Functional Metagenomics Reveals an Overlooked Diversity and Novel Features of Soil-Derived Bacterial Phosphatases and Phytases

Abstract

Phosphorus (P) is a key element involved in numerous cellular processes and essential to meet global food demand. Phosphatases play a major role in cell metabolism and contribute to control the release of P from phosphorylated organic compounds, including phytate. Apart from the relationship with pathogenesis and the enormous economic relevance, phosphatases/phytases are also important for reduction of phosphorus pollution. Almost all known functional phosphatases/phytases are derived from cultured individual microorganisms. We demonstrate here for the first time the potential of functional metagenomics to exploit the phosphatase/phytase pools hidden in environmental soil samples. The recovered diversity of phosphatases/phytases comprises new types and proteins exhibiting largely unknown characteristics, demonstrating the potential of the screening method for retrieving novel target enzymes. The insights gained into the unknown diversity of genes involved in the P cycle highlight the power of function-based metagenomic screening strategies to study Earth’s phosphatase pools.

Functional Metagenomics Reveals a New Catalytic Domain, the Metallo-β-Lactamase Superfamily Domain, Associated with Phytase Activity

“…The Mblp02 activity optimum was 35°C. Similarly, another recently described soil metagenome-originated phytase (Pho07) showed highest activities at lower temperatures (25 to 30°C) (14). The reported pH range of phytase activity also varies (2.2 to 8.0), whereby phytases of bacterial origin revealed optimal activities between pH 6.5 and 7.5.…”

“…coli clones harboring the recombinant plasmids pLP05 (2,496 bp) and pLP12 (5,578 bp) were identified by color change during the functional screening of soil metagenomic libraries using phytic acid as the sole P source (see Fig. S1 in the supplemental material) (14). Sequence analysis of the inserts did not reveal putative genes similar to known ones encoding phosphatase/phytase activity (see Fig.…”

“…However, reported phytase activity is limited to a few protein types, as mentioned above (7). One limiting factor for finding new types of proteins or catalytic domains associated with phytase activity is the almost exclusive usage of individual microorganisms for the isolation and characterization of this type of enzyme (14, 31).…”

“…Other phytases contribute to the virulence potency in human fungal pathogens such as Candida albicans (10–13). The vast majority of reported phytases are derived from a small culturable fraction of microorganisms, but recent reports implementing functional metagenomic approaches demonstrated the potential of environmental samples as source of novel phosphatases/phytases (14, 15).…”

Identification of two novel bacterial phosphatase‐encoding genes inPseudomonas putidastrain P13

“…Functional genomics was proposed as an approach to elucidate the function or activity of novel proteins. Castillo Villamizar et al () suggested that the classical concept comprising four classes of phytases needs modification, since functional metagenomics approaches revealed that novel types of phosphatases/phytases are hidden in the metagenomes of complex environments. Recently, phosphatase gene abundance, diversity and gene activity have been studied (Chen et al ).…”