Interview with the authors: Mega-fire in redwood tanoak forest reduces bacterial and fungal richness and selects for pyrophilous taxa that are phylogenetically conserved

In a recent paper in Molecular Ecology, Enright et al. examined how soil microbiomes are affected by extreme fires. The Soberanes mega-fire provided the authors with an opportunity to study how such extreme events, which are increasingly common with climate-change, can have lasting effects on ecology. By sampling the soil microbiome before and after the Soberanes mega-fire, Enright at al. demonstrated dramatically altered soil communities and a reduction in species richness associated with the mega-fire. There was a clear phylogenetic pattern to the particular microbes that increased or decreased abundance after the fire. Drawing from their results, Enright et al. propose a framework to predict the traits that post-fire microbial communities might exhibit.

We sent some questions to Sydney Glassman, one of the corresponding authors of this work, to get more detail on this new study.

Aerial view of the Soberanes mega-fire. Photo credit: Calfire

What led to your interest in this topic / what was the motivation for this study? 

I had originally been interested in sampling the redwood tanoak forests of Big Sur because I was interested in what the cascading effects of sudden oak death (SOD) induced mortality would be on soil fungal communities during my PhD at UC Berkeley. Prof Dave Rizzo at UC Davis had a large plot network investigating the effects of SOD on plant mortality. I teamed up with him in 2011 to select a subset of plots to collect soils to investigate the impacts on the soil microbial community via amplicon sequencing. Then, in 2016, I learned that half my plots burned in the catastrophic Soberanes Megafire. It’s extremely rare to have pre- and post-fire samples from the same sampling locations before and after a mega-fire. I was really curious about what the impact of a mega-fire would be on soil microbial communities especially since they had never been studied in redwood tanoak forests before. These forests are endemic and charismatic megflora of Califronia that are facing multiple global change factors and it is really unclear how the soil microbial communities will respond to wildfires and how that will influence the recovery of the vegetation. I had already moved to southern California at this time to start a post-doc at UC Irvine, so I asked Kerri Frangioso, who lived in Big Sur, if she would be able to re-sample any of the plots that burned. Using GPS, she was able to collect soils from the exact same sampling locations that I had sampled in 2011 from 3 of the plots (2 burned and 1 unburned) within 30 days of the fire being declared over. She mailed these soils to me, I extracted the DNA, and froze everything until I was able to start my own lab at UC Riverside in 2018.

What difficulties did you run into along the way? 

The terrain in Big Sur is notoriously challenging to traverse. It is extremely steep, lots of windy dirt roads, and there is a lot of poison oak. There is no cell reception in any of our plots and most are at least an hour from the nearest town.  Collecting the soil even before the fire was challenging enough. However, after fires, it is really challenging to access sites because roads are closed, landslides are common, and dead or dying trees are extremely hazardous especially in the case of wind. We were very lucky to be able to re-sample even 3 of our plots so fast after the fire.

What is the biggest or most surprising innovation highlighted in this study? 

I was really surprised that many of the same pyrophilous “fire loving” microbes that have been found to increase in frequency after pine forest fires also increased in frequency after redwood tanoak fires. That indicates that soil microbes are selected for by slightly different pressures than plants because the plants that regenerate post-fire in pine forests vs redwood tanoak forests are very different. It seems more likely that microbes instead survive via temperature thresholds and if fire is high severity enough, similar groups of microbes will respond. We collaborated with Kazuo Isobe to implement the CONSENTRAIT analysis and identified that microbial response to fire was indeed phylogenetically conserved, and it seemed that related groups of bacteria and fungi did indeed positively or negatively respond to fires. This will greatly enhance our ability to predict which microbes will respond to fire in any ecosystem since certain lineages seem evolutionarily adapted to survive fires. We also found that a basidiomycete yeast Basidioascus, dominated the fungal sequences at 30 days post-fire, and that had never been found before, probably because most post-fire sampling historically has been based on fruiting bodies.

Morphological diversity of soil microbes. Photo credit: Jenna Maddox

Moving forward, what are the next steps in this area of research?

