The role of fungi in biogenic weathering in boreal forest soils


In this article we discuss the possible significance of biological processes, and of fungi in particular, in weathering of minerals. We consider biological activity to be a significant driver of mineral weathering in forest ecosystems. In these environments fungi play key roles in organic matter decomposition, uptake, transfer and cycling of organic and inorganic nutrients, biogenic mineral formation, as well as transformation and accumulation of metals. The ability of lichens, mutualistic symbioses between fungi and photobionts such as algae or cyanobacteria, to weather minerals is well documented. The role of mycorrhizal fungi forming symbioses with forest trees is less well understood, but the mineral horizons of boreal forests are intensively colonised by mycorrhizal mycelia which transfer protons and organic metabolites derived from plant photosynthates to mineral surfaces, resulting in mineral dissolution and mobilisation and redistribution of anionic nutrients and metal cations. The mycorrhizal mycelia, in turn provide efficient systems for the uptake and direct transport of mobilised essential nutrients to their host plants which are large sinks. Since almost all (99.99 %) non-suberised lateral plant roots involved in nutrient uptake are covered by ectomycorrhizal fungi, most of this exchange of metabolites must take place through the plant—fungus interface. This idea is still consistent with a linear relationship between soil mineral surface area and weathering rate since the mycelia that emanate from the tree roots will have a larger area of contact with minerals if the mineral surface area is higher. Although empirical models based on bulk soil solution chemistry may fit field data, we argue that biological processes make an important contribution to mineral weathering and that a more detailed mechanistic understanding of these must be developed in order to predict responses to environmental changes and anthropogenic impact.


Finlay, R., Wallander, H., Smits, M., Holmstrom, S., Van Hees, P., Lian, B., Rosling, A. (2009). The role of fungi in biogenic weathering in boreal forest soils. Fungal Biology Reviews: 23; p101-106.


This opinion article discusses in detail mycorrhizal fungi in forest soils and how they influence soil biogeochemical cycling. The article is a little bit old, but it’s emphasis on fungi is what interests me the most. The climax of the article has a figure organizing both symbiotic (mycorrhizal) and saprotrophic fungi in relation to their contributions to soil weathering rate. The figure helps me fit fungus into the larger puzzle of biogeochemical cycling we’ve discussed in class.

Factors limiting bioremediation technologies


The use of microorganisms to destroy, or reduce the concentration of, hazardous wastes on a contaminated site is called bioremediation. Such a biological treatment system has various applications, including, clean up of contaminated sites such as water, soils, sludges, and waste streams. The treatment of the Alaskan shoreline of Prince Williams Sound after the oil spill of Exxon Valdez in 1989 is one common example in which bioremediation methods got public attention. There are numerous other success stories of bioremediation in cleaning up chemical spills, leaking underground storage tanks of gasoline, and many toxic industrial e ‚uents. This paper outlines the various factors, including scientic, non-scientic, and regulatory, that limit the use of bioremediation technologies.


R. Boopathy. (2000). Factors limiting bioremediation technologies. Bioresource technology: 74; p63-67.


This brief article reviews current techniques in bioremediation, as well as scientific and non-scientific factors that limit the progression and implementation of bioremediation technologies. What most interests me is the “Non-technical Criteria” section of the review, where the author details political and economic factors. Discussing solutions to these economic, social, and political problems should be a priority for those of us studying science. Our research wont be very useful if it’s implementation is in question.

Polycyclic aromatic hydrocarbons degradation by marine-derived basidiomycetes: optimization of the degradation process


Pyrene and benzo[a]pyrene (BaP) are high molecular weight polycyclic aromatic hydrocarbons (PAHs) recalcitrant to microbial attack. Although studies related to the microbial degradation of PAHs have been carried out in the last decades, little is known about degradation of these environmental pollutants by fungi from marine origin. Therefore, this study aimed to select one PAHs degrader among three marine-derived basidiomycete fungi and to study its pyrene detoxification/degradation. Marasmiellus sp. CBMAI 1062 showed higher levels of pyrene and BaP degradation and was subjected to studies related to pyrene degradation optimization using experimental design, acute toxicity, organic carbon removal (TOC), and metabolite evaluation. The experimental design resulted in an efficient pyrene degradation, reducing the experiment time while the PAH concentration applied in the assays was increased. The selected fungus was able to degrade almost 100% of pyrene (0.08mgmL−1) after 48h of incubation under saline condition, without generating toxic compounds and with a TOC reduction of 17%. Intermediate metabolites of pyrene degradation were identified, suggesting that the fungus degraded the compound via the cytochrome P450 system and epoxide hydrolases. These results highlight the relevance of marine-derived fungi in the field of PAH bioremediation, adding value to the blue biotechnology.


