MINIREVIEW

Bacterial endophytes: recent developments and applications

Robert P. Ryan1, Kieran Germaine2, Ashley Franks1, David J. Ryan2 & David N. Dowling2
1
BIOMERIT Research Centre, Department of Microbiology, Biosciences Institute, National University of Ireland, Cork, Ireland; and 2Department of
Science & Health, Institute of Technology Carlow, Carlow, Ireland

Correspondence: David N. Dowling, Abstract

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Department Science & Health, Institute of
Technology Carlow, Kilkenny Road, Carlow,
Ireland. Tel.: 1353 59 9170479; fax: 1353 59
9170517; e-mail: dowlingd@itcarlow.ie
Received 9 August 2007; accepted
14 August 2007.
First published online December 2007.
DOI:10.1111/j.1574-6968.2007.00918.x
Editor: Richard Staples
Keywords
bioremediation; plant–microbe interaction;
biocontrol; plant growth promotion.
Endophytic bacteria have been found in virtually every plant studied, where they
colonize the internal tissues of their host plant and can form a range of different
relationships including symbiotic, mutualistic, commensalistic and trophobiotic.
Most endophytes appear to originate from the rhizosphere or phyllosphere; however,
some may be transmitted through the seed. Endophytic bacteria can promote plant
growth and yield and can act as biocontrol agents. Endophytes can also be beneficial
to their host by producing a range of natural products that could be harnessed for
potential use in medicine, agriculture or industry. In addition, it has been shown
that they have the potential to remove soil contaminants by enhancing phytoreme-
diation and may play a role in soil fertility through phosphate solubilization and
nitrogen fixation. There is increasing interest in developing the potential biotechno-
logical applications of endophytes for improving phytoremediation and the sustain-
able production of nonfood crops for biomass and biofuel production.

Introduction Gnanamanickam, 1997), insects (Azevedo et al., 2000) and

Beneficial plant–microbe interactions that promote plant
health and development have been the subject of consider-
able study. Recent work has also investigated their potential
for the enhanced biodegradation of pollutants in soil. Most
of these studies have focused on bacteria from the rhizo-
sphere of plants (Lindow & Brandl, 2003; Kuiper et al., 2004;
Berg et al., 2005). Endophytic bacteria can be defined as
those bacteria that colonize the internal tissue of the plant
showing no external sign of infection or negative effect on
their host (Holliday, 1989; Schulz & Boyle, 2006), and of the
nearly 300 000 plant species that exist on the earth, each
individual plant is host to one or more endophytes (Strobel
et al., 2004). Only a few of these plants have ever been
completely studied relative to their endophytic biology.
Consequently, the opportunity to find new and beneficial
endophytic microorganisms among the diversity of plants in
different ecosystems is considerable.
Bacterial endophytes colonize an ecological niche similar
to that of phytopathogens, which makes them suitable as
biocontrol agents (Berg et al., 2005). Indeed, numerous
reports have shown that endophytic microorganisms can
have the capacity to control plant pathogens (Sturz &
Matheson, 1996; Duijff et al., 1997; Krishnamurthy &
nematodes (Hallmann et al., 1997, 1998). In some cases, they
can also accelerate seedling emergence, promote plant estab-
lishment under adverse conditions (Chanway, 1997) and
enhance plant growth (Bent & Chanway, 1998). Bacterial
endophytes have been shown to prevent disease development
through endophyte-mediated de novo synthesis of novel
compounds and antifungal metabolites. Investigation of the
biodiversity of endophytic strains for novel metabolites may
identity new drugs for effective treatment of diseases in
humans, plants and animals (Strobel et al., 2004).
Along with the production of novel chemicals, many
endophytes have shown a natural capacity for xenobiotic
degradation or may act as vectors to introduce degradative
traits. The ability of some endophytes to show resistance to
heavy metals/antimicrobials and degrade organic com-
pounds probably stems from their exposure to diverse
compounds in the plant/soil niche. This natural ability to
degrade these xenobiotics is being investigated with regard
to improving phytoremediation (Siciliano et al., 2001; Barac
et al., 2004; Germaine et al., 2004, 2006; Porteous-Moore
et al., 2006; Ryan et al., 2007a). This review aims to provide
an overview of the potential applications for bacterial
endophytes particularly in the area of phytoremediation
and sustainable agriculture.

