Comprehensive Phylogenomics of Methylobacterium Reveals Four Evolutionary Distinct Groups and Underappreciated Phyllosphere Diversity

Abstract

Methylobacterium is a group of methylotrophic microbes associated with soil, fresh water, and particularly the phyllosphere, the aerial part of plants that has been well studied in terms of physiology but whose evolutionary history and taxonomy are unclear. Recent work has suggested that Methylobacterium is much more diverse than thought previously, questioning its status as an ecologically and phylogenetically coherent taxonomic genus. However, taxonomic and evolutionary studies of Methylobacterium have mostly been restricted to model species, often isolated from habitats other than the phyllosphere and have yet to utilize comprehensive phylogenomic methods to examine gene trees, gene content, or synteny. By analyzing 189 Methylobacterium genomes from a wide range of habitats, including the phyllosphere, we inferred a robust phylogenetic tree while explicitly accounting for the impact of horizontal gene transfer (HGT). We showed that Methylobacterium contains four evolutionarily distinct groups of bacteria (namely A, B, C, D), characterized by different genome size, GC content, gene content, and genome architecture, revealing the dynamic nature of Methylobacterium genomes. In addition to recovering 59 described species, we identified 45 candidate species, mostly phyllosphere-associated, stressing the significance of plants as a reservoir of Methylobacterium diversity. We inferred an ancient transition from a free-living lifestyle to association with plant roots in Methylobacteriaceae ancestor, followed by phyllosphere association of three of the major groups (A, B, D), whose early branching in Methylobacterium history has been heavily obscured by HGT. Together, our work lays the foundations for a thorough redefinition of Methylobacterium taxonomy, beginning with the abandonment of Methylorubrum.

Significance.

Methylobacterium is an important group of plant-associated bacteria and a model organism in microbiology. Ironically, Methylobacterium diversity and evolution have mostly been studied outside plants. Here, we present the first comprehensive reconstruction of Methylobacterium evolutionary history accounting for gene exchanges typical of Bacteria, and for diversity with known plant association. We demonstrate that Methylobacterium contains four evolutionarily divergent groups of bacteria, also distinguishable by their genome architecture and composition, questioning Methylobacterium taxonomy. We identified 104 Methylobacterium species, of which a large proportion is as of yet undescribed and mostly plant-associated. We also infer an ancient transition in Methylobacterium lifestyle from soil and plant roots, to plant leaves, stressing the significance of plants in Methylobacterium evolution and diversity.

Introduction

For billions of years, bacteria have evolved rapidly through vertical and horizontal gene transmission, mutation, selection, diversification, and extinction. These evolutionary processes allowed bacteria to conquer every biome and living host on Earth and, at the same time, resulted in blurring most traces of their ancient history (Louca et al. 2018). In the past thousands of years, humans have increasingly imposed new selective pressures on bacterial evolution, through bacterial host domestication and ecosystem perturbations (Gillings and Paulsen 2014). Ironically, the human perception of microbial life was until recently limited to the diversity we could “see” (through cultivation) and “use” (through domestication), representing only an infinitesimal proportion of bacterial diversity in nature (Hugenholtz 2002). As a result, bacterial diversity, evolution and speciation concepts remain fuzzy and largely biased (Shapiro et al. 2016). Yet, the advent of high-throughput sequencing technologies and our awakening to the essential role of bacteria in every living system have spurred research into the evolutionary processes shaping the microbial world (Koonin et al. 2021).

Methylobacterium is a well-studied group of bacteria that are abundant and widespread in every plant microbiome (Corpe and Rheem 1989; Keppler et al. 2006). Methylobacterium is part of Methylobacteriaceae (class: Alphaproteobacteria; order: Hyphomycrobiales syn. Rhizobiales [Hördt et al. 2020]), a family including three other genera, mostly isolated from aquifers and soils, sometimes in association with plant roots: Microvirga (Kanso and Patel 2003), Enterovirga (Chen et al. 2017) and Psychroglaciecola (Qu et al. 2014). Easy to isolate and to cultivate, thanks to a pink coloration due to carotenoids and their ability to use methanol as sole carbon source (Clarke 1983; Anthony 1991; Keppler et al. 2006), Methylobacterium are also essential players in plant functions, like growth stimulation (Ivanova et al. 2001; Madhaiyan et al. 2005, 2007), heavy metal sequestration (Madhaiyan et al. 2007), protection against phytopathogens and nitrogen fixation (Dourado et al. 2015), sparking increasing interest in their use in plant biotechnology applications (Ryu et al. 2006; Lee et al. 2006; Madhaiyan et al. 2007).

Recently, Green and Ardley (2018) questioned the taxonomy of Methylobacterium, noticing a “greater degree of phenotypic and genotypic heterogeneity than would normally be expected for a single genus.” Accordingly, these authors proposed to split the genus in three distinct taxa corresponding to monophyletic groups in the 16S rRNA ribosomal gene phylogeny (groups A, B, and C). Group A, containing the Methylobacterium type species M. organophilum, was retained as Methylobacterium. For group B, which included the model species M. extorquens, the authors proposed a new genus: Methylorubrum. Finally, the authors suggested that group C, including M. aquaticum and M. nodulans, should constitute a distinct genus, pending future genetic and phenotypic investigations. The Methylobacterium reclassification has been pointed out as problematic, because of the low phylogenetic resolution of the 16S rRNA gene, and because no genus name was proposed for strains that were not retained in Methylorubrum or Methylobacterium, which could potentially render either new genus as paraphyletic (Hördt et al. 2020; Leducq et al. 2022). Accordingly, the taxonomy of Methylobacterium was reexamined by coupling genome-wide DNA–DNA hybridization and phenotypic information for 63 strains, each representative of a described species (Alessa et al. 2021). Alessa et al. (2021) confirmed Green and Ardley’s (2018) observation that group C was phenotypically and genetically distinct from other groups, but they also showed that Methylorubrum (group B) was embedded within Methylobacterium (group A), forming a homogeneous group, and proposed to merge Methylobacterium and Methylorubrum back into a single genus.

The evolutionary history of Methylobacterium remains poorly resolved for several reasons. First, phylogenetic relationships among and within groups are often inconsistent depending upon the chosen marker gene (Green and Ardley, 2018; Leducq et al. 2022). Such inconsistent phylogenetic signals suggest that these marker genes had different evolutionary histories, perhaps due to horizontal gene transfer (HGT) or incomplete lineage sorting (ILS), illustrating the dynamic nature of bacterial genome evolution and the limitations of bacterial taxonomy based on a limited number of gene phylogenies (Castillo-Ramírez and González 2008; Creevey et al. 2011). Second, Alessa et al. (2021) based their Methylobacterium taxonomy on DNA–DNA hybridization methods, which are widely used to classify prokaryotic species, but are not phylogenetic methods per se, as they do not account for ancestry. They also validated their taxonomy using a phylogenetic tree based on concatenated protein sequences of core genes but did not present evaluations of the uncertainty in the resulting tree. Finally, phylogenies based on concatenated gene alignments assume the same tree for each gene, and thus do not take into account potential ILS and HGT affecting topology and branch lengths differentially in each individual gene trees. With the onset of genomics in evolutionary studies, several coalescent methods have been developed to reconstruct the phylogeny and solve the taxonomy of organisms with complex evolutionary history like bacteria (Davidson et al. 2015). For instance, coalescent-based phylogenetic methods like ASTRAL-III (Mirarab et al. 2014; Zhang et al. 2018) and SVDquartets (Chifman and Kubatko 2014) allow the reconstruction of a consensus tree (the lineage tree) taking into account different levels of ILS and HGT among individual gene trees.

Although more than 60 Methylobacterium species have been described so far (Green and Ardley 2018; Chen et al. 2019; Feng et al. 2020; Jia et al. 2020; Kim, Chhetri, Kim, Lee et al. 2020; Kim, Chhetri, Kim, Kim et al. 2020; Ten et al. 2020; Jiang et al. 2020; Pascual et al. 2020; Alessa et al. 2021), available genomic and phenotypic information was until recently limited to a few model species, mostly from groups B and C, and mostly isolated from anthropogenically impacted environments, and in rare cases from plants (Marx et al. 2012; Tani et al. 2015; Minami et al. 2016; Morohoshi and Ikeda 2016; Belkhelfa et al. 2018). Surveys of Methylobacterium diversity associated with plants have mainly focused on the rhizosphere, especially in crop species (Sy et al. 2001; Jourand et al. 2004; Grossi et al. 2020). Recent studies however revealed that the phyllosphere of model plant species like A. thaliana (Helfrich et al. 2018), of wheat (Zervas et al. 2019), and of natural temperate forests (Leducq et al. 2022) are major reservoirs of undescribed Methylobacterium diversity, most of which belongs to group A (Leducq et al. 2022).

