Ecological Succession and Microbiology

Ecological Succession in the Sibinacocha Watershed

Glaciers are rapidly retreating in the Sibinacocha Watershed leaving behind previously ice-covered lands (Figure 1) that are being slowly colonized by microbes, plants and animals through a process called ecological succession. Studying ecological succession is important not only for understanding the ecology of the biosphere, but also for gaining insight into how organisms build new ecosystems and stabilize soils that are vulnerable to erosion and landslides. Since 2001 researchers have monitored the rate of glacial retreat and the succession of microbes and plants that are colonizing the soils left behind by the massive Puca Glacier. The first scientific analyses of this important work showed that photosynthetic microorganisms rapidly colonize these new soils and carryout important ecosystem processes that stabilize the land and add nutrients to the soil, thus paving the way for plants and animals to also colonize these new lands (Nemerget et al. 2007, Schmidt et al. 2008).




Figure 1. Repeat photography of a site in the Sibinacocha Watershed where glacial retreat is exposing large tracts of
land that are rapidly colonized by microbes (months to years) but only
 slowly colonized by plants (decades to centuries). The top photograph was taken in 2005 and the bottom in 2010 (the person in each photograph is standing in approximately the same location). The photographer was standing at about

5200 m above sea level near the ‘100-m site’ viewable in an aerial photograph of the site previously published in Schmidt
et al. (2009). The distance from the person to the closest edge of the ice is approximately 20 and 200 meters in the top and bottom photos, respectively.

Reprinted from: The Journal of Molecular Ecology, Vol. 23, pg. 254 (2014)




An important observation made during our work on ecosystem succession at the Puca Glacier was that the rate of plant colonization of newly de-glaciated lands in the Sibinacocha Watershed was much slower than it is in recently de-glaciated sites in the Alps and Alaska. At first we hypothesized that the slower rate of succession in the Sibinacocha Watershed was due to the harsher climate (e.g. higher elevation, drier climate etc.) at this site compared to milder climates in the Alps and Alaska. This hypothesis was used to obtain grants from the National Science Foundation and the National Geographic Society to carryout comparative studies of successional processes in Peru, Alaska, Montana and Washington State. The most important finding of this research was that the harsh climate in the Sibinacocha Watershed was not the main factor limiting plant colonization. In fact, evidence is mounting that lack of the nutrient phosphorus is the dominant factor limiting plant colonization in the Sibinacocha watershed. This finding not only contradicted our initial expectations, but also overturned classic theory in the field of ecosystem ecology which posited that nitrogen should be the most limiting nutrient during the initial stages of plant succession. These findings are still being analyzed for final publication, but several papers relating parts of this story have been published (Knelman et al. 2014, Schmidt et al. 2011, 2012, 2014).

The Sibinacocha Watershed as a model system for Astrobiology and Biogeography.

The geographic setting and climatic conditions of the Sibinacocha Watershed make it an ideal location to study how life has adapted to high elevations. We have taken advantage of this “natural laboratory” to study how microbial life is adapting to the unique environmental condition of high elevation landscapes in the tropics. Perhaps the most striking aspect of the microclimate of this site is the occurrence of daily freeze-thaw cycles that occur on a year-round basis. That is, almost every day of the year soil temperatures rise dramatically (due to the high levels of solar radiation) and then plunge to well below zero degrees every night. In one study it was found that soil temperatures can fluctuate from 38°C (100°F) during the day to -12°C (10°F) at night in a single 24 hour period. These extreme temperature fluctuations pose almost insurmountable barriers to life at high elevations, because the enzymes and membranes that all living things possess are usually adapted to higher or lower temperatures depending on the prevailing conditions during the growing season. How microorganisms are able to grow when temperatures cycle dramatically every day is an area of biology that has received very little study. Our initial studies show that there are unique bacteria and fungi that thrive and carry out important ecosystem functions under these extreme conditions (Schmidt et al. 2009, Vimercati et al. 2016). These findings have important implications for understanding the outer limits of where life can occur on Earth and also for understanding if life could exist on planets such as Mars.

Finally, the Sibinacocha Watershed is the centerpiece of a global effort to understand the biogeographic distribution and functioning of microbial life in high elevation and polar regions. This effort was funded through the Microbial Observatories Program at the National Science Foundation and resulted in the establishment of “The Alpine Microbial Observatory” (AMO) ( We have focused the efforts of the AMO on understanding high elevation life in the Andes, Himalayas, Alaska Range and Rocky Mountains, but we have also recently expanded our effort to include Antarctica. Work through the AMO has resulted in many breakthrough discoveries of new life forms in cold environments and has also lead to a better understanding of the biogeography of microbial life on high elevation mountains and in the atmosphere. Examples of articles discussing these findings include Darcy et al. (2011, 2016), Freeman et al. (2009), King et al. (2010), Nemergut et al. (2005, 2013, 2016), Robeson et al. (2011) and Schmidt et al. (2008, 2011b, 2016).

