Comparative Genomics of Exiguobacterium Reveals What Makes a Cosmopolitan Bacterium

Abstract

Although the strategies used by bacteria to adapt to specific environmental conditions are widely reported, fewer studies have addressed how microbes with a cosmopolitan distribution can survive in diverse ecosystems. Exiguobacterium is a versatile genus whose members are commonly found in various habitats. To better understand the mechanisms underlying the universality of Exiguobacterium, we collected 105 strains from diverse environments and performed large-scale metabolic and adaptive ability tests. We found that most Exiguobacterium members have the capacity to survive under wide ranges of temperature, salinity, and pH. According to phylogenetic and average nucleotide identity analyses, we identified 27 putative species and classified two genetic groups: groups I and II. Comparative genomic analysis revealed that the Exiguobacterium members utilize a variety of complex polysaccharides and proteins to support survival in diverse environments and also employ a number of chaperonins and transporters for this purpose. We observed that the group I species can be found in more diverse terrestrial environments and have a larger genome size than the group II species. Our analyses revealed that the expansion of transporter families drove genomic expansion in group I strains, and we identified 25 transporter families, many of which are involved in the transport of important substrates and resistance to environmental stresses and are enriched in group I strains. This study provides important insights into both the overall general genetic basis for the cosmopolitan distribution of a bacterial genus and the evolutionary and adaptive strategies of Exiguobacterium. IMPORTANCE The wide distribution characteristics of Exiguobacterium make it a valuable model for studying the adaptive strategies of bacteria that can survive in multiple habitats. In this study, we reveal that members of the Exiguobacterium genus have a cosmopolitan distribution and share an extensive adaptability that enables them to survive in various environments. The capacities shared by Exiguobacterium members, such as their diverse means of polysaccharide utilization and environmental-stress resistance, provide an important basis for their cosmopolitan distribution. Furthermore, the selective expansion of transporter families has been a main driving force for genomic evolution in Exiguobacterium. Our findings improve our understanding of the adaptive and evolutionary mechanisms of cosmopolitan bacteria and the vital genomic traits that can facilitate niche adaptation.

Keywords: Exiguobacterium; adaptation strategies; cosmopolitan distribution; genomics; polysaccharide utilization; transporters.

FIG 1

Cosmopolitan distribution of Exiguobacterium strains. (A) Relative abundances of various 16S rRNA gene sequences among 13 types of habitats. (B) Isolation sites (pink dots) of 97 Exiguobacterium strains examined in this study. The map was created with ArcGIS 10.6 software. (C) Temperature (°C), pH, and salinity (%) tolerance test results for 105 Exiguobacterium strains. The x axis represents the tolerance range of strains, and “S” represents salinity.

FIG 2

Phylogenetic analysis of Exiguobacterium. The tree was built using IQ-TREE based on the concatenated amino acid sequence alignments of single-copy core genes. Bootstrap support values were calculated from 1,000 replicates. “T” represents the type strain for the following: NIO-1109 for E. enclense, HHS31 for E. indicum, DSM20416 for E. acetylicum, DSM14481 for E. undae, J14376 for E. soli, s128 for E. soli, 7-3 for E. sibiricum, 255-15 for E. sibiricum, s145 for E. artemiae, JCM12280 for E. oxidotolerans, DSM6208 for E. aurantiacum, s122 for “E. himgiriensis,” 12-1 for E. alkaliphilum, J17977 for E. aquaticum, s149 for E. mexicanum, s124 for E. aestuarii, DSM16307 for E. marinum, and s121 for E. profundum. N1 to N12 represent putative new species. Different colors represent different putative species, which were differentiated using the threshold ANI of 95%.

FIG 3

Carbon and nitrogen source utilization. (A to C) Numbers of carbohydrate-active enzymes (CAZymes) (A), plant polysaccharide degradation enzymes (B), and extracellular peptidases (C) encoded in Exiguobacterium genomes. Parentheses enclose the total number of genomes in each Exiguobacterium species. Asterisks indicate CAZymes with a potential secretion signal. The thick black thick line separates the species list into two parts; the species above the line belong to group I, while those below the line belong to group II.

FIG 4

Genes detected across Exiguobacterium genomes are vital for maintaining homeostasis in extreme environments. The heatmap represents the vital gene numbers and their distribution across the 147 genomes. The maximum-likelihood tree was constructed by IQ-TREE as described in Materials and Methods.

FIG 5

Comparison and Spearman’s correlation analysis of genome sizes and transporter numbers. (A) Trends in the genome sizes of Exiguobacterium species (species with at least 5 strains were selected to show the trends). (B) Trends in the transporter numbers of Exiguobacterium species (species with at least 5 strains were selected to show the trends). (C) Comparison of genome sizes between group I and group II. (Black ****, significantly different at a P of <0.0001, as assessed by Wilcoxon tests). (D) Comparison of transporter numbers between group I and group II. (E) Spearman’s correlation analysis of genome sizes, CDS numbers, and transporter numbers. The genome size, CDS number, and transporter number are shown in the central diagonal, and the scatterplots are depicted with a fitted red line. On the corresponding side for each pairing is the Spearman rank correlation coefficient, r_s. (Red ***, P < 0.01).

FIG 6

Comparison of 25 transporter family members between groups I and II. All pairwise comparisons were significantly different (Wilcoxon test). Each dot represents one strain.