ABSTRACT
In this chapter, we review important traits and biotechnological examples of non-pathogenic Pseudomonas species, with a focus on P. putida, a species used for bioremediation, biopolymer production and as host in industrial biotechnology. Explicitly, we review briefly some common and specific features of Pseudomonads biology, including the taxonomy. In Section 10.2, we briefly summarize specialty applications before we review in detail the use of non-pathogenic Pseudomonads as hosts in academic and industrial biocatalysis. Certain traits of particular species and strains of Pseudomonas make them superior to industrially established hosts for specific applications. We will work to contribute to the ongoing developments to lift the potential of Pseudomonas for industrial biotechnology. 10.1.2 TaxonomyThe taxonomy of Pseudomonads is not straightforward, as many species are reported that differ rather little in commonly used features such as the sequence of the 16S rRNA gene (Palleroni, 2010). For biotechnological applications, this is often of little relevance, especially when working in bioremediation with wildtype isolates. In contrast, when working with genetically modified organisms, the risk level matters as the required documentation increases considerably when a facultative pathogen is used as production host. Notably, P. putida was reclassified in Germany in 2011 from safety class 1 to safety class 2 as reports were summarized that indicated strains of this species as human pathogens which can result in mortality upon nosocomial infection (Kim et al., 2012). No other country is known to the authors that placed P. putida into class 2. The only exception is the common lab strain P. putida KT2440, which is also in Germany a class 1 organism. With P. putida KT2440 after 30+ years of extensive work in laboratories around the world no health threat was reported. This might have however different reasons than being a non-pathogenic P. putida. Rather, the evidence for the strain KT2440 to belong to P. putida was questioned previously (Regenhardt et al., 2002). The authors show that KT2440 has a higher 16S rRNA gene sequence similarity to Pseudomonas plecoglossicida (99.8%) than to the P. putida type strains (99.0%), and physiological comparison between P. putida KT2440 and DSM291T also indicate that the two strains are not
similar enough to be called the same species. Important for any future work on the taxonomy of this biotechnologically highly relevant group of organisms is the sequencing of the type strain P. putida DSM291T, which will allow a detailed genomic analysis to highlight the evolutionary relationships between Pseudomonas species and strains, and will likely lead to a re-classification of many of the strains described in this chapter. 10.1.3 Versatile MetabolismThe versatility of metabolism of Pseudomonads and especially of the species used in bioremediation is referenced frequently, suggesting a significantly larger metabolic network when compared to other soil bacteria or bacteria with a comparable genome size of 5.5 to 6.5 Mbp (about 5,400 genes). Notably, the largest genome scale metabolic reconstruction of P. putida KT2440 covers 900 of the about 5,350 genes that are associated with 1,044 metabolites in 1,071 reactions (Sohn et al., 2010). For comparison, the metabolic reconstructions of Klebsiella pneumoniae (Liao et al., 2011) or Clostridium beijerinckii (Milne et al., 2011) with genomes carrying about 5,200 genes include 1,228 and 925 metabolic genes encoding proteins catalyzing 1,970 and 938 reactions with 1,658 and 861 metabolites, respectively. Hence, from the number of enzymes and reactions catalyzed, P. putida is comparable to other bacteria of the same size. Its use in bioremediation and biocatalysis, especially of aromatic molecules with chemical structures that are difficult to bio-degrade, however positions P. putida into the group of organisms with a highly versatile metabolism. Indeed, not only are strains of P. putida used for the most difficult bioremediation challenges, but also enzymes from Pseudomonads are used in in vitro and whole-cell biocatalysis as discussed below.The possibility to degrade aromatic compounds is truly incorporated into the metabolic operation of P. putida as on a benzoate/glucose mixture a diauxic shift occurs, with benzoate being the preferred substrate (Basu et al., 2006). The possibility to degrade such molecules is also based on the bacterial ability to activate the aromatic ring by introducing oxygen via redox reactions (Blank et al., 2010). The ability to frequently use molecular oxygen as substrate in biochemical pathways might correlate with its respiratory lifestyle that is discussed in the next paragraph.
