Complete genome sequence and analysis of Alcaligenes faecalis strain Mc250, a new potential plant bioinoculant

Here we present and analyze the complete genome of Alcaligenes faecalis strain Mc250 (Mc250), a bacterium isolated from the roots of Mimosa calodendron, an endemic plant growing in ferruginous rupestrian grasslands in Minas Gerais State, Brazil. The genome has 4,159,911 bp and 3,719 predicted protein-coding genes, in a single chromosome. Comparison of the Mc250 genome with 36 other Alcaligenes faecalis genomes revealed that there is considerable gene content variation among these strains, with the core genome representing only 39% of the protein-coding gene repertoire of Mc250. Mc250 encodes a complete denitrification pathway, a network of pathways associated with phenolic compounds degradation, and genes associated with HCN and siderophores synthesis; we also found a repertoire of genes associated with metal internalization and metabolism, sulfate/sulfonate and cysteine metabolism, oxidative stress and DNA repair. These findings reveal the genomic basis for the adaptation of this bacterium to the harsh environmental conditions from where it was isolated. Gene clusters associated with ectoine, terpene, resorcinol, and emulsan biosynthesis that can confer some competitive advantage were also found. Experimental results showed that Mc250 was able to reduce (~60%) the virulence phenotype of the plant pathogen Xanthomonas citri subsp. citri when co-inoculated in Citrus sinensis, and was able to eradicate 98% of juveniles and stabilize the hatching rate of eggs to 4% in two species of agricultural nematodes. These results reveal biotechnological potential for the Mc250 strain and warrant its further investigation as a biocontrol and plant growth-promoting bacterium.


Introduction
The Alcaligenes faecalis (Af) species comprises of rod shaped, Gram-negative, aerobic and polyvitric strains that have optimal growth at temperatures ranging from 20 to 37˚C [1]. This bacteria is widely found in water and soil samples and have been shown to be causal agents of opportunistic pathologies in humans and animals [2,3]. Biochemical and molecular studies have demonstrated that some strains of Af have biosurfactant production potential [4], ability to act as denitrifying organisms [5,6], high arsenic oxidizing capacity [7][8][9], and ability to act as biocontrol of nematodes and insects due to their high killing potential against some species of these agricultural pests [10][11][12]. In summary, Af strains have been shown to be valuable as important biofertilizer, bioremediation, and biocontrol agents.
A previous work by our group described Af strain Mc250 (Mc250) isolated from Mimosa calodendron (Fabaceae) roots as part of a prospection study of bacteria associated with plants endemic to ferruginous rupestrian grasslands of the Brazilian Iron Quadrangle [19]. This strain was shown to have high potential as a plant growth promoting bacterium (PGPB), acting mainly as a rhizoremediator of arsenic-contaminated soil [19]. These initial results along with the biotechnological potential reported for strains of this species prompted us to sequence the Mc250 genome and perform a detailed comparison with other published genomes of this species. We identified several metabolic pathways understudied in Af such as those associated with degradation of phenolic compounds, plant hormone synthesis pathways, and pathways related to biomolecules that aid in plant development and those that have the potential to inhibit different plant pathogens and agricultural pests. The latter feature led us to experimentally investigate the inhibitory effects that Mc250 might have against the plant pathogen Xanthomonas citri subsp. citri and two nematodes species that are also plant pathogens, with positive results.

Ethics statement
The field research was approved by the Ministério do Meio Ambiente-MMA; Instituto Chico Mendes de Conservação da Biodiversidade-ICMBio; Sistema de Autorização e Informação em Biodiversidade-SISBIO, field permit number 54015.

