The Genomic Characteristics And Evolution Of Marine Aerobic Anoxygenic Photoheterotrophic Bacteria

Aerobic anoxygenic photoheterotrophic bacteria(AAPB)are the third most abundant phototrophic prokaryote in the ocean,aside from cyanobacteria and proteorhodopsincontaining bacteria.They are widely distributed in various aquatic environments and represent an important group in the microorganism community in the sunlit ocean.AAPB not only make a great contribution to carbon and energy cycles in the ocean,but they also play an important role in the evolution of phototrophic bacteria.AAPB are thought to be a transmit state between anaerobic autophototrophs and aerobic heterotrophs.AAPB harbour photosynthetic gene clusters(PGCs)that contain almost all the photosynthetic genes.Previous studies have shown the independent evolution of PGCs in different AAPB groups and the horizontal gene transfer(HGT)of PGCs between bacteria.Works on characteristics of AAPB genomes,especially their PGCs,are essential to elucidate their evolution.However,those studies are limited to date.In this thesis,we isolated a great number of AAPB strains based on the highthroughput screening system and sequenced 16 genomes of the AAPB strains.Then,we compared Citromoicrobial genomes and analyzed extrachromosomal replicons(ECRs)that carrying PGCs within the Rosebacter clade.Finally,69 AAPB genomes were collected from the database for comprehensive analysis.These studies aim to improve our understanding of genomic characteristics and evolutiona of AAPB.The main progress is as follows:1.High-throughput isolation of AAPB strains.Based on the infra-red screen system,we isolated 84 AAPB Alphaproteobacterial strains from various environments using different mediums.They belonged to 25 genera from four families(Phyllobacteriaceae,Rhodobacteraceae,Erythrobacteraceae,and Sphingomonadaceae),and AAPB members were firstly discovered in 11 of the 25 genera.This work contributed to the AAPB culture collection and our knowledge of AAPB diversity.16 of the 84 AAPB strains have been sequenced for studying their phylogenies and genomic characteristics.The 16 AAPB strains were classified into Alpha-?,Alpha-?,and Alpha-? clusters.Five forms of photosynthetic genes oraganization and two types of the conversed region arrangement were found in the 16 strains.Additionally,PGCs were divided into two or three fragments in the three strains Panimaribius sp.G8,Thalassobius sp.WXO12,and Porphyrobacter sp.YT40.These fragments were conserved,which might be basic units in the process of the PGC recombination.Two strains Tateyamaria sp.Syn59 and Shimia sp.WX04 contained PGCs that carried by extrachromosomal replicons(exPGCs).2.Genomic comparison of Citromicrobial AAPB species.Nine AAPB srains with identical 16S rRNA sequences were isolated from three regions(the South China Sea,the Mediterranean Sea,and the South Atlantic Ocean).The major regions of the nine citromocribial sequences exihibited highly conserved.By comparative genomics analysis,we found nine genetic islands(GIs)that played an essential role in the evolution and divergence of Ciromicrobium strains.These GIs were regarded as originating from HGT,including type ? secretion systems,prophage,flagellar biosynthesis,and integrative conjugative elements.Single-nucleotide polymorphisms(SNP)and genomic average nucleotide identity(ANI)analysis revealed that three RCC strains(RCC1878,RCC1897,and RCC1885)that isolated from the Mediterranean Sea diverged millions of years ago from other strains and have evolved into a novel group.Our results showed that geographical distribution could impact on genomic divergence and local adaptation.Additionally,we confirmed that the coexistence of two different PGCs in Ciromicrobal AAPB strains was prevalent in environmental samples for the first time.The prevalence of the coexistence of two different PGCs might be related to adaptation mechanism for the Ciromicrobal AAPB group in the ocean.This study sheded new light on the genomic evolution and divergence of geographic isolation in Citromicrobal members.The characteristics and evolution of exPGCs in the Roseobacter clade.In addition to bacterial chromosomes,extrachromosomal replicons(ECRs)were found to carry PGCs in the Roseobacter clade.In our study,13 Roseobacter clade members carrying exPGCs were analyzed for their genomes.They belonged to seven genera and were scattered distributed in the 16S rRNA gene phylogeny.The PGC phylogeny revealed that the 13 strains had two origins,corresponding to their two different photosynthetic reaction puf operon organizations(pufXMLABQ and pufCMLABQ).Interestingly,two different puf operon organizations were found to coexist in the same and Jannaschia genera but different strains.Precisely,they were carried by chromosomes and ECRs in the strains,respectively,which provided a clear evidence for the ECRmediated PGC transfer.Based on the codon usage frequency,ECRs that carried PGCs were classified into two types,the plasmid-like and chromid-like ECRs.The plasmidlike ECRs were mainly responsible for the PGC transfer and spread,while chromidlike ECRs were more stable in cells and performed photosynthesis.Three Jannshcia strains(J.faecimaris DSM1004020,J.pohangensis DSM19073,and J.donghaensis CECT 7802)harboured exPGCs whose structures were similar to that of chromosomal PGCs.The PGCs of the three Jannashcia members might represent an initial stage where PGCs transferred from chromosomes into ECRs.Finally,a scenario of the transfer of PGCs mediated by ECRs could explain the scattered distribution of AAPB within the Roseobacter clade.3.The genomic characteristics of different phylogenetic AAPB groups.69 whole genome-sequenced AAPB strains belong to the Alphaproteobacteria(Alpha-?,Alpha-?,Alpha-?,Alpha-?,and Alpha-?),Betaproteobacteria,and Gammaproteobacteria.The novel AAPB group was discovered in the Alpha-? cluster.The PGCs phylogeny showed that the HGT of the PGCs happened in the three Alphaprteobacterial strains Stakelama sp.CH028,Erythrobacter sp.AP23,and Acidisphaera rubrifaciens HP-AP.Moreover,the PGC of Acidisphaera rubrifaciens HP-AP was originated from those of the species belonging to the Betaproteobacteria of AAPB groups.Studies on the PGC structures of the 69 AAPB strains revealed a novel PGC arrangement,forward bch(M)L(H)BNF-pucc-puh plus reverse crtF-bchCXYZ-puf.Additionally,we found five different organizations of the puf operon in which pufQALMC was a novel discovery.The BChl conserved operon of two Paracraurococcus strains was bchFNBL which was missing both bchM and bchH.That suggested the novel BChl biosynthesis pathway in the Paracraurococcus.By comparing AAPB and related non-AAPB genomes,it seemed little significant difference between them as to conserved proteins and metabolic subsystems.Therefore,the main traits of AAPB,except for phototrophic metabolism,might be decided by the phylogenetic group instead of the functional group.Finally,the prophage,integrase,type ? secretion systems and ECR may mediate the PGC transfer as revealed by genomic analysis.