FEMS Microbiol Lett 278 (2008) 1–9

c 2007 Federation of European Microbiological Societies
Published by Blackwell Publishing Ltd. All rights reserved
2 R.P. Ryan et al.
Isolation and biodiversity of bacterial
endophytes
The endophytic niche offers protection from the environ-
ment for those bacteria that can colonize and establish
in planta. These bacteria generally colonize the intercellular
spaces, and they have been isolated from all plant compart-
ments including seeds (Posada & Vega, 2005). Endophytic
bacteria have been isolated from both monocotyledonous
and dicotyledonous plants, ranging from woody tree species,
such as oak and pear, to herbaceous crop plants such as
sugar beet and maize. Classical studies on the diversity of
bacterial endophytes have focused on characterization of
isolates obtained from internal tissues following disinfection
of plant surfaces with sodium hypochlorite or similar agents
(Miche & Balandreau, 2001). A review by Lodewyckx et al.
(2002) highlights the methods used to isolate and character-
ize endophytic bacteria from different plant species. A very
comprehensive list of bacterial endophytes isolated from
a broad range of plants is provided by Rosenblueth &
Martinez-Romero (2006) and Berg & Hallmann (2006),
which updates the groundwork laid by Hallmann et al.
(1997) and Lodewyckx et al. (2002).
A recent study by Porteous-Moore et al. (2006) describes
the diversity of endophytes found in poplar trees, growing at
a phytoremediation field site contaminated with toluene,
with the aim of identifying potential candidates for enhancing
phytoremediation of toluene, ethylbenzene, and xylene
(BTEX) compounds. Endophytic bacteria were isolated from
two varieties of Poplar. The isolated endophytic bacteria were
characterized by comparative sequence analysis of partial 16S
RNA genes, BOX-PCR profiling of genomic DNA and
physiological characterization, with respect to substrate utili-
zation, antibiotics and heavy-metal sensitivities. This study
and those of Germaine et al. (2004, 2006) demonstrated that
within the diverse bacterial communities found in Poplar
trees, several endophytic strains were present that had the
potential to enhance phytoremediation of volatile organics
and herbicides.
Molecular approaches for the isolation and characteriza-
tion of bacterial endophytes and plant-associated bacteria
and communities have been reviewed recently by Franks
et al. (2006). Microbial communities inhabiting stems, roots
and tubers of various varieties of plants were analysed by 16S
rRNA gene-based techniques such as terminal restriction
fragment length polymorphism analysis, denaturing gradi-
ent gel electrophoresis as well as 16S rRNA gene cloning and
sequencing. Five taxa exhibiting the most promising levels
of colonization and an ability to persist were identified as
Cellulomonas, Clavibacter, Curtobacterium, Pseudomonas
and Microbacterium by 16S rRNA gene sequence, fatty acid
and carbon source utilization analyses (Elvira-Recuenco &
van Vuurde, 2000; Zinniel et al., 2002).
c 2007 Federation of European Microbiological Societies
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Studies that make use of both culture-based and culture-
independent techniques can be particularly useful. The
presence and taxonomy of endophytic bacteria of the entire
aerial parts of Crocus (Crocus albiflorus) was investigated by
Reiter & Sessitsch (2006). Their results suggest that Crocus
supports a diverse bacterial microbial communities resem-
bling the microbial communities that have been described
for other plants, but also containing species that have not
been described in association with plants before. A combi-
nation of plating of plant macerates, isolation and 16S rRNA
gene sequence identification of isolates and whole-commu-
nity fingerprinting was used. The results clearly indicated
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that a wide range of bacteria from diverse phylogenetic
affiliation, mainly Gammaproteobacteria and Firmicutes, live
in association with plants of Crocus albiflorus. The commu-
nity composition of the culturable component of the micro-
bial communities was different from that of the 16S rRNA
gene clone library. Only three bacterial divisions were found
in the culture collection, which represented 17 phylotypes,
whereas six divisions were identified in the library analysis
comprising 38 phylotypes. The predominant group in the
culture collection was the low G1C Gram-positive group,
whereas in the clone library, the Gammaproteobacteria pre-
dominated. This study confirms that the culturable endo-
phytes are a subset of total endophyte biodiversity.
Plant colonization and inoculation with
endophytes
Autofluorescent protein (AFP) methods are now a key tool
for studying processes such as microbe–plant interactions
and biofilm formation (for a recent review, see Larrainzar
et al., 2005). These techniques have been utilized to detect
and enumerate microorganisms in situ on plant surfaces
and in planta (Gage et al., 1996; Tombolini et al., 1997;
Tombolini & Jansson, 1998). One of these AFP strategies
uses a marker system, which encodes the green fluorescent
protein (GFP). This technique has shown promise in
monitoring pseudomonads in root tissues (Tombolini
et al., 1997; Tombolini & Jansson, 1998). GFP is a useful
AFP biomarker because it does not require any substrate or
cofactor in order to fluoresce. Workers have developed GFP
cassettes for chromosomal integration and expression of gfp
in a variety of bacteria (Tombolini et al., 1997; Tombolini
& Jansson, 1998; Xi et al., 1999). Bacterial cells with
chromosomal integration of gfp can be identified by
epifluorescence microscopy or confocal laser scanning
microscopy (Villacieros et al., 2003; Germaine et al., 2004).
Germaine et al. (2004) investigated a number of GFP-
labelled Poplar endophytes for their colonization ability and
also explored different methods of inoculation; a simple
‘stick dipping’ method was found to be very efficient,
leading to extensive colonization of the specific tissues of
FEMS Microbiol Lett 278 (2008) 1–9
Bacterial endophytes 3

