Snow microbiome functional analyses reveal novel aspects of microbial metabolism of complex organic compounds

• Published in: MicrobiologyOpen
• Main Authors: Zhu, Chengsheng, Miller, Maximilian, Lusskin, Nicholas, Bergk Pinto, Benoît, Maccario, Lorrie, Häggblom, Max, Vogel, Timothy, Larose, Catherine, Bromberg, Yana
• Other Authors: Rutgers, The State University of New Jersey New Brunswick (RU), Rutgers University System (Rutgers), Ampère, Département Bioingénierie (BioIng), Ampère (AMPERE), École Centrale de Lyon (ECL), Université de Lyon-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-École Centrale de Lyon (ECL), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Copenhagen = Københavns Universitet (UCPH)
• Format: Article in Journal/Newspaper
• Language: English
• Published: HAL CCSD 2020
• Subjects: metatranscriptome; metagenome; mi-faser; snow microbiome; [SDV]Life Sciences [q-bio]; [SDE]Environmental Sciences; Norway; Svalbard
• Online Access: https://hal.science/hal-03080130; https://hal.science/hal-03080130/document; https://hal.science/hal-03080130/file/mbo3.1100.pdf; https://doi.org/10.1002/mbo3.1100

International audience Microbes active in extreme cold are not as well explored as those of other extreme environments. Studies have revealed a substantial microbial diversity and identified cold-specific microbiome molecular functions. We analyzed the metagenomes and metatranscriptomes of 20 snow samples collected in early and late spring in Svalbard, Norway using mi-faser, our read-based computational microbiome function annotation tool. Our results reveal a more diverse microbiome functional capacity and activity in the early- vs. late-spring samples. We also find that functional dissimilarity between the same-sample metagenomes and metatranscriptomes is significantly higher in early than late spring samples. These findings suggest that early spring samples may contain a larger fraction of DNA of dormant (or dead) organisms, while late spring samples reflect a new, metabolically active community. We further show that the abundance of sequencing reads mapping to the fatty acid synthesis-related microbial pathways in late spring metagenomes and metatranscriptomes is significantly correlated with the organic acid levels measured in these samples. Similarly, the organic acid levels correlate with the pathway read abundances of geraniol degradation and inversely correlate with those of styrene degradation, suggesting a possible nutrient change. Our study thus highlights the activity of microbial degradation pathways of complex organic compounds previously unreported at low temperatures.