Here, we explored Methylobacterium diversity from an evolutionary genomic perspective. We de novo annotated 189 Methylobacterium genomes, including 62 strains isolated from temperate forest, wheat, and Arabidopsis phyllosphere, and 127 additional genomes that represent the remainder of the Methylobacterium species described so far. Using different phylogenomic approaches, we reconstructed the Methylobacterium evolutionary tree from 384 Methylobacteriaceae core genes and showed that the genus is consistently constituted of four monophyletic groups: A, B, C, and D. Gene content and especially the highly dynamic core genome architecture predicted the four Methylobacterium groups remarkably well. We estimated that Methylobacterium includes at least 104 species, of which only 59 were previously described. Most of the undescribed species were assigned to groups A and D and were isolated from plant leaves, stressing the significance of the phyllosphere as a reservoir of Methylobacterium diversity. Our inferences of the Methylobacterium evolutionary tree also suggest an ancient transition from a free-living lifestyle to association with plant roots in Methylobacteriaceae ancestor, followed by phyllosphere association of three of the major groups (A, B, D), whose early branching in Methylobacterium history was heavily obscured by HGT. Finally, our comprehensive phylogenetic analysis of Methylobacterium lays the foundation for a profound redefinition of its taxonomy, beginning with the abandonment of Methylorubrum.

Results

Definition of the Methylobacteriaceae Core Genome

We assembled a collection of 213 Methylobacteriaceae genomes, including 189 Methylobacterium and 24 genomes from related genera as outgroups (Microvirga: n = 22; Enterovirga: n = 2). Most Methylobacterium (n = 98) and all outgroup genomes (n = 24) came from distinct studies (supplementary dataset S1, Supplementary Material online). We included 29 genomes from Methylobacterium type strains recently sequenced (Alessa et al. 2021; Bijlani et al. 2021), hence covering most Methylobacterium species described so far. We also included 38 genomes available from two large surveys of the Arabidopsis and wheat phyllospheres (Helfrich et al. 2018; Zervas et al. 2019), and sequenced 24 additional genomes of isolates from a large survey of the temperate forest phyllosphere (Leducq et al. 2022), hence extending our dataset to the leaf-associated Methylobacterium diversity. The 24 newly assembled genomes had 41 to 405 scaffolds (depth: 188–304x) for a total size (5–7Mb) and average GC content (67–70%) in the expected range for Methylobacterium genomes (supplementary dataset S2, Supplementary Material online). We annotated 184 genomes de novo, excluding 29 genomes that were not published at the time of the analysis (Alessa et al. 2021; Bijlani et al. 2021) through the same pipeline (RAST) and after excluding hypothetical proteins, repeat and mobile elements, we identified 9,970 unique gene annotations (i.e., regardless of copy number: supplementary dataset S3, Supplementary Material online), with on average 2637 (SD: 210) unique gene annotations per genome. We identified 893 candidate core genes, i.e., genes that were present in a single copy in at least 90% of Methylobacteriaceae genomes. After filtering for missing data and false duplications attributable to large variations among genome assembly qualities (supplementary figs. S1 and S2, Supplementary Material online), we identified 384 Methylobacteriaceae core genes (supplementary dataset S4, Supplementary Material online) for which the complete nucleotide sequences could be retrieved for at least 181 of 184 genomes. We repeated the RAST annotation for recently sequenced genomes from 29 Methylobacterium species type strains that were not available during our initial survey (Alessa et al. 2021; Bijlani et al. 2021). Doing this, we slightly extended the number of unique gene annotation in Methylobacteriaceae (n = 10,190). We confirmed that the 384 previously identified genes were part of the Methylobacteriaceae core genome and retrieved each core gene nucleotide sequence for at least 26 out of these 29 genomes. Our final dataset consisted of 213 genomes for which we retrieved 327 to 384 core genes nucleotide sequences (average, SD: 381 ± 6).

Inference of the Methylobacteriaceae Lineage Tree

We reconstructed the lineage tree of Methylobacteriaceae from 213 genomes from the 384 core gene nucleotide sequences using three complementary approaches in order to assess the effect of ILS and HGT in the evolutionary history of Methylobacterium. First, we used RAxML to determine a maximum-likelihood (ML) tree (512 replicated tree; bootstraps) from concatenated alignments of the core gene nucleotide sequences, assuming 57 groups of genes (partitions) with different substitution models (partitions determined in IQ-tree; GTRCAT model of substitution), but the same evolutionary tree for all genes, hence not accounting for ILS or HGT (fig. 1a). Second, we used ASTRAL, a coalescent-based method combining ML trees determined for each core gene independently (RAxML, GTRGAMMA model, 1,000 replicated tree), accounting for ILS among genes (fig. 1b; supplementary fig. S3a, Supplementary Material online). Third, we used SVDquartets, a coalescent-based method estimating the tree for each possible combination of four genomes and assuming all nucleotide sites are unlinked in the concatenated alignment of 384 genes, hence accounting for ILS and HGT both within and among genes (fig. 1c; supplementary fig. S3b, Supplementary Material online). In all lineage trees rooted on Microvirga and Enterovirga, Methylobacterium was monophyletic and consisted of four groups of genomes, consistently monophyletic and strongly supported, regardless of the method used (nodal support: 100% in RAxML and SVDquartets trees; local posterior probability: 1.0 in the ASTRAL tree; fig. 1a–c). Group C always formed the most basal group of Methylobacterium, confirming previous observations (Green and Ardley 2018; Alessa et al. 2021; Leducq et al. 2022). Group B regrouped clades B, formerly Methylorubrum (Green and Ardley 2018) and B2 (Alessa et al. 2021; corresponding to clade A4 in Leducq et al. 2022). Most strains previously assigned to clade A (Green and Ardley 2018) were distributed across two distinct monophyletic groups that we named A and D (fig. 1a). Group A included clades A2, A3, A4 and A5 described by Alessa et al. (2021) and corresponded to clades A5, A10, A19 and A7 + A8 described by Leducq et al. (2022), respectively. Group D corresponded to clade A1 proposed by Alessa et al. (2021) and clades A1, A2, and A3 proposed by Leducq et al. (2022).

Fig. 1.

Methylobacteriaceae lineage trees inferred from 213 genomes. (a) Best tree from RAxML ML search on the concatenated alignments of 384 core gene nucleotide sequences (GTRCAT model, 512 replicated trees), rooted on Microvirga and Enterovirga (gray). Correspondence with clades described by previous studies is indicated. (b) ASTRAL tree inferred from 384 core gene ML trees. Each gene ML tree was inferred assuming a GTRgamma model (1,000 replicated trees; nodes with less than 10% of support collapsed) and combined in ASTRAL-III. Branch lengths are in coalescent units. Nodal support values represent local posterior probability. (c) SVD quartet tree inferred from the concatenated alignments of 384 core gene nucleotide sequences. Nodes supported by less than 75% of quartets were collapsed. (d) Main isolation sources of species from Methylobacterium group and Microvirga (see table 1). For each group, ordered according to a consensus tree (see panels B and C), the number of species is indicated in parenthesis.

Groups A, B and D consistently formed a monophyletic group (nodal support: 100% in RAxML and SVDquartets trees; local posterior probability: 1.0 in the ASTRAL tree); however, phylogenetic relationships among groups A, B and D were more challenging to assess. Groups A, B, and D could not be resolved with the RAxML tree (nodal support = 9%; fig. 1a). Group D was sister to groups A and B according to ASTRAL (local posterior probability: 0.8; fig. 1b) and SVDquartets trees (nodal support: 100%; fig. 1c). We evaluated differences between the three lineage tree topologies using the Robinson-Foulds (RF) distance metric in PAUP (Wilgenbusch and Swofford 2003). RAxML and ASTRAL lineage tree topologies were more similar to each other (RF = 0.181) than with the SVDquartets tree (RF = 0.225 and 0.289, respectively; supplementary fig. S4, Supplementary Material online). In order to determine whether the difference between the RAxML and other trees was higher than expected by chance, we estimated the distribution of RF distance between each replicate tree of the RAxML search for the lineage tree (512 replicates). The normalized RF value ranges from 0.028 to 0.113 (RF = 0.069 ± 0.015), indicating that the differences observed between lineage trees were larger than expected by chance (supplementary fig. S4, Supplementary Material online), and suggesting that ILS and HGT among core genes had a significant impact on the Methylobacteriaceae lineage tree. The larger difference between the SVDquartets tree and other trees also suggested that recombination within core genes also occurred during Methylobacteriaceae evolution, although without affecting the relationship among the four major groups (C/D/[A, B]).