Bacterial DNA extraction, sequencing and genome assembly
The strain Alcaligenes faecalis Mc250 (Mc250) was isolated from Mimosa calodendron, an endemic plant of the ferruginous rupestrian grasslands from the Iron Quadrangle [19]. Mc250 was grown in 50 mL of Luria Bertani medium (10 g/L peptone, 10 g/L NaCl, 5 g/L yeast extract, pH 7.0) for 2 days at 28˚C under agitation of 220 rpm, and DNA was extracted using the Wizard Genomic DNA purification™ kit (Promega) according to product specifications. DNA integrity was examined with DNA 7500 chip using 2100 Bioanalyzer, revealing an enrichment of fragments higher than 10 kbp. Sequencing library was prepared with Illumina Nextera DNA library preparation kit (Illumina, Inc., USA) with a total DNA input of 40 ng. After quantification with the KAPA Library Quantification Kit, the library was subjected to one run using the MiSeq Reagent kit v2 (500-cycle format, paired-end (PE) reads). On average, Illumina PE read1 and read2 presented, respectively, >80% and >75% of bases with quality score at least 30 (Q30). Raw reads were trimmed with Trimmomatic v0.35 [20] and assembled with SPAdes v3.12.0 [21]. In addition, the MaSuRCA assembler v3.2.6 [22] was also used. The use of and comparison of different genome assembly algorithm results generally leads to the resolution of the rRNA operons copies and other smaller repeats, permitting the manual extension and junctions of contigs. Therefore, the final genome sequence was generated by the comparisons of both SPAdes and MaSuRCA assembly results by the use of the cross_match software (http:// www.phrap.org), platanus scaffold and gap_close v1.2.4 [23] and special scripts. The trimmed reads were mapped back to the final genome sequence with bowtie2 v2.3.4.1 [24] and the estimated paired-end reads distance were inspected in order to verify misassembled regions and low covered regions. A total of 99.81% of the paired-reads were aligned concordantly, thus supporting a high confidence, complete and circular genome, with an average coverage of 250x.

Genome availability
The sequence of the Mc250 genome is available at GenBank under accession number NZ_CP031012.1, Bioproject PRJNA481026 and Biosample SAMN09655358.

Genome map and genomic islands prediction
The Mc250 genome map was constructed using Artemis DNAPlotter [26] and BRIG [27]. Genomic islands and phage regions were predicted according to Oliveira Alvarenga et al. [28].

FliC phylogenetics and 3D structure prediction
The evolutionary history of the fliC gene was investigated using PSI-Blast [29] search with a hit limit of 1,000 accessions. Multiple alignment of the protein sequences was done using Muscle [30]. Model selection, gene tree Maximum Likelihood estimation, and branch support (by UFBoot) were all performed using IQTree2 [31]. The tridimensional structure prediction of the FliC protein was done using the Phyre 2 program [32].

Pan and core genome analysis
Pan and core genome analysis was done with Roary [33] with a protein identity threshold of 90% [25,33].

In silico metabolic pathways comparison
All comparative analyses involving metabolic pathways and cellular processes were done within the RAST platform [34].

In vitro Xanthomonas citri antagonistic assay
In vitro assays were performed by inoculation of Mc250 over a lawn of Xanthomonas citri subsp. citri strain 306 pathotype A (Xac306) previously made in LB agar plate (90 × 15 mm Petri dish). Halo formation indicated inhibition capacity after 2 days at 28˚C. Serratia marcescens and Escherichia coli were used, respectively, as positive and negative controls. For the formation of the Xanthomonas lawn, 20 μL of a culture in liquid LB medium with OD = 1 was applied onto the surface of the medium and spread homogeneously with a Drigalski handle.

In vivo Xanthomonas citri antagonistic assay
In planta assays to evaluate Mc250 antagonism to Xac306 were carried out by their co-inoculation in sweet orange grafted plants (Citrus sinensis (L.) Osbeck. "Pera Rio"). Twelve-monthold plants were kept in a growth chamber at 28˚C and under a photoperiod of 16 h. Mc250 were inoculated together with Xac306 in the abaxial region of citrus leaves under infiltration pressure 1 mL with needleless syringes. The final concentration of Xac306 and Mc250 suspensions were adjusted to 10 7 CFU/ml in 10 mM MgCl 2 . Plant inoculations with Xac306 alone or MgCl 2 were used, respectively, as positive and negative controls. The infiltrated leaves were photographed 3 and 14 days after inoculation (DAI). The lesions area of five infiltrated leaves (from three independent assays) were quantified, and infected areas were calculated using Image J v1.48 [35].

Phytopathogenic nematodes mortality assay
Mc250 was cultured in LB medium at 28˚C on a shaker (180 rpm) for 48 h. After this time the bacterial culture was centrifuged at 10000 xg for 10 min and the supernatant was used in the following experiments. To determine the effect of Mc250 extracellular metabolites on the nematodes Pratylenchus brachyurus and Panagrellus redivivus, 100 μL of the culture supernatant was transferred to multi well plate previously loaded with a suspension of 100 μL per well containing 100 nematodes of each species previously axenized. The plate was kept at 28˚C for 48 h and nematode mortality was evaluated according to the methodology described by Chen and Dickson [36]. A negative control was performed by replacing the culture supernatant by the same volume of sterile LB medium. The assay was conducted in a randomized design with five replicates per treatment.