Vieira, Gabriela A.L., Magrini, Mariana Juventina, Bonugli-Santos, Rafaella C., Rodrigues, Marili V.N., Sette, Lara D. (2018).  Polycyclic aromatic hydrocarbons degradation by marine-derived basidiomycetes: optimization of the degradation process. Brazilian Journal of Microbiology xxx (2018) p xxx-xxx.


In this article, the researchers investigate the potential of 3 basidiomycete fungal strains isolated from ocean sponges in Brazil to degrade high molecular weight PAHs. One of the three fungal strains showed a much higher potential to degrade pyrene and Benzo(a)pyrene (BaP), so the researchers designed a series of experiments to determine several optimum environmental conditions for the fungal strain to degrade pyrene and BaP. The researchers also tested toxicity of the degradation products using shrimp larvae, and saw a significant decrease in toxicity from a solution of only pyrene, to a solution of pyrene and the degrading fungal strain. The study provides an important look at a fungal strain with enormous potential to degrade toxic PAHs pollution in the environment.

This article interests me because fungi aren’t often the focus of microbiological research, let alone marine fungi. While the paper hasn’t yet been published in print and is so far only available online, I’m interested in seeing if this paper will influence commercial bioaugmentation products in the future.

A Bioremediation fairy tale

Interested in microbial bioremediation? Want to teach your children about it? You’re in luck! Follow the link here to read a children’s story about a small bacterial population who uses the power of plasmids to remediate their island from petroleum pollution!

Pseudomona and the Tale of Bioremediation follows the story of Psuedomona, the daughter of the leader of a population of bacteria, who must travel a great distance to find Psueodmonas putida, the fabled microbe who eats petroleum. Will they be able to save the island together? Find out here!

Lichens and their bacterial microbiome – a thinglink exploration

General summary:

See those spots on the rock face? Those are lichens! These are plants made of algae and fungi living and working together to maintain the health of the whole organism. Frequently, however, lichens contain many different kinds of bacteria that can perform different metabolic processes that can help the lichen thrive. We don’t know a lot about the bacteria that live with lichen, or how and why they associate with lichen. Bates et al. explores the diversity of the bacterial community living with lichen, and their potential contributions to the overall health of a lichen community.

The researchers primarily looked at the bacterial communities to see if they vary based on the species of lichen. Do certain species benefit from certain additional metabolic process? In order to do this, the researchers used both traditional culture based methods – a method which grows the bacteria in a lab –  and modern genetic techniques, which can more accurately describe bacterial communities than culturing.

After collecting and analyzing samples from 4 different species of lichens, the researchers compared the results and discovered that, while some bacterial species were present in all the lichens sampled, there were also certain bacterial species that associated only with certain species of lichen. Bacterial species associated with all the lichens were more likely to be nitrogen fixing bacteria, which provide crucial nitrogen to plants. This research allows us to fill in one small piece of the puzzle that is symbiotic lichens. Do these unique bacterial species contribute to the specific lichen species they associate with? Did they coevolve with the lichen, as the human gut microbiome has coevolved with our species? All these questions remain to be answered by microbiologists in the future.

In-depth, technical summary:

While we traditionally understand lichens to be symbiotic communities of algae and fungi or cyanobacteria, we don’t think of them as organisms having significant microbiomes. This, as it turns out, is false. Bates et al. (2011)  set out to characterize the bacterial microbiomes of 4 species of lichens on 3 different rock outcroppings.