I was able to leverage some of these results and results from my work sampling wildfires in Southern California chaparral to help me acquire a USDA grant from their Agricultural Microbiomes program (described here). The purpose of this grant is to characterize the traits of pyrophilous microbes and begin to get our knowledge of fire adaptation in microbes to that of plants. We understand a lot of the traits that enable plants to survive wildfires (like thick bark, vegetative resprouting, serotinous cones, etc) but we don’t have similar understanding of those traits in microbes. In order to understand these traits, Dylan Enright has begun performing biophysical trait assays on these microbes to determine their traits based on a large culture collection of pyrophilous microbes that I have been developing since I started my lab in July 2018. Over the last four years, 2 lab managers, one PhD student (Dylan Enright), 13 UCR undergraduates, and one part time laboratory technician have been involved in developing this culture collection of over 400 isolates of bacteria and fungi from burned soils from wildfires. Our goal is to characterize their traits with biophysical assays and eventually with genomics.

Have you gone back (or have you any plans to go back) to sample soils in the post-fire period? How long lasting do you think the effects of fire on microbial communities would be? 

Unfortunately, I have not been able to get this particular project funded (despite several attempts) and everything I did for this paper was completely unfunded. So I have not been able to return to these plots to sample again. I would be interested in returning to them eventually. I would predict the effects of the fire on the microbial communities could last decades if not longer, depending on if the plants themselves have been able to recover. Most of the literature on pyrophilous microbes suggests that high severity fire can have long term impacts on soil microbes that can last at least a decade or more. Given that the richness of both bacteria and fungi was reduced by up to 70% in one of our plots, I would predict it will take a long time to recover.

Describe the significance of this research for the general scientific community in one sentence.

Megafires have long lasting impacts on both plants and soil microbes alike, and it is important to understand the impacts on soil microbes since they drive plant and soil regeneration. 

Describe the significance of this research for your scientific community in one sentence.

The pyrophilous microbes that respond to a mega-fire in redwood tanoak forests are similar to those that respond to high severity wildfires in better studied pine forest systems, and the fact that they are phylogenetically conserved indicates that we will be able to predict what microbes will respond to wildfires in any system. Further, we are beginning to identify conserved trait responses that enable wildfire response that are analogous to plants and will help us bin and better understand fire adaptation traits in microbes.

Enright, D. J., Frangioso, K. M., Isobe, K., Rizzo, D. M., & Glassman, S. I. (2022). Mega-fire in redwood tanoak forest reduces bacterial and fungal richness and selects for pyrophilous taxa that are phylogenetically conserved. Molecular Ecology, 31, 2475– 2493.

Interview with the authors

A holobiont view of island biogeography: Unravelling patterns driving the nascent diversification of a Hawaiian spider and its microbial associates

In their recent paper in Molecular Ecology, Armstrong and Perez-Lamarque et al investigated the evolution of the holobiont. The holobiont is the assemblage of species associated with a particular host organism. In the case of this study, the holobiont refers to the stick spider (Ariamnes), its microbiome and its endosymbionts. Taking advantage of the successive colonization of islands in a volcanic archipelego, Armstrong and Perez-Lamarque et al contrasted the evolutionary history of the host species to the different components of the holobiont on different islands in Hawai’i.

We sent some questions to the authors of this work and here’s what Benoît Perez-Lamarque, Rosemary Gillespie and Henrik Krehenwinkel had to say.

Ariames waikula (on the island of Hawaii). Photo credit: George Roderick

What led to your interest in this topic / what was the motivation for this study? 

Gut microbiota play multiple roles in the functioning of animal organisms. In addition, host-associated microbiota composition can be relatively conserved over time and the concept of the “holobiont” has been proposed to describe the ecological unit formed by the host and its associated microbial communities. Yet, it remains unclear how the different components of the holobiont (the hosts and the microbial communities) evolve. This is what spurred our interest. Taking advantages of the chronologically arranged series of volcanic mountains of the Hawaiian archipelago, we were able to tackle this question and could investigate how the different components of the holobiont have changed as the host spiders colonized new locations.   

Can you describe the significance of this research for the general scientific community in one sentence?

The evolution of Hawaiian spider hosts and their associated microbes are differently impacted by the dynamic environment of the volcanic archipelago.
Can you describe the significance of this research for your scientific community in one sentence.

The host and its associated microbiota may not act as a single and homogeneous unit of selection over evolutionary timescales.

Ariames waikula (on the island of Hawaii). Photo credit: George Roderick

What difficulties did you run into along the way? 