Statistical analyses
Statistical analyses were performed using the statistical package GraphPad Prism version 5.00™ (San Diego, CA). The results were submitted to the normality test of Smirnov Kolmogorov and represented as the mean ± SEM (standard error of mean) or mean ± SD (standard deviation). The Student's t-test was used to compare pairs of parametric groups while variance analyses one-way ANOVA was used to compare three or more groups with Tukey post tests for parametric data, while Kruskal-Wallis test was used to compare Dunn's posttests data, considering p <0.05 ( � ), p <0.01 ( �� ), and for p <0.001 ( ��� ).

General characteristics of Mc250 genome
The Alcaligenes faecalis strain Mc250 (Mc250) genome was sequenced using the Illumina MiSeq platform, resulting in 5,867,947 paired-end reads, which were assembled into one circular contig. The Mc250 chromosome has 4,159,911 bp; its automatic annotation resulted in 3,719 protein coding genes, 26 pseudogenes, 57 tRNA sequences, three rRNA operons, four ncRNA genes, and no CRISPR array. No plasmid was identified.

Phylogenomics and pan-and core genome analysis
A Maximum Likelihood (ML) tree showed that Mc250 clusters within others genomes of the Alcaligenes genus, and particularly within one of the A. faecalis clades (Fig 1), hence confirming its classification. For pan-and core genome analysis purposes we compared Mc250 with thirty-six other Alcaligenes faecalis genomes available as of March, 2020 (Table 1). This analysis showed that the pan-genome has just under 11,000 genes, whereas the core genome has 1,459 genes, or about 39% of the complement of protein-coding genes in Mc250 (S1A Fig). The pan-genome curve is clearly ascending (S1B Fig). Both of these results show that there is substantial variation in gene content among known A. faecalis genomes. The Mc250 genome contains 250 specific genes with respect to the other genomes, at the 90% identity threshold (S1 Table).

Genome islands
When compared to 36 A. faecalis genomes (Table 1), a total of 14 genomic islands and two prophage regions were identified in Mc250 (Fig 2A). These regions have horizontal gene  these regions are located in areas where there is no alignment to other Af genomes (S2 Table  and Fig 2A), with a total of 155 genes found only in the Mc250 genome ( Fig 2B). A complete list of the genes found in these regions is presented in S2 Table.

Functional analysis of the Mc250 genome
We now present results of a functional analysis of the Mc250 genome. In these analyses we compared the Mc250 genome with the genomes of twelve other A. faecalis genomes (those that are complete and considered clade representatives based on the phylogeny we obtained (Fig 1)). The information associated with the locus tag and metabolic functions of the genes described in this section are present in the S3 Table.

Metabolism of phenolic compounds
In order to determine what Mc250 genes could help explain its survival capability in contact with the roots of Mimosa calodendrom, a comparative analysis of metabolic pathways involved in phenolic compound degradation was performed. Of the 3,719 protein-coding genes, 94 (2.5%) were categorized into 12 metabolic pathways associated with degradation of these compounds ( Fig 3A). We investigated the presence of the genes in these pathways in 12 other related genomes (Fig 3B and 3C). An integrative analysis of the relationship between these pathways was carried out (Fig 3D).

Resistance to antibiotics and heavy metals
The Mc250 genome has several genes associated with antibiotic resistance. Six genes associated with multidrug efflux pumps (cmeAB, tolC, mdr, macAB, oml and acrB) were identified, ranging from a single copy to six-copy paralogs (S2A Fig). Genes associated with resistance to fluoroquinolones (parCE and gyrAB) were also identified. A repertoire of genes associated with detoxification and metabolism of copper, arsenic, iron, cobalt, and zinc (S2B Fig) was found. The arsRBCH gene cluster, which encodes a transcript regulator, a transporter, and an arsenic resistance gene, respectively, involved arsenate detoxification [38], was identified in genomic island 10.

