Chapter 1

Introduction

Frans J. de BruijnLaboratory of Plant-Microbe Interactions, UMR INRA-CNRS 2594/441, Toulouse,France

The “Rhizosphere” comprises the environment (“sphere”)surrounding or attached to and influenced by the root(“rhizos”) of plants (Hiltner, 1904), consisting of a com-plex mixture of soil particles, microbial communities,fungi, and small eukaryotes, such as nematodes. Theimportance of the rhizosphere can be described by theresemblance to the animal intestine. In both environmentsa large number of hairs (root hairs and villi in plantsand animals, respectively) increase the surface area ofcells and help the plant or animal to take up nutrientsand in both regions large numbers of micro-organismsplay key roles, such as decomposing organic compounds,producing vitamins and/or hormone-like compounds, andinteracting with beneficial and harmful organisms (Unnoand Shinano, Personal Communication).

It has been known that the plant is involved in struc-turing microbial communities and fungi in its rhizosphere,by secreting nutritional compounds, such as carbon, tobe used as growth substrate, enhancing the populationsize and metabolism. It has been estimated that plantstransfer 5–21% of all photosynthetically fixed carbon tothe rhizosphere through root exudates (Bais et al., 2006).This is called “the rhizosphere effect,” but the details onthe changes in microbial populations and their functionsin the rhizosphere are largely unknown, due to the factthat 99% of the microbes in the bulk soil (Skinner et al.,1952) and up to 90% in the rhizosphere (Sorenson, 1997)are presently unculturable. The rhizosphere microbes, inturn, can contribute to plant growth, for example, via bio-logical nitrogen fixation providing fixed nitrogen to theplant. Moreover, selected fungi can solubilise phosphorusand other compounds for use by the plant. In addition,microbial compounds are synthesized which help protect

Molecular Microbial Ecology of the Rhizosphere, Volume 1, First Edition. Edited by Frans J. de Bruijn. 2013 John Wiley & Sons, Inc. Published 2013 by John Wiley & Sons, Inc.

the plant against disease and pathogen attack (biocontrol)or cause plant growth promotion (PGPR).

It is interesting to note that the first plants started tocolonize land as early as 700 million years ago and, sim-ilar to lichens, are hypothesized to have depended on andcoevolved with microbes for stress tolerance and nutrientacquisition (Johnston-Monje and Raizada, 2011).

There is substantial “signaling” occurring betweenmicrobes, and between microbes or fungi and the plant,which activate certain gene sets in these organisms whichplay a role in the biology of the rhizosphere. Althoughthese processes are known to exist, until recently theirmolecular basis has been poorly understood. The soilstructure and dynamics, the composition of the highlycomplex microbial communities, the “interkingdom” sig-naling and the exact pathways of feeding of microbes byplants remain only partially elucidated on a molecularbasis. However, the advent of Molecular MicrobialEcology has caused an explosion of new information,which will be the subject of these Volumes.

The Rhizosphere, and the soil for that matter, havebeen considered “Black Boxes,” but decades of biochem-ical, biophysical, and ecological studies have allowed aglimpse in the Boxes. In addition, with the advent ofmolecular approaches, the rhizosphere has become muchmore tangible and approachable, leading to a real explo-sion of knowledge, especially on the structure and functionof microbial communities, signaling between microbesand between microbes and the host plant, plant control ofmicrobial community in the rhizosphere, and other facetsof plant–microbe interactions. Thus since the Publicationof “The Rhizosphere” by Lynch in 1990 (Lynch, 1990),a wealth of information, has accumulated both on the bulk

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2 Chapter 1 Introduction

soil and the Rhizosphere, which merits a new visitationin the form of these Volumes.

In the present Volumes on the Molecular MicrobialEcology of the Rhizosphere, I would like to focus on asubset of the advances made in the area of the rhizosphere,and highlight those experiments that have been mostlycarried out using molecular approaches from communityfingerprinting to genomics and metagenomics (de Bruijn,2011a, b).

