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Mining the phytomicrobiome to understand how bacterial coinoculations enhance plant growth.

Maymon M, Martínez-Hidalgo P, Tran SS, Ice T, Craemer K, Anbarchian T, Sung T, Hwang LH, Chou M, Fujishige NA, Villella W, Ventosa J, Sikorski J, Sanders ER, Faull KF, Hirsch AM - Front Plant Sci (2015)

Bottom Line: In previous work, we showed that coinoculating Rhizobium leguminosarum bv. viciae 128C53 and Bacillus simplex 30N-5 onto Pisum sativum L. roots resulted in better nodulation and increased plant growth.The exact mechanisms whereby coinoculation results in increased plant growth are incompletely understood, but the synthesis of phytohormones and siderophores, the improved solubilization of inorganic nutrients, and the production of antimicrobial compounds are likely possibilities.Because B. simplex 30N-5 is not widely recognized as a Plant Growth Promoting Bacterial (PGPB) species, after sequencing its genome, we searched for genes proposed to promote plant growth, and then compared these sequences with those from several well studied PGPB species.

View Article: PubMed Central - PubMed

Affiliation: Departments of Molecular, Cell, and Developmental Biology, University of California, Los Angeles Los Angeles, CA, USA.

ABSTRACT
In previous work, we showed that coinoculating Rhizobium leguminosarum bv. viciae 128C53 and Bacillus simplex 30N-5 onto Pisum sativum L. roots resulted in better nodulation and increased plant growth. We now expand this research to include another alpha-rhizobial species as well as a beta-rhizobium, Burkholderia tuberum STM678. We first determined whether the rhizobia were compatible with B. simplex 30N-5 by cross-streaking experiments, and then Medicago truncatula and Melilotus alba were coinoculated with B. simplex 30N-5 and Sinorhizobium (Ensifer) meliloti to determine the effects on plant growth. Similarly, B. simplex 30N-5 and Bu. tuberum STM678 were coinoculated onto Macroptilium atropurpureum. The exact mechanisms whereby coinoculation results in increased plant growth are incompletely understood, but the synthesis of phytohormones and siderophores, the improved solubilization of inorganic nutrients, and the production of antimicrobial compounds are likely possibilities. Because B. simplex 30N-5 is not widely recognized as a Plant Growth Promoting Bacterial (PGPB) species, after sequencing its genome, we searched for genes proposed to promote plant growth, and then compared these sequences with those from several well studied PGPB species. In addition to genes involved in phytohormone synthesis, we detected genes important for the production of volatiles, polyamines, and antimicrobial peptides as well as genes for such plant growth-promoting traits as phosphate solubilization and siderophore production. Experimental evidence is presented to show that some of these traits, such as polyamine synthesis, are functional in B. simplex 30N-5, whereas others, e.g., auxin production, are not.

No MeSH data available.


Related in: MedlinePlus

Homologs of reference set of Plant Growth Promoting (PGP) genes identified in Bacillus and Paenibacillus. Top row, IMG gene ID number; second row, general categories of PGP genes; third row, PGP genes identified in each Bacillus (or Paenibacillus) strain (left column) following comparison with the B. simplex 30N-5 gene (always 100%) and clustered using the K-means algorithm. The highest sequence identity alignment from blastp searches (% values in cells), sequence identities passing the 50% cutoff (cells highlighted in purple) show 3 clusters: cluster 1 (blue), cluster 2 (orange), and cluster 3 (purple). Genes not detected (nd). *Gene names from B. megaterium, B. licheniformis, and B. amyloliquefaciens (see text).
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Figure 1: Homologs of reference set of Plant Growth Promoting (PGP) genes identified in Bacillus and Paenibacillus. Top row, IMG gene ID number; second row, general categories of PGP genes; third row, PGP genes identified in each Bacillus (or Paenibacillus) strain (left column) following comparison with the B. simplex 30N-5 gene (always 100%) and clustered using the K-means algorithm. The highest sequence identity alignment from blastp searches (% values in cells), sequence identities passing the 50% cutoff (cells highlighted in purple) show 3 clusters: cluster 1 (blue), cluster 2 (orange), and cluster 3 (purple). Genes not detected (nd). *Gene names from B. megaterium, B. licheniformis, and B. amyloliquefaciens (see text).

