Microbial highlights from ESA 2014


The Ecological Society of America (ESA) annual conference, once dominated by discussions of lions, tigers and bears (or so I’ll pretend), has become a convergence point for microbial ecologists. From amphibian skin microbiomes to biological soil crusts and more, the diversity of microbial talks this year was astounding.

As the conference winds down, I wanted to share just a few of the coolest microbial findings that stuck with me from the last couple days at ESA. What was your favorite microbial talk of the week? Post about it in the comments, or better yet, tweet about it! And don’t forget to tag me (@themadstone) as well as the official ESA microbial ecology twitter (@ESAmicrobe), if you do 😉

Can dormancy explain microbial biogeography?

Dormancy is a condition that afflicts the best of us.

Dormancy is a condition that affects the best of us.

Dr. Jay Lennon gave a great talk on dormancy; a subject that’s particularly fascinating to me in light of the vast (and probably rather dormant) microbial populations living in deep, subterranean environments.

Dormancy, otherwise known as metabolic inactivity, is an important strategy for surviving stressful environments. Conditions such as extreme drought, cold, or lack of food can cause microbes to enter a dormant state. Dormant microbes are fascinating not only for their ability to survive extreme conditions, but to do so for thousands to millions of years.

Lennon’s research group is particularly interested in applying principles of biogeography- how diversity scales across space- to microbial ecology. But understanding spatial patterns in microbial diversity is tricky because:  1) microorganisms are enormously diverse compared with macroorganisms and 2) unlike, say, mountain lions, which may be very genetically similar across kilometer scales but diverse over thousands of kilometers, genetically distinct populations of microbes can exist at the millimeter scale. Scientists find that microbial communities in soil samples taken 1 centimeter apart from each other can be up to 90% genetically distinct.

Here’s where dormancy comes in. Lennon’s group can separate the active from dormant members of microbial communities, by looking at the number of RNA transcript copies for a ubiquitous bacterial gene. RNA transcripts, the intermediate product between a DNA “blueprint” and an active protein, are well correlated with metabolic activity. Lennon finds differences in how diversity scales with space when examining the dormant versus active portions of a microbial community. Simply put, dormant microbial communities are more homogenous across space than their active counterparts. Furthermore, active microbial communities tend to become dominated by select taxa, probably those with some fitness advantage in the local environment. Dormant communities are less likely to be dominated by a few individual taxa, but rather represent a well-distributed “seed-bank” of genetic diversity.

The difference in how dormant versus active microbial communities scale with space may seem like a nuance, but this information could go a long way toward helping ecologists understand the distribution of microbial diversity across our planet. Lennon’s results suggest dormant microbes may represent up to 40% of a community. That’s no small portion of the total genetic diversity. Furthermore, dormant microbes, as a potentially long-term seed-bank, may help replenish the diversity of a community following extinction events.

Pine needle bacteria that soak up nitrogen

Scots Pine, Poland. Pine needles may host communities of nitrogen fixing bacteria that aid in survival in low-nitrogen environments. Credit: Encyclopedia of Life

Scots Pine, Poland. Pine needles may host communities of nitrogen fixing bacteria that aid in survival in low-nitrogen environments. Credit: Encyclopedia of Life

Did you know that nearly all leaves on Earth host their own microbiomes? Neither did I! But perhaps it’s not too surprising, given we’re now studying the microbiomes of cell phones and sewers. Anyway, it’s pretty cool. It’s extra cool in alpine ecosystems, where scientists are finding that these leaf-dwellers may play an important role in making nitrogen available to plants.

Dr. Carolin Frank’s lab studies nitrogen cycling in high, cold alpine ecosystems dominated by coniferous trees. Alpine ecosystems have long puzzled ecologists, because their soils and vegetation often contain more nitrogen than can be easily explained. Dr. Frank and colleagues hypothesized the “missing nitrogen” might come from nitrogen fixers- bacteria that carry a special enzyme which allows them to convert atmospheric N2 gas to ammonia- found in an unlikely place.