Inference of the Methylobacteriaceae Taxonomy and Species Tree

We classified Methylobacteriaceae genomes into 124 species using a 97% threshold on percentage nucleotide similarity (PNS; analogous to average nucleotide identity; (Mende et al. 2013; Chun and Rainey 2014); supplementary dataset S5, Supplementary Material online) on the core genome (concatenated alignments of 384 core genes; 361,403 bp). In the outgroups, we identified 2 Enterovirga species and 18 Microvirga species. We identified 104 Methylobacterium species (1 to 9 genomes per species), of which 59 included the type strain for at least one described species (table 1; supplementary dataset S5, Supplementary Material online). M. extorquens, M. chloromethanicum and M. dichloromethanicum type strains were assigned to the same species (PNS range: 97.61–99.68%), as previously reported (Alessa et al. 2021). M. populi and M. thiocyanatum type strains were assigned to the same species (PNS range: 98.97%-99.08%), as previously reported (Alessa et al. 2021). M. phyllosphaerae, M. ozyzae and M. fujisawaense type strains were assigned to the same species (99.23–100%), as previously reported (Alessa et al. 2021). We identified 45 candidate species that included no type strain, and thus corresponded to new candidate Methylobacterium species (table 1; supplementary dataset S5, Supplementary Material online). We numbered these candidate species from Methylobacterium sp. 001 to 045. We used the 124 identified species to infer the Methylobacteriaceae species trees with SVDquartets (supplementary fig. S5a, Supplementary Material online) and ASTRAL (supplementary fig. S5b, Supplementary Material online). Although the two species trees were not strictly identical (normalized RF distance = 0.234), the monophyly and relationships among the four main groups was consistent between ASTRAL and SVDquartets species trees (C/D/[AB]; supplementary fig. S5a,b, Supplementary Material online), and with ASTRAL and SVDquartets lineage trees (fig. 1b,c). Each group of genomes assigned to the same species was also monophyletic and strongly supported in lineage trees (fig. 1).

Table 1.

Description and Isolation Source of 104 Methylobacterium Species Distributed in the Four Main Phylogenetic Groups

Group	Description	Species	Genomes	Isolation source						Anthropogenic environments*
				Plant (phyllosphere)	Plant (rhizosphere)	Plant (other)	Water, sediments	Soil	Other
B	Described species	14	33	30%	1%	1%	13%	19%	35%	29%
	(M. aminovorans; M. brachythecii; M. extorquens
	M. gnaphalii; M. haplocladii; M. organophilum
	M. podarium; M. rhodesianum; M. rhodinum
	M. salsuginis; M. suomiense; M. thiocyanatum
	M. thuringiense; M. zatmanii)
	Candidate species (Methylobacterium sp 035 to 041)	7	8	50%	—	7%	29%	—	14%	29%
	All species	21	41	37%	1%	3%	18%	13%	28%	29%
A	Described species	24	45	30%	1%	4%	28%	17%	20%	40%
	(M. aerolatum; M. brachiatum; M. cerastii
	M. dankookense; M. durans; M. fujisawaense
	M. gregans; M. hispanicum; M. jeotgali
	M. komagatae; M. longum; M. mesophilicum
	M. oxalidis; M. persicinum; M. phyllostachyos
	M. planium; M. pseudosasicola; M. radiodurans
	M. radiotolerans; M. segetis; M. soli
	M. symbioticum; M. tardum; M. trifolii)
	Candidate species (Methylobacterium sp 018 to 034)	17	36	80%	10%	10%	—	—	—	—
	All species	41	81	51%	4%	7%	16%	10%	12%	23%
D	Described species	6	10	47%	—	17%	20%	—	17%	17%
	(M. adhaesivum; M. bullatum; M. goesingense
	M. gossipiicola; M. iners; M. marchantiae)
	Candidate species (Methylobacterium sp 001 to 017)	17	32	74%	6%	—	21%	—	—	—
	All species	23	42	67%	4%	4%	20%	—	4%	4%
C	Described species	15	21	8%	10%	7%	27%	33%	15%	55%
	(M. ajmalii; M. aquaticum; M. crusticola; M. currus
	M. frigidaeris; M. indicum; M. isbiliense
	M. nodulans; M. nonmethylotrophicum
	M. oryzihabitans; M. platani; M. tarhaniae
	M. terrae; M. terricola; M. variabile)
	Candidate species (Methylobacterium sp 042 to 045)	4	4	—	25%	25%	—	25%	25%	25%
	All species	19	25	7%	13%	11%	21%	32%	17%	49%
Methylobacterium	All described species	59	109	26%	3%	5%	23%	20%	22%	39%
	All candidate species	45	80	66%	8%	7%	12%	2%	4%	7%
	All species	104	189	43%	5%	6%	18%	12%	14%	25%
Microvirga (all species)		18	24	—	33%	6%	17%	33%	11%	6%
Enterovirga (all species)		2	2	—	—	—	—	50%	50%	—

For each group, the number of species, of genomes, and the proportion of genomes isolated from each main category of environment, are given for described and candidate species (numbered from Methylobacterium sp 001 to 045), separately. Proportions were corrected by the number of genomes per species. Anthropogenic environments include several other isolations sources. —, no observation.

In summary, the Methylobacterium species are distributed across four groups, each of which with somewhat distinct environmental sources of isolation (plant phyllosphere and rhizosphere, water and sediments, soils, others), as well as the proportion of strain isolated from anthropogenic environments (table 1, fig. 1d). Group A contained 62 genomes which fell into 41 species, including 17 new species (Methylobacterium sp. 018 to 034). Group B contained 41 genomes which fell into 21 species, including 7 candidate species (Methylobacterium sp. 035 to 041). Group C contained 25 genomes which fell into 19 species, including 4 new candidate species (Methylobacterium sp. 042 to 045; table 1). Group D contained 42 genomes which fell into 23 species, including 17 new candidate species (Methylobacterium sp. 001 to 017). Species from Microvirga and Enterovirga were mostly isolated from soil samples (65% of species; corrected by the number of genomes per species), often in association with plant roots (Rhizosphere; 30%). Species from Methylobacterium groups B and C were isolated from plants (40 and 31% of genomes, respectively), soil samples (13 and 32%), sediments or water samples (18 and 21%), often in association with anthropogenic environments (29 and 49%). Species from groups A and D were mostly isolated from plants (62 and 75% of species, respectively), especially the phyllosphere (51 and 67%). Of the 45 new candidate Methylobacterium species, most were assigned to groups A (n = 17) and D (n = 17); the majority (81%) was isolated from plants, and especially the phyllosphere (66%; table 1; fig. 1d).

Genome Comparison across Methylobacterium Groups

The four main Methylobacterium groups have consistently contrasting genome characteristics (supplementary fig. S6, Supplementary Material online; table 2). These four groups have significantly different genome sizes (Tukey test, p < 0.001), with group D having smaller genomes (4.99 ± 0.35 Mb; Average ± SD), than groups B (5.58 ± 0.49 Mb), A (6.21 ± 0.59 Mb) and C (7.15 ± 0.66 Mb). Groups D and B had a smaller number of annotated genes (5,224 ± 476 and 5,766 ± 509, respectively) than groups A and C (6,907 ± 821 and 7,670 ± 956, respectively; p < 0.001). The average number of gene annotation copies per genome was significantly different among groups (p < 0.001) and was smaller for group D (1.31 ± 0.04 copies per annotation) than for group B (1.37 ± 0.05), A (1.46 ± 0.07) and C (1.54 ± 0.07). GC content was significantly lower in groups D and B (68.8 ± 1.1 and 69.1 ± 0.8%, respectively) than in group A (70.1 ± 0.8%; p < 0.001) or group C (71.1 ± 0.7%; p < 0.001; supplementary fig. S6, Supplementary Material online, table 2). Although the number of mobile elements per genome was slightly lower in group D (42 ± 21) compared to A (60 ± 34), B (57 ± 31) and C (71 ± 49), these differences were not significant (table 2; Tukey test, p > 0.05). We compared the abundance of 10,187 gene annotations (excluding hypothetical proteins, repeat elements and mobile elements) across the four Methylobacterium groups and outgroups (fig. 2). Methylobacterium genomes clustered according to their gene content and abundance and matched the ASTRAL species tree (fig. 2a). As observed for other genome characteristics, group D had the smaller pan genome size (n = 4,217 ± 70; estimation assuming rarefaction of 15 species per group, mean and standard deviation over 100 replicates; supplementary fig. S7a, Supplementary Material online), followed by group B (n = 4,973 ± 137), group A (n = 4,974 ± 132) and group D (n = 5,636 ± 91 genes; fig. 2b). On the contrary, group D had a larger core genome size (i.e. gene present in a single copy in all species; n = 1,103 ± 29 core genes) than groups A (n = 845 ± 79), B (n = 924 ± 65) and C (n = 843 ± 39; fig. 2c; supplementary fig. S7b, Supplementary Material online). Venn diagrams on shared annotations indicate a limited overlap of gene content among groups, with only 2,863 ± 38 pan genes shared among the four groups (fig. 2b) and 350 ± 32 core genes (fig. 2c).

