Comparative Genomic Analysis Reveals Habitat-Specific Genes and Regulatory Hubs within the Genus Novosphingobium

ABSTRACT This study highlights the significant role of the genetic repertoire of a microorganism in the similarity between Novosphingobium strains. The results suggest that the phylogenetic relationships were mostly influenced by metabolic trait enrichment, which is possibly governed by the microenvironment of each microbe’s respective niche. Using core genome analysis, the enrichment of a certain set of genes specific to a particular habitat was determined, which provided insights on the influence of habitat on the distribution of metabolic traits for Novosphingobium strains. We also identified habitat-specific protein hubs, which suggested delineation of Novosphingobium strains based on their habitat. Examining the available genomes of ecologically diverse bacterial species and analyzing the habitat-specific genes are useful for understanding the distribution and evolution of functional and phylogenetic diversity in the genus Novosphingobium. Species belonging to the genus Novosphingobium are found in many different habitats and have been identified as metabolically versatile. Through comparative genomic analysis, we identified habitat-specific genes and regulatory hubs that could determine habitat selection for Novosphingobium spp. Genomes from 27 Novosphingobium strains isolated from diverse habitats such as rhizosphere soil, plant surfaces, heavily contaminated soils, and marine and freshwater environments were analyzed. Genome size and coding potential were widely variable, differing significantly between habitats. Phylogenetic relationships between strains were less likely to describe functional genotype similarity than the habitat from which they were isolated. In this study, strains (19 out of 27) with a recorded habitat of isolation, and at least 3 representative strains per habitat, comprised four ecological groups—rhizosphere, contaminated soil, marine, and freshwater. Sulfur acquisition and metabolism were the only core genomic traits to differ significantly in proportion between these ecological groups; for example, alkane sulfonate (ssuABCD) assimilation was found exclusively in all of the rhizospheric isolates. When we examined osmolytic regulation in Novosphingobium spp. through ectoine biosynthesis, which was assumed to be marine habitat specific, we found that it was also present in isolates from contaminated soil, suggesting its relevance beyond the marine system. Novosphingobium strains were also found to harbor a wide variety of mono- and dioxygenases, responsible for the metabolism of several aromatic compounds, suggesting their potential to act as degraders of a variety of xenobiotic compounds. Protein-protein interaction analysis revealed β-barrel outer membrane proteins as habitat-specific hubs in each of the four habitats—freshwater (Saro_1868), marine water (PP1Y_AT17644), rhizosphere (PMI02_00367), and soil (V474_17210). These outer membrane proteins could play a key role in habitat demarcation and extend our understanding of the metabolic versatility of the Novosphingobium species. IMPORTANCE This study highlights the significant role of a microorganism’s genetic repertoire in structuring the similarity between Novosphingobium strains. The results suggest that the phylogenetic relationships were mostly influenced by metabolic trait enrichment, which is possibly governed by the microenvironment of each microbe’s respective niche. Using core genome analysis, the enrichment of a certain set of genes specific to a particular habitat was determined, which provided insights on the influence of habitat on the distribution of metabolic traits in Novosphingobium strains. We also identified habitat-specific protein hubs, which suggested delineation of Novosphingobium strains based on their habitat. Examining the available genomes of ecologically diverse bacterial species and analyzing the habitat-specific genes are useful for understanding the distribution and evolution of functional and phylogenetic diversity in the genus Novosphingobium.

Download Full-text

Comparative genomics of the black rot pathogen Xanthomonas campestris pv. campestris and non-pathogenic co-inhabitant Xanthomonas melonis from Trinidad reveal unique pathogenicity determinants and secretion system profiles

PeerJ ◽

10.7717/peerj.12632 ◽

2022 ◽

Vol 9 ◽

pp. e12632

Author(s):

Stephen D. B. Jr. Ramnarine ◽

Jayaraj Jayaraman ◽

Adesh Ramsubhag

Keyword(s):

