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Assessment of functional diversity and structure of phytate-hydrolysing bacterial community in Lolium perenne rhizosphere

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Abstract

Background and aims

Plant growth is frequently limited by the availability of inorganic phosphorus (P) in the soil. In most soils, a considerable amount of the soil P is bound to organic molecules. Of these, phytate is the most abundant identifiable organic P form, but is not readily available to plants. In contrast, microorganisms have been shown to degrade phytate with high efficiency. The current study aims to characterize the members of the phytate-hydrolysing bacterial community in rhizosphere, and the molecular and enzymatic ability of these bacteria to degrade phytate.

Methods and results

The phytate-hydrolysing bacterial community was characterized from the rhizosphere of plants cultivated in the presence or absence of phytate supplementation. Major changes in the bacterial community structure were observed with both culture-dependent and -independent methods, which highlighted the predominance of Proteobacteria and Actinobacteria. Phytase activity was detected for a range of rhizobacterial isolates as well as the presence of, β-propeller phytases (BPP) for both isolates and directly in a soil sample.

Conclusion

A wide taxonomic range of functional phytate utilizers have been discovered, in soil bacterial taxa that were previously not well known for their ability to utilise phytate as P or C sources. This study provides new insights into microbial carbon and phosphorus cycling in soil.

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Acknowledgments

We thank John Hammond and Gary Bending for assistance with soil sampling at Warwick HRI. This project was supported by the Natural Environment Research Council (NERC) and by a research grant from the University of Sydney. We thank John Morton for technical assistance.

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  1. Hervé Sanguin

    Present address: CIRAD, UMR LSTM, F-34398, Montpellier, France

  2. Michael A. Kertesz

    Present address: Faculty of Agriculture, and Environment, University of Sydney, Sydney, New South Wales, 2006, Australia

Authors and Affiliations

  1. Faculty of Life Sciences, University of Manchester, Oxford Rd, Manchester, M13 9PT, UK

    Hervé Sanguin & Michael A. Kertesz

  2. Faculty of Agriculture, and Environment, University of Sydney, Sydney, New South Wales, 2006, Australia

    Neil L. Wilson

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  1. Hervé Sanguin
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Correspondence to Hervé Sanguin.

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Fig. S1

Distribution of phytate-hydrolysing bacteria (OTUs) from L. perenne rhizosphere. Number of bacterial isolates (for each OTU) obtained on PMI (A and C) and PMII (B and D) with (black) or without (white) phytate supplemented is represented for Lindow soil (A and B) and Warwick soil (C and D). The symbols (▲) and (△) indicate the OTUs for which one or two isolates were selected to test their ability to utilize phytate as C source and/or P source. Solid and open triangles indicate the soil treatment, with or without phytate supplemented, respectively. (PPT 225 kb)

Fig. S2

Multiple sequence alignment of amino acids BPP sequences used for the design of phytase-specific PCR primers. The conserved sequence motifs targeted are highlighted in colours and the primer position is indicated at the bottom. The sequences used for the design of each primer are in enclosed boxes. The numbers (I to IIIc) next to the strain names indicate BPP groups defined in Lim et al. (2007). BAP, Bacillus amyloliquefaciens BAP (AAW28542); ATCC14580, Bacillus licheniformis ATCC14580 (YP_090097) ; DS11, Bacillus sp. DS11 (AAC38573); 168, Bacillus subtilis subsp. subtilis 168 (NP_389861); ATCC23134, Microscilla marina ATCC23134 (EAY24393); CB15, Caulobacter crescentus CB15 (AAK23276); RB2256, Sphingomonas alaskensis RB2256 (ABF54827.1); SKA58, Sphingomonas sp. SKA58 (EAT09404); RW1, Sphingomonas wittichii RW1 (YP_001261037); HTCC2633, Oceanicaulis alexandrii HTCC2633 (ZP_00953252); MCS10, Maricaulis maris MCS10 (ABI66660); ATCC15444, Hyphomonas neptunium ATCC15444 (ABI78101); HTCC2503, Parvularcula bermudensis HTCC2503 (EAQ17779); Deepecotype, Alteromonas macleodii ‘Deepecotype’ (YP_002126691); MED297, Reinekea sp. MED297 (EAR10111); S14, Vibrio angustum S14 (EAS63574); HTCC2207, marine gamma proteobacterium HTCC2207 (EAS47070); 2–40, Saccharophagus degradans 2–40 (ABD83254); TAC125, Pseudoalteromonas haloplanktis TAC125 (CAI85536); ANA-3, Shewanella sp. ANA-3 (ABK48437); MR-4, Shewanella sp. MR-4 (ABI39156); MR-7, Shewanella sp. MR-7 (ABI42881); MR-1, Shewanella oneidensis MR-1 (AAN55555); RED65, Oceanobacter sp. RED65 (EAT12633); OS145, Idiomarina baltica OS145 (EAQ32794); L2TR, Idiomarina loihiensis L2TR (AAV80945); Pf-5, Pseudomonas fluorescens Pf-5 (YP_260816); 1448A , Pseudomonas syringae pv. Phaseolicola 1448A (AAZ36343); DC3000, Pseudomonas syringae pv. Tomato DC3000 (AAO56720); ymp, Pseudomonas mendocina ymp (YP_001189542); DJ, Azotobacter vinelandii DJ (YP_002797726). (PPTX 114 kb)

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Sanguin, H., Wilson, N.L. & Kertesz, M.A. Assessment of functional diversity and structure of phytate-hydrolysing bacterial community in Lolium perenne rhizosphere. Plant Soil 401, 151–167 (2016). https://doi.org/10.1007/s11104-015-2512-7

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