Home sweet home: Understanding New York City soil fungal communities in green roofs and city parks

Roof garden

Green roofs are growing more common in urban communities around the world. Besides the cost savings associated with these urban green spaces; they also provide ecosystem benefits such as decreased water run-off and habitats for birds and insects.  While green roofs are well studied for their benefits to urban dwellers of the human species, little is known about the impact of their microscopic inhabitants.

In order to better understand these green roof ecosystems, researchers of a recently published paper dug in and evaluated whether or not green roofs in New York City served as a habitat for fungal communities and compared these fungal communities to the microbial composition of nearby city parks.

Their research uncovered that fungi form a diverse community, with many varieties that belong to groups capable of surviving tough conditions like disturbed and polluted habitats. According to the paper:

 Across roofs, there was significant biogeographical clustering of fungal communities, indicating that community assembly of roof microbes across the greater New York City area is locally variable… While fungal communities were compositionally distinct across green roofs, they did not differentiate by plant community.

When the roof and park soil samples were compared, the researchers found that 54% of the fungal strains where shared between park soil and green roofs.

To read more about this research and about how the fungi living on green roofs could be an undervalued piece of the green roof ecosystem click here.

Citation: McGuire KL, Payne SG, Palmer MI, Gillikin CM, Keefe D, et al. (2013) Digging the New York City Skyline: Soil Fungal Communities in Green Roofs and City Parks. PLoS ONE 8(3): e58020. doi:10.1371/journal.pone.0058020

Image:  Image comes from Figure 2 of the manuscript and is an image of a representative green roof from the study.


Greetings from Lake Socompa! A Diversity of Life in Extreme Conditions

The photo above comes to us from a remote part of the Andes, at the base of the active volcano Socompa. Lake Socompa is situated here and its whitish stomatolites (a type of layered sediment deposit created by microorganisms) are home to an unexpected diversity of bacterial life.

In research published this week in PLOS ONE, scientists from Argentina and Germany travelled to this remote location, 3570 meters above sea level, to study the lake’s stomatolites and the harsh environment in which they are formed. Stomatolites were found only on the southern shore, where a hydrothermal spring feeds acidic water into the lake. This region of the Andes mountain range receives very little annual rainfall and, due to its high elevation, experiences high levels of ultraviolet radiation. Yet, rather than being inhospitable to life, scientists found that the region’s extreme environmental conditions actually helped to foster “rich, diverse and active ecosystems” within the lake’s stomatolites.  According to the research, the Lake Socompa site is the highest altitude, thus far, where stomatolites are found to form.

Citation: Farías ME, Rascovan N, Toneatti DM, Albarracín VH, Flores MR, et al. (2013) The Discovery of Stromatolites Developing at 3570 m above Sea Level in a High-Altitude Volcanic Lake Socompa, Argentinean Andes. PLoS ONE 8(1): e53497. doi:10.1371/journal.pone.0053497


Worth a Thousand Words: Rediscovering an “Extinct” Species

It’s not every day that you come across a living member of an extinct species. Nathan Whelan, a doctoral student at the University of Alabama, had such a day in 2011, when he found specimens of Leptoxis compacta on the banks of the Cahaba River. The last recorded collection of L. compacta more commonly known as the oblong rocksnail, dates back to 1933; the species was formally declared extinct in 2000. The first picture above is Figure 4 from the manuscript, published just last month.

Whelan et al. conducted several tests to confirm that this species above was indeed L. compacta. They compared the shells they found with shells of other known gastropods in the same area. The shells were dissimilar in both pigmentation and pattern. The researchers also compared their findings with archival L. compacta. By using a scanning electron microscope (SEM), they found strong evidence to suggest that they had rediscovered a heretofore “extinct” species.

Citation: Whelan NV, Johnson PD, Harris PM (2012) Rediscovery of Leptoxis compacta (Anthony, 1854) (Gastropoda: Cerithioidea: Pleuroceridae). PLoS ONE 7(8): e42499. doi:10.1371/journal.pone.0042499


Worth a Thousand Words: Handedness in Fish

If you look closely at the image above, you’ll see that the mouths of these cichlid fish, Perissodus microlepis, curve in opposite directions. Similar to left or right handedness in humans, many animals exhibit handedness in behavior or morphology. Whether handed behavior is expressed early in development and produces mouth asymmetry or the opposite, that mouth asymmetry produces handed behavior, however, is not well known. The authors of the study “Handed Foraging Behavior in Scale-Eating Cichlid Fish: Its Potential Role in Shaping Morphological Asymmetry” set out to investigate this question and more. The image above is Figure 1 of the article.