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Fig. 1. Schematic diagram of the different plant–bacterial endophyte interactions that have been studied and their applications

Poplar plants (see Fig. 1) at levels of 102 to 104 CFU g 1

tissue depending on the strain, whereas a seed ‘imbibing’
method was efficient for inoculation of pea plants
(Germaine et al., 2006; Germaine, 2007) (Fig. 2).
Endophyte colonization has also been visualized with the
use of the b-glucuronidase (GUS) reporter system. A GUS-
marked strain of Herbaspirillum seropedicae Z67 was inocu-
lated onto rice seedlings. GUS staining was most intense on
coleoptiles, lateral roots, and also at some of the junctions of
the main and lateral roots (James et al., 2002). This study by
James et al. (2002) showed that endophytes entered the roots
through cracks at the point of lateral root emergence.
Herbaspirillum seropedicae subsequently colonized the root
intercellular spaces, aerenchyma and cortical cells, with a few
penetrating the stele to enter the vascular tissue. The xylem
vessels in leaves and stems were also colonized.
Successful endophyte colonization also involves a compa-
tible host plant. Recently, work by Miche et al. (2006)
investigated the obligate nitrogen-fixing endophyte Azoarcus
sp. strain BH72, which expresses nitrogenase (nif) genes
inside rice roots. They used a proteomic approach to dissect
responses of rice roots toward bacterial colonization and
jasmonic acid treatment (which induces plant defence pro-
teins). Data suggest that induced plant defence responses may
contribute to restricting endophytic colonization in grasses.
Fig. 2. Application of AFPs for studying bacterial endophyte–plant
Few studies have been published describing the molecular
interactions. (a) Xylem tracheid pits of inoculated poplar trees showing
basis of the interactions between endophytic bacteria and colonization by Pseudomonas putida VM1453 cells (  1000) (Germaine
plants. Adapting strategies that have been used to study et al., 2004). Scale bar = 10 mM. (b) Pseudomonas putida VM1450 micro-
bacterial gene expression in the rhizosphere and phyllo- colony within the root cortex of inoculated pea plants exposed to 54 mg
sphere such as in vivo expression technology (IVET) and 2,4-D (  1000) (Germaine et al., 2006).