Table 2.

Methylobacteriaceae Genome Characteristics (Average and Standard Deviation Per Group)

Group	Genomes	Species	Size (Mb)	Annotations	Unique Annotations	Estimated Copy Number	Mobile Elements	% GC
A	81	41	6.21 ± 0.59	6907 ± 821	2696 ± 134	1.457 ± 0.067	60 ± 34	70.1 ± 0.8
B	41	21	5.58 ± 0.49	5766 ± 509	2706 ± 173	1.365 ± 0.048	57 ± 31	69.1 ± 0.8
C	25	19	7.15 ± 0.66	7670 ± 956	2899 ± 122	1.542 ± 0.066	71 ± 49	71.1 ± 0.7
D	42	23	4.99 ± 0.35	5224 ± 476	2421 ± 82	1.312 ± 0.042	42 ± 21	68.8 ± 1.1
Enterovirga	2	2	4.91 ± 0.36	5128 ± 182	2321 ± 14	1.414 ± 0.019	14 ± 10	68.8 ± 0.1
Microvirga	22	18	5.92 ± 1.74	6834 ± 2929	2495 ± 251	1.471 ± 0.173	128 ± 147	63.9 ± 1.6

GC content was estimated from coding sequences. Hypothetical protein, mobile and repeat elements were excluded from unique annotation counts and estimated copy numbers.

Fig. 2.

Gene content comparison among the four main Methylobacterium groups. (a) Occurrence of 10,187 gene annotations (rows) in 124 Methylobacteriaceae species (average occurrence per species; column, ordered according to the ASTRAL species tree, left) and in four Methylobacterium groups and two outgroups (mean occurrence among species within groups; legend in bottom right) are shown. (b and c) Venn diagrams showing the overlap of pan genomes (B) and core genome (c) among four groups. Pan and core genome sizes were estimated assuming 15 species per group (mean and standard deviation over 100 random resampling of 15 species per group). (d) RAxML ML best tree based on annotation occurrence per genome (best ML tree, BINCAT model, 1,001 replicate trees). Main groups are shown and are monophyletic in the gene content tree, but group A: clade A2 (Alessa et al. 2021) and M. jeotgali branched out of group A.

Gene Content Comparison across Methylobacterium Groups

We next asked to what extent gene content evolved concordantly along the core genome phylogeny. We used the Bray-Curtis index to measure the pairwise dissimilarity among genomes based on their gene annotation abundance (BC; Hellinger normalization of gene abundance; supplementary fig. S8, Supplementary Material online). The dissimilarity matrix in gene content among species matched the species tree (supplementary fig. S8, Supplementary Material online). Gene content was more similar among genomes from the same Methylobacterium species (BC range: 0.044 ± 0.017–0.080 ± 0.023) than among species within Methylobacterium groups (BC range: 0.159 ± 0.031–0.197 ± 0.044) or than among Methylobacterium groups (BC range: 0.238 ± 0.025–0.339 ± 0.019; supplementary fig. S8, Supplementary Material online; table 3). We determined the relationships among Methylobacteriaceae members upon their gene content using a ML phylogeny based on the occurrence of the 10,187 gene annotations across 213 genomes (RAxML assuming a BINCAT model; 1,001 replicate trees; figs. 2d; detailed tree in supplementary fig. S9a, Supplementary Material online). The gene content tree supported each of the 124 Methylobacteriaceae species, as well as the monophyly of groups B, C and D (nodal support: 99, 94 and 87%, respectively). Groups A, B and D formed a monophyletic group (nodal support: 100%), making group C the most basal group, as observed for lineage (fig. 1) and species trees (supplementary fig. S5, Supplementary Material online). Most of the species assigned to group A clustered together (nodal support: 77%) but five species formerly assigned to clade A2 (M. planium, M. soli, M. oxalidis, M. durans, M. segetis; Alessa et al. 2021) and M. jeotgali were more similar to groups B and D, which altogether formed a monophyletic group (nodal support: 97%). The normalized RF value between the gene content tree and lineage trees (fig. 1) ranged from 0.429 to 0.469. As a comparison, normalized RF values between the best gene content tree and its 1,001 replicate trees ranged from 0.085 to 0.249 (RF = 0.169 ± 0.026), indicating that the gene content tree had significantly different topology than lineage trees.

Table 3.

Average and Standard Deviation in Gene Content Dissimilarity (BC Index, Hellinger Transformation on Gene Occurrence Per Genome) Per and Among Methylobacterium Group and Outgroups

Group	BC Within S pecies	BC among Species W ithin Groups	BC among Groups
			A	B	C	D	Enterovirga
A	0.06 ± 0.02	0.19 ± 0.05
B	0.08 ± 0.02	0.17 ± 0.05	0.28 ± 0.02
C	0.07 ± 0.03	0.20 ± 0.04	0.29 ± 0.02	0.34 ± 0.02
D	0.04 ± 0.02	0.16 ± 0.03	0.24 ± 0.03	0.24 ± 0.03	0.32 ± 0.02
Enterovirga	—	0.28	0.39 ± 0.01	0.41 ± 0.02	0.36 ± 0.02	0.37 ± 0.01
Microvirga	0.03 ± 0.04	0.26 ± 0.04	0.41 ± 0.02	0.44 ± 0.02	0.38 ± 0.02	0.40 ± 0.02	0.36 ± 0.03

—, no observation.

Core Genome Architecture Comparison (Synteny) across Methylobacteriaceae Genomes

We next evaluated the level of conservation in the architecture of the Methylobacteriaceae core genome to assess the extent of chromosomal rearrangement during Methylobacterium evolution. Most genomes (177 out of 213) were not fully assembled (i.e., the chromosome consisted of more than one scaffold), and we thus inferred the order or the 384 core genes along the chromosome of draft genomes by aligning their scaffolds to the chromosomes of 36 completely assembled Methylobacteriaceae genomes, while conserving the order of core genes within scaffolds. We compared the order of core genes among genomes using a synteny index (SI) calculated as the proportion of pairs of core genes (links) that were neighbors in two genomes, ranging from 0 (no link conserved) to 1 (fully conserved synteny; supplementary fig. S8, Supplementary Material online; table 4). The matrix of synteny among species was generally concordant with the species tree (supplementary fig. S8, Supplementary Material online). In the 213 Methylobacteriaceae genomes, we observed 6,109 different links among the 384 core genes. Core genome architecture was well conserved among genomes from the same Methylobacterium species (SI range: 0.914 ± 0.064–0.995 ± 0.007) but was highly reshuffled among species within Methylobacterium groups (SI range: 0.608 ± 0.118–0.769 ± 0.207; supplementary fig. S8, Supplementary Material online; table 4). As a comparison, the core genome architecture among Microvirga species was remarkably well conserved (SI = 0.913 ± 0.048). Average synteny among Methylobacterium groups A, B, C and D was low (SI range: 0.433 ± 0.025–0.528 ± 0.049) and in the same order of magnitude as synteny between Methylobacterium and Microvirga genomes (SI range: 0.458 ± 0.010–0.525 ± 0.020; supplementary fig. S8, Supplementary Material online; table 4). We identified M. planium (strain YIM132548, group A) as the species having, on average, the highest core genome synteny with other Methylobacterium genomes. Accordingly, we used M. planium as a reference to visualize the conservation of the 384 links identified in its genome across Methylobacterium species (fig. 3a; supplementary fig. S10, Supplementary Material online). We identified 150 links (involving 231 genes; 60.2% of core genes) that were mostly conserved among Methylobacteriaceae genomes. With the exception of a remarkably well-conserved cluster of 26 genes that included ribosomal genes and gene rpoB (fig. 3a; supplementary fig. S10, Supplementary Material online), most of the 150 conserved links were scattered across the M. planium chromosome. We determined the relationships among Methylobacteriaceae members in their core genome architecture using a ML phylogeny based on the occurrence of 6,109 links identified across 213 genomes (RAxML assuming a BINCAT model; 1,001 replicate trees; fig. 3b, detailed tree in supplementary fig. S9b, Supplementary Material online). The synteny tree supported the monophyly of the four major Methylobacterium groups (nodal support = 100%). Groups A, B and D formed a monophyletic group (nodal support: 83%), making group C the most basal group, as observed for lineage trees (fig. 1), species trees (supplementary fig. S5, Supplementary Material online) and the gene content tree (fig. 2d). The normalized RF value between the synteny tree and lineage trees ranged from 0.589 to 0.638. As a comparison, normalized RF values between the best synteny tree and its 1,001 replicate trees ranged from 0.235 to 0.390 (RF = 0.310 ± 0.026), indicating that the synteny tree had a significantly different topology than lineage trees. Interestingly, although M. planium and related species previously assigned to clade A2 (M. soli, M. oxalidis, M. segetis, M. durans; Alessa et al. (2021)) as well as M. jeotgali and M. trifolii were assigned to clade A in the ML synteny tree (fig. 3b), these species had on average higher synteny with species from group D (SI = 0.651 ± 0.045) than with other species from group A (SI = 0.556 ± 0.031; fig. 3c). Accordingly, we identified 29 links involving 54 core genes that were more often conserved between groups A and D than with other Methylobacterium groups. These links, however, were scattered along the M. planium chromosome (figs. 3a, supplementary fig. S10, Supplementary Material online).

