Burkholderia Species Are Major Inhabitants of White Lupin Cluster Roots

Abstract

The formation of cluster roots by plants represents a highly efficient strategy for acquisition of sparingly available phosphate. This particular root type is characterized by a densely branched structure and high exudation of organic acids and protons, which are likely to influence the resident bacterial community. Until now, the identity of the bacterial populations living in cluster roots has not been investigated. We applied cultivation-dependent and cultivation-independent methods to characterize the dominant bacterial genera inhabiting the growing cluster roots of white lupin. We observed a high relative abundance of Burkholderia species (up to 58% of all isolated strains and 44% of all retrieved 16S rRNA sequences) and a significant enrichment with increasing cluster root age. Most of the sequences retrieved clustered together with known plant-or fungus-associated Burkholderia species, while only one of 98 sequences was affiliated with the Burkholderia cepacia complex. In vitro assays revealed that Burkholderia strains were much more tolerant to low pH than non-Burkholderia strains. Moreover, many strains produced large amounts of siderophores and were able to utilize citrate and oxalate as carbon sources. These features seem to represent important traits for the successful colonization and maintenance of Burkholderia species in white lupin cluster roots.To access sparingly available nutrients such as phosphate, plants have evolved several strategies, e.g., mycorrhizal association and cluster root formation. Cluster roots are very densely branched root structures with a particular excretion physiology (20,21,25). They occur in many species of the Proteaceae family and occasionally in the Mimosaceae, Casuarinaceae, or Fabaceae (7). White lupin is the only cluster-rooted species of agricultural importance and has thus been extensively studied (9,17,26,32,33,41,42). In white lupin, cluster root development follows a well-defined pattern: at the juvenile stage, cluster roots secrete small amounts of malate; at the mature stage, high quantities of citrate and protons are excreted, leading to drastic rhizosphere acidification; and at the senescent stage, organic acid excretion decreases. Besides citrate and malate, oxalate and fumarate have also been reported to be exuded by soil-grown lupin plants (6, 41). The close vicinity of growing cluster roots constitutes a highly selective environment, owing to rapid changes in pH and carbon availability. The abundance of bacteria, as well as richness and diversity, has been shown to decrease temporarily in mature cluster roots (40). However, the identity of the populations repressed or enriched during cluster root development has yet to be elucidated. We analyzed the bacterial communities living in the direct vicinity of cluster roots (root surface and inner tissues) by sequencing isolated strains and clone libraries constructed from root-extracted DNA. We then tested relevant physiological properties of isolates to better understand which metabolic abilities might ena...

Response of soil microorganisms to radioactive oil waste: results from a leaching experiment

“…Clones of band 1 (KF926419-KF926422) were phylogenetically similar to Burkholderia strains found in unpolluted and polluted sites (AF247491, DQ465451, FJ210816; Weisskopf et al, 2011;Friedrich et al, 2000), while clones of band 2 (KF926423-926425) were similar to strains of Burkholderia and Bradyrhizobium jicamae (JX010967, JN662515). Bacteria from the genus Burkholderia are typical soil inhabitants, and certain Burkholderia strains are resistant to hydrocarbons and are used in the bioremediation of oil-polluted sites (Bacosa et al, 2012;Weisskopf et al, 2011;Hamamura et al, 2008;Adetutu et al, 2013).…”

“…Clones of band 1 (KF926419-KF926422) were phylogenetically similar to Burkholderia strains found in unpolluted and polluted sites (AF247491, DQ465451, FJ210816; Weisskopf et al, 2011;Friedrich et al, 2000), while clones of band 2 (KF926423-926425) were similar to strains of Burkholderia and Bradyrhizobium jicamae (JX010967, JN662515). Bacteria from the genus Burkholderia are typical soil inhabitants, and certain Burkholderia strains are resistant to hydrocarbons and are used in the bioremediation of oil-polluted sites (Bacosa et al, 2012;Weisskopf et al, 2011;Hamamura et al, 2008;Adetutu et al, 2013). Band 3 (KF926426-KF926429), which is sensitive to oily and radioactive components in the waste samples (not seen in contaminated H -and R-samples), was genetically similar to Hydrogenobacter hydrogenophilus (Z30242) uncultured Acidobacteria isolated from unpolluted grassland and forest soils (HQ598830, HQ599021; Naether et al, 2012) and an uncultured Chlorobiales bacterium found in a uranium mining waste pile (AJ295649, AJ536877; Selenska-Pobell, 2002).…”

Purification, biochemical characterization, and genetic cloning of the phytase produced by <i>Burkholderia</i> sp. strain a13

“…Several reports have indicated a strong association of species from the genus Burkholderia within the rhizosphere of plants (Compant et al, 2008;Oliveira et al, 2009), and have suggested that their presence could contribute to plant growth by liberating phosphates from soil organic compounds like phytic acid (Unno et al, 2005). Although some reports have also suggested that some strains of the genus Burkholderia possess a degrading ability of phytic acid (Hayatsu, 2013;Unno et al, 2005; Weisskopf et al, 2011), to date, there are no reports on the identification and biochemical characterization of phytases from this genus. This study represents the first biochemical characterization of a purified phytase from the genus Burkholderia and may contribute to a better understanding of this class of enzymes and their role in strain a13 metabolism.…”

The mixotrophic nature of photosynthetic plants

“…Cluster roots are considered particularly beneficial in P-depauperate soils (reviewed by Dinkelaker et al 1995;Neumann and Martinoia 2002;Lambers et al 2006). Cluster roots impact a small volume of soil by exuding protons, organic acids, secondary compounds and enzymes (Dinkelaker et al 1995;Shane and Lambers 2005;PaungfooLonhienne et al 2009), and, less well characterised, through interaction with microbes (Marschner et al 2002;Weisskopf et al 2011).…”