All the different components of the holobiont are not as easy to study. For instance, for the host spiders, we used double digest RAD sequencing (ddRAD) to obtain genome-wide single nucleotide polymorphism data. With such data, we could precisely reconstruct the evolutionary histories of the different spider populations in the last couple of million years and tracked the finest changes in their genetic diversity. In contrast, characterizing the composition of the microbial components is much more challenging. We used metabarcoding of a short region of the 16S rRNA gene to identify the bacteria present. However, over such short evolutionary timescales, this DNA region is too conserved to accumulate many differences between isolated populations. Therefore, we had high-resolution data for the spider hosts but comparably low-resolution data for the bacterial communities. To ensure that the observed patterns were not artefactually driven by such differences of resolutions, we complemented our analyses with a range of simulations to assess the robustness of our findings.

What is the biggest or most surprising innovation highlighted in this study? 

We find that the different components of the holobiont (the host spiders, the intracellular endosymbionts, and gut microbial communities) respond in distinct ways to the dynamic environment of the Hawaiian archipelago. While the host spiders have experienced sequential colonizations from older to younger volcanoes, resulting in a strong (phylo)genetic structuring across the archipelago’s chronosequence, the gut microbiota was largely conserved in all populations irrespectively of the archipelago’s chronosequence. More intermediately, we found different endosymbiont genera colonizing the spiders on each island. This suggests that this holobiont does not necessarily evolve as a single unit over long timescales.

In the conclusion to your study, you point out how different components of the holobiont likely contribute differently to selection/colonization history in this system. If you had unlimited resources, what would you do to strengthen this conclusion? 

We indeed suspect that the different components of the holobiont probably did not act as a single and homogeneous unit of selection during the colonization of the Hawaiian archipelago. First, it would be ideal to perform an even broader sampling, targeting more Ariamnes populations and species from older islands, to better characterize the long-term changes of the different holobiont components. Using sequencing technics with better resolution (as detailed below) would also improve our characterization of the microbial component(s) of the holobiont. Second, to properly test for selection, we should perform transplant experiments of the bacterial communities between spider populations/species and measure whether or not it impacts holobiont fitness. We would expect to find a significant impact of the transplant for the endosymbionts, but no or low impact for the gut bacterial communities of these spiders.

The geological history of Hawai’i provides a powerful system to build understanding of the evolution of holobiont. Are you aware of other systems where similar studies could be performed? (I appreciate that this is related to the previous question!).

Many other archipelagos, with similar island chronosequences, like the Canary Islands or the Society Islands, are also ideal for testing hypotheses on the evolution of holobionts. Within the Hawaiian archipelago again, we could replicate our work on other holobiont systems. For instance, among arthropods, plant feeders might rely more importantly on their microbiota for their nutrition, and this might likely translate into different patterns of holobiont evolution.

Moving forward, what are the next steps in this area of research?

As previously said, one main limitation is the low resolution of the 16S rRNA metabarcoding. This prevented us to look at the evolutionary history of the individual bacterial lineages. Using a new model, we have recently tackled this issue of low resolution ( and we reported little evidence of microbial vertical transmission in these holobionts. Yet, the next step would be to move from classical metabarcoding to metabarcoding with longer sequencing reads (e.g. the whole 16S rRNA gene) or even metagenomics. It would provide more resolution for looking at bacterial evolution and would also bring more information on the functioning of these bacterial communities (e.g. are gut microbiota contributing to the digestion of these Hawaiian spiders in natural environments?).

Armstrong, E. E.*, Perez-Lamarque, B.*, Bi, K., Chen, C., Becking, L. E., Lim, J. Y., Linderoth, T., Krehenwinkel, H., & Gillespie, R. G. (2022). A holobiont view of island biogeography: Unravelling patterns driving the nascent diversification of a Hawaiian spider and its microbial associates. Molecular Ecology, 31, 1299– 1316. 

