are well re­cog­niz­ed and of­ten put into prac­tice through "pre­scrib­ed fires." But enor­mous fires are now an im­port­ant so­cie­tal con­cern. With ever in­creas­ing in­ten­si­ty in large part due to cli­mate change, the de­struc­tive pow­er of fires is evi­dent world­wide. Whether it is the un­re­strict­ed burn­ing of the Ama­zon rain­forest or the wild­fires that year­ly af­fect the West­ern half of North Ame­ri­ca, the glo­bal ef­fects of fires con­tinue to in­crease. This aeri­al image (Fi­gure 1) of three ma­jor fires burn­ing out of con­trol in Ca­li­for­nia and Ore­gon this past July make clear the gar­gan­tuan size of these ca­tas­troph­ic events. To get a sense of the mag­ni­tude and reach of these events, I re­com­mend read­ing this and this, two New York Times ar­ticles with im­pres­sive vi­deos in­clud­ed. Af­ter the ra­vag­ing ef­fects of fire, eco­sys­tems ini­tia­te the in­evi­tab­ly much slow­er pro­cess of re­gen­er­a­tion, of­ten in­volv­ing spe­cies suc­ces­sions. While much is do­cu­ment­ed re­gard­ing the post-fire es­tab­lish­ment of plant and ani­mal spe­cies, much less is known about the roles that mi­cro­bial com­mu­ni­ties play in eco­sys­tem re­gen­er­a­tion. But as STC read­ers might sus­pect, it is the mi­crob­es that first po­pu­late burnt eco­sys­tems. En­ter the py­ro­phil­ous fun­gi.
 

FigureFigure 2. Image of Pyronema domes­ti­cum showing the pink fruiting bodies, white hyphae, and some particles of char­coal and soil. Credit Monika Fischer

First a brief aside in the style of our cus­tom­a­ry "Terms in Bio­lo­gy." The term in point is py­ro­phi­ly: thriv­ing in ground or on ma­ter­i­al that has re­cent­ly been scorch­ed or burnt by fire. (Please, ne­ver to be con­fus­ed with the men­tal dis­or­der py­ro­phi­lia.) There are nu­mer­ous plants and ani­mals said to be py­ro­phil­ous, but the clear win­ners in terms of be­ing the first to thrive in re­centl­y burnt are­as are the py­ro­phil­ous fun­gi. That some fun­gi grow well in burnt ma­ter­i­als is ea­sy to note. Per­haps some of you have not­ed fi­la­ment­ous growth of 'fire­place fun­gi' on the char­coal re­main­ing a few days af­ter light­ing a fire in a chim­ney or in an out­doors grill. One genus of py­ro­phil­ous fun­gi, Py­ro­ne­ma, was so named in 1835 from the Greek πῦρ (pyr) = fire and νῆμᾰ (nêma) = thread. The main cha­rac­ter in the pa­ra­graphs that fol­low is Py­ro­ne­ma do­mes­ti­cum (Fi­gure 2). If you look clo­se­ly at the fi­la­ment­ous growth, you'll no­tice it is en­ve­lop­ing bits of char­coal, the re­mains of fire. Py­ro­ne­ma are in­deed, true to their name­sake, the 'threads after the fire.'
 