Iron acquisition and metabolism
We found 12 genes associated with siderophore biosynthesis. These genes are: ybdZ, and immediately downstream, entCEBA, followed by entS, the gene that encodes a siderophore carrier protein; fes, a gene encoding for enterobactin esterase; entF (synthesis component, serine activating enzyme); and the transport system of this compound to the medium (fepAGDCB) (S2B Fig). Eleven genes associated with iron acquisition were also found. Among them four copies of pitADC genes (two of which are complete and in tandem), which correspond respectively to subunits of iron-binding, ATP-binding, and permease proteins of an ABC transporter system. We also found the ABC transport system of ferrichrome/iron (III) dicitrate (fhu/fec), plus a gene for the receptor for hemin (hemR), two copies of the tonB gene, which codes for a periplasmic protein involved with transport of iron-chelated siderophores, a gene coding for a protein that utilizes heme groups (hutX), and two genes coding for paraquat-inducible proteins (parAB).

DNA and RNA metabolism
The Mc250 genome has 95 genes (2.5%) associated with DNA metabolism, of which 71 are involved with DNA repair. Among these, we highlight mutS, mutL, uvrA, uvrB, uvrC and dimeric uvrA, uvrD, a gene coding for photolyase, recA and recX, nine genes associated with the RecFOR pathway (recO, recR, recQ, recA, recA and four copies of ssb), nine genes associated with base excision repair, and two helicases (S3B Fig). As for RNA metabolism, 162 genes (4.3%) were annotated with this function, of which 24 are associated with transcription and 142 associated with RNA processing and modification. In this category, we mention nine genes associated with tRNA modification at position N34 as well as 31 genes associated with queuosine-archeosine biosynthesis, of which 21 are copies of genes coding for permease of drug/metabolite transporter (DMT).

Secondary metabolites production
Secondary metabolites produced by Mc250 were predicted by AntiSmash 3.0 [39] (S4 Table  and Fig 4). Among the 18 gene sets identified, 11 were characterized with Cf-putatives; one cluster associated with Bacillibactin synthesis; one cluster associated with synthesis of T1pks-Cf_saccharide involved with emulsan biosynthesis; one cluster associated with ectoine biosynthesis; one cluster associated with terpene synthesis; two clusters associated with O-antigen synthesis; and one cluster associated with polyhydroxyalkanoate biosynthesis.

Sulfur metabolism
In the Mc250 genome, 75 genes (2%) associated with sulfur metabolism were identified, of which 23 are associated with inorganic sulfur assimilation and 34 with assimilation and use of organic sulfur. Among these34 genes, we mention the genes associated with uptake and use of taurine and alkanesulphonates (S4A and S4B Fig). Integrative analysis of these pathways suggests that Mc250 exhibits high cysteine synthesis capability as a byproduct of the sulfur metabolism (S4B Fig). In addition to being used as a key amino acid for protein synthesis, it is possible that the cysteine surplus produced is used in the synthesis of molecules associated with protection against oxidative stress, as in the case of glutathione (S4C Fig).

Potassium homeostasis
The Mc250 genome codes for several genes related to the influx and efflux of potassium. We found genes coding for the ABC transporters of the Kdp system (kdpFACB) and their regulatory genes, coding for the sensory and regulatory proteins of this system (kdpED) (S4D Fig), all arranged in tandem. In addition, a copy of the kup (low-affinity potassium transport system) gene, two copies of the trkA gene (TrkA system potassium uptake protein) and two copies of the kefA (potassium efflux system KefA) gene were also found. Additionally, we found two copies of a gene coding for the glutathione-regulated potassium efflux system ATP binding protein (kefBC).

Secretion systems
No genes coding for proteins of the T3SS, T5SS, T7SS and T8SS secretory systems could be found. However, eleven genes associated with the T1SS were found (S3E Fig). We found two  Table. https://doi.org/10.1371/journal.pone.0241546.g004 copies of the genes encoding the lapBCD apparatus, with an additional copy of lapD, and four copies of the gene encoding RTX-like adhesins, one of which is located in tandem with one of the labBCD clusters. The Mc250 genome has eleven genes coding for the general secretion pathway of the T2SS (gspGHIJKLMNDEF) arranged in tandem. Fifteen T6SS genes were found, twelve of which were in tandem impABCDFGH-vasDJK-icmF-impM in addition to vgrG (sigma-54 dependent transcriptional regulator), clpB (chaperone protein), and vasH. Genes coding for the twin-arginine translocation (tat) system were also found.

