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Changes in Gene Expression From Long-Term Warming Revealed Using Metatranscriptome Mapping to FAC-Sorted Bacteria

Soil microbiomes play pivotal roles to the health of the environment by maintaining metabolic cycles. One question is how will climate change affect soil bacteria over time and what could the repercussions be. To answer these questions, the Harvard Forest Long-Term Warming Experiment was established to mimic predicted climate change by warming plots of land 5℃ above ambient conditions. In 2017, 14 soil core samples were collected from Barre Woods warming experiment to mark 15 years since the establishment of the soil warming in that location. These samples underwent traditional metatranscriptomics to generate an mRNA library as well as a process coined cell-sorted or mini-metagenomics involving the sorting of single bacterial cells from the environment using FACS. This was followed by pooling into groups of 100 cells for more cost efficient genome recovery. 200 high-quality genomes were compiled, 12 of which were taxonomically identified as Acidobacteria. Acidobacteria are an extremely abundant and diverse phylum of bacteria that were found to be very well represented in the soil samples. Due to their abundance in many different soil environments as well as their known importance in many metabolic cycles, they were chosen as the candidate phylum to further investigate. Using a reference-based read mapping approach with the 12 Acidobacteria genomes and metatranscriptomic data, we identified over 3,000 differentially expressed genes within these organisms as a result of soil warming. Due to the diversity within the phylum itself, many of the genomes indicated different patterns of expression making it difficult to identify phylum-wide differential expression trends. However, the sigma70 factor, an important housekeeping gene used as a transcription regulator, was found to be up-regulated in a majority of the genomes. Over 30 different glycoside hydrolase encoding genes and glycosyltransferases were also found to be differentially expressed across the Acidobacteria reference genomes as well as 23 chemotaxis-related genes. Despite identifying four different groups of genes that showed statistically significant differences in expression levels, there may be more changes occurring in these soil bacteria and the soil microbiome as a whole due to climate change than previously measured by read-based analyses of metatranscriptomic data.
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