Microbes in a warmer world

A major area of research here at Harvard Forest focuses on understanding the ecological changes within the forest due to a rapidly warming climate. These climate conditions are replicated at the forest using several experimentally warmed plots that are heated by resistance cables placed beneath the soil surface. In collaboration with the Marine Biological Labs (MBL), we attempted to understand microbial diversity and function within these manipulated plots, in order to investigate the roles of these microbes in the global carbon cycle in response to warming. 

This study was motivated by prior research that showed initial pulses of soil respiration in the warmed soil plot in Barre Woods.  The respiration flux eventually decreased to control levels within a few years only to then experience a subsequent pulse. In combination with subsequent studies, it is believed that this shift is the result of a shift in microbial community composition, more specifically, away from communities able to break down the easily accessible labile soil carbon and towards communities that are better able to break down tougher recalcitrant carbon sources. Essentially, the easy carbon was used up upon initial heating, and microbes had to adapt to decomposing more difficult carbon sources.  These findings will provide important information which will allow us to better understand this potential feedback system of the carbon cycle.

In a separate project, the microbial function of the community was quantified based on enzyme activity, with specific focus on the production of CO2. Although this is an effective way to understand carbon cycling processes that may be occurring in soil communities, it does not delve deep into the world of microbes that make up a significant component of the soils and are responsible for these processes. Therefore, our overall goal was to understand microbial species diversity and function using a genomics approach. This study utilized genetic sequence data to investigate the microbes that are present within the soil. The Barre Woods experiment is an ongoing process, and therefore, we were unable to conduct any analysis this summer on soil samples collected from that warming plot. However, two unpublished data sets, derived from soil samples collected at Harvard Forest, were provided to us by the National Ecological Observatory Network (NEON) and the Bill Landesman Research Group. We utilized these data sets to develop genomic and computational methods that will be used in future analyses of the data collected from the Barre Woods plots.

Our analysis began by understanding the genes present within the NEON data set, which was derived from a soil sample collected on Prospect Hill. DNA sequences in the data set were compared to known sequences present within online databases, such as NCBI. The resulting alignments provide a gene role and function within the cell based on the matching sequence. We can use the resulting matches to identify proteins that are involved in important ecological processes such as the nitrogen and carbon cycles. At the same time, we specifically searched for enzymes that are able to break down various forms of carbon.

A second approach involved studying microbial diversity, which was done with a similar DNA dataset. This data was processed through a program called QIIME, which integrates a series of scripts that call upon various programs to provide a taxonomic survey of the microbes within the sample based on sequence similarities.

The results from diversity analyses of our two datasets revealed that Proteobacteria and Acidobacteria were the dominant phyla present in the soil. This suggests a high prevalence of microbes that are involved in the nitrogen cycle, the carbon cycle, chemical decomposition, and biomass degradation. The gene analysis of the NEON data revealed that a majority of genes are associated with carbohydrate break down and energy production.

The results provided us with a glimpse into the microbial diversity here at the Harvard Forest. The methods developed using the two provided datasets will be replicated in our analysis of Barre Woods to understand the microbes present in the warming experiment. We expect to see unique microbes that are able to break down a broad range of carbon sources, and adapt to growing in warmer conditions. At the same time, we predict to see an increased prevalence of proteins involved in biomass degradation. This will ultimately be the focus of our research over the course of the following year.

Stay tuned for more results!