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Journal of Advanced Research
Review
Assessment of the structural and functional diversities of plant
microbiota: Achievements and challenges – A review
Anton Hartmanna,, Doreen Fischerb, Linda Kinzelc, Soumitra Paul Chowdhuryd, Andreas Hofmanne,
Jose Ivo Baldanie, Michael Rothballerd,
a Ludwig-Maximilians-Universität (LMU) München, Faculty of Biology, Host-Microbe interactions, Großhaderner Str. 2-4, D-82152 Martinsried, Germany
b Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstr. 1, D-85764 Neuherberg,
Munich, Germany
c Research Unit Microbe-Plant Interactions, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstr. 1, D-85764 Neuherberg,
Munich, Germany
d Institute of Network Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstr. 1, D-85764 Neuherberg, Munich, Germany
e EMBRAPA-Agrobiologia, Br 465, Km 07, Seropédica–RJ–CEP 23891-000, Brazil
h i g h l i g h t s
g r a p h i c a l
a b s t r a c t
 History about the discovery of
endophytes with the focus on
Azospirillum and related diazotrophs.
 Contribution of approaches to reach
highest resolution of microbial
diversity assessment.
 Differentiation of beneficial A.
brasilense and opportunistic human
pathogen R. fauriae.
 Osmoadaption and oxygen tolerance
as major traits for endophytic
bacteria.
 Bacteria-plant communication with
focus on bacterial N-acyl homoserine
lactones.
a r t i c l e
i n f o
a b s t r a c t
Article history:
Analyses of the spatial localization and the functions of bacteria in host plant habitats through in situ
Received 31 January 2019
Revised 23 April 2019
Accepted 24 April 2019
Available online 30 April 2019
identification by immunological and molecular genetic techniques combined with high resolving micro-
scopic tools and 3D-image analysis contributed substantially to a better understanding of the functional
interplay of the microbiota in plants. Among the molecular genetic methods, 16S-rRNA genes were of
central importance to reconstruct the phylogeny of newly isolated bacteria and to localize them
Keywords:
Holobiont
Diazotrophic plant beneficial bacteria
Azospirillum
in situ. However, they usually do not allow resolution for phylogenetic affiliations below genus level.
Especially, the separation of opportunistic human pathogens from plant beneficial strains, currently allo-
cated to the same species, needs genome-based resolving techniques. Whole bacterial genome sequences
allow to discriminate phylogenetically closely related strains. In addition, complete genome sequences
enable strain-specific monitoring for biotechnologically relevant strains. In this mini-review we present
Peer review under responsibility of Cairo University.
Corresponding authors.
2090-1232/ 2019 The Authors. Published by Elsevier B.V. on behalf of Cairo University.
This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).