Xanthomonas Campestris ◽

Bacterial Species ◽

Genomic Analysis ◽

Gene Clusters ◽

Caribbean Region ◽

Future Research ◽

Comparative Genomic ◽

Black Rot ◽

Cell Wall Degrading Enzymes

Black-rot disease caused by the phytopathogen Xanthomonas campestris pv. campestris (Xcc) continues to have considerable impacts on the productivity of cruciferous crops in Trinidad and Tobago and the wider Caribbean region. While the widespread occurrence of resistance of Xcc against bactericidal agrochemicals can contribute to the high disease burdens, the role of virulence and pathogenicity features of local strains on disease prevalence and severity has not been investigated yet. In the present study, a comparative genomic analysis was performed on 6 pathogenic Xcc and 4 co-isolated non-pathogenic Xanthomonas melonis (Xmel) strains from diseased crucifer plants grown in fields with heavy chemical use in Trinidad. Native isolates were grouped into two known and four newly assigned ribosomal sequence types (rST). Mobile genetic elements were identified which belonged to the IS3, IS5 family, Tn3 transposon, resolvases, and tra T4SS gene clusters. Additionally, exogenous plasmid derived sequences with origins from other bacterial species were characterised. Although several instances of genomic rearrangements were observed, native Xcc and Xmel isolates shared a significant level of structural homology with reference genomes, Xcc ATCC 33913 and Xmel CFBP4644, respectively. Complete T1SS hlyDB, T2SS, T4SS vir and T5SS xadA, yapH and estA gene clusters were identified in both species. Only Xmel strains contained a complete T6SS but no T3SS. Both species contained a complex repertoire of extracellular cell wall degrading enzymes. Native Xcc strains contained 37 T3SS and effector genes but a variable and unique profile of 8 avr, 4 xop and 1 hpa genes. Interestingly, Xmel strains contained several T3SS effectors with low similarity to references including avrXccA1 (~89%), hrpG (~73%), hrpX (~90%) and xopAZ (~87%). Furthermore, only Xmel genomes contained a CRISPR-Cas I-F array, but no lipopolysaccharide wxc gene cluster. Xmel strains were confirmed to be non-pathogenic by pathogenicity assays. The results of this study will be useful to guide future research into virulence mechanisms, agrochemical resistance, pathogenomics and the potential role of the co-isolated non-pathogenic Xanthomonas strains on Xcc infections.

Download Full-text

First Steps in the Analysis of Prokaryotic Pan-Genomes

Bioinformatics and Biology Insights ◽

10.1177/1177932220938064 ◽

2020 ◽

Vol 14 ◽

pp. 117793222093806

Author(s):

Sávio Souza Costa ◽

Luís Carlos Guimarães ◽

Artur Silva ◽

Siomar Castro Soares ◽

Rafael Azevedo Baraúna

Keyword(s):

Genome Analysis ◽

Core Genome ◽

Bacterial Species ◽

Genomic Analysis ◽

Gene Families ◽

Specific Group ◽

The Core ◽

Pan Genome ◽

Research Areas ◽

Key Concepts

Pan-genome is defined as the set of orthologous and unique genes of a specific group of organisms. The pan-genome is composed by the core genome, accessory genome, and species- or strain-specific genes. The pan-genome is considered open or closed based on the alpha value of the Heap law. In an open pan-genome, the number of gene families will continuously increase with the addition of new genomes to the analysis, while in a closed pan-genome, the number of gene families will not increase considerably. The first step of a pan-genome analysis is the homogenization of genome annotation. The same software should be used to annotate genomes, such as GeneMark or RAST. Subsequently, several software are used to calculate the pan-genome such as BPGA, GET_HOMOLOGUES, PGAP, among others. This review presents all these initial steps for those who want to perform a pan-genome analysis, explaining key concepts of the area. Furthermore, we present the pan-genomic analysis of 9 bacterial species. These are the species with the highest number of genomes deposited in GenBank. We also show the influence of the identity and coverage parameters on the prediction of orthologous and paralogous genes. Finally, we cite the perspectives of several research areas where pan-genome analysis can be used to answer important issues.

Download Full-text

Role of Hypermutability in the Evolution of the Genus Oenococcus

Journal of Bacteriology ◽

10.1128/jb.01457-07 ◽

2007 ◽

Vol 190 (2) ◽

pp. 564-570 ◽

Cited By ~ 53

Author(s):

Angela M. Marcobal ◽

David A. Sela ◽

Yuri I. Wolf ◽

Kira S. Makarova ◽

David A. Mills

Keyword(s):

