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Molecular and chemical dialogues in bacteria-protozoa interactions.

Song C, Mazzola M, Cheng X, Oetjen J, Alexandrov T, Dorrestein P, Watrous J, van der Voort M, Raaijmakers JM - Sci Rep (2015)

Bottom Line: Lipopeptide (LP) biosynthesis was induced in Pseudomonas upon protozoan grazing and LP accumulation transitioned from homogeneous distributions across bacterial colonies to site-specific accumulation at the bacteria-protist interface.Also putrescine biosynthesis was upregulated in P. fluorescens upon predation.This multifaceted study provides new insights in common and strain-specific responses in bacteria-protozoa interactions, including responses that contribute to bacterial survival in highly competitive soil and rhizosphere environments.

View Article: PubMed Central - PubMed

Affiliation: 1] Laboratory of Phytopathology, Wageningen University, 6708 PB Wageningen, the Netherlands [2] Microbial Ecology Department, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, the Netherlands.

ABSTRACT
Protozoan predation of bacteria can significantly affect soil microbial community composition and ecosystem functioning. Bacteria possess diverse defense strategies to resist or evade protozoan predation. For soil-dwelling Pseudomonas species, several secondary metabolites were proposed to provide protection against different protozoan genera. By combining whole-genome transcriptome analyses with (live) imaging mass spectrometry (IMS), we observed multiple changes in the molecular and chemical dialogues between Pseudomonas fluorescens and the protist Naegleria americana. Lipopeptide (LP) biosynthesis was induced in Pseudomonas upon protozoan grazing and LP accumulation transitioned from homogeneous distributions across bacterial colonies to site-specific accumulation at the bacteria-protist interface. Also putrescine biosynthesis was upregulated in P. fluorescens upon predation. We demonstrated that putrescine induces protozoan trophozoite encystment and adversely affects cyst viability. This multifaceted study provides new insights in common and strain-specific responses in bacteria-protozoa interactions, including responses that contribute to bacterial survival in highly competitive soil and rhizosphere environments.

No MeSH data available.


Related in: MedlinePlus

(A) Transcriptomic analysis of P. fluorescens SS101-N. americana interaction. Each point represents one annotated gene in the SS101 genome, with the X-axis showing the gene order, and the Y-axis showing the log2 of gene transcript abundance in the interaction. The identities of highly modulated, well-characterized gene clusters are shown. 1. massA; 2. massB, massC; 3. alkane oxidation gene clusters; 4. agmatinase encoding gene speB. (B) Organization of the lipopeptide (LP) gene cluster in P. fluorescens SS101. The three LP biosynthesis genes are designated massA, massB and massC. In the boxes of the genes are the fold changes in their expression during P. fluorescens-N. americana interaction. (C) Organization of the alkane oxidation gene cluster in SS101. The reference strain used is P. protegens CHA0 (previously described as P. fluorescens). In the boxes of the genes are the fold changes in their expression during P. fluorescens-N. americana interaction. (D) Organization of the putrescine encoding gene speB and its flanking genes. In the boxes of the genes are the fold changes in their expression during P. fluorescens-N. americana interaction.
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f1: (A) Transcriptomic analysis of P. fluorescens SS101-N. americana interaction. Each point represents one annotated gene in the SS101 genome, with the X-axis showing the gene order, and the Y-axis showing the log2 of gene transcript abundance in the interaction. The identities of highly modulated, well-characterized gene clusters are shown. 1. massA; 2. massB, massC; 3. alkane oxidation gene clusters; 4. agmatinase encoding gene speB. (B) Organization of the lipopeptide (LP) gene cluster in P. fluorescens SS101. The three LP biosynthesis genes are designated massA, massB and massC. In the boxes of the genes are the fold changes in their expression during P. fluorescens-N. americana interaction. (C) Organization of the alkane oxidation gene cluster in SS101. The reference strain used is P. protegens CHA0 (previously described as P. fluorescens). In the boxes of the genes are the fold changes in their expression during P. fluorescens-N. americana interaction. (D) Organization of the putrescine encoding gene speB and its flanking genes. In the boxes of the genes are the fold changes in their expression during P. fluorescens-N. americana interaction.

