Genomic and Genetic Diversity within the <i>Pseudomonas fluorescens</i> Complex

The Pseudomonas fluorescens complex includes Pseudomonas strains that have been taxonomically assigned to more than fifty different species, many of which have been described as plant growth-promoting rhizobacteria (PGPR) with potential applications in biocontrol and biofertilization. So far the phylogeny of this complex has been analyzed according to phenotypic traits, 16S rDNA, MLSA and inferred by whole-genome analysis. However, since most of the type strains have not been fully sequenced and new species are frequently described, correlation between taxonomy and phylogenomic analysis is missing. In recent years, the genomes of a large number of strains have been sequenced, showing important genomic heterogeneity and providing information suitable for genomic studies that are important to understand the genomic and genetic diversity shown by strains of this complex. Based on MLSA and several whole-genome sequence-based analyses of 93 sequenced strains, we have divided the P. fluorescens complex into eight phylogenomic groups that agree with previous works based on type strains. Digital DDH (dDDH) identified 69 species and 75 subspecies within the 93 genomes. The eight groups corresponded to clustering with a threshold of 31.8% dDDH, in full agreement with our MLSA. The Average Nucleotide Identity (ANI) approach showed inconsistencies regarding the assignment to species and to the eight groups. The small core genome of 1,334 CDSs and the large pan-genome of 30,848 CDSs, show the large diversity and genetic heterogeneity of the P. fluorescens complex. However, a low number of strains were enough to explain most of the CDSs diversity at core and strain-specific genomic fractions. Finally, the identification and analysis of group-specific genome and the screening for distinctive characters revealed a phylogenomic distribution of traits among the groups that provided insights into biocontrol and bioremediation applications as well as their role as PGPR.荧光假单胞菌复合体（Pseudomonas fluorescens complex）包含经分类学鉴定归属五十余个不同物种的假单胞菌菌株，其中多数被鉴定为植物促生根际菌（plant growth-promoting rhizobacteria，PGPR），在生物防治与生物施肥领域具备潜在应用价值。迄今为止，针对该复合体的系统发育研究已基于表型性状、16S核糖体DNA（16S rDNA）、多位点序列分析（MLSA）展开，并通过全基因组分析进行推演。然而，由于多数模式菌株尚未完成全基因组测序，且新物种不断被报道，分类学与系统发育基因组学分析之间仍存在关联缺失的问题。近年来，大量菌株的基因组已完成测序，这不仅揭示了该复合体显著的基因组异质性，也为相关基因组学研究提供了可靠数据，有助于深入理解该复合体菌株所呈现的基因组与遗传多样性。本研究基于对93株已测序菌株的多位点序列分析及多项全基因组序列分析，将荧光假单胞菌复合体划分为8个系统发育基因组类群，该划分结果与此前基于模式菌株的研究成果一致。通过数字DNA-DNA杂交（digital DNA-DNA hybridization，dDDH）分析，在93个基因组中共鉴定出69个物种及75个亚种。这8个类群对应31.8% dDDH阈值下的聚类结果，与本研究的多位点序列分析结果完全契合。而平均核苷酸同源性（Average Nucleotide Identity，ANI）方法在物种及8个类群的划分上则表现出不一致性。该复合体的核心基因组仅包含1334个编码序列（Coding Sequences，CDSs），泛基因组则多达30848个CDSs，直观体现了荧光假单胞菌复合体丰富的多样性与遗传异质性。不过，仅需少量菌株即可解释核心基因组与菌株特异性基因组组分中的绝大多数编码序列多样性。最终，通过对组特异性基因组的鉴定与分析，以及对特征性状的筛选，研究发现类群间的性状呈现系统发育基因组学分布特征，这为理解其生物防治、生物修复应用价值以及作为植物促生根际菌的功能角色提供了新的见解。