Final Report Summary - METAECO (Analysing the Impact of Global Climate Change on Ecosystems: A Cross-Scale Metatranscriptomics Approach)
SUMMARY
The project METAECO focuses on investigating the effects of global drivers on both below- and above-ground ecosystems. Using a field experiment, we study how the addition of nitrogen fertilizers and increasing temperatures - alone or in combination - affect both plant communities and microbial communities, and whether there are any interaction effects. We do this using a combination of data on plant community structure and DNA sequencing data of the microbial communities in the soil. We set out to investigate a number of key questions: How do global environmental change drivers such as climate affect microbial diversity in soil? Is the community structure or the relative abundance of specific organisms changed? How do these community-scale changes affect important functional pathways? Can we link these functional traits to specific taxa? What effects do we see in the above-ground plant communities, and do the changes in the above- and below-ground communities match across scale?
PROGRESS
The METAECO project has progressed as planned but is now being terminated early due to the fellow having been offered a new research position in Denmark. The factorial field experiment measures increasing temperatures, added nitrogen fertilizer, both drivers and control plots in replicates. Multiple soil cores were collected from each plot, pooled, sieved, sub-divided into 2 g soil samples and stored at -20 degrees celsius. While collecting soil samples, various other data were measured such as temperature and respiration.
For each plot, total DNA was extracted from three soil samples, pooled and sent to the sequencing center Macrogen for high-throughput sequencing, generating a total of 20 comprehensive metagenome data sets, each containing around 27 million read-pairs of length 100 nucleotides. The DNA data was analyzed by a combination of custom-built programs and previously published metagenome tools from other groups. The analyses looked at both changes in community composition (i.e. which species are present), relative abundance (i.e. do the proportions of individual species change), and functional capacity (i.e. do the presence of specific gene sequences change).
The metagenome data describing the effects of global drivers on microbial communities was subsequently compared to previously collected data on the above-ground plant communities, looking at changes in plant cover, community composition and functional traits.
RESULTS
The preliminary results of the METAECO project were selected for an oral presentation at the ISME meeting (International Symposium on Microbial Ecology) in August 2014. First of, the treatments of the experimental plots significantly changed temperature, moisture and respiration.
When analyzing the above-ground plant data, we see that both drivers significantly alter the composition of tussock grasses, resulting in an overall decrease in diversity. The addition of nitrogen has a significant effect on the plants colonizing the plots by decreasing the richness of colonizers, specifically nitrogen fixing species. Considering both planted tussocks and colonizing plants, nitrogen addition has the largest effect and significantly alters both composition and diversity of plant communities. This also leads to a significant decrease in the functional richness and dispersion of plants.
When analyzing the microbial communities, we do not see the same strong effect of nitrogen addition. Instead, there is a very strong and highly significant effect of warming on community composition all the way from the phylum level and down to individual species. Specifically, this leads to a decrease of Bacteroidetes, Proteobacteria, Chlamydiae and “unclassified bacteria” in the warmed plots. This is coupled with a significant increase of Actinobacteria and Firmicutes in the same plots.
Overall, this translates into an increase of Gram-positive bacteria in the warmed plots. Generally these are characterized as having an oligotrophic lifestyles, meaning that they can live in environments with low levels of nutrients. They exhibit low growth rate and high resource use efficiency, and this could indicate a more stressed community relative to the control plots.
Likewise, at the functional level there is a significant shift in the “functional capacity” of the microbial communities as an effect of warming. This is matched by a significant decrease in the overall richness of enzymes detected in the genomic data. Thus, these communities might be less robust. When comparing the detected shifts at the taxonomic level to the functional changes, they are highly correlated indicating a strong connection between taxa and function.
END GOAL
There are several exciting prospects as to what the METAECO project will produce. It is one of the first studies to link changes in above- and below-ground systems, looking at both community composition and functioning. It also helps us better understand the complex effects of global drivers at an ecosystem level instead of focusing on single species. Furthermore, by investigating both community composition and functional changes, and by combining both above- and below-ground data, the study will generate a comprehensive picture of a complex system. Since it is well-known that there are a lot of interaction between plants and soil microbial communities, this perspective is important for extending our biological understanding of ecosystems. The findings of this and follow-up studies can have great impact on e.g. agriculture and the use of nitrogen containing fertilizers. The study can also help us better understand what changes to expect and, thus, how to potentially prepare for some of the effects of global climate change. Such a study can have both political and economic impacts, and there are multiple avenues for further research.