Using both traditional culture based methods, and 16S rRNA gene amplicon pyrosequencing, Bates et al. (2011)  analyzed the lichen microbiome. They found no trace of archeal 16S rRNA genes, and their sequencing results yielded much more diversity than their culturing results, as can be expected. Using Bray-Curtis NMDS, they discovered that the bacterial communities cluster based on lichen species, rather than outcropping, suggesting that certain bacterial species do associate with certain lichen species. Among the bacteria ubiquitous in the lichen samples, most were potential nitrogen fixing bacteria of the Alphaproteobacteria. This suggests that lichen associate with nitrogen fixing bacteria, however the results are not definitive due to the low accuracy of their species identification, as well as the fact that they did not target functional genes in the lichen microbiome.

This research shows that, while there are certain bacteria present in all lichens just as there are in humans, there are species specific associations between lichen species and the lichen microbiome. Further research into the coevolution and specialized roles of bacteria in the lichen microbiome is required to understand the lichen microbiome, and to understand the full extent of their symbiotic relationships.

Biogeochemical Cycling Paper Suggestion

Coral-Associated Bacteria and Their Role in the Biogeochemical Cycling of Sulfur

Raina, J.B., Tapiolas, D., Willis, B.L., & D.G. Bourne. 2009. Coral-Associated Bacteria and Their Role in the Biogeochemical Cycling of Sulfur. Appl. Env. Microbiology  vol. 75;11. pp3492-3501. doi:  10.1128/AEM.02567-08

Marine bacteria play a central role in the degradation of dimethylsulfoniopropionate (DMSP) to dimethyl sulfide (DMS) and acrylic acid, DMS being critical to cloud formation and thereby cooling effects on the climate. High concentrations of DMSP and DMS have been reported in scleractinian coral tissues although, to date, there have been no investigations into the influence of these organic sulfur compounds on coral-associated bacteria. Two coral species,  Montipora aequituberculata  and  Acropora millepora, were sampled and their bacterial communities were characterized by both culture-dependent and molecular techniques. Four genera,  Roseobacter, Spongiobacter, Vibrio, and  Alteromonas, which were isolated on media with either DMSP or DMS as the sole carbon source, comprised the majority of clones retrieved from coral mucus and tissue 16S rRNA gene clone libraries. Clones affiliated with  Roseobacter  sp. constituted 28% of the  M. aequituberculata  tissue libraries, while 59% of the clones from the  A. millepora  libraries were affiliated with sequences related to the  Spongiobacter  genus.  Vibrio  spp. were commonly isolated from DMS and acrylic acid enrichments and were also present in 16S rRNA gene libraries from coral mucus, suggesting that under “normal’ environmental conditions, they are a natural component of coral-associated communities. Genes homologous to  dddD, and  dddL, previously implicated in DMSP degradation, were also characterized from isolated strains, confirming that bacteria associated with corals have the potential to metabolize this sulfur compound when present in coral tissues. Our results demonstrate that DMSP, DMS, and acrylic acid potentially act as nutrient sources for coral-associated bacteria and that these sulfur compounds are likely to play a role in structuring bacterial communities in corals, with important consequences for the health of both corals and coral reef ecosystems.


I chose this article because of the diversity of microbial analysis methods used in the paper: 16S rRNA amplicon sequencing, traditional culturing, and functional gene amplicon sequencing. In addition, Im very interested in the implications of coral-associated DMS producing bacteria and their affect on climate change, especially given the recent bleaching and mass die off events in teh Great Barrier Reef.

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Assignment A1: Introduction

My name is Patrick Knavel, and I love microbes (And cats)! I have the most perfect, aggressive cat in the world. His name is Sir Pounce-A-Lot, and while he bats at anyone who tries to pet him, he screams at me when I get home until I pick him up and kiss his belly.

I work for the National Park Service in three of Alaska’s National parks: Yukon-Charley national park, Denali National park and Preserve, and Wrangell-St. Elias National Park and Preserve – the largest National park in the US! In these parks, I help monitor Peregrine Falcon and small mammal populations, as well as conduct water quality surveys. I’m very excited to learn more about microbes in relation to wildlife populations and their health!

I thought about posting a picture of my cat, but there are too many good ones and I couldn’t decide on a single one, so here’s a picture of me at the top of Mt. Kinabalu in Borneo in November of 2014! My sister and I climbed the mountain together with a mountain guide, and barely survived the odyssey.

A microbial haiku to commemorate our survival of the mountain:


On top Mt. Kinabalu

I thought I would die