Elucidation of the Photorhabdus temperata Genome and Generation of a Transposon Mutant Library To Identify Motility Mutants Altered in Pathogenesis.

UNLABELLED: The entomopathogenic nematode Heterorhabditis bacteriophora forms a specific mutualistic association with its bacterial partner Photorhabdus temperata. The microbial symbiont is required for nematode growth and development, and symbiont recognition is strain specific. The aim of this study was to sequence the genome of P. temperata and identify genes that plays a role in the pathogenesis of the Photorhabdus-Heterorhabditis symbiosis. A draft genome sequence of P. temperata strain NC19 was generated. The 5.2-Mb genome was organized into 17 scaffolds and contained 4,808 coding sequences (CDS). A genetic approach was also pursued to identify mutants with altered motility. A bank of 10,000 P. temperata transposon mutants was generated and screened for altered motility patterns. Five classes of motility mutants were identified: (i) nonmotile mutants, (ii) mutants with defective or aberrant swimming motility, (iii) mutant swimmers that do not require NaCl or KCl, (iv) hyperswimmer mutants that swim at an accelerated rate, and (v) hyperswarmer mutants that are able to swarm on the surface of 1.25% agar. The transposon insertion sites for these mutants were identified and used to investigate other physiological properties, including insect pathogenesis. The motility-defective mutant P13-7 had an insertion in the RNase II gene and showed reduced virulence and production of extracellular factors. Genetic complementation of this mutant restored wild-type activity. These results demonstrate a role for RNA turnover in insect pathogenesis and other physiological functions. IMPORTANCE: The relationship between Photorhabdus and entomopathogenic nematode Heterorhabditis represents a well-known mutualistic system that has potential as a biological control agent. The elucidation of the genome of the bacterial partner and role that RNase II plays in its life cycle has provided a greater understanding of Photorhabdus as both an insect pathogen and a nematode symbiont.

Genome sequence and comparative analysis of a putative entomopathogenic Serratia isolated from Caenorhabditis briggsae.

BACKGROUND: Entomopathogenic associations between nematodes in the genera Steinernema and Heterorhabdus with their cognate bacteria from the bacterial genera Xenorhabdus and Photorhabdus, respectively, are extensively studied for their potential as biological control agents against invasive insect species. These two highly coevolved associations were results of convergent evolution. Given the natural abundance of bacteria, nematodes and insects, it is surprising that only these two associations with no intermediate forms are widely studied in the entomopathogenic context. Discovering analogous systems involving novel bacterial and nematode species would shed light on the evolutionary processes involved in the transition from free living organisms to obligatory partners in entomopathogenicity. RESULTS: We report the complete genome sequence of a new member of the enterobacterial genus Serratia that forms a putative entomopathogenic complex with Caenorhabditis briggsae. Analysis of the 5.04 MB chromosomal genome predicts 4599 protein coding genes, seven sets of ribosomal RNA genes, 84 tRNA genes and a 64.8 KB plasmid encoding 74 genes. Comparative genomic analysis with three of the previously sequenced Serratia species, S. marcescens DB11 and S. proteamaculans 568, and Serratia sp. AS12, revealed that these four representatives of the genus share a core set of ~3100 genes and extensive structural conservation. The newly identified species shares a more recent common ancestor with S. marcescens with 99% sequence identity in rDNA sequence and orthology across 85.6% of predicted genes. Of the 39 genes/operons implicated in the virulence, symbiosis, recolonization, immune evasion and bioconversion, 21 (53.8%) were present in Serratia while 33 (84.6%) and 35 (89%) were present in Xenorhabdus and Photorhabdus EPN bacteria respectively. CONCLUSION: The majority of unique sequences in Serratia sp. SCBI (South African Caenorhabditis briggsae Isolate) are found in ~29 genomic islands of 5 to 65 genes and are enriched in putative functions that are biologically relevant to an entomopathogenic lifestyle, including non-ribosomal peptide synthetases, bacteriocins, fimbrial biogenesis, ushering proteins, toxins, secondary metabolite secretion and multiple drug resistance/efflux systems. By revealing the early stages of adaptation to this lifestyle, the Serratia sp. SCBI genome underscores the fact that in EPN formation the composite end result - killing, bioconversion, cadaver protection and recolonization- can be achieved by dissimilar mechanisms. This genome sequence will enable further study of the evolution of entomopathogenic nematode-bacteria complexes.