Scale-eating cichlid fish, Perissodus microlepis, from Lake Tanganyika display handed (lateralized) foraging behavior, where an asymmetric ‘left’ mouth morph preferentially feeds on the scales of the right side of its victim fish and a ‘right’ morph bites the scales of the left side. This species has therefore become a textbook example of the astonishing degree of ecological specialization and negative frequency-dependent selection. We investigated the strength of handedness of foraging behavior as well as its interaction with morphological mouth laterality in P. microlepis. In wild-caught adult fish we found that mouth laterality is, as expected, a strong predictor of their preferred attack orientation. Also laboratory-reared juvenile fish exhibited a strong laterality in behavioral preference to feed on scales, even at an early age, although the initial level of mouth asymmetry appeared to be small. This suggests that pronounced mouth asymmetry is not a prerequisite for handed foraging behavior in juvenile scale-eating cichlid fish and might suggest that behavioral preference to attack a particular side of the prey plays a role in facilitating morphological asymmetry of this species.


Citation: Lee HJ, Kusche H, Meyer A (2012) Handed Foraging Behavior in Scale-Eating Cichlid Fish: Its Potential Role in Shaping Morphological Asymmetry. PLoS ONE 7(9): e44670. doi:10.1371/journal.pone.0044670

Observing World Malaria Day 2012: Sustain Gains, Save Lives

Today is the fifth annual World Malaria Day, commemorated every April 25 to recognize and encourage global efforts to control malaria. This year’s theme, “Sustain Gains, Save Lives: Invest in Malaria,” alludes to the many important advances against the malaria parasite that have been achieved in recent years, but also includes a warning: we must continue to invest in malaria research and maintain our vigilance to ensure that painstakingly earned gains are not surrendered to complacency.

Based on the 251 malaria-related PLoS ONE papers published since last year’s World Malaria Day, it’s pretty clear to us that the research community is maintaining its commitment to this disease. Instead of trying to provide an overview of all of these articles, which cover perspectives as diverse as public health, ecology, and microbiology, we decided to observe the day by highlighting a single article that, like this year’s theme, emphasizes the importance of continued research as the parasite proves itself to be a constantly evolving target.

The study, published last October, monitors drug resistance in the causative parasite Plasmodium falciparum in Mozambique over five years, from 2006 to 2010, as the recommended drug treatment was adjusted. The researchers, led by Jaishree Raman of the South African Medical Research Council, found that the incidence of parasitic resistance to the originally recommended drug regimen increased significantly over the course of the study, from 56.2% at the start up to 75.8% in 2010. This approximately 20% leap in resistance suggested that the preferred treatment at the time would become much less effective as its use increased.

However, the Mozambican Ministry of Healthy preempted this scenario by changing their recommended front-line drug treatment in 2008. The authors weren’t able to study the full impact of this policy change, though, because it was not fully deployed until 2010, at which point the study was winding down – further highlighting the need for continued careful monitoring as new treatments are introduced.

You can learn more about World Malaria Day at Roll Back Malaria and the World Health Organization, and read about some additional malaria papers from last year’s World Malaria day post.

Citation: Raman J, Mauff K, Muianga P, Mussa A, Maharaj R, et al. (2011) Five Years of Antimalarial Resistance Marker Surveillance in Gaza Province, Mozambique, Following Artemisinin-Based Combination Therapy Roll Out. PLoS ONE 6(10): e25992. doi:10.1371/journal.pone.0025992

Image source: eyeweed on Flickr

PLoS ONE News and Media Roundup

Emperor penguin – Credit: British Antarctic Survey

This month in PLoS ONE news: Penguin populations recorded from outer space, super strength bacteria discovered in caves, and much more!

Satellite mapping provides the first comprehensive record of the Emperor Penguin population in Antarctica. Scientists found that the overall population is higher than previously estimated; however, other colonies may have disappeared altogether, most likely due to climate change. Wired Scientific American and BBC covered this article.

Strains of previously undiscovered bacteria found deep in the Lechuguilla Cave of New Mexico, show remarkably strong resistance to modern antibiotics. Scientific American, The Los Angeles Times and National Geographic covered this article.

The commonly used Body Mass Index (BMI) measure may vastly underestimate the ongoing obesity epidemic, according to new research. Read this study and more at The Huffington Post, TIME and The Los Angeles Times.

What makes a good athlete? Traits like problem solving, creativity and quick decision making are commonly referred to as “game intelligence” in sports. According to new research, professional soccer players show increased cognitive abilities, which may be linked to such athletic success. New York Times, Wired and CNN discussed this article.

For more in-depth coverage on news and blog articles about PLoS ONE papers, please visit our Media Tracking Project.

The commonly used Body Mass Index (BMI) measure may vastly underestimate the ongoing obesity epidemic, according to new research.