The physico–chemical aspects of the soil per se,although clearly of major importance in the plant–microbe–soil triangle, will not be discussed in detail inthese Volumes. These aspects are covered in a specialissue of Plant and Soil (2009) containing papers presentedat the Rhizosphere 2 Congress in Montpellier, France,and in a corresponding Book published by SpringerVerlag (2010). Moreover, soil aspects will be coveredin a second special issue of Plant and Soil (2012) and aspecial issue of Annals in Botany (2012). The latter twoissues will contain papers presented at the Rhizosphere 3Congress in Perth, Australia (September 2011). Severalpapers from this Meeting are included in these Volumes.For extensive information on the rhizosphere, the reader isreferred to the Internet under the key word “rhizosphere.”

Another important aspect of the rhizosphere, namelyplant pathogens in the rhizosphere, is also not discussedin detail in these Volumes. This is a highly specializedfield and the reader is referred to excellent reviews byRaaijmakers et al. (2009) and Nehl et al. (1996) for furtherdetails on deleterious microbes in the rhizosphere.

The book will have several reviews in each categoryfollowed by research chapters with materials and methodsdetailed enough to carry out similar experiments or clearreferrals to the literature. For each separate topic, severalchapters on the methodology and results will be included.

These can be updates on previously published papersor new original research. The former are generallyderived from papers published since 2008, since in 2010the Book on the Rhizosphere was published by Springer.Most of the chapters will use molecular techniques toapproach a variety of aspects of the rhizosphere, suchas Plant-Mediated Structuring of Bacterial Communitiesin the Rhizosphere, Plant Genetics and RhizomicrobialCommunities, Hormones and Rhizomicrobial Communi-ties and Strains, Endophytes, Symbiotic Plant–MicrobeInteractions, Biocontrol, PGPR, Biofilm Formation,Quorum Sensing and Signaling, Genomic Sequencing,Rhizosphere-Activated Promoters and Genes, Markerand Reporter Genes, Phytoremediation, Climate ChangeEffects, Metagenomics and the Soil/Rhizosphere, andEngineering the Rhizosphere (see Table of Contents).

The Introduction will be followed by several “FocusChapters” describing various central aspects of themolecular microbial ecology of the rhizosphere system,

including two reviews on culture-independent moleculartechniques for soil microbial ecology. More moleculartechniques are discussed in the first two Chapters ofSection 2, which will be on plant-mediated structuring ofbacterial communities in the rhizosphere, a very popularsubject in the field. There will be three review Chaptersfor Section 2 and a number of research chapters describ-ing results obtained in various subhabitats and usingvaried experimental approaches. There is an emphasis onthe “rhizosphere effect” or the role of root exudates instructuring microbial communities in the rhizosphere andthe section ends with a chapter on the question if rootexudates exert more influence on rhizosphere bacterialcommunities than other rhizodeposits. Section 3 willaddress the question of which plant genotype or genesare involved in structuring of microbial communities inthe rhizosphere. The last chapter of this section discussesthe proteomics of roots. The effects of hormones andother signals produced by the plant and/or the microbe onrhizobacterial communities or the plant will be discussedin Section 4. The second chapter in this section describesthe role of small molecules in trans-kingdom communica-tion between plants and rhizobacteria, while the last threereviews in this section discuss the novel class of signalingcompounds and plant hormones called the strigolactones.In Section 5 the properties and roles of endophyticmicrobes will be addressed. This section is prefaced bytwo reviews and features research articles on DNA-basedstable isotope probing for identifying active bacterialendophytes, visualization of endophytes by FISH, theuse of a poplar endophyte to phytoremediate volatilecompounds, nifA gene expression and nitrogen fixationby diazotrophic endophytes, and a study on endophytes inmaize and their transmission. The subsequent Section 6will cover the very important symbiotic plant–microbeinteractions, involving nitrogen-fixing rhizobia and myc-orrhizae, and this vast area of research will be coveredby several review articles addressing the intricaciesof these systems and the similarity in plant–microbesignaling will be highlighted. In Section 7 other beneficialmicrobes will be discussed, including PGPR, biocontrolbacteria, and disease-suppressive bacteria. Three reviewarticles covering PGPR, biocontrol, and biocontrol andosmoprotection will precede several papers on these threetopics, including a chapter on the road from an academ-ically promising result to a commercial product. Afterintroducing this variety of plant–microbe interactions,Section 8 will start to address the mechanistic side ofthings by highlighting the processes of microbial biofilmformation and attachment to roots. This is followedby Section 9 which discusses the important featuresof quorum sensing and signaling in microbe–microbeand microbe–plant interactions. In Chapter 10 variousmolecular approaches are presented as applied to the