Lactic Acid ◽

Leuconostoc Mesenteroides ◽

Genomic Analysis ◽

Oenococcus Oeni ◽

Mutation Rates ◽

Comparative Genomic ◽

Allelic Polymorphism ◽

Resistant Strains ◽

High Level

ABSTRACT Oenococcus oeni is an alcohol-tolerant, acidophilic lactic acid bacterium primarily responsible for malolactic fermentation in wine. A recent comparative genomic analysis of O. oeni PSU-1 with other sequenced lactic acid bacteria indicates that PSU-1 lacks the mismatch repair (MMR) genes mutS and mutL. Consistent with the lack of MMR, mutation rates for O. oeni PSU-1 and a second oenococcal species, O. kitaharae, were higher than those observed for neighboring taxa, Pediococcus pentosaceus and Leuconostoc mesenteroides. Sequence analysis of the rpoB mutations in rifampin-resistant strains from both oenococcal species revealed a high percentage of transition mutations, a result indicative of the lack of MMR. An analysis of common alleles in the two sequenced O. oeni strains, PSU-1 and BAA-1163, also revealed a significantly higher level of transition substitutions than were observed in other Lactobacillales species. These results suggest that the genus Oenococcus is hypermutable due to the loss of mutS and mutL, which occurred with the divergence away from the neighboring Leuconostoc branch. The hypermutable status of the genus Oenococcus explains the observed high level of allelic polymorphism among known O. oeni isolates and likely contributed to the unique adaptation of this genus to acidic and alcoholic environments.

Download Full-text

Comparative Genomic Analysis of Meningitis- and Bacteremia-Causing Pneumococci Identifies a Common Core Genome

Infection and Immunity ◽

10.1128/iai.00814-15 ◽

2015 ◽

Vol 83 (10) ◽

pp. 4165-4173 ◽

Cited By ~ 15

Author(s):

Benard W. Kulohoma ◽

Jennifer E. Cornick ◽

Chrispin Chaguza ◽

Feyruz Yalcin ◽

Simon R. Harris ◽

...

Keyword(s):

Bloodstream Infection ◽

Common Core ◽

Core Genome ◽

Genomic Analysis ◽

Evolutionary Genetics ◽

Comparative Genomic ◽

Accessory Gene ◽

Content Type ◽

Double Exponential ◽

Considerable Pressure

Streptococcus pneumoniaeis a nasopharyngeal commensal that occasionally invades normally sterile sites to cause bloodstream infection and meningitis. Although the pneumococcal population structure and evolutionary genetics are well defined, it is not clear whether pneumococci that cause meningitis are genetically distinct from those that do not. Here, we used whole-genome sequencing of 140 isolates ofS. pneumoniaerecovered from bloodstream infection (n= 70) and meningitis (n= 70) to compare their genetic contents. By fitting a double-exponential decaying-function model, we show that these isolates share a core of 1,427 genes (95% confidence interval [CI], 1,425 to 1,435 genes) and that there is no difference in the core genome or accessory gene content from these disease manifestations. Gene presence/absence alone therefore does not explain the virulence behavior of pneumococci that reach the meninges. Our analysis, however, supports the requirement of a range of previously described virulence factors and vaccine candidates for both meningitis- and bacteremia-causing pneumococci. This high-resolution view suggests that, despite considerable competency for genetic exchange, all pneumococci are under considerable pressure to retain key components advantageous for colonization and transmission and that these components are essential for access to and survival in sterile sites.

Download Full-text

Identification of a Candidate Streptococcus pneumoniae Core Genome and Regions of Diversity Correlated with Invasive Pneumococcal Disease

Infection and Immunity ◽

10.1128/iai.00316-06 ◽

2006 ◽

Vol 74 (8) ◽

pp. 4766-4777 ◽

Cited By ~ 119

Author(s):

Caroline Obert ◽

Jack Sublett ◽

Deepak Kaushal ◽

Ernesto Hinojosa ◽

Theresa Barton ◽

...

Keyword(s):