Permanent Draft Genome Sequence for Frankia sp. Strain Cc1.17, a Nitrogen-Fixing Actinobacterium Isolated from Root Nodules of Colletia cruciata.

Frankia sp. strain Cc1.17 is a member of the Frankia lineage 3, the organisms of which are able to reinfect plants of the Eleagnaceae, Rhamnaceae, and Myricaceae families and the genera Gynmnostoma and Alnus Here, we report the 8.4-Mbp draft genome sequence, with a G+C content of 72.14% and 6,721 candidate protein-coding genes.

Permanent Draft Genome Sequence of Photorhabdus temperata Strain Hm, an Entomopathogenic Bacterium Isolated from Nematodes.

Photorhabdus temperata strain Hm is an entomopathogenic bacterium that forms a symbiotic association with Heterorhabditis nematodes. Here, we report a 5.0-Mbp draft genome sequence for P. temperata strain Hm with a G+C content of 44.1% and containing 4,226 candidate protein-encoding genes.

Draft Genome Sequence of Photorhabdus luminescens subsp. laumondii HP88, an Entomopathogenic Bacterium Isolated from Nematodes.

Photorhabdus luminescens subsp. laumondii HP88 is an entomopathogenic bacterium that forms a symbiotic association with Heterorhabditis nematodes. We report here a 5.27-Mbp draft genome sequence for P. luminescens subsp. laumondii HP88, with a G+C content of 42.4% and containing 4,243 candidate protein-coding genes.

Permanent Draft Genome Sequence of Frankia sp. Strain Allo2, a Salt-Tolerant Nitrogen-Fixing Actinobacterium Isolated from the Root Nodules of Allocasuarina.

Frankia sp. strain Allo2 is a member of Frankia lineage Ib, which is able to reinfect plants of the Casuarinaceae family, and exhibits a high level of salt tolerance compared to other isolates. Here, we report the 5.3-Mbp draft genome sequence of Frankia sp. strain Allo2 with a G+C content of 70.0% and 4,224 candidate protein-encoding genes.

Permanent Draft Genome Sequences for Two Variants of Frankia sp. Strain CpI1, the First Frankia Strain Isolated from Root Nodules of Comptonia peregrina.

Frankia stains CpI1-S and CpI1-P are members of Frankia lineage Ia that are able to reinfect plants of the Betulaceae and Myricaceae families. Here, we report two 7.6-Mbp draft genome sequences with 6,396 and 6,373 candidate protein-coding genes for CpI1-S and CpI1-P, respectively.

Permanent Draft Genome Sequence for Frankia sp. Strain CeD, a Nitrogen-Fixing Actinobacterium Isolated from the Root Nodules of Casuarina equistifolia Grown in Senegal.

Frankiastrain CeD is a member ofFrankialineage Ib that is able to reinfect plants of theCasuarinafamilies. Here, we report a 5.0-Mbp draft genome sequence with a G+C content of 70.1% and 3,847 candidate protein-encoding genes.

Permanent Draft Genome Sequence for Frankia sp. Strain EI5c, a Single-Spore Isolate of a Nitrogen-Fixing Actinobacterium, Isolated from the Root Nodules of Elaeagnus angustifolia.

Frankia sp. strain EI5c is a member of Frankia lineage III, which is able to reinfect plants of the Eleagnaceae, Rhamnaceae, Myricaceae, and Gymnostoma, as well as the genus Alnus Here, we report the 6.6-Mbp draft genome sequence of Frankia sp. strain EI5c with a G+C content of 72.14 % and 5,458 candidate protein-encoding genes.