Table 4.

Average and Standard Deviation in Core Genome Synteny (SI) Per and Among Methylobacterium Group and Outgroups

Group	SI within Species	SI among species Within groups	SI among Groups
			A	B	C	D	Enterovirga
A	0.98 ± 0.03	0.70 ± 0.17
B	0.99 ± 0.01	0.77 ± 0.21	0.46 ± 0.03
C	0.91 ± 0.06	0.61 ± 0.12	0.43 ± 0.03	0.44 ± 0.01
D	0.98 ± 0.02	0.73 ± 0.11	0.53 ± 0.05	0.51 ± 0.02	0.48 ± 0.01
Enterovirga	—	0.47	0.39 ± 0.03	0.39 ± 0.02	0.38 ± 0.02	0.42 ± 0.03
Microvirga	1.00 ± 0.00	0.91 ± 0.05	0.49 ± 0.03	0.48 ± 0.01	0.46 ± 0.01	0.52 ± 0.02	0.52 ± 0.05

—, no observation.

Fig. 3.

Core genome architecture comparison (synteny) among Methylobacteriaceae genomes. (a) Consensus map of the Methylobacterium core genome architecture, and major rearrangements within and among Methylobacterium groups, using M. planium YIM132548 core genome as a reference. The map was drawn as a network using 384 core genes as nodes, and links among neighbor core genes as edges. Only 389 links that were observed in a majority (>50%) of species from a given Methylobacterium group are shown (Venn diagram on top right; 5,720 links discarded). Bold lines indicate links mostly conserved in group A, colored according to their dominance in other groups (legend on bottom right). Thick lines indicate links mostly absent in group A but dominant in other groups. A syntenic island conserved in most Methylobacterium genomes and containing ribosomal genes and gene rpoB is indicated (dotted frame). (b) RAxML ML best tree based on link occurrence per genome (6,109 links; best ML tree, BINCAT model, 1,001 replicate trees). Main groups are shown and are monophyletic in the synteny tree. (c) Detailed synteny plot for the comparison of core genome architecture between seven species from group A and six species from group D (best assembled genome per species). For each pairwise comparison, core gene (black points) are ordered according to their relative position in species 1 genome (x-axis) and are compared with their relative positions in species 2 genome (y-axis). Each plot is colored according to the SI value between species 1 and 2 (scale on top right).

Discussion

Methylobacterium Consists of Four Evolutionarily Divergent Groups of Bacteria

Recent work has suggested that Methylobacterium is much more diverse than thought previously, questioning its genus status (Green and Ardley 2018; Hördt et al. 2020; Alessa et al. 2021; Leducq et al. 2022). Here, we used a comprehensive phylogenomic approach to provide unprecedented insight on the taxonomic diversity of Methylobacterium. Our reconstructions of the Methylobacteriaceae lineage tree based on the core genome confirmed previous comparative genomic and phenotypic studies that group C, including M. nodulans and M. aquaticum, form a distinct and cohesive group at the root of the Methylobacterium phylogeny (Green and Ardley 2018; Hördt et al. 2020; Alessa et al. 2021). On the contrary, we demonstrated that Group B, including the model species M. extorquens, and previously amended as a distinct genus, Methylorubrum (Green and Ardley 2018), formed a monophyletic group with the Methylobacterium type species M. organophilum and other species formerly assigned to group A (e.g. M. oxalidis and M. planium) (Green and Ardley 2018). Our analyses hence support the proposal to extend group B to M. organophilum, M. oxalidis, M. planium, and relatives (Alessa et al. 2021). Although the newly defined group B was monophyletic according to our different inferences of the Methylobacteriaceae species, it was still embedded within former group A (Green and Ardley 2018), making the later paraphyletic, and confirming that Methylorubrum cannot be considered as a distinct genus without breaking apart Methylobacterium (Hördt et al. 2020; Alessa et al. 2021). Accordingly, we support the proposal to abandon “Methylorubrum” as a designation for group B, and to split group A into two monophyletic groups distinct from group B: group A (including M. brachiatum, M. komagatae, M. cerastii, M. jeotgali, M. trifolii, M. planium and relatives) and group D (including M. bullatum, M. gossipicola, M. goesingense, M. iners, and relatives).

We observed that the newly defined monophyletic groups (A, B, C, and D) were characterized by distinct genome sizes and GC content, two metrics that were highly correlated with each other in Methylobacterium, as observed in other bacteria (Nishida 2012). With the exception of a few species from group A (including, M. trifolii, M. jeotgali, M. planium and relatives), the four groups could also be distinguished upon their gene content. GC content, genome size and gene content are widely accepted as criteria for taxonomic definition in prokaryotes (Rosselló-Mora and Amann 2001; Coenye et al. 2005). We also demonstrated that core gene order was highly reshuffled among the four Methylobacterium groups. For instance, we observed the same level of rearrangement in core gene order among Methylobacterium groups, as between Microvirga and Methylobacterium, and the same level of core gene order conservation within Methylobacterium groups as within Microvirga. Core gene order has recently been proposed as a complementary criterion to define bacteria genus and species taxonomy (Chung et al. 2018). The fact that the four groups were monophyletic, regardless of whether we used a concatenated or a coalescent-based approach to infer the Methylobacteriaceae lineage tree and could be consistently distinguished from each other upon different genome characteristics (gene content, core genome architecture, GC content, genome size), supports considering them as distinct genera.

Role of HGT and ILS in the Early Divergence of Groups A, B, and D

The evolution of bacteria is marked by recurrent HGT, gene duplication and loss events, making the reconstruction of bacterial phylogenies challenging. Given that each gene potentially has its own evolutionary history, marked by exchanges among divergent taxa, the evolutionary tree of most bacteria is quite reticulate (Shapiro et al. 2016). The reconstruction of a consensus phylogenetic tree (lineage tree) thus remains highly conceptual in bacteria and could only be achieved by considering a pool of genes assumed to be representative of the prevailing evolutionary history of the considered taxa: the core genome (Sakoparnig et al. 2021). Therefore, HGT and ILS must be considered when attempting to reconstruct bacterial phylogeny. Accordingly, we showed that the concatenated-based reconstruction of Methylobacterium lineage tree, assuming the same evolutionary history for each core gene, significantly differed in its topology from lineages tree reconstructions accounting for ILS and/or HGT among core genes (ASTRAL and SVDquartets lineage trees), indicating that both processes were major drivers of Methylobacterium evolution. While the concatenated tree suggested that groups A and D formed a monophyletic group, coalescent-based estimations from ASTRAL (ILS + HGT among genes) and SVDquartets (ILS + HGT among sites) rather indicated the earlier divergence of group D from the A/B/D group.

A possible explanation of the divergent topology in the concatenated lineage tree is that shared polymorphism was retained by ILS and/or HGT between groups A and D after the A/B divergence. Interestingly, although supporting the four Methylobacterium groups, our phylogeny reconstructed from core genome architecture suggested the closer relationship between groups A and D, in agreement with the concatenated lineage tree, hence supporting the hypothesis of horizontal core gene exchanges having occurred between groups A and D after the A/B divergence. Accordingly, we observed syntenic islands (groups of neighbor core genes) shared between group D and some basal species of group A (M. jeotgali, M. trifolii, M. planium, M. oxalidis and relatives). These islands were scattered across the Methylobacterium chromosome, either suggesting that extensive chromosomal rearrangements occurred after HGT between A and D, or that HGT occurred multiple times during their evolutionary history, potentially among divergent lineages. According to a phylogeny reconstructed from gene occurrence in Methylobacterium, M. jeotgalii, M. planium, M. oxalidis and relatives, belonged to different lineages branching at the root of groups A, B and D, supporting the hypothesis of multiple and independent gene exchanges among distinct Methylobacterium lineages after the divergence of the three groups, blurring their phylogenetic relationships.