The project METAECO focuses on investigating the effects of global drivers on both below- and above-ground ecosystems. Using a field experiment, we study how the addition of nitrogen fertilizers and increasing temperatures - alone or in combination - affect both plant communities and microbial communities, and whether there are any interaction effects. We do this using a combination of data on plant community structure and DNA sequencing data of the microbial communities in the soil. We set out to investigate a number of key questions: How do global environmental change drivers such as climate affect microbial diversity in soil? Is the community structure or the relative abundance of specific organisms changed? How do these community-scale changes affect important functional pathways? Can we link these functional traits to specific taxa? What effects do we see in the above-ground plant communities, and do the changes in the above- and below-ground communities match across scale?
PROGRESS
The METAECO project has progressed as planned but is now being terminated early due to the fellow having been offered a new research position in Denmark. The factorial field experiment measures increasing temperatures, added nitrogen fertilizer, both drivers and control plots in replicates. Multiple soil cores were collected from each plot, pooled, sieved, sub-divided into 2 g soil samples and stored at -20 degrees celsius. While collecting soil samples, various other data were measured such as temperature and respiration.
For each plot, total DNA was extracted from three soil samples, pooled and sent to the sequencing center Macrogen for high-throughput sequencing, generating a total of 20 comprehensive metagenome data sets, each containing around 27 million read-pairs of length 100 nucleotides. The DNA data was analyzed by a combination of custom-built programs and previously published metagenome tools from other groups. The analyses looked at both changes in community composition (i.e. which species are present), relative abundance (i.e. do the proportions of individual species change), and functional capacity (i.e. do the presence of specific gene sequences change).
The metagenome data describing the effects of global drivers on microbial communities was subsequently compared to previously collected data on the above-ground plant communities, looking at changes in plant cover, community composition and functional traits.
RESULTS
The preliminary results of the METAECO project were selected for an oral presentation at the ISME meeting (International Symposium on Microbial Ecology) in August 2014. First of, the treatments of the experimental plots significantly changed temperature, moisture and respiration.
When analyzing the above-ground plant data, we see that both drivers significantly alter the composition of tussock grasses, resulting in an overall decrease in diversity. The addition of nitrogen has a significant effect on the plants colonizing the plots by decreasing the richness of colonizers, specifically nitrogen fixing species. Considering both planted tussocks and colonizing plants, nitrogen addition has the largest effect and significantly alters both composition and diversity of plant communities. This also leads to a significant decrease in the functional richness and dispersion of plants.
When analyzing the microbial communities, we do not see the same strong effect of nitrogen addition. Instead, there is a very strong and highly significant effect of warming on community composition all the way from the phylum level and down to individual species. Specifically, this leads to a decrease of Bacteroidetes, Proteobacteria, Chlamydiae and “unclassified bacteria” in the warmed plots. This is coupled with a significant increase of Actinobacteria and Firmicutes in the same plots.
Overall, this translates into an increase of Gram-positive bacteria in the warmed plots. Generally these are characterized as having an oligotrophic lifestyles, meaning that they can live in environments with low levels of nutrients. They exhibit low growth rate and high resource use efficiency, and this could indicate a more stressed community relative to the control plots.
Likewise, at the functional level there is a significant shift in the “functional capacity” of the microbial communities as an effect of warming. This is matched by a significant decrease in the overall richness of enzymes detected in the genomic data. Thus, these communities might be less robust. When comparing the detected shifts at the taxonomic level to the functional changes, they are highly correlated indicating a strong connection between taxa and function.
END GOAL
There are several exciting prospects as to what the METAECO project will produce. It is one of the first studies to link changes in above- and below-ground systems, looking at both community composition and functioning. It also helps us better understand the complex effects of global drivers at an ecosystem level instead of focusing on single species. Furthermore, by investigating both community composition and functional changes, and by combining both above- and below-ground data, the study will generate a comprehensive picture of a complex system. Since it is well-known that there are a lot of interaction between plants and soil microbial communities, this perspective is important for extending our biological understanding of ecosystems. The findings of this and follow-up studies can have great impact on e.g. agriculture and the use of nitrogen containing fertilizers. The study can also help us better understand what changes to expect and, thus, how to potentially prepare for some of the effects of global climate change. Such a study can have both political and economic impacts, and there are multiple avenues for further research.