Membrane proteins
In addition to the presence of four secretory systems, we identified 52 genes (1.4%) associated with ABC transporters: five genes associated with oligopeptide transport (opp genes), 37 genes associated with branched amino acid transport (livJHMGF) distributed in nine gene clusters, and 10 other genes associated with dipeptide transport (ddpABCDF). We also identified 56 genes (1.5%) associated with TRAP transports. We also found 17 genes associated with tricarboxylate transport, two adjacent copies of tctAB genes, ten copies of tctC, and two copies of tctD. Finally, we found two complete copies of the tonB-exbBD cluster, two tandem copies of exbBD, and a cluster formed by the trp-pal-tolBA-htaS. Regarding membrane proteins involved with metal transport, we found mgtC (Mg 2+ + transport ATPase type C), two copies of the mgtE (Mg/Co/Ni transport protein), three copies of the corC (Mg/Co efflux protein), and four copies of corA (Mg/Co transport protein), three of which are adjacent, and three copies of copA (copper effux protein); the products of these genes are associated with magnesium, cobalt, nickel, or copper transport.

Motility and chemotaxis
Genes associated with biosynthesis (45 genes) and regulation of flagellum activity (18) were found. Although no gene associated with fimbria synthesis was found, eleven genes associated with the tad locus were found, arranged in two clusters (Planet et al. refer to this gene set as the Widespread Colonization Island [40]) A single gene encoding the Flp pilus assembly protein was found.

FliC gene analysis
FliC has been described as an important Microbe-Associated Molecular Pattern (MAMP) protein [41], and when present in pathogenic organisms, it has also been described as a Pathogen-Associated Molecular Pattern (PAMP) protein, capable of modulating defense responses in animal and plant hosts [42,43]. In this context, FliC is directly associated with an intricate bacterial-host interaction system [44].
A multiple alignment of the sequence of fliC from Mc250 with similar sequences from other bacteria of the genus Alcaligenes retrieved from NCBI by a BLAST search showed a wide variation in the composition of residues located between positions 161 and 280 (Fig 5A). In contrast, the amino and carboxy terminal regions in this alignment have high similarity levels (98 and 100%, respectively). In addition, we observed that the length of the FliC proteins in this alignment (mean of 357 residues) was substantially shorter than the length of orthologs in other genera (mean of 490 residues). Multiple alignment of the Mc250 FliC sequence with sequences from orthologs in non-Alcaligenes bacteria revealed that the missing 133 residues constitute an isolated clade identified by dashed lines. Within this clade (see zoomed-in section to the right), Mc250 is in a subgroup together with A. aquatilis and another strain of A. faecalis. https://doi.org/10.1371/journal.pone.0241546.g005

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are located in a position immediately preceding the variable region described above. An analysis based on 3D models suggests that the flagellins in bacteria of the genus Alcaligenes do not have the secondary structure corresponding to secondary structures from β7 to α4, which corresponds to a partial loss of the D3 and D1 domains, and a total loss of the D2 domain ( Fig  5A). As D2 and D3 are domains present on the external face of the flagellum, after polymerization of FliC [45], it is possible that the thickness of the flagella in these bacteria is smaller, as previously described in other bacteria, such as Salmonella (Fig 5B-5E).
This result prompted us to investigate the evolutionary history of fliC. A fliC maximum likelihood tree (Fig 5F) shows Betaproteobacteria homologs clustered in at least five different clades, three of them including only Alcaligenaceae, and the other two having non-Alcaligenaceae genomes only. Four homolog copies belonging to the dipteran insect Lucilia cuprina were also found by PSI-Blast, spread in three different positions across the tree; all four belong to a WGS accession (NW_019410486.1) of Lucilia cuprina strain LS. Three homologs are located in scaffold 12 in the available Lucilia cuprina genome assembly (LOC111676276, LOC111676277, and LOC111676345), whereas the fourth copy is located in scaffold 1053 (LOC111686045).

Plant-Mc250 interactions
In the next sections, we present results related to metabolic pathways and physiological systems inferred from the genome of Mc250 that may play a role in bacteria-plant interactions.