*Authors contributed equally

Interview with the authors: Anthropization level of Lascaux Cave microbiome shown by regional‐scale comparisons of pristine and anthropized caves

Estimated to be around 17,000 years old, the Paleolithic paintings in the Lascaux cave of southwestern France give us a rare insight into the history and culture of communities that existed long before modern society. The conservation of caves such as Lascaux is a high priority for historians, scientists, and the general public. The anthropization, or human use, of caves may have dramatic effects on cave-dwelling macro- and micro-organisms, though few studies have been conducted on this topic. By comparing ‘pristine’ caves with anthropized caves frequently visited by humans, Dr. Lise Alonso and colleagues demonstrate that the anthropization of caves is associated with reduced microbial diversity for bacteria and archaea living on cave walls, though microeukaryotes and arthropods were not as strongly affected. In this post, we go behind-the-scenes with Dr. Yvan Moënne-Loccoz on their recent publication in Molecular Ecology and talk about the importance and challenges of working in cave ecosystems.

Link to the study:

Great Hall of the Bulls in Lascaux Cave. The cables connect to monitoring probes. Source: DRAC Nouvelle Aquitaine

What led to your interest in this topic / what was the motivation for this study? 
Cave conservation is an important issue, especially when dealing with caves displaying Paleolithic artwork, as engravings and particularly paintings can be very fragile. There are many of these caves in Dordogne (South-West of France), some of them listed on the UNESCO World Heritage List ( The most famous Paleolithic cave in Dordogne is the Lascaux Cave, which was closed to the public in the 1960s for conservation reasons. To guide conservation efforts, it is important to understand the ecology and functioning of these caves, especially at the levels of microorganisms and arthropods, which form the main communities present. Against this background, the project was carried out to understand better the biotic communities residing in Lascaux Cave.

Entrance of Lascaux Cave. Source: DRAC Nouvelle Aquitaine

What difficulties did you run into along the way? 
When dealing with microorganisms and arthropods populating soils, sediments or water, in a majority of cases it is rather straightforward to collect samples and there is no restriction on sample size. In caves, taking samples from walls for microbial analyses, using a scalpel, may leave long-lasting marks. This is an issue in all caves, and particularly so in Paleolithic caves. In the Lascaux Cave, the sample list was prepared after discussions with the cave staff and approved by the cave conservator, and the samples were collected (away from ornate surfaces) by qualified restorers, under the guidance of microbial ecologists, so as to avoid any marks on the wall. It also means that only minute samples were available. Restrictions also apply for the type and location of arthropods traps, as sediments at the bottom of caves might contain historical artefacts.

Sampling of rock wall surface in a pristine cave, using a sterile scalpel. Source: B. Bigaï

What is the biggest or most surprising finding from this study? 
Caves are oligotrophic environments, so it is always a surprise to find diversified, rather large microbial communities on cave walls. In this study, the Lascaux Cave was compared with eight other caves from the same region, and these caves were quite different from one another in terms of size, architecture, distance from the soil surface, presence/absence of stream underground, human frequentation patterns, etc. Yet, there were clear distinctions in terms of microbial and arthropod communities when comparing anthropized caves versus non-anthropized (almost pristine) caves, which suggests that anthropization was more influential than these cave-specific features. Finally, we were rather surprised to find that prokaryotes (bacteria and archaea) were comparatively more impacted than eukaryotic residents (fungi, other micro-eukaryotes, arthropods) by cave anthropization.

Pristine cave used for sampling. Source: Y. Moënne-Loccoz

Moving forward, what are the next steps for this research?
This work was carried out with the Lascaux Cave and eight other caves from Dordogne, which corresponds to a relatively small area. There were at the most 35 km between two caves in this study. Therefore, it remains to be seen whether the results of the current investigation are also relevant elsewhere. At a larger geographic scale, several differences in cave properties can be expected, for instance in geological features (e.g. limestone type) and climatic conditions, which have the potential to influence cave biotic communities. In addition, we evidenced parallel variations in the diversity of microbial and arthropod communities, and it will be important to explore and understand better the ecological interactions between both types of cave inhabitants.

What would your message be for students about to start their first research projects in this topic?
First of all, the underground world and the interface between ecology and artwork conservation issues are fascinating, so welcome to the field! More importantly, each cave is different and represents a complex situation of its own, so one can be very busy focusing on a single cave only. This is reflected by the literature on cave microbial ecology, where often a single cave is considered at a time. However, we found that the comparison of different caves, following the path of various groups (e.g. Campbell et al. 2011 J Cave Karst Stud 73:75 ; Hathaway et al. 2014 Geomicrobiol J 31:205 ; De Mandal et al. 2017 BMC Microbiol 17:90 ; Pfendler et al. 2018 Sci Tot Environ 615:1207), brought very interesting insights, so comparative assessments are worth the effort.