Streptococcus Pneumoniae ◽

Invasive Pneumococcal Disease ◽

Pneumococcal Disease ◽

Core Genome ◽

Genomic Analysis ◽

Community Acquired Pneumonia ◽

Comparative Genomic ◽

Virulence Determinants ◽

Wild Type

ABSTRACT Streptococcus pneumoniae is a leading cause of community-acquired pneumonia and gram-positive sepsis. While multiple virulence determinants have been identified, the combination of features that determines the propensity of an isolate to cause invasive pneumococcal disease (IPD) remains unknown. In this study, we determined the genetic composition of 42 invasive and 30 noninvasive clinical isolates of serotypes 6A, 6B, and 14 by comparative genomic hybridization. Comparison of the present/absent gene matrix (i.e., comparative genomic analysis [CGA]) identified a candidate core genome consisting of 1,553 genes (73% of the TIGR4 genome), 154 genes whose presence correlated with the ability to cause IPD, and 176 genes whose presence correlated with the noninvasive phenotype. Genes identified by CGA were cross-referenced with the published signature-tagged mutagenesis studies, which served to identify core and IPD-correlated genes required for in vivo passage. Among these, two pathogenicity islands, region of diversity 8a (RD8a), which encodes a neuraminidase and V-type sodium synthase, and RD10, which encodes PsrP, a protein homologous to the platelet adhesin GspB in Streptococcus gordonii, were identified. Mice infected with a PsrP mutant were delayed in the development of bacteremia and demonstrated reduced mortality versus wild-type-infected controls. Finally, the presence of seven RDs was determined to correlate with the noninvasive phenotype, a finding that suggests some RDs may contribute to asymptomatic colonization. In conclusion, RDs are unequally distributed between invasive and noninvasive isolates, RD8a and RD10 are correlated with the propensity of an isolate to cause IPD, and PsrP is required for full virulence in mice.

Download Full-text

Interaction of two strongly divergent archaellins stabilizes the structure of the Halorubrum archaellum

10.1101/836379 ◽

2019 ◽

Author(s):

Mikhail G. Pyatibratov ◽

Alexey S. Syutkin ◽

Tessa E.F. Quax ◽

Tatjana N. Melnik ◽

R. Thane Papke ◽

...

Keyword(s):

Thermal Stability ◽

Genomic Analysis ◽

Halophilic Archaea ◽

Amino Acid Sequences ◽

Comparative Genomic ◽

Low Salinity ◽

Additional Stabilization ◽

External Conditions ◽

Thermal Stability Of

SUMMARYThe archaellum is a unique motility structure that has only functional similarity to its bacterial counterpart, the flagellum. Archaellar filaments consist of thousands of copies of the protein protomer archaellin. Most euryarchaeal genomes encode multiple homologous archaellins. The role of these multiple archaellin genes remains unclear. Halophilic archaea from the genus Halorubrum possess two archaellin genes, flaB1 and flaB2. Amino acid sequences of the corresponding protein products are extraordinarily diverged (identity of ∼ 40%). To clarify roles for each archaellin, we compared archaella from two natural Halorubrum lacusprofundi strains: the DL18 strain, which possesses both archaellin genes, and the type strain ACAM 34 whose genome contains the flaB2 gene only. Both strains synthesize functional archaella; however, the DL18 strain, where both archaellins are present in comparable amounts, is more motile. In addition, we expressed these different Hrr. lacusprofundi archaellins in a Haloferax volcanii strain from which the endogenous archaellin genes were deleted. Three Hfx. volcanii strains expressing Hrr. lacusprofundi archaellins flaB1, flaB2 or flaB1-flaB2 produced archaellum filaments consisting of only one (FlaB1 or FlaB2) or both (FlaB1/B2) archaellins. All three recombinant Hfx. volcanii strains were motile, although there were profound differences in the efficiency of motility. The recombinant filaments resemble the natural filaments of Hrr. lacusprofundi. Electron microscopy showed that FlaB1 FlaB2-archaella look like typical supercoiled filaments, while with the shape of the FlaB1- and FlaB2-archaella is more variable. Both native and recombinant FlaB1 FlaB2-filaments have greater thermal stability and are more resistant to low salinity stress than single-component filaments. This shows that thermal stability of archaellins depends on the presence of both archaellin types, indicating a close interaction between these subunits in the supramolecular structure. Functional helical Hrr. lacusprofundi archaella can be composed of either single archaellin: FlaB2 or FlaB1; however, the two divergent archaellin subunits in combination provide additional stabilization to the archaellum structure and thus adaptation to a wider range of external conditions. A comparative genomic analysis of archaellins suggests that the described combination of divergent archaellins is not restricted to Hrr. lacusprofundi, but is occurring also in organisms from other haloarchaeal genera.

Download Full-text

Enhanced copper-resistance gene repertoire in Alteromonas macleodii strains isolated from copper-treated marine coatings

PLoS ONE ◽

10.1371/journal.pone.0257800 ◽

2021 ◽

Vol 16 (9) ◽

pp. e0257800

Author(s):

Kathleen Cusick ◽

Ane Iturbide ◽

Pratima Gautam ◽

Amelia Price ◽

Shawn Polson ◽

...