Nitrogen metabolism
Twenty-eight genes were found related to nitrogen metabolism (Fig 6A). Of these, ten (nir-ECFDLGHJES) are associated with dissimilatory nitrite reductase pathway. In addition, we also found 13 genes associated with the ammonia assimilation pathway, including glnD (Protein PII uridyltransferase), glnE (glutamate-ammonia-ligaseadenyltransferase), a gene coding for glutamine synthase type I, a gene coding for a ferrodoxin-dependent glutamate synthase, three copies of a gene coding for nitrogen regulation protein NR (I), two copies of a gene coding for nitrogen regulatory protein P-II (one of which is adjacent to the gene coding for ammonia transporter), two copies of a gene coding for the large subunit of a glutamate synthase (NADPH) (one of which is adjacent to the gene coding for the small subunit). We also found genes coding for a nitrite-sensitive transcriptional repressor (nsrR), a protein involved in response to NO (nnrS), and a quinol-dependent nitric oxide reductase (qnoR). We also found two copies of the gene coding for nitrilase, one associated with plant-induced nitrilase (nit) and the other associated with a transcriptional regulator adjacent to a plant-induced nitrilase gene (reg). We found 26 genes related to nitrification, seven of which form the cluster nirXLYFDZR, plus nirV (nitrite reductase accessory protein), three copies of nirK (Coppercontaining nitrite reductase), qNor (Nitric-oxidase-dependent quinolone), nirS (cytochrome cd1 nitrite reductase), nnrS (involved in the response to NO), and dnr (Fig 6B).

Phosphorus metabolism
Thirty-two genes associated with phosphorus metabolism were identified. Of these, nine are associated with a high affinity system by this semimetal system, including the pstBACS genes ( Fig 6C). This system is regulated by phoBR genes, which encode for a dual regulatory component. In addition, we found the phoU gene, coding for a regulatory protein. Another 21 genes were categorized as being associated with polyphosphate metabolism, including ppx (exopolyphosphatase) and ppk (polyphosphate kinase). These two genes are adjacent to the pstBACS cluster.

Glycerol-3-phosphate and C4-Dicarboxylates uptake and metabolism
Glycerol-3-phosphate (G3P) and C4-dicarboxylates (C4-C) are produced by plants as infectious response signaling molecules [47]. The Mc250 genome has two clusters of the ugpABCE genes encoding the ABC transporter associated with G3P internalization. In addition, genes coding for enzymes encoding glycerophosphoryl diester phosphodiesterase (ugpD), glycerol kinase (glpK), and glycerol-3-phosphate dehydrogenase (glpZ) (two copies) were also found. Regarding the metabolism of C4-C, such as malate, oxaloacetate, and succinate, the Mc250 genome has an ABC transporter and genes that regulate the expression of this system (dctBD, sensor and regulator).

IAA, acetoin and butanediol biosynthesis
No genes capable of converting tryptophan to IAA were identified, but the four genes associated with conversion of anthranilate to tryptophan were identified ( Fig 6C). Likewise, no gene associated with HCN synthesis was found, although a carrier protein of this compound, cynX (cyanate transport protein), was identified. The adaptation of Mc250 in the presence of this compound may be related to the presence of nitrilases (described above in the section on nitrogen metabolism), which can detoxify this compound by providing ammonia to the plant. Finally, although genes coding for major and minor subunits of acetolactate synthase protein were found, the gene coding for acetolactate decarboxylase was not, which suggests that Mc250 may not be able to synthesize acetoin and 2,3-butanediol.

Niacin and choline transport and metabolism
Niacin and choline are byproducts of plant metabolism exuded by roots [48]. In the Mc250 genome we found seven genes associated with niacin and choline transport and metabolism: these are genes coding for choline dehydrogenase, betaine aldehyde dehydrogenase, highaffinity choline uptake protein (betT), niacin transporter (niaP), glycine betaine demethylase subunit (gbcA), nicotinamidase, and the alpha subunit of sarcosine oxidase (Fig 6C).

Mc250 nematicide and bactericide potential
We investigated the ability of Mc250 to act as a biocontrol agent of phytopathogenic nematodes and bacteria. When in contact with juvenile nematodes of the species Panagrellus redivivus and Pratylenchus brachyurus, AfMc50 was able to kill 100% and 95% of the individuals, respectively, after 24 hours of contact (Fig 7A). Mc250 was also able to massively inhibit these species' egg hatching after 24 hours of contact (Fig 7B). In addition, Mc250 was able to reduce the growth of Xanthomonas citri subsp. citri A306 in vitro ( Fig 7C) and in vivo when co-inoculated with A306 in Citrus plants (Fig 7D), decreasing canker lesions by about 60% (Fig 6E).