What have you learned about science over the course of this project? 
The majority of participants to this project usually work on soil or aquatic ecosystems, and we found (once again) that concepts and methodology are applicable across different types of ecosystems. More specifically, we realized that underground systems represent interesting models to investigate ecological perturbations, because they are rather confined environments, where community fluctuations in response to mild environmental variations can be documented.

Describe the significance of this research for the general scientific community in one sentence.
This research shows that microbiome diversity can be used as a bioindicator of the level of cave anthropization.

Alonso L, Pommier T, Kaufmann B, Dubost A, Chapulliot D, Doré J, Douady CJ, Moënne‐Loccoz Y. Anthropization level of Lascaux Cave microbiome shown by regional‐scale comparisons of pristine and anthropized caves. Molecular Ecology, 28(14), 3383-3394.

Summary from the authors: Comparative power law analysis for the spatial heterogeneity scaling of the hot‐spring microbiomes by Lianwei Li and Sam Ma

Spatial heterogeneity is one of the fundamental characteristics of organisms from microbes, animals, plants, to human beings. We humans do not distribute randomly on the earth, and microbes in hot springs do not neither. We aggregate or distribute unevenly on the earth and so our spatial distribution is aggregated or heterogeneous. The study revealed that hot spring microbiomes are distributed heterogeneously and further we discovered that the heterogeneity parameter is invariant with major environmental factors, particularly the hot spring water temperature and acidity (pH-value). This finding indicates that the spatial distribution of hot spring microbiomes is primarily determined by evolutionary forces and is little influenced by environmental factors.

Using an analogy, the heterogeneity scaling parameter for the hot-spring microbiome is similar to the gravitational acceleration constant (g=9.8), which is constant on the earth except for slightly variations on different latitudes but is different on the moon. In the case of the heterogeneity scaling parameter (b), the parameter is constant for the hot spring and is invariant with the water temperature and acidity of the hot spring. However, similar to that earth and moon have different gravitational acceleration constants, the hot spring microbiome and human microbiome exhibited different heterogeneity scaling parameter values (b=1.6 for hot spring microbiome and b=2.0 for the human gut microbiome).

Graphical abstract provided by Sam Ma

The above findings are reported in a paper titled “Comparative Power Law Analysis for the Spatial Heterogeneity Scaling of the Hot‐Spring Microbiomes” published in Molecular Ecology, and authored by Lianwei Li and his PhD adviser Sam Ma. The comparative study was performed based on the extensions of the classic Taylor’s power law [Nature: 1961(vol. 189, 732-735); 1977(vol. 265, 415–421); 1983 (vol. 303,801804)] from population to community ecology by Ma (2015) “Power law analysis of the human microbiome”, also published in Molecular Ecology. – Sam Ma, CAS Center for Excellence in Animal Evolution and Genetics

Learn more about the author’s research here.

Summary from the authors: What do gut microbes do for their hosts?

Despite a flood of recent interest in this question for humans, the answer remains a mystery for the vast majority of animals. Gut microbiota are often assumed to provide nutritional benefits, but many insects acquire the majority of their nutrients during larval feeding, leaving less opportunity for bacterial contributions to adult nutrition. In fact, when food is scarce the adult gut flora might even impose a net reproductive cost.

Photo courtesy of A. Ravenscraft

We tested this prediction in the Mormon fritillary butterfly (Speyeria mormonia), a denizen of mountain meadows in the American Rockies. We experimentally subjected wild caught butterflies to a brief burst of antibiotics to disrupt their gut flora and then maintained them with either ad lib feeding or a 50% starvation diet. Contrary to our
predictions, the number of bacteria in the gut did not correlate with butterfly fitness even if the butterfly was starved, though a few individual bacteria species were associated with increased or decreased lifespan.

Overall, these results suggest that gut bacteria may have little net
effect on some animals. – Alison Ravenscraft, NIH PERT Postdoctoral Fellow, University of Arizona

Ravenscraft A, Kish N, Peay K, Boggs C. No evidence that gut microbiota impose a net cost on their butterfly host. Mol Ecol. 2019;28:2100–2117.