FEMS Microbiol Lett 278 (2008) 1–9

c2007 Federation of European Microbiological Societies
Published by Blackwell Publishing Ltd. All rights reserved
4 R.P. Ryan et al.
recombination in vivo expression technology (Leveau &
Lindow, 2001; Preston et al., 2001; Zhang et al., 2006) may
provide an insight into genes that are required by bacteria to
enter, compete, colonize the plant, suppress pathogens and
generally survive within the plant.
Genomics of endophyte bacteria
To date, few endophytic bacterial genome sequences have
been published; however, genome sequencing of a number
of endophytes including Enterobacter sp.638, Stenotropho-
monas maltophilia R551-3, Pseudomonas putida W619,
Serratia proteamaculans 568 and Methylobacterium populi
BJ001 is underway at the United States Department of
Energy Joint Genome Institute (www.jgi.doe.gov). Recently,
the complete genome sequence of the nitrogen-fixing en-
dophyte, Azoarcus sp. strain BH72 (Hurek & Reinhold-
Hurek, 2003; Krause et al., 2006) has been compared with
that of the related soil bacterium strain Azoarcus sp. strain
EbN1 and other plant-associated bacteria. The BH72 gen-
ome lacks genes encoding type III and type IV secretion
systems, toxins, nodulation factors, common enzymes that
hydrolyses plant cell walls and the N-acyl homoserine
lactone-based quorum-sensing system, which is found
in many plant-associated bacteria and plant pathogens
(Rainey, 1999; Preston et al., 2001; Büttner & Bonas, 2006).
However, Krause et al. (2006) identified other factors
encoded by the BH72 genome that may be involved in the
host interaction. These include type IV pili, surface poly-
saccharides, type I and II protein secretion systems, flagella
and chemotaxis proteins and a large number of ferric-
siderophore uptake systems. The BH72 genome provides
valuable insights into the biology of bacterial endophytes,
and as more endophyte genome sequences become available,
this will provide a rational basis to design experiments
to investigate the mechanisms involved in successful
endophyte colonization.
Plant growth-promoting endophytes
Research has been conducted on the plant growth-promot-
ing abilities of various rhizobacteria. They differ from
biocontrol strains in that they do not necessarily inhibit
pathogens but increase plant growth through the improved
cycling of nutrients and minerals such as nitrogen, phos-
phate and other nutrients.
Endophytes also promote plant growth by a number of
similar mechanisms. These include phosphate solubilization
activity (Verma et al., 2001; Wakelin et al., 2004), indole
acetic acid production (Lee et al., 2004) and the production
of a siderophore (Costa & Loper, 1994). Endophytic organ-
isms can also supply essential vitamins to plants (Pirttila
et al., 2004). Moreover, a number of other beneficial effects
on plant growth have been attributed to endophytes and
c 2007 Federation of European Microbiological Societies
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include osmotic adjustment, stomatal regulation, modifica-
tion of root morphology, enhanced uptake of minerals and
alteration of nitrogen accumulation and metabolism (Com-
pant et al., 2005a, b). The recent areas where these plant
growth-promoting bacterial endophytes are being used are
in the developing areas of forest regeneration and phytor-
emediation of contaminated soils.
Biocontrol and endophytes
Endophytic bacteria are able to lessen or prevent the
deleterious effects of certain pathogenic organisms. The
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beneficial effects of bacterial endophytes on their host plant
appear to occur through similar mechanisms as described
for rhizosphere-associated bacteria. These mechanisms have
been reviewed in great detail by Kloepper et al. (1999) or,
more recently, by Gray & Smith (2005) and Compant et al.
(2005a). Diseases of fungal, bacterial, viral origin and in
some instances even damage caused by insects and nema-
todes can be reduced following prior inoculation with
endophytes (Kerry, 2000; Sturz et al., 2000; Ping & Boland,
2004; Berg & Hallmann, 2006).
It is believed that certain endophyte bacteria trigger
a phenomenon known as induced systemic resistance (ISR),
which is phenotypically similar to systemic-acquired resis-
tance (SAR). SAR develops when plants successfully activate
their defence mechanism in response to primary infection by