The team went out to a high-altitude forest in Colorado, collecting pine needles and bringing them back to the lab. In the lab, they placed the needles in sealed jars and added a chemical called acetylene. Acetylene, a simple carbon compound, can be chemically converted by nitrogenase, the same enzyme used to fix dinitrogen gas. This is a quick and cheap way of assessing whether a sample contains the nitrogenase enzyme, and hence nitrogen-fixing bacteria.

After finding that the pine needles did indeed host nitrogen fixers, the group used genetic techniques to look more closely at who exactly is there. The most prominent bacteria in all pine needle samples was genetically similar to Gluconacetobacter -a nitrogen fixer found in sugarcane.

So, nitrogen fixers are living in pine needles and helping their host trees take up nitrogen. If replicated in other coniferous forests, these findings could transform our understanding of alpine and boreal ecosystems, helping explain how coniferous trees persist on very nitrogen-limited soils.

Ocean acidification and marine calcifiers: it’s more complicated than you thought.

Coccolithophore, a single celled marine phytoplankton that produces calcium carbonate scales. Credit: Encyclopedia of Life

Coccolithophore, a single celled marine phytoplankton that produces calcium carbonate scales. Credit: Encyclopedia of Life

Or at least, it’s much more complicated than an ignorant terrestrial scientist like myself thought. See, my understanding of ocean acidification went something like this: more CO2 in the atmosphere means more CO2 dissolving in the surface ocean. When this CO2 dissolves, it reacts with water to produce acid, lowering the pH of the ocean. This is bad news for organisms that build exoskeletons from calcium carbonate (CaCO3), because the protons that create acidity get in the way of calcium carbonate formation. Sound good?

Well, like most natural phenomena when examined closely, the answer is quite a bit more complicated. Dr. Deborah Iglesias-Rodruigez enlightened me today as to some of that complexity. Iglesias-Rodruigez studies Coccolithophores, a common group of marine phytoplankton (photosynthetic organisms) that precipitate a beautiful, calcium carbonate exoskeleton. But in order for these little guys to create their exoskeletons, they must first take up some form of carbon into their cells.

It turns out Coccolithophores have evolved to take up the predominant form of carbon found in seawater: bicarbonate, or HCO3. And it also turns out this is the particular form of carbon that becomes more abundant during ocean acidification. So- does that mean acidification is good for calcium carbonate formation, after all?

Well, not quite. Although Coccolithophores seem to take up more bicarbonate under more acidic conditions, this isn’t exactly a good thing. Iglesias-Rodruigez finds that, in acidic conditions, Coccolithophores can start over-calcifying: precipitating more calcium carbonate than they need to, which is energetically wasteful. Moreover, once that calcium carbonate is precipitated, it gets slowly eaten away by the more-acidic seawater.

There was more detail to be found in this presentation, including some interesting stuff about differences in microbial cell volume mediating ocean acidification effects, but I’ll leave that for another day. One ocean chemistry lesson today was enough for my brain to juice on.


Combing sloth hair for rainforest fungi, scientists uncover anti-malaria, anti-cancer and antibiotic activity


Hosting the highest biodiversity of any biome on Earth, tropical rainforests may represent a goldmine of “bioactive” compounds- medicinal chemicals produced naturally by plants, insects and microorganisms. Given a full 50% of all medicines introduced between 1981 and 2006 came directly from nature, the notion of “bioprospecting”, or combing the diversity of tropical forests for new drugs, has enticed imaginations for decades. But Big Pharma’s interest in bioprospecting has waned in recent decades due to the slow pace of discovery. However, hope is still alive amongst microbiologists working in the field.  And for good reason. In a study published last week in the journal PLOS ONE, scientists report on a new, highly promising source of bioactive compounds from a rather unusual suspect: the three toed sloth.