Outstanding Methylobacterium Diversity: The Role of the Phyllosphere?

Methylobacterium is frequently associated with the phyllosphere, yet taxonomic and phylogenomic surveys of its diversity have mostly focused on human-impacted environments such as food factories, contaminated soils, air conditioning systems or even the International Space Station. Here we presented the first comprehensive genomic survey of Methylobacterium diversity in the phyllosphere. By including genomes of strains isolated from the phyllosphere of wheat (Zervas et al. 2019), of the model plant A. thaliana (Helfrich et al. 2018), and of trees from natural temperate forests (Leducq et al. 2022), our phylogenomic analysis of Methylobacterium revealed that its evolutionary and taxonomic diversity was larger than previously thought. In addition to recovering the 59 previously described species (Alessa et al. 2021), we identified 45 new (candidate) Methylobacterium species, of which a majority belonged to groups A and D, and were mostly isolated from the phyllosphere. Beyond taxonomic considerations, this result reveals a profound bias in our understanding of natural processes underlying the existing diversity of Methylobacterium, and more generally, of bacteria. For example, the evolutionary distinction between groups A and D, and their importance in Methylobacterium diversity, could not have been revealed without a thorough investigation of diversity in the phyllosphere, from which the majority of candidate species from groups A, B, and D were isolated. A recent survey of Methylobacterium in metagenomes from various biomes (Lee et al. 2022) also suggested the association of groups A (represented by M. pseudosasicola and M. radiotolerans in Lee et al. 2022 study), B and especially D (represented by M. gossipiicola and Methylobacterium sp. Leaf 88) with the aerial part of plants. Similarly, we recently showed that groups A and D were the dominant Methylobacterium groups in the phyllosphere of trees from temperate forests (Leducq et al. 2022). On the contrary, groups B and C included most Methylobacterium model species frequently used in the lab and isolated from anthropogenic environments. While group B is occasionally identified on and isolated from the surface of leaves (Leducq et al. 2022; Lee et al. 2022), group C is rarely, if ever, found in the phyllosphere, and seems to be more widespread in soil and in aquatic environments, often in association with plant roots (Lee et al. 2022). Interestingly, authors from a recent study estimated that Rhizobiales common ancestor likely had a free-living lifestyle, while Methylobacterium groups A, B and D’s common ancestor likely had a plant-associated lifestyle (node 1 in fig. 1 from Wang et al. study (Wang et al. 2020)). The ancestral lifestyle of Methylobacterium, and more widely, of Methylobacteriaceae, is more unclear. The isolation source of group C genomes, as well as the two sister genera of Methylobacterium, Enterovirga and Microvirga, and their survey in metagenomes (Lee et al. 2022) indicate that these three groups are mostly found with soils, sometimes in association with the rhizosphere. These observations suggest that Methylobacteriaceae and Methylobacterium’s ancestors inhabited soils, and were occasionally associated with plants, for instance in the rhizosphere, and that Methylobacterium groups A/B/D’s association with the phyllosphere occurred after divergence from group C. The exact origin and nature of this association is an open question, but the smaller genome size, gene copy number, GC content and to a lower extent, mobile element number, we observed in group A/B/D in comparison with group C could be the genomic signatures of a progressive specialization to life on plants (Nishida 2012; Levy et al. 2018), among other things through the evolution of metabolic pathways in response to contrasted nutrient availability between the soil and the phyllosphere (Lee et al. 2022; Alessa et al. 2021). For instance, some genes involved in the metabolism of aromatic compounds resulting from lignin degradation are present in Microvirga and Methylobacterium group C, but absent from other Methylobacterium groups (Lee et al. 2022), suggesting that these functions essential for ground lifestyle were lost in A/B/D group after they divergence with group C. Inversely, Methylobacterium from group A/B/D arbor a larger panoply of genes allowing the use of methanol, available in the phyllosphere, than group C, while most of these pathways are absent from Microvirga (Alessa et al. 2021), suggesting that the transition from soil to phyllosphere lifestyle in Methylobacterium also coincided with the acquisition and diversification of methylotrophic pathways.

According to our phylogenomic analyses of group A/B/D, group D diverged first, and, like group A, was mostly isolated from the phyllosphere, suggesting that the A/B/D ancestor inhabited the surface of plant leaves. The fact that our analyses support horizontal gene exchanges between groups A, B, and D is also consistent with the hypothesis that these groups lived in the same habitat during their divergence. One can speculate that some horizontally transferred, yet to be discovered, genes may have had shared roles in Methylobacterium adaptation to the phyllosphere. For instance, strains from groups A and D were often identified in the same studies, sometimes isolated from the same plants, indicating that strains from these two groups likely share the same microhabitats on the surface of plant leaves, hence favoring gene exchanges among them and the maintenance of similar molecular pathways and functions. Further identifications of genes exchanges among these groups and the characterization of their functions will be critical to understand evolutionary mechanisms underlying the adaptive role and radiation of Methylobacterium in the phyllosphere.

Conclusion

Our unprecedented phylogenomic analysis of Methylobacterium revealed the outstanding diversity within this taxon, and the role of HGT in its early evolutionary history. Future genomic and functional studies will be needed to characterize the evolutionary and functional features of Methylobacterium adaptation to the phyllosphere. Finally, our work lays the foundation for a thorough taxonomic redefinition of this genus.

Methods

Methylobacteriaceae Genome Collection

We assembled a collection of 213 complete and draft Methylobacteriaceae genomes, including 189 Methylobacterium and 24 genomes from related genera as outgroups (Microvirga: n = 22; Enterovirga: n = 2). Most Methylobacterium (n = 98) and all outgroup genomes (n = 24) came from distinct studies (see references in Leducq et al. (2022)) and corresponded to genomes publicly available in October 2020 on NCBI. We included 29 genomes from Methylobacterium type strains recently published (Alessa et al. 2021; Bijlani et al. 2021) in order to cover most Methylobacterium species described so far. We also included 38 genomes available from two large surveys of the Arabidopsis and wheat phyllospheres (Helfrich et al. 2018; Zervas et al. 2019) and sequenced 24 additional genomes (see “Library Preparation and Genome Assembly of 24 Methylobacterium Strains”) of isolates from a large survey of the temperate forest phyllosphere (Leducq et al. 2022), hence extending our dataset to the leaf-associated Methylobacterium diversity.

Library Preparation and Genome Assembly of 24 Methylobacterium Strains

We performed genome sequencing and de novo assembly of 24 Methylobacterium strains representative of the diversity previously found in the phyllosphere of two temperate forests in the province of Québec, Canada (Leducq et al. (2022); supplementary dataset S2, Supplementary Material online). DNA extraction was performed from culture stocks frozen at −80 °C directly after isolation and identification (Leducq et al. 2022) and thawed 30 min on ice. About 750 μL of cell culture were used for DNA extraction with DNeasy PowerSoil Pro Kit (Qiagen) according to the manufacturer protocol, with the following modification: final elution was repeated twice in 25 μL (total volume: 50 μL). 300 bp paired-end shotgun libraries were prepared from 35 ng genomic DNA with QIAseq FX DNA Library Kit (Qiagen) and protocol was adjusted to target DNA fragments in the range 400–1000 bp. Genomes were assembled from libraries with MEGAHIT (Li et al. 2015) with default parameters. Genome assemblies had 7050–24785 contigs with average depth in the range 188–304 × and a total size in the range 7.2–17.1 Mb. After removing contigs with depth <10x, we obtained 82–411 contigs per genome. Most assemblies had total size (5–7 Mb) and average GC content (67–70%) in the expected range for Methylobacterium genomes (supplementary dataset S2, Supplementary Material online). For three of twenty-four genomes, GC content and depth distribution were clearly bimodal, and total size was much higher (9.5–11.9 Mb) suggesting that these assemblies contained genomes from at least two evolutionary distinct taxa. For these three heterogeneous assemblies, we divided contigs into two pools based on median depth value between two modes (threshold range: 100–150x). For each heterogeneous assembly, the pool with highest average depth (174–241x) had average GC content (67–68%) and total size (5.6–5.8 Mb) in the ranges expected for Methylobacterium. Contigs with lower depth were considered as contaminants and discarded from assemblies.

