TABLE 1.

Summary of transposon insertion sequencing studies of plant growth promoting and plant pathogenic bacteria.

Microbe	Plant host	Method	Main finding	References
Plant and soil colonization
Pseudomonas aeruginosa PGPR2	Corn	INSeq	Identified 108 genes that contribute to fitness during root colonization-amino acid catabolism, stress adaptation, detoxification, signal transduction, and transport functions	Sivakumar et al., 2019
Pseudomonas simiae WCS417r	Arabidopsis thaliana	RB-TnSeq	Identified 115 genes required for colonization of the root system and 243 genes where disruption positively affects colonization – large number of these encode proteins for amino acid transport, suggesting that auxotrophy confers a selective advantage in the plant-associated environment rich with exuded amino acids and sugars	Cole et al., 2017
Pseudomonas syringae pv. syringae B728a	Green bean, Phaseolus vulgaris	RB-TnSeq	Genes for amino acid and polysaccharide biosynthesis are important for fitness on the leaf surface and in the leaf interior (apoplast). Genes for type III secretion system and syringomycin synthesis are important in the apoplast	Helmann et al., 2019a
Bacillus thuringiensis	Clover, Triflorium hybridum	TraDIS	Identified genes required for survival in soil – ability to form spores was a key characteristic for multiplying and colonizing the soil	Bishop et al., 2014
Pseudomonas sp. WCS365	Arabidopsis thaliana	Tn-Seq	Identified novel factors required to evade plant defenses by conducting screens on wild-type and immunocompromised plants – identified 231 genes that increase rhizosphere fitness and verified seven genes involved in avoiding plant defenses	Liu et al., 2018
Rhizobial symbiosis
Rhizobium leguminosarum bv. viciae 3841 Sinorhizobium meliloti RM1021 Agrobacterium tumefaciens UBAPF2	Legumes	INSeq	Used a mariner transposon to mutagenize three members of Rhizobiaceae at high frequency. Generated a saturated mutant library in RLV3841 on rich media and identified essential genes	Perry and Yost, 2014
Rhizobium leguminosarum bv. viciae 3841	Legumes	INSeq	Identified genes required for growth on minimal mannitol containing media. Compared to genes required for growth on rich media and found ∼10% of chromosomal genes required under both growth conditions. Identified plasmid genes encoding functional activities important to central physiology	Perry et al., 2016
Rhizobium leguminosarum bv. viciae 3841	Legumes	INSeq	Identified genes important for growth on minimal media supplemented with glucose or succinate at both 1 or 21% O2. Analyzed central carbon metabolism pathways to examine roles in glucose and succinate metabolism and quantify the ability of pathways to compensate for single mutations	Wheatley et al., 2017
Sinorhizobium meliloti RmP3499	Legumes	Tn-seq	Evaluated the interactions between the chromosomal genes and the extra-chromosomal replicons when grown in defined and rich media – ten percent of chromosomal genes found to functionally interact with the replicons	diCenzo et al., 2018
Sinorhizobium meliloti 1021	Medicago truncatula	Tn-seq	Identified genes and pathways that contribute to sensitivity to NCR247 peptide, a plant signaling peptide with antimicrobial activity which plays a key role during rhizobial differentiation in the nodule – found 78 genes and several pathways that affect sensitivity to NCR247	Arnold et al., 2017
Sinorhizobium meliloti Rm2011	Legumes	Signature tagged mutagenesis combined with next generation sequencing	Identified an additional 4,473 transposon insertion sites in a mutant library, bringing the total number of mutants with known insertion sites to 9,562 – 59% of predicted protein-coding genes have a transposon insertion	Serrania et al., 2017
Pathogenicity and virulence
Dickeya dadantii	Chicory	Tn-Seq	Identified metabolic pathways and genes required for growth of a necrotrophic pathogen in planta – the uridine monophosphate, purine and leucine, cysteine, and lysine biosynthetic pathways are essential for bacterial survival in the plant; RsmC and GcpA are important for regulating the infection process; and glycosylation of flagellin confers fitness during plant infection	Royet et al., 2019