Sloths are famous for their green coloration, a result of the algae that live in their hair and help provide camoflauge

Sloths are famous for their green coloration, a result of the algae that live in their hair and help provide camoflauge

Sloths host entire ecosystems in their thick, coarse hair, including plants (green algae), arthropods (cockroaches, moths and roundworms), bacteria and fungi. Microbiologist Sarah Higgingbotham at the Smithsonian Tropical Research Institute in Panama was interested in finding out whether any of this diversity was medicinally valuable. Of particular interest to Higgingbotham and colleagues were the numerous species of fungi living in sloth hair. Fungi have made substantial contributions to the pool of natural drug products since the discovery of penicillin over 80 years ago.

Fungi are a diverse kingdom of organism from which have come a variety of natural products, including food supplements, antibiotics such as penicillin, and anti-cancer agents.  Credit: National Geographic

Fungi are a diverse kingdom of organisms that produce a variety of economically valuable compounds, such as antioxidants, antibiotics and anti-cancer agents.
Credit: National Geographic

To uncover potential drug-producing fungi, Higgingbotham and colleagues collected samples of the coarse, outer hair from nine unsuspecting three toed sloths found moseying along a road in Soberanía National Park, Panama (yes, aspiring microbiologists, this is something you can actually get paid to do). The hair samples were taken back to their lab, incubated on petri dishes, and checked regularly for fungal growth. Following growth, the researchers collected fungal hyphae from the plates, extracted and sequenced their DNA in order to determine identity. In total, 84 unique fungi were isolated. Although these fungi are a highly diverse group, including several potentially novel species, most fell into the taxonomic class Sordariomycetes – a well documented source of bioactive compounds.

Samples of 70 isolated fungal strains were grown in liquid culture media and tested for “bioactivity” against malaria, Chagas disease and the breast cancer cell line MCF-7, in addition to 15 human pathogenic bacteria. A strain was considered “highly bioactive” if it inhibited growth of a disease by 50% or more. For 50 of these strains, the researchers also constructed “antibiotic activity profiles” – scorecards indicating the degree to which a given fungal strain inhibits a range of bacterial pathogens. Antibiotic activity profiles are commonly used in medicine to determine the efficacy of a particular drug against an infection. Creating antibiotic activity profiles allows scientists to compare novel antibiotics to databases of antibiotics currently on the market and identify new disease-fighting drugs.

Malaria parasite P. falciparum eats its way through the hemoglobin in red blood cells.  Credit: National Geographic

Malaria parasite P. falciparum eats its way through the hemoglobin in red blood cells.
Credit: National Geographic

Overall, two of the fungal isolates were highly bioactive against the malaria parasite Plasmodium falciparum and eight were active against the Chagas parasite Trypanosoma cruzi. Fifteen fungal isolates were highly active against the MCF-7 cell line. Bioactivity against T. cruzi is particularly rare and represents a promising alternative to the two currently used drugs, nitrofurane and benznidazole, both of which can have toxic side effects.

Twenty of the fifty fungal isolates screened were bioactive against at least one bacterial pathogen. An exceptionally promising isolate, Lasiodiplodia sp.1, aggressively reduced the growth of several pathogenic Gram-negative bacteria. Infections caused by multi drug-resistant (MDR) Gram-negative bacteria, such as E.coli and Pseudomonas aeruginosa, are on the rise worldwide due to the overuse of antibiotics in hospitals and clean rooms. There is currently a paucity of drugs in development against MDR Gram-negative bacteria compared with their Gram-positive counterparts. Lasiodiplodia’s bioactivity profile did not match that of any known antibiotics, suggesting a potentially novel disease-fighting mechanism.

What do hospital clean rooms and factory farms have in common? Both use lots of antibiotics, leading to an increase in multidrug-resistant bacteria

What do hospital clean rooms and factory farms have in common? Both use lots of antibiotics, leading to an increase in multidrug-resistant bacteria

Twenty nine of the fungal strains isolated by Higgingbotham and colleagues are known endophytes– fungi that make a home living on plants. Endophytic rainforest fungi have recently made news for other remarkable metabolic features such as the capacity to metabolize plastic . The discovery of endophytic fungi on sloth hair increases our understanding of the habitat range occupied by these diverse organisms. Higgingbotham speculates some her fungi living may be associated with the algae present in sloth hair, forming a symbiosis analogous to that seen in lichen.