Mentions: Draft and finished genome sequences of several PGPB from the Joint Genome Institute IMG/ER (Markowitz et al., 2012) or from NCBI (http://www.ncbi.nlm.nih.gov) were queried by BLAST (Altschul et al., 1990) using sequences of genes encoding known PGPB traits. Thirteen bona fide PGP Bacillus and two Paenibacillus strains were chosen for comparison against B. simplex 30N-5 (Figure 1). The JGI genomes queried included B. simplex 30N-5 (permanent draft), B. simplex II3b11 (permanent draft), B. firmus DS1 (permanent draft), B. licheniformis DSM 13T/ATCC 14580 (finished), B. kribbensis DSM 17871 (permanent draft), B. megaterium DSM 319 (finished), B. amyloliquefaciens subsp. plantarum FZB42T (finished), B. subtilis GB03 (permanent draft), B. subtilis subtilis 168 (finished), B. cereus JM-Mgvxx-63 (permanent draft), B. thuringiensis sv. israelensis (permanent draft), Paenibacillus polymyxa ATCC 12321 (permanent draft), Paenibacillus pini JCM16418 (permanent draft), Pseudomonas fluorescens strains A506 and CHAO (finished), and Azospirillum brasilense FP2 (permanent draft) and Azospirillum sp. B510 (permanent draft). B. simplex 30N-5 was isolated from the Mildred E. Mathias Botanical Garden at UCLA and strain II3b11 belongs to the Putative Ecotype 9 (Koeppel et al., 2008). It originates from the south facing, hot or “African savannah-like” slope of “Evolution Canyon II” in Nahal Keziv, Israel (Sikorski and Nevo, 2005). In addition, the genome of B. simplex strains P558 (Croce et al., 2014) and BA2H3 (Khayi et al., 2015), both from NCBI, were queried when a gene from one or both IMG/ER B. simplex strains was missing. Details of the Bacillus strains studied for the genomic analysis are found in Table 2.


Mining the phytomicrobiome to understand how bacterial coinoculations enhance plant growth.

Maymon M, Martínez-Hidalgo P, Tran SS, Ice T, Craemer K, Anbarchian T, Sung T, Hwang LH, Chou M, Fujishige NA, Villella W, Ventosa J, Sikorski J, Sanders ER, Faull KF, Hirsch AM - Front Plant Sci (2015)

Homologs of reference set of Plant Growth Promoting (PGP) genes identified in Bacillus and Paenibacillus. Top row, IMG gene ID number; second row, general categories of PGP genes; third row, PGP genes identified in each Bacillus (or Paenibacillus) strain (left column) following comparison with the B. simplex 30N-5 gene (always 100%) and clustered using the K-means algorithm. The highest sequence identity alignment from blastp searches (% values in cells), sequence identities passing the 50% cutoff (cells highlighted in purple) show 3 clusters: cluster 1 (blue), cluster 2 (orange), and cluster 3 (purple). Genes not detected (nd). *Gene names from B. megaterium, B. licheniformis, and B. amyloliquefaciens (see text).
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Related In: Results  -  Collection

