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Microbial ecology

Microbial ecology

Talus fields in Green Lakes Valley, photo credit: JG Smith

NWT scientists are finding that an abundance of previously unknown microbes are active beneath the snow at the highest elevations in the continental US, even in rock glaciers high above the tree line in the Rocky Mountains, a barren environment previously thought to be devoid of life. This discovery of microbial activity in even the harshest of alpine environments substantially broadens our understanding of both the diversity and biogeochemical functioning of life in extreme environments.

Research Spotlight

Life in Extreme Environments

In the mostly unvegetated talus fields above NWT’s D1 climate station and Arikaree glacier in the Green Lakes Valley, vascular plant abundance is limited due to persistent snow cover and a short growing season (<20 days in some areas). However, diverse and active microbial communities thrive here (King et al. 2010).  Recent work has shown that heterotrophic soil microbes are predominantly water, C and P limited (King et al. 2008, Schmidt et al. 2015), whereas soil phototrophs (algae and cyanobacteria) are P limited. Opposed to similar high elevation catchments in rapidly de-glaciating areas of the Andes Mountains and the Alaska Range of Denali National Park (Nemergut et al. 2007, Schmidt et al. 2012), N limitation in the barren areas of NWT have been overcome by atmospheric N deposition. At NWT, we find a feed-forward effect of nutrients in a system that was traditionally thought to be water limited (Knelman et al. 2014). Nutrient additions overcome the apparent water limitation by allowing the microbial and plant communities to grow more rapidly in response to pulses of water availability following snowmelt. The degree to which plant-microbe interactions can alleviate P-limitation and thereby facilitate the colonization of these sites by plants as growing season lengthens is the subject of ongoing studies (Knelman et al. 2014).

King AJ, Freeman KR, McCormick KF, Lynch RC, Lozupone C, Knight R and Schmidt SK (2010) Biogeography and habitat modelling of high-alpine bacteria. Nature Communications 1:1-6

Knelman JE, Schmidt SK, Lynch RC, Darcy JL, Castle SC, Cleveland CC and Nemergut DR (2014) Nutrient addition dramatically accelerates microbial community succession. PLOS one 9:e102609

Schmidt SK, King AJ, Meier CL, Bowman WD, Farrer EC, Suding KN and Nemergut DR (2015) Plant–microbe interactions at multiple scales across a high-elevation landscape. Plant Ecology & Diversity 8:703-712

Plant-microbe interactions and response to nitrogen deposition  

Plant community responses to nitrogen (N) are often attributed to altered competitive interactions between plants, but may also be a result of microbial responses to N, particularly root-associated fungi (RAF) and root-associated bacteria (RAB), which are known to affect plant fitness. A long-term N addition and plant species removal experiment was used to investigate the effect of N fertilization on fungal and bacterial symbionts associated with two co-dominant alpine plant species, Geum rossii and Deschampsia cespitosa. Scientists examined whether contrasting host responses to N are associated with altered plant-microbial symbioses, specifically whether microbial communities may explain Geum’s decline. Geum and Deschampsia roots were found to harbor drastically different microbial communities, with only 9% overlap of taxa for fungal communities and 17% overlap for bacterial communities. Endophyte communities also had different responses to N addition: Deschampsia RAF were more responsive to N compared to Geum RAF, and there was a trend that Geum RAB were more responsive to N compared to Deschampsia RAB. Also, one of the main orders of Geum RAF, the Helotiales (a group with many known plant mutualists), declined from 83% to 60% abundance in the N treatment suggesting that loss of mutualists may be causing Geum decline. A few pathogenic RAF taxa also increased in abundance on Geum roots with N (Fig. 1). These results highlight the potential importance of belowground microbial dynamics in plant responses to N deposition.

Dean SL, Farrer EC, Porras-Alfaro A, Suding KN and Sinsabaugh RL (2015) Assembly of root-associated bacteria communities: interactions between abiotic and biotic factors. Environmental Microbiology Reports 7:102-110

Dean SL, Farrer EC, Taylor DL, Porras-Alfaro A, Suding KN and Sinsabaugh RL (2014) Nitrogen deposition alters plant-fungal relationships: linking belowground dynamics to aboveground vegetation change. Molecular Ecology 23:1364-1378

Figure 1. Effect of N treatment on the orders of endophytic fungi in Geum roots; note the decrease in Helotiales (mutualists) and increase of more rare orders in root endophyte communities at high nitrogen. Geum declines strongly at high nitrogen environments; it may be the shift in microbial communities that drive some of this decline (Dean et al. 2014, 2015).

Figure 1. Effect of N treatment on the orders of endophytic fungi in Geum roots; note the decrease in Helotiales (mutualists) and increase of more rare orders in root endophyte communities at high nitrogen. Geum declines strongly at high nitrogen environments; it may be the shift in microbial communities that drive some of this decline (Dean et al. 2014, 2015).

Alpine Microbial Observatory

At Niwot Ridge, the Alpine Microbial Observatory (AMO) is a project focused on studying the seasonal dynamics of soil microorganisms across an extreme environmental gradient ranging from montane forests (2800 m) up to alpine tundra and barren talus slopes (4000 m). These sites represent globally important plant biomes, all of which are covered with snow for part of the year. The snow-covered period is especially important because 35% of Earth's land surface is covered with snow for varying lengths of time each year and research at the AMO has shown that novel soil microorganisms are active under snow where they contribute significantly to gas fluxes and nitrogen pulses to the environment.

At the global scale, research at the AMO will help us to understand how colder regions of the earth function as part of the biosphere and how they will respond to future climate change.

Learn more at the AMO website 

Related Discipline Data:

Microbial ecology

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CU Boulder

This material is based upon work supported by the National Science Foundation under Cooperative Agreement #DEB-1637686. Any opinions, findings, conclusions, or recommendations expressed in the material are those of the author(s) and do not necesarily reflect the views of the National Science Foundation.

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