Gene Annotation

Methylobacteriaceae genomes (n = 213) were individually annotated using RAST (https://rast.nmpdr.org/rast.cgi) (Aziz et al. 2008) with following parameters: genetic code = 11; Annotation scheme = RASTtk; Preserve gene calls = no; Automatically fix errors = yes; Fix frameshifts = no; Backfill gaps = yes. Annotation output from each genome was retrieved separately as Spreadsheet (GFF file in tab-separated text format). Core genome definition was conducted in R (R-Developement-Core-Team 2011). For each genome, we retrieved the abundance of gene annotations (column function in RAST output), excluding Hypothetical proteins, repeat regions and Mobile element proteins (supplementary dataset S3, Supplementary Material online).

Methylobacteriaceae Core Genome Definition

We first defined the Methylobacteriaceae core genome from 184 genomes, excluding 29 genomes that were not yet published nor annotated at the time of the analysis (Alessa et al. 2021; Bijlani et al. 2021). In these 184 genomes, we identified 9,970 unique gene annotations (i.e., regardless copy number: supplementary dataset S3, Supplementary Material online), with on average 2637 ± 210 unique gene annotations per genome. We defined candidate core genes as genes present in one copy in at least 90% of the 184 genomes, resulting in 893 candidate core genes, for which we retrieved the nucleotide sequence (column nucleotide_sequence in RAST output). In order to correct for false gene duplication events that increased consistently with assembly incompleteness (supplementary fig. S1, Supplementary Material online) and to estimate the actual copy number of each candidate core gene, we used 36 complete Methylobacteriaceae genomes as references (defined as genomes with N50 > 3 × 10⁶ Mb). For each candidate core gene, we calculated the average expected nucleotide sequence size observed among 36 complete genomes. Then, for each genome (n = 184) and each candidate core gene, we retrieved all nucleotide sequences (0–10 per gene and genome) and calculated their average size normalized (divided) by the average nucleotide sequence size observed in complete genomes. By doing so, we could distinguish between duplication caused by genome incompleteness (single copy genes divided between different scaffolds) and real duplication events (supplementary fig. S2, Supplementary Material online). We considered 398 genes for which at least one genome had more than one copy with normalized size >0.75 as true duplicates and removed them from candidate core genes. For the 495 remaining candidate core genes, we considered single-copy genes with normalized size >1.3 and gene copies with normalized size <0.7 (regardless copy number) as missing data in the considered genome. After this filter, we removed 111 candidate core genes that were missing in at least 4 genomes, resulting in 384 core genes for which a single full-length copy could be retrieved for at least 181 genomes (out of 184; supplementary dataset S4, Supplementary Material online). Subsequently, we included recently sequenced genomes from 29 Methylobacterium species type strains that were missing from our survey (Alessa et al. 2021; Bijlani et al. 2021). By doing this, we slightly extended the number of unique gene annotations in Methylobacteriaceae (n = 10,190). We confirmed that the 384 previously identified core genes were part of the Methylobacteriaceae core genome and retrieved each core gene nucleotide sequence for at least 26 out of 29 genomes. Our final dataset consisted of 213 genomes for which we retrieved 327 to 384 core genes nucleotide sequences (381 ± 6; mean, SD; supplementary dataset S1, Supplementary Material online).

Core Gene Nucleotide Sequence Alignments

We performed an alignment for each core gene. For each genome (n = 184 + 29 = 213), we first extracted nucleotide sequences of the 384 core genes (when not missing data for the considered genome; column nucleotide_sequence in RAST output) and converted them in sequence fasta files using R package seqinr(). We then performed an alignment for each core gene using R packages seqinr() and msa(). For each gene, nucleotide sequences were translated (function getTrans()) and alignments of amino-acid sequences were performed using ClustalW with default parameters in function msa(). Sequences were converted back in nucleotides (stop codons excluded) and 5″ and 3″ end codons with more than 90% of missing data (gaps of “Ns”) were trimmed. We also constructed an alignment of concatenated core genes nucleotide sequence alignments. In the concatenated alignment, sequences of genes missing for at least one of the 213 genomes (0–6 genomes missing per gene) were replaced by strings of “Ns”.

Inferences of the Methylobacteriaceae Lineage Trees

We reconstructed the lineage tree of Methylobacteriaceae from 213 genomes from the 384 core gene nucleotide sequences using three complementary approaches in order to assess the effect of ILS and HGT in the evolutionary history of Methylobacterium.

First, we used RAxML v. 8.2.8 (Stamatakis 2014) to determine a ML lineage tree from concatenated alignments of the core 384 gene nucleotide sequences assuming a different substitution model for each gene but the same evolutionary tree for all genes (and hence not accounting for ILS or HGT). We used PartitionFinder implemented in IQ-tree2 (Minh et al. 2020) to determine an appropriate bipartitioning scheme allowing us to merge genes evolving under similar nucleotide substitution models (Lanfear et al. 2012). The best-fit partition scheme was determined using TESTMERGERONLY model (option –m) to avoid tree reconstruction, and using the relaxed hierarchical clustering algorithm to reduce the computation burden (Lanfear et al. 2014) by only examining the top 10% partition merging schemes (option –rcluster). We then inferred the Methylobacteriaceae lineage tree from the 384 core gene alignment with RAxML v. 8.2.8 (Stamatakis 2014), using the IQ-tree2 best-scheme output file as partition file (option –q in RAxML). The program performed 512 replicate (bootstrap) searches from independent starting trees with a GTRCAT model of substitution, estimating parameters for each partition separately. Of the 512 trees, the one with the highest ML score (the best-scoring tree) was retained as the lineage tree.

Second, we used ASTRAL-III (Zhang et al. 2018), a coalescent-based method inferring the lineage and the species trees by combining individual core gene trees, hence accounting for ILS and HGT among genes. For each core gene, a gene tree was first inferred from nucleotide sequence alignments with RAxML v. 8.2.8 (Stamatakis 2014). Briefly, for each gene, the program performed 1,000 replicate (bootstrap) searches from independent starting trees assuming a GTRgamma model of nucleotide substitution. Each gene tree in Newick format, including branch length (L: nucleotide substitution per site) and node label (N: nodal support representing the proportion of replicated supporting nodes), was imported in R as a vector. The gene tree in RAxML format: ((():L1[N1]):L2[N2]) was rewritten so that it could be readable in R (package ape [Paradis and Schliep 2019]) and ASTRAL-III: ((():L1)N1:L2)N2. The tree was then reopened in R with function read.tree (package ape) and nodes with < 10% support were collapsed using function collapseUnsupportedEdges (package ips), to optimize accuracy in estimating the lineage and species tree (Zhang et al. 2018). All reformatted gene trees were written in a single file (multiPhylo object), which was used to infer the lineage and the species tree in ASTRAL-III v5.7.7, with default parameters. In ASTRAL trees, branch lengths were measured in coalescent units and nodal support represented local posterior probability (Sayyari and Mirarab 2016).

Third, we used SVDquartets (Chifman and Kubatko 2014) as implemented in PAUP* v4.0a (build 169) (Wilgenbusch and Swofford 2003), a coalescent-based method estimating the tree for each possible combination of four genomes and assuming all sites unlinked in the concatenated alignment of 384 genes. We estimated the lineage tree from the concatenated 213 Methylobacteriaceae core genes by evaluating 2,000,000 random quartets for 100 bootstrap replicates. Phylogenies were estimated under the multispecies coalescent model accounting for ILS and assessing all sites independently to account for recombination within and among loci.

Lineage trees were displayed in Figtree v1.4.4 and rooted on Microvirga and Enterovirga.

Methylobacteriaceae Species Definition and Lineage Tree Inferences

We classified Methylobacteriaceae genomes in species using PNS on the core genome (concatenated alignments on 384 core genes; 361,403 bp), similar to average nucleotide identity (Mende et al. 2013; Chun and Rainey 2014). Briefly, PNS between two genomes was calculated in R as the proportion of conserved nucleotide positions, gaps and “Ns” excluded (supplementary dataset S4, Supplementary Material online). Two genomes were considered from the same species when their PNS was higher or equal to 97%, a threshold similar to what is typically used for bacterial species (96.5% based on nucleotides sequences of 40 marker genes; [Mende et al. 2013; Chun and Rainey 2014]). We inferred the Methylobacteriaceae species tree using both ASTRAL-III (Zhang et al. 2018) and SVDquartets (Chifman and Kubatko 2014), as described above, using individual assignment to species determined from PNS. Species trees were displayed in Figtree v1.4.4 and rooted on Microvirga and Enterovirga.

