Manipulation of beneficial microorganisms in crop rhizospheres - Microbial Ecology in Sustainable Agroecosystems - page 22

chapter 2
Manipulation of beneficial
microorganisms in crop rhizospheres
Richard P. Dick
The Ohio State University
Contents
2.1 Introduction .......................................................................................................................... 23
2.1.1 Microbial ecology, genomics, and synergisms .................................................... 24
2.1.2 Gene pools and microbial diversity ...................................................................... 25
2.1.2.1 Microbial sequencing and metagenomics ............................................. 25
2.1.2.2 Mitigating factors for the power of metagenomics .............................. 26
2.1.3 Signaling ................................................................................................................... 27
2.1.4 Spatial distributions of microorganisms and biofilms 29
2.2 Emerging components of optimized and sustainable rhizospheres............................ 29
2.2.1 Phytostimulators ...................................................................................................... 29
2.2.2 Disease-suppressive soils and plant-protecting microorganisms.................... 30
2.2.3 Biological nutrient enhancement and nitrogen fixation .................................... 32
2.2.3.1 Free-living and endophytic nitrogen-fixing bacteria........................... 32
2.2.3.2 Phosphorus-mineralizing microorganisms .......................................... 34
2.2.4 Manipulating microorganisms to promote drought tolerance on plants........ 36
2.2.5 Companion woody rhizospheres .......................................................................... 37
2.3 Biotechnology within a cultural and agroecosystems context ..................................... 37
2.4 Conclusions........................................................................................................................... 38
References....................................................................................................................................... 40
2.1 Introduction
The rhizosphere (including the endophytic habitat) is a unique microbial environment that
is a critical interface for the growth and maintenance of plants. It encompasses apoplastic
and intracellular root tissue, root surfaces, and the surrounding soil that is influenced
by the root. It is significantly different from bulk soil in terms of chemistry and biology.
Roots release various organic materials that include sloughed dead cellular material and
actively excreted organic compounds. At the same time, they alter the physical environ-
ment, which affects gas and water dynamics and ultimately affects microbial communities
and processes they mediate (Hinsinger et al., 2009).
The endophytic niche requires special recognition because of its unique habitat and
potential to affect plants. Endophytic bacteria can colonize the apoplastic and intracellular
locations in roots without causing negative impacts on the host plant (Schulz and Boyle,
2006). Because of their intimate contact or location within roots, they are more protected
23