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Figure 1: Homologs of reference set of Plant Growth Promoting (PGP) genes identified in Bacillus and Paenibacillus. Top row, IMG gene ID number; second row, general categories of PGP genes; third row, PGP genes identified in each Bacillus (or Paenibacillus) strain (left column) following comparison with the B. simplex 30N-5 gene (always 100%) and clustered using the K-means algorithm. The highest sequence identity alignment from blastp searches (% values in cells), sequence identities passing the 50% cutoff (cells highlighted in purple) show 3 clusters: cluster 1 (blue), cluster 2 (orange), and cluster 3 (purple). Genes not detected (nd). *Gene names from B. megaterium, B. licheniformis, and B. amyloliquefaciens (see text).
Mentions: Draft and finished genome sequences of several PGPB from the Joint Genome Institute IMG/ER (Markowitz et al., 2012) or from NCBI (http://www.ncbi.nlm.nih.gov) were queried by BLAST (Altschul et al., 1990) using sequences of genes encoding known PGPB traits. Thirteen bona fide PGP Bacillus and two Paenibacillus strains were chosen for comparison against B. simplex 30N-5 (Figure 1). The JGI genomes queried included B. simplex 30N-5 (permanent draft), B. simplex II3b11 (permanent draft), B. firmus DS1 (permanent draft), B. licheniformis DSM 13T/ATCC 14580 (finished), B. kribbensis DSM 17871 (permanent draft), B. megaterium DSM 319 (finished), B. amyloliquefaciens subsp. plantarum FZB42T (finished), B. subtilis GB03 (permanent draft), B. subtilis subtilis 168 (finished), B. cereus JM-Mgvxx-63 (permanent draft), B. thuringiensis sv. israelensis (permanent draft), Paenibacillus polymyxa ATCC 12321 (permanent draft), Paenibacillus pini JCM16418 (permanent draft), Pseudomonas fluorescens strains A506 and CHAO (finished), and Azospirillum brasilense FP2 (permanent draft) and Azospirillum sp. B510 (permanent draft). B. simplex 30N-5 was isolated from the Mildred E. Mathias Botanical Garden at UCLA and strain II3b11 belongs to the Putative Ecotype 9 (Koeppel et al., 2008). It originates from the south facing, hot or “African savannah-like” slope of “Evolution Canyon II” in Nahal Keziv, Israel (Sikorski and Nevo, 2005). In addition, the genome of B. simplex strains P558 (Croce et al., 2014) and BA2H3 (Khayi et al., 2015), both from NCBI, were queried when a gene from one or both IMG/ER B. simplex strains was missing. Details of the Bacillus strains studied for the genomic analysis are found in Table 2.

Bottom Line: In previous work, we showed that coinoculating Rhizobium leguminosarum bv. viciae 128C53 and Bacillus simplex 30N-5 onto Pisum sativum L. roots resulted in better nodulation and increased plant growth.The exact mechanisms whereby coinoculation results in increased plant growth are incompletely understood, but the synthesis of phytohormones and siderophores, the improved solubilization of inorganic nutrients, and the production of antimicrobial compounds are likely possibilities.Because B. simplex 30N-5 is not widely recognized as a Plant Growth Promoting Bacterial (PGPB) species, after sequencing its genome, we searched for genes proposed to promote plant growth, and then compared these sequences with those from several well studied PGPB species.

View Article: PubMed Central - PubMed

Affiliation: Departments of Molecular, Cell, and Developmental Biology, University of California, Los Angeles Los Angeles, CA, USA.

ABSTRACT
In previous work, we showed that coinoculating Rhizobium leguminosarum bv. viciae 128C53 and Bacillus simplex 30N-5 onto Pisum sativum L. roots resulted in better nodulation and increased plant growth. We now expand this research to include another alpha-rhizobial species as well as a beta-rhizobium, Burkholderia tuberum STM678. We first determined whether the rhizobia were compatible with B. simplex 30N-5 by cross-streaking experiments, and then Medicago truncatula and Melilotus alba were coinoculated with B. simplex 30N-5 and Sinorhizobium (Ensifer) meliloti to determine the effects on plant growth. Similarly, B. simplex 30N-5 and Bu. tuberum STM678 were coinoculated onto Macroptilium atropurpureum. The exact mechanisms whereby coinoculation results in increased plant growth are incompletely understood, but the synthesis of phytohormones and siderophores, the improved solubilization of inorganic nutrients, and the production of antimicrobial compounds are likely possibilities. Because B. simplex 30N-5 is not widely recognized as a Plant Growth Promoting Bacterial (PGPB) species, after sequencing its genome, we searched for genes proposed to promote plant growth, and then compared these sequences with those from several well studied PGPB species. In addition to genes involved in phytohormone synthesis, we detected genes important for the production of volatiles, polyamines, and antimicrobial peptides as well as genes for such plant growth-promoting traits as phosphate solubilization and siderophore production. Experimental evidence is presented to show that some of these traits, such as polyamine synthesis, are functional in B. simplex 30N-5, whereas others, e.g., auxin production, are not.

No MeSH data available.


Related in: MedlinePlus