Ob­ser­va­tions going back more than a cen­tu­ry point at P. do­mes­ti­cum (and close re­la­tives) as among the first fun­gi whose fruit­ing bo­dies emerge from re­cent­ly burn­ed soils. In pre-fire soils this fun­gus is ba­re­ly de­tec­table, yet it grows ra­pid­ly and ro­bust­ly in pure cul­ture in the lab. How­ever, ear­ly la­bo­ra­to­ry ex­pe­ri­ments sug­gest­ed that Py­ro­ne­ma was a weak com­pe­ti­tor in vitro. So what makes it able to quick­ly take over the soil com­mu­ni­ty post-fires? A re­cent paper by Mo­ni­ka Fischer and Grace Stark, from Matt Trax­ler's lab at UC Ber­ke­ley, and col­leagues pro­vides some ex­cit­ing ans­wers to this key ques­tion. Much prior work al­ready laid a foun­da­tion for the more de­tail­ed re­search pre­sent­ed in this pa­per. For ex­ample, the sur­face com­po­si­tion of re­cent­ly burnt soils is known to con­tain a top lay­er which suf­fered the high­est tem­pe­ra­tures and con­tains most­ly com­ple­te­ly py­ro­lyzed or­gan­ic mat­ter (PyOM). Just be­low is a "ne­cro­mass zone" where the heat is not enough to com­bust or­gan­ic mat­ter but enough to kill and lyse mi­cro­bi­al cells, re­leas­ing pos­sible nu­trients. Some­where in that tem­pe­ra­ture gra­dient of burn­ing soils there is a "Gol­di­locks Zone" where the not-too-hot, not-too-cold tem­pe­ra­tures al­low spores of py­ro­phil­ous fun­gi to sur­vive. Using a py­ro­cosm mo­del sys­tem, Thomas Bruns and col­leagues re­pli­cat­ed in a con­trol­led en­vi­ron­ment Py­ro­ne­ma's abi­li­ty to quick­ly do­mi­nate the fun­gal com­mu­ni­ty after a fire. The ground­work was thus laid down to ask more de­tail­ed ques­tions.
 

Figure(Click to enlarge)
Caption to Figure 3. see below

As the Pyronema grow in burnt soils, what nu­trients do they use to get that com­pe­ti­tive edge? Fischer et al. set out to test the hy­po­the­sis that P. do­mes­ti­cum can grow, in part, be­cause they can hy­dro­lyze PyOM. Mind you PyOM is an enor­mous­ly com­plex mix­ture of re­si­du­al car­bon that con­tains lots of po­ly­aro­mat­ic ring re­si­dues, not an easy-to-break-down ma­ter­ial. It is not even easy to de­fine the struc­ture of PyOM. To ob­tain char­red ma­teri­al in as re­pro­du­cible a way pos­sible, the au­thors col­la­bo­rat­ed with the lab of Thea Whit­man in the Soil Science de­part­ment at the Uni­ver­si­ty of Wis­con­sin, Ma­di­son. There, co-au­thors Naye­la Ze­ba and Ti­mo­thy Ber­ry used a de­vice cal­led a 'char­coal­ator' to pro­duce even­ly py­ro­lyz­ed ma­te­ri­al at 750°C. This ma­te­ri­al al­low­ed the au­thors to car­ry out ele­gant if simple growth ex­pe­ri­ments using dif­fer­ent car­bon sour­ces. Using su­crose as sole car­bon source they ob­served ro­bust fun­gal growth, as ex­pect­ed. But they also ob­serv­ed fun­gal growth when using burnt soil or lab-made PyOM. They then iso­lat­ed the fun­gal bio­mass and per­form­ed RNA-Seq ana­lys­es to de­ter­mine the dif­fer­en­ces in gene ex­pres­sion un­der the dif­fer­ent growth con­di­tions. The first dif­fer­en­tial re­sponse of the fun­gi grow­ing on PyOM they no­ticed was the up re­gu­la­tion of genes for trans­port­ers and the ge­ne­ral stress re­sponse. Those fun­gi, even though they are grow­ing, are show­ing signs of star­va­tion and stress. But the very in­ter­est­ing ob­ser­va­tion was that growth on PyOM in­duced the ex­pres­sion of a co­her­ent set of me­ta­bol­ic path­ways in­vol­ved in aro­ma­tic com­pound de­gra­da­tion (Fi­gure 3). Im­port­ant­ly, they al­so ob­serv­ed the in­creas­ed ex­pres­sion of a gene with se­quence si­mi­la­ri­ty to bapA, a gene from As­per­gil­lus ni­du­lans whose pro­duct oxi­diz­es the po­ly­aro­mat­ic hy­dro­car­bon ben­zo-[a]-py­rene. a carcinogen in humans The pro­duct of the or­tho­lo­gous gene in P. do­mes­ti­cum might pro­vide a first step in the break­down of com­plex po­ly­aro­ma­tic com­ponents of PyOM.
 