Mentions: When challenged with N. americana, up to 2.3% of the SS101 genes exhibited significantly altered expression in cells located at the interaction interface. In total, 128 genes were differentially expressed in SS101 with 55 genes up-regulated and 73 genes down-regulated (fold-change >2.0; P value < 0.05) (Fig. 1A). The LP biosynthesis genes massA, massB and massC in SS101 were more than 2-fold up-regulated (Fig. 1B). This up-regulation is consistent with qRT-PCR results obtained previously24. Also the massetolide-specific luxR-type transcriptional regulatory gene massAR and the downstream ABC-type efflux genes macA and macB were significantly up-regulated (Fig. 1B). Several of the other differentially regulated genes (17 and 29 genes up and down, respectively) were classified as “Function unknown” or “Not in COGs” categories (Figure S1, category S and X, respectively). These results suggest that a large proportion of the bacterial genes expressed in response to N. americana are unknown and remain to be characterized. Thirteen out of sixteen genes from the “Amino acid transport and metabolism” category were up-regulated, including genes associated with arginine and proline metabolism, lysine biosynthesis, degradation of aromatic compounds and phenylalanine metabolism, respectively. The yveA gene, which mediates uptake of both l-aspartate and l-glutamate28, was 3-fold up-regulated in SS101 in interaction with N. americana (Table S1). PflSS101_1522, a homologue gene of ilvB in Pseudomonas protegens, was 4-fold up-regulated in SS101 upon interaction with N. americana. IlvB is a large subunit of acetohydroxyacid synthase (AHAS) which catalyses the first step in the biosynthesis of the essential amino acids isoleucine, leucine and valine in bacteria, as well as in plants, fungi and certain algae2930. The up-regulation of several genes involved in amino acid transport and metabolism suggests that the interaction with N. americana induces changes in primary metabolism of P. fluorescens SS101. In our previous study31, we found indications that amino acids affect the production of the lipopeptide massetolide A in SS101. Hence, the observed transcriptional changes in amino acid metabolism may, via LP biosynthesis, modulate defense against protozoan predation.


Molecular and chemical dialogues in bacteria-protozoa interactions.

Song C, Mazzola M, Cheng X, Oetjen J, Alexandrov T, Dorrestein P, Watrous J, van der Voort M, Raaijmakers JM - Sci Rep (2015)

(A) Transcriptomic analysis of P. fluorescens SS101-N. americana interaction. Each point represents one annotated gene in the SS101 genome, with the X-axis showing the gene order, and the Y-axis showing the log2 of gene transcript abundance in the interaction. The identities of highly modulated, well-characterized gene clusters are shown. 1. massA; 2. massB, massC; 3. alkane oxidation gene clusters; 4. agmatinase encoding gene speB. (B) Organization of the lipopeptide (LP) gene cluster in P. fluorescens SS101. The three LP biosynthesis genes are designated massA, massB and massC. In the boxes of the genes are the fold changes in their expression during P. fluorescens-N. americana interaction. (C) Organization of the alkane oxidation gene cluster in SS101. The reference strain used is P. protegens CHA0 (previously described as P. fluorescens). In the boxes of the genes are the fold changes in their expression during P. fluorescens-N. americana interaction. (D) Organization of the putrescine encoding gene speB and its flanking genes. In the boxes of the genes are the fold changes in their expression during P. fluorescens-N. americana interaction.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4542665&req=5

