Stability of a Pseudomonas putida KT2440 Bacteriophage-Carried Genomic Island and Its Impact on Rhizosphere Fitness

Abstract

<jats:title>ABSTRACT</jats:title><jats:p>The stability of seven genomic islands of<jats:named-content xmlns:xlink="http://www.w3.org/1999/xlink" content-type="genus-species" xlink:type="simple">Pseudomonas putida</jats:named-content>KT2440 with predicted potential for mobilization was studied in bacterial populations associated with the rhizosphere of corn plants by multiplex PCR. DNA rearrangements were detected for only one of them (GI28), which was lost at high frequency. This genomic island of 39.4 kb, with 53 open reading frames, shows the characteristic organization of genes belonging to tailed phages. We present evidence indicating that it corresponds to the lysogenic state of a functional bacteriophage that we have designated Pspu28. Integrated and rarely excised forms of Pspu28 coexist in KT2440 populations. Pspu28 is self-transmissible, and an excisionase is essential for its removal from the bacterial chromosome. The excised Pspu28 forms a circular element that can integrate into the chromosome at a specific location,<jats:italic>att</jats:italic>sites containing a 17-bp direct repeat sequence. Excision/insertion of Pspu28 alters the promoter sequence and changes the expression level of PP_1531, which encodes a predicted arsenate reductase. Finally, we show that the presence of Pspu28 in the lysogenic state has a negative effect on bacterial fitness in the rhizosphere under conditions of intraspecific competition, thus explaining why clones having lost this mobile element are recovered from that environment.</jats:p>

Biotic Interactions Shape the Ecological Distributions of Staphylococcus Species

“…But we did observe substantial variation in the distributions of prophage-encoding genes across the three species. The abundance of prophages within a genome has been shown to decrease the growth of some bacterial species, leading to the notion of a prophage burden (42–44). While S. equorum does have a significantly greater total genome size ( F 2,19 = 26.79, P < 0.001) and a higher total number of coding sequences ( F 2,19 = 15.70, P < 0.001), it also has a higher potential prophage burden, with a significantly higher percentage of total coding sequences being intact phage in S. equorum compared to S. xylosus and S. saprophyticus (Fig.…”

Freeing Pseudomonas putida KT2440 of its proviral load strengthens endurance to environmental stresses

“…This was considered a sound indication that none of the prophages present in P. putida KT2440 matures to the point of becoming infective to other prophage‐free cells. In light of these data, it seems that the capsides observed upon induction of P4 (named Pspu28 by Quesada et al ., ) do not develop into infective viruses. The results also confirm the gain of a fitness advantage of the prophage‐less strain under environmental conditions of DNA damage.…”

“…Finally, prophage 4 (P4) has a size of 40 kb and it includes 53 ORFs; this genetic element is similar to the Pseudomonas phage D3 (Canchaya et al ., ). P4, also named Gi28 by Quesada and colleagues (), has been shown to excise from the genome at an unknown frequency. Interestingly, it encodes an excisionase, two integrases and two holins, but surprisingly not a lytic enzyme (Canchaya et al ., ).…”

“…At the time of starting this work, the activity of some components of the proviral load of P. putida KT2440 had been observed. Quesada and colleagues () reported that the so‐called GI28 genomic island that overlaps with the P4 prophage (see above; Fig. B) was lost spontaneously and originated structures reminiscent of phage capsides.…”

“…the TS1‐TS2 segment of http://onlinelibrary.wiley.com/10.1111/1462-2920.12492/suppinfo), using primers P1532‐XmaI‐P1586‐BamHI (http://onlinelibrary.wiley.com/10.1111/1462-2920.12492/suppinfo), and sequenced the resulting DNA product. This allowed us to confirm that the active P4 prophage encompasses exactly ORFs PP1532–PP1584 as observed by Quesada et al ., (), a segment that does not include the toxin–antitoxin system (PP1585–PP1586; Tamman et al ., ) entertained above. Analysis of the PCR products shown in http://onlinelibrary.wiley.com/10.1111/1462-2920.12492/suppinfo revealed that amplification of the genomic DNA of the wild‐type P. putida KT2440 with primers designed for detection of P4 excision resulted in a faint band of the same size as that coming from the ΔP4 strain P. putida EM371.…”