Keyword(s):

Pseudomonas Syringae ◽

Markov Models ◽

Bacterial Species ◽

Genomic Analysis ◽

Copper Resistance ◽

Comparative Genomic ◽

Gene Repertoire ◽

Ship Hulls ◽

Multiple Copies ◽

Alteromonas Macleodii

Copper is prevalent in coastal ecosystems due to its use as an algaecide and as an anti-fouling agent on ship hulls. Alteromonas spp. have previously been shown to be some of the early colonizers of copper-based anti-fouling paint but little is known about the mechanisms they use to overcome this initial copper challenge. The main models of copper resistance include the Escherichia coli chromosome-based Cue and Cus systems; the plasmid-based E. coli Pco system; and the plasmid-based Pseudomonas syringae Cop system. These were all elucidated from strains isolated from copper-rich environments of agricultural and/or enteric origin. In this work, copper resistance assays demonstrated the ability of Alteromonas macleodii strains CUKW and KCC02 to grow at levels lethal to other marine bacterial species. A custom database of Hidden Markov Models was designed based on proteins from the Cue, Cus, and Cop/Pco systems and used to identify potential copper resistance genes in CUKW and KCC02. Comparative genomic analyses with marine bacterial species and bacterial species isolated from copper-rich environments demonstrated that CUKW and KCC02 possess genetic elements of all systems, oftentimes with multiple copies, distributed throughout the chromosome and mega-plasmids. In particular, two copies of copA (the key player in cytoplasmic detoxification), each with its own apparent MerR-like transcriptional regulator, occur on a mega-plasmid, along with multiple copies of Pco homologs. Genes from both systems were induced upon exposure to elevated copper levels (100 μM– 3 mM). Genomic analysis identified one of the merR-copA clusters occurs on a genomic island (GI) within the plasmid, and comparative genomic analysis found that either of the merR-copA clusters, which also includes genes coding for a cupredoxin domain-containing protein and an isoprenylcysteine methyltransferase, occurs on a GI across diverse bacterial species. These genomic findings combined with the ability of CUKW and KCC02 to grow in copper-challenged conditions are couched within the context of the genome flexibility of the Alteromonas genus.

Download Full-text

Taxonomic scheme of the order Chaetophorales (Chlorophyceae, Chlorophyta) based on Chloroplast genomes

10.21203/rs.2.21773/v1 ◽

2020 ◽

Author(s):

Benwen Liu ◽

Yu Xin Hu ◽

Zheng Yu Hu ◽

Guo Xiang Liu ◽

Huan Zhu

Keyword(s):

Phylogenetic Analysis ◽

Chloroplast Genome ◽

Phylogenetic Relationships ◽

Phylogenetic Analyses ◽

Genome Structure ◽

Genomic Analysis ◽

Comparative Genomic ◽

Rdna Sequences ◽

Chloroplast Genomes ◽

Basal Clade

Abstract Background Order Chaetophorales currently includes six families, namely Schizomeridaceae, Aphanochaetaceae, Barrancaceae, Uronemataceae, Fritschiellaceae, and Chaetophoraceae. Most studies have primarily focused on intergeneric phylogenetic relationships within this order and the phylogenetic relationships with four other Chlorophycean orders (Chaetophorales, Chaetopeltidales and Oedogoniales, and Volvocales). This study aimed to phylogenetically reconstruct order Chaetophorales and determine the taxonomic scheme and to further the current understanding of the evolution of order Chaetophorales. The taxonomic scheme of Chaetophorales has been inferred primarily through phylogenetic analysis based on rDNA sequences and phylogenetic relationships among families in order Chaetophorales remain unclear. Results In present study, seven complete and five fragmentary chloroplast genomes were harvested. Phylogenomic and comparative genomic analysis were performed to determine the taxonomic scheme within Chaetophorales. Consequently, Oedogoniales was found to be a sister to a clade linking Chaetophorales and Chaetopeltidales, Schizomeriaceae, and Aphanochaetaceae clustered into a well-resolved basal clade in Chaetophorales, inconsistent with the results of phylogenetic analysis based on rDNA sequences. Comparative genomic analyses revealed that the chloroplast genomes of Schizomeriaceae and Aphanochaetaceae were highly conserved and homologous, highlighting the closest relationship in this order. Germination types of zoospores precisely correlated with the phylogenetic relationships. Conclusions In conclusion, chloroplast genome structure analyses, synteny analyses, and zoospore germination analyses were concurrent with phylogenetic analyses based on the chloroplast genome, and all of them robustly determined the unique taxonomic scheme of Chaetophorales and the relationships of Oedogoniales, Chaetophorales, and Chaetopeltidales.