Permanent Draft Genome Sequence of Frankia sp. Strain BR, a Nitrogen-Fixing Actinobacterium Isolated from the Root Nodules of Casuarina equisetifolia.

Frankia sp. strain BR is a member of Frankia lineage Ic and is able to reinfect plants of the Casuarinaceae family. Here, we report a 5.2-Mbp draft genome sequence with a G+C content of 70.0% and 4,777 candidate protein-encoding genes.

Permanent Draft Genome Sequence of Frankia sp. Strain ACN1ag, a Nitrogen-Fixing Actinobacterium Isolated from the Root Nodules of Alnus glutinosa.

Frankia strain ACN1(ag) is a member of Frankia lineage Ia, which are able to re-infect plants of the Betulaceae and Myricaceae families. Here, we report a 7.5-Mbp draft genome sequence with a G+C content of 72.35% and 5,687 candidate protein-encoding genes.

Permanent Draft Genome Sequence of Frankia sp. Strain AvcI1, a Nitrogen-Fixing Actinobacterium Isolated from the Root Nodules of Alnus viridis subsp. crispa Grown in Canada.

Frankia strain AvcI1, isolated from root nodules of Alnus viridis subsp. crispa, is a member of Frankia lineage Ia, which is able to reinfect plants of the Betulaceae and Myricaceae families. Here, we report a 7.7-Mbp draft genome sequence with a G+C content of 72.41% and 6,470 candidate protein-encoding genes.

Draft Genome Sequence of Frankia sp. Strain BMG5.23, a Salt-Tolerant Nitrogen-Fixing Actinobacterium Isolated from the Root Nodules of Casuarina glauca Grown in Tunisia.

Nitrogen-fixing actinobacteria of the genus Frankia are symbionts of woody dicotyledonous plants termed actinorhizal plants. We report here a 5.27-Mbp draft genome sequence for Frankia sp. strain BMG5.23, a salt-tolerant nitrogen-fixing actinobacterium isolated from root nodules of Casuarina glauca collected in Tunisia.

Draft Genome Sequence of Photorhabdus luminescens Strain BA1, an Entomopathogenic Bacterium Isolated from Nematodes Found in Egypt.

Photorhabdus luminescens strain BA1 is an entomopathogenic bacterium that forms a symbiotic association with Heterorhabditis nematodes. We report here a 5.0-Mbp draft genome sequence for P. luminscens strain BA1, with a G+C content of 42.46% and 4,250 candidate protein-coding genes.

Draft Genome Sequence of Frankia sp. Strain Thr, a Nitrogen-Fixing Actinobacterium Isolated from the Root Nodules of Casuarina cunninghamiana Grown in Egypt.

Nitrogen-fixing actinobacteria of the genus Frankia are symbionts of woody dicotyledonous plants termed actinorhizal plants. We report here a 5.3-Mbp draft genome sequence for Frankia sp. stain Thr, a nitrogen-fixing actinobacterium isolated from root nodules of Casuarina cunninghamiana collected in Egypt.

Draft Genome Sequence of Photorhabdus temperata Strain Meg1, an Entomopathogenic Bacterium Isolated from Heterorhabditis megidis Nematodes.

Photorhabdus temperata strain Meg1 is an entomopathogenic bacterium that forms a symbiotic association with Heterorhabditis nematodes. We report here a 4.9-Mbp draft genome sequence for P. temperata strain Meg1, with a G+C content of 43.18% and containing 4,340 candidate protein-coding genes.

An insect pathogenic symbiosis between a Caenorhabditis and Serratia.

We described an association between a strain of the nematode Caenorhabditis briggsae, i.e. KT0001, and the bacteria Serratia sp. SCBI (South African Caenorhabditis briggsae isolate), which was able to kill the insect Galleria. Here we show that the Serratia sp. SCBI lines the gut of the nematode, similar to the Heterorhabditis-Photorhabdus complex, indicating that the association is possibly internal. We also expand on the relevance of this tripartite, i.e. insect-nematode-bacteria, interaction in the broader evolutionary context and Caenorhabditis natural history.