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 new clade, Group C, that represents isolates from polar and alpine environments. Group C had a superior ability to grow at -1°C 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 nearly 1000 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. Video Abstract.

Keywords: Alpine environment; Genomics; Metagenomics; Microbial adaptation; Polar environment; Psychrophiles.

Fig. 1

Arthrobacter phylogeny and genome compositional profiling. a Maximum likelihood Arthrobacter phylogenomic tree. The Arthrobacter portion of maximum likelihood Micrococcaceae phylogenomic tree (Additional file 1: Fig. S2a) is reproduced with each leaf marked as polar and alpine (PA, gray highlight) or non-polar and alpine (NPA). The tree has three major clades with the central clade highlighted (purple box). b As for a except Arthrobacter names denoted and font color used to depict Group A (orange font; NPA environments), Group B (olive green font; PA environments clustering with sequences from NPA environments), and Group C (blue font; PA environments that formed an operationally monophyletic lineage with an F measure of 0.95). The specific types of cold environments from where Group C Arthrobacter were isolated are shown to the right of the tree. c Three-dimensional nonmetric multidimensional scaling (NMDS) plot of genome-wide amino acid composition. d Distribution of pairwise average nucleotide identity (ANI). e Distribution of pairwise average amino acid identity (AAI)

Fig. 2

Growth temperature profiles of Group A, B, and C Arthrobacter. OD₆₀₀ growth curves for representative Arthrobacter of Group A (orange symbols and line; A. luteolus, A. globiformis, and A. subterraneus), Group B (olive green symbols and line; Arthrobacter sp. 4R501, Arthrobacter sp. 9E14, and Arthrobacter sp. 08Y14), and Group C (blue symbols and line; A. alpinus, Arthrobacter sp. A3, and Arthrobacter sp. N199823) at a 25 °C, b 5 °C, and c −1 °C

Fig. 3

Overview of genomic characteristics of Group C Arthrobacter. a Box plot of G+C content. Group A (red); Group C (blue); boxes represent the interquartile range with horizontal lines showing maximum and minimum values, excluding outliers. Group C had significantly lower G+C content. b Scatter plot of amino acid composition. Group A (light red circles); Group C (blue circles); ***p < 0.005; *p = 0.05–0.01; ns, not significant. The composition of numerous amino acids varied significantly between Group C and Group A Arthrobacter. c Protein stability predictions calculated using SCooP. Group A (red line); Group C (blue line). The curve is for coenzyme A biosynthesis bifunctional protein, CoaC, and is representative of one of the 32 Group C proteins from a total of 86 which had reduced predicted stability (Additional file 3: Dataset S2 and Additional file 1: Fig. S6) d Box plot of amino acid bias for functional categories. Boxes represent the interquartile range of the Bray-Curtis distances; lines extending from boxes show the maximum and minimum Bray-Curtis distances; dots beyond the lines represent outliers. Biases in amino acid composition (b) were reflected in specific functional categories. e Representation of functional categories. Specific functional categories were over- or under-represented in Group C; arrows indicate relative increases (up arrow) or decreases (down arrow) in functional categories in Group C. f Representation of specific functions. Specific functional processes defined by genes or pathways were characteristic of Group C (up arrow) or had a restricted capacity in Group C (down arrow) compared to Group A (also see Fig. 4)

Fig. 4

Arthrobacter genes typifying the functional potential of Group C. a Maximum likelihood Arthrobacter phylogenomic tree as for Fig. 1. b Heat map of the representation of specific genes in Arthrobacter genomes, highlighting those present in Group C and the central clade. i, branched-chain acyl-CoA dehydrogenase; ii, enoyl-CoA hydratase; iii, biotin repressor; iv, hydrolase in cluster with formaldehyde/S-nitrosomycothiol reductase; v, mycothiol-dependent formaldehyde dehydrogenase

Fig. 5

Metagenome analysis of Group C Arthrobacter. a Depiction of the mean annual temperature (MAT) of surface air at a height of 2 m (European Centre for Medium-Range Weather Forecasts) relative to latitude. The 639 metagenomes are divided into thermal categories: PA (black squares, 196 metagenome), temperate (gray squares, 243 metagenomes), and tropical (purple squares, 200 metagenomes). b Linear regression showing the correlation of the abundance of Group C-specific genes within each of the 639 metagenomes (see panel a) relative to the abundance of Group C-specific genes within the Arthrobacter pan genome. The 95% prediction interval (dark pink band) and 95% confidence interval (light pink band) are shown for each regression line (panels b, c, and e). The upper cluster contains 11 Axel Heiberg Island permafrost metagenomes. c As for panel b, except with the addition of 334 permafrost metagenomes (total 973 metagenomes). The Stordalen Mire (Abisko, Sweden) metagenome is shown by an arrow. d As for panel b, except showing Group B-specific genes. e As for panel b, except showing Group A-specific genes present in PA genomes (lower line) and NPA genomes (upper line). The regression line for the 11 Axel Heiberg Island permafrost metagenomes is not shown