Numbers and locations of native bacteria on field‐grown wheat roots quantified by fluorescence in situ hybridization (FISH)

Abstract

Native bacteria, Pseudomonas and filamentous bacteria were quantified and localized on wheat roots grown in the field using fluorescence in situ hybridization (FISH). Seminal roots were sampled through the season from unploughed soil in a conservation farming system. Such soils are spatially heterogeneous, and many roots grow slowly through hard soil with cracks and pores containing dead roots remnant from previous crops. Root and rhizosphere morphology, and contact with soil particles were preserved, and autofluorescence was avoided by observing sections in the far-red with Cy5 and Cy5.5 fluorochromes. Spatial analyses showed that bacteria were embedded in a stable matrix (biofilm) within 11 microm of the root surface (range 2-30 microm) and were clustered on 40% of roots. Half the clusters co-located with axial grooves between epidermal cells, soil particles, cap cells or root hairs; the other half were not associated with visible features. Across all wheat roots, although variable, bacteria averaged 15.4 x 10(5) cells per mm(3) rhizosphere, and of these, Pseudomonas and filaments comprised 10% and 4%, respectively, with minor effects of sample time, and no effect of plant age. Root caps were most heavily colonized by bacteria along roots, and elongation zones least heavily colonized. Pseudomonas varied little with root development and were 17% of bacteria on the elongation zone. Filamentous bacteria were not found on the elongation zone. The most significant factor to rhizosphere populations along a wheat root, however, was contact with dead root remnants, where Pseudomonas were reduced but filaments increased to 57% of bacteria (P < 0.001). This corresponded with analyses of root remnants showing they were heavily colonized by bacteria, with 48% filaments (P < 0.001) and 1.4%Pseudomonas (P = 0.014). Efforts to manage rhizosphere bacteria for sustainable agricultural systems should continue to focus on root cap and mucilage chemistry, and remnant roots as sources of beneficial bacteria.

Importance of rare taxa for bacterial diversity in the rhizosphere of Bt- and conventional maize varieties

“…With the exception of BEN this was also true at the rank genus. However, at the rank genus differences were detected between bacterial communities from fine and coarse roots, which confirms inhomogeneous colonization of root segments (Watt et al, 2006;DeAngelis et al, 2009). Only the community structure of the 49 most dominant genera was necessary to obtain exactly the same clustering as with all 510 genera.…”

“…The easily available carbon sources exert a great selective power on the enrichment of soil bacteria and may attract both beneficial and detrimental bacteria. Differences in rhizodeposition by the plants are reflected by differently composed bacterial communities in the rhizosphere (Brimecombe et al, 2001) as they become evident between different plant species (Dohrmann and Tebbe, 2005) or cultivars grown in the same soil (Buee et al, 2009) and even across different root sections of the same plant (Watt et al, 2006). GM Bt-maize events produce Cry proteins, typically also in their root tissue.…”

Endophytic actinomycetes: promising source of novel bioactive compounds

“…7,8,10 Furthermore, in comparison of the colony formation from outer and inner part of tissues using two kinds of plant roots, 10 7 CFU g − 1 (dried sample) from near the exterior and 10 3 -10 5 CFU g À 1 (dried sample) from the inside tissue of both samples were detected. The data supported the results detected by FISH.…”

“…6 Bacteria exist on the surface and inside of plant roots, as demonstrated by fluorescence in situ hybridization, scanning electron microscopy or detection of target genes. [7][8][9][10] Numerous bacteria live in rhizospheres, up to 10 6 cells per mm 3 , including filamentous bacteria with actinomycetes accounting for an estimated 4% of the total. 9 This shows the relationship that exists between actinomycetes and plants.…”

Plant exudates improve the mechanical conditions for root penetration through compacted soils

“…Plant roots penetrate and alter the structure of compacted soils through the combined actions of exerting large radial and axial mechanical stresses, enhanced wetting and drying driven by evapotranspiration, as well as the release and secondary microbial decomposition of exudates (Watt et al 2006;Hinsinger et al 2009;Bengough et al 2011;Gregory et al 2013). They are so effective at improving soil physical conditions that biological tillage through the action of plant roots is a growing practice that is advocated in sustainable crop rotations.…”