Download Full-text

Global genomic similarity and core genome sequence diversity of the Streptococcus genus as a toolkit to identify closely related bacterial species in complex environments

PeerJ ◽

10.7717/peerj.6233 ◽

2019 ◽

Vol 6 ◽

pp. e6233 ◽

Cited By ~ 4

Author(s):

Hugo R. Barajas ◽

Miguel F. Romero ◽

Shamayim Martínez-Sánchez ◽

Luis D. Alcaraz

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Core Genome ◽

Bacterial Species ◽

Genomic Diversity ◽

Comparative Genomic ◽

Rrna Gene ◽

Gene Phylogeny ◽

The Core ◽

Core Proteins

Background The Streptococcus genus is relevant to both public health and food safety because of its ability to cause pathogenic infections. It is well-represented (>100 genomes) in publicly available databases. Streptococci are ubiquitous, with multiple sources of isolation, from human pathogens to dairy products. The Streptococcus genus has traditionally been classified by morphology, serum types, the 16S ribosomal RNA (rRNA) gene, and multi-locus sequence types subject to in-depth comparative genomic analysis. Methods Core and pan-genomes described the genomic diversity of 108 strains belonging to 16 Streptococcus species. The core genome nucleotide diversity was calculated and compared to phylogenomic distances within the genus Streptococcus. The core genome was also used as a resource to recruit metagenomic fragment reads from streptococci dominated environments. A conventional 16S rRNA gene phylogeny reconstruction was used as a reference to compare the resulting dendrograms of average nucleotide identity (ANI) and genome similarity score (GSS) dendrograms. Results The core genome, in this work, consists of 404 proteins that are shared by all 108 Streptococcus. The average identity of the pairwise compared core proteins decreases proportionally to GSS lower scores, across species. The GSS dendrogram recovers most of the clades in the 16S rRNA gene phylogeny while distinguishing between 16S polytomies (unresolved nodes). The GSS is a distance metric that can reflect evolutionary history comparing orthologous proteins. Additionally, GSS resulted in the most useful metric for genus and species comparisons, where ANI metrics failed due to false positives when comparing different species. Discussion Understanding of genomic variability and species relatedness is the goal of tools like GSS, which makes use of the maximum pairwise shared orthologous sequences for its calculation. It allows for long evolutionary distances (above species) to be included because of the use of amino acid alignment scores, rather than nucleotides, and normalizing by positive matches. Newly sequenced species and strains could be easily placed into GSS dendrograms to infer overall genomic relatedness. The GSS is not restricted to ubiquitous conservancy of gene features; thus, it reflects the mosaic-structure and dynamism of gene acquisition and loss in bacterial genomes.

Download Full-text

Comparative genomics: Dominant coral-bacterium Endozoicomonas acroporae metabolizes dimethylsulfoniopropionate (DMSP)

10.1101/519546 ◽

2019 ◽

Author(s):

Kshitij Tandon ◽

Pei-Wen Chiang ◽

Chih-Ying Lu ◽

Naohisa Wada ◽

Shan-Hua Yang ◽

...

Keyword(s):

Sole Carbon Source ◽

Genomic Analysis ◽

Sulfur Cycle ◽

Comparative Genomic Analysis ◽

Comparative Genomic ◽

High Quality ◽

Coa Transferase ◽

Complete Genomes ◽

Central Carbon

AbstractDominant coral-associated Endozoicomonas bacteria species are hypothesized to play a role in the coral-sulfur cycle by metabolizing Dimethylsulfoniopropionate (DMSP) into Dimethylsulfide (DMS); however, no sequenced genome to date harbors genes for this process. In this study, we assembled high-quality (>95% complete) genomes of strains of a recently added species Endozoicomonas acroporae (Acr-14T, Acr-1 and Acr-5) isolated from the coral Acropora muricata and performed comparative genomic analysis on genus Endozoicomonas. We identified the first DMSP CoA-transferase/lyase—a dddD gene homolog found in all E. acroporae strains—and functionally characterized bacteria capable of metabolizing DMSP into DMS via the DddD cleavage pathway using RT-qPCR and gas chromatography (GC). Furthermore, we demonstrated that E. acroporae strains can use DMSP as the sole carbon source and have genes arranged in an operon-like manner to link DMSP metabolism to the central carbon cycle. This study confirms the role of Endozoicomonas in the coral sulfur cycle.

Download Full-text