Salmonella enterica serovar Typhimurium ATCC 14028	Campari tomato, Solanum lycopersicum cv. Campari	Tn-Seq	When colonizing tomatoes, Salmonella enterica uses a distinct set of plant-associated genes which only partly overlap with the genes used for virulence in animals and by other phytopathogens during plant infection	de Moraes et al., 2017
Pantoea stewartii ssp. stewartii	Sweetcorn, Zea mays cv. Jubilee	Tn-Seq	In planta study showed 486 genes are important for survival (reduced fitness when mutated) and loss of six genes increased fitness. OmpC, lon and ompA were found to play a role in virulence	Duong et al., 2018
Agrobacterium tumefaciens	Tomato, Solanum lycopersicum	Tn-Seq	Combined plant metabolomics, transcriptomics and Tn-seq to identify genes and pathways involved in host exploitation. On sucrose the pgi, pycA, cisY, and sdhCDA genes are crucial and sucrose breakdown involves the Entner–Doudoroff and tricarboxylic acid (TCA) pathways. When growing on GHB (γ-hydroxybutyric acid) as a carbon source the blc genes are crucial and breakdown requires the TCA cycle and gluconeogenesis	Gonzalez-Mula et al., 2019
Liberibacter crescens BT-1	Mountain papaya	TraDIS	Identified 238 essential genes in common between L. crescens and L. asiaticus (unculturable pathogen of citrus) as potential antimicrobial targets	Lai et al., 2016
Pseudomonas syringae pv. actinidiae	Kiwifruit, Actinidia spp.	TraDIS	Identified auxotrophic, motility and lipopolysaccharide (LPS) biosynthesis mutants using a “phenotype of interest” library. Used a “mutant of interest” library to identify a putative LPS mutant	Mesarich et al., 2017
Bacterial physiology
32 bacteria, including eight plant-associated bacteria: Azospirillum brasilense Sp245 Burkholderia phytofirmans PsJN Desulfovibrio vulgaris Miyazaki F Dyella japonica UNC79MFTsu3.2 Herbaspirillum seropedicae SmR1 Klebsiella michiganensis M5a1 Pseudomonas simiae WCS417 Sinorhizobium meliloti 1021	Wheat roots Onion roots Paddy field Arabidopsis root Cereal root Rice rhizosphere Wheat rhizosphere Alfalfa	RB-TnSeq	Across all 32 bacteria, identified phenotypes for 11,779 genes that are not annotated with a specific function, including 4,135 genes that encode proteins that do not belong to any characterized family in either Pfam or TIGRFAMs. Combined functional associations with comparative sequence analysis to identify putative DNA repair proteins and proposed specific functions for transporter proteins, catabolic enzymes, and domains of unknown function	Price et al., 2018a
Pseudomonas putida KT2440		Tn-Seq	Transposon insertion libraries generated in P. putida KT2440 and P. putida KT2440 Δfcs. P. putida found to be significantly more tolerant than E. coli to p-coumaric acid, a phenolic acid present in soils and plants. Genes involved in maintenance of membrane structure and efflux of solvent compounds were important when exposed to p-coumaric acid	Calero et al., 2017
Pseudomonas syringae pv. syringae B728a	Bean, Phaseolus vulgaris	RB-TnSeq	Identified and used a hyper-susceptible mutant to identify the substrates of redundant transporters. Identified genes that contribute to tolerance of acridine orange, acriflavine and berberine	Helmann et al., 2019b
Herbaspirillum seropedicae SmR1	Rice, maize and sorghum	Tn-Seq	Constructed transposon insertion libraries – identified 395 genes essential for growth in rich media	Rosconi et al., 2016
Pseudomonas putida KT2440	Soil bacteria	Tn-Seq	Transposon insertion libraries generated in P. putida KT2440 and P. putida KT2440 Δfcs. P. putida found to be significantly more tolerant than E. coli to p-coumaric acid, a phenolic acid present in soils and plants. Genes involved in maintenance of membrane structure and efflux of solvent compounds were important when exposed to p-coumaric acid	Calero et al., 2017
Pseudomonas syringae pv. syringae B728a	Bean, Phaseolus vulgaris	RB-TnSeq	Identified and used a hyper-susceptible mutant to identify the substrates of redundant transporters. Identified genes that contribute to tolerance of acridine orange, acriflavine and berberine	Helmann et al., 2019b
Herbaspirillum seropedicae SmR1	Rice, maize and sorghum	Tn-Seq	Constructed transposon insertion libraries – identified 395 genes essential for growth in rich media	Rosconi et al., 2016