On a less happy note, Diana R. Nemergut died of a brain tumor on December 31, 2015. She was a true microbiological pioneer and explorer who led some of the most important studies of high elevation life described above. We all miss her.


For more information of Dr. Steve Schmidt and the Schmidt Laboratory, see:


Publications cited: (pdfs can be downloaded at

Darcy, J.L., et al. 2011. Global distribution of Polaromonas phylotypes – evidence for a highly successful dispersal capacity. PLoS ONE 6: e23742.

Darcy, J.L. et al. 2016. Nutrient limitation of microbial phototrophs on a debris-covered glacier. Soil Biol. Biochemistry 95: 156-163.

Freeman, K.R., D. Karki, et al. 2009. Evidence that chytrids dominate fungal communities in high-elevation soils. Proceedings Natl. Acad. Sci. USA 106: 18315-18320.
King, A.J. et al. 2010. Biogeography and habitat modelling of high-alpine bacteria. Nature Commun. 1:53 doi: 10.1038/ncomms1055.

Knelman J.E. et al. 2014. Nutrient addition dramatically accelerates microbial community succession. PLoS ONE 9: e102609.

Nemergut, D.R. et al. 2005. Structure and function of alpine and arctic soil microbial communities. Res. Microbiology 156: 775-784.

Nemergut, D.R., S.P. Anderson, C.C. Cleveland, A.E. Miller, A. Seimon, S.K. Schmidt. 2007. Microbial community succession in unvegetated, recently-deglaciated soils. Microbial Ecol 53: 110-122.

Nemergut, D.R., T. Fukami et al. 2013. Patterns and processes of microbial community assembly. Microbiol. Molecular Biol. Rev. 77: 342-356.

Nemergut D.R. et al. 2016. Decreases in average bacterial community rRNA operon copy number during succession. ISME Journal 10: 1147-1156.

Rhodes, M. et al. 2013. Structure and Function of Prokaryotic Communities in Soils of Cold Deserts. in E. Rosenberg, E. Delong et al. (eds.), The Prokaryotes, Springer-Verlag, Berlin.

Robeson, M.S. et al. 2011. Soil Rotifer communities are extremely diverse globally but spatially auto-correlated locally. Proceedings Natl. Acad. Sci. USA 108: 4406-4410.

Schmidt, S.K., D.R. Nemergut et al. 2008. The earliest stages of ecosystem succession in high-elevation (5000 m.a.s.l.), recently de-glaciated soils. Proceedings Royal Society B. 275: 2793-2802.

Schmidt, S.K. et al. 2008. Mycorrhizal and dark-septate fungi in plant roots above 4270 meters elevation in the Andes and Rocky Mountains. Arctic, Antarctic and Alpine Res. 40: 576-583.

Schmidt S.K., D.R. Nemergut, et al. 2009. Microbial activity and diversity during extreme freeze-thaw cycles in periglacial soils, 5400 m Elevation, Cordillera Vilcanota, Perú. Extremophiles 13: 807-816.

Schmidt, S.K., D.R. Nemergut, S.C. Reed, A.J. King, P. Sowell. 2011a. Estimating phosphorus availability for microbial growth in an emerging landscape. Geoderma 163: 135-140.

Schmidt, S.K., D. Karki et al. 2011b. Phylogeography of microbial phototrophs in the dry valleys of the high Himalayas and Antarctica. Proceedings Royal Society B. 278: 702-708.

Schmidt, S.K., D.R. Nemergut et al. 2012. A simple method for determining limiting nutrients for photosynthetic crusts. Plant Ecology Diversity 5: 513-519.

Schmidt, S.K., D.R. Nemergut et al. 2014. Do bacterial and fungal communities assemble differently during primary succession? Molecular Ecology 23: 254-258.

Schmidt, S.K. et al. 2016. Biogeochemical stoichiometry reveals P and N limitation across the post-glacial landscape of Denali National Park, Alaska. Ecosystems doi 10.1007/s10021-016-9992-z.

Vimercati L. et al. 2016. Growth of a high-elevation Cryptococcus sp. during extreme freeze-thaw cycles. Extremophiles (doi 10.1007/s00792-016-0844-8).