a pathogen, notably when the latter induces a hypersensitive
reaction through which it becomes limited in a local necrotic
lesion of brown desiccated tissue (van Loon et al., 1998). ISR
is effective against different types of pathogens but differs
from SAR in that the inducing bacterium does not cause
visible symptoms on the host plant (van Loon et al., 1998).
Bacterial endophytes and their role in ISR have been
reviewed recently by Kloepper & Ryu (2006).
Natural products from endophytic
bacteria
Many endophytes are members of common soil bacterial
genera, such as Pseudomonas, Burkholderia and Bacillus
(Lodewyckx et al., 2002). These genera are well known for
their diverse range of secondary metabolic products includ-
ing antibiotics, anticancer compounds, volatile organic
compounds, antifungal, antiviral, insecticidal and immuno-
suppressant agents. While a wide range of biologically active
compounds have been isolated from endophytic organisms,
they still remain a relatively untapped source of novel
natural products.
While most research has focused on fungal-based pro-
duction of antimicrobial products, a number of low-mole-
cular-weight compounds, active at low concentrations
against a range of human, animal and plant pathogenic
FEMS Microbiol Lett 278 (2008) 1–9
Bacterial endophytes
Table 1. Natural products that have been derived or produced from various endophytic bacteria
Organism Plant association
Taxomyces andreanae Taxus brevifolia
Pseudomonas viridiflava Grass
Streptomyces griseus Kandelia candel
Streptomyces NRRL 30562 Kennedia nigriscans
Streptomyces NRRL 30566 Grevillea pteridifolia
Serratia marcescens Rhyncholacis penicillata
Paenibacillus polymyxa Wheat
Lodge pine
Green beans
Arabidopsis thaliana
Canola
Cytonaema sp. Quercus sp. 103
Streptomyces sp. Monstera sp.
bacteria, have been isolated from bacterial endophytes
(Table 1). One member of the plant-associated fluorescent
pseudomonads, Pseudomonas viridiflava, which has
been isolated on and within the tissues of many grass
species (Miller et al., 1998), was found to produce two
novel antimicrobial compounds called ecomycins. Ecomy-
cins represent a family of novel lipopeptides and are
made up of some unusual amino acids including homo-
serine and b-hydroxy aspartic acid. It was found that these
compounds were able to inhibit the human pathogens
Cryptococcus neoformans and Candida albicans (Miller
et al., 1998). While viral inhibitors have been isolated
from Cytomaema sp. of fungi, such as cytonic acids A and
D, these were found to inhibit the human cytomegalovirus
(Guo et al., 2000). However, comprehensive screens for
antiviral compounds from bacterial endophytes have yet
to be reported.
Bioplastics are biomaterials that are receiving increasing
commercial interest. Lemoigne (1926) first described a
bioplastic, poly-3-hydroxybutyrate (PHB) produced by
Bacillus megaterium. They are polyesters, produced by
a range of microorganisms cultured under different nutrient
and environmental conditions. The most widely produced
microbial bioplastics are poly-3-hydroxyalkanoate (PHA)
and PHB. Genomic analysis indicates that many species
of bacteria have the potential to produce bioplastics (Kalia
et al., 2003).
Herbaspirillum seropedicae, a diazotrophic endophyte, can
colonize a variety of higher plants and utilize a diverse range
carbon sources. Catalán et al. (2007) have shown that
H. seropedicae accumulates significant levels of PHB, when
grown on a range of individual carbon sources. The design
and development of bacteria and higher plants able to
accumulate PHAs may also help to streamline cost-effective
production and to produce novel heteropolymers for
a range of applications (Aldor & Keasling, 2003).
FEMS Microbiol Lett 278 (2008) 1–9
5
Active agent Activity Reference
Taxol Anticancer Strobel et al. (1993)
Ecomycins B and C Antimicrobial Miller et al. (1998)
p-Aminoacetophenonic acids Antimicrobial Guan et al. (2005)
Munumbicins Antibiotic Castillo et al. (2002)
Munumbicin D Antimalarial
Kakadumycins Antibiotic Castillo et al. (2003)
Oocydin A Antifungal Strobel et al. (2004)
Fusaricidin A–D Antifungal Beck et al. (2003)
Li et al. (2007)
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Beatty & Jensen (2002)
Cytonic acids A and D Antiviral Guo et al. (2000)
Coronamycin Antimalarial antifungal Ezra et al. (2004)
Endophytic microorganisms with the
potential to improve phytoremediation