Worth a Thousand Words: The Spikerbox

Depiction of the SpikerBox (a) and iPhone running custom open-source iOS software (b) used for electrophysiology experiments in the classroom.

Pictured above is the SpikerBox, a low cost, open-source BioAmplifier developed by a team of scientist/engineers in their quest to bring neuroscience education to the K-12 curricula. The SpikerBox can be built by students and teachers in the classroom and enables a variety of experiments that, in the authors’ words, “provides a great way to learn about how the brain works by letting you hear and even see the electrical impulses of neurons!”

In their manuscript, “The SpikerBox: A Low Cost, Open-Source BioAmplifier for Increasing Public Participation in Neuroscience Inquiry” published last week in PLoS ONE, authors Timothy C. Marzullo and Gregory J. Gage describe the design of the SpikerBox and detail experiments employing the device in a classroom setting. They also provide learning materials and supplemental resources, including an assembly guide and student questions, for use in a lesson plan. Marzullo and Gage’s work is an excellent example of bringing together open-source hardware and openaccess publication to support science education.

From the abstract:

Although people are generally interested in how the brain functions, neuroscience education for the public is hampered by a lack of low cost and engaging teaching materials. To address this, we developed an open-source tool, the SpikerBox, which is appropriate for use in middle/high school educational programs and by amateurs. This device can be used in easy experiments in which students insert sewing pins into the leg of a cockroach, or other invertebrate, to amplify and listen to the electrical activity of neurons. With the cockroach leg preparation, students can hear and see (using a smartphone oscilloscope app we have developed) the dramatic changes in activity caused by touching the mechanosensitive barbs. Students can also experiment with other manipulations such as temperature, drugs, and microstimulation that affect the neural activity. We include teaching guides and other resources in the supplemental materials. These hands-on lessons with the SpikerBox have proven to be effective in teaching basic neuroscience.

Halloween Highlight 2011: An Author Spotlight with David Hughes and Harry Evans

Zombie ant jack o' lantern

In the spirit of Halloween, we’ve asked Dr. David Hughes of Penn State University and  Dr. Harry Evans of  Federal University of Viçosa Brazil to share with us a bit about their manuscript, Hidden Diversity Behind the Zombie-Ant FungusOphiocordyceps unilateralis: Four New Species Described from Carpenter Ants in Minas Gerais, Brazil.   Both were kind enough to oblige and share with us their perspective via email.

The description of ants as zombies is not a pitch to popularity-even at Halloween-  but an orchestrated attempt to identify fungal-infected ants as very different from other ants in the society. Just because something looks, walks and quacks like a duck doesn’t mean it is actually a duck. The sinister thing about parasites which manipulate host behavior is that they can easily go unnoticed. The zombie ant moniker forces us to recall that we are looking at two organisms and the ant is not in the driving seat.

Our study in PLoS ONE, which used micromorphology together with spore function to delimit and describe new species, came about as it was obvious that the diversity of zombie ant fungi must be  higher than previously supposed because ant species diversity is high. We know that ants differ in many important behaviors which of course is due to brain differences. So, if your evolutionary gambit is brain control, then diverse brains will act as diverse selection environments leading to different species. Perhaps the most exciting thing is that we now recognize that these initial descriptions are just the tip of a very large iceberg and that many more zombie-inducing fungi await discovery, especially in tropical forests such as the Brazilian Atlantic rainforest in which we set our study.

In March, our editor wrote an overview of this paper.  To see last year’s Halloween post, click here.

Image by Roel Fleuren and pumpkin carving by Charissa de Bekker.

Worth a Thousand Words

A photographic series covering 5, 15 and 25 years of sessile structural species dwelling on Mediterranean coralligenous outcrops is  this week’s featured image.

This brilliant figure contains frames with sponge and anthozoan species used in the paper, Low Dynamics, High Longevity and Persistence of Sessile Structural Species Dwelling on Mediterranean Coralligenous Outcrops.

In the Abstract the authors write:


There is still limited understanding of the processes underlying benthic species dynamics in marine coastal habitats, which are of disproportionate importance in terms of productivity and biodiversity. The life-history traits of long-lived benthic species in these habitats are particularly poorly documented. In this study, we assessed decadal patterns of population dynamics for ten sponge and anthozoan species that play key structural roles in coralligenous outcrops (~25 m depth) in two areas of the NW Mediterranean Sea.

Methodology/Principle Findings:

This study was based on examination of a unique long-term photographic series, which allowed analysis of population dynamics over extensive spatial and time spans for the very first time. Specifically, 671 individuals were censused annually over periods of 25-, 15-, and 5-years. This long-term study quantitatively revealed a common life-history pattern among the ten studied species, despite the fact they present different growth forms. Low mortality rates (3.4% yr?1 for all species combined) and infrequent recruitment events (mean value of 3.1±0.5 SE recruits yr?1) provided only a very small fraction of the new colonies required to maintain population sizes.