The growth on PyOM and the tran­script­ion re­sults cer­tain­ly point to the pos­si­bi­li­ty that P. do­mes­ti­cum can break down this com­plex sub­stra­te. But could the au­thors prove this di­rect­ly? Once again, the au­thors turn­ed to their col­la­bo­ra­tors in the Whit­man lab, who grew a source of wood, seed­lings of Pi­nus stro­bus (eas­tern white pine), in a 13CO2 at­mo­sphere for two years. They then py­ro­ly­zed the la­bel­ed wood using the char­coal­a­tor to ge­ne­ra­te 13C-PyOM and fed that to P. do­mes­ti­cum. In­deed, they ob­served the pro­duct­ion of 13CO2, prov­ing that P. do­mes­ti­cum di­rect­ly mi­ne­ra­lizes PyOM.
 

The initial growth of P. do­mes­ti­cum in re­cent­ly burnt soils is just the be­gin­ning of the sto­ry. Eco­sys­tem re­ge­ne­ra­tion of course in­volv­es the sub­se­quent suc­ces­sions of many other spe­cies. What do those late com­ers grow on? Since P. do­mes­ti­cum's abun­dance de­creas­es af­ter a few months, it is pos­sible that its bio­mass serves as a food source in the ear­ly sta­ges of suc­ces­sion. This is how the au­thors spe­cu­late on this mat­ter: "Thus, abun­dant Py­ro­ne­ma bio­mass may pro­vide a cri­ti­cal nu­trient source for se­con­da­ry co­lo­niz­ers of post-fire soils, there­by lay­ing the foun­da­tion for suc­ces­sion with­in post-fire com­mu­ni­ties. Im­port­ant­ly, the abil­i­ty of P. do­mes­ti­cum to con­vert some PyOM in­to bio­mass could di­rect­ly fa­ci­li­tate the growth of or­gan­isms that lack the abi­li­ty to me­ta­bo­lize PyOM. Thus, Py­ro­ne­ma may pro­vide an im­port­ant me­chan­ism for ra­pid­ly as­simi­lat­ing some por­tion of new­ly form­ed PyOM back into more rea­di­ly bio­avail­able forms of car­bon in post-fire en­vi­ron­ments." Once again, fun­gi prove to be the world's con­sum­mate re­cyc­lers!
 

Caption to Figure 3.
Metabolic map highlighting aromatic compound metabolism induced by growth on pyrolyzed substrates. Sig­nificantly upregulated genes mapped onto the canonical pathways for aromatic compound metabolism (ad­justed value of p<0.01, fold change >2, n=3). Bolded arrows indicate a fold change >8 on PyOM compared to sucrose. Each gene is indicated as a black-outlined box, and the proteins encoded by these genes are indi­cat­ed as purple text. The color fill of the box indicates the condition(s) in which the gene was upregulated. Multi-colored boxes are slightly larger than mono-color boxes to increase visibility of the colors and to highlight gen­es that are induced in more than one condition. Diagonal parallel lines within a box and associated dash­ed lines indicate genes that were expressed, but not differentially expressed under the tested conditions. Source

 

 
 

 
 

Posted on December 06, 2021 at 01:30 AM in Ecology, Physiology & Genetics | Permalink | Comments (0)

Safeguarding Beetle Development

by Mechas and Roberto  
This is the story of how pursuing a century-old observation led to the recent discovery the chemical ecology involved in protecting a beetle from fungal infection during larval molting. It shall come as no surprise that we would be thrilled by such a story; throughout the lifetime of the blog, we've had posts on insect-microbe symbioses... Read more →

Posted on January 30, 2023 at 12:30 AM in Ecology, Symbioses | Permalink | Comments (0)

Molecular Fossils of Microbial Interactions

by Einat Segev  
Microbes have inhabited our planet for many millions of years. While thriving and dying in almost every niche on Earth, microbes leave behind relics, and some of these relics remain preserved in the geological record. Many cell components are rapidly degraded and do not persist but remains that do are like archives of ancient microbial life. Read more →

