Linking Genomic and Physiological Characteristics of Psychrophilic Arthrobacter to Metagenomic Data to Explain Global Environmental Distribution

Abstract

Background: Microorganisms drive critical global biogeochemical cycles and dominate the biomass in Earth’s expansive cold biosphere. Determining the genomic traits that enable psychrophiles to grow in cold environments informs about their physiology and adaptive responses. However, defining important genomic traits of psychrophiles has proven difficult, with the ability to extrapolate genomic knowledge to environmental relevance proving even more difficult.Results: Here we examined the bacterial genus Arthrobacter, and assisted by genome sequences of new Tibetan Plateau isolates, defined a clade, Group C, that represents isolates from polar and alpine environments. Group C had a superior ability to grow at -1ºC, and possessed genome G+C content, amino acid composition, predicted protein stability and functional capacities (e.g., sulfur metabolism and mycothiol biosynthesis) that distinguished it from non-polar or alpine Group A- Arthrobacter. Interrogation of more than 1,000 metagenomes identified an over-representation of Group C in Canadian permafrost communities from a simulated spring-thaw experiment, indicative of niche adaptation, and an under-representation of Group A in all polar and alpine samples, indicative of a general response to environmental temperature.Conclusion: The findings illustrate a capacity to define genomic markers of specific taxa that potentially have value for environmental monitoring of cold environments, including environmental change arising from anthropogenic impact. More broadly, the study illustrates the challenges involved in extrapolating from genomic and physiological data to an environmental setting.

binny: an automated binning algorithm to recover high-quality genomes from complex metagenomic datasets

“…Real world benchmark data To assess the binning performance in different real-world scenarios with a variety of metagenome sizes, complexities and qualities, 105 metagenomes used in the MetaBAT2 publication [15] for benchmarking were chosen based on the availability of preprocessed read data at the Joint Genome Institute (JGI). The newest available assembly for the metagenomes and the respective preprocessed reads were retrieved from JGI 5 . The read data was processed in the same way as the CAMI data.…”

“…Metagenomeassembled genomes (MAGs) allow the linking of the genetic information at species or strain level: In the absence of cultured isolates, MAGs form an important point of reference. Thereby, study-specific MAGs have led to the discovery of previously uncharacterised microbial taxa [57] and deepened insights into microbial physiology and ecology [14,50]. In addition, large system-wide collections, which have been assembled recently, e.g.…”