Siciliano et al. (2001) showed that plants grown in soil
contaminated with xenobiotics naturally recruited endo-
phytes with the necessary contaminant-degrading genes.
Indeed, in field sites contaminated with nitro-aromatics,
genes encoding for nitro-aromatic compound degradation
were more prevalent in endophytic strains than within
rhizospheric or soil microbial communities. Van Aken et al.
(2004) also showed that a phyto-symbiotic strain of
Methylobacterium, which was isolated from hybrid Poplar
trees (Populus deltoids x nigra), was capable of biodegrading
numerous nitro-aromatic compounds such as 2,4,6-trinitro-
toluene. In the absence of a natural biodegradation ability,
genetically engineered strains can be constructed and tailor-
made for the desired application. Lodewyckx et al. (2001),
demonstrated that endophytes of yellow lupin, genetically
constructed for nickel resistance, were able to increase the
nickel accumulation and tolerance of inoculated plants.
An application of bacterial endophytes with considerable
biotechnological potential was described by Barac et al.
(2004), who showed that engineered Burkholderia cepacia
G4 could increase plant tolerance to toluene, and decrease
the transpiration of toluene to the atmosphere. Because
toluene is one of the four components of BTEX contamina-
tion, this has the potential to improve phyto-remediation by
decreasing toxicity and increasing degradation of the xeno-
biotic (Barac et al., 2004). Table 2 outlines a number of
studies that demonstrate the potential role of endophytes in
phytoremediation.
Germaine et al. (2006) inoculated pea plants with a
Pseudomonas endophyte capable of degrading the organo-
chlorine herbicide, 2,4-dichlorophenoxyacetic acid (2,4-D).
When inoculated plants were exposed to 2,4-D, they showed
no accumulation of the herbicide into their tissues and
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Published by Blackwell Publishing Ltd. All rights reserved
6 R.P. Ryan et al.
Table 2. A non-exhaustive list of pollutants that have been associated with bacterial endophyte phyto-remediation strategies
Compound Plant association
Mono- and dichlorinated Wild rye (Elymus dauricus)
benzoic acids
2,4-D Poplar (Populus) and willow (Salix)
Methane Poplar tissues
(Populus deltoidesnigra DN34)
TNT, RDX, HMX Poplar tissues
(Populus deltoidesnigra DN34)
MTBE, BTEX, TCE Populus cv. Hazendans and
cv. Hoogvorst
Toluene Poplar (Populus)
TCP and PCB Wheat
Volatile organic compounds Yellow lupine (Lupinus luteus L.)
and toluene
TNT, 2,4,6-trinitrotoluene; 2,4-D, 2,4-dichlorophenoxyacetic acid; TNT, 2,4,6-trinitrotoluene; RDX, hexahydro-1,3,5-trinitro-1,3,5-triazene; HMX,
octahydro-1,3,5,7-tetranitro-1,3,5-tetrazocine; NDAB, aliphatic nitramine 4-nitro-2,4-diazabutanal; BTEX, benzene, toluene, ethylbenzene, and
xylene; TCP, 2,3,4,6-tetrachlorophenol; PCB, polychlorinated biphenyl.
experienced little or no signs of phytotoxicity, whereas
uninoculated plants showed significant accumulation of
2,4-D and displayed signs of toxicity including a reduction
in biomass, leaf abscission and callus development on their
roots. Large rhizosphere populations were also observed
during these experiments, which were responsible for en-
hanced degradation of 2,4-D in soil.
The possible advantages of using endophytic microorgan-
isms to improve xenobiotic remediation were summarized
by Newman & Reynolds (2005), a major advantage being
where genetic engineering of a xenobiotic degradation path-
way is required, bacteria are easier to manipulate than plants.
In addition, quantitative gene expression of pollutant
catabolic genes within the endophytic populations could be
a useful monitoring tool for assessing the efficiency of the
remediation process. The unique niche of the interior plant
environment provides the xenobiotic degrader strain with an
ability to reach larger population sizes due to reduced
competition. Another important advantage of using endo-
phytic pollutant degraders is that any toxic xenobiotics taken
up by the plant may be degraded in planta, thereby reducing
phytotoxic effects and eliminating any toxic effects on
herbivorous fauna residing on or near contaminated sites.
The endophyte niche is a hot spot for horizontal gene
transfer (HGT) as demonstrated by Taghavi et al. (2005). In
this study, the degradative plasmid, pTOM-Bu61, was found
to have transferred naturally to a number of different