Posted on January 26, 2023 at 12:30 AM in Ecology, Evolution, Physiology & Genetics | Permalink | Comments (0)

A New Look and Other Changes

by Roberto  
What were you doing seventeen years ago, in 2006? I have a tough time recalling my own actions then, but I sure can tell you what Elio did that year. With his energy, enthusiasm, and relentless itch for writing (along with support from ASM, namely Chris Condayan) he gave birth to this blog. Read more →

Posted on January 23, 2023 at 01:30 AM in Odds & Ends | Permalink | Comments (0)

Christopher T. Walsh (1944–2023)

by Roberto  
Last week, my enthusiastic feelings for the beginning of the new year were greatly dampened when I received the news of Chris Walsh's untimely death, the consequence of a fall. Many of us fortunate enough to have known and interacted with him for many years are still processing... Read more →

Posted on January 19, 2023 at 12:00 AM in Odds & Ends | Permalink | Comments (0)

The Who-Ate-Whom of Terms in Biology: Virovory

by Christoph  
Like with the cus­to­ma­ry New Year's Eve fire­works, eve­ry year we bio­lo­gists are blessed with hi­ther­to un­known or lar­ge­ly un­com­mon sci­en­ti­fic terms. Some stick, others blaze away like said fire­works. How would you guess the term "vi­ro­vo­ry," which was ad­ded to Wi­ki­pe­dia on 29 Decem­ber 2022, will fare? Read more →

Posted on January 16, 2023 at 01:30 AM in Ecology, Protists, Viruses | Permalink | Comments (0)

Winter Vacation


We take advantage of this being the season for re­joic­ing, and em­bark on a three-week win­ter vaca­tion. When we re­turn in 2023, on Ja­nua­ry 16th, we will en­ter the 17th year of Small Things Con­sider­ed. Read more →

Posted on December 22, 2022 at 01:30 AM in Odds & Ends | Permalink | Comments (0)

Retrospective, July to December 2022

by the STC team 
Keeping with tradition, here is a lightly annotated list of our forty-seven posts from the last half year. Read more →

Posted on December 19, 2022 at 01:30 AM in Odds & Ends | Permalink | Comments (0)

Luciferin in Scintillons at Sea

by Janie 
Summer through au­tumn is the time of year for ma­rine di­no­fla­gel­lates' famed light fes­ti­vals. If the con­di­tions are just right, the roll of an ocean wave or the push of a ka­yak paddle or the sway of your legs as you wade in deep­er is enough to set the wa­ters... Read more →

Posted on December 15, 2022 at 01:30 AM in Behavior, Physiology & Genetics, Protists | Permalink | Comments (0)

Applied Molecular Microbiology at Dubrovnik

by Roberto 
If you are interest­ed in any sub­ject re­lated to small mo­le­cule na­tur­al pro­ducts of mi­cro­bi­al ori­gin, the "John In­nes/Rud­jer Boš­ko­vić Sum­mer School in Ap­plied Mo­le­cu­lar Mi­cro­bio­lo­gy" is for you. I know that course name is a mouth­ful so when I am de­scrib­ing the school to mi­cro­bio­lo­gists, I re­fer to it simp­ly as... Read more →

Posted on December 12, 2022 at 01:30 AM in Odds & Ends, Teachers Corner | Permalink | Comments (0)

Scientific Publishing – eLife's Reviewed Preprints

by Roberto 
Just over five years ago, George O'Toole and I had a con­ver­sa­tion about sci­en­ti­fic pub­lish­ing which we posted at STC. After some harsh com­ments cri­tiqu­ing for-pro­fit sci­en­ti­fic pub­lish­ers, jour­nal im­pact fac­tors, and pre­da­to­ry jour­nals, we turned to think­ing about so­lu­tions. George in­di­cat­ed some guard­ed... Read more →

Posted on December 08, 2022 at 01:30 AM in Odds & Ends | Permalink | Comments (0)

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