Overall, annual mortality and recruitment rates did not differ significantly among years; however, some species displayed important mortality events and recruitment pulses, indicating variability among species. Based on the growth rates of these 10 species, we projected their longevity and, obtained a mean estimated age of 25–200 years. Finally, the low to moderate turnover rates (mean value 0.80% yr?1) observed among the coralligenous species were in agreement with their low dynamics and persistence. These results offer solid baseline data and reveal that these habitats are among the most vulnerable to the current increases of anthropogenic disturbances.

This post was written by Raquel Iglesias, a publications assistant at PLoS ONE .  Raquel has been assisting authors, reviewers and academic editors since April of last year.  She also helps ensure our clinical trial submissions move through the review process smoothly.

PLoS ONE News and Blog Round-Up

Researchers find a possible cure for the common cold and more – in this week’s media digest.

Human Pathogen Shown to Cause Disease in the Threatened Eklhorn Coral Acropora palmata was covered by The NewsHour, The New York Times, NPR, and CNN.

CNET, Hindustan Times, and Okezone covered Automatic Prediction of Facial Trait Judgments: Appearance vs. Structural Models.

The paper, Predator Cat Odors Activate Sexual Arousal Pathways in Brains of Toxoplasma gondii Infected Rats, received coverage from The New York Times, Scientific American, TIME’s Healthland, and The Loom.

Broad-Spectrum Antiviral Therapeutics received media coverage from Voice of America, LA Times, and Forbes.

Large Recovery of Fish Biomass in a No-Take Marine Reserve was covered by National Geographic (nice slideshow too), The Christian Science Monitor, Nature News, and KGTV San Diego. The image above, is taken from Figure 4 of this manuscript.

80 Beats covered the article, Artificial Skin – Culturing of Different Skin Cell Lines for Generating an Artificial Skin Substitute on Cross-Weaved Spider Silk Fibres. So did Treehugger.

The article entitled, Scientists Want More Children received media coverage from The Wall Street Journal, TIME’s Ecocentric, Science Career Blog, and Inside Higher Ed.

Elevated Non-Esterified Fatty Acid Concentrations during Bovine Oocyte Maturation Compromise Early Embryo Physiology was covered by Reuters, The Guardian, and The Press Association.

Worth a Thousand Words

Photomicrographs of Glomus versiforme (basionym Endogone versiformis) are this week’s featured image. The colorful figure contains pale spores used in the paper, Revealing Natural Relationships among Arbuscular Mycorrhizal Fungi: Culture Line BEG47 Represents Diversispora epigaea, Not Glomus versiforme.

In the abstract, the authors write:


Understanding the mechanisms underlying biological phenomena, such as evolutionarily conservative trait inheritance, is predicated on knowledge of the natural relationships among organisms. However, despite their enormous ecological significance, many of the ubiquitous soil inhabiting and plant symbiotic arbuscular mycorrhizal fungi (AMF, phylum Glomeromycota) are incorrectly classified.

Methodology/Principal Findings

Here, we focused on a frequently used model AMF registered as culture BEG47. This fungus is a descendent of the ex-type culture-lineage of Glomus epigaeum, which in 1983 was synonymised with Glomus versiforme. It has since then been used as ‘G. versiforme BEG47’. We show by morphological comparisons, based on type material, collected 1860–61, of G. versiforme and on type material and living ex-type cultures of G. epigaeum, that these two AMF species cannot be conspecific, and by molecular phylogenetics that BEG47 is a member of the genus Diversispora.


This study highlights that experimental works published during the last >25 years on an AMF named ‘G. versiforme’ or ‘BEG47’ refer to D. epigaea, a species that is actually evolutionarily separated by hundreds of millions of years from all members of the genera in the Glomerales and thus from most other commonly used AMF ‘laboratory strains’. Detailed redescriptions substantiate the renaming of G. epigaeum (BEG47) as D. epigaea, positioning it systematically in the order Diversisporales, thus enabling an evolutionary understanding of genetical, physiological, and ecological traits, relative to those of other AMF. Diversispora epigaea is widely cultured as a laboratory strain of AMF, whereas G. versiforme appears not to have been cultured nor found in the field since its original description.

All of PLoS ONE’s sporific papers are open access and free for you to read, rate and reuse.

Citation: Schüßler A, Krüger M, Walker C (2011) Revealing Natural Relationships among Arbuscular Mycorrhizal Fungi: Culture Line BEG47 Represents Diversispora epigaea, Not Glomus versiforme. PLoS ONE 6(8): e23333. doi:10.1371/journal.pone.0023333