endophytes in planta. This HGT activity promoted more
efficient degradation of toluene in poplar plants. HGT
in planta is likely to be widespread, as studies in pea with
Pseudomonas endophytes harbouring the plasmids pWWO
and pNAH7 also show high rates of transfer into a range of
autochthonous endophytes (Ryan et al., 2007b; E. Keogh &
D.N. Dowling, unpublished data). This approach may have
practical applications in equipping the natural endophyte
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Published by Blackwell Publishing Ltd. All rights reserved
Organism Reference
Pseudomonas aeruginosa strain R75 Siciliano et al. (1998)
and Pseudomonas savastanoi strain CB35
P. putida VM1450 Germaine et al. (2006)
Methylobacterium populi BJ001 Van Aken et al. (2004)
Methylobacterium populi BJ001 Van Aken et al. (2004)
Pseudomonas sp Germaine et al. (2004),
Porteous-Moore et al. (2006)
B. cepacia Bu61(pTOM-Bu61) Taghavi et al. (2005)
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Herbaspirillum sp. K1 Mannisto et al. (2001)
Burkholderia cepacia G4 Barac et al. (2004)
populations with the capacity to degrade a pollutant and does
not require long-term establishment of the inoculant strain.
It is has been demonstrated that endophytic bacteria
efficiently expressing the necessary catabolic genes can
promote the degradation of xenobiotic compounds or their
metabolites as they are accumulated or while being translo-
cated in the vascular tissues of the host plant. With
phytoremediation playing an ever-increasing role in the
clean-up of contaminated land and water, it is envisaged
that endophytes will play a major role in enhancing both the
range of contaminants that can be remediated and the rate
of their degradation.
The endophyte niche and emerging
pathogens
Various opportunistic bacterial pathogens including
Burkholderia, Enterobacter, Herbaspirillum, Ochrobactrum,
Pseudomonas, Ralstonia, Staphylococcus and Stenotrophomo-
nas have been identified as colonizers of the plant rhizo-
sphere (Berg et al., 2005). Many facultative endophytes are
recruited from the large pool of soil and rhizospheric species
and bacteria adapted for living in planta may include
opportunistic human/animal pathogens. Some bacteria as-
sociated with human infections have been isolated from the
interior of alfalfa (Ponka et al., 1995). This research area
needs further investigation to establish the risks, if any,
associated with the development of the endophytic niche
for biotechnological applications.
Concluding remarks
Exploitation of endophyte–plant interactions can result in
the promotion of plant health and can play a significant role
in low-input sustainable agriculture applications for both
FEMS Microbiol Lett 278 (2008) 1–9
Bacterial endophytes
food and nonfood crops. With the availability of complete
genome sequences of key endophytic bacteria, the genes
governing colonization and establishment of endophytic
bacteria in planta can be identified. This information will
form the foundation for transcriptome and proteome
analysis currently optimized in studying other plant–mic-
robe interactions. Incorporating this information with well-
established techniques such as IVET and recently advanced
‘omic’ technologies offers the ability to search for genes on a
global scale that are found to be induced or repressed during
colonization of plant tissues. An understanding of the
mechanisms enabling these endophytic bacteria to interact
with plants will be essential to fully achieve the biotechno-
logical potential of efficient plant–bacterial partnerships for
a range of applications. One promising area of research for
future studies is developing endophytes (and rhizobacteria)
to promote the sustainable production of biomass and
bioenergy crops in conjunction with phytoremediation of
soil contamination.
Acknowledgements
The authors thank J. Maxwell Dow for useful advice and for
important suggestions and the other members of the BIO-
MERIT Research Centre for comments on this work. The
authors acknowledge the funding by the Technological Sector
Research Strand I and III programmes Higher Education
Authority of Ireland (PRTLI Cycle 3) and Science Founda-
tion of Ireland (SFI) BRG programme, and the DAF Stimulus
programme. A.F. is supported by a fellowship from the Irish
Research Council for Science, Engineering and Technology.
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