Test for HGT and ILS Severity in Lineage and Species Tree Inferences

We tested for the severity of HGT and ILS in our dataset by measuring the differences in tree topologies estimated using different assumptions. To quantify differences between the topologies obtained under different assumptions, we calculated normalized RF distances (Robinson and Foulds 1981), which evaluates the pairwise proportion of unique nodes between tree topologies, between all three lineage trees (RAxML from concatenated core gene alignments, SVDquartets, and ASTRAL) as well as between both species trees (ASTRAL and SVDquartets). RF distances were estimated using the treedist function implemented within PAUP* v4.0 (build 169) (Wilgenbusch and Swofford 2003) using final phylogenies in NEWICK format as input. We also calculated the distribution of RF distances between our best RAxML tree from concatenated core gene alignments and all 512 RAxML bootstrap replicates. We then compared our RF distances between each inference method to this distribution of distances to assess whether discordant topologies among lineage trees are due to different assumptions of methods, or due to phylogenetic uncertainty.

Methylobacteriaceae Genome Characteristics and Gene Content

We analyzed Methylobacteriaceae genome characteristics (size, GC content and gene content) of the coding sequence for each. We first calculated the number of gene annotations, their total nucleotide size (coding genome size), their GC content, the number of unique annotations (excluding hypothetical proteins, repeat elements and mobile elements), the number of mobile elements, and the average copy number of annotations (supplementary dataset S1, Supplementary Material online; table 2). For each statistic, we compared Methylobacterium groups (as defined by lineage trees) and outgroups (Microvirga, Enterovirga) using a Tukey test.

In a heatmap, we displayed the average abundance of 10,187 gene annotations (excluding hypothetical proteins, repeat elements and mobile elements) per Methylobacteriaceae species, per Methylobacterium group and outgroup, ordered according to the ASTRAL species tree (supplementary fig. S5a, Supplementary Material online). For gene abundance per species, we calculated the average occurrence (n) of each gene annotation across genomes assigned to the same species, rounded to 0 (n < 0.5), 1 (0.5 ≤ n < 1.5) or 2 copies (n≥2). For gene abundance per group, we calculated the average occurrence of each gene annotation across species assigned to the same group, using the same principle as for species.

We estimated pan genome and core genome sizes per Methylobacterium group (unknown proteins, repeat and mobile elements excluded; supplementary fig. S7, Supplementary Material online). To deal with biases in size estimations due to the variable number of genomes per group, we applied rarefaction on gene number estimates by randomly sampling 1 to N genomes per group (Park et al. 2019) and by forcing resampling of one genome per species. For each N value and each group, we calculated the average and standard deviation in core genome size (genes in 1:1 copy in each genome of a given group) and in pan genome (any gene present in at least one copy in at least one genome of a given group) over 100 replicates. As pan genome size estimations increased with the number of sampled species per group (supplementary fig. S7a, Supplementary Material online) and core genome size estimations decreased (supplementary fig. S7b, Supplementary Material online), curves of estimates per group did not cross each other, nor reached a plateau, indicating that sizes were either under-estimated (pan genomes) or over-estimated (core genome) but could still be compared among groups. Accordingly, we compared pan and core genome sizes among Methylobacterium groups in a Venn diagram, assuming 15 species per group (figs. 2b,c).

We constructed a phylogeny of Methylobacteriaceae based on gene content (fig. 2d). First, we constructed a matrix of gene occurrence in each genome (0 for absence and 1 for presence) and converted it into a fasta file (one sequence per genome). We inferred an evolutionary tree of based on gene content using with RAxML v. 8.2.8 (Stamatakis 2014). The program performed 1,000 replicate (bootstrap) searches from independent starting trees with a BINCAT model of substitution assuming gene presence of absence as binary data. Of the 1,000 replicate trees, the one with the highest ML score (the best-scoring tree) was considered as the best tree. The tree was displayed in Figtree v1.4.4 and rooted on Microvirga and Enterovirga.

In order to compare Methylobacteriaceae genomes based upon their gene content, we calculated an index of dissimilarity among each pair of genomes from their gene abundance (table 3; supplementary fig. S8b, Supplementary Material online). As no index was available for this purpose, we used the Bray-Curtis (BC) index of dissimilarity, initially developed in ecology for the comparison of communities based on their species abundance (Bray and Curtis 1957). To minimize the effect of higher copy number due to false gene duplications due to genome incompleteness, we applied a normalization on gene abundances (Hellinger normalization; function decostand in R package vegan). We calculated pairwise BC indexes of dissimilarity among normalized gene abundances, using function vegdist in R package vegan.

Core Genome Architecture (Synteny)

We evaluated the level of conservation in core gene organization (synteny) between Methylobacteriaceae genomes. All analyses were performed in R (R-Developement-Core-Team 2011). For each genome, we retrieved core gene coordinates (scaffold name and coordinates in the scaffold). For complete genomes consisting of a single linear scaffold (n = 36), each core gene was paired with its two immediate neighbors, based on shortest distance between gene start and stop coordinates, and core genes located on scaffold edges were also paired together, assuming genome circularity. Hence, for each complete genome, each of the 384 core genes was involved in two links (pairs of neighbor core genes), for a total of N = 384 links per genome. For the 177 draft genomes, core genes were located on different scaffolds, so we predicted scaffold order and orientation using complete genomes as references. The draft genome with the highest completeness was reorganized first. Briefly, for each comparison with a reference genome, and for each scaffold of the draft genome, the list of embedded core genes was retrieved, and a score based on gene average order in the reference genome was calculated. Scaffolds of the draft genome were reordered according to these scores (one per scaffold). Then, each scaffold was eventually reoriented (without affecting gene order within scaffolds) to optimize pairing of edge genes (genes located at the edge of a scaffold) as compared to the reference genome. We repeated the operation for comparisons with the 36 reference genomes. Finally, for each of the 36 new configurations of the draft genome, we calculated a synteny conservation index (SI) with each reference genome, as the proportion of links conserved between two genomes. SI ranged from 0 (no link conserved) to 1 (fully conserved synteny). The draft genome configuration with the highest SI value was conserved for further analyses and added to the list of reference genomes. We repeated this operation for each draft genome, ranked according to their decreasing completeness, hence increasing the number of reference genomes and possible configurations for highly fragmented genomes. Finally, we calculated SI for all possible pairwise comparisons between genomes (supplementary fig. S8b, Supplementary Material online), and average and standard deviation values within and among Methylobacteriaceae species and groups (table 4).

In order to visualize the spatial organization of core genes along the Methylobacteriaceae chromosome, we used two approaches. First, we realized a heatmap of link conservation per species, along a reference genome (supplementary fig. S10, Supplementary Material online). We choose as reference the genome having the highest average SI value with other Methylobacterium genomes. In the heatmap, we displayed the 384 links identified in the reference genome, ordered according to core gene order along its chromosome, and highlighted them when also present in other Methylobacteriaceae species. For each species, we also reported the average SI value with the reference genome. Finally, for each link in the reference genome, we calculated its frequency in each Methylobacterium group. Second, we drew a consensus map of the Methylobacterium core genome architecture, as well as major rearrangements within and among Methylobacterium groups, as a network in Cytoscape v.3.4.0 (Shannon et al. 2003) (fig. 3a). In this network, we represented the 384 core genes as nodes, ordered according to M. planium YIM132548 core genome, and links among neighbor core genes as edges. The network was drawn using 389 links observed in a majority (>50%) of species from a given Methylobacterium group (5,720 links discarded).

In order to reconstruct the evolution of Methylobacteriaceae core genome based on its architecture, we constructed a matrix of occurrence of each possible link observed among genomes (0 for absence and 1 for presence) and converted it into a fasta file. We inferred an ML evolutionary tree of Methylobacteriaceae based on synteny using with RAxML v. 8.2.8 (Stamatakis 2014) with a BINCAT model of substitution assuming pair of core genes presence of absence as binary data, as described for annotations (fig. 3b).

Supplementary Material

Supplementary data are available at Genome Biology and Evolution online.

Author Contributions

J.-B. L., D. S., M. S. and J.M.S. performed the bioinformatic analyses, J.-B. L., D.C.-M., and G.B. performed the experiments, N. C. M.-G., J. A. L., J. A. F. and S. S. provided discussion at the early stage of the study, J.-B. L., B. J. S., S. W. K., J. M. S. and C. J. M. drafted the manuscript, with help from N. C. M.-G., J. A. L. and S. S.

Data Availability

Draft genomes for 24 Methylobacterium strains corresponding to Bioproject PRJNA730554 (Biosamples listed in supplementary dataset S1, Supplementary Material online) were deposited on NCBI under accession numbers JAKSXU000000000 - JAKSYR000000000. R code and related data were deposited on Github (https://github.com/JBLED/methylobacterium-phylogenomics.git).