f1: (A) Transcriptomic analysis of P. fluorescens SS101-N. americana interaction. Each point represents one annotated gene in the SS101 genome, with the X-axis showing the gene order, and the Y-axis showing the log2 of gene transcript abundance in the interaction. The identities of highly modulated, well-characterized gene clusters are shown. 1. massA; 2. massB, massC; 3. alkane oxidation gene clusters; 4. agmatinase encoding gene speB. (B) Organization of the lipopeptide (LP) gene cluster in P. fluorescens SS101. The three LP biosynthesis genes are designated massA, massB and massC. In the boxes of the genes are the fold changes in their expression during P. fluorescens-N. americana interaction. (C) Organization of the alkane oxidation gene cluster in SS101. The reference strain used is P. protegens CHA0 (previously described as P. fluorescens). In the boxes of the genes are the fold changes in their expression during P. fluorescens-N. americana interaction. (D) Organization of the putrescine encoding gene speB and its flanking genes. In the boxes of the genes are the fold changes in their expression during P. fluorescens-N. americana interaction.
Mentions: When challenged with N. americana, up to 2.3% of the SS101 genes exhibited significantly altered expression in cells located at the interaction interface. In total, 128 genes were differentially expressed in SS101 with 55 genes up-regulated and 73 genes down-regulated (fold-change >2.0; P value < 0.05) (Fig. 1A). The LP biosynthesis genes massA, massB and massC in SS101 were more than 2-fold up-regulated (Fig. 1B). This up-regulation is consistent with qRT-PCR results obtained previously24. Also the massetolide-specific luxR-type transcriptional regulatory gene massAR and the downstream ABC-type efflux genes macA and macB were significantly up-regulated (Fig. 1B). Several of the other differentially regulated genes (17 and 29 genes up and down, respectively) were classified as “Function unknown” or “Not in COGs” categories (Figure S1, category S and X, respectively). These results suggest that a large proportion of the bacterial genes expressed in response to N. americana are unknown and remain to be characterized. Thirteen out of sixteen genes from the “Amino acid transport and metabolism” category were up-regulated, including genes associated with arginine and proline metabolism, lysine biosynthesis, degradation of aromatic compounds and phenylalanine metabolism, respectively. The yveA gene, which mediates uptake of both l-aspartate and l-glutamate28, was 3-fold up-regulated in SS101 in interaction with N. americana (Table S1). PflSS101_1522, a homologue gene of ilvB in Pseudomonas protegens, was 4-fold up-regulated in SS101 upon interaction with N. americana. IlvB is a large subunit of acetohydroxyacid synthase (AHAS) which catalyses the first step in the biosynthesis of the essential amino acids isoleucine, leucine and valine in bacteria, as well as in plants, fungi and certain algae2930. The up-regulation of several genes involved in amino acid transport and metabolism suggests that the interaction with N. americana induces changes in primary metabolism of P. fluorescens SS101. In our previous study31, we found indications that amino acids affect the production of the lipopeptide massetolide A in SS101. Hence, the observed transcriptional changes in amino acid metabolism may, via LP biosynthesis, modulate defense against protozoan predation.

Bottom Line: Lipopeptide (LP) biosynthesis was induced in Pseudomonas upon protozoan grazing and LP accumulation transitioned from homogeneous distributions across bacterial colonies to site-specific accumulation at the bacteria-protist interface.Also putrescine biosynthesis was upregulated in P. fluorescens upon predation.This multifaceted study provides new insights in common and strain-specific responses in bacteria-protozoa interactions, including responses that contribute to bacterial survival in highly competitive soil and rhizosphere environments.

View Article: PubMed Central - PubMed

Affiliation: 1] Laboratory of Phytopathology, Wageningen University, 6708 PB Wageningen, the Netherlands [2] Microbial Ecology Department, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, the Netherlands.

ABSTRACT
Protozoan predation of bacteria can significantly affect soil microbial community composition and ecosystem functioning. Bacteria possess diverse defense strategies to resist or evade protozoan predation. For soil-dwelling Pseudomonas species, several secondary metabolites were proposed to provide protection against different protozoan genera. By combining whole-genome transcriptome analyses with (live) imaging mass spectrometry (IMS), we observed multiple changes in the molecular and chemical dialogues between Pseudomonas fluorescens and the protist Naegleria americana. Lipopeptide (LP) biosynthesis was induced in Pseudomonas upon protozoan grazing and LP accumulation transitioned from homogeneous distributions across bacterial colonies to site-specific accumulation at the bacteria-protist interface. Also putrescine biosynthesis was upregulated in P. fluorescens upon predation. We demonstrated that putrescine induces protozoan trophozoite encystment and adversely affects cyst viability. This multifaceted study provides new insights in common and strain-specific responses in bacteria-protozoa interactions, including responses that contribute to bacterial survival in highly competitive soil and rhizosphere environments.

No MeSH data available.


Related in: MedlinePlus