Discussion
The phylogenetic analyses of the Mc250 genome show that this strain belongs to the species Alcaligenes faecalis. The pan-core genome analysis also showed that there is large variation in gene content among the 37 A. faecalis genomes investigated; its "cloud genome" (S1A

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corresponds to more than half of the pan-genome. These results suggest that novel strains of A. faecalis, such as Mc250, can be an important source of new knowledge for the genomics of this versatile species.
We have investigated the metabolic capabilities of Mc250 in detail. Our analyses allowed us to infer that Mc250 is highly adapted to the extreme conditions imposed by the environment in which it was isolated, the ferruginous rock fields in the Iron Quadrangle, as well as to its plant host (Fig 8).
Mc250 has a complex network of pathways associated with the degradation of phenolic compounds. These pathways are interrelated in an intricate adaptive network (Fig 3D). Because virtually all pathways culminate in the synthesis of pyruvate, acetyl-coA or succinyl-coA, intermediates of the glycolytic pathway and TCA, we hypothesize that Mc250 can use, as an alternative source of carbon, various phenolic compounds present in the soil or produced by plants, which generate these as a defense against pathogens. This means that Mc250 is wellsuited to survive in contact with plants, even in the presence of these toxic compounds. In addition, Mc250 apparently can metabolize distinctive carbohydrates, many from plant origin, using a repertoire of genes associated with the acquisition and metabolism of C4-dicarboxylates (malate, succinate, fumarate, succinate), which can be used as alternative carbon source. These compounds have been reported as present in root exudates [49] and may also be associated with chemotactic events in the process of attraction of bacteria associated with plants [50]. Thus, it is possible that the Iron Quadrangle plants can secrete these compounds as a way to attract not only Mc250 but other potential PGPB as an additional adaptation resource in a soil with highly restrictive characteristics to most plants.
Despite this ability to use these plant metabolites, we found that Mc250 possesses all genes of the propanediol pathway, even though it lacks the biosynthesis pathways of IAA, acetoin and butanediol. Mc250 has all genes necessary for complete nitrogen metabolism, which is evidence that Mc250 possesses the ability to act as a denitrifying organism. Although no ability to solubilize phosphate has been identified due to the absence of important genes in this pathway, Mc250 has the potential to internalize G3P produced by the plant through a specialized ABC transporter, based on results that have been reported for Escherichia coli [51]. Although G3Pinput-mediated phosphate acquisition may be a secondary mechanism of phosphate acquisition, Mc250 has the high-affinity Pst system (described in Burkholderia multivorans [52]), and therefore both systems could together provide the bacterium with phosphate, a fundamental component of cellular metabolism. The existence of two such systems in the genome might be explained by the fact that phosphate concentration in the soils of Brazilian rupestrian fields is extremely low [53,54].
The presence of two copies of the apparatus coding for the T1SS, four copies of genes encoding RTX-like adhesins, two gene clusters associated with widespread colonization island, and the presence of a complete T2SS coded by Gsp Proteins, may be associated with broad aggregation capacity and biofilm formation [40,55,56], which could provide protection for Mc250 against other organisms present in the environment, facilitating plant tissue colonization [57]. At the same time, a repertoire of genes associated with metabolism of metals such as zinc, cadmium, copper, and iron, coupled with the proven ability to remove arsenic from the medium [19], provide strong evidence of the tolerance and ability of Mc250 as a bioremediator. This ability of Mc250 could reduce the bioavailability of these metals to plant tissues, even if these plants can bioaccumulate these compounds [58].
In addition to the biotechnological potential to resist and remove pollutants, we have shown that Mc250 is also capable to inhibit important plant pathogens. The culture supernatant of Mc250 was shown to have a nematicide effect, killing up to 100% of the nematodes after 48 hours of immersion in bacterial supernatant. The nematodes of the genus Pratylenchus, also known as nematodes of root lesions, are recognized worldwide as one of the most serious problems in crops of great economic importance, such as soybean, cotton, corn, coffee, and forage [59]. In Brazil, P. brachyurus causes widespread damages, with significant economic losses in several crops and in various regions of the country [60]. Mc250 was also able to inhibit the growth of Xanthomonas citri subsp. citri A306 both in vitro when co-inoculated with this pathogen in leaves of Citrus sinensis. The strain A306 is a causative agent of citrus canker in a wide diversity of citrus hosts, resulting in large losses in the production of fruits and orange juice [61]. Therefore, the ability to tolerate and remove metals [19], to act as a nematicide and bactericide in association with the ability to metabolize phenolic compounds produced by plants suggests that A. faecalis strain Mc250 can be explored as an important bioinoculant of agricultural interest.