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rhizosphere, including complete genomic sequencing ofmicrobes, and different approaches to isolate rhizosphere-activated promoters. This is followed by Section 11 onMarker and Reporter Genes for Plant–Host InteractionStudies. This section starts with a review about designinggenetically engineered bacteria for ecological studies,and covers other microbe detection methods. Section 12introduces the use of rhizobacteria and plants to carryout phytoremediation in the environment. Environmental(climate) change, such as varying CO2 levels and theireffects on microbial communities in the rhizosphere, isbriefly covered in Section 13. The still limited applicationof metagenomic approaches to study the soil/rhizosphereis discussed in Section 14, giving some examples ofongoing projects and their aims. The more esoteric topicof “The Biased Rhizospheres” is reviewed in Section 15.In this scenario attempts are made to “engineer bacterialcompetitiveness and persistence in the phytosphere.”This section is followed by Section 16 containing tworeviews on human pathogenic bacteria in the rhizosphere,a (provocative) chapter on “rhizophagy,” and a synthesischapter.

While obviously this treatise is not complete, I hopethat enough diverse reviews and research articles are pre-sented to give an overview of the topics covered in thistwo volume book and that the chapters and extensive bib-liographies in the chapters will permit the reader to expandher/his horizons in the fields of rhizosphere molecularbiology and plant–microbe interactions.

REFERENCES

Bais HP, Weir TL, Perry LG, Gilroy S, Vivanco JM. The role of rootexudates in rhizosphere interactions with plants and microorganisms.Annu Rev Plant Biol 2006;57:233–266.

de Bruijn FJ, editor. Handbook of Molecular Microbial Ecology I:Metagenomics and Complementary Approaches . Hoboken, NJ, USA:Wiley-Blackwell; 2011a.

de Bruijn FJ, editor. Handbook of Molecular Microbial Ecology II:Metagenomics in Different Habitats . Hoboken, NJ, USA: Wiley-Blackwell; 2011b.

Hiltner L. Uber neuere Erfahrungen und Probleme auf dem Gebietder Bodenbakteriologie und unter besonderer Berucksichtigungder Grundungung und Brache. Arbeiten der Deutschen Land-wirtschaftlichen Gesellschaft 1904;98:59–78.

Johnston-Monje D, Raizada MN. Plant and endophytic relation-ships: nutrient management. In: Moo-Young M, editor. Comprehen-sive Biotechnology . Agricultural and Related Biotechnologies. 2nded. Oxford: Elsevier; 2011. p 713–727.

Lynch JM, editor. The Rhizosphere. Chichester, UK: Wiley Inter-science; 1990.

Nehl DB, Allen SJ, Brown JF. Deleterious rhizosphere bacteria: anintegrated perspective. Appl Soil Ecol 1996;5:1–20.

Raaijmakers JM, Paulitz TC, Steinberg C, Alabouvette C,Moenne-Loccoz Y. The rhizosphere: a playground and battlefieldfor soilborne pathogens and beneficial microorganisms. Plant Soil2009;321:341–361.

Skinner FA, Jones PCT, Mollison JE. Comparison of adirect counting and a plate-counting technique for the quantita-tive estimation of soil micro-organisms. J Gen Microbiol 1952;6:261–271.

Sorenson J. The rhizosphere as a habitat for soil microorganisms. In:van Elsas JD, editor. Modern Soil Microbiology . New York: MarcelDekker, Inc; 1997. p 21–45.